[DOC] render library listing in doc (#505)

* [DATALAD] Added subdataset

* lib in doc

Author: Remi-Gau

.gitignore

@@ -2,6 +2,8 @@
 activities/.DS_Store
 protocols/.DS_Store
 
+__pycache__
+
 .idea/
 
 node_modules

.gitmodules

@@ -0,0 +1,4 @@
+[submodule "library"]
+	path = library
+	url = https://github.com/ReproNim/reproschema-library.git
+	datalad-url = https://github.com/ReproNim/reproschema-library.git

docs/FAQ.md

@@ -53,17 +53,6 @@ once you have opened that page on github that will open this URL:
 If you want to visualize the graph represented by the JSON-LD file,
 we explain how to do this in [From JSON to JSON-LD](#from-json-to-json-ld).
 
-
-### Which assessments tools will/are supporting this standard?
-
-At the moment, all the assessments that support this standard are listed in [this folder](https://github.com/ReproNim/reproschema-library/tree/master/activities) or the [reproschema-library repository](https://github.com/ReproNim/reproschema-library).
-
-If you want to see those different tools in action using our user interface,
-you can explore them on [schema.repronim.org/](https://schema.repronim.org/rl/).
-
-The ReproSchema is also used to develop a checklist to [improve methods and results reporting in neuroimaging](https://github.com/ohbm/cobidas).
-
-
 ## Linked data and semantic web
 
 ## What is the semantic web?

docs/library.md

@@ -0,0 +1,14 @@
+---
+hide:
+    - toc
+---
+# Reproschema library
+
+At the moment, all the assessments that support this standard are listed in [this folder](https://github.com/ReproNim/reproschema-library/tree/master/activities) of the [reproschema-library repository](https://github.com/ReproNim/reproschema-library).
+
+For convenience we are listing them in the table below.
+
+If you want to see those different tools in action using our user interface,
+you can explore them on [schema.repronim.org/](https://schema.repronim.org/rl/).
+
+{{ MACROS___library_table() }}

docs/project-structure.md

@@ -51,8 +51,7 @@ questionnaire for your next participant or patient. Also you can mix and match
 items from this library, knowing that the information is tracked in your protocol.
 
 All assessments are listed in [the `activity` folder](https://github.com/ReproNim/reproschema-library/tree/master/activities)
-and are served [here](https://schema.repronim.org/rl/) if you want to visualize
-them.
+and are served [here](https://schema.repronim.org/rl/) if you want to visualize them.
 
 -   **Standard Alignment:** Each element in the library aligns with the ReproSchema framework, ensuring uniformity in terms and structure and upholding validation protocols for consistency across the ecosystem.
 -   **Research Protocol Integration:** Researchers can utilize these assessments in various combinations to align with specific protocol needs, customizing their application per study objectives. This process can be integrated using the reproschema-protocol-cookiecutter for constructing user interfaces.

docs/tutorials/collecting-demographics-information.md

@@ -0,0 +1,9 @@
+from .macros import (
+    library_table,
+)
+from .main import define_env
+
+__all__ = [
+    "define_env",
+    "library_table",
+]

library

@@ -0,0 +1,68 @@
+from pathlib import Path
+import json
+
+import ruamel.yaml
+from jinja2 import Environment, FileSystemLoader, select_autoescape
+
+yaml = ruamel.yaml.YAML()
+yaml.indent(mapping=2, sequence=4, offset=2)
+
+ROOT = Path(__file__).parents[1]
+
+TEMPLATES_DIR = ROOT / "templates"
+
+LIBRARY_DIR = ROOT / "library"
+
+SCHEMA_DIR = ROOT / "linkml-schema"
+
+
+def return_jinja_env() -> Environment:
+    return Environment(
+        loader=FileSystemLoader(TEMPLATES_DIR),
+        autoescape=select_autoescape(),
+        lstrip_blocks=True,
+        trim_blocks=True,
+    )
+
+
+def library_table() -> str:
+
+    LIBRARY_URL = "https://github.com/ReproNim/reproschema-library"
+
+    activities = []
+
+    for activity_path in (LIBRARY_DIR / "activities").iterdir():
+
+        if not activity_path:
+            continue
+
+        for file in activity_path.glob("*"):
+
+            if file.is_dir() or file is None or "valueConstraints" in file.stem:
+                continue
+
+            with open(file) as f:
+                content = json.load(f)
+
+            activities.append(
+                {
+                    "name": content["@id"],
+                    "description": (
+                        content["description"] if "description" in content else ""
+                    ),
+                    "uri": f"{LIBRARY_URL}/tree/master/activities/{activity_path.stem}/{file.stem}{file.suffix}",
+                }
+            )
+
+    env = return_jinja_env()
+    template = env.get_template("library_table.jinja")
+
+    return template.render(activities=activities)
+
+
+def main():
+    print(library_table())
+
+
+if __name__ == "__main__":
+    main()

macros/__init__.py

@@ -0,0 +1,32 @@
+"""This package is used to build elements from data into
+MarkDown format for the specification text.
+
+Functions decorated in "define_env()" are callable throughout the
+specification and are run/rendered with the mkdocs plugin "macros".
+"""
+
+import os
+import sys
+
+code_path = os.path.abspath(os.path.join(os.path.dirname(__file__)))
+sys.path.append(code_path)
+
+import macros  # noqa E402
+
+
+def define_env(env):
+    """Define variables, macros and filters for the mkdocs-macros plugin.
+
+    Parameters
+    ----------
+    env : :obj:`macros.plugin.MacrosPlugin`
+        An object in which to inject macros, variables, and filters.
+
+    Notes
+    -----
+    "variables" are the dictionary that contains the environment variables
+    "macro" is a decorator function, to declare a macro.
+
+    Macro aliases must start with "MACROS___"
+    """
+    env.macro(macros.library_table, "MACROS___library_table")

macros/macros.py

@@ -54,8 +54,8 @@ nav:
       - Create new items: "tutorials/create-new-items.md"
       - Finalize the protocol: "tutorials/finalizing-the-protocol.md"
       - Translate a questionnaire: "tutorials/translating-an-activity.md"
-      - Demographic information : "tutorials/collecting-demographics-information.md"
-      - Tips to make your life easier: "tutorials/tips-to-make-your-life-easier.md"
+      - Tips: tutorials/tips-to-make-your-life-easier.md
+  - Library: library.md
   - FAQ: "FAQ.md"
   - Contributing: "CONTRIBUTING.md"
 
@@ -75,12 +75,16 @@ markdown_extensions:
   - pymdownx.snippets:
       auto_append:
         - includes/abbreviations.md
+  - tables
   - toc:
       anchorlink: true
 
 watch:
   - includes
+  - linkml-schema
 
 plugins:
   - search
   - tags
+  - macros:
+      module_name: macros/main

macros/main.py

@@ -1,3 +1,5 @@
-rdflib==5.0.0
+mkdocs-macros-plugin
 mkdocs-material
 pymdown-extensions
+rdflib==5.0.0
+ruamel.yaml

mkdocs.yml

@@ -0,0 +1,5 @@
+| Activity | Description | URI |
+| :------  | :---------- | :-- |
+{% for activity in activities %}
+| {{ activity.name }} | {{ activity.description }} | [link]({{ activity.uri }}) |
+{% endfor %}