🎨 order imports, specify relative paths

- in docs the full path will be set based on the directory

Author: enryH

docs/example_data/Earth_microbiome_vuegen_demo_notebook/Earth_microbiome_vuegen_demo_notebook_config.yaml

@@ -1,4 +1,5 @@
 report:
+  title: Earth Microbiome Vuegen Demo Notebook
   description: "The Earth Microbiome Project (EMP) is a systematic attempt to characterize\
     \ global microbial taxonomic and functional diversity for the benefit of the planet\
     \ and humankind. \n  It aimed to sample the Earth\u2019s microbial communities\
@@ -10,152 +11,130 @@ report:
     \ future studies, fostering increasingly complete characterization of Earth\u2019\
     s microbial diversity.\n  \n  You can find more information about the Earth Microbiome\
     \ Project at https://earthmicrobiome.org/ and in the [original article](https://www.nature.com/articles/nature24621).\n"
-  graphical_abstract: ./example_data/Earth_microbiome_vuegen_demo_notebook/emp_logo.png
-  logo: ./example_data/Earth_microbiome_vuegen_demo_notebook/emp_logo.png
-  title: Earth Microbiome Vuegen Demo Notebook
+  graphical_abstract: ''
+  logo: ''
 sections:
-- description: This section contains the exploratory data analysis of the Earth Microbiome
-    Project (EMP) dataset.
+- title: Exploratory Data Analysis
+  description: ''
   subsections:
-  - components:
-    - caption: ''
-      component_type: dataframe
-      delimiter: ','
-      description: ''
-      file_format: csv
-      file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/docs/example_data/Earth_microbiome_vuegen_demo_notebook/1_Exploratory_data_analysis/1_sample_exploration/1_metadata_random_subset.csv
-      title: Metadata Random Subset
-    - caption: ''
-      component_type: plot
-      description: ''
-      file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/docs/example_data/Earth_microbiome_vuegen_demo_notebook/1_Exploratory_data_analysis/1_sample_exploration/2_animal_samples_map.png
-      plot_type: static
-      title: Animal Samples Map
-    - caption: ''
-      component_type: plot
-      description: ''
-      file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/docs/example_data/Earth_microbiome_vuegen_demo_notebook/1_Exploratory_data_analysis/1_sample_exploration/3_plant_samples_map.json
-      plot_type: plotly
-      title: Plant Samples Map
-    - caption: ''
-      component_type: plot
-      description: ''
-      file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/docs/example_data/Earth_microbiome_vuegen_demo_notebook/1_Exploratory_data_analysis/1_sample_exploration/4_saline_samples_map.json
-      plot_type: altair
-      title: Saline Samples Map
-    - caption: Pairwise scatter plots of available physicochemical metadat are shown
-        for temperature, salinity, oxygen, and pH, and for phosphate, nitrate, and
-        ammonium
-      component_type: plot
-      description: ''
-      file_path: https://raw.githubusercontent.com/biocore/emp/master/methods/images/figureED1_physicochemical.png
-      plot_type: static
-      title: Physicochemical properties of the EMP samples
+  - title: Sample Exploration
     description: ''
-    title: Sample Exploration
-  title: Exploratory Data Analysis
-- description: ''
+    components:
+    - title: Metadata Random Subset
+      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/1_Exploratory_data_analysis/1_sample_exploration/1_metadata_random_subset.csv
+      description: ''
+      caption: ''
+      component_type: DATAFRAME
+      file_format: CSV
+      delimiter: ','
+    - title: Animal Samples Map
+      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/1_Exploratory_data_analysis/1_sample_exploration/2_animal_samples_map.png
+      description: ''
+      caption: ''
+      component_type: PLOT
+      plot_type: STATIC
+    - title: Plant Samples Map
+      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/1_Exploratory_data_analysis/1_sample_exploration/3_plant_samples_map.json
+      description: ''
+      caption: ''
+      component_type: PLOT
+      plot_type: PLOTLY
+    - title: Saline Samples Map
+      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/1_Exploratory_data_analysis/1_sample_exploration/4_saline_samples_map.json
+      description: ''
+      caption: ''
+      component_type: PLOT
+      plot_type: ALTAIR
+- title: Metagenomics
+  description: ''
   subsections:
-  - components:
-    - caption: ''
-      component_type: plot
-      description: ''
-      file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/docs/example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/1_alpha_diversity/1_alpha_diversity_host_associated_samples.png
-      plot_type: static
-      title: Alpha Diversity Host Associated Samples
-    - caption: ''
-      component_type: plot
-      description: ''
-      file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/docs/example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/1_alpha_diversity/2_alpha_diversity_free_living_samples.json
-      plot_type: plotly
-      title: Alpha Diversity Free Living Samples
-    description: This subsection contains the alpha diversity analysis of the EMP
-      dataset.
-    title: Alpha Diversity
-  - components:
-    - caption: ''
-      component_type: plot
-      description: ''
-      file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/docs/example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/2_average_copy_number/1_average_copy_number_emp_ontology_level2.png
-      plot_type: static
-      title: Average Copy Number Emp Ontology Level2
-    - caption: ''
-      component_type: plot
-      description: ''
-      file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/docs/example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/2_average_copy_number/2_average_copy_number_emp_ontology_level3.json
-      plot_type: plotly
-      title: Average Copy Number Emp Ontology Level3
+  - title: Alpha Diversity
     description: ''
-    title: Average Copy Number
-  - components:
-    - caption: ''
-      component_type: dataframe
-      delimiter: ','
-      description: ''
-      file_format: csv
-      file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/docs/example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/3_nestedness/1_nestedness_random_subset.csv
-      title: Nestedness Random Subset
-    - caption: ''
-      component_type: plot
-      description: ''
-      file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/docs/example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/3_nestedness/2_all_samples.json
-      plot_type: plotly
-      title: All Samples
-    - caption: ''
-      component_type: plot
-      description: ''
-      file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/docs/example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/3_nestedness/3_plant_samples.json
-      plot_type: plotly
-      title: Plant Samples
-    - caption: ''
-      component_type: plot
-      description: ''
-      file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/docs/example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/3_nestedness/4_animal_samples.png
-      plot_type: static
-      title: Animal Samples
-    - caption: ''
-      component_type: plot
-      description: ''
-      file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/docs/example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/3_nestedness/5_non_saline_samples.png
-      plot_type: static
-      title: Non Saline Samples
+    components:
+    - title: Alpha Diversity Host Associated Samples
+      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/1_alpha_diversity/1_alpha_diversity_host_associated_samples.png
+      description: ''
+      caption: ''
+      component_type: PLOT
+      plot_type: STATIC
+    - title: Alpha Diversity Free Living Samples
+      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/1_alpha_diversity/2_alpha_diversity_free_living_samples.json
+      description: ''
+      caption: ''
+      component_type: PLOT
+      plot_type: PLOTLY
+  - title: Average Copy Number
     description: ''
-    title: Nestedness
-  - components:
-    - caption: a) Environment distribution in all genera and 400 randomly chosen tag
-        sequence. b) and c) Shannon entropy within each taxonomic group.
-      component_type: plot
-      description: ''
-      file_path: https://raw.githubusercontent.com/biocore/emp/master/methods/images/figure4_entropy.png
-      plot_type: static
-      title: Specificity of sequences and higher taxonomic groups for environment
-    description: This subsection contains the Shannon entropy analysis of the EMP
-      dataset.
-    title: Shanon entropy analysis
-  title: Metagenomics
-- description: ''
-  subsections:
-  - components:
-    - caption: ''
-      component_type: dataframe
-      delimiter: ','
+    components:
+    - title: Average Copy Number Emp Ontology Level2
+      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/2_average_copy_number/1_average_copy_number_emp_ontology_level2.png
+      description: ''
+      caption: ''
+      component_type: PLOT
+      plot_type: STATIC
+    - title: Average Copy Number Emp Ontology Level3
+      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/2_average_copy_number/2_average_copy_number_emp_ontology_level3.json
+      description: ''
+      caption: ''
+      component_type: PLOT
+      plot_type: PLOTLY
+  - title: Nestedness
+    description: ''
+    components:
+    - title: Nestedness Random Subset
+      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/3_nestedness/1_nestedness_random_subset.csv
       description: ''
-      file_format: csv
-      file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/docs/example_data/Earth_microbiome_vuegen_demo_notebook/3_Network_analysis/1_phyla_association_networks/1_phyla_counts_subset.csv
-      title: Phyla Counts Subset
-    - caption: ''
-      component_type: plot
-      csv_network_format: edgelist
-      description: ''
-      file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/docs/example_data/Earth_microbiome_vuegen_demo_notebook/3_Network_analysis/1_phyla_association_networks/2_phyla_correlation_network_with_0.5_threshold_edgelist.csv
-      plot_type: interactive_network
-      title: Phyla Correlation Network With 0.5 Threshold Edgelist
-    - caption: ''
-      component_type: plot
-      description: ''
-      file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/docs/example_data/Earth_microbiome_vuegen_demo_notebook/3_Network_analysis/1_phyla_association_networks/3_phyla_correlation_network_with_0.5_threshold.png
-      plot_type: static
-      title: Phyla Correlation Network With 0.5 Threshold
+      caption: ''
+      component_type: DATAFRAME
+      file_format: CSV
+      delimiter: ','
+    - title: All Samples
+      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/3_nestedness/2_all_samples.json
+      description: ''
+      caption: ''
+      component_type: PLOT
+      plot_type: PLOTLY
+    - title: Plant Samples
+      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/3_nestedness/3_plant_samples.json
+      description: ''
+      caption: ''
+      component_type: PLOT
+      plot_type: PLOTLY
+    - title: Animal Samples
+      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/3_nestedness/4_animal_samples.png
+      description: ''
+      caption: ''
+      component_type: PLOT
+      plot_type: STATIC
+    - title: Non Saline Samples
+      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/3_nestedness/5_non_saline_samples.png
+      description: ''
+      caption: ''
+      component_type: PLOT
+      plot_type: STATIC
+- title: Network Analysis
+  description: ''
+  subsections:
+  - title: Phyla Association Networks
     description: ''
-    title: Phyla Association Networks
-  title: Network Analysis
+    components:
+    - title: Phyla Counts Subset
+      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/3_Network_analysis/1_phyla_association_networks/1_phyla_counts_subset.csv
+      description: ''
+      caption: ''
+      component_type: DATAFRAME
+      file_format: CSV
+      delimiter: ','
+    - title: Phyla Correlation Network With 0.5 Threshold Edgelist
+      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/3_Network_analysis/1_phyla_association_networks/2_phyla_correlation_network_with_0.5_threshold_edgelist.csv
+      description: ''
+      caption: ''
+      component_type: PLOT
+      plot_type: INTERACTIVE_NETWORK
+      csv_network_format: EDGELIST
+    - title: Phyla Correlation Network With 0.5 Threshold
+      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/3_Network_analysis/1_phyla_association_networks/3_phyla_correlation_network_with_0.5_threshold.png
+      description: ''
+      caption: ''
+      component_type: PLOT
+      plot_type: STATIC

vuegen/config_manager.py

@@ -1,6 +1,6 @@
-import logging
-import os   
 import json
+import logging
+import os
 from pathlib import Path
 from typing import Dict, List, Optional, Tuple, Union