diff --git a/medcat-trainer/.readthedocs.yaml b/medcat-trainer/.readthedocs.yaml index 4bea1918f..9880b16c9 100644 --- a/medcat-trainer/.readthedocs.yaml +++ b/medcat-trainer/.readthedocs.yaml @@ -5,13 +5,19 @@ version: 2 build: - os: ubuntu-20.04 + os: "ubuntu-24.04" tools: - python: "3.9" + python: "3.13" + jobs: + pre_create_environment: + - cd medcat-trainer/docs + - asdf plugin add uv + - asdf install uv latest + - asdf global uv latest + create_environment: + - uv venv "${READTHEDOCS_VIRTUALENV_PATH}" + install: + - cd medcat-trainer/docs && UV_PROJECT_ENVIRONMENT="${READTHEDOCS_VIRTUALENV_PATH}" uv sync --frozen -sphinx: - configuration: medcat-trainer/docs/conf.py - -python: - install: - - requirements: medcat-trainer/docs/requirements.txt +mkdocs: + configuration: medcat-trainer/mkdocs.yml \ No newline at end of file diff --git a/medcat-trainer/docs/Makefile b/medcat-trainer/docs/Makefile deleted file mode 100644 index d4bb2cbb9..000000000 --- a/medcat-trainer/docs/Makefile +++ /dev/null @@ -1,20 +0,0 @@ -# Minimal makefile for Sphinx documentation -# - -# You can set these variables from the command line, and also -# from the environment for the first two. -SPHINXOPTS ?= -SPHINXBUILD ?= sphinx-build -SOURCEDIR = . -BUILDDIR = _build - -# Put it first so that "make" without argument is like "make help". -help: - @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) - -.PHONY: help Makefile - -# Catch-all target: route all unknown targets to Sphinx using the new -# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). -%: Makefile - @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/medcat-trainer/docs/annotator_guide.md b/medcat-trainer/docs/annotator_guide.md index 32e659031..686441ad1 100644 --- a/medcat-trainer/docs/annotator_guide.md +++ b/medcat-trainer/docs/annotator_guide.md @@ -71,6 +71,9 @@ The sidebar shows details for the currently selected concept, including: If enabled by project settings, a **Comment** field is also available. +!!! tip + If the details are not showing in the sidebar after you've selected one, the issue is likely with an unfinished Project setup. See the section for "Concept lookup index (Solr import)" in the [Project Creation and Management Guide](project_admin.md) for details. + ## Meta annotations and relations Depending on project configuration: diff --git a/medcat-trainer/docs/conf.py b/medcat-trainer/docs/conf.py deleted file mode 100644 index bdd55355a..000000000 --- a/medcat-trainer/docs/conf.py +++ /dev/null @@ -1,88 +0,0 @@ -# Configuration file for the Sphinx documentation builder. -# -# This file only contains a selection of the most common options. For a full -# list see the documentation: -# https://www.sphinx-doc.org/en/master/usage/configuration.html - -# -- Path setup -------------------------------------------------------------- - -# If extensions (or modules to document with autodoc) are in another directory, -# add these directories to sys.path here. If the directory is relative to the -# documentation root, use os.path.abspath to make it absolute, like shown here. -# -import os -import sys -sys.path.insert(0, os.path.abspath('.')) - - -# -- Project information ----------------------------------------------------- - -project = 'MedCATtrainer' -copyright = '2022, CogStack Org' -author = 'CogStack Org' - -# The full version, including alpha/beta/rc tags -release = 'latest' - - -# -- General configuration --------------------------------------------------- - -# Add any Sphinx extension module names here, as strings. They can be -# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom -# ones. -extensions = [ - 'sphinx_rtd_theme', - 'sphinx.ext.autodoc', - 'myst_parser', - 'sphinx.ext.inheritance_diagram', - 'autoapi.extension', -] - -autoapi_type = 'python' -autoapi_dirs = ['../webapp/api/api'] -autodoc_typehints = 'description' -autoapi_template_dir = '_templates/autoapi_templates' - - -# Add any paths that contain templates here, relative to this directory. -templates_path = ['_templates'] - -# List of patterns, relative to source directory, that match files and -# directories to ignore when looking for source files. -# This pattern also affects html_static_path and html_extra_path. -exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] - -source_suffix = { - '.rst': 'restructuredtext', - '.txt': 'markdown', - '.md': 'markdown', -} - -# -- Options for HTML output ------------------------------------------------- - -# The theme to use for HTML and HTML Help pages. See the documentation for -# a list of builtin themes. -# -html_theme = 'sphinx_rtd_theme' - -# Add any paths that contain custom static files (such as style sheets) here, -# relative to this directory. They are copied after the builtin static files, -# so a file named "default.css" will overwrite the builtin "default.css". -html_static_path = ['_static'] - -html_css_files = [ - 'css/overrides.css' -] - -def autoapi_skip_member(app, what, name, obj, skip, options): - # skip: - # log class attributes - # 'private' methods, attributes, functions - exclude = (what == 'attribute' and name == 'log') or \ - (name.startswith('_') and not name.startswith('__')) - return exclude - - -def setup(app): - """Add autoapi-skip-member.""" - app.connect('autoapi-skip-member', autoapi_skip_member) diff --git a/medcat-trainer/docs/demo_page.md b/medcat-trainer/docs/demo_page.md index 3fd397c22..7571d40bb 100644 --- a/medcat-trainer/docs/demo_page.md +++ b/medcat-trainer/docs/demo_page.md @@ -17,8 +17,8 @@ It does **not** persist annotation decisions like a project workflow does. 1. Select a **Model Pack**. 2. Optionally add CUI filters: - - pick concepts from the concept picker, or - - paste a comma-separated CUI list. + - pick concepts from the concept picker, or + - paste a comma-separated CUI list. 3. Optionally enable **Include sub-concepts**. 4. Enter or paste free text. diff --git a/medcat-trainer/docs/main.md b/medcat-trainer/docs/index.md similarity index 73% rename from medcat-trainer/docs/main.md rename to medcat-trainer/docs/index.md index e06bd377f..685cd513c 100644 --- a/medcat-trainer/docs/main.md +++ b/medcat-trainer/docs/index.md @@ -1,4 +1,4 @@ -# Medical oncept Annotation Tool Trainer +# Medical Concept Annotation Tool Trainer MedCATtrainer is a web application for creating, validating, and improving MedCAT concept annotation models on biomedical or clinical text. @@ -10,15 +10,15 @@ review-only workflows (collect annotations without changing the model). - Build annotation projects from CSV/XLSX datasets. - Use either: - - a **Model Pack** (recommended), or - - a **Concept DB + Vocabulary** pair. + - a **Model Pack** (recommended), or + - a **Concept DB + Vocabulary** pair. - Optionally use a **remote MedCAT model service** for document preparation. - Collect concept-level labels: - - Correct - - Incorrect - - Alternative concept - - Terminate - - Irrelevant + - Correct + - Incorrect + - Alternative concept + - Terminate + - Irrelevant - Collect optional **meta annotations** and **relation annotations**. - Use **Project Groups** for multi-annotator setups. - Run **metrics reports** across one or more compatible projects. @@ -27,9 +27,9 @@ review-only workflows (collect annotations without changing the model). ## Typical workflow 1. Install and configure MedCATtrainer. -2. Create users and upload model artifacts (Model Pack or CDB/Vocab). -3. Create a project and assign annotators. -4. Annotate and submit documents. +2. Create users and upload model artifacts (Model Pack or CDB/Vocab). [Administrator Setup](admin_setup.md) +3. Create a project and assign annotators. [Annotation Project Creation and Management](project_admin.md) +4. Annotate and submit documents. [Annotator Guide](annotator_guide.md) 5. Export annotations and evaluate with the metrics tools. ## Documentation map diff --git a/medcat-trainer/docs/index.rst b/medcat-trainer/docs/index.rst deleted file mode 100644 index b7758d22c..000000000 --- a/medcat-trainer/docs/index.rst +++ /dev/null @@ -1,31 +0,0 @@ -.. MedCATtrainer documentation master file, created by - sphinx-quickstart on Fri Feb 18 17:02:13 2022. - You can adapt this file completely to your liking, but it should at least - contain the root `toctree` directive. - -Welcome to MedCATtrainer's documentation! -========================================= - -.. toctree:: - :maxdepth: 2 - :caption: Contents: - - main.md - installation.md - admin_setup.md - project_admin.md - project_group_admin.md - demo_page.md - annotator_guide.md - meta_annotations.md - advanced_usage.md - maintenance.md - client.md - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/medcat-trainer/docs/installation.md b/medcat-trainer/docs/installation.md index 2eda1c2a9..47fbed688 100644 --- a/medcat-trainer/docs/installation.md +++ b/medcat-trainer/docs/installation.md @@ -1,5 +1,13 @@ # Installation +The steps to setup Medcat trainer are as follows: + +1. Run MedCAT Trainer with Docker or Helm +2. Setup the Administrator user with [Administrator Setup](admin_setup.md) +3. Configure annotations Projects + +This page details the initial running of the application with Docker + MedCATtrainer is packaged as a Docker Compose deployment with three core services: @@ -61,6 +69,7 @@ Host-level Compose variables (for example port overrides) can be set by copying | Variable | Description | |---|---| +| `CSRF_TRUSTED_ORIGINS` | Allowed origins to access the admin panel. Mandatory to set if you expose the app over a different URL or port (default `'http://127.0.0.1:8001', 'http://localhost:8001'`). | | `MCTRAINER_PORT` | Host port for the web UI/API (default `8001`). | | `SOLR_PORT` | Host port for Solr admin (default `8983`). | | `MEDCAT_CONFIG_FILE` | MedCAT config file path inside the container. | @@ -129,3 +138,6 @@ An example compose file is available at startup logs. - **Concept picker empty**: confirm Solr is running and concepts were imported for the selected CDB. + +## Next Steps +Now that medcat trainer is installed and running, proceed to [Administrator Setup](admin_setup.md) to create the Admin user. \ No newline at end of file diff --git a/medcat-trainer/docs/maintenance.md b/medcat-trainer/docs/maintenance.md index 6b25dcf4e..ee2290cc0 100644 --- a/medcat-trainer/docs/maintenance.md +++ b/medcat-trainer/docs/maintenance.md @@ -36,8 +36,8 @@ The backup scripts are SQLite-focused (`DB_ENGINE=sqlite3`). - A backup is taken on startup before migrations. - A scheduled backup job also runs regularly. - Backup location is controlled by: - - `DB_PATH` - - `DB_BACKUP_DIR` + - `DB_PATH` + - `DB_BACKUP_DIR` ### Restore process diff --git a/medcat-trainer/docs/make.bat b/medcat-trainer/docs/make.bat deleted file mode 100644 index 8084272b4..000000000 --- a/medcat-trainer/docs/make.bat +++ /dev/null @@ -1,35 +0,0 @@ -@ECHO OFF - -pushd %~dp0 - -REM Command file for Sphinx documentation - -if "%SPHINXBUILD%" == "" ( - set SPHINXBUILD=sphinx-build -) -set SOURCEDIR=. -set BUILDDIR=_build - -if "%1" == "" goto help - -%SPHINXBUILD% >NUL 2>NUL -if errorlevel 9009 ( - echo. - echo.The 'sphinx-build' command was not found. Make sure you have Sphinx - echo.installed, then set the SPHINXBUILD environment variable to point - echo.to the full path of the 'sphinx-build' executable. Alternatively you - echo.may add the Sphinx directory to PATH. - echo. - echo.If you don't have Sphinx installed, grab it from - echo.https://www.sphinx-doc.org/ - exit /b 1 -) - -%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% -goto end - -:help -%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% - -:end -popd diff --git a/medcat-trainer/docs/meta_annotations.md b/medcat-trainer/docs/meta_annotations.md index 069c6512b..be9671aab 100644 --- a/medcat-trainer/docs/meta_annotations.md +++ b/medcat-trainer/docs/meta_annotations.md @@ -16,11 +16,11 @@ Create and manage tasks in Django admin (`/admin`): 1. Create **Meta Task Values** (the allowed label options). 2. Create a **Meta Task**: - - name - - values - - default value (optional) - - description - - ordering + - name + - values + - default value (optional) + - description + - ordering 3. Attach selected tasks to your project (`Project annotate entities`). ## Model-pack predictions vs manual labels diff --git a/medcat-trainer/docs/project_admin.md b/medcat-trainer/docs/project_admin.md index 7ce879bb5..2d3c87cc2 100644 --- a/medcat-trainer/docs/project_admin.md +++ b/medcat-trainer/docs/project_admin.md @@ -10,11 +10,11 @@ MedCATtrainer supports two management surfaces: 1. Open `/project-admin`. 2. Go to the **Projects** tab and select **Create New Project**. 3. Fill in: - - **Basic information** (name, dataset, description, guideline link) - - **Model configuration** - - **Annotation settings** - - **Concept filter (optional)** - - **Members** + - **Basic information** (name, dataset, description, guideline link) + - **Model configuration** + - **Annotation settings** + - **Concept filter (optional)** + - **Members** 4. Save. ### Model configuration options diff --git a/medcat-trainer/docs/pyproject.toml b/medcat-trainer/docs/pyproject.toml new file mode 100644 index 000000000..6e5c4bac6 --- /dev/null +++ b/medcat-trainer/docs/pyproject.toml @@ -0,0 +1,19 @@ +[project] +name = "medcat-trainer-documentation" +version = "0.1.0" +description = "MedCAT Trainer Documentation" +readme = "README.md" +requires-python = ">=3.10" +dependencies = [ + "mkdocs-material>=9.7.0", + "termynal>=0.13.1", +] + +[project.optional-dependencies] +dev = [ + "ruff>=0.12.11", +] + +[tool.ruff] +line-length = 120 + diff --git a/medcat-trainer/docs/requirements.txt b/medcat-trainer/docs/requirements.txt deleted file mode 100644 index 2cdd31719..000000000 --- a/medcat-trainer/docs/requirements.txt +++ /dev/null @@ -1,4 +0,0 @@ -Sphinx==6.2.1 -sphinx-rtd-theme~=1.0 -myst-parser~=0.17 -sphinx-autoapi==3.0.0 \ No newline at end of file diff --git a/medcat-trainer/docs/uv.lock b/medcat-trainer/docs/uv.lock new file mode 100644 index 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/dev/null +++ b/medcat-trainer/mkdocs.yml @@ -0,0 +1,62 @@ +# yaml-language-server: $schema=https://squidfunk.github.io/mkdocs-material/schema.json +site_name: MedCAT Trainer Documentation +site_url: http://localhost:8080/docs/ + +theme: + name: material + favicon: _static/img/cat-logo.svg + logo: _static/img/cat-logo.svg + icon: + logo: _static/img/cat-logo.svg + palette: + primary: white + + features: + - navigation.tabs + - navigation.sections + - navigation.top + - navigation.indexes + - navigation.tracking + - navigation.footer + - header.autohide + - content.tooltips + - search.highlight + - search.share + - search.suggest + - toc.follow + - attr_list + +repo_url: https://github.com/CogStack/cogstack-nlp +repo_name: cogstack-nlp + +docs_dir: docs + +nav: + - Home: index.md + - Getting started: + - Installation: installation.md + - Demo: demo_page.md + - User guide: + - Annotator Guide: annotator_guide.md + - Administratiors Guide: + - Administrator setup: admin_setup.md + - Annotation Project admin: project_admin.md + - Annotation Project group admin: project_group_admin.md + - Meta annotations: meta_annotations.md + - Reference: + - Advanced usage: advanced_usage.md + - Maintenance: maintenance.md + - Client API: client.md + +plugins: + - search + - termynal + +markdown_extensions: + - admonition + - attr_list + - pymdownx.details + - pymdownx.superfences + - pymdownx.emoji: + emoji_index: !!python/name:material.extensions.emoji.twemoji + emoji_generator: !!python/name:material.extensions.emoji.to_svg