Merge pull request #138 from luk27official/docking

Frontend update, add "tasks" including molecular docking
cusbg · Jan 27, 2024 · 4f56790 · 4f56790
2 parents 82ac98e + 1f8e765
commit 4f56790
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diff --git a/.dockerignore b/.dockerignore
@@ -0,0 +1,4 @@
+node_modules
+.dockerignore
+**/.DS_Store
+**/node_modules
diff --git a/.gitignore b/.gitignore
@@ -1,5 +1,6 @@
 #
 .*
+!.dockerignore
 
 # Selected file.
 *.iml

diff --git a/administration/Dockerfile b/administration/Dockerfile
@@ -2,7 +2,7 @@
 # java-tools
 #
 
-FROM debian:bookworm-20211115 as java-tools
+FROM debian:bookworm-20231009 as java-tools
 
 RUN apt-get update \
   && apt-get -y --no-install-recommends install openjdk-17-jdk
@@ -17,17 +17,17 @@ RUN chmod +x ./gradlew && ./gradlew installDist \
 # administration
 #
 
-FROM debian:bookworm-20211115
+FROM debian:bookworm-20231009
 
 ARG UID=5988
 ARG GID=5988
 
 RUN apt-get update \
-   && apt-get -y --no-install-recommends install \
-   wget curl \
-   python3 python3-pip python3-venv \
-   openjdk-17-jre-headless \
-   libgomp1 vim
+  && apt-get -y --no-install-recommends install \
+  wget curl \
+  python3 python3-pip python3-venv \
+  openjdk-17-jre-headless \
+  libgomp1 vim
 
 # https://github.com/python/cpython/issues/102134
 ENV VIRTUAL_ENV=/opt/venv

diff --git a/docker-compose-prankweb.yml b/docker-compose-prankweb.yml
@@ -46,7 +46,8 @@ services:
         GID: ${GID}
     environment:
       CELERY_BROKER_URL: "amqp://${RABBITMQ_DEFAULT_USER}:${RABBITMQ_DEFAULT_PASS}@rabbitmq:5672"
-      PRANKWEB_DATA: "/data/prankweb"
+      PRANKWEB_DATA_PREDICTIONS: "/data/prankweb/predictions/"
+      PRANKWEB_DATA_DOCKING: "/data/prankweb/docking/"
     restart: unless-stopped
     volumes:
       - predictions:/data/prankweb
@@ -60,17 +61,35 @@ services:
       args:
         UID: ${UID}
         GID: ${GID}
-    command: ["celery", "--app=celery_p2rank", "worker", "--concurrency=4", "--hostname=executor-p2rank"]
+    command: ["celery", "--app=celery_p2rank", "worker", "--queues=p2rank", "--concurrency=4", "--hostname=executor-p2rank"]
+    depends_on:
+      rabbitmq:
+        condition: service_healthy
     environment:
       CELERY_BROKER_URL: "amqp://${RABBITMQ_DEFAULT_USER}:${RABBITMQ_DEFAULT_PASS}@rabbitmq:5672"
       LOCK_DIRECTORY: "/data/prankweb/lock"
     restart: unless-stopped
     volumes:
       - conservation:/data/conservation
-      - predictions:/data/prankweb
+      - predictions:/data/prankweb/predictions
+      - docking:/data/prankweb/docking
+  executor-docking:
+    build:
+      context: ./
+      dockerfile: ./executor-docking/Dockerfile
+      args:
+        UID: ${UID}
+        GID: ${GID}
+    command: ["celery", "--app=celery_docking", "worker", "--queues=docking", "--concurrency=4", "--hostname=executor-docking"]
+    environment:
+      CELERY_BROKER_URL: "amqp://${RABBITMQ_DEFAULT_USER}:${RABBITMQ_DEFAULT_PASS}@rabbitmq:5672"
+    restart: unless-stopped
+    volumes:
+      - docking:/data/prankweb/docking
+      - predictions:/data/prankweb/predictions
     depends_on:
       rabbitmq:
-        condition: service_healthy
+        condition: service_healthy   
   monitor:
     build:
       context: ./
@@ -101,3 +120,6 @@ volumes:
   services:
     external: True
     name: prankweb_services
+  docking:
+    external: True
+    name: prankweb_docking
diff --git a/docker-compose.yml b/docker-compose.yml
@@ -31,7 +31,7 @@ services:
     build: https://github.com/mher/flower.git
     command: "celery flower --url_prefix=service/flower"
     environment:
-      CELERY_BROKER_URL: "amqp://${RABBITMQ_DEFAULT_USER}:${RABBITMQ_DEFAULT_PASS}@rabbitmq:5672"
+      CELERY_BROKER_URL: "amqp://${RABBITMQ_DEFAULT_USER:-user}:${RABBITMQ_DEFAULT_PASS:-1234}@rabbitmq:5672"
     depends_on:
       rabbitmq:
           condition: service_healthy
@@ -46,27 +46,47 @@ services:
       rabbitmq:
         condition: service_healthy
     environment:
-      CELERY_BROKER_URL: "amqp://${RABBITMQ_DEFAULT_USER}:${RABBITMQ_DEFAULT_PASS}@rabbitmq:5672"
-      PRANKWEB_DATA: "/data/prankweb"
+      CELERY_BROKER_URL: "amqp://${RABBITMQ_DEFAULT_USER:-user}:${RABBITMQ_DEFAULT_PASS:-1234}@rabbitmq:5672"
+      PRANKWEB_DATA_PREDICTIONS: "/data/prankweb/predictions/"
+      PRANKWEB_DATA_DOCKING: "/data/prankweb/docking/"
     volumes:
-      - predictions:/data/prankweb
+      - predictions:/data/prankweb/predictions
+      - docking:/data/prankweb/docking
   executor-p2rank:
     build:
       context: ./
       dockerfile: ./executor-p2rank/Dockerfile
       args:
         UID: ${UID:-5988}
         GID: ${GID:-5988}
-    command: ["celery", "--app=celery_p2rank", "worker", "--concurrency=4", "--hostname=executor-p2rank"]
+    command: ["celery", "--app=celery_p2rank", "worker", "--queues=p2rank", "--concurrency=4", "--hostname=executor-p2rank"]
     depends_on:
       rabbitmq:
         condition: service_healthy
     environment:
-      CELERY_BROKER_URL: "amqp://${RABBITMQ_DEFAULT_USER}:${RABBITMQ_DEFAULT_PASS}@rabbitmq:5672"
+      CELERY_BROKER_URL: "amqp://${RABBITMQ_DEFAULT_USER:-user}:${RABBITMQ_DEFAULT_PASS:-1234}@rabbitmq:5672"
       LOCK_DIRECTORY: "/data/prankweb/lock"
     volumes:
       - conservation:/data/conservation
-      - predictions:/data/prankweb
+      - predictions:/data/prankweb/predictions
+      - docking:/data/prankweb/docking
+  executor-docking:
+    build:
+      context: ./
+      dockerfile: ./executor-docking/Dockerfile
+      args:
+        UID: ${UID:-5988}
+        GID: ${GID:-5988}
+    command: ["celery", "--app=celery_docking", "worker", "--queues=docking", "--concurrency=4", "--hostname=executor-docking"]
+    environment:
+      CELERY_BROKER_URL: "amqp://${RABBITMQ_DEFAULT_USER:-user}:${RABBITMQ_DEFAULT_PASS:-1234}@rabbitmq:5672"
+    restart: unless-stopped
+    volumes:
+      - docking:/data/prankweb/docking
+      - predictions:/data/prankweb/predictions
+    depends_on:
+      rabbitmq:
+        condition: service_healthy
   prometheus:
     build:
       context: ./
@@ -92,3 +112,6 @@ volumes:
   services:
     external: True
     name: prankweb_services
+  docking:
+    external: True
+    name: prankweb_docking
diff --git a/documentation/prankweb.open-api.yaml b/documentation/prankweb.open-api.yaml
@@ -1,14 +1,14 @@
-openapi: 3.0.0
+openapi: 3.0.2
 
 info:
   title: Prankweb API
-  version: 1.0.0
+  version: 1.0.1
 
 servers:
-  - url: https://prankweb.cz/api/v2/predictions/
+  - url: https://prankweb.cz/api/v2/
 
 paths:
-  /{database}/{task}/:
+  /predictions/{database}/{task}/:
     get:
       parameters:
         - in: path
@@ -28,7 +28,7 @@ paths:
             application/json:
               schema:
                 $ref: '#/components/schemas/Task'
-  /{database}/{task}/log:
+  /predictions/{database}/{task}/log:
     get:
       parameters:
         - in: path
@@ -48,7 +48,7 @@ paths:
             text/plain:
               schema:
                 type: string
-  /{database}/{task}/public/prediction.json:
+  /predictions/{database}/{task}/public/prediction.json:
     get:
       parameters:
         - in: path
@@ -68,6 +68,53 @@ paths:
             application/json:
               schema:
                 $ref: '#/components/schemas/Prediction'
+  /docking/{database}/{task}/tasks:
+    get:
+      parameters:
+        - in: path
+          name: database
+          required: true
+          schema:
+            $ref: '#/components/schemas/DatabaseId'
+        - in: path
+          name: task
+          required: true
+          schema:
+            $ref: '#/components/schemas/TaskId'
+      responses:
+        '200':
+          description: Success
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/DockingTaskList'
+  /docking/{database}/{task}/public/result.json:
+    post:
+      parameters:
+        - in: path
+          name: database
+          required: true
+          schema:
+            $ref: '#/components/schemas/DatabaseId'
+        - in: path
+          name: task
+          required: true
+          schema:
+            $ref: '#/components/schemas/TaskId'
+      requestBody:
+        description: The request needs to contain the hash and the pocket number.
+        required: true
+        content:
+          application/json:
+            schema:
+              $ref: '#/components/schemas/DockingRequest'
+      responses:
+        '200':
+          description: Success
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/DockingResponse'
 
 components:
   schemas:
@@ -148,3 +195,45 @@ components:
                     type: number
                   end:
                     type: number
+    DockingTaskList:
+      type: object
+      properties:
+        identifier:
+          type: string
+        tasks:
+          type: array
+          items:
+            type: object
+            properties:
+              id:
+                type: string
+              created:
+                type: string
+                format: date-time
+              lastChange:
+                type: string
+                format: date-time
+              status:
+                type: string
+                enum: ['queued', 'running', 'failed', 'successful']
+              initialData:
+                type: object
+                properties:
+                  hash:
+                    type: string
+                  pocket:
+                    type: string
+    DockingRequest:
+      type: object
+      properties:
+        hash:
+          type: string
+        pocket:
+          type: number
+    DockingResponse:
+      type: array
+      items:
+        type: object
+        properties:
+          url:
+            type: string