Merge branch 'develop' into csafreen/e2e_etl

Author: csafreen

.github/.voters.yml

@@ -2,5 +2,4 @@
 csafreen: 1
 p-hoffmann: 1
 SantanM: 1
-satish-a0: 1
 suwarnoong: 1 

.github/CODEOWNERS

@@ -2,37 +2,37 @@
 /.github/*                                           @data2evidence/trex
 /.github/workflows                                   @data2evidence/devops
 /.github/workflows/pr-approval.yml                   @data2evidence/trex
-/fhir_functions/                                     @data2evidence/data
-/functions/_shared                                   @data2evidence/analyze
-/functions/alp-usermgmt                              @data2evidence/integrate
-/functions/alpdb                                     @data2evidence/integrate
-/functions/analytics-svc                             @data2evidence/analyze
-/functions/bookmark-svc                              @data2evidence/analyze
-/functions/cdw-svc                                   @data2evidence/analyze
-/functions/code-suggestion                           @data2evidence/data
-/functions/concept-mapping                           @data2evidence/integrate
-/functions/d2e-webapi                                @data2evidence/analyze
-/functions/dataset                                   @data2evidence/integrate
-/functions/demo                                      @data2evidence/integrate
-/functions/files-manager                             @data2evidence/integrate
-/functions/jobplugins                                @data2evidence/integrate
-/functions/strategus-analysis                        @data2evidence/integrate
-/functions/perseus                                   @data2evidence/integrate
-/functions/jobplugins-init                           @data2evidence/integrate
-/functions/supabase-storage-init                     @data2evidence/integrate
-/functions/white-rabbit-init                         @data2evidence/integrate
-/functions/portal-init                               @data2evidence/integrate
-/functions/alp-usermgmt-init                         @data2evidence/integrate
-/functions/strategus-analysis-init                   @data2evidence/integrate
-/functions/perseus-init                              @data2evidence/integrate
-/functions/files-manager-init                        @data2evidence/integrate
-/functions/mri-pa-config                             @data2evidence/analyze
-/functions/mri-pg-config                             @data2evidence/analyze
-/functions/portal                                    @data2evidence/integrate
-/functions/prefect                                   @data2evidence/integrate
-/functions/query-gen-svc                             @data2evidence/analyze
-/functions/terminology-svc                           @data2evidence/analyze
-/functions/alp-dataflow-gen-init                     @data2evidence/data
+/plugins/fhir_functions/                                     @data2evidence/data
+/plugins/functions/_shared                                   @data2evidence/analyze
+/plugins/functions/alp-usermgmt                              @data2evidence/integrate
+/plugins/functions/alpdb                                     @data2evidence/integrate
+/plugins/functions/analytics-svc                             @data2evidence/analyze
+/plugins/functions/bookmark-svc                              @data2evidence/analyze
+/plugins/functions/cdw-svc                                   @data2evidence/analyze
+/plugins/functions/code-suggestion                           @data2evidence/data
+/plugins/functions/concept-mapping                           @data2evidence/integrate
+/plugins/functions/d2e-webapi                                @data2evidence/analyze
+/plugins/functions/dataset                                   @data2evidence/integrate
+/plugins/functions/demo                                      @data2evidence/integrate
+/plugins/functions/files-manager                             @data2evidence/integrate
+/plugins/functions/jobplugins                                @data2evidence/integrate
+/plugins/functions/strategus-analysis                        @data2evidence/integrate
+/plugins/functions/perseus                                   @data2evidence/integrate
+/plugins/functions/jobplugins-init                           @data2evidence/integrate
+/plugins/functions/supabase-storage-init                     @data2evidence/integrate
+/plugins/functions/white-rabbit-init                         @data2evidence/integrate
+/plugins/functions/portal-init                               @data2evidence/integrate
+/plugins/functions/alp-usermgmt-init                         @data2evidence/integrate
+/plugins/functions/strategus-analysis-init                   @data2evidence/integrate
+/plugins/functions/perseus-init                              @data2evidence/integrate
+/plugins/functions/files-manager-init                        @data2evidence/integrate
+/plugins/functions/mri-pa-config                             @data2evidence/analyze
+/plugins/functions/mri-pg-config                             @data2evidence/analyze
+/plugins/functions/portal                                    @data2evidence/integrate
+/plugins/functions/prefect                                   @data2evidence/integrate
+/plugins/functions/query-gen-svc                             @data2evidence/analyze
+/plugins/functions/terminology-svc                           @data2evidence/analyze
+/plugins/functions/alp-dataflow-gen-init                     @data2evidence/data
 /flows                                               @data2evidence/data
 /flows/strategus_plugin                              @data2evidence/integrate
 /scripts                                             @data2evidence/devops
@@ -43,17 +43,18 @@
 /services/alp-db-management                          @data2evidence/data
 /services/envConverter                               @data2evidence/analyze
 /services/mri-db                                     @data2evidence/analyze
+/services/materialize-cohorts                        @data2evidence/analyze
 /services/trex                                       @data2evidence/trex
 /tests                                               @data2evidence/analyze
-/ui                                                  @data2evidence/integrate
-/ui/alp-libs                                         @data2evidence/analyze
-/ui/apps/mri-pa-ui                                   @data2evidence/analyze
-/ui/apps/vue-mri-ui-lib                              @data2evidence/analyze
-/ui/apps/portal/src/plugins/mri                      @data2evidence/analyze
-/ui/apps/portal/src/plugins/Researcher/ConceptSets   @data2evidence/analyze
-/ui/apps/portal/src/plugins/Researcher/Terminology   @data2evidence/analyze
-/ui/apps/concept-sets                                @data2evidence/analyze
-/ui/apps/wizards                                              @data2evidence/analyze
+/plugins/ui                                                  @data2evidence/integrate
+/plugins/ui/alp-libs                                         @data2evidence/analyze
+/plugins/ui/apps/mri-pa-ui                                   @data2evidence/analyze
+/plugins/ui/apps/vue-mri-ui-lib                              @data2evidence/analyze
+/plugins/ui/apps/portal/src/plugins/mri                      @data2evidence/analyze
+/plugins/ui/apps/portal/src/plugins/Researcher/ConceptSets   @data2evidence/analyze
+/plugins/ui/apps/portal/src/plugins/Researcher/Terminology   @data2evidence/analyze
+/plugins/ui/apps/concept-sets                                @data2evidence/analyze
+/plugins/ui/apps/wizards                                              @data2evidence/analyze
 /tests/e2e/tests/02-users                                     @data2evidence/integrate
 /tests/e2e/tests/03-researcher                                @data2evidence/integrate
 /tests/e2e/tests/04-attribute                                 @data2evidence/integrate

.github/CODEOWNERS.src

@@ -1,6 +1,6 @@
-@data2evidence/analyze | @brandantck @jerome-ng @LSriragavan @khairul-syazwan @satish-a0 @p-hoffmann @maggie-li-yd
-@data2evidence/core | @csafreen @SantanM @satish-a0 @suwarnoong @p-hoffmann
+@data2evidence/analyze | @brandantck @jerome-ng @LSriragavan @khairul-syazwan @p-hoffmann @maggie-li-yd
+@data2evidence/core | @csafreen @SantanM @suwarnoong @p-hoffmann
 @data2evidence/data | @alicia-koh @csafreen @Zhimin-arya @p-hoffmann
-@data2evidence/devops | @brandantck @mwaiyee @SantanM @satish-a0 @p-hoffmann
+@data2evidence/devops | @brandantck @mwaiyee @SantanM @p-hoffmann
 @data2evidence/integrate | @hengxian-jiang @KangJingA @SantanM @suwarnoong @p-hoffmann
 @data2evidence/trex | @p-hoffmann

.github/CODEOWNERS.teams

@@ -1,12 +1,12 @@
 ---
-applyTo: "flows/**"
+applyTo: "plugins/flows/**"
 ---
 
 # D2E Flows Development Instructions
 
 ## Quick Plugin Detection
 
-**Auto-detect from file path:** `flows/[plugin_group]/[individual_plugin]/`
+**Auto-detect from file path:** `plugins/flows/[plugin_group]/[individual_plugin]/`
 **Plugin groups:** base, data_management, data_transformation, hades, loyalty_score, search_embedding, i2b2, cohort_survival
 
 **Key indicators:**
@@ -60,7 +60,7 @@ def hello_flow(name: str = "World") -> dict:
 
 ### 2. Package.json Generation
 ```bash
-cd flows
+cd plugins/flows
 python flowinit.py [package_name] [entrypoint] [plugin_type] [-dm]
 ```
 **Required:** package_name, entrypoint (e.g. `path/to/flow.py:function`), plugin_type
@@ -78,18 +78,18 @@ uv add fastapi uvicorn --force
 
 ### 3. Build & Test
 ```bash
-cd flows/[plugin_group]
+cd plugins/flows/[plugin_group]
 yarn build  # Builds Docker image locally with local tag
 ```
 
 **Integration testing with D2E:**
 1. **Directly modify docker-compose-local.yml:**
-   - Uncomment: `- ./flows/[plugin_group]/package.json:/usr/src/plugins/d2e-flows/package.json`
+   - Uncomment: `- ./plugins/flows/[plugin_group]/package.json:/usr/src/plugins/d2e-flows/package.json`
    - Change: `PLUGINS_SEED_UPDATE: ${PLUGINS_SEED_UPDATE:-false}` to `PLUGINS_SEED_UPDATE: ${PLUGINS_SEED_UPDATE:-true}`
 
 2. **Restart trex service:**
    ```bash
-   cd ../..  # Navigate to D2E root folder from flows/[plugin_group]
+   cd ../../..  # Navigate to D2E root folder from plugins/flows/[plugin_group]
    # Restart only trex using yarn (recommended)
    yarn local --services trex start
    ```
@@ -100,7 +100,7 @@ yarn build  # Builds Docker image locally with local tag
 
 ### Directory Structure
 ```
-flows/[plugin_group]/
+plugins/flows/[plugin_group]/
 ├── Dockerfile                   # Uses requirements_[name].txt OR pyproject.toml
 ├── package.json                 # Generated by flowinit.py
 ├── requirements_[name].txt      # Legacy deps (most plugins)