From d30aca898eb45538bd28ede14c4ef947a688edfd Mon Sep 17 00:00:00 2001 From: imedina Date: Tue, 5 Mar 2019 04:16:03 +0000 Subject: [PATCH 01/17] Upgrade JSorolla dependency --- lib/jsorolla | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/jsorolla b/lib/jsorolla index 6b5c62588..537af64dc 160000 --- a/lib/jsorolla +++ b/lib/jsorolla @@ -1 +1 @@ -Subproject commit 6b5c625884d9c51c20b025a1897113a1f93fdadf +Subproject commit 537af64dc7e35589316ce0f307e3e114be011396 From 9fe8559c0776c8c7efcffd9a52f962310fdb7897 Mon Sep 17 00:00:00 2001 From: imedina Date: Tue, 5 Mar 2019 14:03:58 +0000 Subject: [PATCH 02/17] Fix welcome page X and Y chromosomes --- lib/jsorolla | 2 +- src/conf/tools.js | 2 +- src/welcome.html | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/lib/jsorolla b/lib/jsorolla index 537af64dc..13189a9e4 160000 --- a/lib/jsorolla +++ b/lib/jsorolla @@ -1 +1 @@ -Subproject commit 537af64dc7e35589316ce0f307e3e114be011396 +Subproject commit 13189a9e438287dc4fcb2ca1d17a1735527c8639 diff --git a/src/conf/tools.js b/src/conf/tools.js index c90f5edc2..78b49a799 100644 --- a/src/conf/tools.js +++ b/src/conf/tools.js @@ -77,7 +77,7 @@ const filterMenu = { }, { id: "biotype", - title: "Biotype", + title: "Gene Biotype", biotypes: [ "3prime_overlapping_ncrna", "IG_C_gene", "IG_C_pseudogene", "IG_D_gene", "IG_J_gene", "IG_J_pseudogene", "IG_V_gene", "IG_V_pseudogene", "Mt_rRNA", "Mt_tRNA", "TR_C_gene", "TR_D_gene", "TR_J_gene", "TR_J_pseudogene", diff --git a/src/welcome.html b/src/welcome.html index 714b0e526..06bd67136 100644 --- a/src/welcome.html +++ b/src/welcome.html @@ -137,7 +137,7 @@

Note:

let featureId = PolymerUtils.getElementById("welcomeSearchTextBox").value; if (UtilsNew.isNotEmpty(featureId)) { let query = {}; - if (featureId.startsWith("chr") || featureId.match(/^\d/)) { + if (featureId.startsWith("chr") || featureId === "X" || featureId === "Y" || featureId === "MT" || featureId.match(/^\d/)) { if (featureId.split(":").length < 3) { // It's a region, contains only one ':' character query.region = featureId; From 7d122e4a7eda88d9d71d09643537b78133c8558b Mon Sep 17 00:00:00 2001 From: imedina Date: Tue, 12 Mar 2019 11:00:35 +0000 Subject: [PATCH 03/17] Update font-awesome dependency --- lib/jsorolla | 2 +- package.json | 2 +- src/conf/tools.js | 2 ++ src/index.html | 3 ++- 4 files changed, 6 insertions(+), 3 deletions(-) diff --git a/lib/jsorolla b/lib/jsorolla index 13189a9e4..219780234 160000 --- a/lib/jsorolla +++ b/lib/jsorolla @@ -1 +1 @@ -Subproject commit 13189a9e438287dc4fcb2ca1d17a1735527c8639 +Subproject commit 2197802349b3c673c0747ea4250c8b17cb93b976 diff --git a/package.json b/package.json index d0acaa53c..e5aac5e0b 100644 --- a/package.json +++ b/package.json @@ -36,7 +36,7 @@ "crypto-js": "~3.1.9-1", "eonasdan-bootstrap-datetimepicker": "~4.17.43", "file-saver": "~1.3.2", - "font-awesome": "*", + "@fortawesome/fontawesome-free": "^5.6.0", "highcharts": "~4.2.7", "jquery": "~2.2.4", "jquery.json-viewer": "^1.1.0", diff --git a/src/conf/tools.js b/src/conf/tools.js index 78b49a799..095d59a97 100644 --- a/src/conf/tools.js +++ b/src/conf/tools.js @@ -318,6 +318,8 @@ const tools = { active: false, filter: { menu: interpreterMenu, + lof: ["transcript_ablation", "splice_acceptor_variant", "splice_donor_variant", "stop_gained", "frameshift_variant", + "stop_lost", "start_lost", "transcript_amplification", "inframe_insertion", "inframe_deletion"], examples: [ { name: "Tiering (AR)", diff --git a/src/index.html b/src/index.html index fea6f19cb..07ffc1f39 100644 --- a/src/index.html +++ b/src/index.html @@ -85,7 +85,8 @@ - + + From cd1617c7c48aff067bfc8b7db928cbd308fc03d5 Mon Sep 17 00:00:00 2001 From: imedina Date: Wed, 13 Mar 2019 04:08:00 +0000 Subject: [PATCH 04/17] Configuration improvements and minor fixes --- lib/jsorolla | 2 +- src/conf/config.js | 14 +++++++++----- src/conf/tools.js | 31 +++++++++++++------------------ src/iva-app.html | 25 ++++++++++++++++--------- src/welcome.html | 30 +++++++++++++++++++++++------- 5 files changed, 62 insertions(+), 40 deletions(-) diff --git a/lib/jsorolla b/lib/jsorolla index 219780234..9fb90bd75 160000 --- a/lib/jsorolla +++ b/lib/jsorolla @@ -1 +1 @@ -Subproject commit 2197802349b3c673c0747ea4250c8b17cb93b976 +Subproject commit 9fb90bd759df5fc96600d3d91f99bd18de5ee801 diff --git a/src/conf/config.js b/src/conf/config.js index 5cee9dea5..7cfa93376 100644 --- a/src/conf/config.js +++ b/src/conf/config.js @@ -285,7 +285,7 @@ const application = { visible: true, }, settings: { - visibility: "public", + visible: false, }, about: { dropdown: true, @@ -369,12 +369,16 @@ const populationFrequencies = { common: "#0000ff", unobserved: "black" }, + tooltip: `1000 Genomes Only considers variants whose observed allelic frequency in the 1000 genomes phase 3 database + is below (or above) the defined value. Genome-wide allelic frequencies were obtained from more than 2.500 genomes.

+ gnomAD Genomes Only considers variants whose observed allelic frequency in the gnomAD Genomes database is + below (or above) the defined value. Frequencies were calculated from about 15,000 unrelated individuals`, studies: [ { id: "1kG_phase3", title: "1000 Genomes", - tooltip: "Only considers variants whose observed allelic frequency in the 1000 genomes phase 3 database is below (or above) " + - "the defined value. Genome-wide allelic frequencies were obtained from more than 2.500 genomes.", + // tooltip: "Only considers variants whose observed allelic frequency in the 1000 genomes phase 3 database is below (or above) " + + // "the defined value. Genome-wide allelic frequencies were obtained from more than 2.500 genomes.", populations: [ { id: "ALL", title: "All populations [ALL]", @@ -399,8 +403,8 @@ const populationFrequencies = { { id: "GNOMAD_GENOMES", title: "gnomAD Genomes", - tooltip: "Only considers variants whose observed allelic frequency in the gnomAD Genomes database is below (or above) the " + - "defined value. Frequencies were calculated from about 15,000 unrelated individuals.", + // tooltip: "Only considers variants whose observed allelic frequency in the gnomAD Genomes database is below (or above) the " + + // "defined value. Frequencies were calculated from about 15,000 unrelated individuals.", populations: [ { id: "ALL", title: "gnomAD [ALL]", diff --git a/src/conf/tools.js b/src/conf/tools.js index 095d59a97..e78cd313f 100644 --- a/src/conf/tools.js +++ b/src/conf/tools.js @@ -17,6 +17,7 @@ /** * Created by imedina on 05/06/17. */ + const filterMenu = { searchButtonText: "Search", tooltip: { @@ -104,13 +105,7 @@ const filterMenu = { { id: "populationFrequency", title: "Select Population Frequency", - tooltip: "1000 Genomes only considers variants whose observed allelic frequency in the 1000 Genomes " + - "Phase 3 project is below (or above) the defined value. Allele frequencies were obtained from about 2,500 samples." + - "
ExAC only considers variants whose observed allelic frequency in the The Exome Aggregation " + - "Consortium (ExAC) database is below (or above) the defined value. ExAC covers only exomic positions. " + - "The frequencies were obtained using more than 60.000 exomes." + - "
ESP56500 only considers variants whose observed allelic frequency in the Exome Variant Server " + - "(ESP6500) database is below (or above) the defined value. ESP6500 covers only exomic positions from about 6000 exomes" + tooltip: populationFrequencies.tooltip } ] }, @@ -304,13 +299,13 @@ const tools = { { id: "network", component: "reactome-variant-network", - title: "Gene network" + title: "Reactome Pathways" }, - { - id: "template", - component: "opencga-variant-detail-template", - title: "Template" - } + // { + // id: "template", + // component: "opencga-variant-detail-template", + // title: "Template" + // } ] }, interpretation: { @@ -405,11 +400,11 @@ const tools = { // "lovd", "hgmd", "icgc", "sahgp" // ] }, - { - id: "template", - component: "opencga-variant-detail-template", - title: "Template" - } + // { + // id: "template", + // component: "opencga-variant-detail-template", + // title: "Template" + // } ], css: { style: "font-size: 12px" diff --git a/src/iva-app.html b/src/iva-app.html index b35800c15..ea137c33a 100644 --- a/src/iva-app.html +++ b/src/iva-app.html @@ -168,10 +168,12 @@ - -
  • - Settings -
    • + @@ -268,8 +270,11 @@