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Merge pull request #4 from MoseleyBioinformaticsLab/merge_enhancement
Merge enhancement
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‎.gitignore‎

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@@ -12,4 +12,6 @@ dist/
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coverage.xml
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.coverage
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htmlcov/
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README_old.rst
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README_old.rst
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testing_scratch/
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tests/testing_files/new_intermediate_results/

‎README.rst‎

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@@ -124,7 +124,7 @@ and use the example there to create it initially. The add_authors command can he
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with building the Authors section if you already have a csv file with author
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information. A good tool to help track down pesky JSON syntax errors is `here <https://csvjson.com/json_validator>`__.
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There are also examples in the `example_configs <https://github.com/MoseleyBioinformaticsLab/academic_tracker/tree/main/example_configs>`__
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directory of the GitHub repo. There are also more example in the supplemental
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directory of the GitHub repo. There are also more examples in the supplemental
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material of the paper https://doi.org/10.6084/m9.figshare.19412165.
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‎docs/api.rst‎

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:members:
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.. automodule:: academic_tracker.webio
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:members:
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.. automodule:: academic_tracker.emails_and_reports_helpers
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:members:
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‎docs/changelog.rst‎

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Change Log
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==========
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Version 2.0.0
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~~~~~~~~~~~~~
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Changes
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-------
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In the 1.0.0 version each source was queried in a certain order and if later sources found the
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same publicaiton as a previous one it was simply ignored. Now a best attempt is made to try and
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merge information from the previous source with information from later sources. An additional
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"queried_sources" attribute was added to the publication object created for each publication to
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indicate all of the sources where the publication was found. It is a list field, and each source
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is appended to it as it is found.
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Enhancements
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------------
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A "references" attribute was added to the publication object for each publication and the references
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for the publication will appear there if available. It is a list of objects that have the attributes
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"citation", "title", "PMID", "PMCID", and "DOI". Fields that can't be determined will have a null value.
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More information is able to be obtained from PubMed, such as DOI author affiliations, and author ORCIDs.
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Collective authors can now be specified and are handled appropriately when present on information from
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queried sources.
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All new publication attributes were added to the reporting and the documentation updated.
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The raw queries from each source can now be saved using the --save-all-queries option. An "all_results.json"
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file will be saved in the output if the option is given.
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The --keep-duplicates option was added to reference_search. This allows the user to force the search
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not to drop what it deems as duplicates. The default is that they are still dropped automatically, but
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this option allows for an override when the program thinks, incorrectly, that 2 references are the same.
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Bug Fixes
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---------
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Crossref publication dates will now have day and month when available. A bug made it so only the year
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was captured even if month and day were available.
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‎docs/index.rst‎

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api
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license
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todo
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changelog
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Indices and tables

‎docs/jsonschema.rst‎

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The first_name and last_name attributes are for the author's first and last names
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respectively, and are used to validate that the author under search is the same
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as the queried author.
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as the queried author. There is a special type of author known as collective authors.
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These are not individuals, but are instead a collective and are published that way.
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Use the collective_name attribute to indicate that an author is a collective. This
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attribute takes priority, so if it is present the author will be treated as a collective
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author even if they have first_name and last_name attributes.
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pubmed_name_search is used as the query string when querying sources. This is so
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the user can specify exactly what to query rather than simply querying the first
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Validating Schema
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-----------------
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.. code-block:: console
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{
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"$schema": "https://json-schema.org/draft/2020-12/schema",
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"title": "Configuration JSON",
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"description": "Input file that contains information for how the program should run.",
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"type": "object",
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"properties": {
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"project_descriptions" : {
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"type": "object",
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"minProperties": 1,
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"additionalProperties": {
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"type":"object",
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"properties":{
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"grants": {"type": "array", "minItems":1, "items": {"type": "string", "minLength": 1}},
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"cutoff_year": {"type": "integer"},
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"affiliations": {"type": "array", "minItems":1, "items": {"type": "string", "minLength": 1}},
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"project_report": {"type": "object",
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"properties":{
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"columns": {"type": "object",
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"minProperties":1,
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"additionalProperties": {"type": "string", "minLength":1}},
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"sort": {"type": "array", "uniqueItems":True, "items": {"type": "string", "minLength":1}, "minItems":1},
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"separator":{"type":"string", "maxLength":1, "minLength":1},
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"column_order":{"type":"array", "uniqueItems":True, "items": {"type": "string", "minLength":1}, "minItems":1},
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"file_format":{"type":"string", "enum":["csv", "xlsx"]},
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"filename":{"type":"string", "minLength":1},
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"template": {"type": "string", "minLength":1},
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"from_email": {"type": "string", "format": "email"},
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"cc_email": {"type": "array", "items": {"type": "string", "format": "email"}},
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"to_email": {"type": "array", "items": {"type": "string", "format": "email"}},
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"email_body": {"type": "string", "minLength":1},
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"email_subject": {"type": "string", "minLength":1},},
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"dependentRequired":{
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"from_email": ["email_body", "email_subject"],
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"to_email": ["from_email", "email_body", "email_subject"]}},
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"collaborator_report": {"type": "object",
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"properties":{
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"columns": {"type": "object",
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"minProperties":1,
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"additionalProperties": {"type": "string", "minLength":1}},
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"sort": {"type": "array", "uniqueItems":True, "items": {"type": "string", "minLength":1}, "minItems":1},
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"separator":{"type":"string", "maxLength":1, "minLength":1},
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"column_order":{"type":"array", "uniqueItems":True, "items": {"type": "string", "minLength":1}, "minItems":1},
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"file_format":{"type":"string", "enum":["csv", "xlsx"]},
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"filename":{"type":"string", "minLength":1},
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"template": {"type": "string", "minLength":1},
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"from_email": {"type": "string", "format": "email"},
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"cc_email": {"type": "array", "items": {"type": "string", "format": "email"}},
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"to_email": {"type": "array", "items": {"type": "string", "format": "email"}},
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"email_body": {"type": "string", "minLength":1},
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"email_subject": {"type": "string", "minLength":1},},
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"dependentRequired":{
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"from_email": ["email_body", "email_subject"],
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"to_email": ["from_email", "email_body", "email_subject"]},},
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"authors": {"type": "array", "minItems":1, "items": {"type": "string", "minLength": 1}},
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},
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"required": ["grants", "affiliations"]
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}
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},
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"ORCID_search" : {"type":"object",
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"properties": {
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"ORCID_key": {"type": "string", "minLength":1},
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"ORCID_secret": {"type": "string", "minLength":1}},
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"required": ["ORCID_key", "ORCID_secret"]},
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"PubMed_search" : {"type":"object",
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"properties": {
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"PubMed_email": {"type": "string", "format":"email"}},
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"required":["PubMed_email"]},
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"Crossref_search" : {"type":"object",
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"properties": {
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"mailto_email": {"type": "string", "format":"email"}},
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"required":["mailto_email"]},
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"summary_report" : {"type": "object",
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"properties":{
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"columns": {"type": "object",
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"minProperties":1,
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"additionalProperties": {"type": "string", "minLength":1}},
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"sort": {"type": "array", "uniqueItems":True, "items": {"type": "string", "minLength":1}, "minItems":1},
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"separator":{"type":"string", "maxLength":1, "minLength":1},
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"column_order":{"type":"array", "uniqueItems":True, "items": {"type": "string", "minLength":1}, "minItems":1},
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"file_format":{"type":"string", "enum":["csv", "xlsx"]},
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"filename":{"type":"string", "minLength":1},
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"template": {"type": "string", "minLength":1},
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"from_email": {"type": "string", "format": "email"},
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"cc_email": {"type": "array", "items": {"type": "string", "format": "email"}},
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"to_email": {"type": "array", "items": {"type": "string", "format": "email"}},
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"email_body": {"type": "string", "minLength":1},
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"email_subject": {"type": "string", "minLength":1},},
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"dependentRequired":{
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"from_email": ["email_body", "email_subject", "to_email"]}},
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"Authors" : { "type": "object",
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"minProperties": 1,
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"additionalProperties": {
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"type": "object",
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"properties":{
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"first_name": {"type": "string", "minLength":1},
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"last_name":{"type": "string", "minLength":1},
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"pubmed_name_search": {"type": "string", "minLength":1},
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"email":{"type": "string", "format":"email"},
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"ORCID":{"type": "string", "pattern":"^\d{4}-\d{4}-\d{4}-\d{3}[0,1,2,3,4,5,6,7,8,9,X]$"},
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"grants": {"type": "array", "minItems":1, "items": {"type": "string", "minLength": 1}},
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"cutoff_year": {"type": "integer"},
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"affiliations": {"type": "array", "minItems":1, "items": {"type": "string", "minLength": 1}},
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"scholar_id": {"type": "string", "minLength":1},
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"project_report": {"type": "object",
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"properties":{
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"columns": {"type": "object",
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"minProperties":1,
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"additionalProperties": {"type": "string", "minLength":1}},
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"sort": {"type": "array", "uniqueItems":True, "items": {"type": "string", "minLength":1}, "minItems":1},
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"separator":{"type":"string", "maxLength":1, "minLength":1},
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"column_order":{"type":"array", "uniqueItems":True, "items": {"type": "string", "minLength":1}, "minItems":1},
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"file_format":{"type":"string", "enum":["csv", "xlsx"]},
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"filename":{"type":"string", "minLength":1},
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"template": {"type": "string", "minLength":1},
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"from_email": {"type": "string", "format": "email"},
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"cc_email": {"type": "array", "items": {"type": "string", "format": "email"}},
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"to_email": {"type": "array", "items": {"type": "string", "format": "email"}},
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"email_body": {"type": "string", "minLength":1},
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"email_subject": {"type": "string", "minLength":1},},
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"dependentRequired":{
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"from_email": ["email_body", "email_subject"],
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"to_email": ["from_email", "email_body", "email_subject"]}},
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"collaborator_report": {"type": "object",
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"properties":{
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"columns": {"type": "object",
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"minProperties":1,
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"additionalProperties": {"type": "string", "minLength":1}},
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"sort": {"type": "array", "uniqueItems":True, "items": {"type": "string", "minLength":1}, "minItems":1},
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"separator":{"type":"string", "maxLength":1, "minLength":1},
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"column_order":{"type":"array", "uniqueItems":True, "items": {"type": "string", "minLength":1}, "minItems":1},
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"file_format":{"type":"string", "enum":["csv", "xlsx"]},
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"filename":{"type":"string", "minLength":1},
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"template": {"type": "string", "minLength":1},
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"from_email": {"type": "string", "format": "email"},
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"cc_email": {"type": "array", "items": {"type": "string", "format": "email"}},
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"to_email": {"type": "array", "items": {"type": "string", "format": "email"}},
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"email_body": {"type": "string", "minLength":1},
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"email_subject": {"type": "string", "minLength":1},},
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"dependentRequired":{
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"from_email": ["email_body", "email_subject"],
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"to_email": ["from_email", "email_body", "email_subject"]},},
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},
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"required" : ["first_name", "last_name", "pubmed_name_search"]
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}
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}
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},
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"required": ["project_descriptions", "ORCID_search", "PubMed_search", "Crossref_search", "Authors"]
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}
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.. literalinclude:: ../src/academic_tracker/tracker_schema.py
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:start-at: config_schema
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:end-before: ## config_end
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:language: none
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