Merge branch 'TASK-8076' of github.com:opencb/jsorolla into TASK-8076

Author: imedina

src/core/utils-new.js

@@ -645,7 +645,7 @@ export default class UtilsNew {
         const detail = internal.detail;
 
         // Get default filters
-        const defaultFilter = external?.menu?.defaultFilter || {};
+        const defaultFilter = external?.menu?.defaultFilter || null;
 
         if (external?.menu?.sections?.length) {
             sections = UtilsNew.mergeSections(sections, external.menu.sections);

src/webcomponents/clinical/clinical-analysis-browser.js

@@ -226,6 +226,18 @@ export default class ClinicalAnalysisBrowser extends LitElement {
                                 title: "Priority",
                                 description: ""
                             },
+                            {
+                                id: "flags",
+                                title: "Flags",
+                                description: "",
+                                quick: true,
+                            },
+                            {
+                                id: "analysts",
+                                title: "Analysts",
+                                description: "",
+                                quick: true,
+                            },
                             {
                                 id: "creationDate",
                                 title: "Creation Date",

src/webcomponents/commons/filters-toolbar.js

@@ -611,7 +611,7 @@ export default class FiltersToolbar extends LitElement {
     renderFilterItems(items, highlightActiveFilter = true, showFilterDelete = false) {
         return items.map(item => {
             const isActive = highlightActiveFilter && UtilsNew.objectCompare(this.preparedQuery, item.query);
-            const filterParams = Object.keys(item.query)
+            const filterParams = Object.keys(item.query || {})
                 .filter(key => key !== "study" && !!item.query[key]);
             const filterTooltip = filterParams
                 .map(key => `<b>${key}</b> = ${item.query[key]}`)
@@ -827,7 +827,8 @@ export default class FiltersToolbar extends LitElement {
             },
             sections: [],
             examples: [],
-            defaultFilter: {},
+            filters: [],
+            defaultFilter: null,
             searchButton: true,
             searchButtonText: "Search",
             searchButtonIcon: "fas fa-search",

src/webcomponents/commons/opencga-browser-filter.js

@@ -108,6 +108,8 @@ export default class OpencgaBrowserFilter extends LitElement {
             "type": "type",
             "scope": "scope",
             "internalStatus": "internal.status.id",
+            "flags": "flags.id",
+            "analysts": "analysts.id",
         };
     }
 
@@ -162,6 +164,8 @@ export default class OpencgaBrowserFilter extends LitElement {
             case "type":
             case "scope":
             case "internalStatus":
+            case "flags":
+            case "analysts":
                 content = html`
                     <catalog-distinct-autocomplete
                         .value="${preparedQuery[subsection.id]}"

src/webcomponents/variant/interpretation/variant-interpreter-browser-cancer.js

@@ -45,6 +45,9 @@ class VariantInterpreterBrowserCancer extends LitElement {
             title: {
                 type: String,
             },
+            query: {
+                type: Object,
+            },
             settings: {
                 type: Object
             },
@@ -57,11 +60,8 @@ class VariantInterpreterBrowserCancer extends LitElement {
     #init() {
         this.COMPONENT_ID = "variant-interpreter-cancer-snv";
         this._prefix = UtilsNew.randomString(8);
-
-        this.query = {};
-        this.activeFilterFilters = [];
-        this.savedVariants = [];
-
+        this._query = {};
+        this._files = [];
         this._config = this.getDefaultConfig();
     }
 
@@ -90,56 +90,56 @@ class VariantInterpreterBrowserCancer extends LitElement {
     }
 
     clinicalAnalysisObserver() {
+        // Configuration is using the clinicalAnalysis
+        this._config = this.getDefaultConfig();
+
+        let activeFilterFilters = [];
+        let query = {};
+
         // Init the active filters with every new Case opened. Then we add the default filters for the given sample.
-        let _activeFilterFilters;
         if (this.settings?.menu?.examples?.length > 0) {
             // Load custom filters if configured
             // We need to clone to make sure we reset active fields
-            _activeFilterFilters = UtilsNew.objectClone(this.settings.menu.examples);
+            activeFilterFilters = UtilsNew.objectClone(this.settings.menu.examples);
         } else {
             // Load default filters if not custom defined
-            _activeFilterFilters = this._config?.filter?.examples ? [...this._config.filter.examples] : [];
+            activeFilterFilters = this._config?.filter?.examples ? [...this._config.filter.examples] : [];
         }
 
         // Check for adding the examples filters section
-        if (_activeFilterFilters?.length > 0) {
-            _activeFilterFilters.unshift({
+        if (activeFilterFilters?.length > 0) {
+            activeFilterFilters.unshift({
                 category: true,
                 name: "Example Filters",
             });
         }
 
-        this.somaticSample = this.clinicalAnalysis.proband.samples.find(sample => sample.somatic);
-        if (this.somaticSample) {
-            // Init query object if needed
-            if (!this.query) {
-                this.query = {};
-            }
-
+        // get the somatic sample
+        const somaticSample = this.clinicalAnalysis.proband.samples.find(sample => sample.somatic);
+        if (somaticSample) {
             // 1. 'sample' query param: if sample is not defined then we must set the sample and genotype
-            if (!this.query?.sample) {
+            if (!query?.sample) {
                 // We do not add GT filter ":0/1,1/1,NA" in cancer interpreter anymore
                 // because variants with weird GT would not be displayed
-                this.query.sample = this.somaticSample.id;
+                query.sample = somaticSample.id;
             }
 
             // 2. 'panel' query param: add case panels to query object
             if (this.clinicalAnalysis.interpretation?.panels?.length > 0) {
-                this.query.panel = this.clinicalAnalysis.interpretation.panels.map(panel => panel.id).join(",");
+                query.panel = this.clinicalAnalysis.interpretation.panels.map(panel => panel.id).join(",");
             } else {
                 if (this.clinicalAnalysis.panels?.length > 0) {
-                    this.query.panel = this.clinicalAnalysis.panels.map(panel => panel.id).join(",");
+                    query.panel = this.clinicalAnalysis.panels.map(panel => panel.id).join(",");
                 }
             }
 
             // 3. panelIntersection param: if panel lock is enabled, this param should be also enabled
             if (this.clinicalAnalysis.panelLocked) {
-                this.query.panelIntersection = true;
+                query.panelIntersection = true;
             }
 
             // 4. Get all files indexed
-            this.indexedFiles = this.clinicalAnalysis.files
-                .filter(file => file.format.toUpperCase() === "VCF");
+            // const indexedFiles = this.clinicalAnalysis.files.filter(file => file.format.toUpperCase() === "VCF");
 
             // 5. 'fileData' query param: fetch non SV files and set init query
             if (this.opencgaSession?.study?.internal?.configuration?.clinical?.interpretation?.variantCallers?.length > 0) {
@@ -153,50 +153,48 @@ class VariantInterpreterBrowserCancer extends LitElement {
                     .filter(vc => vc.dataFilters.findIndex(filter => !filter.source || filter.source === "FILE") !== -1);
 
                 // Files matching the selected Variant Callers
-                this.files = this.clinicalAnalysis.files
+                this._files = this.clinicalAnalysis.files
                     .filter(file => file.format.toUpperCase() === "VCF")
-                    .filter(file =>
-                        nonSvSomaticVariantCallers.findIndex(vc => vc.id.toUpperCase() === file.software?.name?.toUpperCase()) !== -1);
+                    .filter(file => {
+                        return nonSvSomaticVariantCallers.findIndex(vc => vc.id.toUpperCase() === file.software?.name?.toUpperCase()) !== -1;
+                    });
 
-                if (this.files?.length > 0) {
+                if (this._files?.length > 0) {
                     const fileDataFilters = [];
-                    nonSvSomaticVariantCallers
-                        .forEach(vc => {
-                            const filtersWithDefaultValues = vc.dataFilters
-                                .filter(filter => !filter.source || filter.source === "FILE")
-                                .filter(filter => !!filter.defaultValue)
-                                .map(filter => {
-                                    // Notice that defaultValue includes the comparator, eg. =, >, ...
-                                    return filter.id + (filter.id !== "FILTER" ? filter.defaultValue : "=PASS");
-                                });
-
-                            // Only add this file to the filter if we have at least one default value
-                            if (filtersWithDefaultValues.length > 0) {
-                                // We need to find the file for that caller
-                                const fileId = this.files
-                                    .filter(file => file.internal?.variant?.index?.status?.id === "READY")
-                                    .find(file => file.software.name === vc.id)?.name;
-                                if (fileId) {
-                                    fileDataFilters.push(fileId + ":" + filtersWithDefaultValues.join(";"));
-                                }
+                    nonSvSomaticVariantCallers.forEach(vc => {
+                        const filtersWithDefaultValues = vc.dataFilters
+                            .filter(filter => !filter.source || filter.source === "FILE")
+                            .filter(filter => !!filter.defaultValue)
+                            .map(filter => {
+                                // Notice that defaultValue includes the comparator, eg. =, >, ...
+                                return filter.id + (filter.id !== "FILTER" ? filter.defaultValue : "=PASS");
+                            });
+
+                        // Only add this file to the filter if we have at least one default value
+                        if (filtersWithDefaultValues.length > 0) {
+                            // We need to find the file for that caller
+                            const fileId = this._files
+                                .filter(file => file.internal?.variant?.index?.status?.id === "READY")
+                                .find(file => file.software.name === vc.id)?.name;
+                            if (fileId) {
+                                fileDataFilters.push(fileId + ":" + filtersWithDefaultValues.join(";"));
                             }
-                        });
+                        }
+                    });
 
                     // Update query with default 'fileData' parameters
-                    this.query.fileData = fileDataFilters.join(",");
+                    query.fileData = fileDataFilters.join(",");
                 } else {
-                    this.files = this.clinicalAnalysis.files
-                        .filter(file => file.format.toUpperCase() === "VCF");
+                    this._files = this.clinicalAnalysis.files.filter(file => file.format.toUpperCase() === "VCF");
                 }
             } else {
-                this.files = this.clinicalAnalysis.files
-                    .filter(file => file.format.toUpperCase() === "VCF");
+                this._files = this.clinicalAnalysis.files.filter(file => file.format.toUpperCase() === "VCF");
             }
 
             // 6. Read defaultFilter from browser settings
             if (this.settings?.menu?.defaultFilter) {
-                this.query = {
-                    ...this.query,
+                query = {
+                    ...query,
                     ...this.settings.menu.defaultFilter,
                 };
             }
@@ -207,13 +205,13 @@ class VariantInterpreterBrowserCancer extends LitElement {
 
             // Add filter to Active Filter's menu
             // 1. Add variant stats saved queries to the Active Filters menu
-            if (this.somaticSample.qualityControl?.variant?.variantStats?.length > 0) {
-                _activeFilterFilters.push({
+            if (somaticSample.qualityControl?.variant?.variantStats?.length > 0) {
+                activeFilterFilters.push({
                     category: true,
                     name: "Variant Stats Filters",
                 });
-                _activeFilterFilters.push(
-                    ...this.somaticSample.qualityControl.variant.variantStats.map(variantStat => ({
+                activeFilterFilters.push(
+                    ...somaticSample.qualityControl.variant.variantStats.map(variantStat => ({
                         id: variantStat.id,
                         active: false,
                         query: variantStat.query,
@@ -222,21 +220,21 @@ class VariantInterpreterBrowserCancer extends LitElement {
             }
 
             // 2. Add default initial query the active filter menu
-            _activeFilterFilters.unshift({
+            activeFilterFilters.unshift({
                 id: "Default Filter",
                 active: false,
-                query: this.query,
+                query: query,
             });
 
             // Add 'file' filter if 'fileData' exists
-            if (this.files) {
-                const fileNames = this.files
+            if (this._files) {
+                const fileNames = this._files
                     .filter(file => file.internal?.variant?.index?.status?.id === "READY")
                     .map(f => f.name);
                 // Only filter by file if there are more than 1 file indexed
                 if (fileNames.length > 0) {
                     const joinedFileNames = fileNames.join(",");
-                    for (const filter of _activeFilterFilters) {
+                    for (const filter of activeFilterFilters) {
                         if (filter.query?.fileData && !filter.query?.file) {
                             filter.query.file = joinedFileNames;
                         }
@@ -245,35 +243,39 @@ class VariantInterpreterBrowserCancer extends LitElement {
             }
 
             // Set active filters
-            this._config.filter.activeFilters.filters = _activeFilterFilters;
-            const activeFilter = this._config.filter.activeFilters.filters.find(filter => filter.active);
+            this._config.filter.filters = activeFilterFilters;
+            const activeFilter = this._config.filter.filters.find(filter => filter.active);
             if (activeFilter?.query) {
-                this.query = {...this.query, ...activeFilter.query};
+                query = {
+                    ...query,
+                    ...activeFilter.query,
+                };
             }
         } else {
             // No somatic sample found, this is weird scenario but can happen if a case is created empty.
             // We init active filters anyway.
-            this._config.filter.activeFilters.filters = [];
+            this._config.filter.filters = [];
         }
 
-        this.query = {...this.query};
+        // set the initial query: use the query from the property (to restore the previous query) or the default query
+        this._query = this.query ? UtilsNew.objectClone(this.query) : query;
     }
 
     onQueryChange(event) {
-        this.query = event.detail.query;
+        this._query = event.detail.query;
     }
 
     render() {
         return html`
             <variant-interpreter-browser-template
                 .clinicalAnalysis="${this.clinicalAnalysis}"
-                .query="${this.query}"
+                .query="${this._query}"
                 .opencgaSession="${this.opencgaSession}"
                 .settings="${this.settings}"
                 .toolId="${this.COMPONENT_ID}"
                 .config="${this._config}"
                 .active="${this.active}"
-                @queryChange="${this.onQueryChange}">
+                @queryChange="${event => this.onQueryChange(event)}">
             </variant-interpreter-browser-template>
         `;
     }
@@ -316,9 +318,9 @@ class VariantInterpreterBrowserCancer extends LitElement {
                             {
                                 id: "variant-file",
                                 title: "VCF File Filter",
-                                visible: () => this.files?.length > 1,
+                                visible: () => this._files?.length > 1,
                                 params: {
-                                    files: this.files,
+                                    files: this._files,
                                 },
                                 tooltip: tooltips.vcfFile,
                             },