Updated documentation for current features

.github/copilot-instructions.md

@@ -88,19 +88,7 @@ rm -f soa_builder_web_tests.db*
 ### Pre-commit Hooks
 ```bash
 pre-commit install
-pre-commit run --all-files  # runs black + pytest + flake8
-```
-
-### CLI Commands
-```bash
-# Normalize wide CSV → relational tables
-soa-builder normalize --input files/SoA.csv --out-dir normalized/
-
-# Expand repeating rules → calendar instances
-soa-builder expand --normalized-dir normalized/ --start-date 2025-01-01
-
-# Validate imaging intervals
-soa-builder validate --normalized-dir normalized/
+pre-commit run --all-files  # runs ruff + pytest
 ```
 
 ## Code Conventions

README.md

@@ -1,22 +1,18 @@
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 
-
-
 # SoA Workbench
 
-This workspace provides a Python package `soa_builder` with APIs to:
-
-1. Normalize a wide Schedule of Activities (SoA) matrix into relational tables.
-2. Expand repeating schedule rules into projected calendar instances.
+This workspace provides a Python package `soa_builder` with APIs to create a Schedule of Activites for Clinical Studies.
 
 
 ## Installation
 Recommended: editable install for development.
 ```bash
 python3 -m venv .venv
 source .venv/bin/activate
-pip install -e .
+pip install -r requirements.txt
 pre-commit install
+pre-commit run --all-files
 ```
 
 ## Start web server
@@ -30,13 +26,15 @@ uvicorn soa_builder.web.app:app --reload --port 8000
 ```
 HTML UI:
 - Open http://localhost:8000/ in a browser.
-- Add visits and activities; click cells to toggle status (blank -> X -> blank). 'O' values are not surfaced in the UI; clearing removes the cell row.
-- Use "Generate Normalized Summary" link to produce artifacts.
- - Use export buttons (to be added) or hit endpoints directly for XLSX output.
- - Delete a visit or activity using the ✕ button next to its name (confirmation dialog). Deletion cascades to associated cells and automatically reorders remaining items.
- - View biomedical concepts via the "Concepts" navigation link (`GET /ui/concepts`): renders a table of concept codes, titles and API links (cached; force refresh per study using `POST /ui/soa/{id}/concepts_refresh`).
-
-Biomedical Concepts API Access:
+- Create a new Schedule of Activities for a study or access an existing one.
+	- When a study is chosen, additional navigation links are available in the navigation menu that are unique to the Study context.
+	- More options and parameters for configuring the USDM classes are available through these navigation links.
+- Add Scheduled Activity instances (columns) and activities (rows) to create an SoA matrix on the edit page for a Study; click cells to toggle status (blank -> X -> blank). 'O' values are not surfaced in the UI; clearing removes the cell row.
+ - Use export buttons (to be added) for XLSX output of the Matrix.
+- View avialable biomedical concepts via the "Biomedical Concepts" navigation link to render a table of concept codes, titles and API links (cached; force refresh available).
+- View available data set specializations via the "SDTM Dataset Specializations" navigation link to render a table of specializations and API links to view associated concepts (cached; force refresh available). 
+
+CDISC Library API Access:
 - The concepts list and detail pages call the CDISC Library API.
 - Set one (or both) of: `CDISC_SUBSCRIPTION_KEY`, `CDISC_API_KEY`.
 - The server will send all of these headers when possible:

src/soa_builder/web/templates/help.html

@@ -2,39 +2,95 @@
 {% block content %}
 
 <h2>Steps to Create an SoA Matrix</h2>
+
+
 
 <ol>
     <li>
-        <h3>Create a Schedule Timeline (container)</h3>
+        <h3>Create a new Schedule of Activties on the landing page.</h3>
         <ul>
-            <li>Click <strong>Scheduled Timelines</strong> in the left sidebar</li>
-            <li>Create a Timeline (e.g., Main Timeline)</li>
-            <li>Optionally mark the Timeline as <strong>Main</strong></li>
+            <li>Study Name</li>
+            <li>Study ID</li>
+            <li>Study Label</li>
+            <li>Study Description</li>
+            <li>Create Study</li>
         </ul>
     </li>
+
     <li>
-        <h3>Create Encounters/Visits (Optional, but recommended)</h3>
+        <h3>Create Schedule of Activities Matrix on Study Landing Page</h3>
         <ul>
-            <li>Click <strong>Encounters</strong> in the left sidebar</li>
-            <li>Create visits (e.g., "Visit 1", "Visit 2", "Screening"</quote>)</li>
-            <li>These will appear as column headers in the Matrix</li>
+            <li>
+                A basic Schedule of Activity Matrix can be created on the landing lage once a study is created.
+            </li>
+            <li>Add Scheduled Instances to create coluuns for the SOA Matrix</li>
+            <li>Add Activites to create rows for the SOA Matrix</li>
+            <li>Selecting a cell in the Matrix will add a 'X' indicating the Activity is assigned to the Scheduled Instance</li>
+            <li>Biomedical Concepts can now be assigned to an Activity</li>
         </ul>
+        <p><em>This only creates a rudimentary SOA Matrix. More detail can be added using the links in the navigation menu.</em></p> 
+        <p><em>Links are only available once a study SOA has been chosen.</em></p>
     </li>
     <li>
-        <h3>Create Scheduled Activity Instances (Matrix Columns)</h3>
+        <h3>Create Study Timing</h3>
         <ul>
-            <li>Click <strong>Scheduled Activity Instances</strong> in the left sidebar</li>
-            <li>For each instance created:
+            <li>Click <strong>Study Timing</strong> in the navigation menu</li>
+            <li>There are four configurations available
                 <ul>
-                    <li>Set a <strong>name</strong> (e.g., "Week 1", "Day 1")</li>
-                    <li><strong>IMPORTANT:</strong> Set <strong>Member of Timeline</strong> to the timeline created in Step 1</li>
-                    <li>Optionally link to an encounter from Step 2</li>
-                    <li>Optionally link to an Epoch</li>
+                    <li>Schedule Timelines</li>
+                    <li>Scheduled Activity Instances</li>
+                    <li>Scheduled Decision Instances</li>
+                    <li>Condition Assignments</li>
+                    <li>Timings</li>
                 </ul>
             </li>
-            <li>Each instance becomes a column in the Matrix</li>
         </ul>
     </li>
+    <li>
+        <h3>Create Epochs</h3>
+        <ul>
+            <li>Click <strong>Epochs</strong> in the navigation menu</li>
+
+        </ul>
+    </li>
+    <li>
+        <h3>Create Arms</h3>
+        <ul>
+            <li>Click <strong>Arms</strong> in the navigation menu</li>
+        </ul>
+    </li>
+    <li>
+        <h3>Create Elements</h3>
+        <ul>
+            <li>Click <strong>Elements</strong> in the navigation menu</li>
+        </ul>
+    </li>
+    <li>
+        <h3>Associate Study Epochs and Arms with Elements</h3>
+        <ul>
+            <li>Click <strong>Study Cells</strong></li>
+        </ul>
+    </li>
+    <li>
+        <h3>Create Encounters</h3>
+        <ul>
+            <li>Click <strong>Encounters</strong> in the left sidebar</li>
+        </ul>
+    </li>
+    <li>
+        <h3>Transition Rules for Encounters and Elements can also be defined</h3>
+        <ul>
+            <li>Click <strong>Transition Rules</strong> in the menu navigation menu</li>
+        </ul>
+    </li>
+    <li>
+        <h3>USDM JSON can also be generated</h3>
+        <ul>
+            <li>Click <strong>Generate USDM JSON</strong> in the menu navigation menu</li>
+        </ul>
+        <p><em>Partial JSON can be generated for the different USDM classes.</em></p>
+        <p><em>The full USDM JSON is not complete.  Not all classes required for USDM conformance can be generated with the attributes set in the SOA Workbench</em></p>
+    </li>
     <li>
         <h3>Return to the Edit Page</h3>
         <ul>