diff --git a/src/sites/iva/conf/config.js b/src/sites/iva/conf/config.js index 0d21e3a31..04d5412a7 100644 --- a/src/sites/iva/conf/config.js +++ b/src/sites/iva/conf/config.js @@ -92,8 +92,8 @@ const opencga = { const CATALOG_NAVBAR_MENU = { id: "catalog", name: "Catalog", - visibility: "public", icon: "img/tools/icons/aggregation2.svg", + visibility: "public", submenu: [ // { // id: "projects", @@ -188,6 +188,325 @@ const CATALOG_NAVBAR_MENU = { ] }; +const ANALYSIS_TOOL = { + id: "analysis", + name: "Analysis", + description: "", + icon: "img/tools/icons/aggregation.svg", + visibility: "public", + submenu: [ + { + name: "Analysis Execution", + category: true, + visibility: "public" + }, + { + id: "tool-analysis", + name: "Tool Executor", + description: "", + icon: "", + visibility: "public" + }, + { + id: "custom-tool-builder", + name: "Custom Tool Builder", + description: "", + icon: "", + visibility: "public" + }, + { + id: "workflow-analysis", + name: "Workflow Executor", + description: "", + icon: "", + visibility: "public" + }, + { + separator: true, + visibility: "public" + }, + { + name: "Summary Stats", + category: true, + visibility: "public" + }, + { + id: "sample-variant-stats", + name: "Sample Variant Stats", + acronym: "SVS", + description: "", + icon: "", + visibility: "public" + }, + { + id: "cohort-variant-stats", + name: "Cohort Variant Stats", + acronym: "CS", + description: "", + icon: "", + visibility: "public" + }, + { + separator: true, + visibility: "public" + }, + { + name: "Association Analysis", + category: true, + visibility: "public" + }, + { + id: "gwas", + name: "Genome-Wide Association Study (GWAS)", + acronym: "GWAS", + description: "Study of a genome-wide set of genetic variants in different individuals to see if any variant is associated with a trait", + icon: "img/tools/icons/aggregation.svg", + visibility: "public", + }, + { + separator: true, + visibility: "public" + }, + { + name: "Sample Analysis", + category: true, + visibility: "public" + }, + { + id: "knockout", + name: "Knockout Analysis", + acronym: "KO", + description: "", + icon: "", + visibility: "public" + }, + { + id: "sample-eligibility", + name: "Eligibility Analysis", + description: "", + icon: "", + visibility: "public" + }, + { + separator: true, + visibility: "public" + }, + { + name: "Individual Analysis", + category: true, + visibility: "public" + }, + { + id: "inferred-sex", + name: "Sex Inference", + acronym: "SI", + description: "", + icon: "", + visibility: "public" + }, + { + id: "individual-relatedness", + name: "Relatedness", + acronym: "RL", + description: "", + icon: "", + visibility: "public" + }, + { + id: "mendelian-error", + name: "Mendelian Errors", + acronym: "ME", + description: "", + icon: "", + visibility: "public" + }, + { + separator: true, + visibility: "public" + }, + { + name: "Cancer Analysis", + category: true, + visibility: "public" + }, + { + id: "mutational-signature", + name: "Mutational Signature", + acronym: "SG", + description: "", + icon: "img/tools/icons/aggregation.svg", + visibility: "public" + }, + { + separator: true, + visibility: "public" + }, + { + name: "Quality Control", + category: true, + visibility: "public" + }, + { + id: "sample-qc", + name: "Sample Quality Control", + description: "Calculate different genetic checks and metrics and store data in Sample Catalog", + icon: "img/tools/icons/aggregation.svg", + visibility: "public" + }, + { + id: "individual-qc", + name: "Individual Quality Control", + description: "Calculate different genetic checks and metrics and store data in Individual Catalog", + icon: "", + visibility: "public" + }, + { + id: "family-qc", + name: "Family Quality Control", + description: "Calculate different genetic checks and metrics and store data in Family Catalog", + icon: "", + visibility: "public" + }, + { + separator: true, + visibility: "public" + }, + { + name: "Export", + category: true, + visibility: "public" + }, + { + id: "variant-export", + name: "Variant Export", + acronym: "EX", + description: ` + Filter and export variants, with their annotation and sample genotypes, + from the Variant Storage to a file in multiple supported formats (vcf, json, tped, ensembl vep tab...) + for being shared or processed by an external tool. + `, + icon: "img/tools/icons/aggregation.svg", + visibility: "public" + }, + { + id: "variant-stats-exporter", + name: "Variant Stats Export", + acronym: "VSE", + description: "Export variant stats for different cohorts", + icon: "", + visibility: "public" + }, + { + separator: true, + visibility: "public" + }, + { + name: "External Tools", + category: true, + visibility: "public" + }, + { + id: "beacon", + name: "GA4GH Beacon", + description: ` + `, + thumbnail: "beacon.png", + fa_icon: "fa fa-globe-europe", + icon: "beacon.svg", + visibility: "public" + }, + { + id: "plink", + name: "Plink", + acronym: "Pl", + description: "", + icon: "", + visibility: "public" + }, + { + id: "gatk", + name: "GATK", + acronym: "GT", + description: "", + icon: "", + visibility: "public" + }, + { + id: "bcftools", + name: "BCFtools", + acronym: "GT", + description: "", + icon: "", + visibility: "public" + }, + { + name: "Data Management", + category: true, + visibility: "public" + }, + { + id: "alignment-index", + name: "Alignment Index", + description: "Create a .bai index file.", + icon: "", + visibility: "public" + }, + { + id: "coverage-index", + name: "Coverage Index", + description: "Precompute coverage in a BigWig file", + icon: "", + visibility: "public" + }, + { + separator: true, + visibility: "public" + }, + { + name: "Summary Stats", + category: true, + visibility: "public" + }, + { + id: "alignment-stats", + name: "Alignment Stats", + description: "Compute BAM stats using samtools", + icon: "", + visibility: "public" + }, + { + id: "beacon", + name: "GA4GH Beacon", + description: ` + `, + thumbnail: "beacon.png", + fa_icon: "fa fa-globe-europe", + icon: "beacon.svg", + visibility: "public" + }, + // { + // id: "genomeBrowser", + // title: "Genome Browser", + // acronym: "GB", + // description: ``, + // visibility: "private", + // thumbnail: "screenshot3.png", + // fa_icon: "fa fa-globe-europe", + // icon: "genome_browser.svg" + // + // }, + ] +}; + const SUITE = { id: "suite", name: "OpenCB Suite", @@ -321,7 +640,8 @@ const SUITE = { apps: [ { id: "research", - name: "Research", + name: "Research", // Short name of the app. This is the name that will be displayed in the sidebar + title: "Research Environment", icon: "fa-flask", logo: "img/tools/icons/variant_browser_white.svg", logoAlt: "img/tools/icons/variant_browser.svg", @@ -332,8 +652,8 @@ const SUITE = { titleStyle: "text-align:center;", subtitleStyle: "text-align:center;" }, - title: "Variant Analysis", - subtitle: "Explore variants in real-time and execute analysis", + title: "Research Environment", + subtitle: "Explore variants in real-time and execute analysis and tools", // logo: "img/Zetta_logo.png", logo: "img/tools/icons/variant_browser.svg", content: ` @@ -343,7 +663,9 @@ const SUITE = {

`, links: [ - {title: "Documentation", url: "http://docs.opencb.org/display/iva"}, + { + title: "Documentation", url: "http://docs.opencb.org/display/iva" + }, ] }, menu: [ @@ -362,365 +684,91 @@ const SUITE = { `, }, { - id: "analysis", - name: "Analysis", - description: "", - icon: "img/tools/icons/aggregation.svg", + id: "analysis-tools", + name: "Tools", + icon: "img/tools/icons/variant_browser.svg", visibility: "public", - submenu: [ - { - name: "Analysis Execution", - category: true, - visibility: "public" - }, - { - id: "tool-analysis", - name: "Tool Executor", - description: "", - icon: "", - visibility: "public" - }, - { - id: "custom-tool-builder", - name: "Custom Tool Builder", - description: "", - icon: "", - visibility: "public" - }, - { - id: "workflow-analysis", - name: "Workflow Executor", - description: "", - icon: "", - visibility: "public" - }, - { - separator: true, - visibility: "public" - }, - { - name: "Summary Stats", - category: true, - visibility: "public" - }, - { - id: "sample-variant-stats", - name: "Sample Variant Stats", - acronym: "SVS", - description: "", - icon: "", - visibility: "public" - }, - { - id: "cohort-variant-stats", - name: "Cohort Variant Stats", - acronym: "CS", - description: "", - icon: "", - visibility: "public" - }, - { - separator: true, - visibility: "public" - }, - { - name: "Association Analysis", - category: true, - visibility: "public" - }, - { - id: "gwas", - name: "Genome-Wide Association Study (GWAS)", - acronym: "GWAS", - description: "Study of a genome-wide set of genetic variants in different individuals to see if any variant is associated with a trait", - icon: "img/tools/icons/aggregation.svg", - visibility: "public", - }, - { - separator: true, - visibility: "public" - }, - { - name: "Sample Analysis", - category: true, - visibility: "public" - }, - { - id: "knockout", - name: "Knockout Analysis", - acronym: "KO", - description: "", - icon: "", - visibility: "public" - }, - { - id: "sample-eligibility", - name: "Eligibility Analysis", - description: "", - icon: "", - visibility: "public" - }, - { - separator: true, - visibility: "public" - }, - { - name: "Individual Analysis", - category: true, - visibility: "public" - }, - { - id: "inferred-sex", - name: "Sex Inference", - acronym: "SI", - description: "", - icon: "", - visibility: "public" - }, - { - id: "individual-relatedness", - name: "Relatedness", - acronym: "RL", - description: "", - icon: "", - visibility: "public" - }, - { - id: "mendelian-error", - name: "Mendelian Errors", - acronym: "ME", - description: "", - icon: "", - visibility: "public" - }, - { - separator: true, - visibility: "public" - }, - { - name: "Cancer Analysis", - category: true, - visibility: "public" - }, - { - id: "mutational-signature", - name: "Mutational Signature", - acronym: "SG", - description: "", - icon: "img/tools/icons/aggregation.svg", - visibility: "public" - }, - { - separator: true, - visibility: "public" - }, - { - name: "Quality Control", - category: true, - visibility: "public" - }, - { - id: "sample-qc", - name: "Sample Quality Control", - description: "Calculate different genetic checks and metrics and store data in Sample Catalog", - icon: "img/tools/icons/aggregation.svg", - visibility: "public" - }, - { - id: "individual-qc", - name: "Individual Quality Control", - description: "Calculate different genetic checks and metrics and store data in Individual Catalog", - icon: "", - visibility: "public" - }, - { - id: "family-qc", - name: "Family Quality Control", - description: "Calculate different genetic checks and metrics and store data in Family Catalog", - icon: "", - visibility: "public" - }, - { - separator: true, - visibility: "public" - }, - { - name: "Export", - category: true, - visibility: "public" - }, - { - id: "variant-export", - name: "Variant Export", - acronym: "EX", - description: ` - Filter and export variants, with their annotation and sample genotypes, - from the Variant Storage to a file in multiple supported formats (vcf, json, tped, ensembl vep tab...) - for being shared or processed by an external tool. - `, - icon: "img/tools/icons/aggregation.svg", - visibility: "public" - }, - { - id: "variant-stats-exporter", - name: "Variant Stats Export", - acronym: "VSE", - description: "Export variant stats for different cohorts", - icon: "", - visibility: "public" - }, - { - separator: true, - visibility: "public" - }, - { - name: "External Tools", - category: true, - visibility: "public" - }, - { - id: "beacon", - name: "GA4GH Beacon", - description: ` - `, - thumbnail: "beacon.png", - fa_icon: "fa fa-globe-europe", - icon: "beacon.svg", - visibility: "public" - }, - { - id: "plink", - name: "Plink", - acronym: "Pl", - description: "", - icon: "", - visibility: "public" - }, - { - id: "gatk", - name: "GATK", - acronym: "GT", - description: "", - icon: "", - visibility: "public" - }, - { - id: "bcftools", - name: "BCFtools", - acronym: "GT", - description: "", - icon: "", - visibility: "public" - }, - ] + featured: true, + description: ` +

Explore all variants identified by the current study.

+ + `, }, { - id: "alignment", - name: "Alignment", - description: "", - icon: "img/tools/icons/alignment.svg", - visibility: "none", - submenu: [ - { - name: "Data Management", - category: true, - visibility: "public" - }, - { - id: "alignment-index", - name: "Alignment Index", - description: "Create a .bai index file.", - icon: "", - visibility: "public" - }, - { - id: "coverage-index", - name: "Coverage Index", - description: "Precompute coverage in a BigWig file", - icon: "", - visibility: "public" - }, - { - separator: true, - visibility: "public" - }, - { - name: "Summary Stats", - category: true, - visibility: "public" - }, - { - id: "alignment-stats", - name: "Alignment Stats", - description: "Compute BAM stats using samtools", - icon: "", - visibility: "public" - } - ] + id: "workflow-manager", + name: "Workflow Manager", + icon: "img/tools/icons/variant_browser.svg", + visibility: "public", + featured: true, + description: ` +

Explore all variants identified by the current study.

+ + `, }, { - id: "tools", - name: "Other Tools", + id: "jupyter-notebook", + name: "Jupyter Notebooks", icon: "img/tools/icons/variant_browser.svg", - visibility: "none", - submenu: [ - { - id: "rga", - name: "Recessive Variant Analysis", - acronym: "", - icon: "", - description: "", - visibility: "public" - }, - { - id: "beacon", - name: "GA4GH Beacon", - description: ` - `, - thumbnail: "beacon.png", - fa_icon: "fa fa-globe-europe", - icon: "beacon.svg", - visibility: "public" - } - // { - // id: "genomeBrowser", - // title: "Genome Browser", - // acronym: "GB", - // description: ``, - // visibility: "private", - // thumbnail: "screenshot3.png", - // fa_icon: "fa fa-globe-europe", - // icon: "genome_browser.svg" - // - // }, - ] + visibility: "public", + featured: true, + description: ` +

Explore all variants identified by the current study.

+ + `, + }, + { + id: "my-analysis", + name: "My Analysis", + icon: "img/tools/icons/variant_browser.svg", + visibility: "public", + featured: true, + description: ` +

Explore all variants identified by the current study.

+ + `, + }, + { + id: "file-data-manager", + name: "Data Manager", + icon: "img/tools/icons/variant_browser.svg", + visibility: "public", + featured: true, + description: ` +

Explore all variants identified by the current study.

+ + `, }, - CATALOG_NAVBAR_MENU, ], - fileExplorer: { - visibility: "private" - }, - jobMonitor: { - visibility: "private" - }, - // TODO This option seems to be deprecated, do we need to keep it? - search: { - placeholder: "Search", - visible: false - }, + // fileExplorer: { + // visibility: "private" + // }, + // jobMonitor: { + // visibility: "private" + // }, + // search: { + // placeholder: "Search", + // visible: false + // }, }, { id: "clinical", - name: "Clinical Analysis", + name: "Clinical", + title: "Clinical Analysis", icon: "fa-stethoscope", logo: "img/tools/icons/interpretation_portal_white.svg", logoAlt: "img/tools/icons/interpretation_portal.svg", @@ -744,9 +792,11 @@ const SUITE = { }, menu: [ { - id: "clinicalAnalysisPortal", + id: "clinical-analysis-portal", name: "Case Interpreter Portal", icon: "img/tools/icons/interpretation_portal.svg", + visibility: "public", + featured: true, description: `

Explore and review Clinical Interpretations analysis

`, + thumbnail: "interpretation_portal.png", + }, + { + id: "disease-panel-browser", + name: "Disease Panels", + icon: "img/tools/icons/interpretation_portal.svg", visibility: "public", + featured: true, + description: ` +

Explore and review Clinical Interpretations analysis

+ + `, thumbnail: "interpretation_portal.png", + }, + { + id: "cvdb-browser", + name: "Clinical Variant DB", + icon: "img/tools/icons/interpretation_portal.svg", + visibility: "public", featured: true, + description: ` +

Explore and review Clinical Interpretations analysis

+ + `, + thumbnail: "interpretation_portal.png", }, { - id: "clinical", - name: "Management", + id: "clinical-configuration", + name: "Configuration", icon: "img/tools/icons/interpretation_portal.svg", visibility: "public", - submenu: [ - { - name: "Case Management", - category: true, - visibility: "public" - }, - { - id: "clinical-analysis-create", - name: "Create Case", - icon: "img/tools/icons/genome_browser.svg", - description: ` -

Create a clinical Case

- - `, - visibility: "public", - featured: true, - } - ] + featured: true, + description: ` +

Explore and review Clinical Interpretations analysis

+ + `, + thumbnail: "interpretation_portal.png", }, - CATALOG_NAVBAR_MENU ], - fileExplorer: { - visibility: "private" - }, - jobMonitor: { - visibility: "private" - }, - search: { - placeholder: "Search", - visible: false - }, + // fileExplorer: { + // visibility: "private" + // }, + // jobMonitor: { + // visibility: "private" + // }, + // search: { + // placeholder: "Search", + // visible: false + // }, }, { id: "catalog", - name: "Data Catalog", + name: "Catalog", + title: "Data Catalog", icon: "fa-archive", logo: "img/tools/icons/interpretation_portal_white.svg", logoAlt: "img/tools/icons/interpretation_portal.svg", @@ -824,24 +890,74 @@ const SUITE = { }, menu: [ { - id: "workflow-manager", - name: "Workflow Manager", - icon: "img/tools/icons/interpretation_portal.svg", + id: "sample-browser", + name: "Sample and Individual", + icon: "img/tools/icons/variant_browser.svg", + visibility: "public", + featured: true, description: ` -

Explore and review Clinical Interpretations analysis

+

Explore all variants identified by the current study.

`, + }, + { + id: "individual-browsers", + name: "Browsers", + icon: "img/tools/icons/variant_browser.svg", visibility: "public", - thumbnail: "interpretation_portal.png", + featured: true, + description: ` +

Explore all variants identified by the current study.

+ + `, }, + // { + // id: "workflow-manager", + // name: "Workflow Manager", + // icon: "img/tools/icons/variant_browser.svg", + // visibility: "public", + // featured: true, + // description: ` + //

Explore all variants identified by the current study.

+ // + // `, + // }, { - id: "clinical-configuration", - name: "Configuration", - icon: "img/tools/icons/interpretation_portal.svg", + id: "cohort-browser", + name: "Cohort Builder", + icon: "img/tools/icons/variant_browser.svg", visibility: "public", + featured: true, + description: ` +

Explore all variants identified by the current study.

+ + `, + }, + { + id: "variable-set-browser", + name: "Custom Annotations", + icon: "img/tools/icons/variant_browser.svg", + visibility: "public", + featured: true, + description: ` +

Explore all variants identified by the current study.

+ + `, }, ], // fileExplorer: { @@ -912,7 +1028,7 @@ const SUITE = { icon: "img/tools/icons/variant_browser.svg", description: "", visibility: "public", - featured: false, + featured: true, }, // { // id: "catalog-admin", @@ -951,16 +1067,16 @@ const SUITE = { // featured: true, // }, ], - fileExplorer: { - visibility: "private" - }, - jobMonitor: { - visibility: "none" - }, - search: { - placeholder: "Search", - visible: false - }, + // fileExplorer: { + // visibility: "private" + // }, + // jobMonitor: { + // visibility: "none" + // }, + // search: { + // placeholder: "Search", + // visible: false + // }, } ] }; diff --git a/src/webcomponents/commons/layout/layout-secondary-bar.js b/src/webcomponents/commons/layout/layout-secondary-bar.js index c6650b6d1..12d9d40da 100644 --- a/src/webcomponents/commons/layout/layout-secondary-bar.js +++ b/src/webcomponents/commons/layout/layout-secondary-bar.js @@ -39,7 +39,7 @@ export default class LayoutSecondaryBar extends LitElement {
- ${this.app.name || "-"} + ${this.app.title || this.app.name || "-"}