merging block 3 pipeline

GEO-BON · Oct 7, 2023 · 25921cd · 25921cd
2 parents bba099b + 0d0dce0
commit 25921cd
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diff --git a/.github/workflows/docker_ui.yml b/.github/workflows/docker_ui.yml
@@ -5,35 +5,36 @@ on:
     branches:
       - main
     paths:
-      - 'ui/**'
+      - "ui/**"
 
 jobs:
   ui:
     runs-on: ubuntu-latest
     steps:
-    - name: Check out the repo
-      uses: actions/checkout@v3
-
-    - name: Log in to Docker Hub
-      uses: docker/login-action@v2
-      with:
-        username: ${{ secrets.DOCKER_USERNAME }}
-        password: ${{ secrets.DOCKER_PASSWORD }}
-
-    - name: Extract metadata (tags, labels) for Docker
-      id: meta
-      uses: docker/metadata-action@v4
-      with:
-        images: geobon/bon-in-a-box
-        tags: |
-          type=raw,value=ui
-    
-    - name: Build and push Docker image
-      uses: docker/build-push-action@v3
-      with:
-        context: ui
-        file: ui/Dockerfile.prod
-        push: true
-        tags: ${{ steps.meta.outputs.tags }}
-        labels: ${{ steps.meta.outputs.labels }}
-
+      - name: Check out the repo
+        uses: actions/checkout@v3
+
+      - name: Log in to Docker Hub
+        uses: docker/login-action@v2
+        with:
+          username: ${{ secrets.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_PASSWORD }}
+
+      - run: echo REACT_APP_VIEWER_HOST=/viewer >> ui/.env
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v4
+        with:
+          images: geobon/bon-in-a-box
+          tags: |
+            type=raw,value=ui
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v3
+        with:
+          context: ui
+          file: ui/Dockerfile.prod
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
diff --git a/README.md b/README.md
@@ -7,7 +7,7 @@ A GEO BON project, born from a collaboration between Microsoft, McGill, Humbolt
 ## Contributing
 If you wish to contribute your indicator or EBV code, please let us know at [email protected].
 
-The recommended method is to setup an instance of BON in a Box somewhere you can easily play with the script files, using the local or remote setup below. You can create a fork to save your work. Make sure that the code is general, and will work when used with various parameters, such as in different regions around the globe. Once the integration of the new scripts or pipelines are complete, open a pull request to this repository. The pull request will be peer-reviewed before acceptation.
+The recommended method is to setup an instance of BON in a Box somewhere you can easily play with the script files, using the local or remote setup below. You can create a branch or fork to save your work. Make sure that the code is general, and will work when used with various parameters, such as in different regions around the globe. Once the integration of the new scripts or pipelines are complete, open a pull request to this repository. The pull request will be peer-reviewed before acceptation.
 
 ## Running the servers locally
 Prerequisites : 
@@ -73,6 +73,13 @@ When modifying pipelines in the /pipelines folder, servers do not need to be res
 3. Create a .env file on the server, as above.
 4. Take dockers down and up to load the .env file (this allows accessing GBIF, etc.)
 
+## Running a script or pipeline
+You have an instance of BON in a Box running, either [locally](#running-the-servers-locally) or [remotely](#running-the-servers-remotely), and you want to run your first script or pipeline.
+
+There is one page to run scripts, and one to run pipelines. Select the script or pipelines from the dropdown and fill the form.
+
+The form might ask you for a file. In order to provide a file that you own locally, upload or copy it to the `userdata` folder. You can then refer to it with a url as such: `userdata/myFile.shp`, or `userdata/myFolder/myFile.shp` if there are subfolders.
+
 ## Scripts
 The scripts perform the actual work behind the scenes. They are located in [/scripts folder](/scripts)
 

diff --git a/compose.dev.yml b/compose.dev.yml
@@ -3,23 +3,24 @@
 version: "3.7"
 
 services:
-## UI server to use when developing UI code
+  ## UI server to use when developing UI code
   ui:
     container_name: biab-ui
     build:
       context: ./ui
       dockerfile: Dockerfile.dev
     user: "node"
     volumes:
-      - './ui:/app:rw'
+      - "./ui:/app:rw"
     working_dir: "/app"
     command: sh -c "cd BonInABoxScriptService; npm run build; cd -; npm install; npm start;"
     expose:
-      - '3000'
+      - "3000"
     environment:
-      - CHOKIDAR_USEPOLLING=true 
+      - CHOKIDAR_USEPOLLING=true
       # https://github.com/facebook/create-react-app/issues/11779
       - WDS_SOCKET_PORT=0
+      - REACT_APP_VIEWER_HOST=${REACT_APP_VIEWER_HOST}
     depends_on:
       - script-server
       - tiler
@@ -31,8 +32,8 @@ services:
       - ui
       - openapi_swagger
 
-## In the DEV version, using a volume and a single docker. To rebuild without restarting everything, use
-## docker exec -it biab-script-server sh -c "cd /home/gradle/project/ && gradle build"
+  ## In the DEV version, using a volume and a single docker. To rebuild without restarting everything, use
+  ## docker exec -it biab-script-server sh -c "cd /home/gradle/project/ && gradle build"
   script-server:
     build:
       context: ./script-server
@@ -44,7 +45,7 @@ services:
     environment:
       DEV: true
 
-## Server to use when making changes to the OpenAPI specification.
+  ## Server to use when making changes to the OpenAPI specification.
   openapi_swagger:
     container_name: swagger_editor
     image: swaggerapi/swagger-editor

diff --git a/compose.yml b/compose.yml
@@ -9,12 +9,14 @@ services:
     volumes:
       - ./scripts:/scripts:ro
       - ./pipelines:/pipelines:ro
+      - ./userdata:/userdata:ro
       - ./output:/output:rw
       - /var/run/docker.sock:/var/run/docker.sock
     expose:
       - "8080"
     environment:
       - SCRIPT_LOCATION=/scripts
+      - USERDATA_LOCATION=/userdata
       - PIPELINES_LOCATION=/pipelines
       - OUTPUT_LOCATION=/output
       - HOST_PATH=${PWD}
@@ -37,9 +39,11 @@ services:
     tty: true # Needed to keep the container alive, waiting for requests.
     volumes:
       - ./scripts:/scripts:ro
+      - ./userdata:/userdata:ro
       - ./output:/output:rw
     environment:
       - SCRIPT_LOCATION=/scripts
+      - USERDATA_LOCATION=/userdata
       - OUTPUT_LOCATION=/output
       - JUPYTERHUB_API_TOKEN=${JUPYTERHUB_API_TOKEN}
       - GBIF_USER=${GBIF_USER}
@@ -57,9 +61,11 @@ services:
     tty: true # Needed to keep the container alive, waiting for requests.
     volumes:
       - ./scripts:/scripts:ro
+      - ./userdata:/userdata:ro
       - ./output:/output:rw
     environment:
       - SCRIPT_LOCATION=/scripts
+      - USERDATA_LOCATION=/userdata
       - OUTPUT_LOCATION=/output
 
   http-gateway:
@@ -78,6 +84,7 @@ services:
     image: ghcr.io/developmentseed/titiler:latest
     volumes:
       - ./output:/output:ro
+      - ./userdata:/userdata:ro
     environment:
       - PORT=8000
       - WORKERS_PER_CORE=1