Release v 1.3 by pendingintent · Pull Request #210 · pendingintent/soa-workbench

pendingintent · 2026-05-04T13:22:47Z

No description provided.

… are assigned to the selected timeline

…edicalConcept

…tion

-        return HTMLResponse("", headers={"HX-Redirect": f"/ui/soa/{soa_id}/edit"})
-    return HTMLResponse(f"<script>window.location='/ui/soa/{soa_id}/edit';</script>")
+        return HTMLResponse("", headers={"HX-Redirect": f"/ui/soa/{soa_id}/freezes"})
+    return HTMLResponse(f"<script>window.location='/ui/soa/{soa_id}/freezes';</script>")


+    redirect_url = f"/ui/soa/{soa_id}/edit"
+    if request.headers.get("HX-Request") == "true":
+        return HTMLResponse("", headers={"HX-Redirect": redirect_url})
+    return RedirectResponse(redirect_url, status_code=303)


+    redirect_url = f"/ui/soa/{soa_id}/edit"
+    if request.headers.get("HX-Request") == "true":
+        return HTMLResponse("", headers={"HX-Redirect": redirect_url})
+    return RedirectResponse(redirect_url, status_code=303)


+    redirect_url = f"/ui/soa/{soa_id}/edit"
+    if request.headers.get("HX-Request") == "true":
+        return HTMLResponse("", headers={"HX-Redirect": redirect_url})
+    return RedirectResponse(redirect_url, status_code=303)


Copilot

Pull request overview

This release bundles a broad set of changes across the SoA Workbench: new objective/endpoint authoring in the FastAPI UI/API, richer USDM biomedical concept export data, freeze-page refactoring, and first-pass Azure deployment assets.

Changes:

Added objective and endpoint schemas, routers, edit-page UI, migrations, audits, and tests.
Added USDM biomedical concept property / extension-attribute generation plus related UID helpers and tests.
Moved freeze management to a dedicated page and added Azure deployment scripts/workflow/docs.

Reviewed changes

Copilot reviewed 29 out of 31 changed files in this pull request and generated 7 comments.

Show a summary per file

File	Description
`tests/test_routers_objectives.py`	New API/UI coverage for objectives CRUD and orphaning behavior.
`tests/test_routers_freezes.py`	Added coverage for the dedicated freezes page and delete flow.
`tests/test_routers_endpoints.py`	New API/UI coverage for endpoints CRUD and objective linkage.
`tests/test_generate_extension_attributes.py`	Tests for extension-attribute UID population and export shape.
`tests/test_generate_biomedical_concept_properties.py`	Tests for biomedical concept property persistence and export shape.
`startup.sh`	New App Service startup command using Gunicorn/Uvicorn.
`src/usdm/generate_extension_attributes.py`	New generator for BC extension attributes from DSS mappings.
`src/usdm/generate_biomedical_concepts.py`	Wires properties/extension attributes into BC export.
`src/usdm/generate_biomedical_concept_properties.py`	New persisted BC property generator from CDISC BC metadata.
`src/soa_builder/web/utils.py`	Added UID helpers for BC properties and extension attributes.
`src/soa_builder/web/templates/freezes.html`	New dedicated frozen-versions page and actions.
`src/soa_builder/web/templates/edit.html`	Removed inline freeze bar, added objectives section, filtered matrix rows by timeline.
`src/soa_builder/web/templates/base.html`	Added navigation entry for Frozen Versions.
`src/soa_builder/web/templates/_objectives_section.html`	New edit-page UI for objectives/endpoints CRUD and orphan handling.
`src/soa_builder/web/schemas.py`	Added request models for objectives and endpoints.
`src/soa_builder/web/routers/objectives.py`	New objective API/UI router with audit and level-code handling.
`src/soa_builder/web/routers/freezes.py`	Refactored freeze routes to shared helpers and dedicated listing/delete UI.
`src/soa_builder/web/routers/endpoints.py`	New endpoint API/UI router with parent-objective validation.
`src/soa_builder/web/routers/_freeze_helpers.py`	Extracted freeze/rollback implementation from `app.py`.
`src/soa_builder/web/migrate_database.py`	Added migrations for objectives, endpoints, audits, and extension-attribute UID column.
`src/soa_builder/web/audit.py`	Added objective and endpoint audit writers.
`src/soa_builder/web/app.py`	Registered new routers/migrations and expanded edit-page data loading.
`src/soa_builder.egg-info/top_level.txt`	Refreshed package metadata for additional top-level modules.
`src/soa_builder.egg-info/SOURCES.txt`	Refreshed package source manifest.
`src/soa_builder.egg-info/requires.txt`	Refreshed dependency metadata.
`src/soa_builder.egg-info/PKG-INFO`	Refreshed package metadata/README snapshot.
`scripts/upload_database_to_azure.sh`	Helper script for uploading SQLite data to Azure Files.
`requirements.txt`	Added Gunicorn runtime dependency.
`docs/DEPLOYMENT_AZURE.md`	Large Azure deployment runbook and rollout guidance.
`.gitignore`	Added Azure/deployment and output ignore patterns.
`.github/workflows/azure-deploy.yml`	New GitHub Actions workflow for Azure deployment.

+    snapshot = {
+        "soa_id": soa_id,
+        "soa_name": soa_name,
+        "study_id": study_id_val,
+        "study_label": study_label_val,


+    cur.execute("DELETE FROM matrix_cells WHERE soa_id=?", (soa_id,))
+    cur.execute(
+        "DELETE FROM activity_concept WHERE activity_id IN"
+        " (SELECT id FROM activity WHERE soa_id=? )",
+        (soa_id,),


+    activity_ids_by_timeline: dict = {tl: set() for tl in instances_by_timeline.keys()}
+    for c in cells:
+        tl = instance_timeline.get(c["instance_id"])
+        if tl is None or tl not in activity_ids_by_timeline:
+            continue


+        raise HTTPException(404, "Objective not found")
+    before = _row_to_dict(row)
+
+    new_name = body.name if body.name is not None else before["name"]


+    new_name = body.name if body.name is not None else before["name"]
+    new_label = body.label if body.label is not None else before["label"]
+    new_desc = (
+        body.description if body.description is not None else before["description"]
+    )
+    new_text = body.text if body.text is not None else before["text"]
+    new_purpose = body.purpose if body.purpose is not None else before["purpose"]



 </div>
+
+{% include '_objectives_section.html' %}


+    populate_biomedical_concept_properties(soa_id)
+    populate_extension_attributes(soa_id)


…e cross-site scripting' Co-authored-by: Copilot Autofix powered by AI <62310815+github-advanced-security[bot]@users.noreply.github.com>

-        return HTMLResponse("", headers={"HX-Redirect": f"/ui/soa/{soa_id}/edit"})
-    return HTMLResponse(f"<script>window.location='/ui/soa/{soa_id}/edit';</script>")
+        return HTMLResponse("", headers={"HX-Redirect": f"/ui/soa/{soa_id}/freezes"})
+    return RedirectResponse(url=f"/ui/soa/{soa_id}/freezes", status_code=303)


…e cross-site scripting' Co-authored-by: Copilot Autofix powered by AI <62310815+github-advanced-security[bot]@users.noreply.github.com>

-        return HTMLResponse("", headers={"HX-Redirect": f"/ui/soa/{soa_id}/edit"})
-    return HTMLResponse(f"<script>window.location='/ui/soa/{soa_id}/edit';</script>")
+        return HTMLResponse("", headers={"HX-Redirect": f"/ui/soa/{soa_id}/freezes"})
+    return RedirectResponse(url=f"/ui/soa/{soa_id}/freezes", status_code=303)


Copilot

Pull request overview

Copilot reviewed 29 out of 31 changed files in this pull request and generated 7 comments.

+    # Activities per timeline: an activity is shown in timeline T's matrix
+    # if any matrix_cells row connects it to an instance whose
+    # member_of_timeline == T. The instance->timeline link (set on the
+    # study_timing page) is the authoritative criterion.
+    instance_timeline = {
+        inst["id"]: (inst.get("member_of_timeline") or "unassigned")
+        for inst in instances
+    }
+    activity_ids_by_timeline: dict = {tl: set() for tl in instances_by_timeline.keys()}
+    for c in cells:
+        tl = instance_timeline.get(c["instance_id"])
+        if tl is None or tl not in activity_ids_by_timeline:
+            continue
+        activity_ids_by_timeline[tl].add(c["activity_id"])
+    activities_by_timeline: dict = {
+        tl: [a for a in activities_page if a["id"] in ids]
+        for tl, ids in activity_ids_by_timeline.items()


+    snapshot = {
+        "soa_id": soa_id,
+        "soa_name": soa_name,
+        "study_id": study_id_val,
+        "study_label": study_label_val,
+        "study_description": study_description_val,
+        "version_label": version_label,
+        "frozen_at": datetime.now(timezone.utc).isoformat(),
+        "epochs": epochs,
+        "elements": elements,
+        "visits": visits,
+        "activities": activities,
+        "cells": cells,
+        "activity_concepts": concepts_map,
+    }


+    cur.execute("DELETE FROM biomedical_concept WHERE soa_id=?", (soa_id,))
+    cur.execute("DELETE FROM alias_code WHERE soa_id=?", (soa_id,))
+    cur.execute("DELETE FROM code WHERE soa_id=?", (soa_id,))
+    cur.execute("DELETE FROM code_association WHERE soa_id=?", (soa_id,))


+_migrate_activity_concept_dss_add_extension_attribute_uid()
+_migrate_add_objective_table()
+_migrate_add_objective_audit_table()
+_migrate_add_endpoint_table()
+_migrate_add_endpoint_audit_table()


+<h3 style="margin:0 0 8px;font-size:1em;color:#455a64;">Audit Logs</h3>
+<div style="display:flex;gap:8px;flex-wrap:wrap;font-size:0.85em;">
+  <button hx-get="/ui/soa/{{ soa_id }}/rollback_audit" hx-target="#modal-host" hx-swap="innerHTML" style="background:#37474f;color:#fff;border:none;padding:4px 10px;border-radius:4px;cursor:pointer;">Rollback Audit Log</button>
+  <a href="/soa/{{ soa_id }}/rollback_audit/export/xlsx" style="background:#1976d2;color:#fff;text-decoration:none;padding:4px 10px;border-radius:4px;">Rollback Audit XLSX</a>


+                "isRequired": bool(is_required) if is_required is not None else True,
+                "isEnabled": bool(is_enabled) if is_enabled is not None else True,
+                "datatype": datatype or "",
+                "responseCodes": [],


Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

… remote source' Co-authored-by: Copilot Autofix powered by AI <62310815+github-advanced-security[bot]@users.noreply.github.com>

Copilot

Pull request overview

Copilot reviewed 29 out of 31 changed files in this pull request and generated 11 comments.

+    # Activities per timeline: an activity is shown in timeline T's matrix
+    # if any matrix_cells row connects it to an instance whose
+    # member_of_timeline == T. The instance->timeline link (set on the
+    # study_timing page) is the authoritative criterion.
+    instance_timeline = {
+        inst["id"]: (inst.get("member_of_timeline") or "unassigned")
+        for inst in instances
+    }
+    activity_ids_by_timeline: dict = {tl: set() for tl in instances_by_timeline.keys()}
+    for c in cells:
+        tl = instance_timeline.get(c["instance_id"])
+        if tl is None or tl not in activity_ids_by_timeline:
+            continue
+        activity_ids_by_timeline[tl].add(c["activity_id"])
+    activities_by_timeline: dict = {
+        tl: [a for a in activities_page if a["id"] in ids]
+        for tl, ids in activity_ids_by_timeline.items()


+        "epochs": epochs,
+        "elements": elements,
+        "visits": visits,
+        "activities": activities,
+        "cells": cells,
+        "activity_concepts": concepts_map,


+    cur.execute("DELETE FROM biomedical_concept WHERE soa_id=?", (soa_id,))
+    cur.execute("DELETE FROM alias_code WHERE soa_id=?", (soa_id,))
+    cur.execute("DELETE FROM code WHERE soa_id=?", (soa_id,))
+    cur.execute("DELETE FROM code_association WHERE soa_id=?", (soa_id,))


+<h3 style="margin:0 0 8px;font-size:1em;color:#455a64;">Audit Logs</h3>
+<div style="display:flex;gap:8px;flex-wrap:wrap;font-size:0.85em;">
+  <button hx-get="/ui/soa/{{ soa_id }}/rollback_audit" hx-target="#modal-host" hx-swap="innerHTML" style="background:#37474f;color:#fff;border:none;padding:4px 10px;border-radius:4px;cursor:pointer;">Rollback Audit Log</button>
+  <a href="/soa/{{ soa_id }}/rollback_audit/export/xlsx" style="background:#1976d2;color:#fff;text-decoration:none;padding:4px 10px;border-radius:4px;">Rollback Audit XLSX</a>


+        raise HTTPException(404, "Objective not found")
+    before = _row_to_dict(row)
+
+    new_name = body.name if body.name is not None else before["name"]


+def get_next_extension_attribute_uid(cur: Any, soa_id: int) -> str:
+    """Compute next unique ExtensionAttribute_N for the given SOA.
+
+    Assumes `cur` is a sqlite cursor within an open transaction.
+    """
+    cur.execute(
+        "SELECT extension_attribute_uid FROM activity_concept_dss"
+        " WHERE soa_id=?"
+        " AND extension_attribute_uid LIKE 'ExtensionAttribute_%'",
+        (soa_id,),
+    )
+    existing = [x[0] for x in cur.fetchall() if x[0]]
+    n = 1
+    if existing:
+        try:
+            n = max(int(x.split("_")[1]) for x in existing) + 1
+        except Exception:
+            n = len(existing) + 1
+    return f"ExtensionAttribute_{n}"


+    objective_level_options = sorted({v for v in c188725_map.values() if v})
+    endpoint_level_options = sorted({v for v in c188726_map.values() if v})
+    conn_obj = _connect()
+    cur_obj = conn_obj.cursor()
+    cur_obj.execute(
+        "SELECT code_uid, code FROM code_association "
+        "WHERE soa_id=? AND codelist_code IN ('C188725','C188726')",
+        (soa_id,),
+    )
+    level_code_to_sv: dict = {}
+    for code_uid, code_val in cur_obj.fetchall():
+        level_code_to_sv[code_uid] = code_val or ""


+# Upload database
+echo -e "${YELLOW}Uploading database to Azure Files...${NC}"
+echo "This may take a few moments depending on file size..."
+
+az storage file upload \
+    --account-name "$STORAGE_ACCOUNT" \
+    --account-key "$STORAGE_KEY" \
+    --share-name "$FILE_SHARE" \
+    --source "$LOCAL_DB" \
+    --path soa_builder_web.db \
+    --no-progress


+**⚠️ Important Notes:**
+- **WAL mode files**: SQLite creates `-wal` and `-shm` files in WAL mode. These will be recreated automatically by Azure; you only need to upload the main `.db` file.
+- **Database locking**: Ensure your local app is stopped before uploading the database to avoid corruption.
+- **Schema migrations**: The app will automatically run any pending migrations on startup, so your local database will be updated to match the latest schema.


+        "DELETE FROM activity_concept WHERE activity_id IN"
+        " (SELECT id FROM activity WHERE soa_id=? )",
+        (soa_id,),
+    )


Copilot

Pull request overview

Copilot reviewed 29 out of 31 changed files in this pull request and generated 7 comments.

            "superscript_map": superscript_map,
+            "objectives": objectives,
+            "endpoints_by_objective": endpoints_by_objective,
+            "orphan_endpoints": orphan_endpoints,
+            "objective_level_options": objective_level_options,
+            "endpoint_level_options": endpoint_level_options,


+      <a href="/soa/{{ soa_id }}/freeze/{{ f.id }}" target="_blank" style="background:#37474f;color:#fff;text-decoration:none;padding:2px 8px;border-radius:3px;font-size:0.85em;">JSON</a>
+    </td>
+    <td style="padding:4px;">
+      <form method="post" action="/ui/soa/{{ soa_id }}/freeze/{{ f.id }}/delete" onsubmit="return confirm('Delete frozen version {{ f.version_label }}? This cannot be undone.');" style="display:inline;">


Copilot

Pull request overview

Copilot reviewed 29 out of 31 changed files in this pull request and generated 13 comments.

+    # Activities per timeline: an activity is shown in timeline T's matrix
+    # if any matrix_cells row connects it to an instance whose
+    # member_of_timeline == T. The instance->timeline link (set on the
+    # study_timing page) is the authoritative criterion.
+    instance_timeline = {
+        inst["id"]: (inst.get("member_of_timeline") or "unassigned")
+        for inst in instances
+    }
+    activity_ids_by_timeline: dict = {tl: set() for tl in instances_by_timeline.keys()}
+    for c in cells:
+        tl = instance_timeline.get(c["instance_id"])
+        if tl is None or tl not in activity_ids_by_timeline:
+            continue
+        activity_ids_by_timeline[tl].add(c["activity_id"])
+    activities_by_timeline: dict = {
+        tl: [a for a in activities_page if a["id"] in ids]
+        for tl, ids in activity_ids_by_timeline.items()


+    cur.execute("DELETE FROM biomedical_concept WHERE soa_id=?", (soa_id,))
+    cur.execute("DELETE FROM alias_code WHERE soa_id=?", (soa_id,))
+    cur.execute("DELETE FROM code WHERE soa_id=?", (soa_id,))
+    cur.execute("DELETE FROM code_association WHERE soa_id=?", (soa_id,))


            "superscript_map": superscript_map,
+            "objectives": objectives,
+            "endpoints_by_objective": endpoints_by_objective,
+            "orphan_endpoints": orphan_endpoints,
+            "objective_level_options": objective_level_options,
+            "endpoint_level_options": endpoint_level_options,


+            - name: Azure login
+              uses: azure/login@v1
+              with:
+                creds: ${{ secrets.AZURE_CREDENTIALS }}
+            - name: Stop Azure Web App
+              uses: azure/cli@v1
+              with:
+                azcliversion: 2.36.0
+                inlineScript: |
+                  az webapp stop --name ${{ secrets.AZURE_WEBAPP_NAME }} --resource-group cdisc-soa-workbench-rg
+


+    new_name = body.name if body.name is not None else before["name"]
+    new_label = body.label if body.label is not None else before["label"]
+    new_desc = (
+        body.description if body.description is not None else before["description"]
+    )
+    new_text = body.text if body.text is not None else before["text"]
+
+    new_level_code_uid = before["level_code_uid"]
+    if body.level is not None:
+        new_level = body.level.strip()
+        if not new_level:
+            conn.close()
+            raise HTTPException(400, "Objective level cannot be empty")
+        if before["level_code_uid"]:
+            # Update the submission value in the existing Code_N row.
+            cur.execute(
+                "UPDATE code_association SET code=? WHERE soa_id=? AND code_uid=?",
+                (new_level, soa_id, before["level_code_uid"]),
+            )
+        else:
+            new_level_code_uid = _insert_level_code(cur, soa_id, new_level)
+
+    cur.execute(
+        "UPDATE objective SET name=?, label=?, description=?, text=?, "


+echo "Retrieving storage account key..."
+STORAGE_KEY=$(az storage account keys list \
+    --resource-group "$RESOURCE_GROUP" \
+    --account-name "$STORAGE_ACCOUNT" \
+    --query '[0].value' \
+    --output tsv 2>&1)
+
+if [ $? -ne 0 ]; then
+    echo -e "${RED}Error: Failed to retrieve storage account key${NC}"
+    echo "Please verify:"
+    echo "  1. Resource group '$RESOURCE_GROUP' exists"
+    echo "  2. Storage account '$STORAGE_ACCOUNT' exists"
+    echo "  3. You have permission to access the storage account"
+    exit 1


+    for c in cells:
+        old_vid = c.get("visit_id")
+        old_aid = c.get("activity_id")
+        status = c.get("status", "").strip()
+        if status == "":
+            continue
+        vid = visit_id_map.get(old_vid)
+        aid = activity_id_map.get(old_aid)
+        if vid and aid:
+            cur.execute(
+                "INSERT INTO matrix_cells (soa_id, visit_id, activity_id, status)"
+                " VALUES (?,?,?,?)",
+                (soa_id, vid, aid, status),


+    study_id_val = row[2] if row else None
+    study_label_val = row[3] if row else None
+    study_description_val = row[4] if row else None
+    visits, activities, cells = _fetch_matrix(soa_id)


+    cur.execute(
+        "SELECT id,soa_id,objective_uid,name,label,description,text,"
+        "level_code_uid,order_index "
+        "FROM objective WHERE soa_id=? ORDER BY order_index, id",
+        (soa_id,),
+    )
+    rows = [_row_to_dict(r) for r in cur.fetchall()]
+    conn.close()
+    return JSONResponse(rows)


+    cur.execute(
+        "SELECT id,soa_id,endpoint_uid,objective_uid,name,label,"
+        "description,text,purpose,level_code_uid,order_index "
+        "FROM endpoint WHERE soa_id=? ORDER BY order_index, id",
+        (soa_id,),
+    )
+    rows = [_row_to_dict(r) for r in cur.fetchall()]
+    conn.close()
+    return JSONResponse(rows)


pendingintent added 7 commits April 22, 2026 11:30

Issue #199: SOA Matrix only displays ScheduledActivityInstance's that…

95d1247

… are assigned to the selected timeline

Added objectives and endpoints creation

e875fde

BiomedicalCocneptProperty values are now populated within parent Biom…

60f52ca

…edicalConcept

Added extensionAttributes for BiomedicalConcept

faba830

Fixed Object and Endpoint level display

5b05327

Freezes now on dedicated page presented in table with new delete func…

d270399

…tion

Add Azure deployment configuration

fae7038

pendingintent added this to the v1.3 milestone May 4, 2026

pendingintent self-assigned this May 4, 2026

Copilot AI review requested due to automatic review settings May 4, 2026 13:22

pendingintent added the bug Something isn't working label May 4, 2026

pendingintent added this to @pendingintent's version 1.3 May 4, 2026

pendingintent added documentation Improvements or additions to documentation enhancement New feature or request labels May 4, 2026

github-project-automation Bot moved this to Todo in @pendingintent's version 1.3 May 4, 2026

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Potential fix for pull request finding 'CodeQL / Reflected server-sid…

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Fix Azure package installation and update storage account config

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Added step to stop wunning Azure web app for more robust deployment

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Fixed syntax error

29dea7c

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Fixed syntax error

b66243d

pendingintent had a problem deploying to production May 4, 2026 15:45 — with GitHub Actions Failure

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Added credential to secrets

77668c4

pendingintent had a problem deploying to production May 4, 2026 16:05 — with GitHub Actions Failure

Added credential to secrets

8301475

pendingintent had a problem deploying to production May 4, 2026 16:09 — with GitHub Actions Failure

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pendingintent closed this May 4, 2026

github-project-automation Bot moved this from Todo to Done in @pendingintent's version 1.3 May 4, 2026

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Release v 1.3#210

Release v 1.3#210
pendingintent wants to merge 18 commits into
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pendingintent commented May 4, 2026

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		populate_biomedical_concept_properties(soa_id)
		populate_extension_attributes(soa_id)

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pendingintent commented May 4, 2026

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