From 817ddd98b42d51b8bb1e715eeff7b39f15abbbcc Mon Sep 17 00:00:00 2001 From: Josemi Date: Fri, 31 May 2024 14:07:55 +0200 Subject: [PATCH 01/95] wc: Hide interpretation review step in variant interpreter #TASK-6371 #TASK-5963 --- .../variant/interpretation/variant-interpreter.js | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/webcomponents/variant/interpretation/variant-interpreter.js b/src/webcomponents/variant/interpretation/variant-interpreter.js index 69d341e00..3519119e6 100644 --- a/src/webcomponents/variant/interpretation/variant-interpreter.js +++ b/src/webcomponents/variant/interpretation/variant-interpreter.js @@ -549,7 +549,8 @@ class VariantInterpreter extends LitElement { id: "review", title: "Interpretation Review", description: "", - icon: "fa fa-edit" + icon: "fa fa-edit", + visible: false, }, { id: "report", From dd218527de2e2c9b532e2e9a45faa4aa047253cd Mon Sep 17 00:00:00 2001 From: Josemi Date: Fri, 31 May 2024 14:10:17 +0200 Subject: [PATCH 02/95] wc: Fix displaying headers in interpretation actions dropdown #TASK-6317 #TASK-5963 --- .../variant/interpretation/variant-interpreter.js | 12 ++---------- 1 file changed, 2 insertions(+), 10 deletions(-) diff --git a/src/webcomponents/variant/interpretation/variant-interpreter.js b/src/webcomponents/variant/interpretation/variant-interpreter.js index 3519119e6..8fcf8c30b 100644 --- a/src/webcomponents/variant/interpretation/variant-interpreter.js +++ b/src/webcomponents/variant/interpretation/variant-interpreter.js @@ -422,11 +422,7 @@ class VariantInterpreter extends LitElement { - -
- -
    +
    • Primary Findings From 6e9adebd9c6d7e955f776bbb2757900d959f787b Mon Sep 17 00:00:00 2001 From: Josemi Date: Mon, 1 Jul 2024 16:02:40 +0100 Subject: [PATCH 92/95] wc: Fix comments in save menu actions #TASK-6318 #TASK-5963 --- .../interpretation/variant-interpreter-browser-toolbar.js | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/webcomponents/variant/interpretation/variant-interpreter-browser-toolbar.js b/src/webcomponents/variant/interpretation/variant-interpreter-browser-toolbar.js index ab3550d48..b5e92e3bd 100644 --- a/src/webcomponents/variant/interpretation/variant-interpreter-browser-toolbar.js +++ b/src/webcomponents/variant/interpretation/variant-interpreter-browser-toolbar.js @@ -94,14 +94,14 @@ class VariantInterpreterBrowserToolbar extends LitElement { ], }); // Josemi 20240701 NOTE: this is a terrible and temporal fix to force closing the Save Menu - // when user clicks the 'Filter Variants' button. + // when user clicks the 'Filter Variants' button in the Save menu. this.querySelector(`div#${this._prefix}Save ul.dropdown-menu`)?.classList?.toggle?.("show"); } onResetModifiedVariants() { LitUtils.dispatchCustomEvent(this, "resetVariants", null); // Josemi 20240701 NOTE: this is a terrible and temporal fix to force closing the Save Menu - // when user clicks the 'Filter Variants' button. + // when user clicks the 'Discard Changes' button in the Save menu. this.querySelector(`div#${this._prefix}Save ul.dropdown-menu`)?.classList?.toggle?.("show"); } @@ -110,7 +110,7 @@ class VariantInterpreterBrowserToolbar extends LitElement { comment: event?.detail?.comment || {}, }); // Josemi 20240701 NOTE: this is a terrible and temporal fix to force closing the Save Menu - // when user clicks the 'Filter Variants' button. + // when user clicks the 'Save' button in the Save menu. this.querySelector(`div#${this._prefix}Save ul.dropdown-menu`)?.classList?.toggle?.("show"); } From deb7fc738be35d74063607bdb4f91f0133b65574 Mon Sep 17 00:00:00 2001 From: Josemi Date: Wed, 3 Jul 2024 12:04:46 +0100 Subject: [PATCH 93/95] wc: Include the updated variants in the filter variants list #TASK-6318 #TASK-5963 --- .../interpretation/variant-interpreter-browser-toolbar.js | 1 + 1 file changed, 1 insertion(+) diff --git a/src/webcomponents/variant/interpretation/variant-interpreter-browser-toolbar.js b/src/webcomponents/variant/interpretation/variant-interpreter-browser-toolbar.js index b5e92e3bd..694bcc496 100644 --- a/src/webcomponents/variant/interpretation/variant-interpreter-browser-toolbar.js +++ b/src/webcomponents/variant/interpretation/variant-interpreter-browser-toolbar.js @@ -90,6 +90,7 @@ class VariantInterpreterBrowserToolbar extends LitElement { LitUtils.dispatchCustomEvent(this, "filterVariants", null, { variants: [ ...this.state.addedVariants, + ...this.state.updatedVariants, ...this.state.removedVariants, ], }); From bb5f223f11db3db8addce01a2d5ad569b9f110c0 Mon Sep 17 00:00:00 2001 From: Josemi Date: Wed, 3 Jul 2024 12:05:22 +0100 Subject: [PATCH 94/95] wc: Include unique ids when filtering by changed variants #TASK-6318 #TASK-5963 --- .../interpretation/variant-interpreter-browser-template.js | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/webcomponents/variant/interpretation/variant-interpreter-browser-template.js b/src/webcomponents/variant/interpretation/variant-interpreter-browser-template.js index 997253a2d..6b098ef83 100644 --- a/src/webcomponents/variant/interpretation/variant-interpreter-browser-template.js +++ b/src/webcomponents/variant/interpretation/variant-interpreter-browser-template.js @@ -243,10 +243,10 @@ class VariantInterpreterBrowserTemplate extends LitElement { onFilterVariants(e) { const lockedFields = [...this._config?.filter?.activeFilters?.lockedFields.map(key => key.id), "study"]; - const variantIds = e.detail.variants.map(v => v.id); + const variantIds = new Set(e.detail.variants.map(v => v.id)); this.query = { ...UtilsNew.filterKeys(this.executedQuery, lockedFields), - id: variantIds.join(","), + id: Array.from(variantIds).join(","), }; this.notifyQueryChange(); this.requestUpdate(); From 5873d3a4fcb930af91e127a9077f716dd33e7933 Mon Sep 17 00:00:00 2001 From: Josemi Date: Wed, 3 Jul 2024 12:06:53 +0100 Subject: [PATCH 95/95] iva: Remove commented review step in interpreter settings #TASK-6318 #TASK-5963 --- src/sites/iva/conf/browsers.settings.js | 3 --- src/sites/iva/conf/variant-interpreter.settings.js | 3 --- 2 files changed, 6 deletions(-) diff --git a/src/sites/iva/conf/browsers.settings.js b/src/sites/iva/conf/browsers.settings.js index 836372ca1..8ed956c77 100644 --- a/src/sites/iva/conf/browsers.settings.js +++ b/src/sites/iva/conf/browsers.settings.js @@ -767,9 +767,6 @@ const INTERPRETER_SETTINGS = { }, // hideGenomeBrowser: false }, - // { - // id: "review" - // }, { id: "report" } diff --git a/src/sites/iva/conf/variant-interpreter.settings.js b/src/sites/iva/conf/variant-interpreter.settings.js index 701a66e8b..f8909d17e 100644 --- a/src/sites/iva/conf/variant-interpreter.settings.js +++ b/src/sites/iva/conf/variant-interpreter.settings.js @@ -31,9 +31,6 @@ const VARIANT_INTERPRETER_SETTINGS = { }, // hideGenomeBrowser: false }, - // { - // id: "review" - // }, { id: "report" }