From 2b3c33895cb411de781ff4bfc8d1cc0d8ef18ca5 Mon Sep 17 00:00:00 2001 From: Sandeep Murthy Date: Tue, 12 May 2026 18:44:10 +0100 Subject: [PATCH 1/2] docs: add more Sphinx content, including option list CSV tables --- README.md | 12 ++++++++---- docs/index.rst | 11 ++++++----- docs/sources/{arc.rst => arc-schema.rst} | 19 ++++++++++--------- .../lists/conditions/comorbidities.rst | 11 +++++++++++ .../lists/conditions/complications.rst | 11 +++++++++++ docs/sources/lists/conditions/index.rst | 13 +++++++++++++ docs/sources/lists/conditions/sites.rst | 11 +++++++++++ docs/sources/lists/conditions/symptoms.rst | 11 +++++++++++ docs/sources/lists/demographics/countries.rst | 11 +++++++++++ docs/sources/lists/demographics/index.rst | 12 ++++++++++++ .../lists/demographics/occupations.rst | 11 +++++++++++ docs/sources/lists/demographics/race.rst | 11 +++++++++++ docs/sources/lists/drugs/antibiotics.rst | 11 +++++++++++ docs/sources/lists/drugs/anticoagulants.rst | 11 +++++++++++ docs/sources/lists/drugs/antifungals.rst | 11 +++++++++++ docs/sources/lists/drugs/antivirals.rst | 11 +++++++++++ .../lists/drugs/immunosuppressants.rst | 11 +++++++++++ docs/sources/lists/drugs/index.rst | 18 ++++++++++++++++++ docs/sources/lists/drugs/ivfluids.rst | 11 +++++++++++ docs/sources/lists/drugs/nsaids.rst | 11 +++++++++++ docs/sources/lists/drugs/steroids.rst | 11 +++++++++++ docs/sources/lists/drugs/types.rst | 11 +++++++++++ docs/sources/lists/followup/index.rst | 11 +++++++++++ docs/sources/lists/followup/outcome.rst | 11 +++++++++++ docs/sources/lists/followup/sequelae.rst | 11 +++++++++++ docs/sources/lists/inclusion/diseases.rst | 11 +++++++++++ docs/sources/lists/inclusion/index.rst | 10 ++++++++++ docs/sources/lists/lists.rst | 19 +++++++++++++++++++ docs/sources/lists/outcome/diseases.rst | 11 +++++++++++ docs/sources/lists/outcome/index.rst | 11 +++++++++++ docs/sources/lists/outcome/outcome.rst | 11 +++++++++++ docs/sources/lists/pathogens/all.rst | 11 +++++++++++ .../lists/pathogens/genomic-repository.rst | 11 +++++++++++ docs/sources/lists/pathogens/index.rst | 13 +++++++++++++ docs/sources/lists/pathogens/other.rst | 11 +++++++++++ docs/sources/lists/pathogens/sample-type.rst | 11 +++++++++++ ...ield-types.rst => special-field-types.rst} | 10 +++++++--- ...ariable-naming.rst => variable-naming.rst} | 2 +- 38 files changed, 414 insertions(+), 22 deletions(-) rename docs/sources/{arc.rst => arc-schema.rst} (73%) create mode 100644 docs/sources/lists/conditions/comorbidities.rst create mode 100644 docs/sources/lists/conditions/complications.rst create mode 100644 docs/sources/lists/conditions/index.rst create mode 100644 docs/sources/lists/conditions/sites.rst create mode 100644 docs/sources/lists/conditions/symptoms.rst create mode 100644 docs/sources/lists/demographics/countries.rst create mode 100644 docs/sources/lists/demographics/index.rst create mode 100644 docs/sources/lists/demographics/occupations.rst create mode 100644 docs/sources/lists/demographics/race.rst create mode 100644 docs/sources/lists/drugs/antibiotics.rst create mode 100644 docs/sources/lists/drugs/anticoagulants.rst create mode 100644 docs/sources/lists/drugs/antifungals.rst create mode 100644 docs/sources/lists/drugs/antivirals.rst create mode 100644 docs/sources/lists/drugs/immunosuppressants.rst create mode 100644 docs/sources/lists/drugs/index.rst create mode 100644 docs/sources/lists/drugs/ivfluids.rst create mode 100644 docs/sources/lists/drugs/nsaids.rst create mode 100644 docs/sources/lists/drugs/steroids.rst create mode 100644 docs/sources/lists/drugs/types.rst create mode 100644 docs/sources/lists/followup/index.rst create mode 100644 docs/sources/lists/followup/outcome.rst create mode 100644 docs/sources/lists/followup/sequelae.rst create mode 100644 docs/sources/lists/inclusion/diseases.rst create mode 100644 docs/sources/lists/inclusion/index.rst create mode 100644 docs/sources/lists/lists.rst create mode 100644 docs/sources/lists/outcome/diseases.rst create mode 100644 docs/sources/lists/outcome/index.rst create mode 100644 docs/sources/lists/outcome/outcome.rst create mode 100644 docs/sources/lists/pathogens/all.rst create mode 100644 docs/sources/lists/pathogens/genomic-repository.rst create mode 100644 docs/sources/lists/pathogens/index.rst create mode 100644 docs/sources/lists/pathogens/other.rst create mode 100644 docs/sources/lists/pathogens/sample-type.rst rename docs/sources/{arc-field-types.rst => special-field-types.rst} (95%) rename docs/sources/{arc-variable-naming.rst => variable-naming.rst} (99%) diff --git a/README.md b/README.md index b918827..5ca6d7b 100644 --- a/README.md +++ b/README.md @@ -59,7 +59,7 @@ This way, `arc.csv` serves not only as a **question bank**, but also as a **meta |-------------|-------------------------------------------------------------------------|------------------|-------|--------------|--------------------------|----------------|---------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------|-----------------------------|-------------------------------------------------------------|--------------------------------------|------------------|-------------------------------------| | Presentation | CO-MORBIDITIES AND RISK FACTORS: Existing prior to this current illness and is ongoing | comor_hypertensi | radio | Hypertension | 1, Yes \| 0, No \| 99, Unknown | Cardiovascular | Defined as elevated arterial blood pressure diagnosed clinically (systolic >140 mmHg and/or diastolic >90 mmHg), or treated with medication. | Indicate 'Yes' if this condition existed prior to admission with this current illness and remains an active medical condition. | SNOMED | 38341003, Hypertensive disorder, systemic arterial (disorder) | C0020538, Hypertensive disease | risk_factor_comor | COVID=1, Dengue=1, Mpox=1, H5Nx=1, ARI=1 | -### `lists/` +### `Lists/` A collection of option lists containing standardised reference tables (conditions, demographics, and drugs) that support different response types while ensuring adaptability and consistency in data capture and coding across studies. ## Data Capture Schema @@ -153,11 +153,11 @@ These modules provide shared variables applicable across multiple diseases, impr ## Files - - **Clinical Characterization XML:** This XML file provides a recommended configuration and structure for clinical characterization studies. It includes information about users, events, project settings, and functionality, serving as a reference for setting up clinical characterization studies. +- **Clinical Characterization XML:** This XML file provides a recommended configuration and structure for clinical characterization studies. It includes information about users, events, project settings, and functionality, serving as a reference for setting up clinical characterization studies. - - **ARC:** The "ARC" file is a machine-readable CSV (Comma-Separated Values) file that forms the core of ARC. It contains a comprehensive list of questions that can be asked in a CRF during outbreaks. Each question is defined with specific parameters, including variable names, coded answers, limits, types, skip logic, and more. +- **ARC:** The "ARC" file is a machine-readable CSV (Comma-Separated Values) file that forms the core of ARC. It contains a comprehensive list of questions that can be asked in a CRF during outbreaks. Each question is defined with specific parameters, including variable names, coded answers, limits, types, skip logic, and more. - - **Lists of Standardized Terms:** These files include predefined sets of standardized vocabulary used to describe and categorize various aspects of CRF answers. Standardized terms ensure consistency in data capture, covering items such as comorbidities, symptoms, and medications. +- **Lists of Standardized Terms:** These files include predefined sets of standardized vocabulary used to describe and categorize various aspects of CRF answers. Standardized terms ensure consistency in data capture, covering items such as comorbidities, symptoms, and medications. - **Metadata:** For each version of ARC, a version history file is included. This file contains pertinent information about changes made to ARC over time, allowing for easy tracking of modifications. Typical metadata includes the date of upload of the new version and a description of the changes made. @@ -183,6 +183,10 @@ If you want to use ARC for your research or study, follow these steps: 3. **Contributions**: While contributions to the document are limited to authorized users, you can open issues or discussions for questions, suggestions, or clarifications. +## ARC Documentation + +Key aspects of ARC, including the core schema, and response option lists, are also documented in HTML [here](https://isaric-arc.readthedocs.io/en/latest/index.html). + ## Contributors ### Conceptualization diff --git a/docs/index.rst b/docs/index.rst index b8efdcf..e2d064f 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -23,14 +23,15 @@ ARC is licensed under the open source compliant `MIT license `_ (also shown at the **bottom of this page**) of clinical and research questions. This file provides the standardized structure that ensures interoperability across studies and outbreak contexts. +The ARC schema is made available as a machine-readable `CSV `_ (also as a HTML table **at the bottom of this page**) of clinical and research questions. This file provides the standardized structure that ensures interoperability across studies and outbreak contexts. -Each row in the CSV represents a **variable** used in the Case Report Forms (CRFs). Variables include metadata that ensures **clarity, interoperability, and reusability** across contexts. For more details on variable naming conventions see :ref:`this `, and for details on the variable data types see :ref:`this `. +Each row in the CSV represents a **variable** used in the Case Report Forms (CRFs). Variables include metadata that ensures **clarity, interoperability, and reusability** across contexts. For more details on variable naming conventions see :ref:`this `, and for details on the variable data types see :ref:`this `. For every variable, the following fields are included: @@ -15,11 +15,11 @@ For every variable, the following fields are included: - **Section**: Subdivision within the form that groups related questions (e.g., *Co-morbidities and Risk Factors*,…). - **Type**: Format of the response field (e.g., ``radio``, ``checkbox``, ``text``, ``date``). - **Question**: Human-readable text shown to the data collector (e.g., *Hypertension*). -- **Answer Options**: Permissible responses to the question. These may reference predefined lists in ``/lists`` (e.g., +- **Answer Options**: Permissible responses to the question. These may reference predefined lists in ``/Lists`` (e.g., ``1, Yes | 0, No | 99, Unknown``). - **Validation**: Input rules for the response, such as numeric range or pattern restrictions. - **Minimum / Maximum**: Boundaries for numeric input when applicable. -- **List**: Links to option lists in ``/lists``. +- **List**: Links to option lists in ``/Lists``. - **Skip Logic**: Rules defining when the variable should be displayed, depending on other responses. - **Body System**: Physiological system the variable belongs to (e.g., *Cardiovascular*). - **Definition**: Description of the concept being captured, often linked to clinical definitions. @@ -35,9 +35,10 @@ The CSV serves not only as a **question bank**, but also as a **metadata diction - Mapping to standard vocabularies. - Adaptation for different diseases and study contexts. -.. literalinclude:: ../../ARC.csv - :encoding: latin-1 - :language: csv - :lineno-start: 1 - :emphasize-lines: 1 +The raw CSV is presented below as a HTML table - the display is cut off to the right but you can scroll across the table using the touchpad. +.. csv-table:: + :class: csv-table + :file: ../../ARC.csv + :header-rows: 1 + :width: 100% \ No newline at end of file diff --git a/docs/sources/lists/conditions/comorbidities.rst b/docs/sources/lists/conditions/comorbidities.rst new file mode 100644 index 0000000..bf200c0 --- /dev/null +++ b/docs/sources/lists/conditions/comorbidities.rst @@ -0,0 +1,11 @@ +.. _lists-conditions-comorbidities: + +============= +Comorbidities +============= + +.. csv-table:: + :class: csv-table + :file: ../../../../Lists/conditions/Comorbidities.csv + :header-rows: 1 + :width: 100% diff --git a/docs/sources/lists/conditions/complications.rst b/docs/sources/lists/conditions/complications.rst new file mode 100644 index 0000000..c3a6301 --- /dev/null +++ b/docs/sources/lists/conditions/complications.rst @@ -0,0 +1,11 @@ +.. _lists-conditions-complications: + +============= +Complications +============= + +.. csv-table:: + :class: csv-table + :file: ../../../../Lists/conditions/Complications.csv + :header-rows: 1 + :width: 100% diff --git a/docs/sources/lists/conditions/index.rst b/docs/sources/lists/conditions/index.rst new file mode 100644 index 0000000..a6d485b --- /dev/null +++ b/docs/sources/lists/conditions/index.rst @@ -0,0 +1,13 @@ +.. _lists-conditions-index: + +Conditions +========== + +.. toctree:: + :maxdepth: 1 + :caption: Contents: + + comorbidities + complications + sites + symptoms diff --git a/docs/sources/lists/conditions/sites.rst b/docs/sources/lists/conditions/sites.rst new file mode 100644 index 0000000..6ab16fc --- /dev/null +++ b/docs/sources/lists/conditions/sites.rst @@ -0,0 +1,11 @@ +.. _lists-conditions-sites: + +==== +Site +==== + +.. csv-table:: + :class: csv-table + :file: ../../../../Lists/conditions/Site.csv + :header-rows: 1 + :width: 100% diff --git a/docs/sources/lists/conditions/symptoms.rst b/docs/sources/lists/conditions/symptoms.rst new file mode 100644 index 0000000..efecd64 --- /dev/null +++ b/docs/sources/lists/conditions/symptoms.rst @@ -0,0 +1,11 @@ +.. _lists-conditions-symptoms: + +======== +Symptoms +======== + +.. csv-table:: + :class: csv-table + :file: ../../../../Lists/conditions/Symptoms.csv + :header-rows: 1 + :width: 100% diff --git a/docs/sources/lists/demographics/countries.rst b/docs/sources/lists/demographics/countries.rst new file mode 100644 index 0000000..07ab562 --- /dev/null +++ b/docs/sources/lists/demographics/countries.rst @@ -0,0 +1,11 @@ +.. _lists-demographics-countries: + +======= +Country +======= + +.. csv-table:: + :class: csv-table + :file: ../../../../Lists/demographics/Country.csv + :header-rows: 1 + :width: 100% diff --git a/docs/sources/lists/demographics/index.rst b/docs/sources/lists/demographics/index.rst new file mode 100644 index 0000000..a8cd936 --- /dev/null +++ b/docs/sources/lists/demographics/index.rst @@ -0,0 +1,12 @@ +.. _lists-demographics-index: + +Demographics +============ + +.. toctree:: + :maxdepth: 1 + :caption: Contents: + + countries + occupations + race diff --git a/docs/sources/lists/demographics/occupations.rst b/docs/sources/lists/demographics/occupations.rst new file mode 100644 index 0000000..c2fbea2 --- /dev/null +++ b/docs/sources/lists/demographics/occupations.rst @@ -0,0 +1,11 @@ +.. _lists-demographics-occupations: + +========== +Occupation +========== + +.. csv-table:: + :class: csv-table + :file: ../../../../Lists/demographics/Occupation.csv + :header-rows: 1 + :width: 100% diff --git a/docs/sources/lists/demographics/race.rst b/docs/sources/lists/demographics/race.rst new file mode 100644 index 0000000..7c88411 --- /dev/null +++ b/docs/sources/lists/demographics/race.rst @@ -0,0 +1,11 @@ +.. _lists-demographics-race: + +==== +Race +==== + +.. csv-table:: + :class: csv-table + :file: ../../../../Lists/demographics/Race.csv + :header-rows: 1 + :width: 100% diff --git a/docs/sources/lists/drugs/antibiotics.rst b/docs/sources/lists/drugs/antibiotics.rst new file mode 100644 index 0000000..ba2b304 --- /dev/null +++ b/docs/sources/lists/drugs/antibiotics.rst @@ -0,0 +1,11 @@ +.. _lists-drugs-antibiotics: + +=========== +Antibiotics +=========== + +.. csv-table:: + :class: csv-table + :file: ../../../../Lists/drugs/Antibiotics.csv + :header-rows: 1 + :width: 100% diff --git a/docs/sources/lists/drugs/anticoagulants.rst b/docs/sources/lists/drugs/anticoagulants.rst new file mode 100644 index 0000000..0ca2d48 --- /dev/null +++ b/docs/sources/lists/drugs/anticoagulants.rst @@ -0,0 +1,11 @@ +.. _lists-drugs-anticoagulants: + +============= +Anticoagulant +============= + +.. csv-table:: + :class: csv-table + :file: ../../../../Lists/drugs/Anticoagulant.csv + :header-rows: 1 + :width: 100% diff --git a/docs/sources/lists/drugs/antifungals.rst b/docs/sources/lists/drugs/antifungals.rst new file mode 100644 index 0000000..d5b3947 --- /dev/null +++ b/docs/sources/lists/drugs/antifungals.rst @@ -0,0 +1,11 @@ +.. _lists-drugs-antifungals: + +========== +Antifungal +========== + +.. csv-table:: + :class: csv-table + :file: ../../../../Lists/drugs/Antifungal.csv + :header-rows: 1 + :width: 100% diff --git a/docs/sources/lists/drugs/antivirals.rst b/docs/sources/lists/drugs/antivirals.rst new file mode 100644 index 0000000..68e82a7 --- /dev/null +++ b/docs/sources/lists/drugs/antivirals.rst @@ -0,0 +1,11 @@ +.. _lists-drugs-antivirals: + +========= +Antiviral +========= + +.. csv-table:: + :class: csv-table + :file: ../../../../Lists/drugs/Antiviral.csv + :header-rows: 1 + :width: 100% diff --git a/docs/sources/lists/drugs/immunosuppressants.rst b/docs/sources/lists/drugs/immunosuppressants.rst new file mode 100644 index 0000000..d305409 --- /dev/null +++ b/docs/sources/lists/drugs/immunosuppressants.rst @@ -0,0 +1,11 @@ +.. _lists-drugs-immunosuppressants: + +================== +Immunosuppressants +================== + +.. csv-table:: + :class: csv-table + :file: ../../../../Lists/drugs/Immunosuppressants.csv + :header-rows: 1 + :width: 100% diff --git a/docs/sources/lists/drugs/index.rst b/docs/sources/lists/drugs/index.rst new file mode 100644 index 0000000..90e5d26 --- /dev/null +++ b/docs/sources/lists/drugs/index.rst @@ -0,0 +1,18 @@ +.. _lists-drugs-index: + +Drugs +===== + +.. toctree:: + :maxdepth: 1 + :caption: Contents: + + antibiotics + anticoagulants + antifungals + antivirals + immunosuppressants + ivfluids + nsaids + steroids + types diff --git a/docs/sources/lists/drugs/ivfluids.rst b/docs/sources/lists/drugs/ivfluids.rst new file mode 100644 index 0000000..5818ed1 --- /dev/null +++ b/docs/sources/lists/drugs/ivfluids.rst @@ -0,0 +1,11 @@ +.. _lists-drugs-ivfluids: + +========= +IV Fluids +========= + +.. csv-table:: + :class: csv-table + :file: ../../../../Lists/drugs/IVfluids.csv + :header-rows: 1 + :width: 100% diff --git a/docs/sources/lists/drugs/nsaids.rst b/docs/sources/lists/drugs/nsaids.rst new file mode 100644 index 0000000..0f78285 --- /dev/null +++ b/docs/sources/lists/drugs/nsaids.rst @@ -0,0 +1,11 @@ +.. _lists-drugs-nsaids: + +======= +NS AIDs +======= + +.. csv-table:: + :class: csv-table + :file: ../../../../Lists/drugs/nsaids.csv + :header-rows: 1 + :width: 100% diff --git a/docs/sources/lists/drugs/steroids.rst b/docs/sources/lists/drugs/steroids.rst new file mode 100644 index 0000000..adb60c2 --- /dev/null +++ b/docs/sources/lists/drugs/steroids.rst @@ -0,0 +1,11 @@ +.. _lists-drugs-steroids: + +======== +Steroids +======== + +.. csv-table:: + :class: csv-table + :file: ../../../../Lists/drugs/Steroids.csv + :header-rows: 1 + :width: 100% diff --git a/docs/sources/lists/drugs/types.rst b/docs/sources/lists/drugs/types.rst new file mode 100644 index 0000000..c45fdec --- /dev/null +++ b/docs/sources/lists/drugs/types.rst @@ -0,0 +1,11 @@ +.. _lists-drugs-types: + +==== +Type +==== + +.. csv-table:: + :class: csv-table + :file: ../../../../Lists/drugs/Type.csv + :header-rows: 1 + :width: 100% diff --git a/docs/sources/lists/followup/index.rst b/docs/sources/lists/followup/index.rst new file mode 100644 index 0000000..fb03459 --- /dev/null +++ b/docs/sources/lists/followup/index.rst @@ -0,0 +1,11 @@ +.. _lists-followup-index: + +Follow Up +========= + +.. toctree:: + :maxdepth: 1 + :caption: Contents: + + outcome + sequelae diff --git a/docs/sources/lists/followup/outcome.rst b/docs/sources/lists/followup/outcome.rst new file mode 100644 index 0000000..7d97b87 --- /dev/null +++ b/docs/sources/lists/followup/outcome.rst @@ -0,0 +1,11 @@ +.. _lists-followup-outcomes: + +======= +Outcome +======= + +.. csv-table:: + :class: csv-table + :file: ../../../../Lists/followup/outcome.csv + :header-rows: 1 + :width: 100% diff --git a/docs/sources/lists/followup/sequelae.rst b/docs/sources/lists/followup/sequelae.rst new file mode 100644 index 0000000..6ec8db0 --- /dev/null +++ b/docs/sources/lists/followup/sequelae.rst @@ -0,0 +1,11 @@ +.. _lists-followup-sequelae: + +======== +Sequelae +======== + +.. csv-table:: + :class: csv-table + :file: ../../../../Lists/followup/sequelae.csv + :header-rows: 1 + :width: 100% diff --git a/docs/sources/lists/inclusion/diseases.rst b/docs/sources/lists/inclusion/diseases.rst new file mode 100644 index 0000000..2dba55d --- /dev/null +++ b/docs/sources/lists/inclusion/diseases.rst @@ -0,0 +1,11 @@ +.. _lists-inclusion-diseases: + +======== +Diseases +======== + +.. csv-table:: + :class: csv-table + :file: ../../../../Lists/inclusion/Diseases.csv + :header-rows: 1 + :width: 100% diff --git a/docs/sources/lists/inclusion/index.rst b/docs/sources/lists/inclusion/index.rst new file mode 100644 index 0000000..5322763 --- /dev/null +++ b/docs/sources/lists/inclusion/index.rst @@ -0,0 +1,10 @@ +.. _lists-inclusion-index: + +Inclusion +========= + +.. toctree:: + :maxdepth: 1 + :caption: Contents: + + diseases diff --git a/docs/sources/lists/lists.rst b/docs/sources/lists/lists.rst new file mode 100644 index 0000000..0343127 --- /dev/null +++ b/docs/sources/lists/lists.rst @@ -0,0 +1,19 @@ +.. _lists: + +Lists +===== + +`Option list CSVs `_, which are organised into several categories, can be accessed from the linked pages below. + +.. toctree:: + :maxdepth: 1 + :titlesonly: + :caption: Contents: + + conditions/index + demographics/index + drugs/index + followup/index + inclusion/index + outcome/index + pathogens/index diff --git a/docs/sources/lists/outcome/diseases.rst b/docs/sources/lists/outcome/diseases.rst new file mode 100644 index 0000000..0a70223 --- /dev/null +++ b/docs/sources/lists/outcome/diseases.rst @@ -0,0 +1,11 @@ +.. _lists-outcome-diseases: + +======== +Diseases +======== + +.. csv-table:: + :class: csv-table + :file: ../../../../Lists/outcome/Diseases.csv + :header-rows: 1 + :width: 100% diff --git a/docs/sources/lists/outcome/index.rst b/docs/sources/lists/outcome/index.rst new file mode 100644 index 0000000..79d7409 --- /dev/null +++ b/docs/sources/lists/outcome/index.rst @@ -0,0 +1,11 @@ +.. _lists-outcome-index: + +Outcome +======= + +.. toctree:: + :maxdepth: 1 + :caption: Contents: + + diseases + outcome diff --git a/docs/sources/lists/outcome/outcome.rst b/docs/sources/lists/outcome/outcome.rst new file mode 100644 index 0000000..c4db051 --- /dev/null +++ b/docs/sources/lists/outcome/outcome.rst @@ -0,0 +1,11 @@ +.. _lists-outcome-outcome: + +======= +Outcome +======= + +.. csv-table:: + :class: csv-table + :file: ../../../../Lists/outcome/Outcome.csv + :header-rows: 1 + :width: 100% diff --git a/docs/sources/lists/pathogens/all.rst b/docs/sources/lists/pathogens/all.rst new file mode 100644 index 0000000..9707c47 --- /dev/null +++ b/docs/sources/lists/pathogens/all.rst @@ -0,0 +1,11 @@ +.. _lists-pathogens-all: + +=== +All +=== + +.. csv-table:: + :class: csv-table + :file: ../../../../Lists/pathogens/All.csv + :header-rows: 1 + :width: 100% diff --git a/docs/sources/lists/pathogens/genomic-repository.rst b/docs/sources/lists/pathogens/genomic-repository.rst new file mode 100644 index 0000000..39eeaed --- /dev/null +++ b/docs/sources/lists/pathogens/genomic-repository.rst @@ -0,0 +1,11 @@ +.. _lists-pathogens-genomic-repository: + +================== +Genomic Repository +================== + +.. csv-table:: + :class: csv-table + :file: ../../../../Lists/pathogens/GenomicRepository.csv + :header-rows: 1 + :width: 100% diff --git a/docs/sources/lists/pathogens/index.rst b/docs/sources/lists/pathogens/index.rst new file mode 100644 index 0000000..6af2f5e --- /dev/null +++ b/docs/sources/lists/pathogens/index.rst @@ -0,0 +1,13 @@ +.. _lists-pathogens-index: + +Pathogens +========= + +.. toctree:: + :maxdepth: 1 + :caption: Contents: + + all + genomic-repository + other + sample-type diff --git a/docs/sources/lists/pathogens/other.rst b/docs/sources/lists/pathogens/other.rst new file mode 100644 index 0000000..184d676 --- /dev/null +++ b/docs/sources/lists/pathogens/other.rst @@ -0,0 +1,11 @@ +.. _lists-pathogens-other: + +===== +Other +===== + +.. csv-table:: + :class: csv-table + :file: ../../../../Lists/pathogens/Other.csv + :header-rows: 1 + :width: 100% diff --git a/docs/sources/lists/pathogens/sample-type.rst b/docs/sources/lists/pathogens/sample-type.rst new file mode 100644 index 0000000..2724fee --- /dev/null +++ b/docs/sources/lists/pathogens/sample-type.rst @@ -0,0 +1,11 @@ +.. _lists-pathogens-sample-type: + +=========== +Sample Type +=========== + +.. csv-table:: + :class: csv-table + :file: ../../../../Lists/pathogens/SampleType.csv + :header-rows: 1 + :width: 100% diff --git a/docs/sources/arc-field-types.rst b/docs/sources/special-field-types.rst similarity index 95% rename from docs/sources/arc-field-types.rst rename to docs/sources/special-field-types.rst index b1c232d..c57a36b 100644 --- a/docs/sources/arc-field-types.rst +++ b/docs/sources/special-field-types.rst @@ -1,7 +1,7 @@ -.. _arc-field-types: +.. _special-field-types: -ARC Special Field Types Documentation -===================================== +ARC Special Field Types +======================= This document provides a detailed explanation of the special field types used within the ISARIC ARC (Analysis and Research Compendium) framework to support dynamic, reusable, and semantically structured Case Report Forms (CRFs). These field types extend beyond standard REDCap functionality to enable complex logic, repeated entries, hierarchical lists, and units management. @@ -38,6 +38,7 @@ Example | Variable: ``inclu_disease`` | List source: `Lists/inclusion/Diseases.csv `__ +| :doc:`View list source as HTML Table ` BRIDGE Transformation ~~~~~~~~~~~~~~~~~~~~~ @@ -74,6 +75,7 @@ Example | Variable: ``comor_unlisted`` | List source: `Lists/conditions/Comorbidities.csv `__ +| :doc:`View list source as HTML Table ` .. _bridge-transformation-1: @@ -116,6 +118,7 @@ Example | Variable: ``demog_race`` | List source: `Lists/demographics/Race.csv `__ +| :doc:`View list source as HTML Table ` .. _bridge-transformation-2: @@ -228,5 +231,6 @@ Notes ----- - Lists are stored in the ARC GitHub repo under `/Lists/… `__ +- Lists can also be viewed as HTML tables :doc:`here ` - The transformation is handled automatically during CRF genration from `ISARIC BRIDGE `__ - These structures support modular, scalable, and interoperable CRFs diff --git a/docs/sources/arc-variable-naming.rst b/docs/sources/variable-naming.rst similarity index 99% rename from docs/sources/arc-variable-naming.rst rename to docs/sources/variable-naming.rst index e09a5d7..35d6ab5 100644 --- a/docs/sources/arc-variable-naming.rst +++ b/docs/sources/variable-naming.rst @@ -1,4 +1,4 @@ -.. _arc-variable-naming: +.. _variable-naming: ARC Variable Naming Conventions =============================== From 3092b6f0ddc247731fbebba9542d36cd37540007 Mon Sep 17 00:00:00 2001 From: Sandeep Murthy Date: Tue, 12 May 2026 19:11:36 +0100 Subject: [PATCH 2/2] docs: drop ethical ads sidebar --- docs/conf.py | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/docs/conf.py b/docs/conf.py index a73b91a..980b766 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -220,6 +220,16 @@ } +html_sidebars = { + "**": [ + "sidebar/scroll-start.html", + "sidebar/brand.html", + "sidebar/search.html", + "sidebar/navigation.html", + "sidebar/scroll-end.html", + ] +} + # Force pygments style in dark mode back to the light variant pygments_dark_style = "tango"