From 349037404b0425bcfd79dd5d4f118eb12dad662b Mon Sep 17 00:00:00 2001 From: Luca Fumis Date: Thu, 9 Jun 2022 23:17:19 +0100 Subject: [PATCH 01/10] Update label and tooltip --- src/sections/evidence/OTValidation/Body.js | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/sections/evidence/OTValidation/Body.js b/src/sections/evidence/OTValidation/Body.js index 96878d435..ee3b7a06d 100644 --- a/src/sections/evidence/OTValidation/Body.js +++ b/src/sections/evidence/OTValidation/Body.js @@ -187,7 +187,8 @@ const getColumns = classes => [ }, { id: 'confidence', - label: 'Hit', + label: 'OTVL hit', + tooltip: <>Binary assessment of gene perturbation effect in contrast, renderCell: row => ( ), From cdf48cbb1dc2185c17a541e45b2aa851be1547e9 Mon Sep 17 00:00:00 2001 From: Luca Fumis Date: Thu, 9 Jun 2022 23:17:39 +0100 Subject: [PATCH 02/10] Add tooltip --- src/sections/evidence/OTValidation/Body.js | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/src/sections/evidence/OTValidation/Body.js b/src/sections/evidence/OTValidation/Body.js index ee3b7a06d..f056b7bfc 100644 --- a/src/sections/evidence/OTValidation/Body.js +++ b/src/sections/evidence/OTValidation/Body.js @@ -121,6 +121,11 @@ const getColumns = classes => [ { id: 'projectDescription', label: 'OTAR primary project', + tooltip: ( + <> + Binary assessment of gene perturbation effect in primary project screen + + ), renderCell: row => ( {row.projectDescription} From 26d25f75cfe4ff9fbdf4295d0d241e4cf8df3c49 Mon Sep 17 00:00:00 2001 From: Luca Fumis Date: Mon, 13 Jun 2022 18:03:16 +0100 Subject: [PATCH 03/10] Update chips style --- src/sections/evidence/OTValidation/Body.js | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/src/sections/evidence/OTValidation/Body.js b/src/sections/evidence/OTValidation/Body.js index f056b7bfc..506a16ffd 100644 --- a/src/sections/evidence/OTValidation/Body.js +++ b/src/sections/evidence/OTValidation/Body.js @@ -46,10 +46,6 @@ const useStyles = makeStyles(theme => { hsLegendChip: { width: '32px', }, - hsGreen: { - backgroundColor: '#407253', - border: `1px solid ${theme.palette.grey[600]}`, - }, hsRed: { backgroundColor: '#9e1316', border: `1px solid ${theme.palette.grey[600]}`, @@ -59,8 +55,12 @@ const useStyles = makeStyles(theme => { color: theme.palette.grey[600], border: `1px solid ${theme.palette.grey[600]}`, }, - hsGrey: { - backgroundColor: theme.palette.grey[500], + hsBlack: { + backgroundColor: '#000', + border: `1px solid ${theme.palette.grey[600]}`, + }, + hsBlue: { + backgroundColor: '#3489ca', border: `1px solid ${theme.palette.grey[600]}`, }, }; @@ -87,13 +87,13 @@ const hypothesesStatus = [ status: 'expected but not observed', expected: true, observed: false, - styles: 'hsGrey', + styles: 'hsRed', }, { status: 'observed and expected', expected: true, observed: true, - styles: 'hsGreen', + styles: 'hsBlack', }, { status: 'not expected and not observed', @@ -105,7 +105,7 @@ const hypothesesStatus = [ status: 'observed but not expected', expected: false, observed: true, - styles: 'hsRed', + styles: 'hsBlue', }, ]; From f97959f66287ecf231c34b7d8df4273d6bd43ef0 Mon Sep 17 00:00:00 2001 From: Luca Fumis Date: Mon, 13 Jun 2022 18:23:08 +0100 Subject: [PATCH 04/10] Sort chips and move PAN-CO last --- src/sections/evidence/OTValidation/Body.js | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/sections/evidence/OTValidation/Body.js b/src/sections/evidence/OTValidation/Body.js index 506a16ffd..3267c262d 100644 --- a/src/sections/evidence/OTValidation/Body.js +++ b/src/sections/evidence/OTValidation/Body.js @@ -294,6 +294,9 @@ function Body({ definition, id: { ensgId, efoId }, label: { symbol, name } }) { [] ), 'label' + // sort alphabetically but move 'PAN-CO' at the end of the list + ).sort((a, b) => + b.label === 'PAN-CO' ? -1 : a.label < b.label ? -1 : 1 ); return ( From c1d3b64418cc63dd8782bb53d3293bab5609228b Mon Sep 17 00:00:00 2001 From: Luca Fumis Date: Tue, 14 Jun 2022 12:22:56 +0100 Subject: [PATCH 05/10] Add key to child element in list --- src/sections/evidence/OTEncore/Body.js | 1 + 1 file changed, 1 insertion(+) diff --git a/src/sections/evidence/OTEncore/Body.js b/src/sections/evidence/OTEncore/Body.js index 66570bc51..207d32c77 100644 --- a/src/sections/evidence/OTEncore/Body.js +++ b/src/sections/evidence/OTEncore/Body.js @@ -168,6 +168,7 @@ const getColumns = classes => [ to={`https://cellmodelpassports.sanger.ac.uk/passports/${ diseaseCellLine.id }`} + key={diseaseCellLine.id} > {diseaseCellLine.name} From daca251d1a7f489f6d9a0db10e26918ed6033671 Mon Sep 17 00:00:00 2001 From: Luca Fumis Date: Tue, 14 Jun 2022 17:09:11 +0100 Subject: [PATCH 06/10] Add style for unlikely missing hypotheses --- src/sections/evidence/OTValidation/Body.js | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/src/sections/evidence/OTValidation/Body.js b/src/sections/evidence/OTValidation/Body.js index 3267c262d..239a96fe0 100644 --- a/src/sections/evidence/OTValidation/Body.js +++ b/src/sections/evidence/OTValidation/Body.js @@ -63,6 +63,12 @@ const useStyles = makeStyles(theme => { backgroundColor: '#3489ca', border: `1px solid ${theme.palette.grey[600]}`, }, + // in the unlikely case the hypothesis status is unavailable, + // we don't want to display the primary green (for PPP) + hsUndefined: { + backgroundColor: theme.palette.grey[500], + border: `1px solid ${theme.palette.grey[600]}`, + }, }; }); @@ -286,9 +292,9 @@ function Body({ definition, id: { ensgId, efoId }, label: { symbol, name } }) { tooltip: vht.description, customClass: classes[ - (hypothesesStatus.find(s => s.status === vht.status) - ?.styles) - ] || null, + hypothesesStatus.find(s => s.status === vht.status) + ?.styles || 'hsUndefined' + ], })) ), [] From 53a25a88740eacf475068a2fcccc200fd159760f Mon Sep 17 00:00:00 2001 From: Luca Fumis Date: Tue, 14 Jun 2022 17:32:56 +0100 Subject: [PATCH 07/10] Refactor ambiguous operator --- src/sections/evidence/OTValidation/Body.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/sections/evidence/OTValidation/Body.js b/src/sections/evidence/OTValidation/Body.js index 239a96fe0..5f99ac669 100644 --- a/src/sections/evidence/OTValidation/Body.js +++ b/src/sections/evidence/OTValidation/Body.js @@ -302,7 +302,7 @@ function Body({ definition, id: { ensgId, efoId }, label: { symbol, name } }) { 'label' // sort alphabetically but move 'PAN-CO' at the end of the list ).sort((a, b) => - b.label === 'PAN-CO' ? -1 : a.label < b.label ? -1 : 1 + b.label === 'PAN-CO' ? -1 : (a.label < b.label ? -1 : 1) ); return ( From d3567d8c5eba205c2f80f594b23dcd6c8be5942e Mon Sep 17 00:00:00 2001 From: Luca Fumis Date: Wed, 22 Jun 2022 07:11:11 +0100 Subject: [PATCH 08/10] Update Validation lab widget colour scheme --- src/sections/evidence/OTValidation/Body.js | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/src/sections/evidence/OTValidation/Body.js b/src/sections/evidence/OTValidation/Body.js index 5f99ac669..e6a0a673b 100644 --- a/src/sections/evidence/OTValidation/Body.js +++ b/src/sections/evidence/OTValidation/Body.js @@ -46,6 +46,10 @@ const useStyles = makeStyles(theme => { hsLegendChip: { width: '32px', }, + hsGreen: { + backgroundColor: '#407253', // same as PPP green + border: `1px solid ${theme.palette.grey[600]}`, + }, hsRed: { backgroundColor: '#9e1316', border: `1px solid ${theme.palette.grey[600]}`, @@ -99,13 +103,13 @@ const hypothesesStatus = [ status: 'observed and expected', expected: true, observed: true, - styles: 'hsBlack', + styles: 'hsGreen', }, { status: 'not expected and not observed', expected: false, observed: false, - styles: 'hsWhite', + styles: 'hsBlack', }, { status: 'observed but not expected', @@ -182,6 +186,7 @@ const getColumns = classes => [ items={row.biomarkerList.map(bm => ({ label: bm.name, tooltip: bm.description, + customClass: classes['hsWhite'], }))} /> ); @@ -302,7 +307,7 @@ function Body({ definition, id: { ensgId, efoId }, label: { symbol, name } }) { 'label' // sort alphabetically but move 'PAN-CO' at the end of the list ).sort((a, b) => - b.label === 'PAN-CO' ? -1 : (a.label < b.label ? -1 : 1) + b.label === 'PAN-CO' ? -1 : a.label < b.label ? -1 : 1 ); return ( From cbf90f3193c3e8032991fc7a5b1688e34a16cadb Mon Sep 17 00:00:00 2001 From: Luca Fumis Date: Wed, 22 Jun 2022 11:39:52 +0100 Subject: [PATCH 09/10] Update helper text --- src/sections/evidence/OTValidation/Body.js | 25 +++++++++++++++++++++- 1 file changed, 24 insertions(+), 1 deletion(-) diff --git a/src/sections/evidence/OTValidation/Body.js b/src/sections/evidence/OTValidation/Body.js index e6a0a673b..ab8dc1e63 100644 --- a/src/sections/evidence/OTValidation/Body.js +++ b/src/sections/evidence/OTValidation/Body.js @@ -318,8 +318,31 @@ function Body({ definition, id: { ensgId, efoId }, label: { symbol, name } }) { gutterBottom className={classes.bold} > - OTVL biomarker assessment for {symbol} + + This table provides an overarching summary of the + target-disease association in the context of the listed + biomarkers, based on criteria described{' '} + + here + + , as informed by the target performance across the whole + cell line panel. Colour-coding indicates whether a + dependency was expected to be associated with a biomarker + (based on Project SCORE data) and whether it was observed + as such (based on OTVL data). + + } + showHelpIcon + > + OTVL biomarker assessment for {symbol} + + {/** LEGEND */}
From 88a4de10123f64a1e22e576bb7508a1ac60e29c9 Mon Sep 17 00:00:00 2001 From: Luca Fumis Date: Wed, 22 Jun 2022 11:41:01 +0100 Subject: [PATCH 10/10] update config for TESTING purposes ONLY --- public/index.html | 2 +- src/config.js | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/public/index.html b/public/index.html index 8164bc779..7e42df758 100644 --- a/public/index.html +++ b/public/index.html @@ -45,7 +45,7 @@ --> - + diff --git a/src/config.js b/src/config.js index f4248423e..c78718353 100644 --- a/src/config.js +++ b/src/config.js @@ -2,7 +2,8 @@ const config = { urlApi: window.configUrlApi ?? - 'https://api.platform.dev.opentargets.xyz/api/v4/graphql', + // 'https://api.platform.dev.opentargets.xyz/api/v4/graphql', + 'https://api.partner-platform.dev.opentargets.xyz/api/v4/graphql', googleTagManagerID: window.configGoogleTagManagerID ?? null, efoURL: window.configEFOURL ?? '/data/ontology/efo_json/diseases_efo.jsonl',