diff --git a/ena_upload/templates/ENA_template_samples_ERC000011.xml b/ena_upload/templates/ENA_template_samples_ERC000011.xml index 4731e70..7996915 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000011.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000011.xml @@ -81,16 +81,16 @@ def mandatorytest(row, column, index): ${row['collected_by']} - + - collection date - ${row['collection date']} + collection_date + ${row['collection_date']} - + - geographic location (region and locality) - ${row['geographic location (region and locality)']} + geographic_location_region_and_locality + ${row['geographic_location_region_and_locality']} @@ -117,10 +117,10 @@ def mandatorytest(row, column, index): ${row['sex']} - + - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} + geographic_location_country_andor_sea + ${row['geographic_location_country_andor_sea']} @@ -129,10 +129,10 @@ def mandatorytest(row, column, index): ${row['lab_host']} - + - host scientific name - ${row['host scientific name']} + host_scientific_name + ${row['host_scientific_name']} diff --git a/ena_upload/templates/ENA_template_samples_ERC000012.xml b/ena_upload/templates/ENA_template_samples_ERC000012.xml index 9512c97..40d87c4 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000012.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000012.xml @@ -33,28 +33,28 @@ def mandatorytest(row, column, index): ${row.sample_description} - + - trophic level - ${row['trophic level']} + trophic_level + ${row['trophic_level']} - + - observed biotic relationship - ${row['observed biotic relationship']} + observed_biotic_relationship + ${row['observed_biotic_relationship']} - + - known pathogenicity - ${row['known pathogenicity']} + known_pathogenicity + ${row['known_pathogenicity']} - + - relationship to oxygen - ${row['relationship to oxygen']} + relationship_to_oxygen + ${row['relationship_to_oxygen']} @@ -63,41 +63,41 @@ def mandatorytest(row, column, index): ${row['propagation']} - + - sample collection device - ${row['sample collection device']} + sample_collection_device + ${row['sample_collection_device']} - + - sample collection method - ${row['sample collection method']} + sample_collection_method + ${row['sample_collection_method']} - + - sample storage temperature - ${row['sample storage temperature']} + sample_storage_temperature + ${row['sample_storage_temperature']} °C - + - sample storage location - ${row['sample storage location']} + sample_storage_location + ${row['sample_storage_location']} - + - oxygenation status of sample - ${row['oxygenation status of sample']} + oxygenation_status_of_sample + ${row['oxygenation_status_of_sample']} - + - project name - ${row['project name']} + project_name + ${row['project_name']} @@ -106,70 +106,70 @@ def mandatorytest(row, column, index): ${row['ploidy']} - + - number of replicons - ${row['number of replicons']} + number_of_replicons + ${row['number_of_replicons']} - + - extrachromosomal elements - ${row['extrachromosomal elements']} + extrachromosomal_elements + ${row['extrachromosomal_elements']} - + - estimated size - ${row['estimated size']} + estimated_size + ${row['estimated_size']} - + - target gene - ${row['target gene']} + target_gene + ${row['target_gene']} - + - target subfragment - ${row['target subfragment']} + target_subfragment + ${row['target_subfragment']} - + - multiplex identifiers - ${row['multiplex identifiers']} + multiplex_identifiers + ${row['multiplex_identifiers']} - + - sequence quality check - ${row['sequence quality check']} + sequence_quality_check + ${row['sequence_quality_check']} - + - chimera check software - ${row['chimera check software']} + chimera_check_software + ${row['chimera_check_software']} - + - relevant electronic resources - ${row['relevant electronic resources']} + relevant_electronic_resources + ${row['relevant_electronic_resources']} - + - relevant standard operating procedures - ${row['relevant standard operating procedures']} + relevant_standard_operating_procedures + ${row['relevant_standard_operating_procedures']} - + - collection date - ${row['collection date']} + collection_date + ${row['collection_date']} @@ -179,42 +179,42 @@ def mandatorytest(row, column, index): m - + - geographic location (latitude) - ${row['geographic location (latitude)']} + geographic_location_latitude + ${row['geographic_location_latitude']} DD - + - geographic location (longitude) - ${row['geographic location (longitude)']} + geographic_location_longitude + ${row['geographic_location_longitude']} DD - + - geographic location (region and locality) - ${row['geographic location (region and locality)']} + geographic_location_region_and_locality + ${row['geographic_location_region_and_locality']} - + - broad-scale environmental context - ${row['broad-scale environmental context']} + broadscale_environmental_context + ${row['broadscale_environmental_context']} - + - local environmental context - ${row['local environmental context']} + local_environmental_context + ${row['local_environmental_context']} - + - environmental medium - ${row['environmental medium']} + environmental_medium + ${row['environmental_medium']} @@ -224,60 +224,60 @@ def mandatorytest(row, column, index): m - + - ventilation rate - ${row['ventilation rate']} + ventilation_rate + ${row['ventilation_rate']} m3/min - + - ventilation type - ${row['ventilation type']} + ventilation_type + ${row['ventilation_type']} - + - amount or size of sample collected - ${row['amount or size of sample collected']} - m3 + amount_or_size_of_sample_collected + ${row['amount_or_size_of_sample_collected']} + kg - + - organism count - ${row['organism count']} + organism_count + ${row['organism_count']} - + - sample storage duration - ${row['sample storage duration']} + sample_storage_duration + ${row['sample_storage_duration']} - + - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} + geographic_location_country_andor_sea + ${row['geographic_location_country_andor_sea']} - + - host disease status - ${row['host disease status']} + host_disease_status + ${row['host_disease_status']} - + - host scientific name - ${row['host scientific name']} + host_scientific_name + ${row['host_scientific_name']} - + - barometric pressure - ${row['barometric pressure']} + barometric_pressure + ${row['barometric_pressure']} mm Hg @@ -285,34 +285,34 @@ def mandatorytest(row, column, index): humidity ${row['humidity']} - g/m3 + % pollutants ${row['pollutants']} - mg/L + M/L - + - solar irradiance - ${row['solar irradiance']} + solar_irradiance + ${row['solar_irradiance']} W/m2 - + - wind direction - ${row['wind direction']} + wind_direction + ${row['wind_direction']} - + - wind speed - ${row['wind speed']} - m/s + wind_speed + ${row['wind_speed']} + km/h @@ -322,17 +322,17 @@ def mandatorytest(row, column, index): ºC - + - carbon dioxide - ${row['carbon dioxide']} + carbon_dioxide + ${row['carbon_dioxide']} µmol/L - + - carbon monoxide - ${row['carbon monoxide']} + carbon_monoxide + ${row['carbon_monoxide']} µM/L @@ -340,20 +340,20 @@ def mandatorytest(row, column, index): oxygen ${row['oxygen']} - parts/million + mg/L - + - air particulate matter concentration - ${row['air particulate matter concentration']} + air_particulate_matter_concentration + ${row['air_particulate_matter_concentration']} µg/m3 - + - volatile organic compounds - ${row['volatile organic compounds']} + volatile_organic_compounds + ${row['volatile_organic_compounds']} µg/m3 @@ -371,10 +371,10 @@ def mandatorytest(row, column, index): psu - + - source material identifiers - ${row['source material identifiers']} + source_material_identifiers + ${row['source_material_identifiers']} @@ -383,125 +383,125 @@ def mandatorytest(row, column, index): ${row['perturbation']} - + - negative control type - ${row['negative control type']} + negative_control_type + ${row['negative_control_type']} - + - positive control type - ${row['positive control type']} + positive_control_type + ${row['positive_control_type']} - + - experimental factor - ${row['experimental factor']} + experimental_factor + ${row['experimental_factor']} - + - encoded traits - ${row['encoded traits']} + encoded_traits + ${row['encoded_traits']} - + - subspecific genetic lineage - ${row['subspecific genetic lineage']} + subspecific_genetic_lineage + ${row['subspecific_genetic_lineage']} - + - taxonomic classification - ${row['taxonomic classification']} + taxonomic_classification + ${row['taxonomic_classification']} - + - isolation and growth condition - ${row['isolation and growth condition']} + isolation_and_growth_condition + ${row['isolation_and_growth_condition']} - + - annotation source - ${row['annotation source']} + annotation_source + ${row['annotation_source']} - + - reference for biomaterial - ${row['reference for biomaterial']} + reference_for_biomaterial + ${row['reference_for_biomaterial']} - + - sample material processing - ${row['sample material processing']} + sample_material_processing + ${row['sample_material_processing']} - + - sample volume or weight for DNA extraction - ${row['sample volume or weight for DNA extraction']} - ng + sample_volume_or_weight_for_dna_extraction + ${row['sample_volume_or_weight_for_dna_extraction']} + mL - + - nucleic acid extraction - ${row['nucleic acid extraction']} + nucleic_acid_extraction + ${row['nucleic_acid_extraction']} - + - nucleic acid amplification - ${row['nucleic acid amplification']} + nucleic_acid_amplification + ${row['nucleic_acid_amplification']} - + - library size - ${row['library size']} + library_size + ${row['library_size']} - + - library reads sequenced - ${row['library reads sequenced']} + library_reads_sequenced + ${row['library_reads_sequenced']} - + - library construction method - ${row['library construction method']} + library_construction_method + ${row['library_construction_method']} - + - library vector - ${row['library vector']} + library_vector + ${row['library_vector']} - + - library screening strategy - ${row['library screening strategy']} + library_screening_strategy + ${row['library_screening_strategy']} - + - pcr conditions - ${row['pcr conditions']} + pcr_conditions + ${row['pcr_conditions']} - + - pcr primers - ${row['pcr primers']} + pcr_primers + ${row['pcr_primers']} @@ -510,10 +510,10 @@ def mandatorytest(row, column, index): ${row['adapters']} - + - chemical administration - ${row['chemical administration']} + chemical_administration + ${row['chemical_administration']} diff --git a/ena_upload/templates/ENA_template_samples_ERC000013.xml b/ena_upload/templates/ENA_template_samples_ERC000013.xml index 9ca5147..01b623e 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000013.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000013.xml @@ -33,28 +33,28 @@ def mandatorytest(row, column, index): ${row.sample_description} - + - trophic level - ${row['trophic level']} + trophic_level + ${row['trophic_level']} - + - observed biotic relationship - ${row['observed biotic relationship']} + observed_biotic_relationship + ${row['observed_biotic_relationship']} - + - known pathogenicity - ${row['known pathogenicity']} + known_pathogenicity + ${row['known_pathogenicity']} - + - relationship to oxygen - ${row['relationship to oxygen']} + relationship_to_oxygen + ${row['relationship_to_oxygen']} @@ -63,65 +63,65 @@ def mandatorytest(row, column, index): ${row['propagation']} - + - observed host symbionts - ${row['observed host symbionts']} + observed_host_symbionts + ${row['observed_host_symbionts']} - + - sample collection device - ${row['sample collection device']} + sample_collection_device + ${row['sample_collection_device']} - + - sample collection method - ${row['sample collection method']} + sample_collection_method + ${row['sample_collection_method']} - + - sample storage temperature - ${row['sample storage temperature']} + sample_storage_temperature + ${row['sample_storage_temperature']} °C - + - sample storage location - ${row['sample storage location']} + sample_storage_location + ${row['sample_storage_location']} - + - sample disease stage - ${row['sample disease stage']} + sample_disease_stage + ${row['sample_disease_stage']} - + - oxygenation status of sample - ${row['oxygenation status of sample']} + oxygenation_status_of_sample + ${row['oxygenation_status_of_sample']} - + - sample disease status - ${row['sample disease status']} + sample_disease_status + ${row['sample_disease_status']} - + - sample derived from - ${row['sample derived from']} + sample_derived_from + ${row['sample_derived_from']} - + - project name - ${row['project name']} + project_name + ${row['project_name']} @@ -130,70 +130,70 @@ def mandatorytest(row, column, index): ${row['ploidy']} - + - number of replicons - ${row['number of replicons']} + number_of_replicons + ${row['number_of_replicons']} - + - extrachromosomal elements - ${row['extrachromosomal elements']} + extrachromosomal_elements + ${row['extrachromosomal_elements']} - + - estimated size - ${row['estimated size']} + estimated_size + ${row['estimated_size']} - + - target gene - ${row['target gene']} + target_gene + ${row['target_gene']} - + - target subfragment - ${row['target subfragment']} + target_subfragment + ${row['target_subfragment']} - + - multiplex identifiers - ${row['multiplex identifiers']} + multiplex_identifiers + ${row['multiplex_identifiers']} - + - sequence quality check - ${row['sequence quality check']} + sequence_quality_check + ${row['sequence_quality_check']} - + - chimera check software - ${row['chimera check software']} + chimera_check_software + ${row['chimera_check_software']} - + - relevant electronic resources - ${row['relevant electronic resources']} + relevant_electronic_resources + ${row['relevant_electronic_resources']} - + - relevant standard operating procedures - ${row['relevant standard operating procedures']} + relevant_standard_operating_procedures + ${row['relevant_standard_operating_procedures']} - + - collection date - ${row['collection date']} + collection_date + ${row['collection_date']} @@ -203,42 +203,42 @@ def mandatorytest(row, column, index): m - + - geographic location (latitude) - ${row['geographic location (latitude)']} + geographic_location_latitude + ${row['geographic_location_latitude']} DD - + - geographic location (longitude) - ${row['geographic location (longitude)']} + geographic_location_longitude + ${row['geographic_location_longitude']} DD - + - geographic location (region and locality) - ${row['geographic location (region and locality)']} + geographic_location_region_and_locality + ${row['geographic_location_region_and_locality']} - + - broad-scale environmental context - ${row['broad-scale environmental context']} + broadscale_environmental_context + ${row['broadscale_environmental_context']} - + - local environmental context - ${row['local environmental context']} + local_environmental_context + ${row['local_environmental_context']} - + - environmental medium - ${row['environmental medium']} + environmental_medium + ${row['environmental_medium']} @@ -248,166 +248,166 @@ def mandatorytest(row, column, index): m - + - amount or size of sample collected - ${row['amount or size of sample collected']} - m3 + amount_or_size_of_sample_collected + ${row['amount_or_size_of_sample_collected']} + kg - + - organism count - ${row['organism count']} + organism_count + ${row['organism_count']} - + - sample capture status - ${row['sample capture status']} + sample_capture_status + ${row['sample_capture_status']} - + - biological status - ${row['biological status']} + biological_status + ${row['biological_status']} - + - sample storage duration - ${row['sample storage duration']} + sample_storage_duration + ${row['sample_storage_duration']} - + - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} + geographic_location_country_andor_sea + ${row['geographic_location_country_andor_sea']} - + - host disease status - ${row['host disease status']} + host_disease_status + ${row['host_disease_status']} - + - host common name - ${row['host common name']} + host_common_name + ${row['host_common_name']} - + - host subject id - ${row['host subject id']} + host_subject_id + ${row['host_subject_id']} - + - host age - ${row['host age']} + host_age + ${row['host_age']} years - + - host taxid - ${row['host taxid']} + host_taxid + ${row['host_taxid']} - + - host body habitat - ${row['host body habitat']} + host_body_habitat + ${row['host_body_habitat']} - + - host body site - ${row['host body site']} + host_body_site + ${row['host_body_site']} - + - host life stage - ${row['host life stage']} + host_life_stage + ${row['host_life_stage']} - + - host height - ${row['host height']} - mm + host_height + ${row['host_height']} + m - + - host length - ${row['host length']} - mm + host_length + ${row['host_length']} + m - + - host growth conditions - ${row['host growth conditions']} + host_growth_conditions + ${row['host_growth_conditions']} - + - host substrate - ${row['host substrate']} + host_substrate + ${row['host_substrate']} - + - host total mass - ${row['host total mass']} + host_total_mass + ${row['host_total_mass']} kg - + - host phenotype - ${row['host phenotype']} + host_phenotype + ${row['host_phenotype']} - + - host body temperature - ${row['host body temperature']} + host_body_temperature + ${row['host_body_temperature']} ºC - + - host color - ${row['host color']} + host_color + ${row['host_color']} - + - host shape - ${row['host shape']} + host_shape + ${row['host_shape']} - + - host sex - ${row['host sex']} + host_sex + ${row['host_sex']} - + - host scientific name - ${row['host scientific name']} + host_scientific_name + ${row['host_scientific_name']} - + - host subspecific genetic lineage - ${row['host subspecific genetic lineage']} + host_subspecific_genetic_lineage + ${row['host_subspecific_genetic_lineage']} @@ -424,48 +424,48 @@ def mandatorytest(row, column, index): psu - + - source material identifiers - ${row['source material identifiers']} + source_material_identifiers + ${row['source_material_identifiers']} - + - host blood pressure diastolic - ${row['host blood pressure diastolic']} + host_blood_pressure_diastolic + ${row['host_blood_pressure_diastolic']} mm Hg - + - host blood pressure systolic - ${row['host blood pressure systolic']} + host_blood_pressure_systolic + ${row['host_blood_pressure_systolic']} mm Hg - + - host diet - ${row['host diet']} + host_diet + ${row['host_diet']} - + - host last meal - ${row['host last meal']} + host_last_meal + ${row['host_last_meal']} - + - host family relationship - ${row['host family relationship']} + host_family_relationship + ${row['host_family_relationship']} - + - host genotype - ${row['host genotype']} + host_genotype + ${row['host_genotype']} @@ -474,17 +474,17 @@ def mandatorytest(row, column, index): ${row['gravidity']} - + - host dry mass - ${row['host dry mass']} - mg + host_dry_mass + ${row['host_dry_mass']} + kg - + - host body product - ${row['host body product']} + host_body_product + ${row['host_body_product']} @@ -493,137 +493,137 @@ def mandatorytest(row, column, index): ${row['perturbation']} - + - negative control type - ${row['negative control type']} + negative_control_type + ${row['negative_control_type']} - + - positive control type - ${row['positive control type']} + positive_control_type + ${row['positive_control_type']} - + - experimental factor - ${row['experimental factor']} + experimental_factor + ${row['experimental_factor']} - + - encoded traits - ${row['encoded traits']} + encoded_traits + ${row['encoded_traits']} - + - genetic modification - ${row['genetic modification']} + genetic_modification + ${row['genetic_modification']} - + - subspecific genetic lineage - ${row['subspecific genetic lineage']} + subspecific_genetic_lineage + ${row['subspecific_genetic_lineage']} - + - ancestral data - ${row['ancestral data']} + ancestral_data + ${row['ancestral_data']} - + - taxonomic classification - ${row['taxonomic classification']} + taxonomic_classification + ${row['taxonomic_classification']} - + - isolation and growth condition - ${row['isolation and growth condition']} + isolation_and_growth_condition + ${row['isolation_and_growth_condition']} - + - annotation source - ${row['annotation source']} + annotation_source + ${row['annotation_source']} - + - reference for biomaterial - ${row['reference for biomaterial']} + reference_for_biomaterial + ${row['reference_for_biomaterial']} - + - sample material processing - ${row['sample material processing']} + sample_material_processing + ${row['sample_material_processing']} - + - sample volume or weight for DNA extraction - ${row['sample volume or weight for DNA extraction']} - ng + sample_volume_or_weight_for_dna_extraction + ${row['sample_volume_or_weight_for_dna_extraction']} + mL - + - nucleic acid extraction - ${row['nucleic acid extraction']} + nucleic_acid_extraction + ${row['nucleic_acid_extraction']} - + - nucleic acid amplification - ${row['nucleic acid amplification']} + nucleic_acid_amplification + ${row['nucleic_acid_amplification']} - + - library size - ${row['library size']} + library_size + ${row['library_size']} - + - library reads sequenced - ${row['library reads sequenced']} + library_reads_sequenced + ${row['library_reads_sequenced']} - + - library construction method - ${row['library construction method']} + library_construction_method + ${row['library_construction_method']} - + - library vector - ${row['library vector']} + library_vector + ${row['library_vector']} - + - library screening strategy - ${row['library screening strategy']} + library_screening_strategy + ${row['library_screening_strategy']} - + - pcr conditions - ${row['pcr conditions']} + pcr_conditions + ${row['pcr_conditions']} - + - pcr primers - ${row['pcr primers']} + pcr_primers + ${row['pcr_primers']} @@ -636,13 +636,13 @@ def mandatorytest(row, column, index): depth ${row['depth']} - mm + m - + - chemical administration - ${row['chemical administration']} + chemical_administration + ${row['chemical_administration']} diff --git a/ena_upload/templates/ENA_template_samples_ERC000014.xml b/ena_upload/templates/ENA_template_samples_ERC000014.xml index 75668c8..4eb0bf7 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000014.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000014.xml @@ -33,28 +33,28 @@ def mandatorytest(row, column, index): ${row.sample_description} - + - trophic level - ${row['trophic level']} + trophic_level + ${row['trophic_level']} - + - observed biotic relationship - ${row['observed biotic relationship']} + observed_biotic_relationship + ${row['observed_biotic_relationship']} - + - known pathogenicity - ${row['known pathogenicity']} + known_pathogenicity + ${row['known_pathogenicity']} - + - relationship to oxygen - ${row['relationship to oxygen']} + relationship_to_oxygen + ${row['relationship_to_oxygen']} @@ -63,65 +63,65 @@ def mandatorytest(row, column, index): ${row['propagation']} - + - observed host symbionts - ${row['observed host symbionts']} + observed_host_symbionts + ${row['observed_host_symbionts']} - + - sample collection device - ${row['sample collection device']} + sample_collection_device + ${row['sample_collection_device']} - + - sample collection method - ${row['sample collection method']} + sample_collection_method + ${row['sample_collection_method']} - + - urine/collection method - ${row['urine/collection method']} + urinecollection_method + ${row['urinecollection_method']} - + - sample storage temperature - ${row['sample storage temperature']} + sample_storage_temperature + ${row['sample_storage_temperature']} °C - + - sample storage location - ${row['sample storage location']} + sample_storage_location + ${row['sample_storage_location']} - + - oxygenation status of sample - ${row['oxygenation status of sample']} + oxygenation_status_of_sample + ${row['oxygenation_status_of_sample']} - + - medical history performed - ${row['medical history performed']} + medical_history_performed + ${row['medical_history_performed']} - + - study completion status - ${row['study completion status']} + study_completion_status + ${row['study_completion_status']} - + - project name - ${row['project name']} + project_name + ${row['project_name']} @@ -130,70 +130,70 @@ def mandatorytest(row, column, index): ${row['ploidy']} - + - number of replicons - ${row['number of replicons']} + number_of_replicons + ${row['number_of_replicons']} - + - extrachromosomal elements - ${row['extrachromosomal elements']} + extrachromosomal_elements + ${row['extrachromosomal_elements']} - + - estimated size - ${row['estimated size']} + estimated_size + ${row['estimated_size']} - + - target gene - ${row['target gene']} + target_gene + ${row['target_gene']} - + - target subfragment - ${row['target subfragment']} + target_subfragment + ${row['target_subfragment']} - + - multiplex identifiers - ${row['multiplex identifiers']} + multiplex_identifiers + ${row['multiplex_identifiers']} - + - sequence quality check - ${row['sequence quality check']} + sequence_quality_check + ${row['sequence_quality_check']} - + - chimera check software - ${row['chimera check software']} + chimera_check_software + ${row['chimera_check_software']} - + - relevant electronic resources - ${row['relevant electronic resources']} + relevant_electronic_resources + ${row['relevant_electronic_resources']} - + - relevant standard operating procedures - ${row['relevant standard operating procedures']} + relevant_standard_operating_procedures + ${row['relevant_standard_operating_procedures']} - + - collection date - ${row['collection date']} + collection_date + ${row['collection_date']} @@ -203,42 +203,42 @@ def mandatorytest(row, column, index): m - + - geographic location (latitude) - ${row['geographic location (latitude)']} + geographic_location_latitude + ${row['geographic_location_latitude']} DD - + - geographic location (longitude) - ${row['geographic location (longitude)']} + geographic_location_longitude + ${row['geographic_location_longitude']} DD - + - geographic location (region and locality) - ${row['geographic location (region and locality)']} + geographic_location_region_and_locality + ${row['geographic_location_region_and_locality']} - + - broad-scale environmental context - ${row['broad-scale environmental context']} + broadscale_environmental_context + ${row['broadscale_environmental_context']} - + - local environmental context - ${row['local environmental context']} + local_environmental_context + ${row['local_environmental_context']} - + - environmental medium - ${row['environmental medium']} + environmental_medium + ${row['environmental_medium']} @@ -248,121 +248,121 @@ def mandatorytest(row, column, index): m - + - amount or size of sample collected - ${row['amount or size of sample collected']} - m3 + amount_or_size_of_sample_collected + ${row['amount_or_size_of_sample_collected']} + kg - + - organism count - ${row['organism count']} + organism_count + ${row['organism_count']} - + - sample storage duration - ${row['sample storage duration']} + sample_storage_duration + ${row['sample_storage_duration']} - + - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} + geographic_location_country_andor_sea + ${row['geographic_location_country_andor_sea']} - + - nose/mouth/teeth/throat disorder - ${row['nose/mouth/teeth/throat disorder']} + nosemouthteeththroat_disorder + ${row['nosemouthteeththroat_disorder']} - + - host HIV status - ${row['host HIV status']} + host_hiv_status + ${row['host_hiv_status']} - + - host disease status - ${row['host disease status']} + host_disease_status + ${row['host_disease_status']} - + - lung/pulmonary disorder - ${row['lung/pulmonary disorder']} + lungpulmonary_disorder + ${row['lungpulmonary_disorder']} - + - lung/nose-throat disorder - ${row['lung/nose-throat disorder']} + lungnosethroat_disorder + ${row['lungnosethroat_disorder']} - + - blood/blood disorder - ${row['blood/blood disorder']} + bloodblood_disorder + ${row['bloodblood_disorder']} - + - urine/kidney disorder - ${row['urine/kidney disorder']} + urinekidney_disorder + ${row['urinekidney_disorder']} - + - urine/urogenital tract disorder - ${row['urine/urogenital tract disorder']} + urineurogenital_tract_disorder + ${row['urineurogenital_tract_disorder']} - + - host subject id - ${row['host subject id']} + host_subject_id + ${row['host_subject_id']} - + - IHMC medication code - ${row['IHMC medication code']} + ihmc_medication_code + ${row['ihmc_medication_code']} - + - host age - ${row['host age']} + host_age + ${row['host_age']} years - + - host body site - ${row['host body site']} + host_body_site + ${row['host_body_site']} - + - drug usage - ${row['drug usage']} + drug_usage + ${row['drug_usage']} - + - host height - ${row['host height']} - mm + host_height + ${row['host_height']} + m - + - host body-mass index - ${row['host body-mass index']} + host_bodymass_index + ${row['host_bodymass_index']} kg/m2 @@ -372,48 +372,48 @@ def mandatorytest(row, column, index): ${row['ethnicity']} - + - host occupation - ${row['host occupation']} + host_occupation + ${row['host_occupation']} - + - host total mass - ${row['host total mass']} + host_total_mass + ${row['host_total_mass']} kg - + - host phenotype - ${row['host phenotype']} + host_phenotype + ${row['host_phenotype']} - + - host body temperature - ${row['host body temperature']} + host_body_temperature + ${row['host_body_temperature']} ºC - + - host sex - ${row['host sex']} + host_sex + ${row['host_sex']} - + - host scientific name - ${row['host scientific name']} + host_scientific_name + ${row['host_scientific_name']} - + - presence of pets, animals, or insects - ${row['presence of pets, animals, or insects']} + presence_of_pets_animals_or_insects + ${row['presence_of_pets_animals_or_insects']} @@ -430,10 +430,10 @@ def mandatorytest(row, column, index): psu - + - source material identifiers - ${row['source material identifiers']} + source_material_identifiers + ${row['source_material_identifiers']} @@ -442,90 +442,90 @@ def mandatorytest(row, column, index): ${row['smoker']} - + - major diet change in last six months - ${row['major diet change in last six months']} + major_diet_change_in_last_six_months + ${row['major_diet_change_in_last_six_months']} - + - weight loss in last three months - ${row['weight loss in last three months']} + weight_loss_in_last_three_months + ${row['weight_loss_in_last_three_months']} kg - + - travel outside the country in last six months - ${row['travel outside the country in last six months']} + travel_outside_the_country_in_last_six_months + ${row['travel_outside_the_country_in_last_six_months']} - + - host diet - ${row['host diet']} + host_diet + ${row['host_diet']} - + - twin sibling presence - ${row['twin sibling presence']} + twin_sibling_presence + ${row['twin_sibling_presence']} - + - host last meal - ${row['host last meal']} + host_last_meal + ${row['host_last_meal']} - + - amniotic fluid/gestation state - ${row['amniotic fluid/gestation state']} + amniotic_fluidgestation_state + ${row['amniotic_fluidgestation_state']} - + - host family relationship - ${row['host family relationship']} + host_family_relationship + ${row['host_family_relationship']} - + - amniotic fluid/maternal health status - ${row['amniotic fluid/maternal health status']} + amniotic_fluidmaternal_health_status + ${row['amniotic_fluidmaternal_health_status']} - + - host genotype - ${row['host genotype']} + host_genotype + ${row['host_genotype']} - + - amniotic fluid/foetal health status - ${row['amniotic fluid/foetal health status']} + amniotic_fluidfoetal_health_status + ${row['amniotic_fluidfoetal_health_status']} - + - host pulse - ${row['host pulse']} + host_pulse + ${row['host_pulse']} bpm - + - amniotic fluid/color - ${row['amniotic fluid/color']} + amniotic_fluidcolor + ${row['amniotic_fluidcolor']} - + - host body product - ${row['host body product']} + host_body_product + ${row['host_body_product']} @@ -534,125 +534,125 @@ def mandatorytest(row, column, index): ${row['perturbation']} - + - negative control type - ${row['negative control type']} + negative_control_type + ${row['negative_control_type']} - + - positive control type - ${row['positive control type']} + positive_control_type + ${row['positive_control_type']} - + - experimental factor - ${row['experimental factor']} + experimental_factor + ${row['experimental_factor']} - + - encoded traits - ${row['encoded traits']} + encoded_traits + ${row['encoded_traits']} - + - subspecific genetic lineage - ${row['subspecific genetic lineage']} + subspecific_genetic_lineage + ${row['subspecific_genetic_lineage']} - + - taxonomic classification - ${row['taxonomic classification']} + taxonomic_classification + ${row['taxonomic_classification']} - + - isolation and growth condition - ${row['isolation and growth condition']} + isolation_and_growth_condition + ${row['isolation_and_growth_condition']} - + - annotation source - ${row['annotation source']} + annotation_source + ${row['annotation_source']} - + - reference for biomaterial - ${row['reference for biomaterial']} + reference_for_biomaterial + ${row['reference_for_biomaterial']} - + - sample material processing - ${row['sample material processing']} + sample_material_processing + ${row['sample_material_processing']} - + - sample volume or weight for DNA extraction - ${row['sample volume or weight for DNA extraction']} - ng + sample_volume_or_weight_for_dna_extraction + ${row['sample_volume_or_weight_for_dna_extraction']} + mL - + - nucleic acid extraction - ${row['nucleic acid extraction']} + nucleic_acid_extraction + ${row['nucleic_acid_extraction']} - + - nucleic acid amplification - ${row['nucleic acid amplification']} + nucleic_acid_amplification + ${row['nucleic_acid_amplification']} - + - library size - ${row['library size']} + library_size + ${row['library_size']} - + - library reads sequenced - ${row['library reads sequenced']} + library_reads_sequenced + ${row['library_reads_sequenced']} - + - library construction method - ${row['library construction method']} + library_construction_method + ${row['library_construction_method']} - + - library vector - ${row['library vector']} + library_vector + ${row['library_vector']} - + - library screening strategy - ${row['library screening strategy']} + library_screening_strategy + ${row['library_screening_strategy']} - + - pcr conditions - ${row['pcr conditions']} + pcr_conditions + ${row['pcr_conditions']} - + - pcr primers - ${row['pcr primers']} + pcr_primers + ${row['pcr_primers']} @@ -661,10 +661,10 @@ def mandatorytest(row, column, index): ${row['adapters']} - + - chemical administration - ${row['chemical administration']} + chemical_administration + ${row['chemical_administration']} diff --git a/ena_upload/templates/ENA_template_samples_ERC000015.xml b/ena_upload/templates/ENA_template_samples_ERC000015.xml index 83f5348..1b5fb7d 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000015.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000015.xml @@ -33,28 +33,28 @@ def mandatorytest(row, column, index): ${row.sample_description} - + - trophic level - ${row['trophic level']} + trophic_level + ${row['trophic_level']} - + - observed biotic relationship - ${row['observed biotic relationship']} + observed_biotic_relationship + ${row['observed_biotic_relationship']} - + - known pathogenicity - ${row['known pathogenicity']} + known_pathogenicity + ${row['known_pathogenicity']} - + - relationship to oxygen - ${row['relationship to oxygen']} + relationship_to_oxygen + ${row['relationship_to_oxygen']} @@ -63,53 +63,53 @@ def mandatorytest(row, column, index): ${row['propagation']} - + - observed host symbionts - ${row['observed host symbionts']} + observed_host_symbionts + ${row['observed_host_symbionts']} - + - sample collection device - ${row['sample collection device']} + sample_collection_device + ${row['sample_collection_device']} - + - sample collection method - ${row['sample collection method']} + sample_collection_method + ${row['sample_collection_method']} - + - sample storage temperature - ${row['sample storage temperature']} + sample_storage_temperature + ${row['sample_storage_temperature']} °C - + - sample storage location - ${row['sample storage location']} + sample_storage_location + ${row['sample_storage_location']} - + - oxygenation status of sample - ${row['oxygenation status of sample']} + oxygenation_status_of_sample + ${row['oxygenation_status_of_sample']} - + - medical history performed - ${row['medical history performed']} + medical_history_performed + ${row['medical_history_performed']} - + - project name - ${row['project name']} + project_name + ${row['project_name']} @@ -118,70 +118,70 @@ def mandatorytest(row, column, index): ${row['ploidy']} - + - number of replicons - ${row['number of replicons']} + number_of_replicons + ${row['number_of_replicons']} - + - extrachromosomal elements - ${row['extrachromosomal elements']} + extrachromosomal_elements + ${row['extrachromosomal_elements']} - + - estimated size - ${row['estimated size']} + estimated_size + ${row['estimated_size']} - + - target gene - ${row['target gene']} + target_gene + ${row['target_gene']} - + - target subfragment - ${row['target subfragment']} + target_subfragment + ${row['target_subfragment']} - + - multiplex identifiers - ${row['multiplex identifiers']} + multiplex_identifiers + ${row['multiplex_identifiers']} - + - sequence quality check - ${row['sequence quality check']} + sequence_quality_check + ${row['sequence_quality_check']} - + - chimera check software - ${row['chimera check software']} + chimera_check_software + ${row['chimera_check_software']} - + - relevant electronic resources - ${row['relevant electronic resources']} + relevant_electronic_resources + ${row['relevant_electronic_resources']} - + - relevant standard operating procedures - ${row['relevant standard operating procedures']} + relevant_standard_operating_procedures + ${row['relevant_standard_operating_procedures']} - + - collection date - ${row['collection date']} + collection_date + ${row['collection_date']} @@ -191,42 +191,42 @@ def mandatorytest(row, column, index): m - + - geographic location (latitude) - ${row['geographic location (latitude)']} + geographic_location_latitude + ${row['geographic_location_latitude']} DD - + - geographic location (longitude) - ${row['geographic location (longitude)']} + geographic_location_longitude + ${row['geographic_location_longitude']} DD - + - geographic location (region and locality) - ${row['geographic location (region and locality)']} + geographic_location_region_and_locality + ${row['geographic_location_region_and_locality']} - + - broad-scale environmental context - ${row['broad-scale environmental context']} + broadscale_environmental_context + ${row['broadscale_environmental_context']} - + - local environmental context - ${row['local environmental context']} + local_environmental_context + ${row['local_environmental_context']} - + - environmental medium - ${row['environmental medium']} + environmental_medium + ${row['environmental_medium']} @@ -236,85 +236,85 @@ def mandatorytest(row, column, index): m - + - amount or size of sample collected - ${row['amount or size of sample collected']} - m3 + amount_or_size_of_sample_collected + ${row['amount_or_size_of_sample_collected']} + kg - + - organism count - ${row['organism count']} + organism_count + ${row['organism_count']} - + - sample storage duration - ${row['sample storage duration']} + sample_storage_duration + ${row['sample_storage_duration']} - + - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} + geographic_location_country_andor_sea + ${row['geographic_location_country_andor_sea']} - + - gastrointestinal tract disorder - ${row['gastrointestinal tract disorder']} + gastrointestinal_tract_disorder + ${row['gastrointestinal_tract_disorder']} - + - liver disorder - ${row['liver disorder']} + liver_disorder + ${row['liver_disorder']} - + - host disease status - ${row['host disease status']} + host_disease_status + ${row['host_disease_status']} - + - host subject id - ${row['host subject id']} + host_subject_id + ${row['host_subject_id']} - + - IHMC medication code - ${row['IHMC medication code']} + ihmc_medication_code + ${row['ihmc_medication_code']} - + - host age - ${row['host age']} + host_age + ${row['host_age']} years - + - host body site - ${row['host body site']} + host_body_site + ${row['host_body_site']} - + - host height - ${row['host height']} - mm + host_height + ${row['host_height']} + m - + - host body-mass index - ${row['host body-mass index']} + host_bodymass_index + ${row['host_bodymass_index']} kg/m2 @@ -324,42 +324,42 @@ def mandatorytest(row, column, index): ${row['ethnicity']} - + - host occupation - ${row['host occupation']} + host_occupation + ${row['host_occupation']} - + - host total mass - ${row['host total mass']} + host_total_mass + ${row['host_total_mass']} kg - + - host phenotype - ${row['host phenotype']} + host_phenotype + ${row['host_phenotype']} - + - host body temperature - ${row['host body temperature']} + host_body_temperature + ${row['host_body_temperature']} ºC - + - host sex - ${row['host sex']} + host_sex + ${row['host_sex']} - + - host scientific name - ${row['host scientific name']} + host_scientific_name + ${row['host_scientific_name']} @@ -376,53 +376,53 @@ def mandatorytest(row, column, index): psu - + - source material identifiers - ${row['source material identifiers']} + source_material_identifiers + ${row['source_material_identifiers']} - + - special diet - ${row['special diet']} + special_diet + ${row['special_diet']} - + - host diet - ${row['host diet']} + host_diet + ${row['host_diet']} - + - host last meal - ${row['host last meal']} + host_last_meal + ${row['host_last_meal']} - + - host family relationship - ${row['host family relationship']} + host_family_relationship + ${row['host_family_relationship']} - + - host genotype - ${row['host genotype']} + host_genotype + ${row['host_genotype']} - + - host pulse - ${row['host pulse']} + host_pulse + ${row['host_pulse']} bpm - + - host body product - ${row['host body product']} + host_body_product + ${row['host_body_product']} @@ -431,125 +431,125 @@ def mandatorytest(row, column, index): ${row['perturbation']} - + - negative control type - ${row['negative control type']} + negative_control_type + ${row['negative_control_type']} - + - positive control type - ${row['positive control type']} + positive_control_type + ${row['positive_control_type']} - + - experimental factor - ${row['experimental factor']} + experimental_factor + ${row['experimental_factor']} - + - encoded traits - ${row['encoded traits']} + encoded_traits + ${row['encoded_traits']} - + - subspecific genetic lineage - ${row['subspecific genetic lineage']} + subspecific_genetic_lineage + ${row['subspecific_genetic_lineage']} - + - taxonomic classification - ${row['taxonomic classification']} + taxonomic_classification + ${row['taxonomic_classification']} - + - isolation and growth condition - ${row['isolation and growth condition']} + isolation_and_growth_condition + ${row['isolation_and_growth_condition']} - + - annotation source - ${row['annotation source']} + annotation_source + ${row['annotation_source']} - + - reference for biomaterial - ${row['reference for biomaterial']} + reference_for_biomaterial + ${row['reference_for_biomaterial']} - + - sample material processing - ${row['sample material processing']} + sample_material_processing + ${row['sample_material_processing']} - + - sample volume or weight for DNA extraction - ${row['sample volume or weight for DNA extraction']} - ng + sample_volume_or_weight_for_dna_extraction + ${row['sample_volume_or_weight_for_dna_extraction']} + mL - + - nucleic acid extraction - ${row['nucleic acid extraction']} + nucleic_acid_extraction + ${row['nucleic_acid_extraction']} - + - nucleic acid amplification - ${row['nucleic acid amplification']} + nucleic_acid_amplification + ${row['nucleic_acid_amplification']} - + - library size - ${row['library size']} + library_size + ${row['library_size']} - + - library reads sequenced - ${row['library reads sequenced']} + library_reads_sequenced + ${row['library_reads_sequenced']} - + - library construction method - ${row['library construction method']} + library_construction_method + ${row['library_construction_method']} - + - library vector - ${row['library vector']} + library_vector + ${row['library_vector']} - + - library screening strategy - ${row['library screening strategy']} + library_screening_strategy + ${row['library_screening_strategy']} - + - pcr conditions - ${row['pcr conditions']} + pcr_conditions + ${row['pcr_conditions']} - + - pcr primers - ${row['pcr primers']} + pcr_primers + ${row['pcr_primers']} @@ -558,10 +558,10 @@ def mandatorytest(row, column, index): ${row['adapters']} - + - chemical administration - ${row['chemical administration']} + chemical_administration + ${row['chemical_administration']} diff --git a/ena_upload/templates/ENA_template_samples_ERC000016.xml b/ena_upload/templates/ENA_template_samples_ERC000016.xml index b276c2c..839dd65 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000016.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000016.xml @@ -33,28 +33,28 @@ def mandatorytest(row, column, index): ${row.sample_description} - + - trophic level - ${row['trophic level']} + trophic_level + ${row['trophic_level']} - + - observed biotic relationship - ${row['observed biotic relationship']} + observed_biotic_relationship + ${row['observed_biotic_relationship']} - + - known pathogenicity - ${row['known pathogenicity']} + known_pathogenicity + ${row['known_pathogenicity']} - + - relationship to oxygen - ${row['relationship to oxygen']} + relationship_to_oxygen + ${row['relationship_to_oxygen']} @@ -63,53 +63,53 @@ def mandatorytest(row, column, index): ${row['propagation']} - + - observed host symbionts - ${row['observed host symbionts']} + observed_host_symbionts + ${row['observed_host_symbionts']} - + - sample collection device - ${row['sample collection device']} + sample_collection_device + ${row['sample_collection_device']} - + - sample collection method - ${row['sample collection method']} + sample_collection_method + ${row['sample_collection_method']} - + - sample storage temperature - ${row['sample storage temperature']} + sample_storage_temperature + ${row['sample_storage_temperature']} °C - + - sample storage location - ${row['sample storage location']} + sample_storage_location + ${row['sample_storage_location']} - + - oxygenation status of sample - ${row['oxygenation status of sample']} + oxygenation_status_of_sample + ${row['oxygenation_status_of_sample']} - + - medical history performed - ${row['medical history performed']} + medical_history_performed + ${row['medical_history_performed']} - + - project name - ${row['project name']} + project_name + ${row['project_name']} @@ -118,64 +118,64 @@ def mandatorytest(row, column, index): ${row['ploidy']} - + - number of replicons - ${row['number of replicons']} + number_of_replicons + ${row['number_of_replicons']} - + - extrachromosomal elements - ${row['extrachromosomal elements']} + extrachromosomal_elements + ${row['extrachromosomal_elements']} - + - estimated size - ${row['estimated size']} + estimated_size + ${row['estimated_size']} - + - target gene - ${row['target gene']} + target_gene + ${row['target_gene']} - + - target subfragment - ${row['target subfragment']} + target_subfragment + ${row['target_subfragment']} - + - multiplex identifiers - ${row['multiplex identifiers']} + multiplex_identifiers + ${row['multiplex_identifiers']} - + - sequence quality check - ${row['sequence quality check']} + sequence_quality_check + ${row['sequence_quality_check']} - + - chimera check software - ${row['chimera check software']} + chimera_check_software + ${row['chimera_check_software']} - + - relevant electronic resources - ${row['relevant electronic resources']} + relevant_electronic_resources + ${row['relevant_electronic_resources']} - + - relevant standard operating procedures - ${row['relevant standard operating procedures']} + relevant_standard_operating_procedures + ${row['relevant_standard_operating_procedures']} @@ -184,10 +184,10 @@ def mandatorytest(row, column, index): ${row['lat_lon']} - + - collection date - ${row['collection date']} + collection_date + ${row['collection_date']} @@ -197,42 +197,42 @@ def mandatorytest(row, column, index): m - + - geographic location (latitude) - ${row['geographic location (latitude)']} + geographic_location_latitude + ${row['geographic_location_latitude']} DD - + - geographic location (longitude) - ${row['geographic location (longitude)']} + geographic_location_longitude + ${row['geographic_location_longitude']} DD - + - geographic location (region and locality) - ${row['geographic location (region and locality)']} + geographic_location_region_and_locality + ${row['geographic_location_region_and_locality']} - + - broad-scale environmental context - ${row['broad-scale environmental context']} + broadscale_environmental_context + ${row['broadscale_environmental_context']} - + - local environmental context - ${row['local environmental context']} + local_environmental_context + ${row['local_environmental_context']} - + - environmental medium - ${row['environmental medium']} + environmental_medium + ${row['environmental_medium']} @@ -242,79 +242,79 @@ def mandatorytest(row, column, index): m - + - amount or size of sample collected - ${row['amount or size of sample collected']} - m3 + amount_or_size_of_sample_collected + ${row['amount_or_size_of_sample_collected']} + kg - + - organism count - ${row['organism count']} + organism_count + ${row['organism_count']} - + - sample storage duration - ${row['sample storage duration']} + sample_storage_duration + ${row['sample_storage_duration']} - + - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} + geographic_location_country_andor_sea + ${row['geographic_location_country_andor_sea']} - + - nose/mouth/teeth/throat disorder - ${row['nose/mouth/teeth/throat disorder']} + nosemouthteeththroat_disorder + ${row['nosemouthteeththroat_disorder']} - + - host disease status - ${row['host disease status']} + host_disease_status + ${row['host_disease_status']} - + - host subject id - ${row['host subject id']} + host_subject_id + ${row['host_subject_id']} - + - IHMC medication code - ${row['IHMC medication code']} + ihmc_medication_code + ${row['ihmc_medication_code']} - + - host age - ${row['host age']} + host_age + ${row['host_age']} years - + - host body site - ${row['host body site']} + host_body_site + ${row['host_body_site']} - + - host height - ${row['host height']} - mm + host_height + ${row['host_height']} + m - + - host body-mass index - ${row['host body-mass index']} + host_bodymass_index + ${row['host_bodymass_index']} kg/m2 @@ -324,42 +324,42 @@ def mandatorytest(row, column, index): ${row['ethnicity']} - + - host occupation - ${row['host occupation']} + host_occupation + ${row['host_occupation']} - + - host total mass - ${row['host total mass']} + host_total_mass + ${row['host_total_mass']} kg - + - host phenotype - ${row['host phenotype']} + host_phenotype + ${row['host_phenotype']} - + - host body temperature - ${row['host body temperature']} + host_body_temperature + ${row['host_body_temperature']} ºC - + - host sex - ${row['host sex']} + host_sex + ${row['host_sex']} - + - host scientific name - ${row['host scientific name']} + host_scientific_name + ${row['host_scientific_name']} @@ -376,54 +376,54 @@ def mandatorytest(row, column, index): psu - + - source material identifiers - ${row['source material identifiers']} + source_material_identifiers + ${row['source_material_identifiers']} - + - time since last toothbrushing - ${row['time since last toothbrushing']} + time_since_last_toothbrushing + ${row['time_since_last_toothbrushing']} minutes - + - host diet - ${row['host diet']} + host_diet + ${row['host_diet']} - + - host last meal - ${row['host last meal']} + host_last_meal + ${row['host_last_meal']} - + - host family relationship - ${row['host family relationship']} + host_family_relationship + ${row['host_family_relationship']} - + - host genotype - ${row['host genotype']} + host_genotype + ${row['host_genotype']} - + - host pulse - ${row['host pulse']} + host_pulse + ${row['host_pulse']} bpm - + - host body product - ${row['host body product']} + host_body_product + ${row['host_body_product']} @@ -432,125 +432,125 @@ def mandatorytest(row, column, index): ${row['perturbation']} - + - negative control type - ${row['negative control type']} + negative_control_type + ${row['negative_control_type']} - + - positive control type - ${row['positive control type']} + positive_control_type + ${row['positive_control_type']} - + - experimental factor - ${row['experimental factor']} + experimental_factor + ${row['experimental_factor']} - + - encoded traits - ${row['encoded traits']} + encoded_traits + ${row['encoded_traits']} - + - subspecific genetic lineage - ${row['subspecific genetic lineage']} + subspecific_genetic_lineage + ${row['subspecific_genetic_lineage']} - + - taxonomic classification - ${row['taxonomic classification']} + taxonomic_classification + ${row['taxonomic_classification']} - + - isolation and growth condition - ${row['isolation and growth condition']} + isolation_and_growth_condition + ${row['isolation_and_growth_condition']} - + - annotation source - ${row['annotation source']} + annotation_source + ${row['annotation_source']} - + - reference for biomaterial - ${row['reference for biomaterial']} + reference_for_biomaterial + ${row['reference_for_biomaterial']} - + - sample material processing - ${row['sample material processing']} + sample_material_processing + ${row['sample_material_processing']} - + - sample volume or weight for DNA extraction - ${row['sample volume or weight for DNA extraction']} - ng + sample_volume_or_weight_for_dna_extraction + ${row['sample_volume_or_weight_for_dna_extraction']} + mL - + - nucleic acid extraction - ${row['nucleic acid extraction']} + nucleic_acid_extraction + ${row['nucleic_acid_extraction']} - + - nucleic acid amplification - ${row['nucleic acid amplification']} + nucleic_acid_amplification + ${row['nucleic_acid_amplification']} - + - library size - ${row['library size']} + library_size + ${row['library_size']} - + - library reads sequenced - ${row['library reads sequenced']} + library_reads_sequenced + ${row['library_reads_sequenced']} - + - library construction method - ${row['library construction method']} + library_construction_method + ${row['library_construction_method']} - + - library vector - ${row['library vector']} + library_vector + ${row['library_vector']} - + - library screening strategy - ${row['library screening strategy']} + library_screening_strategy + ${row['library_screening_strategy']} - + - pcr conditions - ${row['pcr conditions']} + pcr_conditions + ${row['pcr_conditions']} - + - pcr primers - ${row['pcr primers']} + pcr_primers + ${row['pcr_primers']} @@ -559,10 +559,10 @@ def mandatorytest(row, column, index): ${row['adapters']} - + - chemical administration - ${row['chemical administration']} + chemical_administration + ${row['chemical_administration']} diff --git a/ena_upload/templates/ENA_template_samples_ERC000017.xml b/ena_upload/templates/ENA_template_samples_ERC000017.xml index 96a13cb..7717530 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000017.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000017.xml @@ -33,28 +33,28 @@ def mandatorytest(row, column, index): ${row.sample_description} - + - trophic level - ${row['trophic level']} + trophic_level + ${row['trophic_level']} - + - observed biotic relationship - ${row['observed biotic relationship']} + observed_biotic_relationship + ${row['observed_biotic_relationship']} - + - known pathogenicity - ${row['known pathogenicity']} + known_pathogenicity + ${row['known_pathogenicity']} - + - relationship to oxygen - ${row['relationship to oxygen']} + relationship_to_oxygen + ${row['relationship_to_oxygen']} @@ -63,53 +63,53 @@ def mandatorytest(row, column, index): ${row['propagation']} - + - observed host symbionts - ${row['observed host symbionts']} + observed_host_symbionts + ${row['observed_host_symbionts']} - + - sample collection device - ${row['sample collection device']} + sample_collection_device + ${row['sample_collection_device']} - + - sample collection method - ${row['sample collection method']} + sample_collection_method + ${row['sample_collection_method']} - + - sample storage temperature - ${row['sample storage temperature']} + sample_storage_temperature + ${row['sample_storage_temperature']} °C - + - sample storage location - ${row['sample storage location']} + sample_storage_location + ${row['sample_storage_location']} - + - oxygenation status of sample - ${row['oxygenation status of sample']} + oxygenation_status_of_sample + ${row['oxygenation_status_of_sample']} - + - medical history performed - ${row['medical history performed']} + medical_history_performed + ${row['medical_history_performed']} - + - project name - ${row['project name']} + project_name + ${row['project_name']} @@ -118,70 +118,70 @@ def mandatorytest(row, column, index): ${row['ploidy']} - + - number of replicons - ${row['number of replicons']} + number_of_replicons + ${row['number_of_replicons']} - + - extrachromosomal elements - ${row['extrachromosomal elements']} + extrachromosomal_elements + ${row['extrachromosomal_elements']} - + - estimated size - ${row['estimated size']} + estimated_size + ${row['estimated_size']} - + - target gene - ${row['target gene']} + target_gene + ${row['target_gene']} - + - target subfragment - ${row['target subfragment']} + target_subfragment + ${row['target_subfragment']} - + - multiplex identifiers - ${row['multiplex identifiers']} + multiplex_identifiers + ${row['multiplex_identifiers']} - + - sequence quality check - ${row['sequence quality check']} + sequence_quality_check + ${row['sequence_quality_check']} - + - chimera check software - ${row['chimera check software']} + chimera_check_software + ${row['chimera_check_software']} - + - relevant electronic resources - ${row['relevant electronic resources']} + relevant_electronic_resources + ${row['relevant_electronic_resources']} - + - relevant standard operating procedures - ${row['relevant standard operating procedures']} + relevant_standard_operating_procedures + ${row['relevant_standard_operating_procedures']} - + - collection date - ${row['collection date']} + collection_date + ${row['collection_date']} @@ -191,42 +191,42 @@ def mandatorytest(row, column, index): m - + - geographic location (latitude) - ${row['geographic location (latitude)']} + geographic_location_latitude + ${row['geographic_location_latitude']} DD - + - geographic location (longitude) - ${row['geographic location (longitude)']} + geographic_location_longitude + ${row['geographic_location_longitude']} DD - + - geographic location (region and locality) - ${row['geographic location (region and locality)']} + geographic_location_region_and_locality + ${row['geographic_location_region_and_locality']} - + - broad-scale environmental context - ${row['broad-scale environmental context']} + broadscale_environmental_context + ${row['broadscale_environmental_context']} - + - local environmental context - ${row['local environmental context']} + local_environmental_context + ${row['local_environmental_context']} - + - environmental medium - ${row['environmental medium']} + environmental_medium + ${row['environmental_medium']} @@ -236,79 +236,79 @@ def mandatorytest(row, column, index): m - + - amount or size of sample collected - ${row['amount or size of sample collected']} - m3 + amount_or_size_of_sample_collected + ${row['amount_or_size_of_sample_collected']} + kg - + - organism count - ${row['organism count']} + organism_count + ${row['organism_count']} - + - sample storage duration - ${row['sample storage duration']} + sample_storage_duration + ${row['sample_storage_duration']} - + - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} + geographic_location_country_andor_sea + ${row['geographic_location_country_andor_sea']} - + - dermatology disorder - ${row['dermatology disorder']} + dermatology_disorder + ${row['dermatology_disorder']} - + - host disease status - ${row['host disease status']} + host_disease_status + ${row['host_disease_status']} - + - host subject id - ${row['host subject id']} + host_subject_id + ${row['host_subject_id']} - + - IHMC medication code - ${row['IHMC medication code']} + ihmc_medication_code + ${row['ihmc_medication_code']} - + - host age - ${row['host age']} + host_age + ${row['host_age']} years - + - host body site - ${row['host body site']} + host_body_site + ${row['host_body_site']} - + - host height - ${row['host height']} - mm + host_height + ${row['host_height']} + m - + - host body-mass index - ${row['host body-mass index']} + host_bodymass_index + ${row['host_bodymass_index']} kg/m2 @@ -318,42 +318,42 @@ def mandatorytest(row, column, index): ${row['ethnicity']} - + - host occupation - ${row['host occupation']} + host_occupation + ${row['host_occupation']} - + - host total mass - ${row['host total mass']} + host_total_mass + ${row['host_total_mass']} kg - + - host phenotype - ${row['host phenotype']} + host_phenotype + ${row['host_phenotype']} - + - host body temperature - ${row['host body temperature']} + host_body_temperature + ${row['host_body_temperature']} ºC - + - host sex - ${row['host sex']} + host_sex + ${row['host_sex']} - + - host scientific name - ${row['host scientific name']} + host_scientific_name + ${row['host_scientific_name']} @@ -370,60 +370,60 @@ def mandatorytest(row, column, index): psu - + - source material identifiers - ${row['source material identifiers']} + source_material_identifiers + ${row['source_material_identifiers']} - + - time since last wash - ${row['time since last wash']} + time_since_last_wash + ${row['time_since_last_wash']} minutes - + - dominant hand - ${row['dominant hand']} + dominant_hand + ${row['dominant_hand']} - + - host diet - ${row['host diet']} + host_diet + ${row['host_diet']} - + - host last meal - ${row['host last meal']} + host_last_meal + ${row['host_last_meal']} - + - host family relationship - ${row['host family relationship']} + host_family_relationship + ${row['host_family_relationship']} - + - host genotype - ${row['host genotype']} + host_genotype + ${row['host_genotype']} - + - host pulse - ${row['host pulse']} + host_pulse + ${row['host_pulse']} bpm - + - host body product - ${row['host body product']} + host_body_product + ${row['host_body_product']} @@ -432,125 +432,125 @@ def mandatorytest(row, column, index): ${row['perturbation']} - + - negative control type - ${row['negative control type']} + negative_control_type + ${row['negative_control_type']} - + - positive control type - ${row['positive control type']} + positive_control_type + ${row['positive_control_type']} - + - experimental factor - ${row['experimental factor']} + experimental_factor + ${row['experimental_factor']} - + - encoded traits - ${row['encoded traits']} + encoded_traits + ${row['encoded_traits']} - + - subspecific genetic lineage - ${row['subspecific genetic lineage']} + subspecific_genetic_lineage + ${row['subspecific_genetic_lineage']} - + - taxonomic classification - ${row['taxonomic classification']} + taxonomic_classification + ${row['taxonomic_classification']} - + - isolation and growth condition - ${row['isolation and growth condition']} + isolation_and_growth_condition + ${row['isolation_and_growth_condition']} - + - annotation source - ${row['annotation source']} + annotation_source + ${row['annotation_source']} - + - reference for biomaterial - ${row['reference for biomaterial']} + reference_for_biomaterial + ${row['reference_for_biomaterial']} - + - sample material processing - ${row['sample material processing']} + sample_material_processing + ${row['sample_material_processing']} - + - sample volume or weight for DNA extraction - ${row['sample volume or weight for DNA extraction']} - ng + sample_volume_or_weight_for_dna_extraction + ${row['sample_volume_or_weight_for_dna_extraction']} + mL - + - nucleic acid extraction - ${row['nucleic acid extraction']} + nucleic_acid_extraction + ${row['nucleic_acid_extraction']} - + - nucleic acid amplification - ${row['nucleic acid amplification']} + nucleic_acid_amplification + ${row['nucleic_acid_amplification']} - + - library size - ${row['library size']} + library_size + ${row['library_size']} - + - library reads sequenced - ${row['library reads sequenced']} + library_reads_sequenced + ${row['library_reads_sequenced']} - + - library construction method - ${row['library construction method']} + library_construction_method + ${row['library_construction_method']} - + - library vector - ${row['library vector']} + library_vector + ${row['library_vector']} - + - library screening strategy - ${row['library screening strategy']} + library_screening_strategy + ${row['library_screening_strategy']} - + - pcr conditions - ${row['pcr conditions']} + pcr_conditions + ${row['pcr_conditions']} - + - pcr primers - ${row['pcr primers']} + pcr_primers + ${row['pcr_primers']} @@ -559,10 +559,10 @@ def mandatorytest(row, column, index): ${row['adapters']} - + - chemical administration - ${row['chemical administration']} + chemical_administration + ${row['chemical_administration']} diff --git a/ena_upload/templates/ENA_template_samples_ERC000018.xml b/ena_upload/templates/ENA_template_samples_ERC000018.xml index c8f99dc..16f0691 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000018.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000018.xml @@ -33,28 +33,28 @@ def mandatorytest(row, column, index): ${row.sample_description} - + - trophic level - ${row['trophic level']} + trophic_level + ${row['trophic_level']} - + - observed biotic relationship - ${row['observed biotic relationship']} + observed_biotic_relationship + ${row['observed_biotic_relationship']} - + - known pathogenicity - ${row['known pathogenicity']} + known_pathogenicity + ${row['known_pathogenicity']} - + - relationship to oxygen - ${row['relationship to oxygen']} + relationship_to_oxygen + ${row['relationship_to_oxygen']} @@ -63,53 +63,53 @@ def mandatorytest(row, column, index): ${row['propagation']} - + - observed host symbionts - ${row['observed host symbionts']} + observed_host_symbionts + ${row['observed_host_symbionts']} - + - sample collection device - ${row['sample collection device']} + sample_collection_device + ${row['sample_collection_device']} - + - sample collection method - ${row['sample collection method']} + sample_collection_method + ${row['sample_collection_method']} - + - sample storage temperature - ${row['sample storage temperature']} + sample_storage_temperature + ${row['sample_storage_temperature']} °C - + - sample storage location - ${row['sample storage location']} + sample_storage_location + ${row['sample_storage_location']} - + - oxygenation status of sample - ${row['oxygenation status of sample']} + oxygenation_status_of_sample + ${row['oxygenation_status_of_sample']} - + - medical history performed - ${row['medical history performed']} + medical_history_performed + ${row['medical_history_performed']} - + - project name - ${row['project name']} + project_name + ${row['project_name']} @@ -118,70 +118,70 @@ def mandatorytest(row, column, index): ${row['ploidy']} - + - number of replicons - ${row['number of replicons']} + number_of_replicons + ${row['number_of_replicons']} - + - extrachromosomal elements - ${row['extrachromosomal elements']} + extrachromosomal_elements + ${row['extrachromosomal_elements']} - + - estimated size - ${row['estimated size']} + estimated_size + ${row['estimated_size']} - + - target gene - ${row['target gene']} + target_gene + ${row['target_gene']} - + - target subfragment - ${row['target subfragment']} + target_subfragment + ${row['target_subfragment']} - + - multiplex identifiers - ${row['multiplex identifiers']} + multiplex_identifiers + ${row['multiplex_identifiers']} - + - sequence quality check - ${row['sequence quality check']} + sequence_quality_check + ${row['sequence_quality_check']} - + - chimera check software - ${row['chimera check software']} + chimera_check_software + ${row['chimera_check_software']} - + - relevant electronic resources - ${row['relevant electronic resources']} + relevant_electronic_resources + ${row['relevant_electronic_resources']} - + - relevant standard operating procedures - ${row['relevant standard operating procedures']} + relevant_standard_operating_procedures + ${row['relevant_standard_operating_procedures']} - + - collection date - ${row['collection date']} + collection_date + ${row['collection_date']} @@ -191,42 +191,42 @@ def mandatorytest(row, column, index): m - + - geographic location (latitude) - ${row['geographic location (latitude)']} + geographic_location_latitude + ${row['geographic_location_latitude']} DD - + - geographic location (longitude) - ${row['geographic location (longitude)']} + geographic_location_longitude + ${row['geographic_location_longitude']} DD - + - geographic location (region and locality) - ${row['geographic location (region and locality)']} + geographic_location_region_and_locality + ${row['geographic_location_region_and_locality']} - + - broad-scale environmental context - ${row['broad-scale environmental context']} + broadscale_environmental_context + ${row['broadscale_environmental_context']} - + - local environmental context - ${row['local environmental context']} + local_environmental_context + ${row['local_environmental_context']} - + - environmental medium - ${row['environmental medium']} + environmental_medium + ${row['environmental_medium']} @@ -236,85 +236,85 @@ def mandatorytest(row, column, index): m - + - amount or size of sample collected - ${row['amount or size of sample collected']} - m3 + amount_or_size_of_sample_collected + ${row['amount_or_size_of_sample_collected']} + kg - + - organism count - ${row['organism count']} + organism_count + ${row['organism_count']} - + - sample storage duration - ${row['sample storage duration']} + sample_storage_duration + ${row['sample_storage_duration']} - + - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} + geographic_location_country_andor_sea + ${row['geographic_location_country_andor_sea']} - + - gynecological disorder - ${row['gynecological disorder']} + gynecological_disorder + ${row['gynecological_disorder']} - + - urogenital disorder - ${row['urogenital disorder']} + urogenital_disorder + ${row['urogenital_disorder']} - + - host disease status - ${row['host disease status']} + host_disease_status + ${row['host_disease_status']} - + - host subject id - ${row['host subject id']} + host_subject_id + ${row['host_subject_id']} - + - IHMC medication code - ${row['IHMC medication code']} + ihmc_medication_code + ${row['ihmc_medication_code']} - + - host age - ${row['host age']} + host_age + ${row['host_age']} years - + - host body site - ${row['host body site']} + host_body_site + ${row['host_body_site']} - + - host height - ${row['host height']} - mm + host_height + ${row['host_height']} + m - + - host body-mass index - ${row['host body-mass index']} + host_bodymass_index + ${row['host_bodymass_index']} kg/m2 @@ -324,42 +324,42 @@ def mandatorytest(row, column, index): ${row['ethnicity']} - + - host occupation - ${row['host occupation']} + host_occupation + ${row['host_occupation']} - + - host total mass - ${row['host total mass']} + host_total_mass + ${row['host_total_mass']} kg - + - host phenotype - ${row['host phenotype']} + host_phenotype + ${row['host_phenotype']} - + - host body temperature - ${row['host body temperature']} + host_body_temperature + ${row['host_body_temperature']} ºC - + - host sex - ${row['host sex']} + host_sex + ${row['host_sex']} - + - host scientific name - ${row['host scientific name']} + host_scientific_name + ${row['host_scientific_name']} @@ -369,10 +369,10 @@ def mandatorytest(row, column, index): ºC - + - sample salinity - ${row['sample salinity']} + sample_salinity + ${row['sample_salinity']} psu @@ -383,10 +383,10 @@ def mandatorytest(row, column, index): psu - + - source material identifiers - ${row['source material identifiers']} + source_material_identifiers + ${row['source_material_identifiers']} @@ -395,10 +395,10 @@ def mandatorytest(row, column, index): ${row['menarche']} - + - sexual activity - ${row['sexual activity']} + sexual_activity + ${row['sexual_activity']} @@ -413,10 +413,10 @@ def mandatorytest(row, column, index): ${row['douche']} - + - birth control - ${row['birth control']} + birth_control + ${row['birth_control']} @@ -425,10 +425,10 @@ def mandatorytest(row, column, index): ${row['menopause']} - + - HRT - ${row['HRT']} + hrt + ${row['hrt']} @@ -437,41 +437,41 @@ def mandatorytest(row, column, index): ${row['hysterectomy']} - + - host diet - ${row['host diet']} + host_diet + ${row['host_diet']} - + - host last meal - ${row['host last meal']} + host_last_meal + ${row['host_last_meal']} - + - host family relationship - ${row['host family relationship']} + host_family_relationship + ${row['host_family_relationship']} - + - host genotype - ${row['host genotype']} + host_genotype + ${row['host_genotype']} - + - host pulse - ${row['host pulse']} + host_pulse + ${row['host_pulse']} bpm - + - host body product - ${row['host body product']} + host_body_product + ${row['host_body_product']} @@ -480,125 +480,125 @@ def mandatorytest(row, column, index): ${row['perturbation']} - + - negative control type - ${row['negative control type']} + negative_control_type + ${row['negative_control_type']} - + - positive control type - ${row['positive control type']} + positive_control_type + ${row['positive_control_type']} - + - experimental factor - ${row['experimental factor']} + experimental_factor + ${row['experimental_factor']} - + - encoded traits - ${row['encoded traits']} + encoded_traits + ${row['encoded_traits']} - + - subspecific genetic lineage - ${row['subspecific genetic lineage']} + subspecific_genetic_lineage + ${row['subspecific_genetic_lineage']} - + - taxonomic classification - ${row['taxonomic classification']} + taxonomic_classification + ${row['taxonomic_classification']} - + - isolation and growth condition - ${row['isolation and growth condition']} + isolation_and_growth_condition + ${row['isolation_and_growth_condition']} - + - annotation source - ${row['annotation source']} + annotation_source + ${row['annotation_source']} - + - reference for biomaterial - ${row['reference for biomaterial']} + reference_for_biomaterial + ${row['reference_for_biomaterial']} - + - sample material processing - ${row['sample material processing']} + sample_material_processing + ${row['sample_material_processing']} - + - sample volume or weight for DNA extraction - ${row['sample volume or weight for DNA extraction']} - ng + sample_volume_or_weight_for_dna_extraction + ${row['sample_volume_or_weight_for_dna_extraction']} + mL - + - nucleic acid extraction - ${row['nucleic acid extraction']} + nucleic_acid_extraction + ${row['nucleic_acid_extraction']} - + - nucleic acid amplification - ${row['nucleic acid amplification']} + nucleic_acid_amplification + ${row['nucleic_acid_amplification']} - + - library size - ${row['library size']} + library_size + ${row['library_size']} - + - library reads sequenced - ${row['library reads sequenced']} + library_reads_sequenced + ${row['library_reads_sequenced']} - + - library construction method - ${row['library construction method']} + library_construction_method + ${row['library_construction_method']} - + - library vector - ${row['library vector']} + library_vector + ${row['library_vector']} - + - library screening strategy - ${row['library screening strategy']} + library_screening_strategy + ${row['library_screening_strategy']} - + - pcr conditions - ${row['pcr conditions']} + pcr_conditions + ${row['pcr_conditions']} - + - pcr primers - ${row['pcr primers']} + pcr_primers + ${row['pcr_primers']} @@ -607,10 +607,10 @@ def mandatorytest(row, column, index): ${row['adapters']} - + - chemical administration - ${row['chemical administration']} + chemical_administration + ${row['chemical_administration']} diff --git a/ena_upload/templates/ENA_template_samples_ERC000019.xml b/ena_upload/templates/ENA_template_samples_ERC000019.xml index 48595bb..e370393 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000019.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000019.xml @@ -33,28 +33,28 @@ def mandatorytest(row, column, index): ${row.sample_description} - + - trophic level - ${row['trophic level']} + trophic_level + ${row['trophic_level']} - + - observed biotic relationship - ${row['observed biotic relationship']} + observed_biotic_relationship + ${row['observed_biotic_relationship']} - + - known pathogenicity - ${row['known pathogenicity']} + known_pathogenicity + ${row['known_pathogenicity']} - + - relationship to oxygen - ${row['relationship to oxygen']} + relationship_to_oxygen + ${row['relationship_to_oxygen']} @@ -63,41 +63,41 @@ def mandatorytest(row, column, index): ${row['propagation']} - + - sample collection device - ${row['sample collection device']} + sample_collection_device + ${row['sample_collection_device']} - + - sample collection method - ${row['sample collection method']} + sample_collection_method + ${row['sample_collection_method']} - + - sample storage temperature - ${row['sample storage temperature']} + sample_storage_temperature + ${row['sample_storage_temperature']} °C - + - sample storage location - ${row['sample storage location']} + sample_storage_location + ${row['sample_storage_location']} - + - oxygenation status of sample - ${row['oxygenation status of sample']} + oxygenation_status_of_sample + ${row['oxygenation_status_of_sample']} - + - project name - ${row['project name']} + project_name + ${row['project_name']} @@ -106,70 +106,70 @@ def mandatorytest(row, column, index): ${row['ploidy']} - + - number of replicons - ${row['number of replicons']} + number_of_replicons + ${row['number_of_replicons']} - + - extrachromosomal elements - ${row['extrachromosomal elements']} + extrachromosomal_elements + ${row['extrachromosomal_elements']} - + - estimated size - ${row['estimated size']} + estimated_size + ${row['estimated_size']} - + - target gene - ${row['target gene']} + target_gene + ${row['target_gene']} - + - target subfragment - ${row['target subfragment']} + target_subfragment + ${row['target_subfragment']} - + - multiplex identifiers - ${row['multiplex identifiers']} + multiplex_identifiers + ${row['multiplex_identifiers']} - + - sequence quality check - ${row['sequence quality check']} + sequence_quality_check + ${row['sequence_quality_check']} - + - chimera check software - ${row['chimera check software']} + chimera_check_software + ${row['chimera_check_software']} - + - relevant electronic resources - ${row['relevant electronic resources']} + relevant_electronic_resources + ${row['relevant_electronic_resources']} - + - relevant standard operating procedures - ${row['relevant standard operating procedures']} + relevant_standard_operating_procedures + ${row['relevant_standard_operating_procedures']} - + - collection date - ${row['collection date']} + collection_date + ${row['collection_date']} @@ -179,42 +179,42 @@ def mandatorytest(row, column, index): m - + - geographic location (latitude) - ${row['geographic location (latitude)']} + geographic_location_latitude + ${row['geographic_location_latitude']} DD - + - geographic location (longitude) - ${row['geographic location (longitude)']} + geographic_location_longitude + ${row['geographic_location_longitude']} DD - + - geographic location (region and locality) - ${row['geographic location (region and locality)']} + geographic_location_region_and_locality + ${row['geographic_location_region_and_locality']} - + - broad-scale environmental context - ${row['broad-scale environmental context']} + broadscale_environmental_context + ${row['broadscale_environmental_context']} - + - local environmental context - ${row['local environmental context']} + local_environmental_context + ${row['local_environmental_context']} - + - environmental medium - ${row['environmental medium']} + environmental_medium + ${row['environmental_medium']} @@ -224,61 +224,61 @@ def mandatorytest(row, column, index): m - + - amount or size of sample collected - ${row['amount or size of sample collected']} - m3 + amount_or_size_of_sample_collected + ${row['amount_or_size_of_sample_collected']} + kg biomass ${row['biomass']} - t + kg - + - organism count - ${row['organism count']} + organism_count + ${row['organism_count']} - + - sample storage duration - ${row['sample storage duration']} + sample_storage_duration + ${row['sample_storage_duration']} - + - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} + geographic_location_country_andor_sea + ${row['geographic_location_country_andor_sea']} - + - host disease status - ${row['host disease status']} + host_disease_status + ${row['host_disease_status']} - + - host scientific name - ${row['host scientific name']} + host_scientific_name + ${row['host_scientific_name']} - + - mean friction velocity - ${row['mean friction velocity']} + mean_friction_velocity + ${row['mean_friction_velocity']} m/s - + - mean peak friction velocity - ${row['mean peak friction velocity']} + mean_peak_friction_velocity + ${row['mean_peak_friction_velocity']} m/s @@ -286,7 +286,7 @@ def mandatorytest(row, column, index): pressure ${row['pressure']} - bar + atm @@ -303,30 +303,30 @@ def mandatorytest(row, column, index): NTU - + - pH - ${row['pH']} + ph + ${row['ph']} - + - water content - ${row['water content']} + water_content + ${row['water_content']} g/g - + - alkyl diethers - ${row['alkyl diethers']} + alkyl_diethers + ${row['alkyl_diethers']} µg/L - + - aminopeptidase activity - ${row['aminopeptidase activity']} + aminopeptidase_activity + ${row['aminopeptidase_activity']} mol/L/h @@ -337,10 +337,10 @@ def mandatorytest(row, column, index): µmol/L - + - bacterial carbon production - ${row['bacterial carbon production']} + bacterial_carbon_production + ${row['bacterial_carbon_production']} ng/h @@ -348,7 +348,7 @@ def mandatorytest(row, column, index): bishomohopanol ${row['bishomohopanol']} - µg/g + µg/L @@ -362,13 +362,13 @@ def mandatorytest(row, column, index): calcium ${row['calcium']} - µmol/L + mg/L - + - carbon/nitrogen ratio - ${row['carbon/nitrogen ratio']} + carbonnitrogen_ratio + ${row['carbonnitrogen_ratio']} @@ -385,45 +385,45 @@ def mandatorytest(row, column, index): µg/L - + - diether lipids - ${row['diether lipids']} + diether_lipids + ${row['diether_lipids']} ng/L - + - dissolved carbon dioxide - ${row['dissolved carbon dioxide']} + dissolved_carbon_dioxide + ${row['dissolved_carbon_dioxide']} µmol/L - + - dissolved hydrogen - ${row['dissolved hydrogen']} + dissolved_hydrogen + ${row['dissolved_hydrogen']} µmol/L - + - dissolved inorganic carbon - ${row['dissolved inorganic carbon']} + dissolved_inorganic_carbon + ${row['dissolved_inorganic_carbon']} µg/L - + - dissolved organic carbon - ${row['dissolved organic carbon']} + dissolved_organic_carbon + ${row['dissolved_organic_carbon']} µmol/L - + - dissolved organic nitrogen - ${row['dissolved organic nitrogen']} + dissolved_organic_nitrogen + ${row['dissolved_organic_nitrogen']} µg/L @@ -434,17 +434,17 @@ def mandatorytest(row, column, index): µM/L - + - dissolved oxygen - ${row['dissolved oxygen']} + dissolved_oxygen + ${row['dissolved_oxygen']} µmol/kg - + - glucosidase activity - ${row['glucosidase activity']} + glucosidase_activity + ${row['glucosidase_activity']} mol/L/h @@ -452,13 +452,13 @@ def mandatorytest(row, column, index): magnesium ${row['magnesium']} - parts/million + mg/L - + - n-alkanes - ${row['n-alkanes']} + nalkanes + ${row['nalkanes']} µmol/L @@ -476,45 +476,45 @@ def mandatorytest(row, column, index): µmol/L - + - total nitrogen concentration - ${row['total nitrogen concentration']} + total_nitrogen_concentration + ${row['total_nitrogen_concentration']} µmol/L - + - organic carbon - ${row['organic carbon']} + organic_carbon + ${row['organic_carbon']} µmol/L - + - organic matter - ${row['organic matter']} + organic_matter + ${row['organic_matter']} µg/L - + - organic nitrogen - ${row['organic nitrogen']} + organic_nitrogen + ${row['organic_nitrogen']} µg/L - + - particulate organic carbon - ${row['particulate organic carbon']} + particulate_organic_carbon + ${row['particulate_organic_carbon']} µg/L - + - petroleum hydrocarbon - ${row['petroleum hydrocarbon']} + petroleum_hydrocarbon + ${row['petroleum_hydrocarbon']} µmol/L @@ -532,10 +532,10 @@ def mandatorytest(row, column, index): µmol/L - + - phospholipid fatty acid - ${row['phospholipid fatty acid']} + phospholipid_fatty_acid + ${row['phospholipid_fatty_acid']} mol/g @@ -546,10 +546,10 @@ def mandatorytest(row, column, index): µmol/L - + - redox potential - ${row['redox potential']} + redox_potential + ${row['redox_potential']} mV @@ -560,10 +560,10 @@ def mandatorytest(row, column, index): psu - + - total carbon - ${row['total carbon']} + total_carbon + ${row['total_carbon']} µg/L @@ -581,10 +581,10 @@ def mandatorytest(row, column, index): µmol/L - + - total organic carbon - ${row['total organic carbon']} + total_organic_carbon + ${row['total_organic_carbon']} g/kg @@ -592,21 +592,21 @@ def mandatorytest(row, column, index): sulfate ${row['sulfate']} - µmol/L + mg/L sulfide ${row['sulfide']} - µmol/L + mg/L - + - total nitrogen content - ${row['total nitrogen content']} - µmol/L + total_nitrogen_content + ${row['total_nitrogen_content']} + µg/L @@ -616,10 +616,10 @@ def mandatorytest(row, column, index): mEq/L - + - source material identifiers - ${row['source material identifiers']} + source_material_identifiers + ${row['source_material_identifiers']} @@ -628,125 +628,125 @@ def mandatorytest(row, column, index): ${row['perturbation']} - + - negative control type - ${row['negative control type']} + negative_control_type + ${row['negative_control_type']} - + - positive control type - ${row['positive control type']} + positive_control_type + ${row['positive_control_type']} - + - experimental factor - ${row['experimental factor']} + experimental_factor + ${row['experimental_factor']} - + - encoded traits - ${row['encoded traits']} + encoded_traits + ${row['encoded_traits']} - + - subspecific genetic lineage - ${row['subspecific genetic lineage']} + subspecific_genetic_lineage + ${row['subspecific_genetic_lineage']} - + - taxonomic classification - ${row['taxonomic classification']} + taxonomic_classification + ${row['taxonomic_classification']} - + - isolation and growth condition - ${row['isolation and growth condition']} + isolation_and_growth_condition + ${row['isolation_and_growth_condition']} - + - annotation source - ${row['annotation source']} + annotation_source + ${row['annotation_source']} - + - reference for biomaterial - ${row['reference for biomaterial']} + reference_for_biomaterial + ${row['reference_for_biomaterial']} - + - sample material processing - ${row['sample material processing']} + sample_material_processing + ${row['sample_material_processing']} - + - sample volume or weight for DNA extraction - ${row['sample volume or weight for DNA extraction']} - ng + sample_volume_or_weight_for_dna_extraction + ${row['sample_volume_or_weight_for_dna_extraction']} + mL - + - nucleic acid extraction - ${row['nucleic acid extraction']} + nucleic_acid_extraction + ${row['nucleic_acid_extraction']} - + - nucleic acid amplification - ${row['nucleic acid amplification']} + nucleic_acid_amplification + ${row['nucleic_acid_amplification']} - + - library size - ${row['library size']} + library_size + ${row['library_size']} - + - library reads sequenced - ${row['library reads sequenced']} + library_reads_sequenced + ${row['library_reads_sequenced']} - + - library construction method - ${row['library construction method']} + library_construction_method + ${row['library_construction_method']} - + - library vector - ${row['library vector']} + library_vector + ${row['library_vector']} - + - library screening strategy - ${row['library screening strategy']} + library_screening_strategy + ${row['library_screening_strategy']} - + - pcr conditions - ${row['pcr conditions']} + pcr_conditions + ${row['pcr_conditions']} - + - pcr primers - ${row['pcr primers']} + pcr_primers + ${row['pcr_primers']} @@ -759,13 +759,13 @@ def mandatorytest(row, column, index): depth ${row['depth']} - mm + m - + - chemical administration - ${row['chemical administration']} + chemical_administration + ${row['chemical_administration']} diff --git a/ena_upload/templates/ENA_template_samples_ERC000020.xml b/ena_upload/templates/ENA_template_samples_ERC000020.xml index 3823752..16ef234 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000020.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000020.xml @@ -33,28 +33,28 @@ def mandatorytest(row, column, index): ${row.sample_description} - + - trophic level - ${row['trophic level']} + trophic_level + ${row['trophic_level']} - + - observed biotic relationship - ${row['observed biotic relationship']} + observed_biotic_relationship + ${row['observed_biotic_relationship']} - + - known pathogenicity - ${row['known pathogenicity']} + known_pathogenicity + ${row['known_pathogenicity']} - + - relationship to oxygen - ${row['relationship to oxygen']} + relationship_to_oxygen + ${row['relationship_to_oxygen']} @@ -63,65 +63,65 @@ def mandatorytest(row, column, index): ${row['propagation']} - + - observed host symbionts - ${row['observed host symbionts']} + observed_host_symbionts + ${row['observed_host_symbionts']} - + - sample collection device - ${row['sample collection device']} + sample_collection_device + ${row['sample_collection_device']} - + - sample collection method - ${row['sample collection method']} + sample_collection_method + ${row['sample_collection_method']} - + - sample storage temperature - ${row['sample storage temperature']} + sample_storage_temperature + ${row['sample_storage_temperature']} °C - + - sample storage location - ${row['sample storage location']} + sample_storage_location + ${row['sample_storage_location']} - + - growth facility - ${row['growth facility']} + growth_facility + ${row['growth_facility']} - + - sample disease stage - ${row['sample disease stage']} + sample_disease_stage + ${row['sample_disease_stage']} - + - oxygenation status of sample - ${row['oxygenation status of sample']} + oxygenation_status_of_sample + ${row['oxygenation_status_of_sample']} - + - sample disease status - ${row['sample disease status']} + sample_disease_status + ${row['sample_disease_status']} - + - project name - ${row['project name']} + project_name + ${row['project_name']} @@ -130,70 +130,70 @@ def mandatorytest(row, column, index): ${row['ploidy']} - + - number of replicons - ${row['number of replicons']} + number_of_replicons + ${row['number_of_replicons']} - + - extrachromosomal elements - ${row['extrachromosomal elements']} + extrachromosomal_elements + ${row['extrachromosomal_elements']} - + - estimated size - ${row['estimated size']} + estimated_size + ${row['estimated_size']} - + - target gene - ${row['target gene']} + target_gene + ${row['target_gene']} - + - target subfragment - ${row['target subfragment']} + target_subfragment + ${row['target_subfragment']} - + - multiplex identifiers - ${row['multiplex identifiers']} + multiplex_identifiers + ${row['multiplex_identifiers']} - + - sequence quality check - ${row['sequence quality check']} + sequence_quality_check + ${row['sequence_quality_check']} - + - chimera check software - ${row['chimera check software']} + chimera_check_software + ${row['chimera_check_software']} - + - relevant electronic resources - ${row['relevant electronic resources']} + relevant_electronic_resources + ${row['relevant_electronic_resources']} - + - relevant standard operating procedures - ${row['relevant standard operating procedures']} + relevant_standard_operating_procedures + ${row['relevant_standard_operating_procedures']} - + - collection date - ${row['collection date']} + collection_date + ${row['collection_date']} @@ -203,42 +203,42 @@ def mandatorytest(row, column, index): m - + - geographic location (latitude) - ${row['geographic location (latitude)']} + geographic_location_latitude + ${row['geographic_location_latitude']} DD - + - geographic location (longitude) - ${row['geographic location (longitude)']} + geographic_location_longitude + ${row['geographic_location_longitude']} DD - + - geographic location (region and locality) - ${row['geographic location (region and locality)']} + geographic_location_region_and_locality + ${row['geographic_location_region_and_locality']} - + - broad-scale environmental context - ${row['broad-scale environmental context']} + broadscale_environmental_context + ${row['broadscale_environmental_context']} - + - local environmental context - ${row['local environmental context']} + local_environmental_context + ${row['local_environmental_context']} - + - environmental medium - ${row['environmental medium']} + environmental_medium + ${row['environmental_medium']} @@ -248,147 +248,147 @@ def mandatorytest(row, column, index): m - + - amount or size of sample collected - ${row['amount or size of sample collected']} - m3 + amount_or_size_of_sample_collected + ${row['amount_or_size_of_sample_collected']} + kg - + - organism count - ${row['organism count']} + organism_count + ${row['organism_count']} - + - sample capture status - ${row['sample capture status']} + sample_capture_status + ${row['sample_capture_status']} - + - growth habit - ${row['growth habit']} + growth_habit + ${row['growth_habit']} - + - plant sex - ${row['plant sex']} + plant_sex + ${row['plant_sex']} - + - plant structure - ${row['plant structure']} + plant_structure + ${row['plant_structure']} - + - sample storage duration - ${row['sample storage duration']} + sample_storage_duration + ${row['sample_storage_duration']} - + - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} + geographic_location_country_andor_sea + ${row['geographic_location_country_andor_sea']} - + - host disease status - ${row['host disease status']} + host_disease_status + ${row['host_disease_status']} - + - host common name - ${row['host common name']} + host_common_name + ${row['host_common_name']} - + - host age - ${row['host age']} + host_age + ${row['host_age']} years - + - host taxid - ${row['host taxid']} + host_taxid + ${row['host_taxid']} - + - host life stage - ${row['host life stage']} + host_life_stage + ${row['host_life_stage']} - + - host height - ${row['host height']} - mm + host_height + ${row['host_height']} + m - + - host length - ${row['host length']} - mm + host_length + ${row['host_length']} + m - + - plant body site - ${row['plant body site']} + plant_body_site + ${row['plant_body_site']} - + - host total mass - ${row['host total mass']} + host_total_mass + ${row['host_total_mass']} kg - + - host phenotype - ${row['host phenotype']} + host_phenotype + ${row['host_phenotype']} - + - host scientific name - ${row['host scientific name']} + host_scientific_name + ${row['host_scientific_name']} - + - host subspecific genetic lineage - ${row['host subspecific genetic lineage']} + host_subspecific_genetic_lineage + ${row['host_subspecific_genetic_lineage']} - + - climate environment - ${row['climate environment']} + climate_environment + ${row['climate_environment']} - + - gaseous environment - ${row['gaseous environment']} + gaseous_environment + ${row['gaseous_environment']} - + - seasonal environment - ${row['seasonal environment']} + seasonal_environment + ${row['seasonal_environment']} @@ -405,30 +405,30 @@ def mandatorytest(row, column, index): psu - + - source material identifiers - ${row['source material identifiers']} + source_material_identifiers + ${row['source_material_identifiers']} - + - host genotype - ${row['host genotype']} + host_genotype + ${row['host_genotype']} - + - host dry mass - ${row['host dry mass']} - mg + host_dry_mass + ${row['host_dry_mass']} + kg - + - host wet mass - ${row['host wet mass']} - mg + host_wet_mass + ${row['host_wet_mass']} + kg @@ -437,197 +437,197 @@ def mandatorytest(row, column, index): ${row['perturbation']} - + - negative control type - ${row['negative control type']} + negative_control_type + ${row['negative_control_type']} - + - positive control type - ${row['positive control type']} + positive_control_type + ${row['positive_control_type']} - + - experimental factor - ${row['experimental factor']} + experimental_factor + ${row['experimental_factor']} - + - encoded traits - ${row['encoded traits']} + encoded_traits + ${row['encoded_traits']} - + - genetic modification - ${row['genetic modification']} + genetic_modification + ${row['genetic_modification']} - + - subspecific genetic lineage - ${row['subspecific genetic lineage']} + subspecific_genetic_lineage + ${row['subspecific_genetic_lineage']} - + - ancestral data - ${row['ancestral data']} + ancestral_data + ${row['ancestral_data']} - + - taxonomic classification - ${row['taxonomic classification']} + taxonomic_classification + ${row['taxonomic_classification']} - + - plant growth medium - ${row['plant growth medium']} + plant_growth_medium + ${row['plant_growth_medium']} - + - rooting conditions - ${row['rooting conditions']} + rooting_conditions + ${row['rooting_conditions']} - + - culture rooting medium - ${row['culture rooting medium']} + culture_rooting_medium + ${row['culture_rooting_medium']} - + - rooting medium macronutrients - ${row['rooting medium macronutrients']} + rooting_medium_macronutrients + ${row['rooting_medium_macronutrients']} - + - rooting medium micronutrients - ${row['rooting medium micronutrients']} + rooting_medium_micronutrients + ${row['rooting_medium_micronutrients']} - + - rooting medium organic supplements - ${row['rooting medium organic supplements']} + rooting_medium_organic_supplements + ${row['rooting_medium_organic_supplements']} - + - rooting medium carbon - ${row['rooting medium carbon']} + rooting_medium_carbon + ${row['rooting_medium_carbon']} - + - rooting medium regulators - ${row['rooting medium regulators']} + rooting_medium_regulators + ${row['rooting_medium_regulators']} - + - rooting medium solidifier - ${row['rooting medium solidifier']} + rooting_medium_solidifier + ${row['rooting_medium_solidifier']} - + - rooting medium pH - ${row['rooting medium pH']} + rooting_medium_ph + ${row['rooting_medium_ph']} - + - isolation and growth condition - ${row['isolation and growth condition']} + isolation_and_growth_condition + ${row['isolation_and_growth_condition']} - + - annotation source - ${row['annotation source']} + annotation_source + ${row['annotation_source']} - + - reference for biomaterial - ${row['reference for biomaterial']} + reference_for_biomaterial + ${row['reference_for_biomaterial']} - + - sample material processing - ${row['sample material processing']} + sample_material_processing + ${row['sample_material_processing']} - + - sample volume or weight for DNA extraction - ${row['sample volume or weight for DNA extraction']} - ng + sample_volume_or_weight_for_dna_extraction + ${row['sample_volume_or_weight_for_dna_extraction']} + mL - + - nucleic acid extraction - ${row['nucleic acid extraction']} + nucleic_acid_extraction + ${row['nucleic_acid_extraction']} - + - nucleic acid amplification - ${row['nucleic acid amplification']} + nucleic_acid_amplification + ${row['nucleic_acid_amplification']} - + - library size - ${row['library size']} + library_size + ${row['library_size']} - + - library reads sequenced - ${row['library reads sequenced']} + library_reads_sequenced + ${row['library_reads_sequenced']} - + - library construction method - ${row['library construction method']} + library_construction_method + ${row['library_construction_method']} - + - library vector - ${row['library vector']} + library_vector + ${row['library_vector']} - + - library screening strategy - ${row['library screening strategy']} + library_screening_strategy + ${row['library_screening_strategy']} - + - pcr conditions - ${row['pcr conditions']} + pcr_conditions + ${row['pcr_conditions']} - + - pcr primers - ${row['pcr primers']} + pcr_primers + ${row['pcr_primers']} @@ -636,47 +636,47 @@ def mandatorytest(row, column, index): ${row['adapters']} - + - plant product - ${row['plant product']} + plant_product + ${row['plant_product']} depth ${row['depth']} - mm + m - + - air temperature regimen - ${row['air temperature regimen']} + air_temperature_regimen + ${row['air_temperature_regimen']} - + - antibiotic regimen - ${row['antibiotic regimen']} + antibiotic_regimen + ${row['antibiotic_regimen']} - + - chemical mutagen - ${row['chemical mutagen']} + chemical_mutagen + ${row['chemical_mutagen']} - + - fertilizer administration - ${row['fertilizer administration']} + fertilizer_administration + ${row['fertilizer_administration']} - + - fungicide regimen - ${row['fungicide regimen']} + fungicide_regimen + ${row['fungicide_regimen']} @@ -685,118 +685,118 @@ def mandatorytest(row, column, index): ${row['gravity']} - + - growth hormone regimen - ${row['growth hormone regimen']} + growth_hormone_regimen + ${row['growth_hormone_regimen']} - + - growth media - ${row['growth media']} + growth_media + ${row['growth_media']} - + - herbicide regimen - ${row['herbicide regimen']} + herbicide_regimen + ${row['herbicide_regimen']} - + - humidity regimen - ${row['humidity regimen']} + humidity_regimen + ${row['humidity_regimen']} - + - mineral nutrient regimen - ${row['mineral nutrient regimen']} + mineral_nutrient_regimen + ${row['mineral_nutrient_regimen']} - + - non-mineral nutrient regimen - ${row['non-mineral nutrient regimen']} + nonmineral_nutrient_regimen + ${row['nonmineral_nutrient_regimen']} - + - pesticide regimen - ${row['pesticide regimen']} + pesticide_regimen + ${row['pesticide_regimen']} - + - pH regimen - ${row['pH regimen']} + ph_regimen + ${row['ph_regimen']} - + - radiation regimen - ${row['radiation regimen']} + radiation_regimen + ${row['radiation_regimen']} - + - rainfall regimen - ${row['rainfall regimen']} + rainfall_regimen + ${row['rainfall_regimen']} - + - salt regimen - ${row['salt regimen']} + salt_regimen + ${row['salt_regimen']} - + - standing water regimen - ${row['standing water regimen']} + standing_water_regimen + ${row['standing_water_regimen']} - + - tissue culture growth media - ${row['tissue culture growth media']} + tissue_culture_growth_media + ${row['tissue_culture_growth_media']} - + - watering regimen - ${row['watering regimen']} + watering_regimen + ${row['watering_regimen']} - + - water temperature regimen - ${row['water temperature regimen']} + water_temperature_regimen + ${row['water_temperature_regimen']} - + - light regimen - ${row['light regimen']} + light_regimen + ${row['light_regimen']} - + - biotic regimen - ${row['biotic regimen']} + biotic_regimen + ${row['biotic_regimen']} - + - mechanical damage - ${row['mechanical damage']} + mechanical_damage + ${row['mechanical_damage']} - + - chemical administration - ${row['chemical administration']} + chemical_administration + ${row['chemical_administration']} diff --git a/ena_upload/templates/ENA_template_samples_ERC000021.xml b/ena_upload/templates/ENA_template_samples_ERC000021.xml index 4e758fe..62eb631 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000021.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000021.xml @@ -33,28 +33,28 @@ def mandatorytest(row, column, index): ${row.sample_description} - + - trophic level - ${row['trophic level']} + trophic_level + ${row['trophic_level']} - + - observed biotic relationship - ${row['observed biotic relationship']} + observed_biotic_relationship + ${row['observed_biotic_relationship']} - + - known pathogenicity - ${row['known pathogenicity']} + known_pathogenicity + ${row['known_pathogenicity']} - + - relationship to oxygen - ${row['relationship to oxygen']} + relationship_to_oxygen + ${row['relationship_to_oxygen']} @@ -63,47 +63,47 @@ def mandatorytest(row, column, index): ${row['propagation']} - + - sample collection device - ${row['sample collection device']} + sample_collection_device + ${row['sample_collection_device']} - + - sample collection method - ${row['sample collection method']} + sample_collection_method + ${row['sample_collection_method']} - + - sample storage temperature - ${row['sample storage temperature']} + sample_storage_temperature + ${row['sample_storage_temperature']} °C - + - sample storage location - ${row['sample storage location']} + sample_storage_location + ${row['sample_storage_location']} - + - particle classification - ${row['particle classification']} + particle_classification + ${row['particle_classification']} - + - sediment type - ${row['sediment type']} + sediment_type + ${row['sediment_type']} - + - oxygenation status of sample - ${row['oxygenation status of sample']} + oxygenation_status_of_sample + ${row['oxygenation_status_of_sample']} @@ -113,10 +113,10 @@ def mandatorytest(row, column, index): g/m3 - + - project name - ${row['project name']} + project_name + ${row['project_name']} @@ -125,70 +125,70 @@ def mandatorytest(row, column, index): ${row['ploidy']} - + - number of replicons - ${row['number of replicons']} + number_of_replicons + ${row['number_of_replicons']} - + - extrachromosomal elements - ${row['extrachromosomal elements']} + extrachromosomal_elements + ${row['extrachromosomal_elements']} - + - estimated size - ${row['estimated size']} + estimated_size + ${row['estimated_size']} - + - target gene - ${row['target gene']} + target_gene + ${row['target_gene']} - + - target subfragment - ${row['target subfragment']} + target_subfragment + ${row['target_subfragment']} - + - multiplex identifiers - ${row['multiplex identifiers']} + multiplex_identifiers + ${row['multiplex_identifiers']} - + - sequence quality check - ${row['sequence quality check']} + sequence_quality_check + ${row['sequence_quality_check']} - + - chimera check software - ${row['chimera check software']} + chimera_check_software + ${row['chimera_check_software']} - + - relevant electronic resources - ${row['relevant electronic resources']} + relevant_electronic_resources + ${row['relevant_electronic_resources']} - + - relevant standard operating procedures - ${row['relevant standard operating procedures']} + relevant_standard_operating_procedures + ${row['relevant_standard_operating_procedures']} - + - collection date - ${row['collection date']} + collection_date + ${row['collection_date']} @@ -198,42 +198,42 @@ def mandatorytest(row, column, index): m - + - geographic location (latitude) - ${row['geographic location (latitude)']} + geographic_location_latitude + ${row['geographic_location_latitude']} DD - + - geographic location (longitude) - ${row['geographic location (longitude)']} + geographic_location_longitude + ${row['geographic_location_longitude']} DD - + - geographic location (region and locality) - ${row['geographic location (region and locality)']} + geographic_location_region_and_locality + ${row['geographic_location_region_and_locality']} - + - broad-scale environmental context - ${row['broad-scale environmental context']} + broadscale_environmental_context + ${row['broadscale_environmental_context']} - + - local environmental context - ${row['local environmental context']} + local_environmental_context + ${row['local_environmental_context']} - + - environmental medium - ${row['environmental medium']} + environmental_medium + ${row['environmental_medium']} @@ -243,61 +243,61 @@ def mandatorytest(row, column, index): m - + - amount or size of sample collected - ${row['amount or size of sample collected']} - m3 + amount_or_size_of_sample_collected + ${row['amount_or_size_of_sample_collected']} + kg biomass ${row['biomass']} - t + kg - + - organism count - ${row['organism count']} + organism_count + ${row['organism_count']} - + - sample storage duration - ${row['sample storage duration']} + sample_storage_duration + ${row['sample_storage_duration']} - + - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} + geographic_location_country_andor_sea + ${row['geographic_location_country_andor_sea']} - + - host disease status - ${row['host disease status']} + host_disease_status + ${row['host_disease_status']} - + - host scientific name - ${row['host scientific name']} + host_scientific_name + ${row['host_scientific_name']} - + - mean friction velocity - ${row['mean friction velocity']} + mean_friction_velocity + ${row['mean_friction_velocity']} m/s - + - mean peak friction velocity - ${row['mean peak friction velocity']} + mean_peak_friction_velocity + ${row['mean_peak_friction_velocity']} m/s @@ -305,7 +305,7 @@ def mandatorytest(row, column, index): pressure ${row['pressure']} - bar + atm @@ -315,10 +315,10 @@ def mandatorytest(row, column, index): ºC - + - tidal stage - ${row['tidal stage']} + tidal_stage + ${row['tidal_stage']} @@ -328,37 +328,37 @@ def mandatorytest(row, column, index): NTU - + - pH - ${row['pH']} + ph + ${row['ph']} - + - total depth of water column - ${row['total depth of water column']} + total_depth_of_water_column + ${row['total_depth_of_water_column']} m - + - water content - ${row['water content']} + water_content + ${row['water_content']} g/g - + - alkyl diethers - ${row['alkyl diethers']} + alkyl_diethers + ${row['alkyl_diethers']} µg/L - + - aminopeptidase activity - ${row['aminopeptidase activity']} + aminopeptidase_activity + ${row['aminopeptidase_activity']} mol/L/h @@ -369,10 +369,10 @@ def mandatorytest(row, column, index): µmol/L - + - bacterial carbon production - ${row['bacterial carbon production']} + bacterial_carbon_production + ${row['bacterial_carbon_production']} ng/h @@ -380,7 +380,7 @@ def mandatorytest(row, column, index): bishomohopanol ${row['bishomohopanol']} - µg/g + µg/L @@ -394,13 +394,13 @@ def mandatorytest(row, column, index): calcium ${row['calcium']} - µmol/L + mg/L - + - carbon/nitrogen ratio - ${row['carbon/nitrogen ratio']} + carbonnitrogen_ratio + ${row['carbonnitrogen_ratio']} @@ -417,45 +417,45 @@ def mandatorytest(row, column, index): µg/L - + - diether lipids - ${row['diether lipids']} + diether_lipids + ${row['diether_lipids']} ng/L - + - dissolved carbon dioxide - ${row['dissolved carbon dioxide']} + dissolved_carbon_dioxide + ${row['dissolved_carbon_dioxide']} µmol/L - + - dissolved hydrogen - ${row['dissolved hydrogen']} + dissolved_hydrogen + ${row['dissolved_hydrogen']} µmol/L - + - dissolved inorganic carbon - ${row['dissolved inorganic carbon']} + dissolved_inorganic_carbon + ${row['dissolved_inorganic_carbon']} µg/L - + - dissolved organic carbon - ${row['dissolved organic carbon']} + dissolved_organic_carbon + ${row['dissolved_organic_carbon']} µmol/L - + - dissolved organic nitrogen - ${row['dissolved organic nitrogen']} + dissolved_organic_nitrogen + ${row['dissolved_organic_nitrogen']} µg/L @@ -466,17 +466,17 @@ def mandatorytest(row, column, index): µM/L - + - dissolved oxygen - ${row['dissolved oxygen']} + dissolved_oxygen + ${row['dissolved_oxygen']} µmol/kg - + - glucosidase activity - ${row['glucosidase activity']} + glucosidase_activity + ${row['glucosidase_activity']} mol/L/h @@ -484,13 +484,13 @@ def mandatorytest(row, column, index): magnesium ${row['magnesium']} - parts/million + mg/L - + - n-alkanes - ${row['n-alkanes']} + nalkanes + ${row['nalkanes']} µmol/L @@ -508,45 +508,45 @@ def mandatorytest(row, column, index): µmol/L - + - total nitrogen concentration - ${row['total nitrogen concentration']} + total_nitrogen_concentration + ${row['total_nitrogen_concentration']} µmol/L - + - organic carbon - ${row['organic carbon']} + organic_carbon + ${row['organic_carbon']} µmol/L - + - organic matter - ${row['organic matter']} + organic_matter + ${row['organic_matter']} µg/L - + - organic nitrogen - ${row['organic nitrogen']} + organic_nitrogen + ${row['organic_nitrogen']} µg/L - + - particulate organic carbon - ${row['particulate organic carbon']} + particulate_organic_carbon + ${row['particulate_organic_carbon']} µg/L - + - petroleum hydrocarbon - ${row['petroleum hydrocarbon']} + petroleum_hydrocarbon + ${row['petroleum_hydrocarbon']} µmol/L @@ -564,10 +564,10 @@ def mandatorytest(row, column, index): µmol/L - + - phospholipid fatty acid - ${row['phospholipid fatty acid']} + phospholipid_fatty_acid + ${row['phospholipid_fatty_acid']} mol/g @@ -578,10 +578,10 @@ def mandatorytest(row, column, index): µmol/L - + - redox potential - ${row['redox potential']} + redox_potential + ${row['redox_potential']} mV @@ -592,10 +592,10 @@ def mandatorytest(row, column, index): psu - + - total carbon - ${row['total carbon']} + total_carbon + ${row['total_carbon']} µg/L @@ -613,10 +613,10 @@ def mandatorytest(row, column, index): µmol/L - + - total organic carbon - ${row['total organic carbon']} + total_organic_carbon + ${row['total_organic_carbon']} g/kg @@ -624,21 +624,21 @@ def mandatorytest(row, column, index): sulfate ${row['sulfate']} - µmol/L + mg/L sulfide ${row['sulfide']} - µmol/L + mg/L - + - total nitrogen content - ${row['total nitrogen content']} - µmol/L + total_nitrogen_content + ${row['total_nitrogen_content']} + µg/L @@ -648,10 +648,10 @@ def mandatorytest(row, column, index): mEq/L - + - source material identifiers - ${row['source material identifiers']} + source_material_identifiers + ${row['source_material_identifiers']} @@ -660,125 +660,125 @@ def mandatorytest(row, column, index): ${row['perturbation']} - + - negative control type - ${row['negative control type']} + negative_control_type + ${row['negative_control_type']} - + - positive control type - ${row['positive control type']} + positive_control_type + ${row['positive_control_type']} - + - experimental factor - ${row['experimental factor']} + experimental_factor + ${row['experimental_factor']} - + - encoded traits - ${row['encoded traits']} + encoded_traits + ${row['encoded_traits']} - + - subspecific genetic lineage - ${row['subspecific genetic lineage']} + subspecific_genetic_lineage + ${row['subspecific_genetic_lineage']} - + - taxonomic classification - ${row['taxonomic classification']} + taxonomic_classification + ${row['taxonomic_classification']} - + - isolation and growth condition - ${row['isolation and growth condition']} + isolation_and_growth_condition + ${row['isolation_and_growth_condition']} - + - annotation source - ${row['annotation source']} + annotation_source + ${row['annotation_source']} - + - reference for biomaterial - ${row['reference for biomaterial']} + reference_for_biomaterial + ${row['reference_for_biomaterial']} - + - sample material processing - ${row['sample material processing']} + sample_material_processing + ${row['sample_material_processing']} - + - sample volume or weight for DNA extraction - ${row['sample volume or weight for DNA extraction']} - ng + sample_volume_or_weight_for_dna_extraction + ${row['sample_volume_or_weight_for_dna_extraction']} + mL - + - nucleic acid extraction - ${row['nucleic acid extraction']} + nucleic_acid_extraction + ${row['nucleic_acid_extraction']} - + - nucleic acid amplification - ${row['nucleic acid amplification']} + nucleic_acid_amplification + ${row['nucleic_acid_amplification']} - + - library size - ${row['library size']} + library_size + ${row['library_size']} - + - library reads sequenced - ${row['library reads sequenced']} + library_reads_sequenced + ${row['library_reads_sequenced']} - + - library construction method - ${row['library construction method']} + library_construction_method + ${row['library_construction_method']} - + - library vector - ${row['library vector']} + library_vector + ${row['library_vector']} - + - library screening strategy - ${row['library screening strategy']} + library_screening_strategy + ${row['library_screening_strategy']} - + - pcr conditions - ${row['pcr conditions']} + pcr_conditions + ${row['pcr_conditions']} - + - pcr primers - ${row['pcr primers']} + pcr_primers + ${row['pcr_primers']} @@ -797,13 +797,13 @@ def mandatorytest(row, column, index): depth ${row['depth']} - mm + m - + - chemical administration - ${row['chemical administration']} + chemical_administration + ${row['chemical_administration']} diff --git a/ena_upload/templates/ENA_template_samples_ERC000022.xml b/ena_upload/templates/ENA_template_samples_ERC000022.xml index 8ba9520..0e47127 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000022.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000022.xml @@ -33,28 +33,28 @@ def mandatorytest(row, column, index): ${row.sample_description} - + - trophic level - ${row['trophic level']} + trophic_level + ${row['trophic_level']} - + - observed biotic relationship - ${row['observed biotic relationship']} + observed_biotic_relationship + ${row['observed_biotic_relationship']} - + - known pathogenicity - ${row['known pathogenicity']} + known_pathogenicity + ${row['known_pathogenicity']} - + - relationship to oxygen - ${row['relationship to oxygen']} + relationship_to_oxygen + ${row['relationship_to_oxygen']} @@ -63,78 +63,78 @@ def mandatorytest(row, column, index): ${row['propagation']} - + - sample collection device - ${row['sample collection device']} + sample_collection_device + ${row['sample_collection_device']} - + - sample collection method - ${row['sample collection method']} + sample_collection_method + ${row['sample_collection_method']} - + - sample storage conditions - ${row['sample storage conditions']} + sample_storage_conditions + ${row['sample_storage_conditions']} - + - soil_taxonomic/FAO classification - ${row['soil_taxonomic/FAO classification']} + soil_taxonomicfao_classification + ${row['soil_taxonomicfao_classification']} - + - soil_taxonomic/local classification - ${row['soil_taxonomic/local classification']} + soil_taxonomiclocal_classification + ${row['soil_taxonomiclocal_classification']} - + - soil_taxonomic/local classification method - ${row['soil_taxonomic/local classification method']} + soil_taxonomiclocal_classification_method + ${row['soil_taxonomiclocal_classification_method']} - + - soil type - ${row['soil type']} + soil_type + ${row['soil_type']} - + - soil type method - ${row['soil type method']} + soil_type_method + ${row['soil_type_method']} - + - soil texture measurement - ${row['soil texture measurement']} + soil_texture_measurement + ${row['soil_texture_measurement']} % sand/silt/clay - + - soil texture method - ${row['soil texture method']} + soil_texture_method + ${row['soil_texture_method']} - + - microbial biomass - ${row['microbial biomass']} + microbial_biomass + ${row['microbial_biomass']} g/kg - + - project name - ${row['project name']} + project_name + ${row['project_name']} @@ -143,70 +143,70 @@ def mandatorytest(row, column, index): ${row['ploidy']} - + - number of replicons - ${row['number of replicons']} + number_of_replicons + ${row['number_of_replicons']} - + - extrachromosomal elements - ${row['extrachromosomal elements']} + extrachromosomal_elements + ${row['extrachromosomal_elements']} - + - estimated size - ${row['estimated size']} + estimated_size + ${row['estimated_size']} - + - target gene - ${row['target gene']} + target_gene + ${row['target_gene']} - + - target subfragment - ${row['target subfragment']} + target_subfragment + ${row['target_subfragment']} - + - multiplex identifiers - ${row['multiplex identifiers']} + multiplex_identifiers + ${row['multiplex_identifiers']} - + - sequence quality check - ${row['sequence quality check']} + sequence_quality_check + ${row['sequence_quality_check']} - + - chimera check software - ${row['chimera check software']} + chimera_check_software + ${row['chimera_check_software']} - + - relevant electronic resources - ${row['relevant electronic resources']} + relevant_electronic_resources + ${row['relevant_electronic_resources']} - + - relevant standard operating procedures - ${row['relevant standard operating procedures']} + relevant_standard_operating_procedures + ${row['relevant_standard_operating_procedures']} - + - collection date - ${row['collection date']} + collection_date + ${row['collection_date']} @@ -216,42 +216,42 @@ def mandatorytest(row, column, index): m - + - geographic location (latitude) - ${row['geographic location (latitude)']} + geographic_location_latitude + ${row['geographic_location_latitude']} DD - + - geographic location (longitude) - ${row['geographic location (longitude)']} + geographic_location_longitude + ${row['geographic_location_longitude']} DD - + - geographic location (region and locality) - ${row['geographic location (region and locality)']} + geographic_location_region_and_locality + ${row['geographic_location_region_and_locality']} - + - broad-scale environmental context - ${row['broad-scale environmental context']} + broadscale_environmental_context + ${row['broadscale_environmental_context']} - + - local environmental context - ${row['local environmental context']} + local_environmental_context + ${row['local_environmental_context']} - + - environmental medium - ${row['environmental medium']} + environmental_medium + ${row['environmental_medium']} @@ -261,11 +261,11 @@ def mandatorytest(row, column, index): m - + - amount or size of sample collected - ${row['amount or size of sample collected']} - m3 + amount_or_size_of_sample_collected + ${row['amount_or_size_of_sample_collected']} + kg @@ -274,107 +274,107 @@ def mandatorytest(row, column, index): ${row['sieving']} - + - microbial biomass method - ${row['microbial biomass method']} + microbial_biomass_method + ${row['microbial_biomass_method']} - + - horizon method - ${row['horizon method']} + horizon_method + ${row['horizon_method']} - + - extreme_unusual_properties/heavy metals - ${row['extreme_unusual_properties/heavy metals']} + extreme_unusual_propertiesheavy_metals + ${row['extreme_unusual_propertiesheavy_metals']} - + - extreme_unusual_properties/heavy metals method - ${row['extreme_unusual_properties/heavy metals method']} + extreme_unusual_propertiesheavy_metals_method + ${row['extreme_unusual_propertiesheavy_metals_method']} - + - extreme_unusual_properties/Al saturation - ${row['extreme_unusual_properties/Al saturation']} + extreme_unusual_propertiesal_saturation + ${row['extreme_unusual_propertiesal_saturation']} % - + - extreme_unusual_properties/Al saturation method - ${row['extreme_unusual_properties/Al saturation method']} + extreme_unusual_propertiesal_saturation_method + ${row['extreme_unusual_propertiesal_saturation_method']} - + - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} + geographic_location_country_andor_sea + ${row['geographic_location_country_andor_sea']} - + - host disease status - ${row['host disease status']} + host_disease_status + ${row['host_disease_status']} - + - host scientific name - ${row['host scientific name']} + host_scientific_name + ${row['host_scientific_name']} - + - link to climate information - ${row['link to climate information']} + link_to_climate_information + ${row['link_to_climate_information']} - + - link to classification information - ${row['link to classification information']} + link_to_classification_information + ${row['link_to_classification_information']} - + - links to additional analysis - ${row['links to additional analysis']} + links_to_additional_analysis + ${row['links_to_additional_analysis']} - + - current land use - ${row['current land use']} + current_land_use + ${row['current_land_use']} - + - current vegetation - ${row['current vegetation']} + current_vegetation + ${row['current_vegetation']} - + - current vegetation method - ${row['current vegetation method']} + current_vegetation_method + ${row['current_vegetation_method']} - + - soil horizon - ${row['soil horizon']} + soil_horizon + ${row['soil_horizon']} - + - drainage classification - ${row['drainage classification']} + drainage_classification + ${row['drainage_classification']} @@ -384,182 +384,182 @@ def mandatorytest(row, column, index): ºC - + - pH - ${row['pH']} + ph + ${row['ph']} - + - pH method - ${row['pH method']} + ph_method + ${row['ph_method']} - + - water content - ${row['water content']} + water_content + ${row['water_content']} g/g - + - slope gradient - ${row['slope gradient']} + slope_gradient + ${row['slope_gradient']} % - + - slope aspect - ${row['slope aspect']} + slope_aspect + ${row['slope_aspect']} - + - profile position - ${row['profile position']} + profile_position + ${row['profile_position']} - + - water content method - ${row['water content method']} + water_content_method + ${row['water_content_method']} - + - total organic carbon method - ${row['total organic carbon method']} + total_organic_carbon_method + ${row['total_organic_carbon_method']} - + - total nitrogen content method - ${row['total nitrogen content method']} + total_nitrogen_content_method + ${row['total_nitrogen_content_method']} - + - organic matter - ${row['organic matter']} + organic_matter + ${row['organic_matter']} µg/L - + - organic nitrogen - ${row['organic nitrogen']} + organic_nitrogen + ${row['organic_nitrogen']} µg/L - + - total organic carbon - ${row['total organic carbon']} + total_organic_carbon + ${row['total_organic_carbon']} g/kg - + - total nitrogen content - ${row['total nitrogen content']} - µmol/L + total_nitrogen_content + ${row['total_nitrogen_content']} + µg/L - + - salinity method - ${row['salinity method']} + salinity_method + ${row['salinity_method']} - + - source material identifiers - ${row['source material identifiers']} + source_material_identifiers + ${row['source_material_identifiers']} - + - history/previous land use - ${row['history/previous land use']} + historyprevious_land_use + ${row['historyprevious_land_use']} - + - previous land use method - ${row['previous land use method']} + previous_land_use_method + ${row['previous_land_use_method']} - + - history/crop rotation - ${row['history/crop rotation']} + historycrop_rotation + ${row['historycrop_rotation']} - + - history/agrochemical additions - ${row['history/agrochemical additions']} + historyagrochemical_additions + ${row['historyagrochemical_additions']} - + - history/tillage - ${row['history/tillage']} + historytillage + ${row['historytillage']} - + - history/fire - ${row['history/fire']} + historyfire + ${row['historyfire']} - + - history/flooding - ${row['history/flooding']} + historyflooding + ${row['historyflooding']} - + - history/extreme events - ${row['history/extreme events']} + historyextreme_events + ${row['historyextreme_events']} - + - mean seasonal temperature - ${row['mean seasonal temperature']} + mean_seasonal_temperature + ${row['mean_seasonal_temperature']} °C - + - mean seasonal precipitation - ${row['mean seasonal precipitation']} + mean_seasonal_precipitation + ${row['mean_seasonal_precipitation']} mm - + - mean annual precipitation - ${row['mean annual precipitation']} + mean_annual_precipitation + ${row['mean_annual_precipitation']} mm - + - mean annual temperature - ${row['mean annual temperature']} + mean_annual_temperature + ${row['mean_annual_temperature']} ºC - + - host specificity or range - ${row['host specificity or range']} + host_specificity_or_range + ${row['host_specificity_or_range']} @@ -568,131 +568,131 @@ def mandatorytest(row, column, index): ${row['perturbation']} - + - negative control type - ${row['negative control type']} + negative_control_type + ${row['negative_control_type']} - + - positive control type - ${row['positive control type']} + positive_control_type + ${row['positive_control_type']} - + - experimental factor - ${row['experimental factor']} + experimental_factor + ${row['experimental_factor']} - + - encoded traits - ${row['encoded traits']} + encoded_traits + ${row['encoded_traits']} - + - subspecific genetic lineage - ${row['subspecific genetic lineage']} + subspecific_genetic_lineage + ${row['subspecific_genetic_lineage']} - + - taxonomic classification - ${row['taxonomic classification']} + taxonomic_classification + ${row['taxonomic_classification']} - + - isolation and growth condition - ${row['isolation and growth condition']} + isolation_and_growth_condition + ${row['isolation_and_growth_condition']} - + - annotation source - ${row['annotation source']} + annotation_source + ${row['annotation_source']} - + - reference for biomaterial - ${row['reference for biomaterial']} + reference_for_biomaterial + ${row['reference_for_biomaterial']} - + - sample pooling - ${row['sample pooling']} + sample_pooling + ${row['sample_pooling']} - + - sample material processing - ${row['sample material processing']} + sample_material_processing + ${row['sample_material_processing']} - + - sample volume or weight for DNA extraction - ${row['sample volume or weight for DNA extraction']} - ng + sample_volume_or_weight_for_dna_extraction + ${row['sample_volume_or_weight_for_dna_extraction']} + mL - + - nucleic acid extraction - ${row['nucleic acid extraction']} + nucleic_acid_extraction + ${row['nucleic_acid_extraction']} - + - nucleic acid amplification - ${row['nucleic acid amplification']} + nucleic_acid_amplification + ${row['nucleic_acid_amplification']} - + - library size - ${row['library size']} + library_size + ${row['library_size']} - + - library reads sequenced - ${row['library reads sequenced']} + library_reads_sequenced + ${row['library_reads_sequenced']} - + - library construction method - ${row['library construction method']} + library_construction_method + ${row['library_construction_method']} - + - library vector - ${row['library vector']} + library_vector + ${row['library_vector']} - + - library screening strategy - ${row['library screening strategy']} + library_screening_strategy + ${row['library_screening_strategy']} - + - pcr conditions - ${row['pcr conditions']} + pcr_conditions + ${row['pcr_conditions']} - + - pcr primers - ${row['pcr primers']} + pcr_primers + ${row['pcr_primers']} @@ -705,7 +705,7 @@ def mandatorytest(row, column, index): depth ${row['depth']} - mm + m diff --git a/ena_upload/templates/ENA_template_samples_ERC000023.xml b/ena_upload/templates/ENA_template_samples_ERC000023.xml index a018865..cba9562 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000023.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000023.xml @@ -33,28 +33,28 @@ def mandatorytest(row, column, index): ${row.sample_description} - + - trophic level - ${row['trophic level']} + trophic_level + ${row['trophic_level']} - + - observed biotic relationship - ${row['observed biotic relationship']} + observed_biotic_relationship + ${row['observed_biotic_relationship']} - + - known pathogenicity - ${row['known pathogenicity']} + known_pathogenicity + ${row['known_pathogenicity']} - + - relationship to oxygen - ${row['relationship to oxygen']} + relationship_to_oxygen + ${row['relationship_to_oxygen']} @@ -63,41 +63,41 @@ def mandatorytest(row, column, index): ${row['propagation']} - + - sample collection device - ${row['sample collection device']} + sample_collection_device + ${row['sample_collection_device']} - + - sample collection method - ${row['sample collection method']} + sample_collection_method + ${row['sample_collection_method']} - + - sample storage temperature - ${row['sample storage temperature']} + sample_storage_temperature + ${row['sample_storage_temperature']} °C - + - sample storage location - ${row['sample storage location']} + sample_storage_location + ${row['sample_storage_location']} - + - oxygenation status of sample - ${row['oxygenation status of sample']} + oxygenation_status_of_sample + ${row['oxygenation_status_of_sample']} - + - project name - ${row['project name']} + project_name + ${row['project_name']} @@ -106,70 +106,70 @@ def mandatorytest(row, column, index): ${row['ploidy']} - + - number of replicons - ${row['number of replicons']} + number_of_replicons + ${row['number_of_replicons']} - + - extrachromosomal elements - ${row['extrachromosomal elements']} + extrachromosomal_elements + ${row['extrachromosomal_elements']} - + - estimated size - ${row['estimated size']} + estimated_size + ${row['estimated_size']} - + - target gene - ${row['target gene']} + target_gene + ${row['target_gene']} - + - target subfragment - ${row['target subfragment']} + target_subfragment + ${row['target_subfragment']} - + - multiplex identifiers - ${row['multiplex identifiers']} + multiplex_identifiers + ${row['multiplex_identifiers']} - + - sequence quality check - ${row['sequence quality check']} + sequence_quality_check + ${row['sequence_quality_check']} - + - chimera check software - ${row['chimera check software']} + chimera_check_software + ${row['chimera_check_software']} - + - relevant electronic resources - ${row['relevant electronic resources']} + relevant_electronic_resources + ${row['relevant_electronic_resources']} - + - relevant standard operating procedures - ${row['relevant standard operating procedures']} + relevant_standard_operating_procedures + ${row['relevant_standard_operating_procedures']} - + - collection date - ${row['collection date']} + collection_date + ${row['collection_date']} @@ -179,42 +179,42 @@ def mandatorytest(row, column, index): m - + - geographic location (latitude) - ${row['geographic location (latitude)']} + geographic_location_latitude + ${row['geographic_location_latitude']} DD - + - geographic location (longitude) - ${row['geographic location (longitude)']} + geographic_location_longitude + ${row['geographic_location_longitude']} DD - + - geographic location (region and locality) - ${row['geographic location (region and locality)']} + geographic_location_region_and_locality + ${row['geographic_location_region_and_locality']} - + - broad-scale environmental context - ${row['broad-scale environmental context']} + broadscale_environmental_context + ${row['broadscale_environmental_context']} - + - local environmental context - ${row['local environmental context']} + local_environmental_context + ${row['local_environmental_context']} - + - environmental medium - ${row['environmental medium']} + environmental_medium + ${row['environmental_medium']} @@ -224,111 +224,111 @@ def mandatorytest(row, column, index): m - + - amount or size of sample collected - ${row['amount or size of sample collected']} - m3 + amount_or_size_of_sample_collected + ${row['amount_or_size_of_sample_collected']} + kg - + - organism count - ${row['organism count']} + organism_count + ${row['organism_count']} - + - sample storage duration - ${row['sample storage duration']} + sample_storage_duration + ${row['sample_storage_duration']} - + - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} + geographic_location_country_andor_sea + ${row['geographic_location_country_andor_sea']} - + - biochemical oxygen demand - ${row['biochemical oxygen demand']} + biochemical_oxygen_demand + ${row['biochemical_oxygen_demand']} mg/L (over 5 days at 20C) - + - chemical oxygen demand - ${row['chemical oxygen demand']} + chemical_oxygen_demand + ${row['chemical_oxygen_demand']} mg/L (over 5 days at 20C) - + - pre-treatment - ${row['pre-treatment']} + pretreatment + ${row['pretreatment']} - + - primary treatment - ${row['primary treatment']} + primary_treatment + ${row['primary_treatment']} - + - reactor type - ${row['reactor type']} + reactor_type + ${row['reactor_type']} - + - secondary treatment - ${row['secondary treatment']} + secondary_treatment + ${row['secondary_treatment']} - + - sludge retention time - ${row['sludge retention time']} - weeks + sludge_retention_time + ${row['sludge_retention_time']} + days - + - tertiary treatment - ${row['tertiary treatment']} + tertiary_treatment + ${row['tertiary_treatment']} - + - host disease status - ${row['host disease status']} + host_disease_status + ${row['host_disease_status']} - + - host scientific name - ${row['host scientific name']} + host_scientific_name + ${row['host_scientific_name']} - + - industrial effluent percent - ${row['industrial effluent percent']} + industrial_effluent_percent + ${row['industrial_effluent_percent']} % - + - sewage type - ${row['sewage type']} + sewage_type + ${row['sewage_type']} - + - wastewater type - ${row['wastewater type']} + wastewater_type + ${row['wastewater_type']} @@ -338,16 +338,16 @@ def mandatorytest(row, column, index): ºC - + - pH - ${row['pH']} + ph + ${row['ph']} - + - efficiency percent - ${row['efficiency percent']} + efficiency_percent + ${row['efficiency_percent']} % @@ -358,53 +358,53 @@ def mandatorytest(row, column, index): µg/L - + - gaseous substances - ${row['gaseous substances']} + gaseous_substances + ${row['gaseous_substances']} µmol/L - + - inorganic particles - ${row['inorganic particles']} - mol/L + inorganic_particles + ${row['inorganic_particles']} + mg/L - + - organic particles - ${row['organic particles']} + organic_particles + ${row['organic_particles']} g/L - + - soluble inorganic material - ${row['soluble inorganic material']} - parts/million + soluble_inorganic_material + ${row['soluble_inorganic_material']} + g/L - + - soluble organic material - ${row['soluble organic material']} - parts/million + soluble_organic_material + ${row['soluble_organic_material']} + g/L - + - suspended solids - ${row['suspended solids']} - parts/million + suspended_solids + ${row['suspended_solids']} + g/L - + - total phosphate - ${row['total phosphate']} - µmol/L + total_phosphate + ${row['total_phosphate']} + µg/L @@ -414,10 +414,10 @@ def mandatorytest(row, column, index): µmol/L - + - total nitrogen concentration - ${row['total nitrogen concentration']} + total_nitrogen_concentration + ${row['total_nitrogen_concentration']} µmol/L @@ -442,11 +442,11 @@ def mandatorytest(row, column, index): µmol/L - + - total nitrogen content - ${row['total nitrogen content']} - µmol/L + total_nitrogen_content + ${row['total_nitrogen_content']} + µg/L @@ -456,10 +456,10 @@ def mandatorytest(row, column, index): mEq/L - + - source material identifiers - ${row['source material identifiers']} + source_material_identifiers + ${row['source_material_identifiers']} @@ -468,125 +468,125 @@ def mandatorytest(row, column, index): ${row['perturbation']} - + - negative control type - ${row['negative control type']} + negative_control_type + ${row['negative_control_type']} - + - positive control type - ${row['positive control type']} + positive_control_type + ${row['positive_control_type']} - + - experimental factor - ${row['experimental factor']} + experimental_factor + ${row['experimental_factor']} - + - encoded traits - ${row['encoded traits']} + encoded_traits + ${row['encoded_traits']} - + - subspecific genetic lineage - ${row['subspecific genetic lineage']} + subspecific_genetic_lineage + ${row['subspecific_genetic_lineage']} - + - taxonomic classification - ${row['taxonomic classification']} + taxonomic_classification + ${row['taxonomic_classification']} - + - isolation and growth condition - ${row['isolation and growth condition']} + isolation_and_growth_condition + ${row['isolation_and_growth_condition']} - + - annotation source - ${row['annotation source']} + annotation_source + ${row['annotation_source']} - + - reference for biomaterial - ${row['reference for biomaterial']} + reference_for_biomaterial + ${row['reference_for_biomaterial']} - + - sample material processing - ${row['sample material processing']} + sample_material_processing + ${row['sample_material_processing']} - + - sample volume or weight for DNA extraction - ${row['sample volume or weight for DNA extraction']} - ng + sample_volume_or_weight_for_dna_extraction + ${row['sample_volume_or_weight_for_dna_extraction']} + mL - + - nucleic acid extraction - ${row['nucleic acid extraction']} + nucleic_acid_extraction + ${row['nucleic_acid_extraction']} - + - nucleic acid amplification - ${row['nucleic acid amplification']} + nucleic_acid_amplification + ${row['nucleic_acid_amplification']} - + - library size - ${row['library size']} + library_size + ${row['library_size']} - + - library reads sequenced - ${row['library reads sequenced']} + library_reads_sequenced + ${row['library_reads_sequenced']} - + - library construction method - ${row['library construction method']} + library_construction_method + ${row['library_construction_method']} - + - library vector - ${row['library vector']} + library_vector + ${row['library_vector']} - + - library screening strategy - ${row['library screening strategy']} + library_screening_strategy + ${row['library_screening_strategy']} - + - pcr conditions - ${row['pcr conditions']} + pcr_conditions + ${row['pcr_conditions']} - + - pcr primers - ${row['pcr primers']} + pcr_primers + ${row['pcr_primers']} @@ -599,13 +599,13 @@ def mandatorytest(row, column, index): depth ${row['depth']} - mm + m - + - chemical administration - ${row['chemical administration']} + chemical_administration + ${row['chemical_administration']} diff --git a/ena_upload/templates/ENA_template_samples_ERC000024.xml b/ena_upload/templates/ENA_template_samples_ERC000024.xml index 5b8e71d..88ac38c 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000024.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000024.xml @@ -33,28 +33,28 @@ def mandatorytest(row, column, index): ${row.sample_description} - + - trophic level - ${row['trophic level']} + trophic_level + ${row['trophic_level']} - + - observed biotic relationship - ${row['observed biotic relationship']} + observed_biotic_relationship + ${row['observed_biotic_relationship']} - + - known pathogenicity - ${row['known pathogenicity']} + known_pathogenicity + ${row['known_pathogenicity']} - + - relationship to oxygen - ${row['relationship to oxygen']} + relationship_to_oxygen + ${row['relationship_to_oxygen']} @@ -63,49 +63,49 @@ def mandatorytest(row, column, index): ${row['propagation']} - + - sample collection device - ${row['sample collection device']} + sample_collection_device + ${row['sample_collection_device']} - + - sample collection method - ${row['sample collection method']} + sample_collection_method + ${row['sample_collection_method']} - + - sample storage temperature - ${row['sample storage temperature']} + sample_storage_temperature + ${row['sample_storage_temperature']} °C - + - sample storage location - ${row['sample storage location']} + sample_storage_location + ${row['sample_storage_location']} - + - size-fraction lower threshold - ${row['size-fraction lower threshold']} - µm + sizefraction_lower_threshold + ${row['sizefraction_lower_threshold']} + nm - + - size-fraction upper threshold - ${row['size-fraction upper threshold']} - µm + sizefraction_upper_threshold + ${row['sizefraction_upper_threshold']} + nm - + - oxygenation status of sample - ${row['oxygenation status of sample']} + oxygenation_status_of_sample + ${row['oxygenation_status_of_sample']} @@ -115,10 +115,10 @@ def mandatorytest(row, column, index): g/m3 - + - project name - ${row['project name']} + project_name + ${row['project_name']} @@ -127,70 +127,70 @@ def mandatorytest(row, column, index): ${row['ploidy']} - + - number of replicons - ${row['number of replicons']} + number_of_replicons + ${row['number_of_replicons']} - + - extrachromosomal elements - ${row['extrachromosomal elements']} + extrachromosomal_elements + ${row['extrachromosomal_elements']} - + - estimated size - ${row['estimated size']} + estimated_size + ${row['estimated_size']} - + - target gene - ${row['target gene']} + target_gene + ${row['target_gene']} - + - target subfragment - ${row['target subfragment']} + target_subfragment + ${row['target_subfragment']} - + - multiplex identifiers - ${row['multiplex identifiers']} + multiplex_identifiers + ${row['multiplex_identifiers']} - + - sequence quality check - ${row['sequence quality check']} + sequence_quality_check + ${row['sequence_quality_check']} - + - chimera check software - ${row['chimera check software']} + chimera_check_software + ${row['chimera_check_software']} - + - relevant electronic resources - ${row['relevant electronic resources']} + relevant_electronic_resources + ${row['relevant_electronic_resources']} - + - relevant standard operating procedures - ${row['relevant standard operating procedures']} + relevant_standard_operating_procedures + ${row['relevant_standard_operating_procedures']} - + - collection date - ${row['collection date']} + collection_date + ${row['collection_date']} @@ -200,42 +200,42 @@ def mandatorytest(row, column, index): m - + - geographic location (latitude) - ${row['geographic location (latitude)']} + geographic_location_latitude + ${row['geographic_location_latitude']} DD - + - geographic location (longitude) - ${row['geographic location (longitude)']} + geographic_location_longitude + ${row['geographic_location_longitude']} DD - + - geographic location (region and locality) - ${row['geographic location (region and locality)']} + geographic_location_region_and_locality + ${row['geographic_location_region_and_locality']} - + - broad-scale environmental context - ${row['broad-scale environmental context']} + broadscale_environmental_context + ${row['broadscale_environmental_context']} - + - local environmental context - ${row['local environmental context']} + local_environmental_context + ${row['local_environmental_context']} - + - environmental medium - ${row['environmental medium']} + environmental_medium + ${row['environmental_medium']} @@ -245,54 +245,54 @@ def mandatorytest(row, column, index): m - + - amount or size of sample collected - ${row['amount or size of sample collected']} - m3 + amount_or_size_of_sample_collected + ${row['amount_or_size_of_sample_collected']} + kg biomass ${row['biomass']} - t + kg - + - organism count - ${row['organism count']} + organism_count + ${row['organism_count']} - + - sample storage duration - ${row['sample storage duration']} + sample_storage_duration + ${row['sample_storage_duration']} - + - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} + geographic_location_country_andor_sea + ${row['geographic_location_country_andor_sea']} - + - host disease status - ${row['host disease status']} + host_disease_status + ${row['host_disease_status']} - + - host scientific name - ${row['host scientific name']} + host_scientific_name + ${row['host_scientific_name']} - + - atmospheric data - ${row['atmospheric data']} + atmospheric_data + ${row['atmospheric_data']} @@ -302,11 +302,11 @@ def mandatorytest(row, column, index): mS/cm - + - water current - ${row['water current']} - m3/s + water_current + ${row['water_current']} + knot @@ -316,38 +316,38 @@ def mandatorytest(row, column, index): mg Chla/m3 - + - light intensity - ${row['light intensity']} + light_intensity + ${row['light_intensity']} lux - + - mean friction velocity - ${row['mean friction velocity']} + mean_friction_velocity + ${row['mean_friction_velocity']} m/s - + - mean peak friction velocity - ${row['mean peak friction velocity']} + mean_peak_friction_velocity + ${row['mean_peak_friction_velocity']} m/s - + - downward PAR - ${row['downward PAR']} + downward_par + ${row['downward_par']} µE/m2/s - + - photon flux - ${row['photon flux']} + photon_flux + ${row['photon_flux']} µmol/m2/s @@ -355,7 +355,7 @@ def mandatorytest(row, column, index): pressure ${row['pressure']} - bar + atm @@ -365,10 +365,10 @@ def mandatorytest(row, column, index): ºC - + - tidal stage - ${row['tidal stage']} + tidal_stage + ${row['tidal_stage']} @@ -378,30 +378,30 @@ def mandatorytest(row, column, index): NTU - + - pH - ${row['pH']} + ph + ${row['ph']} - + - total depth of water column - ${row['total depth of water column']} + total_depth_of_water_column + ${row['total_depth_of_water_column']} m - + - alkyl diethers - ${row['alkyl diethers']} + alkyl_diethers + ${row['alkyl_diethers']} µg/L - + - aminopeptidase activity - ${row['aminopeptidase activity']} + aminopeptidase_activity + ${row['aminopeptidase_activity']} mol/L/h @@ -412,24 +412,24 @@ def mandatorytest(row, column, index): µmol/L - + - bacterial carbon production - ${row['bacterial carbon production']} + bacterial_carbon_production + ${row['bacterial_carbon_production']} ng/h - + - bacterial production - ${row['bacterial production']} + bacterial_production + ${row['bacterial_production']} mg/m3/d - + - bacterial respiration - ${row['bacterial respiration']} + bacterial_respiration + ${row['bacterial_respiration']} mg/m3/d @@ -437,7 +437,7 @@ def mandatorytest(row, column, index): bishomohopanol ${row['bishomohopanol']} - µg/g + µg/L @@ -451,13 +451,13 @@ def mandatorytest(row, column, index): calcium ${row['calcium']} - µmol/L + mg/L - + - carbon/nitrogen ratio - ${row['carbon/nitrogen ratio']} + carbonnitrogen_ratio + ${row['carbonnitrogen_ratio']} @@ -474,73 +474,73 @@ def mandatorytest(row, column, index): µg/L - + - diether lipids - ${row['diether lipids']} + diether_lipids + ${row['diether_lipids']} ng/L - + - dissolved carbon dioxide - ${row['dissolved carbon dioxide']} + dissolved_carbon_dioxide + ${row['dissolved_carbon_dioxide']} µmol/L - + - dissolved hydrogen - ${row['dissolved hydrogen']} + dissolved_hydrogen + ${row['dissolved_hydrogen']} µmol/L - + - dissolved inorganic carbon - ${row['dissolved inorganic carbon']} + dissolved_inorganic_carbon + ${row['dissolved_inorganic_carbon']} µg/L - + - dissolved inorganic nitrogen - ${row['dissolved inorganic nitrogen']} + dissolved_inorganic_nitrogen + ${row['dissolved_inorganic_nitrogen']} µg/L - + - dissolved inorganic phosphorus - ${row['dissolved inorganic phosphorus']} + dissolved_inorganic_phosphorus + ${row['dissolved_inorganic_phosphorus']} µg/L - + - dissolved organic carbon - ${row['dissolved organic carbon']} + dissolved_organic_carbon + ${row['dissolved_organic_carbon']} µmol/L - + - dissolved organic nitrogen - ${row['dissolved organic nitrogen']} + dissolved_organic_nitrogen + ${row['dissolved_organic_nitrogen']} µg/L - + - dissolved oxygen - ${row['dissolved oxygen']} + dissolved_oxygen + ${row['dissolved_oxygen']} µmol/kg - + - glucosidase activity - ${row['glucosidase activity']} + glucosidase_activity + ${row['glucosidase_activity']} mol/L/h @@ -548,13 +548,13 @@ def mandatorytest(row, column, index): magnesium ${row['magnesium']} - parts/million + mg/L - + - n-alkanes - ${row['n-alkanes']} + nalkanes + ${row['nalkanes']} µmol/L @@ -572,52 +572,52 @@ def mandatorytest(row, column, index): µmol/L - + - total nitrogen concentration - ${row['total nitrogen concentration']} + total_nitrogen_concentration + ${row['total_nitrogen_concentration']} µmol/L - + - organic carbon - ${row['organic carbon']} + organic_carbon + ${row['organic_carbon']} µmol/L - + - organic matter - ${row['organic matter']} + organic_matter + ${row['organic_matter']} µg/L - + - organic nitrogen - ${row['organic nitrogen']} + organic_nitrogen + ${row['organic_nitrogen']} µg/L - + - particulate organic carbon - ${row['particulate organic carbon']} + particulate_organic_carbon + ${row['particulate_organic_carbon']} µg/L - + - particulate organic nitrogen - ${row['particulate organic nitrogen']} + particulate_organic_nitrogen + ${row['particulate_organic_nitrogen']} µg/L - + - petroleum hydrocarbon - ${row['petroleum hydrocarbon']} + petroleum_hydrocarbon + ${row['petroleum_hydrocarbon']} µmol/L @@ -635,10 +635,10 @@ def mandatorytest(row, column, index): µmol/L - + - phospholipid fatty acid - ${row['phospholipid fatty acid']} + phospholipid_fatty_acid + ${row['phospholipid_fatty_acid']} mol/g @@ -649,17 +649,17 @@ def mandatorytest(row, column, index): µmol/L - + - primary production - ${row['primary production']} - mg/m3/day + primary_production + ${row['primary_production']} + g/m2/day - + - redox potential - ${row['redox potential']} + redox_potential + ${row['redox_potential']} mV @@ -684,10 +684,10 @@ def mandatorytest(row, column, index): µmol/L - + - soluble reactive phosphorus - ${row['soluble reactive phosphorus']} + soluble_reactive_phosphorus + ${row['soluble_reactive_phosphorus']} µmol/L @@ -695,62 +695,62 @@ def mandatorytest(row, column, index): sulfate ${row['sulfate']} - µmol/L + mg/L sulfide ${row['sulfide']} - µmol/L + mg/L - + - suspended particulate matter - ${row['suspended particulate matter']} + suspended_particulate_matter + ${row['suspended_particulate_matter']} mg/L - + - total dissolved nitrogen - ${row['total dissolved nitrogen']} + total_dissolved_nitrogen + ${row['total_dissolved_nitrogen']} µg/L - + - total inorganic nitrogen - ${row['total inorganic nitrogen']} + total_inorganic_nitrogen + ${row['total_inorganic_nitrogen']} µg/L - + - total nitrogen content - ${row['total nitrogen content']} - µmol/L + total_nitrogen_content + ${row['total_nitrogen_content']} + µg/L - + - total particulate carbon - ${row['total particulate carbon']} - µmol/L + total_particulate_carbon + ${row['total_particulate_carbon']} + µg/L - + - total phosphorus - ${row['total phosphorus']} + total_phosphorus + ${row['total_phosphorus']} µmol/L - + - alkalinity method - ${row['alkalinity method']} + alkalinity_method + ${row['alkalinity_method']} m2 @@ -761,10 +761,10 @@ def mandatorytest(row, column, index): mEq/L - + - source material identifiers - ${row['source material identifiers']} + source_material_identifiers + ${row['source_material_identifiers']} @@ -773,125 +773,125 @@ def mandatorytest(row, column, index): ${row['perturbation']} - + - negative control type - ${row['negative control type']} + negative_control_type + ${row['negative_control_type']} - + - positive control type - ${row['positive control type']} + positive_control_type + ${row['positive_control_type']} - + - experimental factor - ${row['experimental factor']} + experimental_factor + ${row['experimental_factor']} - + - encoded traits - ${row['encoded traits']} + encoded_traits + ${row['encoded_traits']} - + - subspecific genetic lineage - ${row['subspecific genetic lineage']} + subspecific_genetic_lineage + ${row['subspecific_genetic_lineage']} - + - taxonomic classification - ${row['taxonomic classification']} + taxonomic_classification + ${row['taxonomic_classification']} - + - isolation and growth condition - ${row['isolation and growth condition']} + isolation_and_growth_condition + ${row['isolation_and_growth_condition']} - + - annotation source - ${row['annotation source']} + annotation_source + ${row['annotation_source']} - + - reference for biomaterial - ${row['reference for biomaterial']} + reference_for_biomaterial + ${row['reference_for_biomaterial']} - + - sample material processing - ${row['sample material processing']} + sample_material_processing + ${row['sample_material_processing']} - + - sample volume or weight for DNA extraction - ${row['sample volume or weight for DNA extraction']} - ng + sample_volume_or_weight_for_dna_extraction + ${row['sample_volume_or_weight_for_dna_extraction']} + mL - + - nucleic acid extraction - ${row['nucleic acid extraction']} + nucleic_acid_extraction + ${row['nucleic_acid_extraction']} - + - nucleic acid amplification - ${row['nucleic acid amplification']} + nucleic_acid_amplification + ${row['nucleic_acid_amplification']} - + - library size - ${row['library size']} + library_size + ${row['library_size']} - + - library reads sequenced - ${row['library reads sequenced']} + library_reads_sequenced + ${row['library_reads_sequenced']} - + - library construction method - ${row['library construction method']} + library_construction_method + ${row['library_construction_method']} - + - library vector - ${row['library vector']} + library_vector + ${row['library_vector']} - + - library screening strategy - ${row['library screening strategy']} + library_screening_strategy + ${row['library_screening_strategy']} - + - pcr conditions - ${row['pcr conditions']} + pcr_conditions + ${row['pcr_conditions']} - + - pcr primers - ${row['pcr primers']} + pcr_primers + ${row['pcr_primers']} @@ -904,13 +904,13 @@ def mandatorytest(row, column, index): depth ${row['depth']} - mm + m - + - chemical administration - ${row['chemical administration']} + chemical_administration + ${row['chemical_administration']} diff --git a/ena_upload/templates/ENA_template_samples_ERC000025.xml b/ena_upload/templates/ENA_template_samples_ERC000025.xml index 2ce7413..7f923a6 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000025.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000025.xml @@ -33,28 +33,28 @@ def mandatorytest(row, column, index): ${row.sample_description} - + - trophic level - ${row['trophic level']} + trophic_level + ${row['trophic_level']} - + - observed biotic relationship - ${row['observed biotic relationship']} + observed_biotic_relationship + ${row['observed_biotic_relationship']} - + - known pathogenicity - ${row['known pathogenicity']} + known_pathogenicity + ${row['known_pathogenicity']} - + - relationship to oxygen - ${row['relationship to oxygen']} + relationship_to_oxygen + ${row['relationship_to_oxygen']} @@ -63,35 +63,35 @@ def mandatorytest(row, column, index): ${row['propagation']} - + - sample collection device - ${row['sample collection device']} + sample_collection_device + ${row['sample_collection_device']} - + - sample collection method - ${row['sample collection method']} + sample_collection_method + ${row['sample_collection_method']} - + - sample storage temperature - ${row['sample storage temperature']} + sample_storage_temperature + ${row['sample_storage_temperature']} °C - + - sample storage location - ${row['sample storage location']} + sample_storage_location + ${row['sample_storage_location']} - + - oxygenation status of sample - ${row['oxygenation status of sample']} + oxygenation_status_of_sample + ${row['oxygenation_status_of_sample']} @@ -101,10 +101,10 @@ def mandatorytest(row, column, index): g/m3 - + - project name - ${row['project name']} + project_name + ${row['project_name']} @@ -113,70 +113,70 @@ def mandatorytest(row, column, index): ${row['ploidy']} - + - number of replicons - ${row['number of replicons']} + number_of_replicons + ${row['number_of_replicons']} - + - extrachromosomal elements - ${row['extrachromosomal elements']} + extrachromosomal_elements + ${row['extrachromosomal_elements']} - + - estimated size - ${row['estimated size']} + estimated_size + ${row['estimated_size']} - + - target gene - ${row['target gene']} + target_gene + ${row['target_gene']} - + - target subfragment - ${row['target subfragment']} + target_subfragment + ${row['target_subfragment']} - + - multiplex identifiers - ${row['multiplex identifiers']} + multiplex_identifiers + ${row['multiplex_identifiers']} - + - sequence quality check - ${row['sequence quality check']} + sequence_quality_check + ${row['sequence_quality_check']} - + - chimera check software - ${row['chimera check software']} + chimera_check_software + ${row['chimera_check_software']} - + - relevant electronic resources - ${row['relevant electronic resources']} + relevant_electronic_resources + ${row['relevant_electronic_resources']} - + - relevant standard operating procedures - ${row['relevant standard operating procedures']} + relevant_standard_operating_procedures + ${row['relevant_standard_operating_procedures']} - + - collection date - ${row['collection date']} + collection_date + ${row['collection_date']} @@ -186,42 +186,42 @@ def mandatorytest(row, column, index): m - + - geographic location (latitude) - ${row['geographic location (latitude)']} + geographic_location_latitude + ${row['geographic_location_latitude']} DD - + - geographic location (longitude) - ${row['geographic location (longitude)']} + geographic_location_longitude + ${row['geographic_location_longitude']} DD - + - geographic location (region and locality) - ${row['geographic location (region and locality)']} + geographic_location_region_and_locality + ${row['geographic_location_region_and_locality']} - + - broad-scale environmental context - ${row['broad-scale environmental context']} + broadscale_environmental_context + ${row['broadscale_environmental_context']} - + - local environmental context - ${row['local environmental context']} + local_environmental_context + ${row['local_environmental_context']} - + - environmental medium - ${row['environmental medium']} + environmental_medium + ${row['environmental_medium']} @@ -231,62 +231,62 @@ def mandatorytest(row, column, index): m - + - amount or size of sample collected - ${row['amount or size of sample collected']} - m3 + amount_or_size_of_sample_collected + ${row['amount_or_size_of_sample_collected']} + kg biomass ${row['biomass']} - t + kg - + - organism count - ${row['organism count']} + organism_count + ${row['organism_count']} - + - sample storage duration - ${row['sample storage duration']} + sample_storage_duration + ${row['sample_storage_duration']} - + - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} + geographic_location_country_andor_sea + ${row['geographic_location_country_andor_sea']} - + - host disease status - ${row['host disease status']} + host_disease_status + ${row['host_disease_status']} - + - host scientific name - ${row['host scientific name']} + host_scientific_name + ${row['host_scientific_name']} - + - water current - ${row['water current']} - m3/s + water_current + ${row['water_current']} + knot pressure ${row['pressure']} - bar + atm @@ -296,10 +296,10 @@ def mandatorytest(row, column, index): ºC - + - pH - ${row['pH']} + ph + ${row['ph']} @@ -320,7 +320,7 @@ def mandatorytest(row, column, index): calcium ${row['calcium']} - µmol/L + mg/L @@ -337,45 +337,45 @@ def mandatorytest(row, column, index): µg/L - + - diether lipids - ${row['diether lipids']} + diether_lipids + ${row['diether_lipids']} ng/L - + - dissolved carbon dioxide - ${row['dissolved carbon dioxide']} + dissolved_carbon_dioxide + ${row['dissolved_carbon_dioxide']} µmol/L - + - dissolved hydrogen - ${row['dissolved hydrogen']} + dissolved_hydrogen + ${row['dissolved_hydrogen']} µmol/L - + - dissolved inorganic carbon - ${row['dissolved inorganic carbon']} + dissolved_inorganic_carbon + ${row['dissolved_inorganic_carbon']} µg/L - + - dissolved organic nitrogen - ${row['dissolved organic nitrogen']} + dissolved_organic_nitrogen + ${row['dissolved_organic_nitrogen']} µg/L - + - dissolved oxygen - ${row['dissolved oxygen']} + dissolved_oxygen + ${row['dissolved_oxygen']} µmol/kg @@ -393,31 +393,31 @@ def mandatorytest(row, column, index): µmol/L - + - total nitrogen concentration - ${row['total nitrogen concentration']} + total_nitrogen_concentration + ${row['total_nitrogen_concentration']} µmol/L - + - organic carbon - ${row['organic carbon']} + organic_carbon + ${row['organic_carbon']} µmol/L - + - organic matter - ${row['organic matter']} + organic_matter + ${row['organic_matter']} µg/L - + - organic nitrogen - ${row['organic nitrogen']} + organic_nitrogen + ${row['organic_nitrogen']} µg/L @@ -428,10 +428,10 @@ def mandatorytest(row, column, index): µmol/L - + - phospholipid fatty acid - ${row['phospholipid fatty acid']} + phospholipid_fatty_acid + ${row['phospholipid_fatty_acid']} mol/g @@ -467,14 +467,14 @@ def mandatorytest(row, column, index): sulfate ${row['sulfate']} - µmol/L + mg/L sulfide ${row['sulfide']} - µmol/L + mg/L @@ -484,10 +484,10 @@ def mandatorytest(row, column, index): mEq/L - + - source material identifiers - ${row['source material identifiers']} + source_material_identifiers + ${row['source_material_identifiers']} @@ -496,125 +496,125 @@ def mandatorytest(row, column, index): ${row['perturbation']} - + - negative control type - ${row['negative control type']} + negative_control_type + ${row['negative_control_type']} - + - positive control type - ${row['positive control type']} + positive_control_type + ${row['positive_control_type']} - + - experimental factor - ${row['experimental factor']} + experimental_factor + ${row['experimental_factor']} - + - encoded traits - ${row['encoded traits']} + encoded_traits + ${row['encoded_traits']} - + - subspecific genetic lineage - ${row['subspecific genetic lineage']} + subspecific_genetic_lineage + ${row['subspecific_genetic_lineage']} - + - taxonomic classification - ${row['taxonomic classification']} + taxonomic_classification + ${row['taxonomic_classification']} - + - isolation and growth condition - ${row['isolation and growth condition']} + isolation_and_growth_condition + ${row['isolation_and_growth_condition']} - + - annotation source - ${row['annotation source']} + annotation_source + ${row['annotation_source']} - + - reference for biomaterial - ${row['reference for biomaterial']} + reference_for_biomaterial + ${row['reference_for_biomaterial']} - + - sample material processing - ${row['sample material processing']} + sample_material_processing + ${row['sample_material_processing']} - + - sample volume or weight for DNA extraction - ${row['sample volume or weight for DNA extraction']} - ng + sample_volume_or_weight_for_dna_extraction + ${row['sample_volume_or_weight_for_dna_extraction']} + mL - + - nucleic acid extraction - ${row['nucleic acid extraction']} + nucleic_acid_extraction + ${row['nucleic_acid_extraction']} - + - nucleic acid amplification - ${row['nucleic acid amplification']} + nucleic_acid_amplification + ${row['nucleic_acid_amplification']} - + - library size - ${row['library size']} + library_size + ${row['library_size']} - + - library reads sequenced - ${row['library reads sequenced']} + library_reads_sequenced + ${row['library_reads_sequenced']} - + - library construction method - ${row['library construction method']} + library_construction_method + ${row['library_construction_method']} - + - library vector - ${row['library vector']} + library_vector + ${row['library_vector']} - + - library screening strategy - ${row['library screening strategy']} + library_screening_strategy + ${row['library_screening_strategy']} - + - pcr conditions - ${row['pcr conditions']} + pcr_conditions + ${row['pcr_conditions']} - + - pcr primers - ${row['pcr primers']} + pcr_primers + ${row['pcr_primers']} @@ -627,13 +627,13 @@ def mandatorytest(row, column, index): depth ${row['depth']} - mm + m - + - chemical administration - ${row['chemical administration']} + chemical_administration + ${row['chemical_administration']} diff --git a/ena_upload/templates/ENA_template_samples_ERC000027.xml b/ena_upload/templates/ENA_template_samples_ERC000027.xml index 7cca27b..9bb2ec7 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000027.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000027.xml @@ -33,62 +33,62 @@ def mandatorytest(row, column, index): ${row.sample_description} - + - Latitude Start - ${row['Latitude Start']} + latitude_start + ${row['latitude_start']} DD - + - Longitude Start - ${row['Longitude Start']} + longitude_start + ${row['longitude_start']} DD - + - Latitude End - ${row['Latitude End']} + latitude_end + ${row['latitude_end']} DD - + - Longitude End - ${row['Longitude End']} + longitude_end + ${row['longitude_end']} DD - + - Protocol Label - ${row['Protocol Label']} + protocol_label + ${row['protocol_label']} - + - trophic level - ${row['trophic level']} + trophic_level + ${row['trophic_level']} - + - observed biotic relationship - ${row['observed biotic relationship']} + observed_biotic_relationship + ${row['observed_biotic_relationship']} - + - known pathogenicity - ${row['known pathogenicity']} + known_pathogenicity + ${row['known_pathogenicity']} - + - relationship to oxygen - ${row['relationship to oxygen']} + relationship_to_oxygen + ${row['relationship_to_oxygen']} @@ -97,29 +97,29 @@ def mandatorytest(row, column, index): ${row['propagation']} - + - sample collection method - ${row['sample collection method']} + sample_collection_method + ${row['sample_collection_method']} - + - sample storage temperature - ${row['sample storage temperature']} + sample_storage_temperature + ${row['sample_storage_temperature']} °C - + - sample storage location - ${row['sample storage location']} + sample_storage_location + ${row['sample_storage_location']} - + - oxygenation status of sample - ${row['oxygenation status of sample']} + oxygenation_status_of_sample + ${row['oxygenation_status_of_sample']} @@ -129,16 +129,16 @@ def mandatorytest(row, column, index): g/m3 - + - project name - ${row['project name']} + project_name + ${row['project_name']} - + - finishing strategy - ${row['finishing strategy']} + finishing_strategy + ${row['finishing_strategy']} @@ -147,175 +147,175 @@ def mandatorytest(row, column, index): ${row['ploidy']} - + - number of replicons - ${row['number of replicons']} + number_of_replicons + ${row['number_of_replicons']} - + - extrachromosomal elements - ${row['extrachromosomal elements']} + extrachromosomal_elements + ${row['extrachromosomal_elements']} - + - estimated size - ${row['estimated size']} + estimated_size + ${row['estimated_size']} - + - target gene - ${row['target gene']} + target_gene + ${row['target_gene']} - + - target subfragment - ${row['target subfragment']} + target_subfragment + ${row['target_subfragment']} - + - multiplex identifiers - ${row['multiplex identifiers']} + multiplex_identifiers + ${row['multiplex_identifiers']} - + - sequence quality check - ${row['sequence quality check']} + sequence_quality_check + ${row['sequence_quality_check']} - + - chimera check software - ${row['chimera check software']} + chimera_check_software + ${row['chimera_check_software']} - + - relevant electronic resources - ${row['relevant electronic resources']} + relevant_electronic_resources + ${row['relevant_electronic_resources']} - + - relevant standard operating procedures - ${row['relevant standard operating procedures']} + relevant_standard_operating_procedures + ${row['relevant_standard_operating_procedures']} - + - environmental package - ${row['environmental package']} + environmental_package + ${row['environmental_package']} - + - collection date - ${row['collection date']} + collection_date + ${row['collection_date']} - + - broad-scale environmental context - ${row['broad-scale environmental context']} + broadscale_environmental_context + ${row['broadscale_environmental_context']} - + - local environmental context - ${row['local environmental context']} + local_environmental_context + ${row['local_environmental_context']} - + - environmental medium - ${row['environmental medium']} + environmental_medium + ${row['environmental_medium']} - + - Sampling Campaign - ${row['Sampling Campaign']} + sampling_campaign + ${row['sampling_campaign']} - + - Sampling Site - ${row['Sampling Site']} + sampling_site + ${row['sampling_site']} - + - Sampling Platform - ${row['Sampling Platform']} + sampling_platform + ${row['sampling_platform']} - + - amount or size of sample collected - ${row['amount or size of sample collected']} - m3 + amount_or_size_of_sample_collected + ${row['amount_or_size_of_sample_collected']} + kg biomass ${row['biomass']} - t + kg - + - organism count - ${row['organism count']} + organism_count + ${row['organism_count']} - + - Marine Region - ${row['Marine Region']} + marine_region + ${row['marine_region']} - + - water temperature - ${row['water temperature']} + water_temperature + ${row['water_temperature']} ºC - + - sample storage duration - ${row['sample storage duration']} + sample_storage_duration + ${row['sample_storage_duration']} - + - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} + geographic_location_country_andor_sea + ${row['geographic_location_country_andor_sea']} - + - specific host - ${row['specific host']} + specific_host + ${row['specific_host']} - + - health or disease status of specific host - ${row['health or disease status of specific host']} + health_or_disease_status_of_specific_host + ${row['health_or_disease_status_of_specific_host']} - + - atmospheric data - ${row['atmospheric data']} + atmospheric_data + ${row['atmospheric_data']} @@ -325,11 +325,11 @@ def mandatorytest(row, column, index): mS/cm - + - water current - ${row['water current']} - m3/s + water_current + ${row['water_current']} + knot @@ -339,38 +339,38 @@ def mandatorytest(row, column, index): mg Chla/m3 - + - light intensity - ${row['light intensity']} + light_intensity + ${row['light_intensity']} lux - + - mean friction velocity - ${row['mean friction velocity']} + mean_friction_velocity + ${row['mean_friction_velocity']} m/s - + - mean peak friction velocity - ${row['mean peak friction velocity']} + mean_peak_friction_velocity + ${row['mean_peak_friction_velocity']} m/s - + - downward PAR - ${row['downward PAR']} + downward_par + ${row['downward_par']} µE/m2/s - + - photon flux - ${row['photon flux']} + photon_flux + ${row['photon_flux']} µmol/m2/s @@ -378,13 +378,13 @@ def mandatorytest(row, column, index): pressure ${row['pressure']} - bar + atm - + - tidal stage - ${row['tidal stage']} + tidal_stage + ${row['tidal_stage']} @@ -394,30 +394,30 @@ def mandatorytest(row, column, index): NTU - + - pH - ${row['pH']} + ph + ${row['ph']} - + - total depth of water column - ${row['total depth of water column']} + total_depth_of_water_column + ${row['total_depth_of_water_column']} m - + - alkyl diethers - ${row['alkyl diethers']} + alkyl_diethers + ${row['alkyl_diethers']} µg/L - + - aminopeptidase activity - ${row['aminopeptidase activity']} + aminopeptidase_activity + ${row['aminopeptidase_activity']} mol/L/h @@ -428,24 +428,24 @@ def mandatorytest(row, column, index): µmol/L - + - bacterial carbon production - ${row['bacterial carbon production']} + bacterial_carbon_production + ${row['bacterial_carbon_production']} ng/h - + - bacterial production - ${row['bacterial production']} + bacterial_production + ${row['bacterial_production']} mg/m3/d - + - bacterial respiration - ${row['bacterial respiration']} + bacterial_respiration + ${row['bacterial_respiration']} mg/m3/d @@ -453,7 +453,7 @@ def mandatorytest(row, column, index): bishomohopanol ${row['bishomohopanol']} - µg/g + µg/L @@ -467,13 +467,13 @@ def mandatorytest(row, column, index): calcium ${row['calcium']} - µmol/L + mg/L - + - carbon/nitrogen ratio - ${row['carbon/nitrogen ratio']} + carbonnitrogen_ratio + ${row['carbonnitrogen_ratio']} @@ -490,73 +490,73 @@ def mandatorytest(row, column, index): µg/L - + - diether lipids - ${row['diether lipids']} + diether_lipids + ${row['diether_lipids']} ng/L - + - dissolved carbon dioxide - ${row['dissolved carbon dioxide']} + dissolved_carbon_dioxide + ${row['dissolved_carbon_dioxide']} µmol/L - + - dissolved hydrogen - ${row['dissolved hydrogen']} + dissolved_hydrogen + ${row['dissolved_hydrogen']} µmol/L - + - dissolved inorganic carbon - ${row['dissolved inorganic carbon']} + dissolved_inorganic_carbon + ${row['dissolved_inorganic_carbon']} µg/L - + - dissolved inorganic nitrogen - ${row['dissolved inorganic nitrogen']} + dissolved_inorganic_nitrogen + ${row['dissolved_inorganic_nitrogen']} µg/L - + - dissolved inorganic phosphorus - ${row['dissolved inorganic phosphorus']} + dissolved_inorganic_phosphorus + ${row['dissolved_inorganic_phosphorus']} µg/L - + - dissolved organic carbon - ${row['dissolved organic carbon']} + dissolved_organic_carbon + ${row['dissolved_organic_carbon']} µmol/L - + - dissolved organic nitrogen - ${row['dissolved organic nitrogen']} + dissolved_organic_nitrogen + ${row['dissolved_organic_nitrogen']} µg/L - + - dissolved oxygen - ${row['dissolved oxygen']} + dissolved_oxygen + ${row['dissolved_oxygen']} µmol/kg - + - glucosidase activity - ${row['glucosidase activity']} + glucosidase_activity + ${row['glucosidase_activity']} mol/L/h @@ -564,13 +564,13 @@ def mandatorytest(row, column, index): magnesium ${row['magnesium']} - parts/million + mg/L - + - n-alkanes - ${row['n-alkanes']} + nalkanes + ${row['nalkanes']} µmol/L @@ -588,52 +588,52 @@ def mandatorytest(row, column, index): µmol/L - + - total nitrogen concentration - ${row['total nitrogen concentration']} + total_nitrogen_concentration + ${row['total_nitrogen_concentration']} µmol/L - + - organic carbon - ${row['organic carbon']} + organic_carbon + ${row['organic_carbon']} µmol/L - + - organic matter - ${row['organic matter']} + organic_matter + ${row['organic_matter']} µg/L - + - organic nitrogen - ${row['organic nitrogen']} + organic_nitrogen + ${row['organic_nitrogen']} µg/L - + - particulate organic carbon - ${row['particulate organic carbon']} + particulate_organic_carbon + ${row['particulate_organic_carbon']} µg/L - + - particulate organic nitrogen - ${row['particulate organic nitrogen']} + particulate_organic_nitrogen + ${row['particulate_organic_nitrogen']} µg/L - + - petroleum hydrocarbon - ${row['petroleum hydrocarbon']} + petroleum_hydrocarbon + ${row['petroleum_hydrocarbon']} µmol/L @@ -651,10 +651,10 @@ def mandatorytest(row, column, index): µmol/L - + - phospholipid fatty acid - ${row['phospholipid fatty acid']} + phospholipid_fatty_acid + ${row['phospholipid_fatty_acid']} mol/g @@ -665,17 +665,17 @@ def mandatorytest(row, column, index): µmol/L - + - primary production - ${row['primary production']} - mg/m3/day + primary_production + ${row['primary_production']} + g/m2/day - + - redox potential - ${row['redox potential']} + redox_potential + ${row['redox_potential']} mV @@ -700,10 +700,10 @@ def mandatorytest(row, column, index): µmol/L - + - soluble reactive phosphorus - ${row['soluble reactive phosphorus']} + soluble_reactive_phosphorus + ${row['soluble_reactive_phosphorus']} µmol/L @@ -711,55 +711,55 @@ def mandatorytest(row, column, index): sulfate ${row['sulfate']} - µmol/L + mg/L sulfide ${row['sulfide']} - µmol/L + mg/L - + - suspended particulate matter - ${row['suspended particulate matter']} + suspended_particulate_matter + ${row['suspended_particulate_matter']} mg/L - + - total dissolved nitrogen - ${row['total dissolved nitrogen']} + total_dissolved_nitrogen + ${row['total_dissolved_nitrogen']} µg/L - + - total inorganic nitrogen - ${row['total inorganic nitrogen']} + total_inorganic_nitrogen + ${row['total_inorganic_nitrogen']} µg/L - + - total nitrogen content - ${row['total nitrogen content']} - µmol/L + total_nitrogen_content + ${row['total_nitrogen_content']} + µg/L - + - total particulate carbon - ${row['total particulate carbon']} - µmol/L + total_particulate_carbon + ${row['total_particulate_carbon']} + µg/L - + - total phosphorus - ${row['total phosphorus']} + total_phosphorus + ${row['total_phosphorus']} µmol/L @@ -770,16 +770,16 @@ def mandatorytest(row, column, index): mEq/L - + - source material identifiers - ${row['source material identifiers']} + source_material_identifiers + ${row['source_material_identifiers']} - + - miscellaneous parameter - ${row['miscellaneous parameter']} + miscellaneous_parameter + ${row['miscellaneous_parameter']} @@ -788,107 +788,107 @@ def mandatorytest(row, column, index): ${row['perturbation']} - + - experimental factor - ${row['experimental factor']} + experimental_factor + ${row['experimental_factor']} - + - encoded traits - ${row['encoded traits']} + encoded_traits + ${row['encoded_traits']} - + - subspecific genetic lineage - ${row['subspecific genetic lineage']} + subspecific_genetic_lineage + ${row['subspecific_genetic_lineage']} - + - isolation and growth condition - ${row['isolation and growth condition']} + isolation_and_growth_condition + ${row['isolation_and_growth_condition']} - + - annotation source - ${row['annotation source']} + annotation_source + ${row['annotation_source']} - + - reference for biomaterial - ${row['reference for biomaterial']} + reference_for_biomaterial + ${row['reference_for_biomaterial']} - + - sample material processing - ${row['sample material processing']} + sample_material_processing + ${row['sample_material_processing']} - + - sample volume or weight for DNA extraction - ${row['sample volume or weight for DNA extraction']} - ng + sample_volume_or_weight_for_dna_extraction + ${row['sample_volume_or_weight_for_dna_extraction']} + mL - + - nucleic acid extraction - ${row['nucleic acid extraction']} + nucleic_acid_extraction + ${row['nucleic_acid_extraction']} - + - nucleic acid amplification - ${row['nucleic acid amplification']} + nucleic_acid_amplification + ${row['nucleic_acid_amplification']} - + - library size - ${row['library size']} + library_size + ${row['library_size']} - + - library reads sequenced - ${row['library reads sequenced']} + library_reads_sequenced + ${row['library_reads_sequenced']} - + - library construction method - ${row['library construction method']} + library_construction_method + ${row['library_construction_method']} - + - library vector - ${row['library vector']} + library_vector + ${row['library_vector']} - + - library screening strategy - ${row['library screening strategy']} + library_screening_strategy + ${row['library_screening_strategy']} - + - pcr conditions - ${row['pcr conditions']} + pcr_conditions + ${row['pcr_conditions']} - + - pcr primers - ${row['pcr primers']} + pcr_primers + ${row['pcr_primers']} @@ -901,13 +901,13 @@ def mandatorytest(row, column, index): depth ${row['depth']} - mm + m - + - chemical administration - ${row['chemical administration']} + chemical_administration + ${row['chemical_administration']} diff --git a/ena_upload/templates/ENA_template_samples_ERC000028.xml b/ena_upload/templates/ENA_template_samples_ERC000028.xml index 9ab9ddf..8569955 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000028.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000028.xml @@ -51,16 +51,16 @@ def mandatorytest(row, column, index): ${row['collected_by']} - + - collection date - ${row['collection date']} + collection_date + ${row['collection_date']} - + - geographic location (region and locality) - ${row['geographic location (region and locality)']} + geographic_location_region_and_locality + ${row['geographic_location_region_and_locality']} @@ -81,16 +81,16 @@ def mandatorytest(row, column, index): ${row['mating_type']} - + - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} + geographic_location_country_andor_sea + ${row['geographic_location_country_andor_sea']} - + - host health state - ${row['host health state']} + host_health_state + ${row['host_health_state']} @@ -99,10 +99,10 @@ def mandatorytest(row, column, index): ${row['lab_host']} - + - host scientific name - ${row['host scientific name']} + host_scientific_name + ${row['host_scientific_name']} diff --git a/ena_upload/templates/ENA_template_samples_ERC000029.xml b/ena_upload/templates/ENA_template_samples_ERC000029.xml index 0013e1b..5879180 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000029.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000029.xml @@ -33,34 +33,34 @@ def mandatorytest(row, column, index): ${row.sample_description} - + - sample storage conditions - ${row['sample storage conditions']} + sample_storage_conditions + ${row['sample_storage_conditions']} - + - subject exposure - ${row['subject exposure']} + subject_exposure + ${row['subject_exposure']} - + - travel-relation - ${row['travel-relation']} + travelrelation + ${row['travelrelation']} - + - clinical setting - ${row['clinical setting']} + clinical_setting + ${row['clinical_setting']} - + - country of travel - ${row['country of travel']} + country_of_travel + ${row['country_of_travel']} @@ -69,10 +69,10 @@ def mandatorytest(row, column, index): ${row['collected_by']} - + - collection date - ${row['collection date']} + collection_date + ${row['collection_date']} @@ -82,24 +82,24 @@ def mandatorytest(row, column, index): m - + - geographic location (latitude) - ${row['geographic location (latitude)']} + geographic_location_latitude + ${row['geographic_location_latitude']} DD - + - geographic location (longitude) - ${row['geographic location (longitude)']} + geographic_location_longitude + ${row['geographic_location_longitude']} DD - + - geographic location (region and locality) - ${row['geographic location (region and locality)']} + geographic_location_region_and_locality + ${row['geographic_location_region_and_locality']} @@ -108,18 +108,18 @@ def mandatorytest(row, column, index): ${row['identified_by']} - + - subject exposure duration - ${row['subject exposure duration']} - year + subject_exposure_duration + ${row['subject_exposure_duration']} + day - + - amount or size of sample collected - ${row['amount or size of sample collected']} - m3 + amount_or_size_of_sample_collected + ${row['amount_or_size_of_sample_collected']} + kg @@ -140,59 +140,59 @@ def mandatorytest(row, column, index): ${row['pathotype']} - + - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} + geographic_location_country_andor_sea + ${row['geographic_location_country_andor_sea']} - + - host disease status - ${row['host disease status']} + host_disease_status + ${row['host_disease_status']} - + - host disease outcome - ${row['host disease outcome']} + host_disease_outcome + ${row['host_disease_outcome']} - + - host subject id - ${row['host subject id']} + host_subject_id + ${row['host_subject_id']} - + - host age - ${row['host age']} + host_age + ${row['host_age']} years - + - host taxid - ${row['host taxid']} + host_taxid + ${row['host_taxid']} - + - host life stage - ${row['host life stage']} + host_life_stage + ${row['host_life_stage']} - + - host health state - ${row['host health state']} + host_health_state + ${row['host_health_state']} - + - host sex - ${row['host sex']} + host_sex + ${row['host_sex']} @@ -201,10 +201,10 @@ def mandatorytest(row, column, index): ${row['lab_host']} - + - host scientific name - ${row['host scientific name']} + host_scientific_name + ${row['host_scientific_name']} @@ -213,10 +213,10 @@ def mandatorytest(row, column, index): ${row['passage_history']} - + - Is the sequenced pathogen host associated? - ${row['Is the sequenced pathogen host associated?']} + is_the_sequenced_pathogen_host_associated + ${row['is_the_sequenced_pathogen_host_associated']} @@ -279,22 +279,22 @@ def mandatorytest(row, column, index): ${row['strain']} - + - host disease stage - ${row['host disease stage']} + host_disease_stage + ${row['host_disease_stage']} - + - isolation source host-associated - ${row['isolation source host-associated']} + isolation_source_hostassociated + ${row['isolation_source_hostassociated']} - + - host description - ${row['host description']} + host_description + ${row['host_description']} @@ -303,17 +303,17 @@ def mandatorytest(row, column, index): ${row['genotype']} - + - isolation source non-host-associated - ${row['isolation source non-host-associated']} + isolation_source_nonhostassociated + ${row['isolation_source_nonhostassociated']} depth ${row['depth']} - mm + m diff --git a/ena_upload/templates/ENA_template_samples_ERC000030.xml b/ena_upload/templates/ENA_template_samples_ERC000030.xml index 3a394cb..3c005e4 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000030.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000030.xml @@ -33,214 +33,214 @@ def mandatorytest(row, column, index): ${row.sample_description} - + - Event Label - ${row['Event Label']} + event_label + ${row['event_label']} - + - Event Date/Time Start - ${row['Event Date/Time Start']} + event_datetime_start + ${row['event_datetime_start']} - + - Event Date/Time End - ${row['Event Date/Time End']} + event_datetime_end + ${row['event_datetime_end']} - + - Latitude Start - ${row['Latitude Start']} + latitude_start + ${row['latitude_start']} DD - + - Longitude Start - ${row['Longitude Start']} + longitude_start + ${row['longitude_start']} DD - + - Latitude End - ${row['Latitude End']} + latitude_end + ${row['latitude_end']} DD - + - Longitude End - ${row['Longitude End']} + longitude_end + ${row['longitude_end']} DD - + - Protocol Label - ${row['Protocol Label']} + protocol_label + ${row['protocol_label']} - + - Sample Status - ${row['Sample Status']} + sample_status + ${row['sample_status']} - + - Last Update Date - ${row['Last Update Date']} + last_update_date + ${row['last_update_date']} - + - sample collection device - ${row['sample collection device']} + sample_collection_device + ${row['sample_collection_device']} - + - sample storage device - ${row['sample storage device']} + sample_storage_device + ${row['sample_storage_device']} - + - size-fraction lower threshold - ${row['size-fraction lower threshold']} - µm + sizefraction_lower_threshold + ${row['sizefraction_lower_threshold']} + nm - + - size-fraction upper threshold - ${row['size-fraction upper threshold']} - µm + sizefraction_upper_threshold + ${row['sizefraction_upper_threshold']} + nm - + - project name - ${row['project name']} + project_name + ${row['project_name']} - + - environmental package - ${row['environmental package']} + environmental_package + ${row['environmental_package']} - + - collection date - ${row['collection date']} + collection_date + ${row['collection_date']} - + - broad-scale environmental context - ${row['broad-scale environmental context']} + broadscale_environmental_context + ${row['broadscale_environmental_context']} - + - local environmental context - ${row['local environmental context']} + local_environmental_context + ${row['local_environmental_context']} - + - environmental medium - ${row['environmental medium']} + environmental_medium + ${row['environmental_medium']} - + - Sampling Campaign - ${row['Sampling Campaign']} + sampling_campaign + ${row['sampling_campaign']} - + - Sampling Station - ${row['Sampling Station']} + sampling_station + ${row['sampling_station']} - + - Sampling Platform - ${row['Sampling Platform']} + sampling_platform + ${row['sampling_platform']} - + - Marine Region - ${row['Marine Region']} + marine_region + ${row['marine_region']} - + - Salinity Sensor - ${row['Salinity Sensor']} + salinity_sensor + ${row['salinity_sensor']} psu - + - Oxygen Sensor - ${row['Oxygen Sensor']} + oxygen_sensor + ${row['oxygen_sensor']} µmol/kg - + - Nitrate Sensor - ${row['Nitrate Sensor']} + nitrate_sensor + ${row['nitrate_sensor']} µmol/L - + - water temperature - ${row['water temperature']} + water_temperature + ${row['water_temperature']} ºC - + - Chlorophyll Sensor - ${row['Chlorophyll Sensor']} + chlorophyll_sensor + ${row['chlorophyll_sensor']} mg Chl/m3 - + - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} + geographic_location_country_andor_sea + ${row['geographic_location_country_andor_sea']} - + - Citation - ${row['Citation']} + citation + ${row['citation']} - + - Further Details - ${row['Further Details']} + further_details + ${row['further_details']} depth ${row['depth']} - mm + m diff --git a/ena_upload/templates/ENA_template_samples_ERC000031.xml b/ena_upload/templates/ENA_template_samples_ERC000031.xml index 67496f2..4b26d2e 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000031.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000031.xml @@ -33,34 +33,34 @@ def mandatorytest(row, column, index): ${row.sample_description} - + - number of inoculated individuals - ${row['number of inoculated individuals']} + number_of_inoculated_individuals + ${row['number_of_inoculated_individuals']} - + - trophic level - ${row['trophic level']} + trophic_level + ${row['trophic_level']} - + - observed biotic relationship - ${row['observed biotic relationship']} + observed_biotic_relationship + ${row['observed_biotic_relationship']} - + - known pathogenicity - ${row['known pathogenicity']} + known_pathogenicity + ${row['known_pathogenicity']} - + - relationship to oxygen - ${row['relationship to oxygen']} + relationship_to_oxygen + ${row['relationship_to_oxygen']} @@ -69,28 +69,28 @@ def mandatorytest(row, column, index): ${row['propagation']} - + - sample collection device - ${row['sample collection device']} + sample_collection_device + ${row['sample_collection_device']} - + - sample collection method - ${row['sample collection method']} + sample_collection_method + ${row['sample_collection_method']} - + - project name - ${row['project name']} + project_name + ${row['project_name']} - + - frequency of cooking - ${row['frequency of cooking']} + frequency_of_cooking + ${row['frequency_of_cooking']} @@ -99,70 +99,70 @@ def mandatorytest(row, column, index): ${row['ploidy']} - + - number of replicons - ${row['number of replicons']} + number_of_replicons + ${row['number_of_replicons']} - + - extrachromosomal elements - ${row['extrachromosomal elements']} + extrachromosomal_elements + ${row['extrachromosomal_elements']} - + - estimated size - ${row['estimated size']} + estimated_size + ${row['estimated_size']} - + - target gene - ${row['target gene']} + target_gene + ${row['target_gene']} - + - target subfragment - ${row['target subfragment']} + target_subfragment + ${row['target_subfragment']} - + - multiplex identifiers - ${row['multiplex identifiers']} + multiplex_identifiers + ${row['multiplex_identifiers']} - + - sequence quality check - ${row['sequence quality check']} + sequence_quality_check + ${row['sequence_quality_check']} - + - chimera check software - ${row['chimera check software']} + chimera_check_software + ${row['chimera_check_software']} - + - relevant electronic resources - ${row['relevant electronic resources']} + relevant_electronic_resources + ${row['relevant_electronic_resources']} - + - relevant standard operating procedures - ${row['relevant standard operating procedures']} + relevant_standard_operating_procedures + ${row['relevant_standard_operating_procedures']} - + - collection date - ${row['collection date']} + collection_date + ${row['collection_date']} @@ -172,42 +172,42 @@ def mandatorytest(row, column, index): m - + - geographic location (latitude) - ${row['geographic location (latitude)']} + geographic_location_latitude + ${row['geographic_location_latitude']} DD - + - geographic location (longitude) - ${row['geographic location (longitude)']} + geographic_location_longitude + ${row['geographic_location_longitude']} DD - + - geographic location (region and locality) - ${row['geographic location (region and locality)']} + geographic_location_region_and_locality + ${row['geographic_location_region_and_locality']} - + - broad-scale environmental context - ${row['broad-scale environmental context']} + broadscale_environmental_context + ${row['broadscale_environmental_context']} - + - local environmental context - ${row['local environmental context']} + local_environmental_context + ${row['local_environmental_context']} - + - environmental medium - ${row['environmental medium']} + environmental_medium + ${row['environmental_medium']} @@ -217,149 +217,149 @@ def mandatorytest(row, column, index): m - + - sampling time outside - ${row['sampling time outside']} + sampling_time_outside + ${row['sampling_time_outside']} - + - temperature outside house - ${row['temperature outside house']} + temperature_outside_house + ${row['temperature_outside_house']} °C - + - train station collection location - ${row['train station collection location']} + train_station_collection_location + ${row['train_station_collection_location']} - + - train stop collection location - ${row['train stop collection location']} + train_stop_collection_location + ${row['train_stop_collection_location']} - + - surface material - ${row['surface material']} + surface_material + ${row['surface_material']} - + - surface-air contaminant - ${row['surface-air contaminant']} + surfaceair_contaminant + ${row['surfaceair_contaminant']} - + - indoor surface - ${row['indoor surface']} + indoor_surface + ${row['indoor_surface']} - + - indoor space - ${row['indoor space']} + indoor_space + ${row['indoor_space']} - + - filter type - ${row['filter type']} + filter_type + ${row['filter_type']} - + - heating and cooling system type - ${row['heating and cooling system type']} + heating_and_cooling_system_type + ${row['heating_and_cooling_system_type']} - + - substructure type - ${row['substructure type']} + substructure_type + ${row['substructure_type']} - + - light type - ${row['light type']} + light_type + ${row['light_type']} - + - building setting - ${row['building setting']} + building_setting + ${row['building_setting']} - + - building occupancy type - ${row['building occupancy type']} + building_occupancy_type + ${row['building_occupancy_type']} - + - space typical state - ${row['space typical state']} + space_typical_state + ${row['space_typical_state']} - + - typical occupant density - ${row['typical occupant density']} + typical_occupant_density + ${row['typical_occupant_density']} - + - occupancy at sampling - ${row['occupancy at sampling']} + occupancy_at_sampling + ${row['occupancy_at_sampling']} - + - occupant density at sampling - ${row['occupant density at sampling']} + occupant_density_at_sampling + ${row['occupant_density_at_sampling']} - + - ventilation type - ${row['ventilation type']} + ventilation_type + ${row['ventilation_type']} - + - rooms that are on the same hallway - ${row['rooms that are on the same hallway']} + rooms_that_are_on_the_same_hallway + ${row['rooms_that_are_on_the_same_hallway']} - + - wall surface treatment - ${row['wall surface treatment']} + wall_surface_treatment + ${row['wall_surface_treatment']} - + - wall area - ${row['wall area']} + wall_area + ${row['wall_area']} - + - elevator count - ${row['elevator count']} + elevator_count + ${row['elevator_count']} - + - floor area - ${row['floor area']} + floor_area + ${row['floor_area']} @@ -368,547 +368,547 @@ def mandatorytest(row, column, index): ${row['furniture']} - + - water feature type - ${row['water feature type']} + water_feature_type + ${row['water_feature_type']} - + - room door distance - ${row['room door distance']} + room_door_distance + ${row['room_door_distance']} - + - room type - ${row['room type']} + room_type + ${row['room_type']} - + - window location - ${row['window location']} + window_location + ${row['window_location']} - + - ceiling type - ${row['ceiling type']} + ceiling_type + ${row['ceiling_type']} - + - door direction of opening - ${row['door direction of opening']} + door_direction_of_opening + ${row['door_direction_of_opening']} - + - exposed pipes - ${row['exposed pipes']} + exposed_pipes + ${row['exposed_pipes']} - + - wall height - ${row['wall height']} + wall_height + ${row['wall_height']} - + - door type, metal - ${row['door type, metal']} + door_type_metal + ${row['door_type_metal']} - + - inside lux light - ${row['inside lux light']} + inside_lux_light + ${row['inside_lux_light']} kg s−3 - + - exposed ductwork - ${row['exposed ductwork']} + exposed_ductwork + ${row['exposed_ductwork']} kg s−3 - + - door material - ${row['door material']} + door_material + ${row['door_material']} kg s−3 - + - adjacent rooms - ${row['adjacent rooms']} + adjacent_rooms + ${row['adjacent_rooms']} - + - wall thermal mass - ${row['wall thermal mass']} + wall_thermal_mass + ${row['wall_thermal_mass']} J/°C - + - ceiling signs of water/mold - ${row['ceiling signs of water/mold']} + ceiling_signs_of_watermold + ${row['ceiling_signs_of_watermold']} J/°C - + - window status - ${row['window status']} + window_status + ${row['window_status']} % - + - door location - ${row['door location']} - year + door_location + ${row['door_location']} + minute - + - window signs of water/mold - ${row['window signs of water/mold']} - year + window_signs_of_watermold + ${row['window_signs_of_watermold']} + minute - + - window type - ${row['window type']} + window_type + ${row['window_type']} ppm - + - window material - ${row['window material']} - g/m3 + window_material + ${row['window_material']} + % - + - window horizontal position - ${row['window horizontal position']} + window_horizontal_position + ${row['window_horizontal_position']} - + - room condition - ${row['room condition']} - mm + room_condition + ${row['room_condition']} + m - + - window area/size - ${row['window area/size']} - mm + window_areasize + ${row['window_areasize']} + m - + - sampling floor - ${row['sampling floor']} + sampling_floor + ${row['sampling_floor']} °C - + - room count - ${row['room count']} + room_count + ${row['room_count']} - + - average daily occupancy - ${row['average daily occupancy']} + average_daily_occupancy + ${row['average_daily_occupancy']} °C - + - floor condition - ${row['floor condition']} + floor_condition + ${row['floor_condition']} °C - + - door type, wood - ${row['door type, wood']} + door_type_wood + ${row['door_type_wood']} °C - + - door condition - ${row['door condition']} + door_condition + ${row['door_condition']} - + - door movement - ${row['door movement']} + door_movement + ${row['door_movement']} - + - interior wall condition - ${row['interior wall condition']} + interior_wall_condition + ${row['interior_wall_condition']} - + - floor signs of water/mold - ${row['floor signs of water/mold']} + floor_signs_of_watermold + ${row['floor_signs_of_watermold']} - + - ceiling structure - ${row['ceiling structure']} + ceiling_structure + ${row['ceiling_structure']} m - + - wall texture - ${row['wall texture']} + wall_texture + ${row['wall_texture']} m - + - floor thermal mass - ${row['floor thermal mass']} + floor_thermal_mass + ${row['floor_thermal_mass']} J/°C - + - room air exchange rate - ${row['room air exchange rate']} + room_air_exchange_rate + ${row['room_air_exchange_rate']} year - + - bathroom count - ${row['bathroom count']} + bathroom_count + ${row['bathroom_count']} year - + - shading device signs of water/mold - ${row['shading device signs of water/mold']} + shading_device_signs_of_watermold + ${row['shading_device_signs_of_watermold']} year - + - window covering - ${row['window covering']} + window_covering + ${row['window_covering']} year - + - ceiling texture - ${row['ceiling texture']} + ceiling_texture + ${row['ceiling_texture']} year - + - maximum occupancy - ${row['maximum occupancy']} + maximum_occupancy + ${row['maximum_occupancy']} year - + - gender of restroom - ${row['gender of restroom']} + gender_of_restroom + ${row['gender_of_restroom']} year - + - ceiling condition - ${row['ceiling condition']} + ceiling_condition + ${row['ceiling_condition']} year - + - floor structure - ${row['floor structure']} - year + floor_structure + ${row['floor_structure']} + minute - + - rooms that share a wall with sampling room - ${row['rooms that share a wall with sampling room']} - year + rooms_that_share_a_wall_with_sampling_room + ${row['rooms_that_share_a_wall_with_sampling_room']} + minute - + - wall finish material - ${row['wall finish material']} - year + wall_finish_material + ${row['wall_finish_material']} + minute - + - room occupancy - ${row['room occupancy']} - year + room_occupancy + ${row['room_occupancy']} + minute - + - room location in building - ${row['room location in building']} - year + room_location_in_building + ${row['room_location_in_building']} + minute - + - floor finish material - ${row['floor finish material']} - year + floor_finish_material + ${row['floor_finish_material']} + minute - + - room window count - ${row['room window count']} - year + room_window_count + ${row['room_window_count']} + minute - + - sampling room id or name - ${row['sampling room id or name']} - year + sampling_room_id_or_name + ${row['sampling_room_id_or_name']} + day - + - height carpet fiber mat - ${row['height carpet fiber mat']} - mm + height_carpet_fiber_mat + ${row['height_carpet_fiber_mat']} + cm - + - ceiling area - ${row['ceiling area']} + ceiling_area + ${row['ceiling_area']} m2 - + - heating system delivery method - ${row['heating system delivery method']} + heating_system_delivery_method + ${row['heating_system_delivery_method']} m2 - + - room sampling position - ${row['room sampling position']} + room_sampling_position + ${row['room_sampling_position']} m2 - + - room moisture damage or mold history - ${row['room moisture damage or mold history']} + room_moisture_damage_or_mold_history + ${row['room_moisture_damage_or_mold_history']} °C - + - door signs of water/mold - ${row['door signs of water/mold']} + door_signs_of_watermold + ${row['door_signs_of_watermold']} minute - + - room net area - ${row['room net area']} + room_net_area + ${row['room_net_area']} m2 - + - ceiling thermal mass - ${row['ceiling thermal mass']} + ceiling_thermal_mass + ${row['ceiling_thermal_mass']} J/°C - + - rooms that share a door with sampling room - ${row['rooms that share a door with sampling room']} - year + rooms_that_share_a_door_with_sampling_room + ${row['rooms_that_share_a_door_with_sampling_room']} + day - + - orientations of exterior window - ${row['orientations of exterior window']} - year + orientations_of_exterior_window + ${row['orientations_of_exterior_window']} + day - + - wall location - ${row['wall location']} + wall_location + ${row['wall_location']} °C - + - room volume - ${row['room volume']} + room_volume + ${row['room_volume']} m2 - + - door type, composite - ${row['door type, composite']} + door_type_composite + ${row['door_type_composite']} m2 - + - bedroom count - ${row['bedroom count']} + bedroom_count + ${row['bedroom_count']} m2 - + - wall construction type - ${row['wall construction type']} + wall_construction_type + ${row['wall_construction_type']} m2 - + - wall signs of water/mold - ${row['wall signs of water/mold']} + wall_signs_of_watermold + ${row['wall_signs_of_watermold']} m2 - + - window condition - ${row['window condition']} + window_condition + ${row['window_condition']} m2 - + - escalator count - ${row['escalator count']} + escalator_count + ${row['escalator_count']} m2 - + - cooling system identifier - ${row['cooling system identifier']} + cooling_system_identifier + ${row['cooling_system_identifier']} °C - + - quadrant position - ${row['quadrant position']} + quadrant_position + ${row['quadrant_position']} °C - + - number of pets - ${row['number of pets']} + number_of_pets + ${row['number_of_pets']} °C - + - window vertical position - ${row['window vertical position']} + window_vertical_position + ${row['window_vertical_position']} °C - + - fireplace type - ${row['fireplace type']} + fireplace_type + ${row['fireplace_type']} °C - + - heating delivery locations - ${row['heating delivery locations']} + heating_delivery_locations + ${row['heating_delivery_locations']} °C - + - ceiling finish material - ${row['ceiling finish material']} + ceiling_finish_material + ${row['ceiling_finish_material']} °C - + - door type - ${row['door type']} + door_type + ${row['door_type']} °C - + - number of houseplants - ${row['number of houseplants']} + number_of_houseplants + ${row['number_of_houseplants']} °C - + - floor age - ${row['floor age']} + floor_age + ${row['floor_age']} year - + - rooms connected by a doorway - ${row['rooms connected by a doorway']} + rooms_connected_by_a_doorway + ${row['rooms_connected_by_a_doorway']} year @@ -918,56 +918,56 @@ def mandatorytest(row, column, index): ${row['specifications']} - + - specific humidity - ${row['specific humidity']} + specific_humidity + ${row['specific_humidity']} g/m3 - + - window open frequency - ${row['window open frequency']} + window_open_frequency + ${row['window_open_frequency']} m - + - room dimensions - ${row['room dimensions']} + room_dimensions + ${row['room_dimensions']} - + - water feature size - ${row['water feature size']} - m2 + water_feature_size + ${row['water_feature_size']} + ha - + - amount or size of sample collected - ${row['amount or size of sample collected']} - m3 + amount_or_size_of_sample_collected + ${row['amount_or_size_of_sample_collected']} + kg - + - sample size sorting method - ${row['sample size sorting method']} + sample_size_sorting_method + ${row['sample_size_sorting_method']} - + - organism count - ${row['organism count']} + organism_count + ${row['organism_count']} - + - mechanical structure - ${row['mechanical structure']} + mechanical_structure + ${row['mechanical_structure']} @@ -977,76 +977,76 @@ def mandatorytest(row, column, index): year - + - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} + geographic_location_country_andor_sea + ${row['geographic_location_country_andor_sea']} - + - host disease status - ${row['host disease status']} + host_disease_status + ${row['host_disease_status']} - + - host scientific name - ${row['host scientific name']} + host_scientific_name + ${row['host_scientific_name']} - + - relative air humidity - ${row['relative air humidity']} + relative_air_humidity + ${row['relative_air_humidity']} % - + - absolute air humidity - ${row['absolute air humidity']} + absolute_air_humidity + ${row['absolute_air_humidity']} kg - + - surface humidity - ${row['surface humidity']} + surface_humidity + ${row['surface_humidity']} % - + - air temperature - ${row['air temperature']} + air_temperature + ${row['air_temperature']} ºC - + - surface temperature - ${row['surface temperature']} + surface_temperature + ${row['surface_temperature']} ºC - + - surface moisture - ${row['surface moisture']} + surface_moisture + ${row['surface_moisture']} parts/million - + - surface moisture pH - ${row['surface moisture pH']} + surface_moisture_ph + ${row['surface_moisture_ph']} - + - dew point - ${row['dew point']} + dew_point + ${row['dew_point']} ºC @@ -1057,50 +1057,50 @@ def mandatorytest(row, column, index): ºC - + - last time swept/mopped/vacuumed - ${row['last time swept/mopped/vacuumed']} + last_time_sweptmoppedvacuumed + ${row['last_time_sweptmoppedvacuumed']} - + - number of residents - ${row['number of residents']} + number_of_residents + ${row['number_of_residents']} m - + - average dew point - ${row['average dew point']} + average_dew_point + ${row['average_dew_point']} °C - + - frequency of cleaning - ${row['frequency of cleaning']} - year + frequency_of_cleaning + ${row['frequency_of_cleaning']} + minute - + - carbon dioxide - ${row['carbon dioxide']} + carbon_dioxide + ${row['carbon_dioxide']} µmol/L - + - source material identifiers - ${row['source material identifiers']} + source_material_identifiers + ${row['source_material_identifiers']} - + - seasonal use - ${row['seasonal use']} + seasonal_use + ${row['seasonal_use']} year @@ -1110,16 +1110,16 @@ def mandatorytest(row, column, index): ${row['season']} - + - average temperature - ${row['average temperature']} + average_temperature + ${row['average_temperature']} - + - host specificity or range - ${row['host specificity or range']} + host_specificity_or_range + ${row['host_specificity_or_range']} @@ -1128,125 +1128,125 @@ def mandatorytest(row, column, index): ${row['perturbation']} - + - negative control type - ${row['negative control type']} + negative_control_type + ${row['negative_control_type']} - + - positive control type - ${row['positive control type']} + positive_control_type + ${row['positive_control_type']} - + - experimental factor - ${row['experimental factor']} + experimental_factor + ${row['experimental_factor']} - + - encoded traits - ${row['encoded traits']} + encoded_traits + ${row['encoded_traits']} - + - subspecific genetic lineage - ${row['subspecific genetic lineage']} + subspecific_genetic_lineage + ${row['subspecific_genetic_lineage']} - + - taxonomic classification - ${row['taxonomic classification']} + taxonomic_classification + ${row['taxonomic_classification']} - + - isolation and growth condition - ${row['isolation and growth condition']} + isolation_and_growth_condition + ${row['isolation_and_growth_condition']} - + - annotation source - ${row['annotation source']} + annotation_source + ${row['annotation_source']} - + - reference for biomaterial - ${row['reference for biomaterial']} + reference_for_biomaterial + ${row['reference_for_biomaterial']} - + - sample material processing - ${row['sample material processing']} + sample_material_processing + ${row['sample_material_processing']} - + - sample volume or weight for DNA extraction - ${row['sample volume or weight for DNA extraction']} - ng + sample_volume_or_weight_for_dna_extraction + ${row['sample_volume_or_weight_for_dna_extraction']} + mL - + - nucleic acid extraction - ${row['nucleic acid extraction']} + nucleic_acid_extraction + ${row['nucleic_acid_extraction']} - + - nucleic acid amplification - ${row['nucleic acid amplification']} + nucleic_acid_amplification + ${row['nucleic_acid_amplification']} - + - library size - ${row['library size']} + library_size + ${row['library_size']} - + - library reads sequenced - ${row['library reads sequenced']} + library_reads_sequenced + ${row['library_reads_sequenced']} - + - library construction method - ${row['library construction method']} + library_construction_method + ${row['library_construction_method']} - + - library vector - ${row['library vector']} + library_vector + ${row['library_vector']} - + - library screening strategy - ${row['library screening strategy']} + library_screening_strategy + ${row['library_screening_strategy']} - + - pcr conditions - ${row['pcr conditions']} + pcr_conditions + ${row['pcr_conditions']} - + - pcr primers - ${row['pcr primers']} + pcr_primers + ${row['pcr_primers']} @@ -1255,146 +1255,146 @@ def mandatorytest(row, column, index): ${row['adapters']} - + - date last rain - ${row['date last rain']} + date_last_rain + ${row['date_last_rain']} - + - sampling day weather - ${row['sampling day weather']} - g/m3 + sampling_day_weather + ${row['sampling_day_weather']} + % - + - amount of light - ${row['amount of light']} + amount_of_light + ${row['amount_of_light']} W/m2 - + - train line - ${row['train line']} + train_line + ${row['train_line']} °C - + - outside relative humidity - ${row['outside relative humidity']} - g/m3 + outside_relative_humidity + ${row['outside_relative_humidity']} + % depth ${row['depth']} - mm + m - + - door area or size - ${row['door area or size']} + door_area_or_size + ${row['door_area_or_size']} - + - visual media - ${row['visual media']} + visual_media + ${row['visual_media']} - + - built structure setting - ${row['built structure setting']} + built_structure_setting + ${row['built_structure_setting']} - + - built structure type - ${row['built structure type']} + built_structure_type + ${row['built_structure_type']} m - + - exterior door count - ${row['exterior door count']} + exterior_door_count + ${row['exterior_door_count']} °C - + - design, construction, and operation documents - ${row['design, construction, and operation documents']} + design_construction_and_operation_documents + ${row['design_construction_and_operation_documents']} year - + - shading device condition - ${row['shading device condition']} + shading_device_condition + ${row['shading_device_condition']} year - + - occupancy documentation - ${row['occupancy documentation']} - year + occupancy_documentation + ${row['occupancy_documentation']} + minute - + - floor count - ${row['floor count']} - year + floor_count + ${row['floor_count']} + minute - + - shading device material - ${row['shading device material']} - year + shading_device_material + ${row['shading_device_material']} + minute - + - built structure age - ${row['built structure age']} - year + built_structure_age + ${row['built_structure_age']} + day - + - hallway/corridor count - ${row['hallway/corridor count']} - g/m3 + hallwaycorridor_count + ${row['hallwaycorridor_count']} + % - + - architectural structure - ${row['architectural structure']} + architectural_structure + ${row['architectural_structure']} m2 - + - shading device type - ${row['shading device type']} + shading_device_type + ${row['shading_device_type']} m2 - + - shading device location - ${row['shading device location']} + shading_device_location + ${row['shading_device_location']} °C @@ -1411,16 +1411,16 @@ def mandatorytest(row, column, index): ${row['address']} - + - room architectural elements - ${row['room architectural elements']} + room_architectural_elements + ${row['room_architectural_elements']} - + - aerospace structure - ${row['aerospace structure']} + aerospace_structure + ${row['aerospace_structure']} diff --git a/ena_upload/templates/ENA_template_samples_ERC000032.xml b/ena_upload/templates/ENA_template_samples_ERC000032.xml index 5e87477..d532ce1 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000032.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000032.xml @@ -33,52 +33,52 @@ def mandatorytest(row, column, index): ${row.sample_description} - + - number of inoculated individuals - ${row['number of inoculated individuals']} + number_of_inoculated_individuals + ${row['number_of_inoculated_individuals']} - + - inoculation route - ${row['inoculation route']} + inoculation_route + ${row['inoculation_route']} - + - inoculation dose - ${row['inoculation dose']} + inoculation_dose + ${row['inoculation_dose']} - + - inoculation stock availability - ${row['inoculation stock availability']} + inoculation_stock_availability + ${row['inoculation_stock_availability']} - + - sample storage conditions - ${row['sample storage conditions']} + sample_storage_conditions + ${row['sample_storage_conditions']} - + - subject exposure - ${row['subject exposure']} + subject_exposure + ${row['subject_exposure']} - + - type exposure - ${row['type exposure']} + type_exposure + ${row['type_exposure']} - + - personal protective equipment - ${row['personal protective equipment']} + personal_protective_equipment + ${row['personal_protective_equipment']} @@ -87,266 +87,266 @@ def mandatorytest(row, column, index): ${row['hospitalisation']} - + - antiviral treatment - ${row['antiviral treatment']} + antiviral_treatment + ${row['antiviral_treatment']} - + - antiviral treatment initiation - ${row['antiviral treatment initiation']} + antiviral_treatment_initiation + ${row['antiviral_treatment_initiation']} - + - antiviral treatment dosage - ${row['antiviral treatment dosage']} + antiviral_treatment_dosage + ${row['antiviral_treatment_dosage']} - + - antiviral treatment duration - ${row['antiviral treatment duration']} + antiviral_treatment_duration + ${row['antiviral_treatment_duration']} - + - influenza vaccination type - ${row['influenza vaccination type']} + influenza_vaccination_type + ${row['influenza_vaccination_type']} - + - influenza vaccination date - ${row['influenza vaccination date']} + influenza_vaccination_date + ${row['influenza_vaccination_date']} - + - source of vaccination information - ${row['source of vaccination information']} + source_of_vaccination_information + ${row['source_of_vaccination_information']} - + - vaccine lot number - ${row['vaccine lot number']} + vaccine_lot_number + ${row['vaccine_lot_number']} - + - vaccine manufacturer - ${row['vaccine manufacturer']} + vaccine_manufacturer + ${row['vaccine_manufacturer']} - + - vaccine dosage - ${row['vaccine dosage']} + vaccine_dosage + ${row['vaccine_dosage']} - + - influenza-like illness at the time of sample collection - ${row['influenza-like illness at the time of sample collection']} + influenzalike_illness_at_the_time_of_sample_collection + ${row['influenzalike_illness_at_the_time_of_sample_collection']} - + - illness onset date - ${row['illness onset date']} + illness_onset_date + ${row['illness_onset_date']} - + - illness duration - ${row['illness duration']} + illness_duration + ${row['illness_duration']} - + - illness symptoms - ${row['illness symptoms']} + illness_symptoms + ${row['illness_symptoms']} - + - collection date - ${row['collection date']} + collection_date + ${row['collection_date']} - + - geographic location (latitude) - ${row['geographic location (latitude)']} + geographic_location_latitude + ${row['geographic_location_latitude']} DD - + - geographic location (longitude) - ${row['geographic location (longitude)']} + geographic_location_longitude + ${row['geographic_location_longitude']} DD - + - geographic location (region and locality) - ${row['geographic location (region and locality)']} + geographic_location_region_and_locality + ${row['geographic_location_region_and_locality']} - + - subject exposure duration - ${row['subject exposure duration']} - year + subject_exposure_duration + ${row['subject_exposure_duration']} + day - + - sample capture status - ${row['sample capture status']} + sample_capture_status + ${row['sample_capture_status']} - + - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} + geographic_location_country_andor_sea + ${row['geographic_location_country_andor_sea']} - + - host disease outcome - ${row['host disease outcome']} + host_disease_outcome + ${row['host_disease_outcome']} - + - host common name - ${row['host common name']} + host_common_name + ${row['host_common_name']} - + - host subject id - ${row['host subject id']} + host_subject_id + ${row['host_subject_id']} - + - host age - ${row['host age']} + host_age + ${row['host_age']} years - + - host health state - ${row['host health state']} + host_health_state + ${row['host_health_state']} - + - host sex - ${row['host sex']} + host_sex + ${row['host_sex']} - + - host scientific name - ${row['host scientific name']} + host_scientific_name + ${row['host_scientific_name']} - + - influenza test method - ${row['influenza test method']} + influenza_test_method + ${row['influenza_test_method']} - + - influenza test result - ${row['influenza test result']} + influenza_test_result + ${row['influenza_test_result']} - + - other pathogens tested - ${row['other pathogens tested']} + other_pathogens_tested + ${row['other_pathogens_tested']} - + - other pathogens test result - ${row['other pathogens test result']} + other_pathogens_test_result + ${row['other_pathogens_test_result']} - + - influenza virus type - ${row['influenza virus type']} + influenza_virus_type + ${row['influenza_virus_type']} - + - virus identifier - ${row['virus identifier']} + virus_identifier + ${row['virus_identifier']} - + - influenza strain unique number - ${row['influenza strain unique number']} + influenza_strain_unique_number + ${row['influenza_strain_unique_number']} - + - WHO/OIE/FAO clade (required for HPAI H5N1 viruses) - ${row['WHO/OIE/FAO clade (required for HPAI H5N1 viruses)']} + whooiefao_clade_required_for_hpai_h5n1_viruses + ${row['whooiefao_clade_required_for_hpai_h5n1_viruses']} - + - lineage:swl (required for H1N1 viruses) - ${row['lineage:swl (required for H1N1 viruses)']} + lineageswl_required_for_h1n1_viruses + ${row['lineageswl_required_for_h1n1_viruses']} - + - collector name - ${row['collector name']} + collector_name + ${row['collector_name']} - + - collecting institution - ${row['collecting institution']} + collecting_institution + ${row['collecting_institution']} - + - receipt date - ${row['receipt date']} + receipt_date + ${row['receipt_date']} - + - definition for seropositive sample - ${row['definition for seropositive sample']} + definition_for_seropositive_sample + ${row['definition_for_seropositive_sample']} - + - meaning of cut off value - ${row['meaning of cut off value']} + meaning_of_cut_off_value + ${row['meaning_of_cut_off_value']} - + - serotype (required for a seropositive sample) - ${row['serotype (required for a seropositive sample)']} + serotype_required_for_a_seropositive_sample + ${row['serotype_required_for_a_seropositive_sample']} @@ -355,22 +355,22 @@ def mandatorytest(row, column, index): ${row['strain']} - + - host habitat - ${row['host habitat']} + host_habitat + ${row['host_habitat']} - + - isolation source host-associated - ${row['isolation source host-associated']} + isolation_source_hostassociated + ${row['isolation_source_hostassociated']} - + - host description - ${row['host description']} + host_description + ${row['host_description']} @@ -379,16 +379,16 @@ def mandatorytest(row, column, index): ${row['gravidity']} - + - host behaviour - ${row['host behaviour']} + host_behaviour + ${row['host_behaviour']} - + - isolation source non-host-associated - ${row['isolation source non-host-associated']} + isolation_source_nonhostassociated + ${row['isolation_source_nonhostassociated']} diff --git a/ena_upload/templates/ENA_template_samples_ERC000033.xml b/ena_upload/templates/ENA_template_samples_ERC000033.xml index bed2ce4..056215b 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000033.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000033.xml @@ -33,28 +33,28 @@ def mandatorytest(row, column, index): ${row.sample_description} - + - sample storage conditions - ${row['sample storage conditions']} + sample_storage_conditions + ${row['sample_storage_conditions']} - + - subject exposure - ${row['subject exposure']} + subject_exposure + ${row['subject_exposure']} - + - type exposure - ${row['type exposure']} + type_exposure + ${row['type_exposure']} - + - personal protective equipment - ${row['personal protective equipment']} + personal_protective_equipment + ${row['personal_protective_equipment']} @@ -63,98 +63,98 @@ def mandatorytest(row, column, index): ${row['hospitalisation']} - + - illness duration - ${row['illness duration']} + illness_duration + ${row['illness_duration']} - + - illness symptoms - ${row['illness symptoms']} + illness_symptoms + ${row['illness_symptoms']} - + - collection date - ${row['collection date']} + collection_date + ${row['collection_date']} - + - geographic location (latitude) - ${row['geographic location (latitude)']} + geographic_location_latitude + ${row['geographic_location_latitude']} DD - + - geographic location (longitude) - ${row['geographic location (longitude)']} + geographic_location_longitude + ${row['geographic_location_longitude']} DD - + - geographic location (region and locality) - ${row['geographic location (region and locality)']} + geographic_location_region_and_locality + ${row['geographic_location_region_and_locality']} - + - subject exposure duration - ${row['subject exposure duration']} - year + subject_exposure_duration + ${row['subject_exposure_duration']} + day - + - sample capture status - ${row['sample capture status']} + sample_capture_status + ${row['sample_capture_status']} - + - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} + geographic_location_country_andor_sea + ${row['geographic_location_country_andor_sea']} - + - host disease outcome - ${row['host disease outcome']} + host_disease_outcome + ${row['host_disease_outcome']} - + - host common name - ${row['host common name']} + host_common_name + ${row['host_common_name']} - + - host subject id - ${row['host subject id']} + host_subject_id + ${row['host_subject_id']} - + - host age - ${row['host age']} + host_age + ${row['host_age']} years - + - host health state - ${row['host health state']} + host_health_state + ${row['host_health_state']} - + - host sex - ${row['host sex']} + host_sex + ${row['host_sex']} @@ -163,46 +163,46 @@ def mandatorytest(row, column, index): ${row['lab_host']} - + - host scientific name - ${row['host scientific name']} + host_scientific_name + ${row['host_scientific_name']} - + - virus identifier - ${row['virus identifier']} + virus_identifier + ${row['virus_identifier']} - + - collector name - ${row['collector name']} + collector_name + ${row['collector_name']} - + - collecting institution - ${row['collecting institution']} + collecting_institution + ${row['collecting_institution']} - + - receipt date - ${row['receipt date']} + receipt_date + ${row['receipt_date']} - + - definition for seropositive sample - ${row['definition for seropositive sample']} + definition_for_seropositive_sample + ${row['definition_for_seropositive_sample']} - + - serotype (required for a seropositive sample) - ${row['serotype (required for a seropositive sample)']} + serotype_required_for_a_seropositive_sample + ${row['serotype_required_for_a_seropositive_sample']} @@ -217,22 +217,22 @@ def mandatorytest(row, column, index): ${row['strain']} - + - host habitat - ${row['host habitat']} + host_habitat + ${row['host_habitat']} - + - isolation source host-associated - ${row['isolation source host-associated']} + isolation_source_hostassociated + ${row['isolation_source_hostassociated']} - + - host description - ${row['host description']} + host_description + ${row['host_description']} @@ -241,16 +241,16 @@ def mandatorytest(row, column, index): ${row['gravidity']} - + - host behaviour - ${row['host behaviour']} + host_behaviour + ${row['host_behaviour']} - + - isolation source non-host-associated - ${row['isolation source non-host-associated']} + isolation_source_nonhostassociated + ${row['isolation_source_nonhostassociated']} diff --git a/ena_upload/templates/ENA_template_samples_ERC000034.xml b/ena_upload/templates/ENA_template_samples_ERC000034.xml index 6810291..fffbf12 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000034.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000034.xml @@ -39,10 +39,10 @@ def mandatorytest(row, column, index): ${row['tissue_type']} - + - collection date - ${row['collection date']} + collection_date + ${row['collection_date']} @@ -51,16 +51,16 @@ def mandatorytest(row, column, index): ${row['sex']} - + - date of birth - ${row['date of birth']} + date_of_birth + ${row['date_of_birth']} - + - date of death - ${row['date of death']} + date_of_death + ${row['date_of_death']} @@ -69,10 +69,10 @@ def mandatorytest(row, column, index): ${row['diagnosis']} - + - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} + geographic_location_country_andor_sea + ${row['geographic_location_country_andor_sea']} @@ -81,35 +81,35 @@ def mandatorytest(row, column, index): ${row['strain']} - + - tumor grading (OBI_0600002) - ${row['tumor grading (OBI_0600002)']} + tumor_grading_obi_0600002 + ${row['tumor_grading_obi_0600002']} - + - treatment agent - ${row['treatment agent']} + treatment_agent + ${row['treatment_agent']} - + - treatment dose - ${row['treatment dose']} - picomolar + treatment_dose + ${row['treatment_dose']} + molar - + - treatment date - ${row['treatment date']} + treatment_date + ${row['treatment_date']} - + - Further Details - ${row['Further Details']} + further_details + ${row['further_details']} diff --git a/ena_upload/templates/ENA_template_samples_ERC000035.xml b/ena_upload/templates/ENA_template_samples_ERC000035.xml index 78ec6f1..e143d50 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000035.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000035.xml @@ -45,10 +45,10 @@ def mandatorytest(row, column, index): ${row['dev_stage']} - + - organism part - ${row['organism part']} + organism_part + ${row['organism_part']} @@ -63,22 +63,22 @@ def mandatorytest(row, column, index): ${row['infect']} - + - collection date - ${row['collection date']} + collection_date + ${row['collection_date']} - + - sampling time point - ${row['sampling time point']} + sampling_time_point + ${row['sampling_time_point']} - + - initial time point - ${row['initial time point']} + initial_time_point + ${row['initial_time_point']} @@ -93,10 +93,10 @@ def mandatorytest(row, column, index): ${row['age']} - + - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} + geographic_location_country_andor_sea + ${row['geographic_location_country_andor_sea']} @@ -105,10 +105,10 @@ def mandatorytest(row, column, index): ${row['phenotype']} - + - cellular component - ${row['cellular component']} + cellular_component + ${row['cellular_component']} @@ -117,10 +117,10 @@ def mandatorytest(row, column, index): ${row['individual']} - + - disease staging - ${row['disease staging']} + disease_staging + ${row['disease_staging']} @@ -171,40 +171,40 @@ def mandatorytest(row, column, index): ${row['dose']} - + - chemical compound - ${row['chemical compound']} + chemical_compound + ${row['chemical_compound']} - + - experimental factor 1 - ${row['experimental factor 1']} + experimental_factor_1 + ${row['experimental_factor_1']} - + - experimental factor 2 - ${row['experimental factor 2']} + experimental_factor_2 + ${row['experimental_factor_2']} - + - experimental factor 3 - ${row['experimental factor 3']} + experimental_factor_3 + ${row['experimental_factor_3']} - + - experimental factor 4 - ${row['experimental factor 4']} + experimental_factor_4 + ${row['experimental_factor_4']} - + - experimental factor 5 - ${row['experimental factor 5']} + experimental_factor_5 + ${row['experimental_factor_5']} @@ -219,10 +219,10 @@ def mandatorytest(row, column, index): ${row['genotype']} - + - genetic modification - ${row['genetic modification']} + genetic_modification + ${row['genetic_modification']} @@ -231,22 +231,22 @@ def mandatorytest(row, column, index): ${row['protocol']} - + - environmental stress - ${row['environmental stress']} + environmental_stress + ${row['environmental_stress']} - + - environmental history - ${row['environmental history']} + environmental_history + ${row['environmental_history']} - + - growth condition - ${row['growth condition']} + growth_condition + ${row['growth_condition']} diff --git a/ena_upload/templates/ENA_template_samples_ERC000036.xml b/ena_upload/templates/ENA_template_samples_ERC000036.xml index e664dcd..0f02bcd 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000036.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000036.xml @@ -33,123 +33,123 @@ def mandatorytest(row, column, index): ${row.sample_description} - + - sample transportation date - ${row['sample transportation date']} + sample_transportation_date + ${row['sample_transportation_date']} - + - sample transportation temperature - ${row['sample transportation temperature']} + sample_transportation_temperature + ${row['sample_transportation_temperature']} °C - + - sample transportation time - ${row['sample transportation time']} + sample_transportation_time + ${row['sample_transportation_time']} - + - sample storage temperature - ${row['sample storage temperature']} + sample_storage_temperature + ${row['sample_storage_temperature']} °C - + - sample storage location - ${row['sample storage location']} + sample_storage_location + ${row['sample_storage_location']} - + - name of the sampling site - ${row['name of the sampling site']} + name_of_the_sampling_site + ${row['name_of_the_sampling_site']} - + - area of sampling site - ${row['area of sampling site']} + area_of_sampling_site + ${row['area_of_sampling_site']} - + - investigation type - ${row['investigation type']} + investigation_type + ${row['investigation_type']} - + - surveillance target - ${row['surveillance target']} + surveillance_target + ${row['surveillance_target']} - + - collection date - ${row['collection date']} + collection_date + ${row['collection_date']} - + - geographic location (latitude) - ${row['geographic location (latitude)']} + geographic_location_latitude + ${row['geographic_location_latitude']} DD - + - geographic location (longitude) - ${row['geographic location (longitude)']} + geographic_location_longitude + ${row['geographic_location_longitude']} DD - + - geographic location (region and locality) - ${row['geographic location (region and locality)']} + geographic_location_region_and_locality + ${row['geographic_location_region_and_locality']} - + - amount or size of sample collected - ${row['amount or size of sample collected']} - m3 + amount_or_size_of_sample_collected + ${row['amount_or_size_of_sample_collected']} + kg - + - sampling time point - ${row['sampling time point']} + sampling_time_point + ${row['sampling_time_point']} - + - sample storage duration - ${row['sample storage duration']} + sample_storage_duration + ${row['sample_storage_duration']} - + - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} + geographic_location_country_andor_sea + ${row['geographic_location_country_andor_sea']} - + - receipt date - ${row['receipt date']} + receipt_date + ${row['receipt_date']} - + - sewage type - ${row['sewage type']} + sewage_type + ${row['sewage_type']} @@ -159,28 +159,28 @@ def mandatorytest(row, column, index): ºC - + - size of the catchment area - ${row['size of the catchment area']} + size_of_the_catchment_area + ${row['size_of_the_catchment_area']} - + - population size of the catchment area - ${row['population size of the catchment area']} + population_size_of_the_catchment_area + ${row['population_size_of_the_catchment_area']} - + - nucleic acid extraction - ${row['nucleic acid extraction']} + nucleic_acid_extraction + ${row['nucleic_acid_extraction']} - + - nucleic acid amplification - ${row['nucleic acid amplification']} + nucleic_acid_amplification + ${row['nucleic_acid_amplification']} diff --git a/ena_upload/templates/ENA_template_samples_ERC000037.xml b/ena_upload/templates/ENA_template_samples_ERC000037.xml index c0f1b25..8e0a02b 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000037.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000037.xml @@ -33,10 +33,10 @@ def mandatorytest(row, column, index): ${row.sample_description} - + - observed biotic relationship - ${row['observed biotic relationship']} + observed_biotic_relationship + ${row['observed_biotic_relationship']} @@ -45,138 +45,138 @@ def mandatorytest(row, column, index): ${row['propagation']} - + - sample collection method - ${row['sample collection method']} + sample_collection_method + ${row['sample_collection_method']} - + - sample storage temperature - ${row['sample storage temperature']} + sample_storage_temperature + ${row['sample_storage_temperature']} °C - + - sample storage location - ${row['sample storage location']} + sample_storage_location + ${row['sample_storage_location']} - + - soil_taxonomic/FAO classification - ${row['soil_taxonomic/FAO classification']} + soil_taxonomicfao_classification + ${row['soil_taxonomicfao_classification']} - + - soil_taxonomic/local classification - ${row['soil_taxonomic/local classification']} + soil_taxonomiclocal_classification + ${row['soil_taxonomiclocal_classification']} - + - soil_taxonomic/local classification method - ${row['soil_taxonomic/local classification method']} + soil_taxonomiclocal_classification_method + ${row['soil_taxonomiclocal_classification_method']} - + - soil type - ${row['soil type']} + soil_type + ${row['soil_type']} - + - soil type method - ${row['soil type method']} + soil_type_method + ${row['soil_type_method']} - + - soil texture measurement - ${row['soil texture measurement']} + soil_texture_measurement + ${row['soil_texture_measurement']} % sand/silt/clay - + - soil texture method - ${row['soil texture method']} + soil_texture_method + ${row['soil_texture_method']} - + - soil pH - ${row['soil pH']} + soil_ph + ${row['soil_ph']} - + - growth facility - ${row['growth facility']} + growth_facility + ${row['growth_facility']} - + - plant developmental stage - ${row['plant developmental stage']} + plant_developmental_stage + ${row['plant_developmental_stage']} - + - sampled age - ${row['sampled age']} + sampled_age + ${row['sampled_age']} - + - sample health state - ${row['sample health state']} + sample_health_state + ${row['sample_health_state']} - + - sample wet mass - ${row['sample wet mass']} + sample_wet_mass + ${row['sample_wet_mass']} - + - sample disease stage - ${row['sample disease stage']} + sample_disease_stage + ${row['sample_disease_stage']} - + - sample length - ${row['sample length']} + sample_length + ${row['sample_length']} - + - sample height - ${row['sample height']} + sample_height + ${row['sample_height']} - + - sample dry mass - ${row['sample dry mass']} + sample_dry_mass + ${row['sample_dry_mass']} - + - sample disease status - ${row['sample disease status']} + sample_disease_status + ${row['sample_disease_status']} - + - sample phenotype - ${row['sample phenotype']} + sample_phenotype + ${row['sample_phenotype']} @@ -185,22 +185,22 @@ def mandatorytest(row, column, index): ${row['ploidy']} - + - number of replicons - ${row['number of replicons']} + number_of_replicons + ${row['number_of_replicons']} - + - extrachromosomal elements - ${row['extrachromosomal elements']} + extrachromosomal_elements + ${row['extrachromosomal_elements']} - + - estimated size - ${row['estimated size']} + estimated_size + ${row['estimated_size']} @@ -209,10 +209,10 @@ def mandatorytest(row, column, index): ${row['collected_by']} - + - collection date - ${row['collection date']} + collection_date + ${row['collection_date']} @@ -222,24 +222,24 @@ def mandatorytest(row, column, index): m - + - geographic location (latitude) - ${row['geographic location (latitude)']} + geographic_location_latitude + ${row['geographic_location_latitude']} DD - + - geographic location (longitude) - ${row['geographic location (longitude)']} + geographic_location_longitude + ${row['geographic_location_longitude']} DD - + - geographic location (region and locality) - ${row['geographic location (region and locality)']} + geographic_location_region_and_locality + ${row['geographic_location_region_and_locality']} @@ -248,16 +248,16 @@ def mandatorytest(row, column, index): ${row['identified_by']} - + - broad-scale environmental context - ${row['broad-scale environmental context']} + broadscale_environmental_context + ${row['broadscale_environmental_context']} - + - local environmental context - ${row['local environmental context']} + local_environmental_context + ${row['local_environmental_context']} @@ -267,101 +267,101 @@ def mandatorytest(row, column, index): m - + - amount or size of sample collected - ${row['amount or size of sample collected']} - m3 + amount_or_size_of_sample_collected + ${row['amount_or_size_of_sample_collected']} + kg - + - sampling time point - ${row['sampling time point']} + sampling_time_point + ${row['sampling_time_point']} - + - sample capture status - ${row['sample capture status']} + sample_capture_status + ${row['sample_capture_status']} - + - organism common name - ${row['organism common name']} + organism_common_name + ${row['organism_common_name']} - + - biological status - ${row['biological status']} + biological_status + ${row['biological_status']} - + - growth habit - ${row['growth habit']} + growth_habit + ${row['growth_habit']} - + - plant sex - ${row['plant sex']} + plant_sex + ${row['plant_sex']} - + - plant structure - ${row['plant structure']} + plant_structure + ${row['plant_structure']} - + - sample storage duration - ${row['sample storage duration']} + sample_storage_duration + ${row['sample_storage_duration']} - + - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} + geographic_location_country_andor_sea + ${row['geographic_location_country_andor_sea']} - + - climate environment - ${row['climate environment']} + climate_environment + ${row['climate_environment']} - + - gaseous environment - ${row['gaseous environment']} + gaseous_environment + ${row['gaseous_environment']} - + - seasonal environment - ${row['seasonal environment']} + seasonal_environment + ${row['seasonal_environment']} - + - drainage classification - ${row['drainage classification']} + drainage_classification + ${row['drainage_classification']} - + - source material identifiers - ${row['source material identifiers']} + source_material_identifiers + ${row['source_material_identifiers']} - + - source material description - ${row['source material description']} + source_material_description + ${row['source_material_description']} @@ -376,150 +376,150 @@ def mandatorytest(row, column, index): ${row['genotype']} - + - genetic modification - ${row['genetic modification']} + genetic_modification + ${row['genetic_modification']} - + - subspecific genetic lineage rank - ${row['subspecific genetic lineage rank']} + subspecific_genetic_lineage_rank + ${row['subspecific_genetic_lineage_rank']} - + - subspecific genetic lineage name - ${row['subspecific genetic lineage name']} + subspecific_genetic_lineage_name + ${row['subspecific_genetic_lineage_name']} - + - organism phenotype - ${row['organism phenotype']} + organism_phenotype + ${row['organism_phenotype']} - + - ancestral data - ${row['ancestral data']} + ancestral_data + ${row['ancestral_data']} - + - plant growth medium - ${row['plant growth medium']} + plant_growth_medium + ${row['plant_growth_medium']} - + - rooting conditions - ${row['rooting conditions']} + rooting_conditions + ${row['rooting_conditions']} - + - culture rooting medium - ${row['culture rooting medium']} + culture_rooting_medium + ${row['culture_rooting_medium']} - + - rooting medium macronutrients - ${row['rooting medium macronutrients']} + rooting_medium_macronutrients + ${row['rooting_medium_macronutrients']} - + - rooting medium micronutrients - ${row['rooting medium micronutrients']} + rooting_medium_micronutrients + ${row['rooting_medium_micronutrients']} - + - rooting medium organic supplements - ${row['rooting medium organic supplements']} + rooting_medium_organic_supplements + ${row['rooting_medium_organic_supplements']} - + - rooting medium carbon - ${row['rooting medium carbon']} + rooting_medium_carbon + ${row['rooting_medium_carbon']} - + - rooting medium regulators - ${row['rooting medium regulators']} + rooting_medium_regulators + ${row['rooting_medium_regulators']} - + - rooting medium solidifier - ${row['rooting medium solidifier']} + rooting_medium_solidifier + ${row['rooting_medium_solidifier']} - + - rooting medium pH - ${row['rooting medium pH']} + rooting_medium_ph + ${row['rooting_medium_ph']} - + - isolation and growth condition - ${row['isolation and growth condition']} + isolation_and_growth_condition + ${row['isolation_and_growth_condition']} - + - sample material processing - ${row['sample material processing']} + sample_material_processing + ${row['sample_material_processing']} - + - sample volume or weight for DNA extraction - ${row['sample volume or weight for DNA extraction']} - ng + sample_volume_or_weight_for_dna_extraction + ${row['sample_volume_or_weight_for_dna_extraction']} + mL depth ${row['depth']} - mm + m - + - air temperature regimen - ${row['air temperature regimen']} + air_temperature_regimen + ${row['air_temperature_regimen']} - + - antibiotic regimen - ${row['antibiotic regimen']} + antibiotic_regimen + ${row['antibiotic_regimen']} - + - chemical mutagen - ${row['chemical mutagen']} + chemical_mutagen + ${row['chemical_mutagen']} - + - fertilizer administration - ${row['fertilizer administration']} + fertilizer_administration + ${row['fertilizer_administration']} - + - fungicide regimen - ${row['fungicide regimen']} + fungicide_regimen + ${row['fungicide_regimen']} @@ -528,112 +528,112 @@ def mandatorytest(row, column, index): ${row['gravity']} - + - growth hormone regimen - ${row['growth hormone regimen']} + growth_hormone_regimen + ${row['growth_hormone_regimen']} - + - herbicide regimen - ${row['herbicide regimen']} + herbicide_regimen + ${row['herbicide_regimen']} - + - humidity regimen - ${row['humidity regimen']} + humidity_regimen + ${row['humidity_regimen']} - + - mineral nutrient regimen - ${row['mineral nutrient regimen']} + mineral_nutrient_regimen + ${row['mineral_nutrient_regimen']} - + - non-mineral nutrient regimen - ${row['non-mineral nutrient regimen']} + nonmineral_nutrient_regimen + ${row['nonmineral_nutrient_regimen']} - + - pesticide regimen - ${row['pesticide regimen']} + pesticide_regimen + ${row['pesticide_regimen']} - + - pH regimen - ${row['pH regimen']} + ph_regimen + ${row['ph_regimen']} - + - radiation regimen - ${row['radiation regimen']} + radiation_regimen + ${row['radiation_regimen']} - + - rainfall regimen - ${row['rainfall regimen']} + rainfall_regimen + ${row['rainfall_regimen']} - + - salt regimen - ${row['salt regimen']} + salt_regimen + ${row['salt_regimen']} - + - standing water regimen - ${row['standing water regimen']} + standing_water_regimen + ${row['standing_water_regimen']} - + - watering regimen - ${row['watering regimen']} + watering_regimen + ${row['watering_regimen']} - + - water temperature regimen - ${row['water temperature regimen']} + water_temperature_regimen + ${row['water_temperature_regimen']} - + - plant treatment - ${row['plant treatment']} + plant_treatment + ${row['plant_treatment']} - + - light regimen - ${row['light regimen']} + light_regimen + ${row['light_regimen']} - + - biotic regimen - ${row['biotic regimen']} + biotic_regimen + ${row['biotic_regimen']} - + - mechanical damage - ${row['mechanical damage']} + mechanical_damage + ${row['mechanical_damage']} - + - chemical administration - ${row['chemical administration']} + chemical_administration + ${row['chemical_administration']} diff --git a/ena_upload/templates/ENA_template_samples_ERC000038.xml b/ena_upload/templates/ENA_template_samples_ERC000038.xml index 7dde69e..bdf6317 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000038.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000038.xml @@ -33,137 +33,137 @@ def mandatorytest(row, column, index): ${row.sample_description} - + - Latitude Start - ${row['Latitude Start']} + latitude_start + ${row['latitude_start']} DD - + - Longitude Start - ${row['Longitude Start']} + longitude_start + ${row['longitude_start']} DD - + - Protocol Label - ${row['Protocol Label']} + protocol_label + ${row['protocol_label']} - + - sample storage conditions - ${row['sample storage conditions']} + sample_storage_conditions + ${row['sample_storage_conditions']} - + - aquaculture origin - ${row['aquaculture origin']} + aquaculture_origin + ${row['aquaculture_origin']} - + - shellfish total weight - ${row['shellfish total weight']} + shellfish_total_weight + ${row['shellfish_total_weight']} g - + - shellfish soft tissue weight - ${row['shellfish soft tissue weight']} + shellfish_soft_tissue_weight + ${row['shellfish_soft_tissue_weight']} g - + - shell length - ${row['shell length']} + shell_length + ${row['shell_length']} g - + - shell width - ${row['shell width']} + shell_width + ${row['shell_width']} g - + - shell markings - ${row['shell markings']} + shell_markings + ${row['shell_markings']} g - + - sample health state - ${row['sample health state']} + sample_health_state + ${row['sample_health_state']} - + - sample disease status - ${row['sample disease status']} + sample_disease_status + ${row['sample_disease_status']} - + - collection date - ${row['collection date']} + collection_date + ${row['collection_date']} - + - broad-scale environmental context - ${row['broad-scale environmental context']} + broadscale_environmental_context + ${row['broadscale_environmental_context']} - + - local environmental context - ${row['local environmental context']} + local_environmental_context + ${row['local_environmental_context']} - + - environmental medium - ${row['environmental medium']} + environmental_medium + ${row['environmental_medium']} - + - Sampling Campaign - ${row['Sampling Campaign']} + sampling_campaign + ${row['sampling_campaign']} - + - Sampling Station - ${row['Sampling Station']} + sampling_station + ${row['sampling_station']} - + - Sampling Platform - ${row['Sampling Platform']} + sampling_platform + ${row['sampling_platform']} - + - Marine Region - ${row['Marine Region']} + marine_region + ${row['marine_region']} - + - seabed habitat - ${row['seabed habitat']} + seabed_habitat + ${row['seabed_habitat']} @@ -172,50 +172,50 @@ def mandatorytest(row, column, index): ${row['age']} - + - adductor weight - ${row['adductor weight']} + adductor_weight + ${row['adductor_weight']} g - + - gonad weight - ${row['gonad weight']} + gonad_weight + ${row['gonad_weight']} g - + - toxin burden - ${row['toxin burden']} - mg + toxin_burden + ${row['toxin_burden']} + kg - + - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} + geographic_location_country_andor_sea + ${row['geographic_location_country_andor_sea']} - + - treatment agent - ${row['treatment agent']} + treatment_agent + ${row['treatment_agent']} - + - chemical compound - ${row['chemical compound']} + chemical_compound + ${row['chemical_compound']} depth ${row['depth']} - mm + m diff --git a/ena_upload/templates/ENA_template_samples_ERC000039.xml b/ena_upload/templates/ENA_template_samples_ERC000039.xml index a6622cb..fde58d0 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000039.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000039.xml @@ -39,134 +39,134 @@ def mandatorytest(row, column, index): ${row['dev_stage']} - + - known pathogenicity - ${row['known pathogenicity']} + known_pathogenicity + ${row['known_pathogenicity']} - + - sample storage conditions - ${row['sample storage conditions']} + sample_storage_conditions + ${row['sample_storage_conditions']} - + - subject exposure - ${row['subject exposure']} + subject_exposure + ${row['subject_exposure']} - + - travel-relation - ${row['travel-relation']} + travelrelation + ${row['travelrelation']} - + - clinical setting - ${row['clinical setting']} + clinical_setting + ${row['clinical_setting']} - + - country of travel - ${row['country of travel']} + country_of_travel + ${row['country_of_travel']} - + - collection date - ${row['collection date']} + collection_date + ${row['collection_date']} - + - geographic location (latitude) - ${row['geographic location (latitude)']} + geographic_location_latitude + ${row['geographic_location_latitude']} DD - + - geographic location (longitude) - ${row['geographic location (longitude)']} + geographic_location_longitude + ${row['geographic_location_longitude']} DD - + - geographic location (region and locality) - ${row['geographic location (region and locality)']} + geographic_location_region_and_locality + ${row['geographic_location_region_and_locality']} - + - subject exposure duration - ${row['subject exposure duration']} - year + subject_exposure_duration + ${row['subject_exposure_duration']} + day - + - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} + geographic_location_country_andor_sea + ${row['geographic_location_country_andor_sea']} - + - host disease outcome - ${row['host disease outcome']} + host_disease_outcome + ${row['host_disease_outcome']} - + - host common name - ${row['host common name']} + host_common_name + ${row['host_common_name']} - + - host subject id - ${row['host subject id']} + host_subject_id + ${row['host_subject_id']} - + - host age - ${row['host age']} + host_age + ${row['host_age']} years - + - host health state - ${row['host health state']} + host_health_state + ${row['host_health_state']} - + - host sex - ${row['host sex']} + host_sex + ${row['host_sex']} - + - host scientific name - ${row['host scientific name']} + host_scientific_name + ${row['host_scientific_name']} - + - collector name - ${row['collector name']} + collector_name + ${row['collector_name']} - + - collecting institution - ${row['collecting institution']} + collecting_institution + ${row['collecting_institution']} @@ -181,16 +181,16 @@ def mandatorytest(row, column, index): ${row['strain']} - + - isolation source host-associated - ${row['isolation source host-associated']} + isolation_source_hostassociated + ${row['isolation_source_hostassociated']} - + - diagnostic method - ${row['diagnostic method']} + diagnostic_method + ${row['diagnostic_method']} @@ -199,10 +199,10 @@ def mandatorytest(row, column, index): ${row['genotype']} - + - isolation source non-host-associated - ${row['isolation source non-host-associated']} + isolation_source_nonhostassociated + ${row['isolation_source_nonhostassociated']} diff --git a/ena_upload/templates/ENA_template_samples_ERC000040.xml b/ena_upload/templates/ENA_template_samples_ERC000040.xml index e6b3f0f..c3c9bed 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000040.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000040.xml @@ -33,36 +33,36 @@ def mandatorytest(row, column, index): ${row.sample_description} - + - sample collection method - ${row['sample collection method']} + sample_collection_method + ${row['sample_collection_method']} - + - size-fraction lower threshold - ${row['size-fraction lower threshold']} - µm + sizefraction_lower_threshold + ${row['sizefraction_lower_threshold']} + nm - + - size-fraction upper threshold - ${row['size-fraction upper threshold']} - µm + sizefraction_upper_threshold + ${row['sizefraction_upper_threshold']} + nm - + - target gene - ${row['target gene']} + target_gene + ${row['target_gene']} - + - target subfragment - ${row['target subfragment']} + target_subfragment + ${row['target_subfragment']} @@ -77,10 +77,10 @@ def mandatorytest(row, column, index): ${row['collected_by']} - + - collection date - ${row['collection date']} + collection_date + ${row['collection_date']} @@ -90,42 +90,42 @@ def mandatorytest(row, column, index): m - + - geographic location (latitude) - ${row['geographic location (latitude)']} + geographic_location_latitude + ${row['geographic_location_latitude']} DD - + - geographic location (longitude) - ${row['geographic location (longitude)']} + geographic_location_longitude + ${row['geographic_location_longitude']} DD - + - geographic location (region and locality) - ${row['geographic location (region and locality)']} + geographic_location_region_and_locality + ${row['geographic_location_region_and_locality']} - + - broad-scale environmental context - ${row['broad-scale environmental context']} + broadscale_environmental_context + ${row['broadscale_environmental_context']} - + - local environmental context - ${row['local environmental context']} + local_environmental_context + ${row['local_environmental_context']} - + - environmental medium - ${row['environmental medium']} + environmental_medium + ${row['environmental_medium']} @@ -134,10 +134,10 @@ def mandatorytest(row, column, index): ${row['environmental_sample']} - + - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} + geographic_location_country_andor_sea + ${row['geographic_location_country_andor_sea']} @@ -147,23 +147,23 @@ def mandatorytest(row, column, index): psu - + - Further Details - ${row['Further Details']} + further_details + ${row['further_details']} - + - pcr primers - ${row['pcr primers']} + pcr_primers + ${row['pcr_primers']} depth ${row['depth']} - mm + m diff --git a/ena_upload/templates/ENA_template_samples_ERC000041.xml b/ena_upload/templates/ENA_template_samples_ERC000041.xml index 149c363..ca95d8f 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000041.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000041.xml @@ -33,54 +33,54 @@ def mandatorytest(row, column, index): ${row.sample_description} - + - sample transportation date - ${row['sample transportation date']} + sample_transportation_date + ${row['sample_transportation_date']} - + - sample transportation temperature - ${row['sample transportation temperature']} + sample_transportation_temperature + ${row['sample_transportation_temperature']} °C - + - sample transportation time - ${row['sample transportation time']} + sample_transportation_time + ${row['sample_transportation_time']} - + - sample storage temperature - ${row['sample storage temperature']} + sample_storage_temperature + ${row['sample_storage_temperature']} °C - + - sample storage location - ${row['sample storage location']} + sample_storage_location + ${row['sample_storage_location']} - + - instrument for DNA concentration measurement - ${row['instrument for DNA concentration measurement']} + instrument_for_dna_concentration_measurement + ${row['instrument_for_dna_concentration_measurement']} - + - read quality filter - ${row['read quality filter']} + read_quality_filter + ${row['read_quality_filter']} - + - DNA concentration - ${row['DNA concentration']} + dna_concentration + ${row['dna_concentration']} ng/µl @@ -90,53 +90,53 @@ def mandatorytest(row, column, index): ${row['isolation_source']} - + - collection date - ${row['collection date']} + collection_date + ${row['collection_date']} - + - geographic location (region and locality) - ${row['geographic location (region and locality)']} + geographic_location_region_and_locality + ${row['geographic_location_region_and_locality']} - + - amount or size of sample collected - ${row['amount or size of sample collected']} - m3 + amount_or_size_of_sample_collected + ${row['amount_or_size_of_sample_collected']} + kg - + - sampling time point - ${row['sampling time point']} + sampling_time_point + ${row['sampling_time_point']} - + - sample storage duration - ${row['sample storage duration']} + sample_storage_duration + ${row['sample_storage_duration']} - + - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} + geographic_location_country_andor_sea + ${row['geographic_location_country_andor_sea']} - + - receipt date - ${row['receipt date']} + receipt_date + ${row['receipt_date']} - + - links to additional analysis - ${row['links to additional analysis']} + links_to_additional_analysis + ${row['links_to_additional_analysis']} @@ -151,22 +151,22 @@ def mandatorytest(row, column, index): ${row['sub_species']} - + - Further Details - ${row['Further Details']} + further_details + ${row['further_details']} - + - nucleic acid extraction - ${row['nucleic acid extraction']} + nucleic_acid_extraction + ${row['nucleic_acid_extraction']} - + - library construction method - ${row['library construction method']} + library_construction_method + ${row['library_construction_method']} diff --git a/ena_upload/templates/ENA_template_samples_ERC000043.xml b/ena_upload/templates/ENA_template_samples_ERC000043.xml index c7b12de..64e5864 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000043.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000043.xml @@ -33,22 +33,22 @@ def mandatorytest(row, column, index): ${row.sample_description} - + - sample collection method - ${row['sample collection method']} + sample_collection_method + ${row['sample_collection_method']} - + - sample storage conditions - ${row['sample storage conditions']} + sample_storage_conditions + ${row['sample_storage_conditions']} - + - sample storage temperature - ${row['sample storage temperature']} + sample_storage_temperature + ${row['sample_storage_temperature']} °C @@ -58,63 +58,63 @@ def mandatorytest(row, column, index): ${row['collected_by']} - + - collection date - ${row['collection date']} + collection_date + ${row['collection_date']} - + - geographic location (latitude) - ${row['geographic location (latitude)']} + geographic_location_latitude + ${row['geographic_location_latitude']} DD - + - geographic location (longitude) - ${row['geographic location (longitude)']} + geographic_location_longitude + ${row['geographic_location_longitude']} DD - + - amount or size of sample collected - ${row['amount or size of sample collected']} - m3 + amount_or_size_of_sample_collected + ${row['amount_or_size_of_sample_collected']} + kg - + - water temperature - ${row['water temperature']} + water_temperature + ${row['water_temperature']} ºC - + - sample storage duration - ${row['sample storage duration']} + sample_storage_duration + ${row['sample_storage_duration']} - + - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} + geographic_location_country_andor_sea + ${row['geographic_location_country_andor_sea']} - + - light intensity - ${row['light intensity']} + light_intensity + ${row['light_intensity']} lux - + - pH - ${row['pH']} + ph + ${row['ph']} @@ -136,29 +136,29 @@ def mandatorytest(row, column, index): ${row['strain']} - + - Further Details - ${row['Further Details']} + further_details + ${row['further_details']} - + - isolation and growth condition - ${row['isolation and growth condition']} + isolation_and_growth_condition + ${row['isolation_and_growth_condition']} depth ${row['depth']} - mm + m - + - growth condition - ${row['growth condition']} + growth_condition + ${row['growth_condition']} diff --git a/ena_upload/templates/ENA_template_samples_ERC000044.xml b/ena_upload/templates/ENA_template_samples_ERC000044.xml index 572fb38..6482073 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000044.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000044.xml @@ -33,28 +33,28 @@ def mandatorytest(row, column, index): ${row.sample_description} - + - subject exposure - ${row['subject exposure']} + subject_exposure + ${row['subject_exposure']} - + - travel-relation - ${row['travel-relation']} + travelrelation + ${row['travelrelation']} - + - clinical setting - ${row['clinical setting']} + clinical_setting + ${row['clinical_setting']} - + - country of travel - ${row['country of travel']} + country_of_travel + ${row['country_of_travel']} @@ -63,47 +63,47 @@ def mandatorytest(row, column, index): ${row['collected_by']} - + - collection date - ${row['collection date']} + collection_date + ${row['collection_date']} - + - geographic location (region and locality) - ${row['geographic location (region and locality)']} + geographic_location_region_and_locality + ${row['geographic_location_region_and_locality']} - + - subject exposure duration - ${row['subject exposure duration']} - year + subject_exposure_duration + ${row['subject_exposure_duration']} + day - + - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} + geographic_location_country_andor_sea + ${row['geographic_location_country_andor_sea']} - + - host disease status - ${row['host disease status']} + host_disease_status + ${row['host_disease_status']} - + - host disease outcome - ${row['host disease outcome']} + host_disease_outcome + ${row['host_disease_outcome']} - + - host scientific name - ${row['host scientific name']} + host_scientific_name + ${row['host_scientific_name']} @@ -124,16 +124,16 @@ def mandatorytest(row, column, index): ${row['serovar']} - + - serovar_in-silico - ${row['serovar_in-silico']} + serovar_insilico + ${row['serovar_insilico']} - + - isolation source host-associated - ${row['isolation source host-associated']} + isolation_source_hostassociated + ${row['isolation_source_hostassociated']} diff --git a/ena_upload/templates/ENA_template_samples_ERC000045.xml b/ena_upload/templates/ENA_template_samples_ERC000045.xml index 93fc3a5..f4d0143 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000045.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000045.xml @@ -45,28 +45,28 @@ def mandatorytest(row, column, index): ${row['collected_by']} - + - collection date - ${row['collection date']} + collection_date + ${row['collection_date']} - + - geographic location (region and locality) - ${row['geographic location (region and locality)']} + geographic_location_region_and_locality + ${row['geographic_location_region_and_locality']} - + - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} + geographic_location_country_andor_sea + ${row['geographic_location_country_andor_sea']} - + - receipt date - ${row['receipt date']} + receipt_date + ${row['receipt_date']} diff --git a/ena_upload/templates/ENA_template_samples_ERC000047.xml b/ena_upload/templates/ENA_template_samples_ERC000047.xml index 13160c9..1e58afe 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000047.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000047.xml @@ -33,175 +33,175 @@ def mandatorytest(row, column, index): ${row.sample_description} - + - relationship to oxygen - ${row['relationship to oxygen']} + relationship_to_oxygen + ${row['relationship_to_oxygen']} - + - sample collection device - ${row['sample collection device']} + sample_collection_device + ${row['sample_collection_device']} - + - sample collection method - ${row['sample collection method']} + sample_collection_method + ${row['sample_collection_method']} - + - metagenomic source - ${row['metagenomic source']} + metagenomic_source + ${row['metagenomic_source']} - + - sample derived from - ${row['sample derived from']} + sample_derived_from + ${row['sample_derived_from']} - + - project name - ${row['project name']} + project_name + ${row['project_name']} - + - multiplex identifiers - ${row['multiplex identifiers']} + multiplex_identifiers + ${row['multiplex_identifiers']} - + - relevant electronic resources - ${row['relevant electronic resources']} + relevant_electronic_resources + ${row['relevant_electronic_resources']} - + - relevant standard operating procedures - ${row['relevant standard operating procedures']} + relevant_standard_operating_procedures + ${row['relevant_standard_operating_procedures']} - + - number of standard tRNAs extracted - ${row['number of standard tRNAs extracted']} + number_of_standard_trnas_extracted + ${row['number_of_standard_trnas_extracted']} - + - feature prediction - ${row['feature prediction']} + feature_prediction + ${row['feature_prediction']} - + - similarity search method - ${row['similarity search method']} + similarity_search_method + ${row['similarity_search_method']} - + - 16s recovered - ${row['16s recovered']} + _16s_recovered + ${row['_16s_recovered']} - + - 16S recovery software - ${row['16S recovery software']} + _16s_recovery_software + ${row['_16s_recovery_software']} - + - tRNA extraction software - ${row['tRNA extraction software']} + trna_extraction_software + ${row['trna_extraction_software']} - + - completeness score - ${row['completeness score']} + completeness_score + ${row['completeness_score']} % - + - completeness software - ${row['completeness software']} + completeness_software + ${row['completeness_software']} - + - completeness approach - ${row['completeness approach']} + completeness_approach + ${row['completeness_approach']} - + - contamination score - ${row['contamination score']} + contamination_score + ${row['contamination_score']} % - + - contamination screening input - ${row['contamination screening input']} + contamination_screening_input + ${row['contamination_screening_input']} - + - contamination screening parameters - ${row['contamination screening parameters']} + contamination_screening_parameters + ${row['contamination_screening_parameters']} - + - decontamination software - ${row['decontamination software']} + decontamination_software + ${row['decontamination_software']} - + - binning software - ${row['binning software']} + binning_software + ${row['binning_software']} - + - reassembly post binning - ${row['reassembly post binning']} + reassembly_post_binning + ${row['reassembly_post_binning']} Yes - + - MAG coverage software - ${row['MAG coverage software']} + mag_coverage_software + ${row['mag_coverage_software']} - + - assembly quality - ${row['assembly quality']} + assembly_quality + ${row['assembly_quality']} - + - binning parameters - ${row['binning parameters']} + binning_parameters + ${row['binning_parameters']} - + - taxonomic identity marker - ${row['taxonomic identity marker']} + taxonomic_identity_marker + ${row['taxonomic_identity_marker']} @@ -210,10 +210,10 @@ def mandatorytest(row, column, index): ${row['isolation_source']} - + - collection date - ${row['collection date']} + collection_date + ${row['collection_date']} @@ -223,42 +223,42 @@ def mandatorytest(row, column, index): m - + - geographic location (latitude) - ${row['geographic location (latitude)']} + geographic_location_latitude + ${row['geographic_location_latitude']} DD - + - geographic location (longitude) - ${row['geographic location (longitude)']} + geographic_location_longitude + ${row['geographic_location_longitude']} DD - + - geographic location (region and locality) - ${row['geographic location (region and locality)']} + geographic_location_region_and_locality + ${row['geographic_location_region_and_locality']} - + - broad-scale environmental context - ${row['broad-scale environmental context']} + broadscale_environmental_context + ${row['broadscale_environmental_context']} - + - local environmental context - ${row['local environmental context']} + local_environmental_context + ${row['local_environmental_context']} - + - environmental medium - ${row['environmental medium']} + environmental_medium + ${row['environmental_medium']} @@ -268,107 +268,107 @@ def mandatorytest(row, column, index): m - + - amount or size of sample collected - ${row['amount or size of sample collected']} - m3 + amount_or_size_of_sample_collected + ${row['amount_or_size_of_sample_collected']} + kg - + - size fraction selected - ${row['size fraction selected']} + size_fraction_selected + ${row['size_fraction_selected']} - + - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} + geographic_location_country_andor_sea + ${row['geographic_location_country_andor_sea']} - + - source material identifiers - ${row['source material identifiers']} + source_material_identifiers + ${row['source_material_identifiers']} - + - experimental factor - ${row['experimental factor']} + experimental_factor + ${row['experimental_factor']} - + - taxonomic classification - ${row['taxonomic classification']} + taxonomic_classification + ${row['taxonomic_classification']} - + - annotation source - ${row['annotation source']} + annotation_source + ${row['annotation_source']} - + - reference for biomaterial - ${row['reference for biomaterial']} + reference_for_biomaterial + ${row['reference_for_biomaterial']} - + - reference database(s) - ${row['reference database(s)']} + reference_databases + ${row['reference_databases']} - + - sample material processing - ${row['sample material processing']} + sample_material_processing + ${row['sample_material_processing']} - + - nucleic acid extraction - ${row['nucleic acid extraction']} + nucleic_acid_extraction + ${row['nucleic_acid_extraction']} - + - nucleic acid amplification - ${row['nucleic acid amplification']} + nucleic_acid_amplification + ${row['nucleic_acid_amplification']} - + - library size - ${row['library size']} + library_size + ${row['library_size']} - + - library reads sequenced - ${row['library reads sequenced']} + library_reads_sequenced + ${row['library_reads_sequenced']} - + - library vector - ${row['library vector']} + library_vector + ${row['library_vector']} - + - library screening strategy - ${row['library screening strategy']} + library_screening_strategy + ${row['library_screening_strategy']} - + - assembly software - ${row['assembly software']} + assembly_software + ${row['assembly_software']} @@ -381,7 +381,7 @@ def mandatorytest(row, column, index): depth ${row['depth']} - mm + m diff --git a/ena_upload/templates/ENA_template_samples_ERC000048.xml b/ena_upload/templates/ENA_template_samples_ERC000048.xml index 82b5a92..ee130c5 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000048.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000048.xml @@ -33,150 +33,150 @@ def mandatorytest(row, column, index): ${row.sample_description} - + - relationship to oxygen - ${row['relationship to oxygen']} + relationship_to_oxygen + ${row['relationship_to_oxygen']} - + - sample collection device - ${row['sample collection device']} + sample_collection_device + ${row['sample_collection_device']} - + - sample collection method - ${row['sample collection method']} + sample_collection_method + ${row['sample_collection_method']} - + - metagenomic source - ${row['metagenomic source']} + metagenomic_source + ${row['metagenomic_source']} - + - sample derived from - ${row['sample derived from']} + sample_derived_from + ${row['sample_derived_from']} - + - project name - ${row['project name']} + project_name + ${row['project_name']} - + - multiplex identifiers - ${row['multiplex identifiers']} + multiplex_identifiers + ${row['multiplex_identifiers']} - + - relevant electronic resources - ${row['relevant electronic resources']} + relevant_electronic_resources + ${row['relevant_electronic_resources']} - + - relevant standard operating procedures - ${row['relevant standard operating procedures']} + relevant_standard_operating_procedures + ${row['relevant_standard_operating_procedures']} - + - number of standard tRNAs extracted - ${row['number of standard tRNAs extracted']} + number_of_standard_trnas_extracted + ${row['number_of_standard_trnas_extracted']} - + - feature prediction - ${row['feature prediction']} + feature_prediction + ${row['feature_prediction']} - + - similarity search method - ${row['similarity search method']} + similarity_search_method + ${row['similarity_search_method']} - + - 16s recovered - ${row['16s recovered']} + _16s_recovered + ${row['_16s_recovered']} - + - 16S recovery software - ${row['16S recovery software']} + _16s_recovery_software + ${row['_16s_recovery_software']} - + - tRNA extraction software - ${row['tRNA extraction software']} + trna_extraction_software + ${row['trna_extraction_software']} - + - completeness score - ${row['completeness score']} + completeness_score + ${row['completeness_score']} % - + - completeness software - ${row['completeness software']} + completeness_software + ${row['completeness_software']} - + - completeness approach - ${row['completeness approach']} + completeness_approach + ${row['completeness_approach']} - + - contamination score - ${row['contamination score']} + contamination_score + ${row['contamination_score']} % - + - contamination screening input - ${row['contamination screening input']} + contamination_screening_input + ${row['contamination_screening_input']} - + - contamination screening parameters - ${row['contamination screening parameters']} + contamination_screening_parameters + ${row['contamination_screening_parameters']} - + - decontamination software - ${row['decontamination software']} + decontamination_software + ${row['decontamination_software']} - + - assembly quality - ${row['assembly quality']} + assembly_quality + ${row['assembly_quality']} - + - taxonomic identity marker - ${row['taxonomic identity marker']} + taxonomic_identity_marker + ${row['taxonomic_identity_marker']} @@ -185,10 +185,10 @@ def mandatorytest(row, column, index): ${row['isolation_source']} - + - collection date - ${row['collection date']} + collection_date + ${row['collection_date']} @@ -198,42 +198,42 @@ def mandatorytest(row, column, index): m - + - geographic location (latitude) - ${row['geographic location (latitude)']} + geographic_location_latitude + ${row['geographic_location_latitude']} DD - + - geographic location (longitude) - ${row['geographic location (longitude)']} + geographic_location_longitude + ${row['geographic_location_longitude']} DD - + - geographic location (region and locality) - ${row['geographic location (region and locality)']} + geographic_location_region_and_locality + ${row['geographic_location_region_and_locality']} - + - broad-scale environmental context - ${row['broad-scale environmental context']} + broadscale_environmental_context + ${row['broadscale_environmental_context']} - + - local environmental context - ${row['local environmental context']} + local_environmental_context + ${row['local_environmental_context']} - + - environmental medium - ${row['environmental medium']} + environmental_medium + ${row['environmental_medium']} @@ -243,137 +243,137 @@ def mandatorytest(row, column, index): m - + - amount or size of sample collected - ${row['amount or size of sample collected']} - m3 + amount_or_size_of_sample_collected + ${row['amount_or_size_of_sample_collected']} + kg - + - size fraction selected - ${row['size fraction selected']} + size_fraction_selected + ${row['size_fraction_selected']} - + - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} + geographic_location_country_andor_sea + ${row['geographic_location_country_andor_sea']} - + - source material identifiers - ${row['source material identifiers']} + source_material_identifiers + ${row['source_material_identifiers']} - + - experimental factor - ${row['experimental factor']} + experimental_factor + ${row['experimental_factor']} - + - taxonomic classification - ${row['taxonomic classification']} + taxonomic_classification + ${row['taxonomic_classification']} - + - annotation source - ${row['annotation source']} + annotation_source + ${row['annotation_source']} - + - reference for biomaterial - ${row['reference for biomaterial']} + reference_for_biomaterial + ${row['reference_for_biomaterial']} - + - reference database(s) - ${row['reference database(s)']} + reference_databases + ${row['reference_databases']} - + - single cell or viral particle lysis approach - ${row['single cell or viral particle lysis approach']} + single_cell_or_viral_particle_lysis_approach + ${row['single_cell_or_viral_particle_lysis_approach']} - + - single cell or viral particle lysis kit protocol - ${row['single cell or viral particle lysis kit protocol']} + single_cell_or_viral_particle_lysis_kit_protocol + ${row['single_cell_or_viral_particle_lysis_kit_protocol']} - + - sample material processing - ${row['sample material processing']} + sample_material_processing + ${row['sample_material_processing']} - + - nucleic acid extraction - ${row['nucleic acid extraction']} + nucleic_acid_extraction + ${row['nucleic_acid_extraction']} - + - nucleic acid amplification - ${row['nucleic acid amplification']} + nucleic_acid_amplification + ${row['nucleic_acid_amplification']} - + - library size - ${row['library size']} + library_size + ${row['library_size']} - + - library reads sequenced - ${row['library reads sequenced']} + library_reads_sequenced + ${row['library_reads_sequenced']} - + - library vector - ${row['library vector']} + library_vector + ${row['library_vector']} - + - library screening strategy - ${row['library screening strategy']} + library_screening_strategy + ${row['library_screening_strategy']} - + - assembly software - ${row['assembly software']} + assembly_software + ${row['assembly_software']} - + - WGA amplification approach - ${row['WGA amplification approach']} + wga_amplification_approach + ${row['wga_amplification_approach']} - + - WGA amplification kit - ${row['WGA amplification kit']} + wga_amplification_kit + ${row['wga_amplification_kit']} - + - sorting technology - ${row['sorting technology']} + sorting_technology + ${row['sorting_technology']} @@ -386,7 +386,7 @@ def mandatorytest(row, column, index): depth ${row['depth']} - mm + m diff --git a/ena_upload/templates/ENA_template_samples_ERC000049.xml b/ena_upload/templates/ENA_template_samples_ERC000049.xml index b5ef07a..37e8d83 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000049.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000049.xml @@ -33,198 +33,198 @@ def mandatorytest(row, column, index): ${row.sample_description} - + - observed biotic relationship - ${row['observed biotic relationship']} + observed_biotic_relationship + ${row['observed_biotic_relationship']} - + - known pathogenicity - ${row['known pathogenicity']} + known_pathogenicity + ${row['known_pathogenicity']} - + - sample collection device - ${row['sample collection device']} + sample_collection_device + ${row['sample_collection_device']} - + - sample collection method - ${row['sample collection method']} + sample_collection_method + ${row['sample_collection_method']} - + - metagenomic source - ${row['metagenomic source']} + metagenomic_source + ${row['metagenomic_source']} - + - sample derived from - ${row['sample derived from']} + sample_derived_from + ${row['sample_derived_from']} - + - project name - ${row['project name']} + project_name + ${row['project_name']} - + - estimated size - ${row['estimated size']} + estimated_size + ${row['estimated_size']} - + - multiplex identifiers - ${row['multiplex identifiers']} + multiplex_identifiers + ${row['multiplex_identifiers']} - + - relevant electronic resources - ${row['relevant electronic resources']} + relevant_electronic_resources + ${row['relevant_electronic_resources']} - + - relevant standard operating procedures - ${row['relevant standard operating procedures']} + relevant_standard_operating_procedures + ${row['relevant_standard_operating_procedures']} - + - number of standard tRNAs extracted - ${row['number of standard tRNAs extracted']} + number_of_standard_trnas_extracted + ${row['number_of_standard_trnas_extracted']} - + - feature prediction - ${row['feature prediction']} + feature_prediction + ${row['feature_prediction']} - + - similarity search method - ${row['similarity search method']} + similarity_search_method + ${row['similarity_search_method']} - + - tRNA extraction software - ${row['tRNA extraction software']} + trna_extraction_software + ${row['trna_extraction_software']} - + - completeness score - ${row['completeness score']} + completeness_score + ${row['completeness_score']} % - + - completeness software - ${row['completeness software']} + completeness_software + ${row['completeness_software']} - + - completeness approach - ${row['completeness approach']} + completeness_approach + ${row['completeness_approach']} - + - binning software - ${row['binning software']} + binning_software + ${row['binning_software']} - + - reassembly post binning - ${row['reassembly post binning']} + reassembly_post_binning + ${row['reassembly_post_binning']} Yes - + - MAG coverage software - ${row['MAG coverage software']} + mag_coverage_software + ${row['mag_coverage_software']} - + - binning parameters - ${row['binning parameters']} + binning_parameters + ${row['binning_parameters']} - + - taxonomic identity marker - ${row['taxonomic identity marker']} + taxonomic_identity_marker + ${row['taxonomic_identity_marker']} - + - source of UViGs - ${row['source of UViGs']} + source_of_uvigs + ${row['source_of_uvigs']} - + - predicted genome type - ${row['predicted genome type']} + predicted_genome_type + ${row['predicted_genome_type']} - + - predicted genome structure - ${row['predicted genome structure']} + predicted_genome_structure + ${row['predicted_genome_structure']} - + - detection type - ${row['detection type']} + detection_type + ${row['detection_type']} - + - viral identification software - ${row['viral identification software']} + viral_identification_software + ${row['viral_identification_software']} - + - OTU classification approach - ${row['OTU classification approach']} + otu_classification_approach + ${row['otu_classification_approach']} - + - OTU sequence comparison approach - ${row['OTU sequence comparison approach']} + otu_sequence_comparison_approach + ${row['otu_sequence_comparison_approach']} - + - OTU database - ${row['OTU database']} + otu_database + ${row['otu_database']} - + - UViG assembly quality - ${row['UViG assembly quality']} + uvig_assembly_quality + ${row['uvig_assembly_quality']} @@ -233,10 +233,10 @@ def mandatorytest(row, column, index): ${row['isolation_source']} - + - collection date - ${row['collection date']} + collection_date + ${row['collection_date']} @@ -246,42 +246,42 @@ def mandatorytest(row, column, index): m - + - geographic location (latitude) - ${row['geographic location (latitude)']} + geographic_location_latitude + ${row['geographic_location_latitude']} DD - + - geographic location (longitude) - ${row['geographic location (longitude)']} + geographic_location_longitude + ${row['geographic_location_longitude']} DD - + - geographic location (region and locality) - ${row['geographic location (region and locality)']} + geographic_location_region_and_locality + ${row['geographic_location_region_and_locality']} - + - broad-scale environmental context - ${row['broad-scale environmental context']} + broadscale_environmental_context + ${row['broadscale_environmental_context']} - + - local environmental context - ${row['local environmental context']} + local_environmental_context + ${row['local_environmental_context']} - + - environmental medium - ${row['environmental medium']} + environmental_medium + ${row['environmental_medium']} @@ -291,161 +291,161 @@ def mandatorytest(row, column, index): m - + - amount or size of sample collected - ${row['amount or size of sample collected']} - m3 + amount_or_size_of_sample_collected + ${row['amount_or_size_of_sample_collected']} + kg - + - size fraction selected - ${row['size fraction selected']} + size_fraction_selected + ${row['size_fraction_selected']} - + - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} + geographic_location_country_andor_sea + ${row['geographic_location_country_andor_sea']} - + - host scientific name - ${row['host scientific name']} + host_scientific_name + ${row['host_scientific_name']} - + - source material identifiers - ${row['source material identifiers']} + source_material_identifiers + ${row['source_material_identifiers']} - + - host prediction approach - ${row['host prediction approach']} + host_prediction_approach + ${row['host_prediction_approach']} - + - host prediction estimated accuracy - ${row['host prediction estimated accuracy']} + host_prediction_estimated_accuracy + ${row['host_prediction_estimated_accuracy']} - + - experimental factor - ${row['experimental factor']} + experimental_factor + ${row['experimental_factor']} - + - taxonomic classification - ${row['taxonomic classification']} + taxonomic_classification + ${row['taxonomic_classification']} - + - annotation source - ${row['annotation source']} + annotation_source + ${row['annotation_source']} - + - reference for biomaterial - ${row['reference for biomaterial']} + reference_for_biomaterial + ${row['reference_for_biomaterial']} - + - reference database(s) - ${row['reference database(s)']} + reference_databases + ${row['reference_databases']} - + - single cell or viral particle lysis approach - ${row['single cell or viral particle lysis approach']} + single_cell_or_viral_particle_lysis_approach + ${row['single_cell_or_viral_particle_lysis_approach']} - + - single cell or viral particle lysis kit protocol - ${row['single cell or viral particle lysis kit protocol']} + single_cell_or_viral_particle_lysis_kit_protocol + ${row['single_cell_or_viral_particle_lysis_kit_protocol']} - + - sample material processing - ${row['sample material processing']} + sample_material_processing + ${row['sample_material_processing']} - + - nucleic acid extraction - ${row['nucleic acid extraction']} + nucleic_acid_extraction + ${row['nucleic_acid_extraction']} - + - nucleic acid amplification - ${row['nucleic acid amplification']} + nucleic_acid_amplification + ${row['nucleic_acid_amplification']} - + - library size - ${row['library size']} + library_size + ${row['library_size']} - + - library reads sequenced - ${row['library reads sequenced']} + library_reads_sequenced + ${row['library_reads_sequenced']} - + - library vector - ${row['library vector']} + library_vector + ${row['library_vector']} - + - library screening strategy - ${row['library screening strategy']} + library_screening_strategy + ${row['library_screening_strategy']} - + - assembly software - ${row['assembly software']} + assembly_software + ${row['assembly_software']} - + - WGA amplification approach - ${row['WGA amplification approach']} + wga_amplification_approach + ${row['wga_amplification_approach']} - + - WGA amplification kit - ${row['WGA amplification kit']} + wga_amplification_kit + ${row['wga_amplification_kit']} - + - sorting technology - ${row['sorting technology']} + sorting_technology + ${row['sorting_technology']} - + - virus enrichment approach - ${row['virus enrichment approach']} + virus_enrichment_approach + ${row['virus_enrichment_approach']} @@ -458,7 +458,7 @@ def mandatorytest(row, column, index): depth ${row['depth']} - mm + m diff --git a/ena_upload/templates/ENA_template_samples_ERC000050.xml b/ena_upload/templates/ENA_template_samples_ERC000050.xml index bab10f0..dbdd75c 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000050.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000050.xml @@ -33,163 +33,163 @@ def mandatorytest(row, column, index): ${row.sample_description} - + - relationship to oxygen - ${row['relationship to oxygen']} + relationship_to_oxygen + ${row['relationship_to_oxygen']} - + - sample collection method - ${row['sample collection method']} + sample_collection_method + ${row['sample_collection_method']} - + - metagenomic source - ${row['metagenomic source']} + metagenomic_source + ${row['metagenomic_source']} - + - sample derived from - ${row['sample derived from']} + sample_derived_from + ${row['sample_derived_from']} - + - project name - ${row['project name']} + project_name + ${row['project_name']} - + - multiplex identifiers - ${row['multiplex identifiers']} + multiplex_identifiers + ${row['multiplex_identifiers']} - + - relevant electronic resources - ${row['relevant electronic resources']} + relevant_electronic_resources + ${row['relevant_electronic_resources']} - + - relevant standard operating procedures - ${row['relevant standard operating procedures']} + relevant_standard_operating_procedures + ${row['relevant_standard_operating_procedures']} - + - number of standard tRNAs extracted - ${row['number of standard tRNAs extracted']} + number_of_standard_trnas_extracted + ${row['number_of_standard_trnas_extracted']} - + - 16s recovered - ${row['16s recovered']} + _16s_recovered + ${row['_16s_recovered']} - + - 16S recovery software - ${row['16S recovery software']} + _16s_recovery_software + ${row['_16s_recovery_software']} - + - tRNA extraction software - ${row['tRNA extraction software']} + trna_extraction_software + ${row['trna_extraction_software']} - + - completeness score - ${row['completeness score']} + completeness_score + ${row['completeness_score']} % - + - completeness software - ${row['completeness software']} + completeness_software + ${row['completeness_software']} - + - completeness approach - ${row['completeness approach']} + completeness_approach + ${row['completeness_approach']} - + - contamination score - ${row['contamination score']} + contamination_score + ${row['contamination_score']} % - + - contamination screening input - ${row['contamination screening input']} + contamination_screening_input + ${row['contamination_screening_input']} - + - contamination screening parameters - ${row['contamination screening parameters']} + contamination_screening_parameters + ${row['contamination_screening_parameters']} - + - decontamination software - ${row['decontamination software']} + decontamination_software + ${row['decontamination_software']} - + - binning software - ${row['binning software']} + binning_software + ${row['binning_software']} - + - reassembly post binning - ${row['reassembly post binning']} + reassembly_post_binning + ${row['reassembly_post_binning']} Yes - + - MAG coverage software - ${row['MAG coverage software']} + mag_coverage_software + ${row['mag_coverage_software']} - + - assembly quality - ${row['assembly quality']} + assembly_quality + ${row['assembly_quality']} - + - investigation type - ${row['investigation type']} + investigation_type + ${row['investigation_type']} - + - binning parameters - ${row['binning parameters']} + binning_parameters + ${row['binning_parameters']} - + - taxonomic identity marker - ${row['taxonomic identity marker']} + taxonomic_identity_marker + ${row['taxonomic_identity_marker']} @@ -198,10 +198,10 @@ def mandatorytest(row, column, index): ${row['isolation_source']} - + - collection date - ${row['collection date']} + collection_date + ${row['collection_date']} @@ -211,36 +211,36 @@ def mandatorytest(row, column, index): m - + - geographic location (latitude) - ${row['geographic location (latitude)']} + geographic_location_latitude + ${row['geographic_location_latitude']} DD - + - geographic location (longitude) - ${row['geographic location (longitude)']} + geographic_location_longitude + ${row['geographic_location_longitude']} DD - + - broad-scale environmental context - ${row['broad-scale environmental context']} + broadscale_environmental_context + ${row['broadscale_environmental_context']} - + - local environmental context - ${row['local environmental context']} + local_environmental_context + ${row['local_environmental_context']} - + - environmental medium - ${row['environmental medium']} + environmental_medium + ${row['environmental_medium']} @@ -250,95 +250,95 @@ def mandatorytest(row, column, index): m - + - amount or size of sample collected - ${row['amount or size of sample collected']} - m3 + amount_or_size_of_sample_collected + ${row['amount_or_size_of_sample_collected']} + kg - + - size fraction selected - ${row['size fraction selected']} + size_fraction_selected + ${row['size_fraction_selected']} - + - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} + geographic_location_country_andor_sea + ${row['geographic_location_country_andor_sea']} - + - source material identifiers - ${row['source material identifiers']} + source_material_identifiers + ${row['source_material_identifiers']} - + - experimental factor - ${row['experimental factor']} + experimental_factor + ${row['experimental_factor']} - + - taxonomic classification - ${row['taxonomic classification']} + taxonomic_classification + ${row['taxonomic_classification']} - + - reference for biomaterial - ${row['reference for biomaterial']} + reference_for_biomaterial + ${row['reference_for_biomaterial']} - + - sample material processing - ${row['sample material processing']} + sample_material_processing + ${row['sample_material_processing']} - + - nucleic acid extraction - ${row['nucleic acid extraction']} + nucleic_acid_extraction + ${row['nucleic_acid_extraction']} - + - nucleic acid amplification - ${row['nucleic acid amplification']} + nucleic_acid_amplification + ${row['nucleic_acid_amplification']} - + - library size - ${row['library size']} + library_size + ${row['library_size']} - + - library reads sequenced - ${row['library reads sequenced']} + library_reads_sequenced + ${row['library_reads_sequenced']} - + - library vector - ${row['library vector']} + library_vector + ${row['library_vector']} - + - library screening strategy - ${row['library screening strategy']} + library_screening_strategy + ${row['library_screening_strategy']} - + - assembly software - ${row['assembly software']} + assembly_software + ${row['assembly_software']} @@ -351,7 +351,7 @@ def mandatorytest(row, column, index): depth ${row['depth']} - mm + m diff --git a/ena_upload/templates/ENA_template_samples_ERC000051.xml b/ena_upload/templates/ENA_template_samples_ERC000051.xml index d9b2741..e1dc9f3 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000051.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000051.xml @@ -33,100 +33,100 @@ def mandatorytest(row, column, index): ${row.sample_description} - + - sample origin - ${row['sample origin']} + sample_origin + ${row['sample_origin']} - + - sample material - ${row['sample material']} + sample_material + ${row['sample_material']} - + - sample taxon name - ${row['sample taxon name']} + sample_taxon_name + ${row['sample_taxon_name']} - + - sample unique ID - ${row['sample unique ID']} + sample_unique_id + ${row['sample_unique_id']} - + - patient tumor type - ${row['patient tumor type']} + patient_tumor_type + ${row['patient_tumor_type']} - + - collection date - ${row['collection date']} + collection_date + ${row['collection_date']} - + - engrafted tumor sample passage - ${row['engrafted tumor sample passage']} + engrafted_tumor_sample_passage + ${row['engrafted_tumor_sample_passage']} - + - engrafted tumor collection site - ${row['engrafted tumor collection site']} + engrafted_tumor_collection_site + ${row['engrafted_tumor_collection_site']} - + - patient tumor site of collection - ${row['patient tumor site of collection']} + patient_tumor_site_of_collection + ${row['patient_tumor_site_of_collection']} - + - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} + geographic_location_country_andor_sea + ${row['geographic_location_country_andor_sea']} - + - engraftment host strain name - ${row['engraftment host strain name']} + engraftment_host_strain_name + ${row['engraftment_host_strain_name']} - + - patient age at collection of tumor - ${row['patient age at collection of tumor']} + patient_age_at_collection_of_tumor + ${row['patient_age_at_collection_of_tumor']} - + - patient tumor diagnosis at time of collection - ${row['patient tumor diagnosis at time of collection']} + patient_tumor_diagnosis_at_time_of_collection + ${row['patient_tumor_diagnosis_at_time_of_collection']} - + - patient tumor primary site - ${row['patient tumor primary site']} + patient_tumor_primary_site + ${row['patient_tumor_primary_site']} - + - was the PDX model humanised? - ${row['was the PDX model humanised?']} + was_the_pdx_model_humanised + ${row['was_the_pdx_model_humanised']} - + - patient sex - ${row['patient sex']} + patient_sex + ${row['patient_sex']} diff --git a/ena_upload/templates/ENA_template_samples_ERC000052.xml b/ena_upload/templates/ENA_template_samples_ERC000052.xml index 6745c95..0d63e44 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000052.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000052.xml @@ -33,213 +33,213 @@ def mandatorytest(row, column, index): ${row.sample_description} - + - sample storage temperature - ${row['sample storage temperature']} + sample_storage_temperature + ${row['sample_storage_temperature']} °C - + - sample storage buffer - ${row['sample storage buffer']} + sample_storage_buffer + ${row['sample_storage_buffer']} - + - sample storage device - ${row['sample storage device']} + sample_storage_device + ${row['sample_storage_device']} - + - sample storage location - ${row['sample storage location']} + sample_storage_location + ${row['sample_storage_location']} - + - project name - ${row['project name']} + project_name + ${row['project_name']} - + - reference host genome for decontamination - ${row['reference host genome for decontamination']} + reference_host_genome_for_decontamination + ${row['reference_host_genome_for_decontamination']} - + - collection date - ${row['collection date']} + collection_date + ${row['collection_date']} - + - geographic location (latitude) - ${row['geographic location (latitude)']} + geographic_location_latitude + ${row['geographic_location_latitude']} DD - + - geographic location (longitude) - ${row['geographic location (longitude)']} + geographic_location_longitude + ${row['geographic_location_longitude']} DD - + - geographic location (region and locality) - ${row['geographic location (region and locality)']} + geographic_location_region_and_locality + ${row['geographic_location_region_and_locality']} - + - trial length - ${row['trial length']} + trial_length + ${row['trial_length']} years - + - trial timepoint - ${row['trial timepoint']} + trial_timepoint + ${row['trial_timepoint']} years - + - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} + geographic_location_country_andor_sea + ${row['geographic_location_country_andor_sea']} - + - host disease status - ${row['host disease status']} + host_disease_status + ${row['host_disease_status']} - + - host common name - ${row['host common name']} + host_common_name + ${row['host_common_name']} - + - host subject id - ${row['host subject id']} + host_subject_id + ${row['host_subject_id']} - + - host taxid - ${row['host taxid']} + host_taxid + ${row['host_taxid']} - + - host body site - ${row['host body site']} + host_body_site + ${row['host_body_site']} - + - host length - ${row['host length']} - mm + host_length + ${row['host_length']} + m - + - host total mass - ${row['host total mass']} + host_total_mass + ${row['host_total_mass']} kg - + - host sex - ${row['host sex']} + host_sex + ${row['host_sex']} - + - host scientific name - ${row['host scientific name']} + host_scientific_name + ${row['host_scientific_name']} - + - host breed - ${row['host breed']} + host_breed + ${row['host_breed']} - + - host gutted mass - ${row['host gutted mass']} + host_gutted_mass + ${row['host_gutted_mass']} kg - + - host diet - ${row['host diet']} + host_diet + ${row['host_diet']} - + - host diet treatment - ${row['host diet treatment']} + host_diet_treatment + ${row['host_diet_treatment']} - + - host diet treatment concentration - ${row['host diet treatment concentration']} + host_diet_treatment_concentration + ${row['host_diet_treatment_concentration']} % mass - + - host storage container - ${row['host storage container']} + host_storage_container + ${row['host_storage_container']} - + - host storage container pH - ${row['host storage container pH']} + host_storage_container_ph + ${row['host_storage_container_ph']} - + - host storage container temperature - ${row['host storage container temperature']} + host_storage_container_temperature + ${row['host_storage_container_temperature']} °C - + - sample volume or weight for DNA extraction - ${row['sample volume or weight for DNA extraction']} - ng + sample_volume_or_weight_for_dna_extraction + ${row['sample_volume_or_weight_for_dna_extraction']} + mL - + - nucleic acid extraction - ${row['nucleic acid extraction']} + nucleic_acid_extraction + ${row['nucleic_acid_extraction']} - + - pcr primers - ${row['pcr primers']} + pcr_primers + ${row['pcr_primers']} diff --git a/ena_upload/templates/ENA_template_samples_ERC000053.xml b/ena_upload/templates/ENA_template_samples_ERC000053.xml index 5e78e73..5813bde 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000053.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000053.xml @@ -33,38 +33,38 @@ def mandatorytest(row, column, index): ${row.sample_description} - + - Latitude Start - ${row['Latitude Start']} + latitude_start + ${row['latitude_start']} DD - + - Longitude Start - ${row['Longitude Start']} + longitude_start + ${row['longitude_start']} DD - + - Latitude End - ${row['Latitude End']} + latitude_end + ${row['latitude_end']} DD - + - Longitude End - ${row['Longitude End']} + longitude_end + ${row['longitude_end']} DD - + - organism part - ${row['organism part']} + organism_part + ${row['organism_part']} @@ -79,10 +79,10 @@ def mandatorytest(row, column, index): ${row['relationship']} - + - sample symbiont of - ${row['sample symbiont of']} + sample_symbiont_of + ${row['sample_symbiont_of']} @@ -91,40 +91,40 @@ def mandatorytest(row, column, index): ${row['symbiont']} - + - sample collection method - ${row['sample collection method']} + sample_collection_method + ${row['sample_collection_method']} - + - sample coordinator affiliation - ${row['sample coordinator affiliation']} + sample_coordinator_affiliation + ${row['sample_coordinator_affiliation']} - + - sample same as - ${row['sample same as']} + sample_same_as + ${row['sample_same_as']} - + - sample derived from - ${row['sample derived from']} + sample_derived_from + ${row['sample_derived_from']} - + - project name - ${row['project name']} + project_name + ${row['project_name']} - + - barcoding center - ${row['barcoding center']} + barcoding_center + ${row['barcoding_center']} @@ -139,30 +139,30 @@ def mandatorytest(row, column, index): ${row['collected_by']} - + - collection date - ${row['collection date']} + collection_date + ${row['collection_date']} - + - geographic location (latitude) - ${row['geographic location (latitude)']} + geographic_location_latitude + ${row['geographic_location_latitude']} DD - + - geographic location (longitude) - ${row['geographic location (longitude)']} + geographic_location_longitude + ${row['geographic_location_longitude']} DD - + - geographic location (region and locality) - ${row['geographic location (region and locality)']} + geographic_location_region_and_locality + ${row['geographic_location_region_and_locality']} @@ -190,36 +190,36 @@ def mandatorytest(row, column, index): ${row['identifier_affiliation']} - + - original collection date - ${row['original collection date']} + original_collection_date + ${row['original_collection_date']} - + - original geographic location - ${row['original geographic location']} + original_geographic_location + ${row['original_geographic_location']} - + - original geographic location (latitude) - ${row['original geographic location (latitude)']} + original_geographic_location_latitude + ${row['original_geographic_location_latitude']} DD - + - original geographic location (longitude) - ${row['original geographic location (longitude)']} + original_geographic_location_longitude + ${row['original_geographic_location_longitude']} DD - + - sample coordinator - ${row['sample coordinator']} + sample_coordinator + ${row['sample_coordinator']} @@ -228,22 +228,22 @@ def mandatorytest(row, column, index): ${row['sex']} - + - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} + geographic_location_country_andor_sea + ${row['geographic_location_country_andor_sea']} - + - collecting institution - ${row['collecting institution']} + collecting_institution + ${row['collecting_institution']} - + - GAL - ${row['GAL']} + gal + ${row['gal']} @@ -252,22 +252,22 @@ def mandatorytest(row, column, index): ${row['specimen_id']} - + - GAL_sample_id - ${row['GAL_sample_id']} + gal_sample_id + ${row['gal_sample_id']} - + - proxy voucher - ${row['proxy voucher']} + proxy_voucher + ${row['proxy_voucher']} - + - proxy biomaterial - ${row['proxy biomaterial']} + proxy_biomaterial + ${row['proxy_biomaterial']} @@ -292,7 +292,7 @@ def mandatorytest(row, column, index): depth ${row['depth']} - mm + m diff --git a/ena_upload/templates/ENA_template_samples_ERC000055.xml b/ena_upload/templates/ENA_template_samples_ERC000055.xml index 36d8470..7ee8f8e 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000055.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000055.xml @@ -33,28 +33,28 @@ def mandatorytest(row, column, index): ${row.sample_description} - + - biotic relationship [deprecated] - ${row['biotic relationship [deprecated]']} + biotic_relationship_deprecated + ${row['biotic_relationship_deprecated']} - + - trophic level - ${row['trophic level']} + trophic_level + ${row['trophic_level']} - + - known pathogenicity - ${row['known pathogenicity']} + known_pathogenicity + ${row['known_pathogenicity']} - + - relationship to oxygen - ${row['relationship to oxygen']} + relationship_to_oxygen + ${row['relationship_to_oxygen']} @@ -63,190 +63,190 @@ def mandatorytest(row, column, index): ${row['propagation']} - + - observed host symbionts - ${row['observed host symbionts']} + observed_host_symbionts + ${row['observed_host_symbionts']} - + - sample collection device - ${row['sample collection device']} + sample_collection_device + ${row['sample_collection_device']} - + - sample collection method - ${row['sample collection method']} + sample_collection_method + ${row['sample_collection_method']} - + - sample storage temperature - ${row['sample storage temperature']} + sample_storage_temperature + ${row['sample_storage_temperature']} °C - + - sample storage location - ${row['sample storage location']} + sample_storage_location + ${row['sample_storage_location']} - + - size-fraction lower threshold - ${row['size-fraction lower threshold']} - µm + sizefraction_lower_threshold + ${row['sizefraction_lower_threshold']} + nm - + - size-fraction upper threshold - ${row['size-fraction upper threshold']} - µm + sizefraction_upper_threshold + ${row['sizefraction_upper_threshold']} + nm - + - soil_taxonomic/FAO classification - ${row['soil_taxonomic/FAO classification']} + soil_taxonomicfao_classification + ${row['soil_taxonomicfao_classification']} - + - soil_taxonomic/local classification - ${row['soil_taxonomic/local classification']} + soil_taxonomiclocal_classification + ${row['soil_taxonomiclocal_classification']} - + - soil_taxonomic/local classification method - ${row['soil_taxonomic/local classification method']} + soil_taxonomiclocal_classification_method + ${row['soil_taxonomiclocal_classification_method']} - + - soil type - ${row['soil type']} + soil_type + ${row['soil_type']} - + - soil type method - ${row['soil type method']} + soil_type_method + ${row['soil_type_method']} - + - soil texture measurement - ${row['soil texture measurement']} + soil_texture_measurement + ${row['soil_texture_measurement']} % sand/silt/clay - + - soil texture method - ${row['soil texture method']} + soil_texture_method + ${row['soil_texture_method']} - + - soil pH - ${row['soil pH']} + soil_ph + ${row['soil_ph']} - + - soil cover - ${row['soil cover']} + soil_cover + ${row['soil_cover']} - + - oxygenation status of sample - ${row['oxygenation status of sample']} + oxygenation_status_of_sample + ${row['oxygenation_status_of_sample']} - + - microbial biomass - ${row['microbial biomass']} + microbial_biomass + ${row['microbial_biomass']} g/kg - + - project name - ${row['project name']} + project_name + ${row['project_name']} - + - farm equipment sanitization - ${row['farm equipment sanitization']} + farm_equipment_sanitization + ${row['farm_equipment_sanitization']} - + - equipment shared with other farms - ${row['equipment shared with other farms']} + equipment_shared_with_other_farms + ${row['equipment_shared_with_other_farms']} - + - farm equipment used - ${row['farm equipment used']} + farm_equipment_used + ${row['farm_equipment_used']} - + - farm watering water source - ${row['farm watering water source']} + farm_watering_water_source + ${row['farm_watering_water_source']} - + - food production system characteristics - ${row['food production system characteristics']} + food_production_system_characteristics + ${row['food_production_system_characteristics']} - + - animal water delivery method - ${row['animal water delivery method']} + animal_water_delivery_method + ${row['animal_water_delivery_method']} - + - plant water delivery method - ${row['plant water delivery method']} + plant_water_delivery_method + ${row['plant_water_delivery_method']} - + - food harvesting process - ${row['food harvesting process']} + food_harvesting_process + ${row['food_harvesting_process']} - + - food production characteristics - ${row['food production characteristics']} + food_production_characteristics + ${row['food_production_characteristics']} °C - + - fertilizer administration date - ${row['fertilizer administration date']} + fertilizer_administration_date + ${row['fertilizer_administration_date']} - + - crop yield - ${row['crop yield']} + crop_yield + ${row['crop_yield']} @@ -255,82 +255,82 @@ def mandatorytest(row, column, index): ${row['ploidy']} - + - number of replicons - ${row['number of replicons']} + number_of_replicons + ${row['number_of_replicons']} - + - extrachromosomal elements - ${row['extrachromosomal elements']} + extrachromosomal_elements + ${row['extrachromosomal_elements']} - + - estimated size - ${row['estimated size']} + estimated_size + ${row['estimated_size']} - + - target gene - ${row['target gene']} + target_gene + ${row['target_gene']} - + - target subfragment - ${row['target subfragment']} + target_subfragment + ${row['target_subfragment']} - + - multiplex identifiers - ${row['multiplex identifiers']} + multiplex_identifiers + ${row['multiplex_identifiers']} - + - sequence quality check - ${row['sequence quality check']} + sequence_quality_check + ${row['sequence_quality_check']} - + - chimera check software - ${row['chimera check software']} + chimera_check_software + ${row['chimera_check_software']} - + - relevant electronic resources - ${row['relevant electronic resources']} + relevant_electronic_resources + ${row['relevant_electronic_resources']} - + - relevant standard operating procedures - ${row['relevant standard operating procedures']} + relevant_standard_operating_procedures + ${row['relevant_standard_operating_procedures']} - + - 16s recovered - ${row['16s recovered']} + _16s_recovered + ${row['_16s_recovered']} - + - 16S recovery software - ${row['16S recovery software']} + _16s_recovery_software + ${row['_16s_recovery_software']} - + - collection date - ${row['collection date']} + collection_date + ${row['collection_date']} @@ -340,42 +340,42 @@ def mandatorytest(row, column, index): m - + - geographic location (latitude) - ${row['geographic location (latitude)']} + geographic_location_latitude + ${row['geographic_location_latitude']} DD - + - geographic location (longitude) - ${row['geographic location (longitude)']} + geographic_location_longitude + ${row['geographic_location_longitude']} DD - + - geographic location (region and locality) - ${row['geographic location (region and locality)']} + geographic_location_region_and_locality + ${row['geographic_location_region_and_locality']} - + - broad-scale environmental context - ${row['broad-scale environmental context']} + broadscale_environmental_context + ${row['broadscale_environmental_context']} - + - local environmental context - ${row['local environmental context']} + local_environmental_context + ${row['local_environmental_context']} - + - environmental medium - ${row['environmental medium']} + environmental_medium + ${row['environmental_medium']} @@ -385,10 +385,10 @@ def mandatorytest(row, column, index): m - + - culture isolation date - ${row['culture isolation date']} + culture_isolation_date + ${row['culture_isolation_date']} @@ -397,190 +397,190 @@ def mandatorytest(row, column, index): ${row['sieving']} - + - microbial biomass method - ${row['microbial biomass method']} + microbial_biomass_method + ${row['microbial_biomass_method']} - + - organism count - ${row['organism count']} + organism_count + ${row['organism_count']} - + - horizon method - ${row['horizon method']} + horizon_method + ${row['horizon_method']} - + - extreme_unusual_properties/heavy metals - ${row['extreme_unusual_properties/heavy metals']} + extreme_unusual_propertiesheavy_metals + ${row['extreme_unusual_propertiesheavy_metals']} - + - extreme_unusual_properties/heavy metals method - ${row['extreme_unusual_properties/heavy metals method']} + extreme_unusual_propertiesheavy_metals_method + ${row['extreme_unusual_propertiesheavy_metals_method']} - + - plant structure - ${row['plant structure']} + plant_structure + ${row['plant_structure']} - + - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} + geographic_location_country_andor_sea + ${row['geographic_location_country_andor_sea']} - + - host disease status - ${row['host disease status']} + host_disease_status + ${row['host_disease_status']} - + - host common name - ${row['host common name']} + host_common_name + ${row['host_common_name']} - + - host age - ${row['host age']} + host_age + ${row['host_age']} years - + - host taxid - ${row['host taxid']} + host_taxid + ${row['host_taxid']} - + - host life stage - ${row['host life stage']} + host_life_stage + ${row['host_life_stage']} - + - host height - ${row['host height']} - mm + host_height + ${row['host_height']} + m - + - host length - ${row['host length']} - mm + host_length + ${row['host_length']} + m - + - host total mass - ${row['host total mass']} + host_total_mass + ${row['host_total_mass']} kg - + - host phenotype - ${row['host phenotype']} + host_phenotype + ${row['host_phenotype']} - + - host scientific name - ${row['host scientific name']} + host_scientific_name + ${row['host_scientific_name']} - + - host subspecific genetic lineage - ${row['host subspecific genetic lineage']} + host_subspecific_genetic_lineage + ${row['host_subspecific_genetic_lineage']} - + - link to climate information - ${row['link to climate information']} + link_to_climate_information + ${row['link_to_climate_information']} - + - link to classification information - ${row['link to classification information']} + link_to_classification_information + ${row['link_to_classification_information']} - + - climate environment - ${row['climate environment']} + climate_environment + ${row['climate_environment']} - + - presence of pets, animals, or insects - ${row['presence of pets, animals, or insects']} + presence_of_pets_animals_or_insects + ${row['presence_of_pets_animals_or_insects']} - + - current vegetation - ${row['current vegetation']} + current_vegetation + ${row['current_vegetation']} - + - gaseous environment - ${row['gaseous environment']} + gaseous_environment + ${row['gaseous_environment']} humidity ${row['humidity']} - g/m3 + % - + - current vegetation method - ${row['current vegetation method']} + current_vegetation_method + ${row['current_vegetation_method']} - + - seasonal environment - ${row['seasonal environment']} + seasonal_environment + ${row['seasonal_environment']} - + - soil horizon - ${row['soil horizon']} + soil_horizon + ${row['soil_horizon']} - + - solar irradiance - ${row['solar irradiance']} + solar_irradiance + ${row['solar_irradiance']} W/m2 - + - drainage classification - ${row['drainage classification']} + drainage_classification + ${row['drainage_classification']} @@ -590,161 +590,161 @@ def mandatorytest(row, column, index): ºC - + - pH method - ${row['pH method']} + ph_method + ${row['ph_method']} - + - slope gradient - ${row['slope gradient']} + slope_gradient + ${row['slope_gradient']} % - + - slope aspect - ${row['slope aspect']} + slope_aspect + ${row['slope_aspect']} - + - profile position - ${row['profile position']} + profile_position + ${row['profile_position']} - + - total organic carbon method - ${row['total organic carbon method']} + total_organic_carbon_method + ${row['total_organic_carbon_method']} - + - total nitrogen content method - ${row['total nitrogen content method']} + total_nitrogen_content_method + ${row['total_nitrogen_content_method']} - + - total phosphate - ${row['total phosphate']} - µmol/L + total_phosphate + ${row['total_phosphate']} + µg/L - + - total nitrogen concentration - ${row['total nitrogen concentration']} + total_nitrogen_concentration + ${row['total_nitrogen_concentration']} µmol/L - + - total carbon - ${row['total carbon']} + total_carbon + ${row['total_carbon']} µg/L - + - total organic carbon - ${row['total organic carbon']} + total_organic_carbon + ${row['total_organic_carbon']} g/kg - + - water pH - ${row['water pH']} + water_ph + ${row['water_ph']} - + - photosynthetic activity method - ${row['photosynthetic activity method']} + photosynthetic_activity_method + ${row['photosynthetic_activity_method']} - + - photosynthetic activity - ${row['photosynthetic activity']} + photosynthetic_activity + ${row['photosynthetic_activity']} - + - source material identifiers - ${row['source material identifiers']} + source_material_identifiers + ${row['source_material_identifiers']} - + - history/previous land use - ${row['history/previous land use']} + historyprevious_land_use + ${row['historyprevious_land_use']} - + - previous land use method - ${row['previous land use method']} + previous_land_use_method + ${row['previous_land_use_method']} - + - history/crop rotation - ${row['history/crop rotation']} + historycrop_rotation + ${row['historycrop_rotation']} - + - history/agrochemical additions - ${row['history/agrochemical additions']} + historyagrochemical_additions + ${row['historyagrochemical_additions']} - + - history/tillage - ${row['history/tillage']} + historytillage + ${row['historytillage']} - + - history/fire - ${row['history/fire']} + historyfire + ${row['historyfire']} - + - history/flooding - ${row['history/flooding']} + historyflooding + ${row['historyflooding']} - + - history/extreme events - ${row['history/extreme events']} + historyextreme_events + ${row['historyextreme_events']} - + - mean seasonal humidity - ${row['mean seasonal humidity']} - g/m3 + mean_seasonal_humidity + ${row['mean_seasonal_humidity']} + % - + - mean seasonal temperature - ${row['mean seasonal temperature']} + mean_seasonal_temperature + ${row['mean_seasonal_temperature']} °C - + - mean seasonal precipitation - ${row['mean seasonal precipitation']} + mean_seasonal_precipitation + ${row['mean_seasonal_precipitation']} mm @@ -754,43 +754,43 @@ def mandatorytest(row, column, index): ${row['season']} - + - mean annual precipitation - ${row['mean annual precipitation']} + mean_annual_precipitation + ${row['mean_annual_precipitation']} mm - + - mean annual temperature - ${row['mean annual temperature']} + mean_annual_temperature + ${row['mean_annual_temperature']} ºC - + - host genotype - ${row['host genotype']} + host_genotype + ${row['host_genotype']} - + - host specificity or range - ${row['host specificity or range']} + host_specificity_or_range + ${row['host_specificity_or_range']} - + - host dry mass - ${row['host dry mass']} - mg + host_dry_mass + ${row['host_dry_mass']} + kg - + - spike-in microbial strain - ${row['spike-in microbial strain']} + spikein_microbial_strain + ${row['spikein_microbial_strain']} @@ -799,204 +799,204 @@ def mandatorytest(row, column, index): ${row['perturbation']} - + - negative control type - ${row['negative control type']} + negative_control_type + ${row['negative_control_type']} - + - positive control type - ${row['positive control type']} + positive_control_type + ${row['positive_control_type']} - + - experimental factor - ${row['experimental factor']} + experimental_factor + ${row['experimental_factor']} - + - encoded traits - ${row['encoded traits']} + encoded_traits + ${row['encoded_traits']} - + - genetic modification - ${row['genetic modification']} + genetic_modification + ${row['genetic_modification']} - + - subspecific genetic lineage - ${row['subspecific genetic lineage']} + subspecific_genetic_lineage + ${row['subspecific_genetic_lineage']} - + - ancestral data - ${row['ancestral data']} + ancestral_data + ${row['ancestral_data']} - + - taxonomic classification - ${row['taxonomic classification']} + taxonomic_classification + ${row['taxonomic_classification']} - + - plant growth medium - ${row['plant growth medium']} + plant_growth_medium + ${row['plant_growth_medium']} - + - rooting medium macronutrients - ${row['rooting medium macronutrients']} + rooting_medium_macronutrients + ${row['rooting_medium_macronutrients']} - + - rooting medium carbon - ${row['rooting medium carbon']} + rooting_medium_carbon + ${row['rooting_medium_carbon']} - + - isolation and growth condition - ${row['isolation and growth condition']} + isolation_and_growth_condition + ${row['isolation_and_growth_condition']} - + - annotation source - ${row['annotation source']} + annotation_source + ${row['annotation_source']} - + - reference for biomaterial - ${row['reference for biomaterial']} + reference_for_biomaterial + ${row['reference_for_biomaterial']} - + - sequencing location - ${row['sequencing location']} + sequencing_location + ${row['sequencing_location']} - + - enrichment protocol - ${row['enrichment protocol']} + enrichment_protocol + ${row['enrichment_protocol']} - + - library preparation kit - ${row['library preparation kit']} + library_preparation_kit + ${row['library_preparation_kit']} - + - sample pooling - ${row['sample pooling']} + sample_pooling + ${row['sample_pooling']} - + - lot number - ${row['lot number']} + lot_number + ${row['lot_number']} % - + - single cell or viral particle lysis approach - ${row['single cell or viral particle lysis approach']} + single_cell_or_viral_particle_lysis_approach + ${row['single_cell_or_viral_particle_lysis_approach']} - + - single cell or viral particle lysis kit protocol - ${row['single cell or viral particle lysis kit protocol']} + single_cell_or_viral_particle_lysis_kit_protocol + ${row['single_cell_or_viral_particle_lysis_kit_protocol']} - + - pooled DNA extract total - ${row['pooled DNA extract total']} + pooled_dna_extract_total + ${row['pooled_dna_extract_total']} - + - sample material processing - ${row['sample material processing']} + sample_material_processing + ${row['sample_material_processing']} - + - sample volume or weight for DNA extraction - ${row['sample volume or weight for DNA extraction']} - ng + sample_volume_or_weight_for_dna_extraction + ${row['sample_volume_or_weight_for_dna_extraction']} + mL - + - nucleic acid extraction - ${row['nucleic acid extraction']} + nucleic_acid_extraction + ${row['nucleic_acid_extraction']} - + - nucleic acid amplification - ${row['nucleic acid amplification']} + nucleic_acid_amplification + ${row['nucleic_acid_amplification']} - + - library size - ${row['library size']} + library_size + ${row['library_size']} - + - library reads sequenced - ${row['library reads sequenced']} + library_reads_sequenced + ${row['library_reads_sequenced']} - + - library construction method - ${row['library construction method']} + library_construction_method + ${row['library_construction_method']} - + - library vector - ${row['library vector']} + library_vector + ${row['library_vector']} - + - library screening strategy - ${row['library screening strategy']} + library_screening_strategy + ${row['library_screening_strategy']} - + - pcr conditions - ${row['pcr conditions']} + pcr_conditions + ${row['pcr_conditions']} - + - pcr primers - ${row['pcr primers']} + pcr_primers + ${row['pcr_primers']} @@ -1005,46 +1005,46 @@ def mandatorytest(row, column, index): ${row['adapters']} - + - food shipping transportation vehicle - ${row['food shipping transportation vehicle']} + food_shipping_transportation_vehicle + ${row['food_shipping_transportation_vehicle']} - + - water source shared - ${row['water source shared']} + water_source_shared + ${row['water_source_shared']} - + - food source - ${row['food source']} + food_source + ${row['food_source']} - + - food shipping transportation method - ${row['food shipping transportation method']} + food_shipping_transportation_method + ${row['food_shipping_transportation_method']} - + - food product type - ${row['food product type']} + food_product_type + ${row['food_product_type']} - + - plant product - ${row['plant product']} + plant_product + ${row['plant_product']} - + - relative location of sample - ${row['relative location of sample']} + relative_location_of_sample + ${row['relative_location_of_sample']} @@ -1057,73 +1057,73 @@ def mandatorytest(row, column, index): depth ${row['depth']} - mm + m - + - environment adjacent to site - ${row['environment adjacent to site']} + environment_adjacent_to_site + ${row['environment_adjacent_to_site']} - + - fungicide regimen - ${row['fungicide regimen']} + fungicide_regimen + ${row['fungicide_regimen']} - + - herbicide regimen - ${row['herbicide regimen']} + herbicide_regimen + ${row['herbicide_regimen']} - + - non-mineral nutrient regimen - ${row['non-mineral nutrient regimen']} + nonmineral_nutrient_regimen + ${row['nonmineral_nutrient_regimen']} - + - pesticide regimen - ${row['pesticide regimen']} + pesticide_regimen + ${row['pesticide_regimen']} - + - pH regimen - ${row['pH regimen']} + ph_regimen + ${row['ph_regimen']} - + - salt regimen - ${row['salt regimen']} + salt_regimen + ${row['salt_regimen']} - + - standing water regimen - ${row['standing water regimen']} + standing_water_regimen + ${row['standing_water_regimen']} - + - watering regimen - ${row['watering regimen']} + watering_regimen + ${row['watering_regimen']} - + - water temperature regimen - ${row['water temperature regimen']} + water_temperature_regimen + ${row['water_temperature_regimen']} - + - chemical administration - ${row['chemical administration']} + chemical_administration + ${row['chemical_administration']} diff --git a/ena_upload/templates/ENA_template_samples_ERC000056.xml b/ena_upload/templates/ENA_template_samples_ERC000056.xml index 91cadb1..29527a3 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000056.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000056.xml @@ -33,66 +33,66 @@ def mandatorytest(row, column, index): ${row.sample_description} - + - culture result - ${row['culture result']} + culture_result + ${row['culture_result']} - + - culture result organism - ${row['culture result organism']} + culture_result_organism + ${row['culture_result_organism']} m2 - + - culture target microbial analyte - ${row['culture target microbial analyte']} + culture_target_microbial_analyte + ${row['culture_target_microbial_analyte']} - + - biological sample replicate - ${row['biological sample replicate']} + biological_sample_replicate + ${row['biological_sample_replicate']} year - + - technical sample replicate - ${row['technical sample replicate']} + technical_sample_replicate + ${row['technical_sample_replicate']} - + - purpose of sampling - ${row['purpose of sampling']} + purpose_of_sampling + ${row['purpose_of_sampling']} - + - trophic level - ${row['trophic level']} + trophic_level + ${row['trophic_level']} - + - observed biotic relationship - ${row['observed biotic relationship']} + observed_biotic_relationship + ${row['observed_biotic_relationship']} - + - known pathogenicity - ${row['known pathogenicity']} + known_pathogenicity + ${row['known_pathogenicity']} - + - relationship to oxygen - ${row['relationship to oxygen']} + relationship_to_oxygen + ${row['relationship_to_oxygen']} @@ -101,269 +101,269 @@ def mandatorytest(row, column, index): ${row['propagation']} - + - sample transportation temperature - ${row['sample transportation temperature']} + sample_transportation_temperature + ${row['sample_transportation_temperature']} °C - + - sample transport container - ${row['sample transport container']} + sample_transport_container + ${row['sample_transport_container']} J/°C - + - sample transport duration - ${row['sample transport duration']} + sample_transport_duration + ${row['sample_transport_duration']} year - + - sample collection device - ${row['sample collection device']} + sample_collection_device + ${row['sample_collection_device']} - + - sample collection method - ${row['sample collection method']} + sample_collection_method + ${row['sample_collection_method']} - + - sample storage temperature - ${row['sample storage temperature']} + sample_storage_temperature + ${row['sample_storage_temperature']} °C - + - sample storage device - ${row['sample storage device']} + sample_storage_device + ${row['sample_storage_device']} - + - sample storage location - ${row['sample storage location']} + sample_storage_location + ${row['sample_storage_location']} - + - size-fraction lower threshold - ${row['size-fraction lower threshold']} - µm + sizefraction_lower_threshold + ${row['sizefraction_lower_threshold']} + nm - + - size-fraction upper threshold - ${row['size-fraction upper threshold']} - µm + sizefraction_upper_threshold + ${row['sizefraction_upper_threshold']} + nm - + - soil type - ${row['soil type']} + soil_type + ${row['soil_type']} - + - soil type method - ${row['soil type method']} + soil_type_method + ${row['soil_type_method']} - + - soil texture method - ${row['soil texture method']} + soil_texture_method + ${row['soil_texture_method']} - + - soil pH - ${row['soil pH']} + soil_ph + ${row['soil_ph']} - + - soil cover - ${row['soil cover']} + soil_cover + ${row['soil_cover']} - + - soil texture classification - ${row['soil texture classification']} + soil_texture_classification + ${row['soil_texture_classification']} °C - + - soil sediment porosity - ${row['soil sediment porosity']} + soil_sediment_porosity + ${row['soil_sediment_porosity']} - + - soil conductivity - ${row['soil conductivity']} + soil_conductivity + ${row['soil_conductivity']} - + - facility type - ${row['facility type']} + facility_type + ${row['facility_type']} - + - collection site geographic feature - ${row['collection site geographic feature']} - m2 + collection_site_geographic_feature + ${row['collection_site_geographic_feature']} + ha - + - area sampled size - ${row['area sampled size']} + area_sampled_size + ${row['area_sampled_size']} ml - + - sample name - ${row['sample name']} + sample_name + ${row['sample_name']} - + - study design - ${row['study design']} + study_design + ${row['study_design']} kg s−3 - + - project name - ${row['project name']} + project_name + ${row['project_name']} - + - farm equipment sanitization - ${row['farm equipment sanitization']} + farm_equipment_sanitization + ${row['farm_equipment_sanitization']} - + - equipment shared with other farms - ${row['equipment shared with other farms']} + equipment_shared_with_other_farms + ${row['equipment_shared_with_other_farms']} - + - farm equipment used - ${row['farm equipment used']} + farm_equipment_used + ${row['farm_equipment_used']} - + - farm equipment sanitization frequency - ${row['farm equipment sanitization frequency']} + farm_equipment_sanitization_frequency + ${row['farm_equipment_sanitization_frequency']} m2 - + - farm watering water source - ${row['farm watering water source']} + farm_watering_water_source + ${row['farm_watering_water_source']} - + - food production system characteristics - ${row['food production system characteristics']} + food_production_system_characteristics + ${row['food_production_system_characteristics']} - + - animal water delivery method - ${row['animal water delivery method']} + animal_water_delivery_method + ${row['animal_water_delivery_method']} - + - plant water delivery method - ${row['plant water delivery method']} + plant_water_delivery_method + ${row['plant_water_delivery_method']} - + - food harvesting process - ${row['food harvesting process']} + food_harvesting_process + ${row['food_harvesting_process']} - + - food animal source diet - ${row['food animal source diet']} + food_animal_source_diet + ${row['food_animal_source_diet']} - + - food production characteristics - ${row['food production characteristics']} + food_production_characteristics + ${row['food_production_characteristics']} °C - + - food animal group size - ${row['food animal group size']} + food_animal_group_size + ${row['food_animal_group_size']} year - + - fertilizer administration date - ${row['fertilizer administration date']} + fertilizer_administration_date + ${row['fertilizer_administration_date']} - + - animal feeding equipment - ${row['animal feeding equipment']} + animal_feeding_equipment + ${row['animal_feeding_equipment']} - + - crop yield - ${row['crop yield']} + crop_yield + ${row['crop_yield']} - + - water delivery frequency - ${row['water delivery frequency']} + water_delivery_frequency + ${row['water_delivery_frequency']} - + - animal housing system - ${row['animal housing system']} + animal_housing_system + ${row['animal_housing_system']} - + - environmental feature adjacent water source - ${row['environmental feature adjacent water source']} + environmental_feature_adjacent_water_source + ${row['environmental_feature_adjacent_water_source']} @@ -372,113 +372,113 @@ def mandatorytest(row, column, index): ${row['ploidy']} - + - number of replicons - ${row['number of replicons']} + number_of_replicons + ${row['number_of_replicons']} - + - extrachromosomal elements - ${row['extrachromosomal elements']} + extrachromosomal_elements + ${row['extrachromosomal_elements']} - + - estimated size - ${row['estimated size']} + estimated_size + ${row['estimated_size']} - + - target gene - ${row['target gene']} + target_gene + ${row['target_gene']} - + - target subfragment - ${row['target subfragment']} + target_subfragment + ${row['target_subfragment']} - + - multiplex identifiers - ${row['multiplex identifiers']} + multiplex_identifiers + ${row['multiplex_identifiers']} - + - sequence quality check - ${row['sequence quality check']} + sequence_quality_check + ${row['sequence_quality_check']} - + - chimera check software - ${row['chimera check software']} + chimera_check_software + ${row['chimera_check_software']} - + - relevant electronic resources - ${row['relevant electronic resources']} + relevant_electronic_resources + ${row['relevant_electronic_resources']} - + - relevant standard operating procedures - ${row['relevant standard operating procedures']} + relevant_standard_operating_procedures + ${row['relevant_standard_operating_procedures']} - + - 16s recovered - ${row['16s recovered']} + _16s_recovered + ${row['_16s_recovered']} - + - 16S recovery software - ${row['16S recovery software']} + _16s_recovery_software + ${row['_16s_recovery_software']} - + - completeness score - ${row['completeness score']} + completeness_score + ${row['completeness_score']} % - + - completeness software - ${row['completeness software']} + completeness_software + ${row['completeness_software']} - + - completeness approach - ${row['completeness approach']} + completeness_approach + ${row['completeness_approach']} - + - assembly quality - ${row['assembly quality']} + assembly_quality + ${row['assembly_quality']} - + - assembly name - ${row['assembly name']} + assembly_name + ${row['assembly_name']} - + - collection date - ${row['collection date']} + collection_date + ${row['collection_date']} @@ -488,42 +488,42 @@ def mandatorytest(row, column, index): m - + - geographic location (latitude) - ${row['geographic location (latitude)']} + geographic_location_latitude + ${row['geographic_location_latitude']} DD - + - geographic location (longitude) - ${row['geographic location (longitude)']} + geographic_location_longitude + ${row['geographic_location_longitude']} DD - + - geographic location (region and locality) - ${row['geographic location (region and locality)']} + geographic_location_region_and_locality + ${row['geographic_location_region_and_locality']} - + - broad-scale environmental context - ${row['broad-scale environmental context']} + broadscale_environmental_context + ${row['broadscale_environmental_context']} - + - local environmental context - ${row['local environmental context']} + local_environmental_context + ${row['local_environmental_context']} - + - environmental medium - ${row['environmental medium']} + environmental_medium + ${row['environmental_medium']} @@ -533,209 +533,209 @@ def mandatorytest(row, column, index): m - + - culture isolation date - ${row['culture isolation date']} + culture_isolation_date + ${row['culture_isolation_date']} - + - time course duration - ${row['time course duration']} - year + time_course_duration + ${row['time_course_duration']} + day - + - number of samples collected - ${row['number of samples collected']} + number_of_samples_collected + ${row['number_of_samples_collected']} - + - surface material - ${row['surface material']} + surface_material + ${row['surface_material']} - + - ventilation rate - ${row['ventilation rate']} + ventilation_rate + ${row['ventilation_rate']} m3/min - + - indoor surface - ${row['indoor surface']} + indoor_surface + ${row['indoor_surface']} - + - ventilation type - ${row['ventilation type']} + ventilation_type + ${row['ventilation_type']} - + - sampling room sterilization method - ${row['sampling room sterilization method']} + sampling_room_sterilization_method + ${row['sampling_room_sterilization_method']} - + - sampling floor - ${row['sampling floor']} + sampling_floor + ${row['sampling_floor']} °C - + - average daily occupancy - ${row['average daily occupancy']} + average_daily_occupancy + ${row['average_daily_occupancy']} °C - + - sample surface moisture - ${row['sample surface moisture']} - year + sample_surface_moisture + ${row['sample_surface_moisture']} + minute - + - sampling room id or name - ${row['sampling room id or name']} - year + sampling_room_id_or_name + ${row['sampling_room_id_or_name']} + day - + - fermentation relative humidity - ${row['fermentation relative humidity']} - g/m3 + fermentation_relative_humidity + ${row['fermentation_relative_humidity']} + % - + - room dimensions - ${row['room dimensions']} + room_dimensions + ${row['room_dimensions']} - + - amount or size of sample collected - ${row['amount or size of sample collected']} - m3 + amount_or_size_of_sample_collected + ${row['amount_or_size_of_sample_collected']} + kg - + - organism count - ${row['organism count']} + organism_count + ${row['organism_count']} - + - sampling time point - ${row['sampling time point']} + sampling_time_point + ${row['sampling_time_point']} - + - growth habit - ${row['growth habit']} + growth_habit + ${row['growth_habit']} - + - sample storage duration - ${row['sample storage duration']} + sample_storage_duration + ${row['sample_storage_duration']} - + - sequencing kit - ${row['sequencing kit']} + sequencing_kit + ${row['sequencing_kit']} - + - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} + geographic_location_country_andor_sea + ${row['geographic_location_country_andor_sea']} - + - host disease status - ${row['host disease status']} + host_disease_status + ${row['host_disease_status']} - + - host age - ${row['host age']} + host_age + ${row['host_age']} years - + - host taxid - ${row['host taxid']} + host_taxid + ${row['host_taxid']} - + - host height - ${row['host height']} - mm + host_height + ${row['host_height']} + m - + - host length - ${row['host length']} - mm + host_length + ${row['host_length']} + m - + - host total mass - ${row['host total mass']} + host_total_mass + ${row['host_total_mass']} kg - + - host phenotype - ${row['host phenotype']} + host_phenotype + ${row['host_phenotype']} - + - host scientific name - ${row['host scientific name']} + host_scientific_name + ${row['host_scientific_name']} - + - host subspecific genetic lineage - ${row['host subspecific genetic lineage']} + host_subspecific_genetic_lineage + ${row['host_subspecific_genetic_lineage']} - + - serovar or serotype - ${row['serovar or serotype']} + serovar_or_serotype + ${row['serovar_or_serotype']} humidity ${row['humidity']} - g/m3 + % @@ -745,24 +745,24 @@ def mandatorytest(row, column, index): mS/cm - + - solar irradiance - ${row['solar irradiance']} + solar_irradiance + ${row['solar_irradiance']} W/m2 - + - wind direction - ${row['wind direction']} + wind_direction + ${row['wind_direction']} - + - wind speed - ${row['wind speed']} - m/s + wind_speed + ${row['wind_speed']} + km/h @@ -779,61 +779,61 @@ def mandatorytest(row, column, index): NTU - + - pH - ${row['pH']} + ph + ${row['ph']} - + - pH method - ${row['pH method']} + ph_method + ${row['ph_method']} - + - fermentation vessel - ${row['fermentation vessel']} + fermentation_vessel + ${row['fermentation_vessel']} - + - fermentation headspace oxygen - ${row['fermentation headspace oxygen']} + fermentation_headspace_oxygen + ${row['fermentation_headspace_oxygen']} m2 - + - frequency of cleaning - ${row['frequency of cleaning']} - year + frequency_of_cleaning + ${row['frequency_of_cleaning']} + minute - + - total organic carbon method - ${row['total organic carbon method']} + total_organic_carbon_method + ${row['total_organic_carbon_method']} - + - air particulate matter concentration - ${row['air particulate matter concentration']} + air_particulate_matter_concentration + ${row['air_particulate_matter_concentration']} µg/m3 - + - total nitrogen content method - ${row['total nitrogen content method']} + total_nitrogen_content_method + ${row['total_nitrogen_content_method']} - + - total nitrogen concentration - ${row['total nitrogen concentration']} + total_nitrogen_concentration + ${row['total_nitrogen_concentration']} µmol/L @@ -844,50 +844,50 @@ def mandatorytest(row, column, index): psu - + - total carbon - ${row['total carbon']} + total_carbon + ${row['total_carbon']} µg/L - + - total organic carbon - ${row['total organic carbon']} + total_organic_carbon + ${row['total_organic_carbon']} g/kg - + - total nitrogen content - ${row['total nitrogen content']} - µmol/L + total_nitrogen_content + ${row['total_nitrogen_content']} + µg/L - + - water pH - ${row['water pH']} + water_ph + ${row['water_ph']} - + - fermentation ph - ${row['fermentation ph']} + fermentation_ph + ${row['fermentation_ph']} - + - bacteria density - ${row['bacteria density']} - g/m3 + bacteria_density + ${row['bacteria_density']} + % - + - salinity method - ${row['salinity method']} + salinity_method + ${row['salinity_method']} @@ -896,68 +896,68 @@ def mandatorytest(row, column, index): ${row['bio_material']} - + - source material identifiers - ${row['source material identifiers']} + source_material_identifiers + ${row['source_material_identifiers']} - + - sample source material category - ${row['sample source material category']} + sample_source_material_category + ${row['sample_source_material_category']} - + - history/previous land use - ${row['history/previous land use']} + historyprevious_land_use + ${row['historyprevious_land_use']} - + - history/crop rotation - ${row['history/crop rotation']} + historycrop_rotation + ${row['historycrop_rotation']} - + - history/tillage - ${row['history/tillage']} + historytillage + ${row['historytillage']} - + - mean seasonal humidity - ${row['mean seasonal humidity']} - g/m3 + mean_seasonal_humidity + ${row['mean_seasonal_humidity']} + % - + - mean seasonal temperature - ${row['mean seasonal temperature']} + mean_seasonal_temperature + ${row['mean_seasonal_temperature']} °C - + - mean seasonal precipitation - ${row['mean seasonal precipitation']} + mean_seasonal_precipitation + ${row['mean_seasonal_precipitation']} mm - + - extreme weather date - ${row['extreme weather date']} + extreme_weather_date + ${row['extreme_weather_date']} J/°C - + - extreme weather event - ${row['extreme weather event']} + extreme_weather_event + ${row['extreme_weather_event']} m @@ -967,151 +967,151 @@ def mandatorytest(row, column, index): ${row['season']} - + - host genotype - ${row['host genotype']} + host_genotype + ${row['host_genotype']} - + - host specificity or range - ${row['host specificity or range']} + host_specificity_or_range + ${row['host_specificity_or_range']} - + - host dry mass - ${row['host dry mass']} - mg + host_dry_mass + ${row['host_dry_mass']} + kg - + - host prediction approach - ${row['host prediction approach']} + host_prediction_approach + ${row['host_prediction_approach']} - + - host prediction estimated accuracy - ${row['host prediction estimated accuracy']} + host_prediction_estimated_accuracy + ${row['host_prediction_estimated_accuracy']} - + - spike-in microbial strain - ${row['spike-in microbial strain']} + spikein_microbial_strain + ${row['spikein_microbial_strain']} - + - fermentation chemical additives - ${row['fermentation chemical additives']} + fermentation_chemical_additives + ${row['fermentation_chemical_additives']} J/°C - + - fermentation chemical additives percentage - ${row['fermentation chemical additives percentage']} + fermentation_chemical_additives_percentage + ${row['fermentation_chemical_additives_percentage']} % - + - study treatment - ${row['study treatment']} + study_treatment + ${row['study_treatment']} % - + - spike-in organism - ${row['spike-in organism']} - g/m3 + spikein_organism + ${row['spikein_organism']} + % - + - spike-in organism count - ${row['spike-in organism count']} - mm + spikein_organism_count + ${row['spikein_organism_count']} + m - + - fermentation temperature - ${row['fermentation temperature']} + fermentation_temperature + ${row['fermentation_temperature']} °C - + - spike-in with heavy metals - ${row['spike-in with heavy metals']} + spikein_with_heavy_metals + ${row['spikein_with_heavy_metals']} year - + - microbial starter inoculation - ${row['microbial starter inoculation']} + microbial_starter_inoculation + ${row['microbial_starter_inoculation']} m3/day - + - microbial starter source - ${row['microbial starter source']} - year + microbial_starter_source + ${row['microbial_starter_source']} + minute - + - microbial starter preparation - ${row['microbial starter preparation']} - year + microbial_starter_preparation + ${row['microbial_starter_preparation']} + minute - + - spike-in bacterial serovar or serotype - ${row['spike-in bacterial serovar or serotype']} - year + spikein_bacterial_serovar_or_serotype + ${row['spikein_bacterial_serovar_or_serotype']} + minute - + - antimicrobial phenotype of spike-in bacteria - ${row['antimicrobial phenotype of spike-in bacteria']} + antimicrobial_phenotype_of_spikein_bacteria + ${row['antimicrobial_phenotype_of_spikein_bacteria']} - + - fermentation time - ${row['fermentation time']} - year + fermentation_time + ${row['fermentation_time']} + minute - + - microbial starter organism count - ${row['microbial starter organism count']} + microbial_starter_organism_count + ${row['microbial_starter_organism_count']} m2 - + - spike-in with antibiotics - ${row['spike-in with antibiotics']} + spikein_with_antibiotics + ${row['spikein_with_antibiotics']} m2 - + - study incubation temperature - ${row['study incubation temperature']} + study_incubation_temperature + ${row['study_incubation_temperature']} °C @@ -1121,11 +1121,11 @@ def mandatorytest(row, column, index): ${row['perturbation']} - + - study incubation duration - ${row['study incubation duration']} - year + study_incubation_duration + ${row['study_incubation_duration']} + minute @@ -1135,257 +1135,256 @@ def mandatorytest(row, column, index): °C - + - negative control type - ${row['negative control type']} + negative_control_type + ${row['negative_control_type']} - + - positive control type - ${row['positive control type']} + positive_control_type + ${row['positive_control_type']} - + - experimental factor - ${row['experimental factor']} + experimental_factor + ${row['experimental_factor']} - + - encoded traits - ${row['encoded traits']} + encoded_traits + ${row['encoded_traits']} - + - genetic modification - ${row['genetic modification']} + genetic_modification + ${row['genetic_modification']} - + - subspecific genetic lineage - ${row['subspecific genetic lineage']} + subspecific_genetic_lineage + ${row['subspecific_genetic_lineage']} - + - ancestral data - ${row['ancestral data']} + ancestral_data + ${row['ancestral_data']} - + - taxonomic classification - ${row['taxonomic classification']} + taxonomic_classification + ${row['taxonomic_classification']} - + - plant growth medium - ${row['plant growth medium']} + plant_growth_medium + ${row['plant_growth_medium']} - + - rooting conditions - ${row['rooting conditions']} + rooting_conditions + ${row['rooting_conditions']} - + - rooting medium macronutrients - ${row['rooting medium macronutrients']} + rooting_medium_macronutrients + ${row['rooting_medium_macronutrients']} - + - rooting medium micronutrients - ${row['rooting medium micronutrients']} + rooting_medium_micronutrients + ${row['rooting_medium_micronutrients']} - + - rooting medium carbon - ${row['rooting medium carbon']} + rooting_medium_carbon + ${row['rooting_medium_carbon']} - + - rooting medium pH - ${row['rooting medium pH']} + rooting_medium_ph + ${row['rooting_medium_ph']} - + - microbiological culture medium - ${row['microbiological culture medium']} - Pa + microbiological_culture_medium + ${row['microbiological_culture_medium']} + N/m2 - + - spike-in growth medium - ${row['spike-in growth medium']} + spikein_growth_medium + ${row['spikein_growth_medium']} W/m2 - + - fermentation medium - ${row['fermentation medium']} + fermentation_medium + ${row['fermentation_medium']} m - + - growth medium - ${row['growth medium']} + growth_medium + ${row['growth_medium']} year - + - isolation and growth condition - ${row['isolation and growth condition']} + isolation_and_growth_condition + ${row['isolation_and_growth_condition']} - + - annotation source - ${row['annotation source']} + annotation_source + ${row['annotation_source']} - + - reference for biomaterial - ${row['reference for biomaterial']} + reference_for_biomaterial + ${row['reference_for_biomaterial']} - + - sequencing location - ${row['sequencing location']} + sequencing_location + ${row['sequencing_location']} - + - enrichment protocol - ${row['enrichment protocol']} + enrichment_protocol + ${row['enrichment_protocol']} - + - library preparation kit - ${row['library preparation kit']} + library_preparation_kit + ${row['library_preparation_kit']} - + - nucleic acid extraction kit - ${row['nucleic acid extraction kit']} - ppm + nucleic_acid_extraction_kit + ${row['nucleic_acid_extraction_kit']} - + - sample pooling - ${row['sample pooling']} + sample_pooling + ${row['sample_pooling']} - + - lot number - ${row['lot number']} + lot_number + ${row['lot_number']} % - + - single cell or viral particle lysis approach - ${row['single cell or viral particle lysis approach']} + single_cell_or_viral_particle_lysis_approach + ${row['single_cell_or_viral_particle_lysis_approach']} - + - single cell or viral particle lysis kit protocol - ${row['single cell or viral particle lysis kit protocol']} + single_cell_or_viral_particle_lysis_kit_protocol + ${row['single_cell_or_viral_particle_lysis_kit_protocol']} - + - pooled DNA extract total - ${row['pooled DNA extract total']} + pooled_dna_extract_total + ${row['pooled_dna_extract_total']} - + - sample material processing - ${row['sample material processing']} + sample_material_processing + ${row['sample_material_processing']} - + - sample volume or weight for DNA extraction - ${row['sample volume or weight for DNA extraction']} - ng + sample_volume_or_weight_for_dna_extraction + ${row['sample_volume_or_weight_for_dna_extraction']} + mL - + - nucleic acid extraction - ${row['nucleic acid extraction']} + nucleic_acid_extraction + ${row['nucleic_acid_extraction']} - + - nucleic acid amplification - ${row['nucleic acid amplification']} + nucleic_acid_amplification + ${row['nucleic_acid_amplification']} - + - library size - ${row['library size']} + library_size + ${row['library_size']} - + - library reads sequenced - ${row['library reads sequenced']} + library_reads_sequenced + ${row['library_reads_sequenced']} - + - library vector - ${row['library vector']} + library_vector + ${row['library_vector']} - + - library screening strategy - ${row['library screening strategy']} + library_screening_strategy + ${row['library_screening_strategy']} - + - pcr conditions - ${row['pcr conditions']} + pcr_conditions + ${row['pcr_conditions']} - + - assembly software - ${row['assembly software']} + assembly_software + ${row['assembly_software']} - + - pcr primers - ${row['pcr primers']} + pcr_primers + ${row['pcr_primers']} @@ -1394,391 +1393,391 @@ def mandatorytest(row, column, index): ${row['adapters']} - + - food animal antimicrobial - ${row['food animal antimicrobial']} + food_animal_antimicrobial + ${row['food_animal_antimicrobial']} - + - food shipping transportation vehicle - ${row['food shipping transportation vehicle']} + food_shipping_transportation_vehicle + ${row['food_shipping_transportation_vehicle']} - + - water source shared - ${row['water source shared']} + water_source_shared + ${row['water_source_shared']} - + - food source - ${row['food source']} + food_source + ${row['food_source']} - + - food shipping transportation method - ${row['food shipping transportation method']} + food_shipping_transportation_method + ${row['food_shipping_transportation_method']} - + - material of contact prior to food packaging - ${row['material of contact prior to food packaging']} + material_of_contact_prior_to_food_packaging + ${row['material_of_contact_prior_to_food_packaging']} - + - food product name legal status - ${row['food product name legal status']} + food_product_name_legal_status + ${row['food_product_name_legal_status']} - + - food quality date - ${row['food quality date']} + food_quality_date + ${row['food_quality_date']} - + - food cleaning process - ${row['food cleaning process']} + food_cleaning_process + ${row['food_cleaning_process']} m - + - hygienic food production area - ${row['hygienic food production area']} + hygienic_food_production_area + ${row['hygienic_food_production_area']} kg s−3 - + - food contact surface - ${row['food contact surface']} + food_contact_surface + ${row['food_contact_surface']} J/°C - + - food cooking process - ${row['food cooking process']} + food_cooking_process + ${row['food_cooking_process']} % - + - food product by quality - ${row['food product by quality']} - year + food_product_by_quality + ${row['food_product_by_quality']} + minute - + - food animal antimicrobial route of administration - ${row['food animal antimicrobial route of administration']} - m2 + food_animal_antimicrobial_route_of_administration + ${row['food_animal_antimicrobial_route_of_administration']} + ha - + - food allergen labeling - ${row['food allergen labeling']} + food_allergen_labeling + ${row['food_allergen_labeling']} W/m2 - + - food product type - ${row['food product type']} + food_product_type + ${row['food_product_type']} - + - food animal source sex category - ${row['food animal source sex category']} + food_animal_source_sex_category + ${row['food_animal_source_sex_category']} °C - + - animal intrusion near sample source - ${row['animal intrusion near sample source']} + animal_intrusion_near_sample_source + ${row['animal_intrusion_near_sample_source']} °C - + - food packing medium integrity - ${row['food packing medium integrity']} + food_packing_medium_integrity + ${row['food_packing_medium_integrity']} °C - + - microbial starter - ${row['microbial starter']} + microbial_starter + ${row['microbial_starter']} °C - + - food treatment process - ${row['food treatment process']} + food_treatment_process + ${row['food_treatment_process']} - + - food preservation process - ${row['food preservation process']} + food_preservation_process + ${row['food_preservation_process']} J/°C - + - microbial starter ncbi taxonomy id - ${row['microbial starter ncbi taxonomy id']} + microbial_starter_ncbi_taxonomy_id + ${row['microbial_starter_ncbi_taxonomy_id']} - + - interagency food safety analytics collaboration (ifsac) category - ${row['interagency food safety analytics collaboration (ifsac) category']} + interagency_food_safety_analytics_collaboration_ifsac_category + ${row['interagency_food_safety_analytics_collaboration_ifsac_category']} - + - food animal body condition - ${row['food animal body condition']} + food_animal_body_condition + ${row['food_animal_body_condition']} - + - food product synonym - ${row['food product synonym']} + food_product_synonym + ${row['food_product_synonym']} - + - food ingredient - ${row['food ingredient']} + food_ingredient + ${row['food_ingredient']} year - + - food stored by consumer (storage duration) - ${row['food stored by consumer (storage duration)']} - year + food_stored_by_consumer_storage_duration + ${row['food_stored_by_consumer_storage_duration']} + minute - + - food animal antimicrobial duration - ${row['food animal antimicrobial duration']} - year + food_animal_antimicrobial_duration + ${row['food_animal_antimicrobial_duration']} + minute - + - part of plant or animal - ${row['part of plant or animal']} - year + part_of_plant_or_animal + ${row['part_of_plant_or_animal']} + minute - + - hazard analysis critical control points (haccp) guide food safety term - ${row['hazard analysis critical control points (haccp) guide food safety term']} - year + hazard_analysis_critical_control_points_haccp_guide_food_safety_term + ${row['hazard_analysis_critical_control_points_haccp_guide_food_safety_term']} + minute - + - dietary claim or use - ${row['dietary claim or use']} + dietary_claim_or_use + ${row['dietary_claim_or_use']} - + - degree of plant part maturity - ${row['degree of plant part maturity']} - year + degree_of_plant_part_maturity + ${row['degree_of_plant_part_maturity']} + day - + - food production environmental monitoring zone - ${row['food production environmental monitoring zone']} + food_production_environmental_monitoring_zone + ${row['food_production_environmental_monitoring_zone']} - + - plant reproductive part - ${row['plant reproductive part']} + plant_reproductive_part + ${row['plant_reproductive_part']} - + - food traceability list category - ${row['food traceability list category']} - mm + food_traceability_list_category + ${row['food_traceability_list_category']} + cm - + - food animal antimicrobial frequency - ${row['food animal antimicrobial frequency']} + food_animal_antimicrobial_frequency + ${row['food_animal_antimicrobial_frequency']} m2 - + - intended consumer - ${row['intended consumer']} + intended_consumer + ${row['intended_consumer']} m2 - + - quantity purchased - ${row['quantity purchased']} + quantity_purchased + ${row['quantity_purchased']} - + - food container or wrapping - ${row['food container or wrapping']} + food_container_or_wrapping + ${row['food_container_or_wrapping']} °C - + - food additive - ${row['food additive']} - g/m3 + food_additive + ${row['food_additive']} + % - + - food source age - ${row['food source age']} - year + food_source_age + ${row['food_source_age']} + day - + - food animal antimicrobial intended use - ${row['food animal antimicrobial intended use']} - year + food_animal_antimicrobial_intended_use + ${row['food_animal_antimicrobial_intended_use']} + day - + - food packing medium - ${row['food packing medium']} + food_packing_medium + ${row['food_packing_medium']} m2 - + - specific intended consumer - ${row['specific intended consumer']} + specific_intended_consumer + ${row['specific_intended_consumer']} m2 - + - purchase date - ${row['purchase date']} + purchase_date + ${row['purchase_date']} m2 - + - food stored by consumer (storage temperature) - ${row['food stored by consumer (storage temperature)']} + food_stored_by_consumer_storage_temperature + ${row['food_stored_by_consumer_storage_temperature']} °C - + - food package capacity - ${row['food package capacity']} + food_package_capacity + ${row['food_package_capacity']} year - + - food distribution point geographic location (city) - ${row['food distribution point geographic location (city)']} + food_distribution_point_geographic_location_city + ${row['food_distribution_point_geographic_location_city']} - + - food product origin geographic location - ${row['food product origin geographic location']} + food_product_origin_geographic_location + ${row['food_product_origin_geographic_location']} m - + - food distribution point geographic location - ${row['food distribution point geographic location']} + food_distribution_point_geographic_location + ${row['food_distribution_point_geographic_location']} m - + - production labeling claims - ${row['production labeling claims']} + production_labeling_claims + ${row['production_labeling_claims']} - + - relative location of sample - ${row['relative location of sample']} + relative_location_of_sample + ${row['relative_location_of_sample']} depth ${row['depth']} - mm + m - + - environment adjacent to site - ${row['environment adjacent to site']} + environment_adjacent_to_site + ${row['environment_adjacent_to_site']} - + - fertilizer administration - ${row['fertilizer administration']} + fertilizer_administration + ${row['fertilizer_administration']} - + - biotic regimen - ${row['biotic regimen']} + biotic_regimen + ${row['biotic_regimen']} - + - mechanical damage - ${row['mechanical damage']} + mechanical_damage + ${row['mechanical_damage']} - + - chemical administration - ${row['chemical administration']} + chemical_administration + ${row['chemical_administration']} diff --git a/ena_upload/templates/ENA_template_samples_ERC000057.xml b/ena_upload/templates/ENA_template_samples_ERC000057.xml index d6b397a..b021fce 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000057.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000057.xml @@ -33,28 +33,28 @@ def mandatorytest(row, column, index): ${row.sample_description} - + - trophic level - ${row['trophic level']} + trophic_level + ${row['trophic_level']} - + - observed biotic relationship - ${row['observed biotic relationship']} + observed_biotic_relationship + ${row['observed_biotic_relationship']} - + - known pathogenicity - ${row['known pathogenicity']} + known_pathogenicity + ${row['known_pathogenicity']} - + - relationship to oxygen - ${row['relationship to oxygen']} + relationship_to_oxygen + ${row['relationship_to_oxygen']} @@ -63,53 +63,53 @@ def mandatorytest(row, column, index): ${row['propagation']} - + - host of the symbiont role - ${row['host of the symbiont role']} + host_of_the_symbiont_role + ${row['host_of_the_symbiont_role']} - + - sample symbiont of - ${row['sample symbiont of']} + sample_symbiont_of + ${row['sample_symbiont_of']} - + - sample collection method - ${row['sample collection method']} + sample_collection_method + ${row['sample_collection_method']} - + - sample storage temperature - ${row['sample storage temperature']} + sample_storage_temperature + ${row['sample_storage_temperature']} °C - + - sample storage location - ${row['sample storage location']} + sample_storage_location + ${row['sample_storage_location']} - + - sample storage solution - ${row['sample storage solution']} + sample_storage_solution + ${row['sample_storage_solution']} - + - oxygenation status of sample - ${row['oxygenation status of sample']} + oxygenation_status_of_sample + ${row['oxygenation_status_of_sample']} - + - project name - ${row['project name']} + project_name + ${row['project_name']} @@ -118,82 +118,82 @@ def mandatorytest(row, column, index): ${row['ploidy']} - + - number of replicons - ${row['number of replicons']} + number_of_replicons + ${row['number_of_replicons']} - + - extrachromosomal elements - ${row['extrachromosomal elements']} + extrachromosomal_elements + ${row['extrachromosomal_elements']} - + - estimated size - ${row['estimated size']} + estimated_size + ${row['estimated_size']} - + - target gene - ${row['target gene']} + target_gene + ${row['target_gene']} - + - target subfragment - ${row['target subfragment']} + target_subfragment + ${row['target_subfragment']} - + - multiplex identifiers - ${row['multiplex identifiers']} + multiplex_identifiers + ${row['multiplex_identifiers']} - + - sequence quality check - ${row['sequence quality check']} + sequence_quality_check + ${row['sequence_quality_check']} - + - chimera check software - ${row['chimera check software']} + chimera_check_software + ${row['chimera_check_software']} - + - relevant electronic resources - ${row['relevant electronic resources']} + relevant_electronic_resources + ${row['relevant_electronic_resources']} - + - relevant standard operating procedures - ${row['relevant standard operating procedures']} + relevant_standard_operating_procedures + ${row['relevant_standard_operating_procedures']} - + - 16s recovered - ${row['16s recovered']} + _16s_recovered + ${row['_16s_recovered']} - + - 16S recovery software - ${row['16S recovery software']} + _16s_recovery_software + ${row['_16s_recovery_software']} - + - collection date - ${row['collection date']} + collection_date + ${row['collection_date']} @@ -203,42 +203,42 @@ def mandatorytest(row, column, index): m - + - geographic location (latitude) - ${row['geographic location (latitude)']} + geographic_location_latitude + ${row['geographic_location_latitude']} DD - + - geographic location (longitude) - ${row['geographic location (longitude)']} + geographic_location_longitude + ${row['geographic_location_longitude']} DD - + - geographic location (region and locality) - ${row['geographic location (region and locality)']} + geographic_location_region_and_locality + ${row['geographic_location_region_and_locality']} - + - broad-scale environmental context - ${row['broad-scale environmental context']} + broadscale_environmental_context + ${row['broadscale_environmental_context']} - + - local environmental context - ${row['local environmental context']} + local_environmental_context + ${row['local_environmental_context']} - + - environmental medium - ${row['environmental medium']} + environmental_medium + ${row['environmental_medium']} @@ -248,179 +248,179 @@ def mandatorytest(row, column, index): m - + - amount or size of sample collected - ${row['amount or size of sample collected']} - m3 + amount_or_size_of_sample_collected + ${row['amount_or_size_of_sample_collected']} + kg - + - organism count - ${row['organism count']} + organism_count + ${row['organism_count']} - + - sample storage duration - ${row['sample storage duration']} + sample_storage_duration + ${row['sample_storage_duration']} - + - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} + geographic_location_country_andor_sea + ${row['geographic_location_country_andor_sea']} - + - host disease status - ${row['host disease status']} + host_disease_status + ${row['host_disease_status']} - + - host of the symbiotic host disease status - ${row['host of the symbiotic host disease status']} + host_of_the_symbiotic_host_disease_status + ${row['host_of_the_symbiotic_host_disease_status']} - + - host common name - ${row['host common name']} + host_common_name + ${row['host_common_name']} - + - host subject id - ${row['host subject id']} + host_subject_id + ${row['host_subject_id']} - + - host age - ${row['host age']} + host_age + ${row['host_age']} years - + - host taxid - ${row['host taxid']} + host_taxid + ${row['host_taxid']} - + - host body habitat - ${row['host body habitat']} + host_body_habitat + ${row['host_body_habitat']} - + - host body site - ${row['host body site']} + host_body_site + ${row['host_body_site']} - + - host life stage - ${row['host life stage']} + host_life_stage + ${row['host_life_stage']} - + - host height - ${row['host height']} - mm + host_height + ${row['host_height']} + m - + - host length - ${row['host length']} - mm + host_length + ${row['host_length']} + m - + - host growth conditions - ${row['host growth conditions']} + host_growth_conditions + ${row['host_growth_conditions']} - + - host substrate - ${row['host substrate']} + host_substrate + ${row['host_substrate']} - + - host total mass - ${row['host total mass']} + host_total_mass + ${row['host_total_mass']} kg - + - host infra-specific name - ${row['host infra-specific name']} + host_infraspecific_name + ${row['host_infraspecific_name']} - + - host infra-specific rank - ${row['host infra-specific rank']} + host_infraspecific_rank + ${row['host_infraspecific_rank']} - + - host phenotype - ${row['host phenotype']} + host_phenotype + ${row['host_phenotype']} - + - host color - ${row['host color']} + host_color + ${row['host_color']} - + - host shape - ${row['host shape']} + host_shape + ${row['host_shape']} - + - host sex - ${row['host sex']} + host_sex + ${row['host_sex']} - + - host scientific name - ${row['host scientific name']} + host_scientific_name + ${row['host_scientific_name']} - + - host of the symbiotic host subject id - ${row['host of the symbiotic host subject id']} + host_of_the_symbiotic_host_subject_id + ${row['host_of_the_symbiotic_host_subject_id']} year - + - host of the symbiotic host taxon id - ${row['host of the symbiotic host taxon id']} + host_of_the_symbiotic_host_taxon_id + ${row['host_of_the_symbiotic_host_taxon_id']} - + - duration of association with the host - ${row['duration of association with the host']} - year + duration_of_association_with_the_host + ${row['duration_of_association_with_the_host']} + minute @@ -430,29 +430,29 @@ def mandatorytest(row, column, index): ºC - + - sample salinity - ${row['sample salinity']} + sample_salinity + ${row['sample_salinity']} psu - + - source material identifiers - ${row['source material identifiers']} + source_material_identifiers + ${row['source_material_identifiers']} - + - host family relationship - ${row['host family relationship']} + host_family_relationship + ${row['host_family_relationship']} - + - host genotype - ${row['host genotype']} + host_genotype + ${row['host_genotype']} @@ -461,129 +461,129 @@ def mandatorytest(row, column, index): ${row['gravidity']} - + - host specificity or range - ${row['host specificity or range']} + host_specificity_or_range + ${row['host_specificity_or_range']} - + - host of the symbiotic host phenotype - ${row['host of the symbiotic host phenotype']} + host_of_the_symbiotic_host_phenotype + ${row['host_of_the_symbiotic_host_phenotype']} - + - mode of transmission - ${row['mode of transmission']} + mode_of_transmission + ${row['mode_of_transmission']} - + - symbiotic host organism life cycle type - ${row['symbiotic host organism life cycle type']} + symbiotic_host_organism_life_cycle_type + ${row['symbiotic_host_organism_life_cycle_type']} - + - host dependence - ${row['host dependence']} + host_dependence + ${row['host_dependence']} - + - host specificity - ${row['host specificity']} + host_specificity + ${row['host_specificity']} - + - host cellular location - ${row['host cellular location']} + host_cellular_location + ${row['host_cellular_location']} % - + - host of the symbiotic host infra-specific rank - ${row['host of the symbiotic host infra-specific rank']} + host_of_the_symbiotic_host_infraspecific_rank + ${row['host_of_the_symbiotic_host_infraspecific_rank']} °C - + - type of symbiosis - ${row['type of symbiosis']} + type_of_symbiosis + ${row['type_of_symbiosis']} °C - + - observed coinfecting organisms in host of host - ${row['observed coinfecting organisms in host of host']} + observed_coinfecting_organisms_in_host_of_host + ${row['observed_coinfecting_organisms_in_host_of_host']} year - + - host of the symbiotic host infra-specific name - ${row['host of the symbiotic host infra-specific name']} + host_of_the_symbiotic_host_infraspecific_name + ${row['host_of_the_symbiotic_host_infraspecific_name']} year - + - host of the symbiotic host total mass - ${row['host of the symbiotic host total mass']} - µg + host_of_the_symbiotic_host_total_mass + ${row['host_of_the_symbiotic_host_total_mass']} + kg - + - host of the symbiotic host local environmental context - ${row['host of the symbiotic host local environmental context']} - g/m3 + host_of_the_symbiotic_host_local_environmental_context + ${row['host_of_the_symbiotic_host_local_environmental_context']} + % - + - host of the symbiotic host common name - ${row['host of the symbiotic host common name']} + host_of_the_symbiotic_host_common_name + ${row['host_of_the_symbiotic_host_common_name']} °C - + - host of the symbiotic host genotype - ${row['host of the symbiotic host genotype']} + host_of_the_symbiotic_host_genotype + ${row['host_of_the_symbiotic_host_genotype']} year - + - route of transmission - ${row['route of transmission']} + route_of_transmission + ${row['route_of_transmission']} mm - + - host dry mass - ${row['host dry mass']} - mg + host_dry_mass + ${row['host_dry_mass']} + kg - + - host body product - ${row['host body product']} + host_body_product + ${row['host_body_product']} - + - host number individual - ${row['host number individual']} + host_number_individual + ${row['host_number_individual']} @@ -592,131 +592,131 @@ def mandatorytest(row, column, index): ${row['perturbation']} - + - negative control type - ${row['negative control type']} + negative_control_type + ${row['negative_control_type']} - + - positive control type - ${row['positive control type']} + positive_control_type + ${row['positive_control_type']} - + - experimental factor - ${row['experimental factor']} + experimental_factor + ${row['experimental_factor']} - + - encoded traits - ${row['encoded traits']} + encoded_traits + ${row['encoded_traits']} - + - subspecific genetic lineage - ${row['subspecific genetic lineage']} + subspecific_genetic_lineage + ${row['subspecific_genetic_lineage']} - + - taxonomic classification - ${row['taxonomic classification']} + taxonomic_classification + ${row['taxonomic_classification']} - + - isolation and growth condition - ${row['isolation and growth condition']} + isolation_and_growth_condition + ${row['isolation_and_growth_condition']} - + - annotation source - ${row['annotation source']} + annotation_source + ${row['annotation_source']} - + - reference for biomaterial - ${row['reference for biomaterial']} + reference_for_biomaterial + ${row['reference_for_biomaterial']} - + - single cell or viral particle lysis approach - ${row['single cell or viral particle lysis approach']} + single_cell_or_viral_particle_lysis_approach + ${row['single_cell_or_viral_particle_lysis_approach']} - + - single cell or viral particle lysis kit protocol - ${row['single cell or viral particle lysis kit protocol']} + single_cell_or_viral_particle_lysis_kit_protocol + ${row['single_cell_or_viral_particle_lysis_kit_protocol']} - + - sample material processing - ${row['sample material processing']} + sample_material_processing + ${row['sample_material_processing']} - + - sample volume or weight for DNA extraction - ${row['sample volume or weight for DNA extraction']} - ng + sample_volume_or_weight_for_dna_extraction + ${row['sample_volume_or_weight_for_dna_extraction']} + mL - + - nucleic acid extraction - ${row['nucleic acid extraction']} + nucleic_acid_extraction + ${row['nucleic_acid_extraction']} - + - nucleic acid amplification - ${row['nucleic acid amplification']} + nucleic_acid_amplification + ${row['nucleic_acid_amplification']} - + - library size - ${row['library size']} + library_size + ${row['library_size']} - + - library reads sequenced - ${row['library reads sequenced']} + library_reads_sequenced + ${row['library_reads_sequenced']} - + - library vector - ${row['library vector']} + library_vector + ${row['library_vector']} - + - library screening strategy - ${row['library screening strategy']} + library_screening_strategy + ${row['library_screening_strategy']} - + - pcr conditions - ${row['pcr conditions']} + pcr_conditions + ${row['pcr_conditions']} - + - pcr primers - ${row['pcr primers']} + pcr_primers + ${row['pcr_primers']} @@ -729,13 +729,13 @@ def mandatorytest(row, column, index): depth ${row['depth']} - mm + m - + - chemical administration - ${row['chemical administration']} + chemical_administration + ${row['chemical_administration']} diff --git a/ena_upload/templates/ENA_template_samples_ERC000058.xml b/ena_upload/templates/ENA_template_samples_ERC000058.xml index e35e49a..9a98819 100644 --- a/ena_upload/templates/ENA_template_samples_ERC000058.xml +++ b/ena_upload/templates/ENA_template_samples_ERC000058.xml @@ -33,34 +33,34 @@ def mandatorytest(row, column, index): ${row.sample_description} - + - sample true vertical depth subsea - ${row['sample true vertical depth subsea']} + sample_true_vertical_depth_subsea + ${row['sample_true_vertical_depth_subsea']} - + - trophic level - ${row['trophic level']} + trophic_level + ${row['trophic_level']} - + - observed biotic relationship - ${row['observed biotic relationship']} + observed_biotic_relationship + ${row['observed_biotic_relationship']} - + - known pathogenicity - ${row['known pathogenicity']} + known_pathogenicity + ${row['known_pathogenicity']} - + - relationship to oxygen - ${row['relationship to oxygen']} + relationship_to_oxygen + ${row['relationship_to_oxygen']} @@ -69,74 +69,74 @@ def mandatorytest(row, column, index): ${row['propagation']} - + - sample transport conditions - ${row['sample transport conditions']} - m2 + sample_transport_conditions + ${row['sample_transport_conditions']} + ha - + - sample collection device - ${row['sample collection device']} + sample_collection_device + ${row['sample_collection_device']} - + - sample collection method - ${row['sample collection method']} + sample_collection_method + ${row['sample_collection_method']} - + - sample storage temperature - ${row['sample storage temperature']} + sample_storage_temperature + ${row['sample_storage_temperature']} °C - + - sample storage location - ${row['sample storage location']} + sample_storage_location + ${row['sample_storage_location']} - + - source rock depositional environment - ${row['source rock depositional environment']} + source_rock_depositional_environment + ${row['source_rock_depositional_environment']} - + - sample measured depth - ${row['sample measured depth']} - mm + sample_measured_depth + ${row['sample_measured_depth']} + m - + - corrosion rate at sample location - ${row['corrosion rate at sample location']} + corrosion_rate_at_sample_location + ${row['corrosion_rate_at_sample_location']} - + - sample collection point - ${row['sample collection point']} + sample_collection_point + ${row['sample_collection_point']} - + - depth (tvdss) of hydrocarbon resource temperature - ${row['depth (tvdss) of hydrocarbon resource temperature']} + depth_tvdss_of_hydrocarbon_resource_temperature + ${row['depth_tvdss_of_hydrocarbon_resource_temperature']} m - + - oxygenation status of sample - ${row['oxygenation status of sample']} + oxygenation_status_of_sample + ${row['oxygenation_status_of_sample']} @@ -146,16 +146,16 @@ def mandatorytest(row, column, index): g/m3 - + - sample well name - ${row['sample well name']} + sample_well_name + ${row['sample_well_name']} - + - project name - ${row['project name']} + project_name + ${row['project_name']} @@ -164,103 +164,103 @@ def mandatorytest(row, column, index): ${row['ploidy']} - + - number of replicons - ${row['number of replicons']} + number_of_replicons + ${row['number_of_replicons']} - + - extrachromosomal elements - ${row['extrachromosomal elements']} + extrachromosomal_elements + ${row['extrachromosomal_elements']} - + - estimated size - ${row['estimated size']} + estimated_size + ${row['estimated_size']} - + - target gene - ${row['target gene']} + target_gene + ${row['target_gene']} - + - target subfragment - ${row['target subfragment']} + target_subfragment + ${row['target_subfragment']} - + - multiplex identifiers - ${row['multiplex identifiers']} + multiplex_identifiers + ${row['multiplex_identifiers']} - + - sequence quality check - ${row['sequence quality check']} + sequence_quality_check + ${row['sequence_quality_check']} - + - chimera check software - ${row['chimera check software']} + chimera_check_software + ${row['chimera_check_software']} - + - relevant electronic resources - ${row['relevant electronic resources']} + relevant_electronic_resources + ${row['relevant_electronic_resources']} - + - relevant standard operating procedures - ${row['relevant standard operating procedures']} + relevant_standard_operating_procedures + ${row['relevant_standard_operating_procedures']} - + - 16s recovered - ${row['16s recovered']} + _16s_recovered + ${row['_16s_recovered']} - + - well identification number - ${row['well identification number']} - year + well_identification_number + ${row['well_identification_number']} + minute - + - water cut - ${row['water cut']} - year + water_cut + ${row['water_cut']} + minute - + - production rate - ${row['production rate']} + production_rate + ${row['production_rate']} °C - + - field name - ${row['field name']} + field_name + ${row['field_name']} - + - collection date - ${row['collection date']} + collection_date + ${row['collection_date']} @@ -270,42 +270,42 @@ def mandatorytest(row, column, index): m - + - geographic location (latitude) - ${row['geographic location (latitude)']} + geographic_location_latitude + ${row['geographic_location_latitude']} DD - + - geographic location (longitude) - ${row['geographic location (longitude)']} + geographic_location_longitude + ${row['geographic_location_longitude']} DD - + - geographic location (region and locality) - ${row['geographic location (region and locality)']} + geographic_location_region_and_locality + ${row['geographic_location_region_and_locality']} - + - broad-scale environmental context - ${row['broad-scale environmental context']} + broadscale_environmental_context + ${row['broadscale_environmental_context']} - + - local environmental context - ${row['local environmental context']} + local_environmental_context + ${row['local_environmental_context']} - + - environmental medium - ${row['environmental medium']} + environmental_medium + ${row['environmental_medium']} @@ -315,75 +315,75 @@ def mandatorytest(row, column, index): m - + - secondary and tertiary recovery methods and start date - ${row['secondary and tertiary recovery methods and start date']} + secondary_and_tertiary_recovery_methods_and_start_date + ${row['secondary_and_tertiary_recovery_methods_and_start_date']} - + - amount or size of sample collected - ${row['amount or size of sample collected']} - m3 + amount_or_size_of_sample_collected + ${row['amount_or_size_of_sample_collected']} + kg - + - organism count - ${row['organism count']} + organism_count + ${row['organism_count']} - + - organism count qpcr information - ${row['organism count qpcr information']} + organism_count_qpcr_information + ${row['organism_count_qpcr_information']} year - + - hydrocarbon type produced - ${row['hydrocarbon type produced']} - year + hydrocarbon_type_produced + ${row['hydrocarbon_type_produced']} + minute - + - api gravity - ${row['api gravity']} + api_gravity + ${row['api_gravity']} °C - + - sample storage duration - ${row['sample storage duration']} + sample_storage_duration + ${row['sample_storage_duration']} - + - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} + geographic_location_country_andor_sea + ${row['geographic_location_country_andor_sea']} - + - host disease status - ${row['host disease status']} + host_disease_status + ${row['host_disease_status']} - + - host scientific name - ${row['host scientific name']} + host_scientific_name + ${row['host_scientific_name']} pressure ${row['pressure']} - bar + atm @@ -393,10 +393,10 @@ def mandatorytest(row, column, index): ºC - + - pH - ${row['pH']} + ph + ${row['ph']} @@ -409,27 +409,27 @@ def mandatorytest(row, column, index): permeability ${row['permeability']} - mm + m - + - oil water contact depth - ${row['oil water contact depth']} + oil_water_contact_depth + ${row['oil_water_contact_depth']} m - + - hydrocarbon resource original pressure - ${row['hydrocarbon resource original pressure']} - Pa + hydrocarbon_resource_original_pressure + ${row['hydrocarbon_resource_original_pressure']} + N/m2 - + - source rock geological age - ${row['source rock geological age']} + source_rock_geological_age + ${row['source_rock_geological_age']} °C @@ -440,10 +440,10 @@ def mandatorytest(row, column, index): µmol/L - + - sample salinity - ${row['sample salinity']} + sample_salinity + ${row['sample_salinity']} psu @@ -451,7 +451,7 @@ def mandatorytest(row, column, index): calcium ${row['calcium']} - µmol/L + mg/L @@ -461,38 +461,38 @@ def mandatorytest(row, column, index): mg/L - + - suspended solids - ${row['suspended solids']} - parts/million + suspended_solids + ${row['suspended_solids']} + g/L - + - dissolved carbon dioxide - ${row['dissolved carbon dioxide']} + dissolved_carbon_dioxide + ${row['dissolved_carbon_dioxide']} µmol/L - + - dissolved inorganic carbon - ${row['dissolved inorganic carbon']} + dissolved_inorganic_carbon + ${row['dissolved_inorganic_carbon']} µg/L - + - dissolved inorganic phosphorus - ${row['dissolved inorganic phosphorus']} + dissolved_inorganic_phosphorus + ${row['dissolved_inorganic_phosphorus']} µg/L - + - dissolved organic carbon - ${row['dissolved organic carbon']} + dissolved_organic_carbon + ${row['dissolved_organic_carbon']} µmol/L @@ -500,7 +500,7 @@ def mandatorytest(row, column, index): magnesium ${row['magnesium']} - parts/million + mg/L @@ -517,10 +517,10 @@ def mandatorytest(row, column, index): µmol/L - + - total nitrogen concentration - ${row['total nitrogen concentration']} + total_nitrogen_concentration + ${row['total_nitrogen_concentration']} µmol/L @@ -549,66 +549,66 @@ def mandatorytest(row, column, index): sulfate ${row['sulfate']} - µmol/L + mg/L sulfide ${row['sulfide']} - µmol/L + mg/L - + - total phosphorus - ${row['total phosphorus']} + total_phosphorus + ${row['total_phosphorus']} µmol/L - + - total iron - ${row['total iron']} + total_iron + ${row['total_iron']} - + - volatile fatty acids - ${row['volatile fatty acids']} + volatile_fatty_acids + ${row['volatile_fatty_acids']} - + - dissolved iron - ${row['dissolved iron']} + dissolved_iron + ${row['dissolved_iron']} µl/L - + - resins wt% - ${row['resins wt%']} + resins_wt + ${row['resins_wt']} - + - dissolved oxygen in fluids - ${row['dissolved oxygen in fluids']} - µmol/kg + dissolved_oxygen_in_fluids + ${row['dissolved_oxygen_in_fluids']} + µg/L - + - total sulfur - ${row['total sulfur']} - µmol/L + total_sulfur + ${row['total_sulfur']} + µg/L - + - injection water fraction - ${row['injection water fraction']} + injection_water_fraction + ${row['injection_water_fraction']} % @@ -616,40 +616,40 @@ def mandatorytest(row, column, index): ethylbenzene ${row['ethylbenzene']} - µmol/L + µg/L - + - vfa in formation water - ${row['vfa in formation water']} + vfa_in_formation_water + ${row['vfa_in_formation_water']} - + - total acid number - ${row['total acid number']} + total_acid_number + ${row['total_acid_number']} year - + - sulfate in formation water - ${row['sulfate in formation water']} - year + sulfate_in_formation_water + ${row['sulfate_in_formation_water']} + minute toluene ${row['toluene']} - year + minute - + - asphaltenes wt% - ${row['asphaltenes wt%']} + asphaltenes_wt + ${row['asphaltenes_wt']} % @@ -660,10 +660,10 @@ def mandatorytest(row, column, index): m2 - + - alkalinity method - ${row['alkalinity method']} + alkalinity_method + ${row['alkalinity_method']} m2 @@ -681,195 +681,195 @@ def mandatorytest(row, column, index): mEq/L - + - source material identifiers - ${row['source material identifiers']} + source_material_identifiers + ${row['source_material_identifiers']} - + - source rock lithology - ${row['source rock lithology']} - year + source_rock_lithology + ${row['source_rock_lithology']} + minute - + - sample material type - ${row['sample material type']} + sample_material_type + ${row['sample_material_type']} - + - host of the symbiotic host phenotype - ${row['host of the symbiotic host phenotype']} + host_of_the_symbiotic_host_phenotype + ${row['host_of_the_symbiotic_host_phenotype']} - + - biocide administration method - ${row['biocide administration method']} + biocide_administration_method + ${row['biocide_administration_method']} - + - chemical treatment - ${row['chemical treatment']} + chemical_treatment + ${row['chemical_treatment']} - + - biocide administration - ${row['biocide administration']} - year + biocide_administration + ${row['biocide_administration']} + minute - + - chemical treatment method - ${row['chemical treatment method']} + chemical_treatment_method + ${row['chemical_treatment_method']} J/K - + - negative control type - ${row['negative control type']} + negative_control_type + ${row['negative_control_type']} - + - positive control type - ${row['positive control type']} + positive_control_type + ${row['positive_control_type']} - + - experimental factor - ${row['experimental factor']} + experimental_factor + ${row['experimental_factor']} - + - encoded traits - ${row['encoded traits']} + encoded_traits + ${row['encoded_traits']} - + - subspecific genetic lineage - ${row['subspecific genetic lineage']} + subspecific_genetic_lineage + ${row['subspecific_genetic_lineage']} - + - taxonomic classification - ${row['taxonomic classification']} + taxonomic_classification + ${row['taxonomic_classification']} - + - isolation and growth condition - ${row['isolation and growth condition']} + isolation_and_growth_condition + ${row['isolation_and_growth_condition']} - + - annotation source - ${row['annotation source']} + annotation_source + ${row['annotation_source']} - + - reference for biomaterial - ${row['reference for biomaterial']} + reference_for_biomaterial + ${row['reference_for_biomaterial']} - + - sample subtype - ${row['sample subtype']} + sample_subtype + ${row['sample_subtype']} m2 - + - preservative added to sample - ${row['preservative added to sample']} + preservative_added_to_sample + ${row['preservative_added_to_sample']} - + - single cell or viral particle lysis approach - ${row['single cell or viral particle lysis approach']} + single_cell_or_viral_particle_lysis_approach + ${row['single_cell_or_viral_particle_lysis_approach']} - + - single cell or viral particle lysis kit protocol - ${row['single cell or viral particle lysis kit protocol']} + single_cell_or_viral_particle_lysis_kit_protocol + ${row['single_cell_or_viral_particle_lysis_kit_protocol']} - + - sample material processing - ${row['sample material processing']} + sample_material_processing + ${row['sample_material_processing']} - + - sample volume or weight for DNA extraction - ${row['sample volume or weight for DNA extraction']} - ng + sample_volume_or_weight_for_dna_extraction + ${row['sample_volume_or_weight_for_dna_extraction']} + mL - + - nucleic acid extraction - ${row['nucleic acid extraction']} + nucleic_acid_extraction + ${row['nucleic_acid_extraction']} - + - nucleic acid amplification - ${row['nucleic acid amplification']} + nucleic_acid_amplification + ${row['nucleic_acid_amplification']} - + - library size - ${row['library size']} + library_size + ${row['library_size']} - + - library reads sequenced - ${row['library reads sequenced']} + library_reads_sequenced + ${row['library_reads_sequenced']} - + - library vector - ${row['library vector']} + library_vector + ${row['library_vector']} - + - library screening strategy - ${row['library screening strategy']} + library_screening_strategy + ${row['library_screening_strategy']} - + - pcr conditions - ${row['pcr conditions']} + pcr_conditions + ${row['pcr_conditions']} - + - pcr primers - ${row['pcr primers']} + pcr_primers + ${row['pcr_primers']} @@ -878,24 +878,24 @@ def mandatorytest(row, column, index): ${row['adapters']} - + - production start date - ${row['production start date']} + production_start_date + ${row['production_start_date']} m - + - aromatics wt% - ${row['aromatics wt%']} + aromatics_wt + ${row['aromatics_wt']} % - + - saturates wt% - ${row['saturates wt%']} + saturates_wt + ${row['saturates_wt']} % @@ -905,65 +905,65 @@ def mandatorytest(row, column, index): ${row['porosity']} - + - formation water salinity - ${row['formation water salinity']} + formation_water_salinity + ${row['formation_water_salinity']} ppm - + - basin name - ${row['basin name']} - g/m3 + basin_name + ${row['basin_name']} + % - + - pour point - ${row['pour point']} + pour_point + ${row['pour_point']} °C - + - reservoir name - ${row['reservoir name']} + reservoir_name + ${row['reservoir_name']} °C - + - hydrocarbon resource geological age - ${row['hydrocarbon resource geological age']} + hydrocarbon_resource_geological_age + ${row['hydrocarbon_resource_geological_age']} - + - depositional environment - ${row['depositional environment']} + depositional_environment + ${row['depositional_environment']} m - + - source rock kerogen type - ${row['source rock kerogen type']} + source_rock_kerogen_type + ${row['source_rock_kerogen_type']} year - + - hydrocarbon resource type - ${row['hydrocarbon resource type']} + hydrocarbon_resource_type + ${row['hydrocarbon_resource_type']} year - + - water production rate - ${row['water production rate']} + water_production_rate + ${row['water_production_rate']} m3/day @@ -971,13 +971,13 @@ def mandatorytest(row, column, index): lithology ${row['lithology']} - year + minute - + - hydrocarbon resource original temperature - ${row['hydrocarbon resource original temperature']} + hydrocarbon_resource_original_temperature + ${row['hydrocarbon_resource_original_temperature']} °C @@ -985,13 +985,13 @@ def mandatorytest(row, column, index): depth ${row['depth']} - mm + m - + - injection water breakthrough date of specific well - ${row['injection water breakthrough date of specific well']} + injection_water_breakthrough_date_of_specific_well + ${row['injection_water_breakthrough_date_of_specific_well']} % diff --git a/ena_upload/templates/ENA_template_samples_ERC000059.xml b/ena_upload/templates/ENA_template_samples_ERC000059.xml new file mode 100644 index 0000000..ab5ad19 --- /dev/null +++ b/ena_upload/templates/ENA_template_samples_ERC000059.xml @@ -0,0 +1,351 @@ + + + + + + + ${row.title} + + + + ${row.taxon_id} + + ${row.scientific_name} + + ${row.common_name} + + + + ${row.sample_description} + + + + + project_name + ${row['project_name']} + + + + + sample_collection_device + ${row['sample_collection_device']} + + + + + sample_collection_method + ${row['sample_collection_method']} + + + + + sample_storage_location + ${row['sample_storage_location']} + + + + + sample_storage_device + ${row['sample_storage_device']} + + + + + sample_storage_conditions + ${row['sample_storage_conditions']} + + + + + collection_date + ${row['collection_date']} + + + + + geographic_location_region_and_locality + ${row['geographic_location_region_and_locality']} + + + + + geographic_location_latitude + ${row['geographic_location_latitude']} + DD + + + + + geographic_location_longitude + ${row['geographic_location_longitude']} + DD + + + + + broadscale_environmental_context + ${row['broadscale_environmental_context']} + + + + + local_environmental_context + ${row['local_environmental_context']} + + + + + environmental_medium + ${row['environmental_medium']} + + + + + elevation + ${row['elevation']} + m + + + + + collected_by + ${row['collected_by']} + + + + + geographic_location_country_andor_sea + ${row['geographic_location_country_andor_sea']} + + + + + depth + ${row['depth']} + m + + + + + total_depth_of_water_column + ${row['total_depth_of_water_column']} + m + + + + + source_material_identifiers + ${row['source_material_identifiers']} + + + + + negative_control_status + ${row['negative_control_status']} + + + + + negative_control_of + ${row['negative_control_of']} + + + + + negative_control_type + ${row['negative_control_type']} + + + + + sample_volume_or_weight_for_dna_extraction + ${row['sample_volume_or_weight_for_dna_extraction']} + mL + + + + + nucleic_acid_extraction + ${row['nucleic_acid_extraction']} + + + + + nucleic_acid_extraction_kit + ${row['nucleic_acid_extraction_kit']} + + + + + nucleic_acid_extraction_date + ${row['nucleic_acid_extraction_date']} + + + + + damage_treatment + ${row['damage_treatment']} + + + + + master_core_sample_id + ${row['master_core_sample_id']} + + + + + sample_age_range_youngest_limit + ${row['sample_age_range_youngest_limit']} + Ka + + + + + sample_age_range_oldest_limit + ${row['sample_age_range_oldest_limit']} + Ka + + + + + sample_age_inference_method + ${row['sample_age_inference_method']} + + + + + sample_age_inference_description + ${row['sample_age_inference_description']} + + + + + host_body_preservation_state + ${row['host_body_preservation_state']} + + + + + cultural_era + ${row['cultural_era']} + + + + + palaeopathology_status + ${row['palaeopathology_status']} + + + + + sample_decontamination_pretreatment + ${row['sample_decontamination_pretreatment']} + + + + + geological_epoch + ${row['geological_epoch']} + + + + + past_broadscale_environmental_context + ${row['past_broadscale_environmental_context']} + + + + + recovery_date + ${row['recovery_date']} + + + + + preservational_treatment + ${row['preservational_treatment']} + + + + + sample_composed_of + ${row['sample_composed_of']} + + + + + collecting_institution + ${row['collecting_institution']} + + + + + past_local_environmental_context + ${row['past_local_environmental_context']} + + + + + sample_same_as + ${row['sample_same_as']} + + + + + sample_derived_from + ${row['sample_derived_from']} + + + + + sample_coordinator + ${row['sample_coordinator']} + + + + + sample_coordinator_affiliation + ${row['sample_coordinator_affiliation']} + + + + + sample_material_type + ${row['sample_material_type']} + + + + + + ${tag} + ${row[header]} + + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file