move flows to plugins

.github/CODEOWNERS

@@ -23,8 +23,8 @@
 /functions/query-gen-svc                             @brandantck @jerome-ng @LSriragavan @khairul-syazwan @satish-a0 @p-hoffmann @maggie-li-yd
 /functions/terminology-svc                           @brandantck @jerome-ng @LSriragavan @khairul-syazwan @satish-a0 @p-hoffmann @maggie-li-yd
 /functions/alp-dataflow-gen-init                     @alicia-koh @csafreen @Zhimin-arya @p-hoffmann
-/flows                                               @alicia-koh @csafreen @Zhimin-arya @p-hoffmann
-/flows/strategus_plugin                              @hengxian-jiang @KangJingA @SantanM @suwarnoong @p-hoffmann
+/plugins/flows                                       @alicia-koh @csafreen @Zhimin-arya @p-hoffmann
+/plugins/flows/strategus_plugin                      @hengxian-jiang @KangJingA @SantanM @suwarnoong @p-hoffmann
 /scripts                                             @brandantck @mwaiyee @SantanM @satish-a0 @p-hoffmann
 /services/alp-dataflow-gen                           @alicia-koh @csafreen @Zhimin-arya @p-hoffmann
 /services/alp-dataflow-gen-worker                    @alicia-koh @csafreen @Zhimin-arya @p-hoffmann

.github/CODEOWNERS.src

@@ -23,8 +23,8 @@
 /functions/query-gen-svc                             @data2evidence/analyze
 /functions/terminology-svc                           @data2evidence/analyze
 /functions/alp-dataflow-gen-init                     @data2evidence/data
-/flows                                               @data2evidence/data
-/flows/strategus_plugin                              @data2evidence/integrate
+/plugins/flows                                       @data2evidence/data
+/plugins/flows/strategus_plugin                      @data2evidence/integrate
 /scripts                                             @data2evidence/devops
 /services/alp-dataflow-gen                           @data2evidence/data
 /services/alp-dataflow-gen-worker                    @data2evidence/data

.github/instructions/flows.instructions.md

@@ -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)

.github/workflows/d2e-demosetup-dev.yml

@@ -68,33 +68,33 @@ jobs:
           initial-fetch-depth: 1
           filters: |
             flow_base:
-              - "flows/base/**"
+              - "plugins/flows/base/**"
             flow_i2b2:
-              - "flows/i2b2/**"
+              - "plugins/flows/i2b2/**"
             flow_data_management:
-              - "flows/data_management/**"
+              - "plugins/flows/data_management/**"
             flow_package_json:
-              - "flows/base/package.json"
+              - "plugins/flows/base/package.json"
             ui: 
               - "ui/**"
 
       - name: Build Flow base docker image
         if: steps.file_changes.outputs.flow_base == 'true'
         id: build_flow_base_image
         run: |
-          docker build --build-arg GIT_COMMIT_ARG=${{ github.sha }} --build-arg BUILD_TYPE=OSS --build-arg GITHUB_PAT=${{ secrets.GITHUB_TOKEN }} --file ./flows/base/Dockerfile --platform linux/amd64 --attest type=provenance,disabled=true --tag ghcr.io/ohdsi/d2e/flow-base:develop ./flows
+          docker build --build-arg GIT_COMMIT_ARG=${{ github.sha }} --build-arg BUILD_TYPE=OSS --build-arg GITHUB_PAT=${{ secrets.GITHUB_TOKEN }} --file ./plugins/flows/base/Dockerfile --platform linux/amd64 --attest type=provenance,disabled=true --tag ghcr.io/ohdsi/d2e/flow-base:develop ./plugins/flows
 
       - name: Build i2b2 docker image
         if: steps.file_changes.outputs.flow_i2b2 == 'true'
         id: build_i2b2_image
         run: |
-          docker build --build-arg GIT_COMMIT_ARG=${{ github.sha }} --build-arg BUILD_TYPE=OSS --build-arg GITHUB_PAT=${{ secrets.GITHUB_TOKEN }} --file ./flows/i2b2/Dockerfile --platform linux/amd64 --attest type=provenance,disabled=true --tag ghcr.io/ohdsi/d2e/flow-i2b2:develop ./flows
+          docker build --build-arg GIT_COMMIT_ARG=${{ github.sha }} --build-arg BUILD_TYPE=OSS --build-arg GITHUB_PAT=${{ secrets.GITHUB_TOKEN }} --file ./plugins/flows/i2b2/Dockerfile --platform linux/amd64 --attest type=provenance,disabled=true --tag ghcr.io/ohdsi/d2e/flow-i2b2:develop ./plugins/flows
 
       - name: Build data management docker image
         if: steps.file_changes.outputs.flow_data_management == 'true'
         id: build_dm_image
         run: |
-          docker build --build-arg GIT_COMMIT_ARG=${{ github.sha }} --build-arg BUILD_TYPE=OSS --build-arg GITHUB_PAT=${{ secrets.GITHUB_TOKEN }} --file ./flows/data_management/Dockerfile --platform linux/amd64 --attest type=provenance,disabled=true --tag ghcr.io/ohdsi/d2e/flow-data-management:develop ./flows
+          docker build --build-arg GIT_COMMIT_ARG=${{ github.sha }} --build-arg BUILD_TYPE=OSS --build-arg GITHUB_PAT=${{ secrets.GITHUB_TOKEN }} --file ./plugins/flows/data_management/Dockerfile --platform linux/amd64 --attest type=provenance,disabled=true --tag ghcr.io/ohdsi/d2e/flow-data-management:develop ./plugins/flows
 
       - name: Build docker images
         if: success() || failure()
@@ -200,7 +200,7 @@ jobs:
       - name: Flow base docker-compose-local
         if: ${{ steps.file_changes.outputs.flow_package_json == 'true' }}
         run: |
-          sed -i 's|# - ./flows/base/package.json:/usr/src/plugins/d2e-flows/package.json|- ./flows/base/package.json:/usr/src/plugins/d2e-flows/package.json|' docker-compose-local.yml
+          sed -i 's|# - ./plugins/flows/base/package.json:/usr/src/plugins/d2e-flows/package.json|- ./plugins/flows/base/package.json:/usr/src/plugins/d2e-flows/package.json|' docker-compose-local.yml
 
       - name: Restart d2e services
         if: success() || failure()

.github/workflows/d2e-demosetup-hana.yml

@@ -73,13 +73,13 @@ jobs:
           initial-fetch-depth: 1
           filters: |
             src:
-              - "flows/base/**"
+              - "plugins/flows/base/**"
 
       - name: Build Flow base docker image
         if: steps.flow_file_changes.outputs.src == 'true'
         id: build_flow_base_image
         run: |
-          docker build --build-arg GIT_COMMIT_ARG=${{ github.sha }} --build-arg BUILD_TYPE=OSS --build-arg GITHUB_PAT=${{ secrets.GITHUB_TOKEN }} --file ./flows/base/Dockerfile --platform linux/amd64 --attest type=provenance,disabled=true --tag ghcr.io/ohdsi/d2e/flow-base:develop ./flows
+          docker build --build-arg GIT_COMMIT_ARG=${{ github.sha }} --build-arg BUILD_TYPE=OSS --build-arg GITHUB_PAT=${{ secrets.GITHUB_TOKEN }} --file ./plugins/flows/base/Dockerfile --platform linux/amd64 --attest type=provenance,disabled=true --tag ghcr.io/ohdsi/d2e/flow-base:develop ./plugins/flows
 
       - name: Build docker images
         if: success() || failure()

.github/workflows/docker-build-push.yaml

@@ -64,16 +64,16 @@ jobs:
           initial-fetch-depth: 1
           filters: |
             src:
-              - "flows/**"
+              - "plugins/flows/**"
               - "services/**"
               - "package.json"
               - "docker-compose.yml"
             rkernel:
               - "./services/enterprise-gateway/CustomKernelManager/**"
               - "./services/enterprise-gateway/kernels/**"
               - "./services/enterprise-gateway/r-strategus-lib/**"
-              - "./flows/hades/renv.lock"
-              - "./flows/_shared_flow_utils/postgresql-42.3.1.jar"
+              - "./plugins/flows/hades/renv.lock"
+              - "./plugins/flows/_shared_flow_utils/postgresql-42.3.1.jar"
               - ".github/workflows/docker-build-push.yaml"
 
   bld:
@@ -93,26 +93,26 @@ jobs:
       matrix:
         include:
           - AZ_REG_REPOSITORY: d2e/flow-base
-            DOCKER_BUILD_CONTEXT_PATH: ./flows
-            DOCKER_BUILD_FILE_PATH: ./flows/base/Dockerfile
+            DOCKER_BUILD_CONTEXT_PATH: ./plugins/flows
+            DOCKER_BUILD_FILE_PATH: ./plugins/flows/base/Dockerfile
           - AZ_REG_REPOSITORY: d2e/flow-i2b2
-            DOCKER_BUILD_CONTEXT_PATH: ./flows
-            DOCKER_BUILD_FILE_PATH: ./flows/i2b2/Dockerfile
+            DOCKER_BUILD_CONTEXT_PATH: ./plugins/flows
+            DOCKER_BUILD_FILE_PATH: ./plugins/flows/i2b2/Dockerfile
           - AZ_REG_REPOSITORY: d2e/flow-search-embedding
-            DOCKER_BUILD_CONTEXT_PATH: ./flows
-            DOCKER_BUILD_FILE_PATH: ./flows/search_embedding/Dockerfile
+            DOCKER_BUILD_CONTEXT_PATH: ./plugins/flows
+            DOCKER_BUILD_FILE_PATH: ./plugins/flows/search_embedding/Dockerfile
           - AZ_REG_REPOSITORY: d2e/flow-data-management
-            DOCKER_BUILD_CONTEXT_PATH: ./flows
-            DOCKER_BUILD_FILE_PATH: ./flows/data_management/Dockerfile
+            DOCKER_BUILD_CONTEXT_PATH: ./plugins/flows
+            DOCKER_BUILD_FILE_PATH: ./plugins/flows/data_management/Dockerfile
           - AZ_REG_REPOSITORY: d2e/flow-loyalty-score
-            DOCKER_BUILD_CONTEXT_PATH: ./flows
-            DOCKER_BUILD_FILE_PATH: ./flows/loyalty_score/Dockerfile
+            DOCKER_BUILD_CONTEXT_PATH: ./plugins/flows
+            DOCKER_BUILD_FILE_PATH: ./plugins/flows/loyalty_score/Dockerfile
           - AZ_REG_REPOSITORY: d2e/flow-hades
-            DOCKER_BUILD_CONTEXT_PATH: ./flows
-            DOCKER_BUILD_FILE_PATH: ./flows/hades/Dockerfile
+            DOCKER_BUILD_CONTEXT_PATH: ./plugins/flows
+            DOCKER_BUILD_FILE_PATH: ./plugins/flows/hades/Dockerfile
           - AZ_REG_REPOSITORY: d2e/flow-data-transformation
-            DOCKER_BUILD_CONTEXT_PATH: ./flows
-            DOCKER_BUILD_FILE_PATH: ./flows/data_transformation/Dockerfile
+            DOCKER_BUILD_CONTEXT_PATH: ./plugins/flows
+            DOCKER_BUILD_FILE_PATH: ./plugins/flows/data_transformation/Dockerfile
           - AZ_REG_REPOSITORY: d2e-pg-mgmt-init
             DOCKER_BUILD_FILE_PATH: ./services/alp-pg-management/Dockerfile
             DOCKER_BUILD_CONTEXT_PATH: ./services/alp-pg-management

.github/workflows/plugin-ci.yml

@@ -67,7 +67,7 @@ jobs:
           initial-fetch-depth: 1
           filters: |
             src:
-              - "flows/**"
+              - "plugins/flows/**"
               - "package.json"
               - "docker-compose.yml"
               - "ui/**"
@@ -93,13 +93,13 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - PKGPATH: ./flows/base/
-          - PKGPATH: ./flows/i2b2/
-          - PKGPATH: ./flows/search_embedding/
-          - PKGPATH: ./flows/data_management/
-          - PKGPATH: ./flows/hades/
-          - PKGPATH: ./flows/loyalty_score/
-          - PKGPATH: ./flows/data_transformation/
+          - PKGPATH: ./plugins/flows/base/
+          - PKGPATH: ./plugins/flows/i2b2/
+          - PKGPATH: ./plugins/flows/search_embedding/
+          - PKGPATH: ./plugins/flows/data_management/
+          - PKGPATH: ./plugins/flows/hades/
+          - PKGPATH: ./plugins/flows/loyalty_score/
+          - PKGPATH: ./plugins/flows/data_transformation/
           - PKGPATH: ./ui
             NPM: bun
           - PKGPATH: ./functions/

.github/workflows/test_strategus_nodes.yml

@@ -27,7 +27,7 @@ jobs:
         with:
           filters: |
             has_strategus_changes:
-              - 'flows/hades/strategus_plugin/**'
+              - 'plugins/flows/hades/strategus_plugin/**'
 
       - name: Determine condition to run
         env:
@@ -39,4 +39,4 @@ jobs:
         if: env.WF_RUN == 'true'
         run: |
           docker pull --platform linux/amd64 ghcr.io/ohdsi/d2e/flow-hades:develop
-          docker compose -f ./flows/hades/strategus_plugin/dc-local.yml up
+          docker compose -f ./plugins/flows/hades/strategus_plugin/dc-local.yml up

.vscode/launch.json

@@ -46,7 +46,7 @@
       },
       "pathMappings": [
         {
-          "localRoot": "${workspaceFolder}/flows",
+          "localRoot": "${workspaceFolder}/plugins/flows",
           "remoteRoot": "./flows"
         }
       ]

docker-compose-local.yml

@@ -17,7 +17,7 @@ services:
       - ./ui/resources:/usr/src/local-resources # For local ui development only
       # - ./services/trex/core:/usr/src/core # For debugging trex with local code
       # - ./services/trex/deno.json:/usr/src/deno.json 
-      # - ./flows/base/package.json:/usr/src/plugins/d2e-flows/package.json # For local flows development only
+      # - ./plugins/flows/base/package.json:/usr/src/plugins/d2e-flows/package.json # For local flows development only
     environment:
       RUST_LOG: info
       RUST_BACKTRACE: full