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TASK-5120 - Port Patch 1.6.5 -> 1.10.0 #824

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merged 39 commits into from
Oct 27, 2023
Merged

TASK-5120 - Port Patch 1.6.5 -> 1.10.0 #824

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c78b51f
wc - Added logic for exluding columns from Settings
gpveronica Jul 7, 2023
d502a66
wc - Excluded from settings Actions and Select in Variant browser grid
gpveronica Jul 7, 2023
5a9db5b
wc - Excluded from settings select and actions in variant interpreter…
gpveronica Jul 19, 2023
dcf3c25
wc: added missing import of clinical-analysis-review in variant-inter…
jmjuanes Aug 1, 2023
a36d92b
wc - Excluded from settings column review in Variant Interpreter Grid
gpveronica Aug 1, 2023
0d6be15
wc - Fixed HGVS, exomiser and Role in Cancer
gpveronica Aug 8, 2023
30922b5
Merged release-2.8.x in TASK-4497
gpveronica Aug 9, 2023
07b6c0d
wc - Minor style fix
gpveronica Aug 9, 2023
edb2547
Upgrade release to 2.8.5-dev
imedina Aug 16, 2023
d8e0bda
wc - Removed or moved to deprecated tests and files with tokenize2 de…
gpveronica Aug 25, 2023
7214e91
wc - Removed tokenize2 dependency
gpveronica Aug 25, 2023
5831a60
wc - Revomed test folder from variant/analysis/deprecated
gpveronica Aug 25, 2023
90b220f
Merge pull request #811 from opencb/TASK-4900-1.6.5
gpveronica Aug 25, 2023
a1c2e5d
wc - Added visibility condition for parent column in Variant Browser
gpveronica Sep 7, 2023
d6191e9
wc - Added visibility condition for parent column in Variant Interpreter
gpveronica Sep 8, 2023
faa5721
iva: add new configuration for interpretation methods #TASK-4753
jmjuanes Sep 26, 2023
017792c
wc: add a settings property to interpreter methods #TASK-4753
jmjuanes Sep 26, 2023
49a1ef6
wc: generate available methods from settings #TASK-4753
jmjuanes Sep 26, 2023
afce281
wc: display a warning message if no methods have been configured #TAS…
jmjuanes Sep 26, 2023
6c3b8c9
Merge branch 'release-2.8.x' into TASK-4497
gpveronica Sep 26, 2023
ef785fa
Merge branch 'release-2.8.x' into TASK-4821
jmjuanes Sep 26, 2023
024f90d
wc: remove unused imports in variant-interpreter-methods #TASK-4753
jmjuanes Sep 26, 2023
7f308ea
iva: rename case option in methods configuration to items #TASK-4753
jmjuanes Sep 27, 2023
e983f90
wc: rename cases to items in methods tool settings #TASK-4753
jmjuanes Sep 27, 2023
31a0983
wc: removed unused config property in variant-interpreter-methods #TA…
jmjuanes Sep 27, 2023
c811008
wc: using visible key instead of hidden for displaying interpretation…
jmjuanes Sep 27, 2023
41a1da7
Merge pull request #803 from opencb/TASK-4821
jmjuanes Sep 27, 2023
afc9c36
Merge branch 'release-2.8.x' into TASK-4753
jmjuanes Sep 28, 2023
4403910
Merge branch 'release-2.8.x' into TASK-4497
gpveronica Sep 28, 2023
e233480
Merge pull request #809 from opencb/TASK-4497
gpveronica Sep 28, 2023
5732164
Merge branch 'release-2.8.x' into TASK-4753
jmjuanes Sep 28, 2023
bff933b
Merge pull request #820 from opencb/TASK-4753
jmjuanes Oct 2, 2023
d537ef1
wc - Merge branch 'release-2.8.x' into TASK-4937
gpveronica Oct 2, 2023
1308205
wc - Fixed mistake in resolving conflicts for exomiser
gpveronica Oct 2, 2023
002cace
Merge pull request #817 from opencb/TASK-4937
gpveronica Oct 3, 2023
2936122
Prepare release v2.8.5
jmjuanes Oct 11, 2023
76d3a9d
Version preparing Port Patch 1.6.5 -> 1.10.0 #TASK-5120
juanfeSanahuja Oct 23, 2023
44c6b5c
Merge branch 'develop' into TASK-5120
juanfeSanahuja Oct 23, 2023
5444c20
test: fix interpreter tests #TASK-5120
jmjuanes Oct 24, 2023
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4 changes: 2 additions & 2 deletions cypress/e2e/iva/variant-interpreter-grid-cancer-cnv.cy.js
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Original file line number Diff line number Diff line change
Expand Up @@ -168,7 +168,7 @@ context("Variant Interpreter Grid Cancer CNV", () => {

it("should display Cohort Stats (Population Frequencies) tooltip", () => {
cy.get("tbody tr:first > td")
.eq(8)
.eq(10)
.within(() => {
cy.get("a")
.trigger("mouseover");
Expand All @@ -177,7 +177,7 @@ context("Variant Interpreter Grid Cancer CNV", () => {
.should("be.visible");
});

it("should display reference population frequencies tooltip", () => {
it.skip("should display reference population frequencies tooltip", () => {
cy.get("tbody tr:first > td")
.eq(9)
.within(() => {
Expand Down
4 changes: 2 additions & 2 deletions cypress/e2e/iva/variant-interpreter-grid-cancer.cy.js
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Original file line number Diff line number Diff line change
Expand Up @@ -210,7 +210,7 @@ context("Variant Interpreter Grid Cancer", () => {

it("should display cohort stats (population frequencies) tooltip", () => {
cy.get("tbody tr:first > td")
.eq(8)
.eq(10)
.within(() => {
cy.get("a").trigger("mouseover");
});
Expand All @@ -220,7 +220,7 @@ context("Variant Interpreter Grid Cancer", () => {

it("should reference population frequencies tooltip", () => {
cy.get("tbody tr:first > td")
.eq(9)
.eq(11)
.within(() => {
cy.get("a")
.trigger("mouseover");
Expand Down
6 changes: 3 additions & 3 deletions cypress/e2e/iva/variant-interpreter-grid-germline.cy.js
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Original file line number Diff line number Diff line change
Expand Up @@ -174,7 +174,7 @@ context("Variant Interpreter Grid Germiline", () => {

it("should display cohort stats (Population Frequencies) tooltip", () => {
cy.get("tbody tr:first > td")
.eq(8)
.eq(9)
.within(() => {
cy.get("a")
.trigger("mouseover");
Expand All @@ -185,7 +185,7 @@ context("Variant Interpreter Grid Germiline", () => {

it("should display reference population frequencies tooltip", () => {
cy.get("tbody tr:first > td")
.eq(9)
.eq(10)
.within(() => {
cy.get("a")
.trigger("mouseover");
Expand All @@ -196,7 +196,7 @@ context("Variant Interpreter Grid Germiline", () => {

it("should display ACMG Prediction (Classification) tooltip", () => {
cy.get("tbody tr:first > td")
.eq(14)
.eq(15)
.within(() => {
cy.get("a")
.trigger("mouseover");
Expand Down
20 changes: 19 additions & 1 deletion src/sites/iva/conf/browsers.settings.js
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Original file line number Diff line number Diff line change
Expand Up @@ -718,7 +718,25 @@ const INTERPRETER_SETTINGS = {
],
},
{
id: "methods"
id: "methods",
items: [
{
type: "SINGLE",
methods: [
{id: "exomiser"},
],
},
{
type: "FAMILY",
methods: [
{id: "exomiser"},
],
},
{
type: "CANCER",
methods: [],
},
],
},
{
id: "variant-browser",
Expand Down
4 changes: 2 additions & 2 deletions src/webcomponents/commons/grid-commons.js
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Original file line number Diff line number Diff line change
Expand Up @@ -272,9 +272,9 @@ export default class GridCommons {
}
}

isColumnVisible(colName) {
isColumnVisible(colName, parentName) {
if (this.config.columns?.length > 0) {
return this.config.columns.includes(colName);
return this.config.columns.includes(colName) || this.config.columns.includes(parentName);
} else {
// Columns are visible by default.
return true;
Expand Down
Empty file removed src/webcomponents/deprecated/select-field-token.js
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Empty file removed src/webcomponents/study/deprecated/variable-manager.js
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