From 449d9da03a3660e216ea0447f39d5704e5d9f46e Mon Sep 17 00:00:00 2001 From: gpveronica Date: Mon, 29 May 2023 11:12:07 +0200 Subject: [PATCH 01/17] wc - Fixed region MoI view Signed-off-by: gpveronica --- .../disease-panel-region-view.js | 40 +++++++++++++------ 1 file changed, 27 insertions(+), 13 deletions(-) diff --git a/src/webcomponents/disease-panel/disease-panel-region-view.js b/src/webcomponents/disease-panel/disease-panel-region-view.js index f222d41072..e66b75a753 100644 --- a/src/webcomponents/disease-panel/disease-panel-region-view.js +++ b/src/webcomponents/disease-panel/disease-panel-region-view.js @@ -131,10 +131,25 @@ export default class DiseasePanelRegionView extends LitElement { formatter: (value, row) => `${row.id}`, halign: this._config.header.horizontalAlign, }, + // { + // id: "modeOfInheritance", + // title: "Mode of Inheritance", + // field: "modeOfInheritance", + // }, { - id: "modeOfInheritance", + id: "modesOfInheritance", title: "Mode of Inheritance", - field: "modeOfInheritance", + field: "modesOfInheritance", + formatter: (value, row) => { + const modesOfInheritanceContent = this.generateList(row.modesOfInheritance, ""); + return String.raw ` + ${modesOfInheritanceContent ? String.raw ` + ` : "-" + } + `; + }, }, { id: "confidence", @@ -190,17 +205,16 @@ export default class DiseasePanelRegionView extends LitElement { render() { return html` - ${this._config.showToolbar ? - html` - - ` : nothing - } + ${this._config.showToolbar ? html` + + + ` : nothing}
From 4baf7d2fa437240f6572f48f8f7a09ed2c3e1981 Mon Sep 17 00:00:00 2001 From: gpveronica Date: Mon, 29 May 2023 12:59:25 +0200 Subject: [PATCH 02/17] wc - Added region and variant coordinates Signed-off-by: gpveronica --- .../disease-panel/disease-panel-create.js | 49 ++++++++++++++++--- .../disease-panel/disease-panel-update.js | 41 ++++++++++++++-- 2 files changed, 80 insertions(+), 10 deletions(-) diff --git a/src/webcomponents/disease-panel/disease-panel-create.js b/src/webcomponents/disease-panel/disease-panel-create.js index 6285554aa5..a336a11afe 100644 --- a/src/webcomponents/disease-panel/disease-panel-create.js +++ b/src/webcomponents/disease-panel/disease-panel-create.js @@ -83,7 +83,8 @@ export default class DiseasePanelCreate extends LitElement { const params = { exclude: "transcripts,annotation", }; - this.opencgaSession.cellbaseClient.getGeneClient(gene.name, "info", params) + this.opencgaSession.cellbaseClient + .getGeneClient(gene.name, "info", params) .then(res => { const g = res.responses[0].results[0]; gene.id = g.id; @@ -106,6 +107,34 @@ export default class DiseasePanelCreate extends LitElement { } } } + // Set the region coordinates if needed: location, assembly, and source + if (e.detail?.data?.regions?.length > 0) { + for (const region of e.detail.data.regions) { + if (!region?.coordinates?.location) { + region.coordinates = [ + { + location: region.id, + assembly: this.opencgaSession?.project?.organism?.assembly || "", + // source: region.source || "", + } + ]; + } + } + } + // Set the variant coordinates if needed: location, assembly, and source + if (e.detail?.data?.variants?.length > 0) { + for (const variant of e.detail.data.variants) { + if (!variant?.coordinates?.location) { + variant.coordinates = [ + { + location: variant.id, + assembly: this.opencgaSession?.project?.organism?.assembly || "", + // source: region.source || "", + } + ]; + } + } + } this.diseasePanel = {...e.detail.data}; // force to refresh the object-list this.requestUpdate(); } @@ -297,7 +326,7 @@ export default class DiseasePanelCreate extends LitElement { view: gene => html`
${gene?.name} (${gene?.id})
-
MoI: ${gene?.modeOfInheritance || "NA"} (Confidence: ${gene.confidence || "NA"})
+
MoI: ${gene?.modesOfInheritance?.join(", ") || "-"} (Confidence: ${gene.confidence || "NA"})
${gene.coordinates?.[0]?.location}
`, @@ -366,8 +395,11 @@ export default class DiseasePanelCreate extends LitElement { display: { style: "border-left: 2px solid #0c2f4c; padding-left: 12px; margin-bottom:24px", collapsedUpdate: true, - view: region => html` -
${region.id} - ${region?.modeOfInheritance || "-"}
+ view: region => html ` +
+
${region?.id}
+
MoI: ${region?.modesOfInheritance?.join(", ") || "-"} (Confidence: ${region?.confidence || "NA"})
+
`, }, elements: [ @@ -376,7 +408,7 @@ export default class DiseasePanelCreate extends LitElement { field: "regions[].id", type: "input-text", display: { - placeholder: "Add region...", + placeholder: "Add a region location (e.g. 1:134545:2324234) ...", } }, { @@ -384,7 +416,7 @@ export default class DiseasePanelCreate extends LitElement { field: "regions[].modesOfInheritance", type: "select", multiple: true, - save: value => value.split(","), // Array when select and multiple + save: value => value?.split(","), // Array when select and multiple allowedValues: MODE_OF_INHERITANCE, display: { placeholder: "Select a mode of inheritance..." @@ -414,7 +446,10 @@ export default class DiseasePanelCreate extends LitElement { style: "border-left: 2px solid #0c2f4c; padding-left: 12px; margin-bottom:24px", collapsedUpdate: true, view: variant => html` -
${variant.id} - ${variant?.modeOfInheritance || "-"}
+
+
${variant.id}
+
MoI: ${variant?.modesOfInheritance?.join(", ") || "-"}
+
`, }, elements: [ diff --git a/src/webcomponents/disease-panel/disease-panel-update.js b/src/webcomponents/disease-panel/disease-panel-update.js index efdbb6e033..eb83b2c9b1 100644 --- a/src/webcomponents/disease-panel/disease-panel-update.js +++ b/src/webcomponents/disease-panel/disease-panel-update.js @@ -117,6 +117,35 @@ export default class DiseasePanelUpdate extends LitElement { } } } + + // Set the region coordinates if needed: location, assembly, and source + if (e.detail?.component?.regions?.length > 0) { + for (const region of e.detail.component.regions) { + if (!region?.coordinates?.location) { + region.coordinates = [ + { + location: region.id, + assembly: this.opencgaSession?.project?.organism?.assembly || "", + // source: region.source || "", + } + ]; + } + } + } + + if (e.detail?.component?.variants?.length > 0) { + for (const variant of e.detail.component.variants) { + if (!variant?.coordinates?.location) { + variant.coordinates = [ + { + location: variant.id, + assembly: this.opencgaSession?.project?.organism?.assembly || "", + // source: region.source || "", + } + ]; + } + } + } } render() { @@ -342,7 +371,10 @@ export default class DiseasePanelUpdate extends LitElement { style: "border-left: 2px solid #0c2f4c; padding-left: 12px; margin-bottom:24px", collapsedUpdate: true, view: region => html ` -
${region.id} - ${region?.modesOfInheritance.join(", ") || "-"}
+
+
${region?.id}
+
MoI: ${region?.modesOfInheritance?.join(", ") || "-"} (Confidence: ${region?.confidence || "NA"})
+
`, }, elements: [ @@ -351,7 +383,7 @@ export default class DiseasePanelUpdate extends LitElement { field: "regions[].id", type: "input-text", display: { - placeholder: "Add region...", + placeholder: "Add a region location (e.g. 1:134545:2324234) ...", } }, { @@ -389,7 +421,10 @@ export default class DiseasePanelUpdate extends LitElement { style: "border-left: 2px solid #0c2f4c; padding-left: 12px; margin-bottom:24px", collapsedUpdate: true, view: variant => html` -
${variant.id} - ${variant?.modesOfInheritance.join(", ") || "-"}
+
+
${variant.id}
+
MoI: ${variant?.modesOfInheritance?.join(", ") || "-"}
+
`, }, elements: [ From 9489fd22c2b1db074ed35fa78235d9b9a0757e55 Mon Sep 17 00:00:00 2001 From: gpveronica Date: Tue, 30 May 2023 15:41:29 +0200 Subject: [PATCH 03/17] wc - Minor code clean Signed-off-by: gpveronica --- src/webcomponents/disease-panel/disease-panel-region-view.js | 5 ----- 1 file changed, 5 deletions(-) diff --git a/src/webcomponents/disease-panel/disease-panel-region-view.js b/src/webcomponents/disease-panel/disease-panel-region-view.js index e66b75a753..52af5aaa73 100644 --- a/src/webcomponents/disease-panel/disease-panel-region-view.js +++ b/src/webcomponents/disease-panel/disease-panel-region-view.js @@ -131,11 +131,6 @@ export default class DiseasePanelRegionView extends LitElement { formatter: (value, row) => `${row.id}`, halign: this._config.header.horizontalAlign, }, - // { - // id: "modeOfInheritance", - // title: "Mode of Inheritance", - // field: "modeOfInheritance", - // }, { id: "modesOfInheritance", title: "Mode of Inheritance", From 4bca310b476bd3793b7619dc501f0b774591a82c Mon Sep 17 00:00:00 2001 From: gpveronica Date: Tue, 30 May 2023 15:44:09 +0200 Subject: [PATCH 04/17] wc - Fixed condition for setting and visualising coordinates --- .../disease-panel/disease-panel-create.js | 66 +++++++++++++------ .../disease-panel/disease-panel-update.js | 57 +++++++++++----- 2 files changed, 85 insertions(+), 38 deletions(-) diff --git a/src/webcomponents/disease-panel/disease-panel-create.js b/src/webcomponents/disease-panel/disease-panel-create.js index a336a11afe..3bee039b17 100644 --- a/src/webcomponents/disease-panel/disease-panel-create.js +++ b/src/webcomponents/disease-panel/disease-panel-create.js @@ -107,31 +107,44 @@ export default class DiseasePanelCreate extends LitElement { } } } + debugger // Set the region coordinates if needed: location, assembly, and source if (e.detail?.data?.regions?.length > 0) { for (const region of e.detail.data.regions) { - if (!region?.coordinates?.location) { - region.coordinates = [ - { - location: region.id, - assembly: this.opencgaSession?.project?.organism?.assembly || "", - // source: region.source || "", - } - ]; + if (region.id) { + if (region.id !== region.coordinates?.[0]?.location) { + region.coordinates = [ + { + location: region.id, + assembly: this.opencgaSession?.project?.organism?.assembly || "", + // source: region.source || "", + } + ]; + } + } else { + if (region.coordinates) { + region.coordinates = null; + } } } } // Set the variant coordinates if needed: location, assembly, and source if (e.detail?.data?.variants?.length > 0) { for (const variant of e.detail.data.variants) { - if (!variant?.coordinates?.location) { - variant.coordinates = [ - { - location: variant.id, - assembly: this.opencgaSession?.project?.organism?.assembly || "", - // source: region.source || "", - } - ]; + if (variant.id) { + if (variant.id !== variant.coordinates?.[0]?.location) { + variant.coordinates = [ + { + location: variant.id, + assembly: this.opencgaSession?.project?.organism?.assembly || "", + // source: region.source || "", + } + ]; + } + } else { + if (variant.coordinates) { + variant.coordinates = null; + } } } } @@ -327,7 +340,10 @@ export default class DiseasePanelCreate extends LitElement {
${gene?.name} (${gene?.id})
MoI: ${gene?.modesOfInheritance?.join(", ") || "-"} (Confidence: ${gene.confidence || "NA"})
-
${gene.coordinates?.[0]?.location}
+
+ Location: ${gene.coordinates?.[0]?.location || "-"}, + Assembly: ${gene.coordinates?.[0]?.assembly || "-"}, +
`, }, @@ -399,16 +415,20 @@ export default class DiseasePanelCreate extends LitElement {
${region?.id}
MoI: ${region?.modesOfInheritance?.join(", ") || "-"} (Confidence: ${region?.confidence || "NA"})
+
+ Location: ${region.coordinates?.[0]?.location || "-"}, + Assembly: ${region.coordinates?.[0]?.assembly || "-"}, +
`, }, elements: [ { - title: "Region ID", + title: "Region ID/Location", field: "regions[].id", type: "input-text", display: { - placeholder: "Add a region location (e.g. 1:134545:2324234) ...", + placeholder: "Add a region ID/Location (e.g. 1:134545:2324234) ...", } }, { @@ -449,16 +469,20 @@ export default class DiseasePanelCreate extends LitElement {
${variant.id}
MoI: ${variant?.modesOfInheritance?.join(", ") || "-"}
+
+ Location: ${variant.coordinates?.[0]?.location || "-"}, + Assembly: ${variant.coordinates?.[0]?.assembly || "-"}, +
`, }, elements: [ { - title: "Variant ID", + title: "Variant ID/Location", field: "variants[].id", type: "input-text", display: { - placeholder: "Add variant ID...", + placeholder: "Add the variant ID/Location...", } }, { diff --git a/src/webcomponents/disease-panel/disease-panel-update.js b/src/webcomponents/disease-panel/disease-panel-update.js index eb83b2c9b1..dd7a7d938e 100644 --- a/src/webcomponents/disease-panel/disease-panel-update.js +++ b/src/webcomponents/disease-panel/disease-panel-update.js @@ -121,28 +121,40 @@ export default class DiseasePanelUpdate extends LitElement { // Set the region coordinates if needed: location, assembly, and source if (e.detail?.component?.regions?.length > 0) { for (const region of e.detail.component.regions) { - if (!region?.coordinates?.location) { - region.coordinates = [ - { - location: region.id, - assembly: this.opencgaSession?.project?.organism?.assembly || "", - // source: region.source || "", - } - ]; + if (region.id) { + if (region.id !== region.coordinates?.[0]?.location) { + region.coordinates = [ + { + location: region.id, + assembly: this.opencgaSession?.project?.organism?.assembly || "", + // source: region.source || "", + } + ]; + } + } else { + if (region.coordinates) { + region.coordinates = null; + } } } } if (e.detail?.component?.variants?.length > 0) { for (const variant of e.detail.component.variants) { - if (!variant?.coordinates?.location) { - variant.coordinates = [ - { - location: variant.id, - assembly: this.opencgaSession?.project?.organism?.assembly || "", - // source: region.source || "", - } - ]; + if (variant.id) { + if (variant.id !== variant.coordinates?.[0]?.location) { + variant.coordinates = [ + { + location: variant.id, + assembly: this.opencgaSession?.project?.organism?.assembly || "", + // source: region.source || "", + } + ]; + } + } else { + if (variant.coordinates) { + variant.coordinates = null; + } } } } @@ -302,7 +314,10 @@ export default class DiseasePanelUpdate extends LitElement {
${gene?.name} (${gene?.id})
MoI: ${gene?.modesOfInheritance.join(", ") || "NA"} (Confidence: ${gene.confidence || "NA"})
-
${gene.coordinates?.[0]?.location}
+
+ Location: ${gene.coordinates?.[0]?.location || "-"}, + Assembly: ${gene.coordinates?.[0]?.assembly || "-"}, +
`, }, @@ -374,6 +389,10 @@ export default class DiseasePanelUpdate extends LitElement {
${region?.id}
MoI: ${region?.modesOfInheritance?.join(", ") || "-"} (Confidence: ${region?.confidence || "NA"})
+
+ Location: ${region.coordinates?.[0]?.location || "-"}, + Assembly: ${region.coordinates?.[0]?.assembly || "-"}, +
`, }, @@ -424,6 +443,10 @@ export default class DiseasePanelUpdate extends LitElement {
${variant.id}
MoI: ${variant?.modesOfInheritance?.join(", ") || "-"}
+
+ Location: ${variant.coordinates?.[0]?.location || "-"}, + Assembly: ${variant.coordinates?.[0]?.assembly || "-"}, +
`, }, From a34dfddaa26d945263bf90b24b61ecdbbb30598e Mon Sep 17 00:00:00 2001 From: gpveronica Date: Tue, 30 May 2023 15:44:58 +0200 Subject: [PATCH 05/17] wc - Minor code clean Signed-off-by: gpveronica --- src/webcomponents/disease-panel/disease-panel-create.js | 1 - 1 file changed, 1 deletion(-) diff --git a/src/webcomponents/disease-panel/disease-panel-create.js b/src/webcomponents/disease-panel/disease-panel-create.js index 3bee039b17..e5ceebc28d 100644 --- a/src/webcomponents/disease-panel/disease-panel-create.js +++ b/src/webcomponents/disease-panel/disease-panel-create.js @@ -107,7 +107,6 @@ export default class DiseasePanelCreate extends LitElement { } } } - debugger // Set the region coordinates if needed: location, assembly, and source if (e.detail?.data?.regions?.length > 0) { for (const region of e.detail.data.regions) { From 6ec7741c9446784a532cd2c0359b46ac4f64cffe Mon Sep 17 00:00:00 2001 From: Josemi Date: Wed, 31 May 2023 11:19:29 +0200 Subject: [PATCH 06/17] wc: fix displaying pedigree in clinical analysis create #TASK-4501 --- .../clinical/clinical-analysis-create.js | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/src/webcomponents/clinical/clinical-analysis-create.js b/src/webcomponents/clinical/clinical-analysis-create.js index 161baab6e7..90c13a51d7 100644 --- a/src/webcomponents/clinical/clinical-analysis-create.js +++ b/src/webcomponents/clinical/clinical-analysis-create.js @@ -22,6 +22,7 @@ import UtilsNew from "../../core/utils-new.js"; import "../commons/forms/data-form.js"; import "../commons/filters/disease-panel-filter.js"; import "../commons/filters/catalog-search-autocomplete.js"; +import "../commons/image-viewer.js"; import "./filters/clinical-priority-filter.js"; import "./filters/clinical-flag-filter.js"; @@ -651,11 +652,15 @@ export default class ClinicalAnalysisCreate extends LitElement { title: "Pedigree", type: "custom", display: { - // defaultLayout: "vertical", render: data => { - if (data.family) { - return html``; + if (data?.family?.pedigreeGraph?.base64) { + return html` + + + `; } + return "-"; }, errorMessage: "No family selected", } From 369c64c61bd1e4ceb9bb17257f073b1cca066456 Mon Sep 17 00:00:00 2001 From: gpveronica Date: Wed, 31 May 2023 18:57:27 +0200 Subject: [PATCH 07/17] wc - Fixed returned value when value is undefined Signed-off-by: gpveronica --- src/webcomponents/disease-panel/disease-panel-create.js | 8 ++++---- src/webcomponents/disease-panel/disease-panel-update.js | 8 ++++---- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/src/webcomponents/disease-panel/disease-panel-create.js b/src/webcomponents/disease-panel/disease-panel-create.js index e5ceebc28d..952c43ef40 100644 --- a/src/webcomponents/disease-panel/disease-panel-create.js +++ b/src/webcomponents/disease-panel/disease-panel-create.js @@ -370,7 +370,7 @@ export default class DiseasePanelCreate extends LitElement { field: "genes[].modesOfInheritance", type: "select", multiple: true, - save: value => value.split(","), // Array when select and multiple + save: value => value?.split(",") || [], // Array when select and multiple allowedValues: MODE_OF_INHERITANCE, display: { placeholder: "Select a mode of inheritance..." @@ -390,7 +390,7 @@ export default class DiseasePanelCreate extends LitElement { field: "genes[].cancer.roles", type: "select", multiple: true, - save: value => value.split(","), // Array when select and multiple + save: value => value?.split(",") || [], // Array when select and multiple allowedValues: ROLE_IN_CANCER, display: { placeholder: "Select role in cancer..." @@ -435,7 +435,7 @@ export default class DiseasePanelCreate extends LitElement { field: "regions[].modesOfInheritance", type: "select", multiple: true, - save: value => value?.split(","), // Array when select and multiple + save: value => value?.split(",") || [], // Array when select and multiple allowedValues: MODE_OF_INHERITANCE, display: { placeholder: "Select a mode of inheritance..." @@ -489,7 +489,7 @@ export default class DiseasePanelCreate extends LitElement { field: "variants[].modesOfInheritance", type: "select", multiple: true, - save: value => value.split(","), // Array when select and multiple + save: value => value?.split(",") || [], // Array when select and multiple allowedValues: MODE_OF_INHERITANCE, display: { placeholder: "Select a mode of inheritance..." diff --git a/src/webcomponents/disease-panel/disease-panel-update.js b/src/webcomponents/disease-panel/disease-panel-update.js index dd7a7d938e..21c5209fbd 100644 --- a/src/webcomponents/disease-panel/disease-panel-update.js +++ b/src/webcomponents/disease-panel/disease-panel-update.js @@ -345,7 +345,7 @@ export default class DiseasePanelUpdate extends LitElement { field: "genes[].modesOfInheritance", type: "select", multiple: true, - save: value => value.split(","), // Array when select and multiple + save: value => value?.split(",") || [], // Array when select and multiple allowedValues: MODE_OF_INHERITANCE, display: { placeholder: "Select a mode of inheritance..." @@ -365,7 +365,7 @@ export default class DiseasePanelUpdate extends LitElement { field: "genes[].cancer.roles", type: "select", multiple: true, - save: value => value.split(","), // Array when select and multiple + save: value => value?.split(",") || [], // Array when select and multiple allowedValues: ROLE_IN_CANCER, display: { placeholder: "Select role in cancer..." @@ -410,7 +410,7 @@ export default class DiseasePanelUpdate extends LitElement { field: "regions[].modesOfInheritance", type: "select", multiple: true, - save: value => value.split(","), // Array when select and multiple + save: value => value?.split(",") || [], // Array when select and multiple allowedValues: MODE_OF_INHERITANCE, display: { placeholder: "Select a mode of inheritance..." @@ -464,7 +464,7 @@ export default class DiseasePanelUpdate extends LitElement { field: "variants[].modesOfInheritance", type: "select", multiple: true, - save: value => value.split(","), // Array when select and multiple + save: value => value?.split(",") || [], // Array when select and multiple allowedValues: MODE_OF_INHERITANCE, display: { placeholder: "Select a mode of inheritance..." From 2bbfccee9c339298618d6b57436114482dbf5f29 Mon Sep 17 00:00:00 2001 From: gpveronica Date: Wed, 7 Jun 2023 11:01:04 +0200 Subject: [PATCH 08/17] wc - Fixed visibility of Cohort Stats and Population Frequencies nested columns --- src/webcomponents/variant/variant-browser-grid.js | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/webcomponents/variant/variant-browser-grid.js b/src/webcomponents/variant/variant-browser-grid.js index dc74128ee9..98c9914093 100644 --- a/src/webcomponents/variant/variant-browser-grid.js +++ b/src/webcomponents/variant/variant-browser-grid.js @@ -574,7 +574,8 @@ export default class VariantBrowserGrid extends LitElement { colspan: 1, formatter: this.cohortFormatter, align: "center", - eligible: true + eligible: true, + visible: this.gridCommons.isColumnVisible(study.id), }); } } @@ -614,6 +615,7 @@ export default class VariantBrowserGrid extends LitElement { colspan: 1, formatter: this.populationFrequenciesFormatter, align: "center", + visible: this.gridCommons.isColumnVisible(this.populationFrequencies.studies[j].id), }); } } From 7aa1f3d113610d304dc155995513091ed4c12dda Mon Sep 17 00:00:00 2001 From: Rodiel Martinez <10471758+Rodielm@users.noreply.github.com> Date: Wed, 7 Jun 2023 13:13:48 +0200 Subject: [PATCH 09/17] wc: Fix typo in the fullTextSearch Field message within the ClinVar section filter #TASK-4030 --- src/sites/iva/conf/opencga-variant-constants.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/sites/iva/conf/opencga-variant-constants.js b/src/sites/iva/conf/opencga-variant-constants.js index e256c5efa8..808470a2eb 100644 --- a/src/sites/iva/conf/opencga-variant-constants.js +++ b/src/sites/iva/conf/opencga-variant-constants.js @@ -868,7 +868,7 @@ const tooltips = { "This knowledge is both human-readable and machine-readable, and is a foundation for computational analysis of large-scale molecular biology and genetics experiments in biomedical research.", hpo: "The Human Phenotype Ontology (HPO) provides a standardized vocabulary of phenotypic abnormalities encountered in human disease.", clinvar: "Filter out variants falling outside the genomic features (gene, transcript, SNP, etc.) defined", - fullTextSearch: "Filter out variants falling outside the genomic features (gene, transcript, SNP, etc.) defined", + fullTextSearch: "Filter out variants that do not match with the IDs or the full text provided", cadd: "Raw values have relative meaning, with higher values indicating that a variant is more likely to be " + "simulated (or not observed) and therefore more likely to have deleterious effects. If discovering causal variants " + "within an individual, or small groups, of exomes or genomes te use of the scaled CADD score is recommended", From c79c2fe73310ba546028273d75cb4d1e0311e264 Mon Sep 17 00:00:00 2001 From: gpveronica Date: Thu, 8 Jun 2023 16:56:59 +0200 Subject: [PATCH 10/17] wc - Added visibility to samples column --- src/webcomponents/variant/variant-browser-grid.js | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/webcomponents/variant/variant-browser-grid.js b/src/webcomponents/variant/variant-browser-grid.js index 98c9914093..3bccb63207 100644 --- a/src/webcomponents/variant/variant-browser-grid.js +++ b/src/webcomponents/variant/variant-browser-grid.js @@ -549,7 +549,8 @@ export default class VariantBrowserGrid extends LitElement { colspan: 1, formatter: VariantInterpreterGridFormatter.sampleGenotypeFormatter, align: "center", - nucleotideGenotype: true + nucleotideGenotype: true, + visible: this.gridCommons.isColumnVisible(this.samples[i].id), }); } } From f994dbfd8bbbd7b6d53a2934142e84e3a08da475 Mon Sep 17 00:00:00 2001 From: imedina Date: Fri, 9 Jun 2023 01:56:36 +0100 Subject: [PATCH 11/17] Increment version to 2.8.3-dev --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index 083dfe85cf..a98d2f0ae4 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "jsorolla", - "version": "2.8.2", + "version": "2.8.3-dev", "description": "JSorolla is a JavaScript bioinformatic library for data analysis and genomic visualization", "repository": { "type": "git", From ca439064b44775f7b97c198a2180ae726ea9eb23 Mon Sep 17 00:00:00 2001 From: Josemi Date: Wed, 14 Jun 2023 13:40:56 +0200 Subject: [PATCH 12/17] wc: fix saving proband info for family type in clinical-analysis-create #TASK-4573 --- .../clinical/clinical-analysis-create.js | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/src/webcomponents/clinical/clinical-analysis-create.js b/src/webcomponents/clinical/clinical-analysis-create.js index 3af0f02b37..c63b6074e3 100644 --- a/src/webcomponents/clinical/clinical-analysis-create.js +++ b/src/webcomponents/clinical/clinical-analysis-create.js @@ -107,14 +107,17 @@ export default class ClinicalAnalysisCreate extends LitElement { } // In FAMILY, changing the proband only sets the 'proband.id' field of the clinicalAnalysis object - // We have to add also the disorders list to 'proband.disorders'. + // We need to save the full member object in proband. if (e.detail.param === "proband.id" && this.clinicalAnalysis.type === "FAMILY") { + // Changing the 'proband.id' means we have to reset the disorder field + delete this.clinicalAnalysis.disorder; if (this.clinicalAnalysis.proband?.id) { const proband = this.clinicalAnalysis.family.members.find(member => member.id === this.clinicalAnalysis.proband?.id); - this.clinicalAnalysis.proband.disorders = proband?.disorders || []; - } else if (this.clinicalAnalysis.proband?.disorders) { - // If we have remove the 'proband.id', we have to remove also the 'proband.disorders' field - delete this.clinicalAnalysis.proband.disorders; + this.clinicalAnalysis.proband = UtilsNew.objectClone(proband); + this.clinicalAnalysis.proband.disorders = this.clinicalAnalysis.proband.disorders || []; + } else { + // If we have removed the 'proband.id' field, we have to remove also the full proband object + delete this.clinicalAnalysis.proband; } } @@ -175,7 +178,7 @@ export default class ClinicalAnalysisCreate extends LitElement { if (this.clinicalAnalysis.family && this.clinicalAnalysis.family.members) { for (const member of this.clinicalAnalysis.family.members) { if (member.disorders && member.disorders.length > 0 && member.father.id && member.mother.id) { - this.clinicalAnalysis.proband = member; + this.clinicalAnalysis.proband = UtilsNew.objectClone(member); break; } } From fc75ce80c8706543c716225768c20fed280f343e Mon Sep 17 00:00:00 2001 From: gpveronica Date: Thu, 22 Jun 2023 08:23:53 +0200 Subject: [PATCH 13/17] wc - Changed placeholder in Regions Signed-off-by: gpveronica --- src/webcomponents/disease-panel/disease-panel-create.js | 2 +- src/webcomponents/disease-panel/disease-panel-update.js | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/webcomponents/disease-panel/disease-panel-create.js b/src/webcomponents/disease-panel/disease-panel-create.js index 952c43ef40..dfac1ddead 100644 --- a/src/webcomponents/disease-panel/disease-panel-create.js +++ b/src/webcomponents/disease-panel/disease-panel-create.js @@ -427,7 +427,7 @@ export default class DiseasePanelCreate extends LitElement { field: "regions[].id", type: "input-text", display: { - placeholder: "Add a region ID/Location (e.g. 1:134545:2324234) ...", + placeholder: "Add a region ID/Location (e.g. 1:10100-10110)...", } }, { diff --git a/src/webcomponents/disease-panel/disease-panel-update.js b/src/webcomponents/disease-panel/disease-panel-update.js index 21c5209fbd..14ef5b8994 100644 --- a/src/webcomponents/disease-panel/disease-panel-update.js +++ b/src/webcomponents/disease-panel/disease-panel-update.js @@ -402,7 +402,7 @@ export default class DiseasePanelUpdate extends LitElement { field: "regions[].id", type: "input-text", display: { - placeholder: "Add a region location (e.g. 1:134545:2324234) ...", + placeholder: "Add a region location (e.g. 1:10100-10110)...", } }, { From b8b525e5055237a300105d0803f91582f19b9250 Mon Sep 17 00:00:00 2001 From: Josemi Date: Mon, 26 Jun 2023 14:57:23 +0200 Subject: [PATCH 14/17] Prepare release 2.8.3 --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index a98d2f0ae4..c5a63c7fe1 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "jsorolla", - "version": "2.8.3-dev", + "version": "2.8.3", "description": "JSorolla is a JavaScript bioinformatic library for data analysis and genomic visualization", "repository": { "type": "git", From 1b63df5f7b9068bfe1d45ba2d95a9baa638b6a38 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 27 Jun 2023 16:17:43 +0200 Subject: [PATCH 15/17] 2.9.2-dev --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index 2d43d23075..7e1e0dfc6e 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "jsorolla", - "version": "2.9.1-dev", + "version": "2.9.2-dev", "description": "JSorolla is a JavaScript bioinformatic library for data analysis and genomic visualization", "repository": { "type": "git", From ab75d430b699eb3999e8c7f41a27b958e9ffedf9 Mon Sep 17 00:00:00 2001 From: Josemi Date: Tue, 25 Jul 2023 12:26:55 +0200 Subject: [PATCH 16/17] Prepare release 2.9.2 --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index 7e1e0dfc6e..6cfe4d9c7f 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "jsorolla", - "version": "2.9.2-dev", + "version": "2.9.2", "description": "JSorolla is a JavaScript bioinformatic library for data analysis and genomic visualization", "repository": { "type": "git", From 45b6d3a4355864e73f51c10dd32e58d8660e2209 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 1 Aug 2023 17:47:16 +0200 Subject: [PATCH 17/17] Prepare Port Patch 1.7.2 -> 1.8.1 #TASK-4668 --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index 6cfe4d9c7f..83691cd617 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "jsorolla", - "version": "2.9.2", + "version": "2.10.1-dev", "description": "JSorolla is a JavaScript bioinformatic library for data analysis and genomic visualization", "repository": { "type": "git",