Merge branch 'release-2.3.x'

.github/workflows/build-jsorolla-workflow.yml

@@ -14,7 +14,14 @@ jobs:
     outputs:
       version: ${{ steps.package.outputs.version }}
     steps:
-      - uses: actions/checkout@v2
+      - name: "Checkout JSorolla"
+        uses: actions/checkout@v2
+#      - name: "Checkout private custom sites repo inside JSorolla"
+#        uses: actions/checkout@v2
+#        if: ${{ github.repository != 'opencb/jsorolla' }}
+#        with:
+#          repository: ${{ secrets.JSOROLLA_CUSTOM_SITES_REPOSITORY }}
+#          path: custom-sites
       - uses: actions/setup-node@v2
         with:
           node-version: "16"
@@ -44,4 +51,3 @@ jobs:
           # TODO: we should rename the iva-VERSION.tar.gz file as jsorolla-VERSION.tar.gz
           path: iva-${{ steps.package.outputs.version }}.tar.gz
           retention-days: 1
-

.github/workflows/develop.yml

@@ -16,9 +16,14 @@ jobs:
     secrets:
       DOCKER_HUB_USER: ${{ secrets.DOCKER_HUB_USER }}
       DOCKER_HUB_PASSWORD: ${{ secrets.DOCKER_HUB_PASSWORD }}
+      DOCKER_HUB_ORGANISATION: ${{ secrets.DOCKER_HUB_ORGANISATION }}
+      DOCKER_IMAGES_JSOROLLA: ${{ secrets.DOCKER_IMAGES_JSOROLLA }}
+      JSOROLLA_CUSTOM_SITES_REPOSITORY: ${{ secrets.JSOROLLA_CUSTOM_SITES_REPOSITORY }}
+      GH_PRIVATE_TOKEN: ${{ secrets.GH_PRIVATE_TOKEN }}
 
   deploy:
     needs: build
+    if: ${{ github.repository == 'opencb/jsorolla' }}
     uses: opencb/jsorolla/.github/workflows/deploy-jsorolla-workflow.yml@develop
     with:
       version: ${{ needs.build.outputs.version }}

.github/workflows/docker-jsorolla-workflow.yml

@@ -7,13 +7,30 @@ on:
         required: true
       DOCKER_HUB_PASSWORD:
         required: true
-
+      DOCKER_HUB_ORGANISATION:
+        required: true
+      DOCKER_IMAGES_JSOROLLA:
+        required: true
+      JSOROLLA_CUSTOM_SITES_REPOSITORY:
+        required: true
+      GH_PRIVATE_TOKEN:
+        required: true
+
 jobs:
   docker-jsorolla-workflow:
     name: Publish JSorolla Docker
     runs-on: ubuntu-20.04
     steps:
-      - uses: actions/checkout@v2
+      - name: "Checkout JSorolla"
+        uses: actions/checkout@v2
+      - name: "Checkout private custom sites repo inside JSorolla"
+        uses: actions/checkout@v2
+        if: ${{ github.repository != 'opencb/jsorolla' }}
+        with:
+          token: ${{ secrets.GH_PRIVATE_TOKEN }}
+          repository: ${{ secrets.JSOROLLA_CUSTOM_SITES_REPOSITORY }}
+          ref: main
+          path: custom-sites
       - uses: actions/download-artifact@v2
         with:
           name: jsorolla-build
@@ -22,5 +39,4 @@ jobs:
         with:
           username: ${{ secrets.DOCKER_HUB_USER }}
           password: ${{ secrets.DOCKER_HUB_PASSWORD }}
-      - run: python3 ./docker/docker-build.py push --images app
-
+      - run: python3 ./docker/docker-build.py push --organisation ${{ secrets.DOCKER_HUB_ORGANISATION }} --images ${{ secrets.DOCKER_IMAGES_JSOROLLA }}

.github/workflows/release.yml

@@ -15,6 +15,10 @@ jobs:
     secrets:
       DOCKER_HUB_USER: ${{ secrets.DOCKER_HUB_USER }}
       DOCKER_HUB_PASSWORD: ${{ secrets.DOCKER_HUB_PASSWORD }}
+      DOCKER_HUB_ORGANISATION: ${{ secrets.DOCKER_HUB_ORGANISATION }}
+      DOCKER_IMAGES_JSOROLLA: ${{ secrets.DOCKER_IMAGES_JSOROLLA }}
+      JSOROLLA_CUSTOM_SITES_REPOSITORY: ${{ secrets.JSOROLLA_CUSTOM_SITES_REPOSITORY }}
+      GH_PRIVATE_TOKEN: ${{ secrets.GH_PRIVATE_TOKEN }}
 
   release:
     needs: [build, docker]
@@ -25,6 +29,7 @@ jobs:
 
   deploy:
     needs: build
+    if: github.repository == "opencb/jsorolla"
     uses: opencb/jsorolla/.github/workflows/deploy-jsorolla-workflow.yml@develop
     with:
       version: ${{ needs.build.outputs.version }}

docker/iva-app/Dockerfile

@@ -26,6 +26,8 @@ COPY    ./build/iva                 /usr/local/apache2/htdocs/iva
 COPY    ./${SITE}/iva/conf          /usr/local/apache2/htdocs/iva/conf/
 COPY    ./${SITE}/iva/img           /usr/local/apache2/htdocs/iva/img/
 
+RUN true
+
 ## API
 COPY    ./build/api                 /usr/local/apache2/htdocs/api
 COPY    ./${SITE}/api/conf          /usr/local/apache2/htdocs/api/conf/

package.json

@@ -1,6 +1,6 @@
 {
   "name": "jsorolla",
-  "version": "2.3.0",
+  "version": "2.3.1",
   "description": "JSorolla is a JavaScript bioinformatic library for data analysis and genomics visualization",
   "repository": {
     "type": "git",

src/core/clients/cellbase/cellbase-client.js

@@ -72,7 +72,7 @@ export class CellBaseClient {
             })
             .catch(e => {
                 console.error(e);
-                globalEvent("signingInError", {value: "Cellbase host not available."});
+                // globalEvent("signingInError", {value: "Cellbase host not available."});
                 globalEvent("hostInit", {host: "cellbase", value: "NOT AVAILABLE"});
             });
     }

src/core/clients/opencga/api/Admin.js

@@ -10,12 +10,12 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  * WARNING: AUTOGENERATED CODE
- *
+ * 
  * This code was generated by a tool.
- * Autogenerated on: 2021-04-30 10:42:30
- *
+ * Autogenerated on: 2022-05-20 02:30:03
+ * 
  * Manual changes to this file may cause unexpected behavior in your application.
- * Manual changes to this file will be overwritten if the code is regenerated.
+ * Manual changes to this file will be overwritten if the code is regenerated. 
  *
 **/
 
@@ -115,4 +115,4 @@ export default class Admin extends OpenCGAParentClass {
         return this._post("admin", null, "users", null, "sync", data);
     }
 
-}
+}

src/core/clients/opencga/api/Alignment.js

@@ -10,12 +10,12 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  * WARNING: AUTOGENERATED CODE
- *
+ * 
  * This code was generated by a tool.
- * Autogenerated on: 2021-04-30 10:42:30
- *
+ * Autogenerated on: 2022-05-20 02:30:03
+ * 
  * Manual changes to this file may cause unexpected behavior in your application.
- * Manual changes to this file will be overwritten if the code is regenerated.
+ * Manual changes to this file will be overwritten if the code is regenerated. 
  *
 **/
 
@@ -62,6 +62,21 @@ export default class Alignment extends OpenCGAParentClass {
         return this._post("analysis", null, "alignment/coverage/index", null, "run", data, params);
     }
 
+    /** Compute gene coverage stats for a given alignment file and a list of genes
+    * @param {Object} data - Gene coverage stats parameters for a given BAM file and a list of genes.
+    * @param {Object} [params] - The Object containing the following optional parameters:
+    * @param {String} [params.study] - study.
+    * @param {String} [params.jobId] - Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not
+    *     provided.
+    * @param {String} [params.jobDependsOn] - Comma separated list of existing job IDs the job will depend on.
+    * @param {String} [params.jobDescription] - Job description.
+    * @param {String} [params.jobTags] - Job tags.
+    * @returns {Promise} Promise object in the form of RestResponse instance.
+    */
+    coverageQcGeneCoverageStatsRun(data, params) {
+        return this._post("analysis", null, "alignment/coverage/qc/geneCoverageStats", null, "run", data, params);
+    }
+
     /** Query the coverage of an alignment file for regions or genes
     * @param {String} file - File ID.
     * @param {Object} [params] - The Object containing the following optional parameters:
@@ -113,7 +128,7 @@ export default class Alignment extends OpenCGAParentClass {
 
     /** Deeptools is a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as
     * ChIP-seq, RNA-seq or MNase-seq.
-    * @param {Object} data - Deeptools parameters.
+    * @param {Object} data - Deeptools parameters. Supported Deeptools commands: bamCoverage, bamCompare.
     * @param {Object} [params] - The Object containing the following optional parameters:
     * @param {String} [params.study] - study.
     * @param {String} [params.jobId] - Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not
@@ -159,7 +174,7 @@ export default class Alignment extends OpenCGAParentClass {
 
     /** Picard is a set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as
     * SAM/BAM/CRAM and VCF. Supported Picard commands: CollectHsMetrics, CollectWgsMetrics, BedToIntervalList
-    * @param {Object} data - Picard parameters.
+    * @param {Object} data - Picard parameters. Supported Picard commands: CollectHsMetrics, CollectWgsMetrics, BedToIntervalList.
     * @param {Object} [params] - The Object containing the following optional parameters:
     * @param {String} [params.study] - study.
     * @param {String} [params.jobId] - Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not
@@ -173,24 +188,10 @@ export default class Alignment extends OpenCGAParentClass {
         return this._post("analysis", null, "alignment/picard", null, "run", data, params);
     }
 
-    /** Compute gene coverage stats for a given alignment file and a list of genes
-    * @param {Object} data - Gene coverage stats parameters for a given BAM file and a list of genes.
-    * @param {Object} [params] - The Object containing the following optional parameters:
-    * @param {String} [params.study] - study.
-    * @param {String} [params.jobId] - Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not
-    *     provided.
-    * @param {String} [params.jobDependsOn] - Comma separated list of existing job IDs the job will depend on.
-    * @param {String} [params.jobDescription] - Job description.
-    * @param {String} [params.jobTags] - Job tags.
-    * @returns {Promise} Promise object in the form of RestResponse instance.
-    */
-    genecoveragestatsQc(data, params) {
-        return this._post("analysis", null, "alignment/qc", null, "genecoveragestats", data, params);
-    }
-
     /** Compute quality control (QC) metrics for a given alignment file (including samtools stats, samtools flag stats, FastQC and HS metrics)
-    * @param {Object} data - Alignment quality control (QC) parameters. The BAM file is mandatory ever but the BED file and the dictionary
-    *     files are only mandatory for computing hybrid-selection (HS) metrics.
+    * @param {Object} data - Alignment quality control (QC) parameters. It computes: stats, flag stats, fastqc and hybrid-selection metrics.
+    *     The BAM file is mandatory ever but the BED fileand the dictionary files are only mandatory for computing hybrid-selection (HS)
+    *     metrics. In order to skip some metrics, use the following keywords (separated by commas): stats, flagstats, fastqc and hsmetrics.
     * @param {Object} [params] - The Object containing the following optional parameters:
     * @param {String} [params.study] - study.
     * @param {String} [params.jobId] - Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not
@@ -235,7 +236,8 @@ export default class Alignment extends OpenCGAParentClass {
 
     /** Samtools is a program for interacting with high-throughput sequencing data in SAM, BAM and CRAM formats. Supported Samtools commands:
     * sort, index, view, stats, flagstat, dict, faidx, depth, plot-bamstats
-    * @param {Object} data - Samtoolstools parameters.
+    * @param {Object} data - Samtools parameters. Supported Samtools commands: sort, index, view, stats, flagstat, dict, faidx, depth, plot-
+    *     bamstats.
     * @param {Object} [params] - The Object containing the following optional parameters:
     * @param {String} [params.study] - study.
     * @param {String} [params.jobId] - Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not
@@ -249,4 +251,4 @@ export default class Alignment extends OpenCGAParentClass {
         return this._post("analysis", null, "alignment/samtools", null, "run", data, params);
     }
 
-}
+}