Merge branch 'release-2.12.x' into TASK-5693

opencb · Apr 1, 2024 · 1125efa · 1125efa
2 parents 69a8809 + a120256
commit 1125efa
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Showing 32 changed files with 390 additions and 419 deletions.
diff --git a/docker/docker-build.py b/docker/docker-build.py
@@ -15,6 +15,7 @@
 parser.add_argument('--images', help="comma separated list of images to be made, e.g. app", default="app")
 parser.add_argument('--tag', help="the tag for this code, e.g. v2.0.0")
 parser.add_argument('--build-folder', help="the location of the build folder, if not default location")
+parser.add_argument('--platform', help="specify the target platform for the build image, e.g. 'linux/amd64'", default="linux/amd64")
 parser.add_argument('--username', help="credentials for dockerhub (REQUIRED if deleting from DockerHub)")
 parser.add_argument('--password', help="credentials for dockerhub (REQUIRED if deleting from DockerHub)")
 
@@ -81,7 +82,7 @@ def build():
             site = "build/custom-sites" + "/" + image
 
         print(shell_colors['blue'] + "Building " + organisation + "/iva-" + image + ":" + tag + " ..." + shell_colors['reset'])
-        run("docker build -t " + organisation + "/iva-" + image + ":" + tag + " --build-arg SITE=" + site + " -f " + build_folder + "/docker/iva-app/Dockerfile " + build_folder)
+        run("docker build --platform " + platform + " -t " + organisation + "/iva-" + image + ":" + tag + " --build-arg SITE=" + site + " -f " + build_folder + "/docker/iva-app/Dockerfile " + build_folder)
 
 def tag_latest(image):
     latest_tag = os.popen(("curl -s https://registry.hub.docker.com/v1/repositories/" + organisation + "/iva-" + image + "/tags"
@@ -163,6 +164,11 @@ def delete():
 else:
     images = args.images.split(",")
 
+# 5. init platform: set platform to default value if not set
+if args.platform is not None:
+    platform = args.platform
+else:
+    platform = "linux/amd64"
 
 ## Execute the action
 if args.action == "build":

diff --git a/src/sites/iva/conf/config.js b/src/sites/iva/conf/config.js
@@ -22,7 +22,7 @@ const hosts = [
         url: "https://ws.opencb.org/opencga-prod"
     },
     {
-        id: "test",
+        id: "test1",
         url: "https://demo.app.zettagenomics.com/opencga"
     },
     {

diff --git a/src/sites/iva/iva-app.js b/src/sites/iva/iva-app.js
@@ -1839,7 +1839,7 @@ class IvaApp extends LitElement {
                     <div class="content col-md-8 col-md-offset-2" id="inferred-sex-analysis">
                         <inferred-sex-analysis
                             .opencgaSession="${this.opencgaSession}"
-                            .title="">
+                            .config=${{title: ""}}>
                         </inferred-sex-analysis>
                     </div>
                 ` : null}
@@ -1848,7 +1848,7 @@ class IvaApp extends LitElement {
                     <div class="content col-md-8 col-md-offset-2" id="individual-relatedness-analysis">
                         <individual-relatedness-analysis
                             .opencgaSession="${this.opencgaSession}"
-                            .title="">
+                            .config=${{title: ""}}>
                         </individual-relatedness-analysis>
                     </div>
                 ` : null}
@@ -1863,7 +1863,7 @@ class IvaApp extends LitElement {
                     <div class="content col-md-8 col-md-offset-2" id="sample-qc-analysis">
                         <sample-qc-analysis
                             .opencgaSession="${this.opencgaSession}"
-                            .title="">
+                            .config=${{title: ""}}>
                         </sample-qc-analysis>
                     </div>
                 ` : null}
@@ -1872,7 +1872,7 @@ class IvaApp extends LitElement {
                     <div class="content col-md-8 col-md-offset-2" id="individual-qc-analysis">
                         <individual-qc-analysis
                             .opencgaSession="${this.opencgaSession}"
-                            .title="">
+                            .config=${{title: ""}}>
                         </individual-qc-analysis>
                     </div>
                 ` : null}
@@ -1881,7 +1881,7 @@ class IvaApp extends LitElement {
                     <div class="content col-md-8 col-md-offset-2" id="family-qc-analysis">
                         <family-qc-analysis
                             .opencgaSession="${this.opencgaSession}"
-                            .title="">
+                            .config=${{title: ""}}>
                         </family-qc-analysis>
                     </div>
                 ` : null}

diff --git a/src/webcomponents/clinical/analysis/exomiser-analysis.js b/src/webcomponents/clinical/analysis/exomiser-analysis.js
@@ -15,7 +15,6 @@
  */
 
 import {LitElement, html} from "lit";
-import FormUtils from "../../commons/forms/form-utils";
 import AnalysisUtils from "../../commons/analysis/analysis-utils.js";
 import UtilsNew from "../../../core/utils-new.js";
 import "../../commons/forms/data-form.js";
@@ -40,16 +39,16 @@ export default class ExomiserAnalysis extends LitElement {
             opencgaSession: {
                 type: Object
             },
-            title: {
-                type: String
+            config: {
+                type: Object
             },
         };
     }
 
     #init() {
-        this.TOOL = "interpreter-exomiser";
-        this.TITLE = "Interpreter Exomiser";
-        this.DESCRIPTION = "Executes an Exomiser Interpretation analysis";
+        this.ANALYSIS_TOOL = "interpreter-exomiser";
+        this.ANALYSIS_TITLE = "Interpreter Exomiser";
+        this.ANALYSIS_DESCRIPTION = "Executes an Exomiser Interpretation analysis";
 
         this.DEFAULT_TOOLPARAMS = {};
         // Make a deep copy to avoid modifying default object.
@@ -130,10 +129,10 @@ export default class ExomiserAnalysis extends LitElement {
         };
         const params = {
             study: this.opencgaSession.study.fqn,
-            ...AnalysisUtils.fillJobParams(this.toolParams, this.TOOL),
+            ...AnalysisUtils.fillJobParams(this.toolParams, this.ANALYSIS_TOOL),
         };
         AnalysisUtils.submit(
-            this.TITLE,
+            this.ANALYSIS_TITLE,
             this.opencgaSession.opencgaClient.clinical()
                 .runInterpreterExomiser(toolParams, params),
             this,
@@ -189,11 +188,12 @@ export default class ExomiserAnalysis extends LitElement {
         ];
 
         return AnalysisUtils.getAnalysisConfiguration(
-            this.TOOL,
-            this.title ?? this.TITLE,
-            this.DESCRIPTION,
+            this.ANALYSIS_TOOL,
+            this.ANALYSIS_TITLE,
+            this.ANALYSIS_DESCRIPTION,
             params,
             this.check(),
+            this.config
         );
     }
 

diff --git a/src/webcomponents/clinical/analysis/hrdetect-analysis.js b/src/webcomponents/clinical/analysis/hrdetect-analysis.js
@@ -40,12 +40,12 @@ export default class HRDetectAnalysis extends LitElement {
             opencgaSession: {
                 type: Object
             },
-            title: {
-                type: String
-            },
             active: {
                 type: Boolean,
             },
+            config: {
+                type: Object
+            },
         };
     }
 
@@ -339,10 +339,11 @@ export default class HRDetectAnalysis extends LitElement {
 
         return AnalysisUtils.getAnalysisConfiguration(
             this.ANALYSIS_TOOL,
-            this.title ?? this.ANALYSIS_TITLE,
+            this.ANALYSIS_TITLE,
             this.ANALYSIS_DESCRIPTION,
             params,
-            this.check()
+            this.check(),
+            this.config
         );
     }
 

diff --git a/src/webcomponents/clinical/analysis/mutational-signature-analysis.js b/src/webcomponents/clinical/analysis/mutational-signature-analysis.js
@@ -42,12 +42,12 @@ export default class MutationalSignatureAnalysis extends LitElement {
             opencgaSession: {
                 type: Object
             },
-            title: {
-                type: String
-            },
             active: {
                 type: Boolean,
             },
+            config: {
+                type: Object
+            },
         };
     }
 
@@ -451,10 +451,11 @@ export default class MutationalSignatureAnalysis extends LitElement {
 
         return AnalysisUtils.getAnalysisConfiguration(
             this.ANALYSIS_TOOL,
-            this.title ?? this.ANALYSIS_TITLE,
+            this.ANALYSIS_TITLE,
             this.ANALYSIS_DESCRIPTION,
             params,
             this.check(),
+            this.config
         );
     }
 

diff --git a/src/webcomponents/clinical/analysis/rd-tiering-analysis.js b/src/webcomponents/clinical/analysis/rd-tiering-analysis.js
@@ -41,16 +41,16 @@ export default class RdTieringAnalysis extends LitElement {
             opencgaSession: {
                 type: Object,
             },
-            title: {
-                type: String
+            config: {
+                type: Object
             },
         };
     }
 
     #init() {
-        this.TOOL = "rd-tiering";
-        this.TITLE = "RD Tiering Interpretation";
-        this.DESCRIPTION = "Executes an RD Tiering Interpreation analysis job";
+        this.ANALYSIS_TOOL = "rd-tiering";
+        this.ANALYSIS_TITLE = "RD Tiering Interpretation";
+        this.ANALYSIS_DESCRIPTION = "Executes an RD Tiering Interpreation analysis job";
 
         this.DEFAULT_TOOLPARAMS = {};
         // Make a deep copy to avoid modifying default object.
@@ -98,10 +98,10 @@ export default class RdTieringAnalysis extends LitElement {
         };
         const params = {
             study: this.opencgaSession.study.fqn,
-            ...AnalysisUtils.fillJobParams(this.toolParams, this.TOOL),
+            ...AnalysisUtils.fillJobParams(this.toolParams, this.ANALYSIS_TOOL),
         };
         AnalysisUtils.submit(
-            this.TITLE,
+            this.ANALYSIS_TITLE,
             this.opencgaSession.opencgaClient.clinical()
                 .runInterpreterTiering(toolParams, params),
             this,
@@ -193,11 +193,12 @@ export default class RdTieringAnalysis extends LitElement {
         ];
 
         return AnalysisUtils.getAnalysisConfiguration(
-            this.TOOL,
-            this.title ?? this.TITLE,
-            this.DESCRIPTION,
+            this.ANALYSIS_TOOL,
+            this.ANALYSIS_TITLE,
+            this.ANALYSIS_DESCRIPTION,
             params,
-            this.check()
+            this.check(),
+            this.config
         );
     }
 

diff --git a/src/webcomponents/commons/analysis/analysis-utils.js b/src/webcomponents/commons/analysis/analysis-utils.js
@@ -111,13 +111,15 @@ export default class AnalysisUtils {
         ];
     }
 
-    static getAnalysisConfiguration(id, title, description, paramSections, check) {
+    static getAnalysisConfiguration(id, title, description, paramSections, check, config = {}) {
         return {
             id: id,
-            title: title,
-            description: description,
+            icon: config.icon,
+            title: config.title || title,
+            description: config.description || description,
             display: {
                 // defaultLayout: "vertical"
+                ...config.display
             },
             sections: [
                 {

diff --git a/src/webcomponents/commons/filters/variant-file-format-filter.js b/src/webcomponents/commons/filters/variant-file-format-filter.js
@@ -108,7 +108,7 @@ export default class VariantFileFormatFilter extends LitElement {
     render() {
         return html`
             <data-form
-                .data=${this._sampleData}
+                .data="${this._sampleData}"
                 .config="${this._config}"
                 @fieldChange="${this.filterChange}">
             </data-form>
@@ -124,7 +124,7 @@ export default class VariantFileFormatFilter extends LitElement {
                 collapsable: true,
                 titleVisible: false,
                 titleWidth: 2,
-                defaultValue: "-",
+                defaultValue: "",
                 defaultLayout: "vertical"
             },
             sections: [
@@ -141,9 +141,9 @@ export default class VariantFileFormatFilter extends LitElement {
                             type: "input-number",
                             comparators: this.depthIndex?.type === "RANGE_LT" ? "<,>=" : "<=,>",
                             allowedValues: this.depthIndex?.thresholds,
-                            defaultValue: "",
                             display: {
-                                visible: () => this.depthIndex?.thresholds?.length > 0
+                                defaultValue: "",
+                                visible: () => this.depthIndex?.thresholds?.length > 0,
                             }
                         },
                         {
@@ -152,9 +152,9 @@ export default class VariantFileFormatFilter extends LitElement {
                             type: "input-number",
                             comparators: this.afIndex?.type === "RANGE_LT" ? "<,>=" : "<=,>",
                             allowedValues: this.afIndex?.thresholds,
-                            defaultValue: "",
                             display: {
-                                visible: () => this.afIndex?.thresholds?.length > 0
+                                defaultValue: "",
+                                visible: () => this.afIndex?.thresholds?.length > 0,
                             }
                         },
                         {
@@ -163,9 +163,9 @@ export default class VariantFileFormatFilter extends LitElement {
                             type: "input-number",
                             comparators: this.extVafIndex?.type === "RANGE_LT" ? "<,>=" : "<=,>",
                             allowedValues: this.extVafIndex?.thresholds,
-                            defaultValue: "",
                             display: {
-                                visible: () => this.extVafIndex?.thresholds?.length > 0
+                                defaultValue: "",
+                                visible: () => this.extVafIndex?.thresholds?.length > 0,
                             }
                         }
                     ]

diff --git a/src/webcomponents/commons/filters/variant-file-info-filter.js b/src/webcomponents/commons/filters/variant-file-info-filter.js
@@ -427,7 +427,7 @@ export default class VariantFileInfoFilter extends LitElement {
     render() {
         return html`
             <data-form
-                .data=${this.fileDataQuery}
+                .data="${this.fileDataQuery}"
                 .config="${this._config}"
                 @fieldChange="${this.filterChange}">
             </data-form>
@@ -469,7 +469,9 @@ export default class VariantFileInfoFilter extends LitElement {
                         allowedValues: field.allowedValues,
                         multiple: field.multiple ?? false,
                         maxOptions: field.maxOptions ?? 1,
-                        defaultValue: "",
+                        display: {
+                            defaultValue: "",
+                        },
                     }))
                 ],
             };
@@ -483,7 +485,7 @@ export default class VariantFileInfoFilter extends LitElement {
                 collapsable: true,
                 titleVisible: false,
                 titleWidth: 2,
-                defaultValue: "-",
+                defaultValue: "",
                 defaultLayout: "vertical"
             },
             sections: _sections,

diff --git a/src/webcomponents/variant/analysis/cohort-variant-stats-analysis.js b/src/webcomponents/variant/analysis/cohort-variant-stats-analysis.js
@@ -16,7 +16,6 @@
 
 import {LitElement, html} from "lit";
 import AnalysisUtils from "../../commons/analysis/analysis-utils.js";
-import FormUtils from "../../commons/forms/form-utils.js";
 import UtilsNew from "../../../core/utils-new.js";
 import "../../commons/forms/data-form.js";
 
@@ -40,8 +39,8 @@ export default class CohortVariantStatsAnalysis extends LitElement {
             opencgaSession: {
                 type: Object
             },
-            title: {
-                type: String
+            config: {
+                type: Object
             },
         };
     }
@@ -191,10 +190,11 @@ export default class CohortVariantStatsAnalysis extends LitElement {
 
         return AnalysisUtils.getAnalysisConfiguration(
             this.ANALYSIS_TOOL,
-            this.title ?? this.ANALYSIS_TITLE,
+            this.ANALYSIS_TITLE,
             this.ANALYSIS_DESCRIPTION,
             params,
-            this.check()
+            this.check(),
+            this.config
         );
     }