ready to deploy

guigolab · Oct 1, 2024 · 5e5b2fc · 5e5b2fc
1 parent b9a7eea
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diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -0,0 +1,38 @@
+variables:
+  APP_NAME_FRONT: rnaget-nginx
+  APP_NAME_BACK: rnaget-server
+  BASE_PATH: /rnaget-beacon
+
+stages: 
+  - build
+  - deploy
+
+build_containers:
+  only:
+    - master
+
+  tags:
+    - docker
+    - monstre
+
+  stage: build
+  image: docker:latest
+
+  before_script:
+    - echo $CI_REGISTRY_PASSWORD | docker login $CI_REGISTRY -u $CI_REGISTRY_USER --password-stdin
+
+  script:
+    - docker build --build-arg BASE_PATH="$BASE_PATH" -t gitlab.linux.crg.es:5005/monstre/rnaget-implementation/$APP_NAME_FRONT ./nginx
+    - docker push gitlab.linux.crg.es:5005/monstre/rnaget-implementation/$APP_NAME_FRONT
+    - docker build -t gitlab.linux.crg.es:5005/monstre/rnaget-implementation/$APP_NAME_BACK ./server
+    - docker push gitlab.linux.crg.es:5005/monstre/rnaget-implementation/$APP_NAME_BACK
+
+deploy_containers:
+  stage: deploy
+  tags:
+    - shell
+    - monstre
+  script:
+    - cat $ENV_FILE > .env
+    - docker-compose -f docker-compose.yml down -v
+    - docker-compose -f docker-compose.yml up -d
diff --git a/dist/favicon-16x16.png b/dist/favicon-16x16.png
diff --git a/dist/favicon-32x32.png b/dist/favicon-32x32.png
diff --git a/dist/index.css b/dist/index.css
@@ -0,0 +1,16 @@
+html {
+    box-sizing: border-box;
+    overflow: -moz-scrollbars-vertical;
+    overflow-y: scroll;
+}
+
+*,
+*:before,
+*:after {
+    box-sizing: inherit;
+}
+
+body {
+    margin: 0;
+    background: #fafafa;
+}
diff --git a/dist/oauth2-redirect.html b/dist/oauth2-redirect.html
@@ -0,0 +1,79 @@
+<!doctype html>
+<html lang="en-US">
+<head>
+    <title>Swagger UI: OAuth2 Redirect</title>
+</head>
+<body>
+<script>
+    'use strict';
+    function run () {
+        var oauth2 = window.opener.swaggerUIRedirectOauth2;
+        var sentState = oauth2.state;
+        var redirectUrl = oauth2.redirectUrl;
+        var isValid, qp, arr;
+
+        if (/code|token|error/.test(window.location.hash)) {
+            qp = window.location.hash.substring(1).replace('?', '&');
+        } else {
+            qp = location.search.substring(1);
+        }
+
+        arr = qp.split("&");
+        arr.forEach(function (v,i,_arr) { _arr[i] = '"' + v.replace('=', '":"') + '"';});
+        qp = qp ? JSON.parse('{' + arr.join() + '}',
+                function (key, value) {
+                    return key === "" ? value : decodeURIComponent(value);
+                }
+        ) : {};
+
+        isValid = qp.state === sentState;
+
+        if ((
+          oauth2.auth.schema.get("flow") === "accessCode" ||
+          oauth2.auth.schema.get("flow") === "authorizationCode" ||
+          oauth2.auth.schema.get("flow") === "authorization_code"
+        ) && !oauth2.auth.code) {
+            if (!isValid) {
+                oauth2.errCb({
+                    authId: oauth2.auth.name,
+                    source: "auth",
+                    level: "warning",
+                    message: "Authorization may be unsafe, passed state was changed in server. The passed state wasn't returned from auth server."
+                });
+            }
+
+            if (qp.code) {
+                delete oauth2.state;
+                oauth2.auth.code = qp.code;
+                oauth2.callback({auth: oauth2.auth, redirectUrl: redirectUrl});
+            } else {
+                let oauthErrorMsg;
+                if (qp.error) {
+                    oauthErrorMsg = "["+qp.error+"]: " +
+                        (qp.error_description ? qp.error_description+ ". " : "no accessCode received from the server. ") +
+                        (qp.error_uri ? "More info: "+qp.error_uri : "");
+                }
+
+                oauth2.errCb({
+                    authId: oauth2.auth.name,
+                    source: "auth",
+                    level: "error",
+                    message: oauthErrorMsg || "[Authorization failed]: no accessCode received from the server."
+                });
+            }
+        } else {
+            oauth2.callback({auth: oauth2.auth, token: qp, isValid: isValid, redirectUrl: redirectUrl});
+        }
+        window.close();
+    }
+
+    if (document.readyState !== 'loading') {
+        run();
+    } else {
+        document.addEventListener('DOMContentLoaded', function () {
+            run();
+        });
+    }
+</script>
+</body>
+</html>
diff --git a/dist/swagger-initializer.js b/dist/swagger-initializer.js
@@ -0,0 +1,20 @@
+window.onload = function() {
+  //<editor-fold desc="Changeable Configuration Block">
+
+  // the following lines will be replaced by docker/configurator, when it runs in a docker-container
+  window.ui = SwaggerUIBundle({
+    url: "rnaget-beacon-schema.yaml",
+    dom_id: '#swagger-ui',
+    deepLinking: true,
+    presets: [
+      SwaggerUIBundle.presets.apis,
+      SwaggerUIStandalonePreset
+    ],
+    plugins: [
+      SwaggerUIBundle.plugins.DownloadUrl
+    ],
+    layout: "StandaloneLayout"
+  });
+
+  //</editor-fold>
+};
diff --git a/dist/swagger-ui-bundle.js b/dist/swagger-ui-bundle.js
diff --git a/dist/swagger-ui-bundle.js.map b/dist/swagger-ui-bundle.js.map
diff --git a/dist/swagger-ui-es-bundle-core.js b/dist/swagger-ui-es-bundle-core.js
diff --git a/dist/swagger-ui-es-bundle-core.js.map b/dist/swagger-ui-es-bundle-core.js.map
diff --git a/dist/swagger-ui-es-bundle.js b/dist/swagger-ui-es-bundle.js
diff --git a/dist/swagger-ui-es-bundle.js.map b/dist/swagger-ui-es-bundle.js.map
diff --git a/dist/swagger-ui-standalone-preset.js b/dist/swagger-ui-standalone-preset.js
diff --git a/dist/swagger-ui-standalone-preset.js.map b/dist/swagger-ui-standalone-preset.js.map
diff --git a/dist/swagger-ui.css b/dist/swagger-ui.css
diff --git a/dist/swagger-ui.css.map b/dist/swagger-ui.css.map
diff --git a/dist/swagger-ui.js b/dist/swagger-ui.js
diff --git a/dist/swagger-ui.js.map b/dist/swagger-ui.js.map
diff --git a/docker-compose.yml b/docker-compose.yml
@@ -1,65 +1,75 @@
 version: '3'
 
 services:
-
-  nginx:
-    build:
-      context: ./nginx
-      dockerfile: Dockerfile
-      args:
-        - BASE_PATH=$BASE_PATH
-    container_name: ${NGINX_HOST}
-    restart: always
-    environment:
-      - API_PORT=${API_PORT}
-      - API_HOST=${API_HOST}
-      - BASE_PATH=${BASE_PATH}
-    ports:
-        - "94:${API_PORT}"
 
-  mongo:
+  rnaget-mongo:
     image: mongo:6.0
     container_name: "${DB_HOST}"
     env_file:
       - .env
     restart: always
     volumes:
      - ./mongo-init.sh:/docker-entrypoint-initdb.d/mongo-init.sh
-     - mongodb-data:${MONGODB_DATA_DIR}
+      - /data/rnaget-data:/data/db
     ports:
       - "${DB_PORT}:27017"
+    networks:
+      - monstre
+
+  rnaget-nginx:
+    image: gitlab.linux.crg.es:5005/monstre/rnaget-implementation/rnaget-nginx
+    container_name: ${NGINX_HOST}
+    restart: always
+    environment:
+      - API_PORT=${API_PORT}
+      - API_HOST=${API_HOST}
+      - BASE_PATH=${BASE_PATH}
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.rnaget-nginx.rule=(Host(`genome.crg.es`) || Host(`genome.crg.cat`) || Host(`genome.crg.eu`)) && PathPrefix(`/rnaget-beacon`)"
+      - "traefik.http.routers.rnaget-nginx.tls=true"
+      - "traefik.http.routers.rnaget-nginx.entrypoints=web_https"
+      - "traefik.http.services.rnaget-nginx.loadBalancer.server.port=80"
+    ports:
+        - "94:${API_PORT}"
+    networks:
+      - monstre
 
-  server:
-    build: ./server
+  rnaget-server:
+    image: gitlab.linux.crg.es:5005/monstre/rnaget-implementation/rnaget-server
     container_name: ${API_HOST}
     restart: always
     volumes:
       - ./server:/server
     env_file:
       - .env
     depends_on:
-      - redis
-    ports:
-      - "5000:5000"  # Expose
+      - rnaget-redis
+    networks:
+      - monstre
 
-  celery:
-    build: ./server
+  rnaget-celery:
+    image: gitlab.linux.crg.es:5005/monstre/rnaget-implementation/rnaget-server
     command: celery --app app.celery_app worker --loglevel=info --autoscale=1,1 --max-tasks-per-child=1
     restart: always
     volumes:
       - ./server:/server
     env_file:
       - .env
     depends_on:
-      - server
-      - mongo
-      - redis
+      - rnaget-server
+      - rnaget-mongo
+      - rnaget-redis
+    networks:
+      - monstre
 
-  redis:
+  rnaget-redis:
     image: "redis:alpine"
-
-volumes:
-  app:
-  mongodb-data:
-  node_modules:
-  shared_files:
+    expose:
+      - "6378"
+    networks:
+      - monstre
+networks:
+  monstre:
+    external:
+      name: monstre
diff --git a/index.html b/index.html
@@ -0,0 +1,19 @@
+<!-- HTML for static distribution bundle build -->
+<!DOCTYPE html>
+<html lang="en">
+  <head>
+    <meta charset="UTF-8">
+    <title>Swagger UI</title>
+    <link rel="stylesheet" type="text/css" href="dist/swagger-ui.css" />
+    <link rel="stylesheet" type="text/css" href="index.css" />
+    <link rel="icon" type="image/png" href="dist/favicon-32x32.png" sizes="32x32" />
+    <link rel="icon" type="image/png" href="dist/favicon-16x16.png" sizes="16x16" />
+  </head>
+
+  <body>
+    <div id="swagger-ui"></div>
+    <script src="dist/swagger-ui-bundle.js" charset="UTF-8"> </script>
+    <script src="dist/swagger-ui-standalone-preset.js" charset="UTF-8"> </script>
+    <script src="dist/swagger-initializer.js" charset="UTF-8"> </script>
+  </body>
+</html>
diff --git a/ranaget-beacon-schema.yaml b/ranaget-beacon-schema.yaml
@@ -1,11 +1,15 @@
 openapi: 3.0.0
 
 info:
-  version: "2.0.0"
+  version: "1.0.0"
   title: "RNAget Extension for BeaconV2 API"
   contact:
     email: "[email protected]"
 
+servers:
+  - url: https://genome.crg.es/rnaget-beacon/api
+    description: Demo server containing some gene expression data to test rnaget-beaconV2 API implementation
+
 tags:
 - name: "matrices"
 - name: "features"
@@ -348,12 +352,65 @@ paths:
                   data:
                     type: "array"
                     items:
-                      $ref: "#/components/schemas/BioSample"
+                      $ref: "#/components/schemas/ExpressionValue"
                   total:
                     type: "number"
         "404":
           description: "Matrix not found"
 
+    post:
+      tags:
+        - "matrices"
+      summary: "Endpoint to retrieve a paginated list of expression values from a matrix id"
+      parameters:
+        - in: "path"
+          name: "id"
+          required: true
+          schema:
+            type: "string"
+      requestBody:
+        required: true
+        content:
+          application/json:
+            schema:
+              type: "object"
+              properties:
+                skip:
+                  type: "number"
+                  default: 0
+                  description: "Number of records to skip for pagination"
+                limit:
+                  type: "number"
+                  default: 10
+                  description: "Maximum number of records to return"
+                featureIDList:
+                  type: "string"
+                  description: "Comma-separated list of feature IDs to filter the results"
+                biosampleIDList:
+                  type: "string"
+                  description: "Comma-separated list of biosample IDs to filter the results"
+                maxValue:
+                  type: "number"
+                  description: "Maximum expression count value to filter in the results"
+                minValue:
+                  type: "number"
+                  description: "Minimum expression count value to filter in the results"
+      responses:
+        "200":
+          description: "successful operation"
+          content:
+            application/json:
+              schema:
+                type: "object"
+                properties:
+                  data:
+                    type: "array"
+                    items:
+                      $ref: "#/components/schemas/ExpressionValue"
+                  total:
+                    type: "number"
+        "404":
+          description: "Matrix not found"
 
 components:
   schemas: