diff --git a/packages/sections/src/constants.js b/packages/sections/src/constants.js
index df86ed383..f8ad9d89b 100644
--- a/packages/sections/src/constants.js
+++ b/packages/sections/src/constants.js
@@ -7,6 +7,7 @@ export const appCanonicalUrl = "https://platform.opentargets.org";
// Chunk sizes for server side pagination/download.
export const tableChunkSize = 100;
export const downloaderChunkSize = 2500;
+export const sectionsBaseSizeQuery = 3500;
// NA label.
export const naLabel = "N/A";
@@ -38,7 +39,7 @@ const clinicalPhases = {
4: "Phase IV",
};
-export const phaseMap = (clinicalPhase) => {
+export const phaseMap = clinicalPhase => {
const clinicalPhaseId = String(clinicalPhase);
return clinicalPhases[clinicalPhaseId];
};
diff --git a/packages/sections/src/evidence/CRISPR/Body.jsx b/packages/sections/src/evidence/CRISPR/Body.jsx
index dfd24f4c2..40189dd86 100644
--- a/packages/sections/src/evidence/CRISPR/Body.jsx
+++ b/packages/sections/src/evidence/CRISPR/Body.jsx
@@ -3,7 +3,7 @@ import { useQuery } from "@apollo/client";
import { Link } from "@mui/material";
import { SectionItem, DataTable, TableDrawer } from "ui";
import { dataTypesMap } from "../../dataTypes";
-import { naLabel } from "../../constants";
+import { naLabel, sectionsBaseSizeQuery } from "../../constants";
import Description from "./Description";
import { definition } from ".";
@@ -24,7 +24,7 @@ const columns = [
renderCell: ({ diseaseCellLines, diseaseFromSource }) => {
if (!diseaseCellLines) return naLabel;
- const cellLines = diseaseCellLines.map((line) => ({
+ const cellLines = diseaseCellLines.map(line => ({
name: line.name,
url: `https://cellmodelpassports.sanger.ac.uk/passports/${line.id}`,
group: "Cancer Cell Lines",
@@ -52,6 +52,7 @@ function Body({ id, label, entity }) {
const variables = {
ensemblId: ensgId,
efoId,
+ size: sectionsBaseSizeQuery,
};
const request = useQuery(CRISPR_QUERY, {
@@ -64,9 +65,7 @@ function Body({ id, label, entity }) {
chipText={dataTypesMap.affected_pathway}
request={request}
entity={entity}
- renderDescription={() => (
-
- )}
+ renderDescription={() => }
renderBody={({ disease }) => {
const { rows } = disease.crisprSummary;
return (
diff --git a/packages/sections/src/evidence/CRISPR/CrisprQuery.gql b/packages/sections/src/evidence/CRISPR/CrisprQuery.gql
index 38d8095ed..62789bdd0 100644
--- a/packages/sections/src/evidence/CRISPR/CrisprQuery.gql
+++ b/packages/sections/src/evidence/CRISPR/CrisprQuery.gql
@@ -1,10 +1,11 @@
-query CrisprQuery($ensemblId: String!, $efoId: String!) {
+query CrisprQuery($ensemblId: String!, $efoId: String!, $size: Int!) {
disease(efoId: $efoId) {
id
crisprSummary: evidences(
ensemblIds: [$ensemblId]
enableIndirect: true
datasourceIds: ["crispr"]
+ size: $size
) {
count
rows {
diff --git a/packages/sections/src/evidence/CRISPRScreen/Body.jsx b/packages/sections/src/evidence/CRISPRScreen/Body.jsx
index 9919612aa..b49f0e89c 100644
--- a/packages/sections/src/evidence/CRISPRScreen/Body.jsx
+++ b/packages/sections/src/evidence/CRISPRScreen/Body.jsx
@@ -5,7 +5,7 @@ import { Tooltip, SectionItem, TooltipStyledLabel, Link, DataTable } from "ui";
import { dataTypesMap } from "../../dataTypes";
import Description from "./Description";
import { PublicationsDrawer } from "ui";
-import { defaultRowsPerPageOptions, naLabel } from "../../constants";
+import { defaultRowsPerPageOptions, naLabel, sectionsBaseSizeQuery } from "../../constants";
import { definition } from ".";
import CRISPR_QUERY from "./CrisprScreenQuery.gql";
@@ -20,32 +20,23 @@ const sources = {
// format the diseaseFromSource field: remove the "essential genes" info
// this might be sorted at data level at some point
-const parseDiseaseName = (d) =>
- d.toLowerCase().replace("essential genes / ", "");
+const parseDiseaseName = d => d.toLowerCase().replace("essential genes / ", "");
-const getColumns = (label) => [
+const getColumns = label => [
{
id: "diseaseFromSourceMappedId",
label: "Reported disease",
- renderCell: (row) => {
+ renderCell: row => {
const disease = parseDiseaseName(row.diseaseFromSource);
- return (
-
- {_.capitalize(disease)}
-
- );
+ return {_.capitalize(disease)};
},
- filterValue: (row) =>
- row.diseaseFromSource + ", " + row.diseaseFromSourceMappedId,
+ filterValue: row => row.diseaseFromSource + ", " + row.diseaseFromSourceMappedId,
},
{
id: "studyId",
label: "Study Identifier",
- renderCell: (row) => (
-
+ renderCell: row => (
+
{row.studyId}
),
@@ -53,7 +44,7 @@ const getColumns = (label) => [
{
id: "contrast",
label: "Contrast / Study overview",
- renderCell: (row) => {
+ renderCell: row => {
// trim the last '.' - this could also be addressed at data level perhaps?
const overview = row.studyOverview?.endsWith(".")
? row.studyOverview.slice(0, -1)
@@ -63,10 +54,7 @@ const getColumns = (label) => [
+
}
>
@@ -80,28 +68,26 @@ const getColumns = (label) => [
return {overview};
}
},
- filterValue: (row) => row.contrast + "; " + row.studyOverview,
+ filterValue: row => row.contrast + "; " + row.studyOverview,
},
{
id: "cellType",
label: "Cell type",
- renderCell: (row) => row.cellType,
- filterValue: (row) => row.cellType,
+ renderCell: row => row.cellType,
+ filterValue: row => row.cellType,
width: "12%",
},
{
id: "log2FoldChangeValue",
label: "log2 fold change",
- renderCell: (row) =>
- row.log2FoldChangeValue
- ? parseFloat(row.log2FoldChangeValue.toFixed(6))
- : naLabel,
+ renderCell: row =>
+ row.log2FoldChangeValue ? parseFloat(row.log2FoldChangeValue.toFixed(6)) : naLabel,
width: "9%",
},
{
id: "resourceScore",
label: "Significance",
- renderCell: (row) => {
+ renderCell: row => {
if (row.resourceScore && row.statisticalTestTail) {
return (
[
);
} else {
- return row.resourceScore
- ? parseFloat(row.resourceScore.toFixed(6))
- : naLabel;
+ return row.resourceScore ? parseFloat(row.resourceScore.toFixed(6)) : naLabel;
}
},
- filterValue: (row) => row.resourceScore + "; " + row.statisticalTestTail,
+ filterValue: row => row.resourceScore + "; " + row.statisticalTestTail,
width: "9%",
},
{
id: "projectId",
label: "Source",
- renderCell: (row) => (
+ renderCell: row => (
{sources[row.projectId].name}
),
- filterValue: (row) => row.projectId,
+ filterValue: row => row.projectId,
width: "9%",
},
{
@@ -157,57 +141,59 @@ const getColumns = (label) => [
const exportColumns = [
{
label: "disease",
- exportValue: (row) => parseDiseaseName(row.diseaseFromSource),
+ exportValue: row => parseDiseaseName(row.diseaseFromSource),
},
{
label: "disease id",
- exportValue: (row) => row.diseaseFromSourceMappedId,
+ exportValue: row => row.diseaseFromSourceMappedId,
},
{
label: "study identifier",
- exportValue: (row) => row.studyId,
+ exportValue: row => row.studyId,
},
{
label: "contrast",
- exportValue: (row) => row.contrast,
+ exportValue: row => row.contrast,
},
{
label: "study overview",
- exportValue: (row) => row.studyOverview,
+ exportValue: row => row.studyOverview,
},
{
label: "cell type",
- exportValue: (row) => row.cellType,
+ exportValue: row => row.cellType,
},
{
label: "log2 fold change",
- exportValue: (row) => row.log2FoldChangeValue,
+ exportValue: row => row.log2FoldChangeValue,
},
{
label: "significance",
- exportValue: (row) => row.resourceScore,
+ exportValue: row => row.resourceScore,
},
{
label: "statistical test tail",
- exportValue: (row) => row.statisticalTestTail,
+ exportValue: row => row.statisticalTestTail,
},
{
label: "source",
- exportValue: (row) => row.projectId,
+ exportValue: row => row.projectId,
},
{
label: "publication",
- exportValue: (row) => row.literature.join(", "),
+ exportValue: row => row.literature.join(", "),
},
];
function Body({ id, label, entity }) {
const { ensgId, efoId } = id;
+ const variables = {
+ ensemblId: ensgId,
+ efoId,
+ size: sectionsBaseSizeQuery,
+ };
const request = useQuery(CRISPR_QUERY, {
- variables: {
- ensemblId: ensgId,
- efoId,
- },
+ variables,
});
const columns = getColumns(label);
@@ -218,9 +204,7 @@ function Body({ id, label, entity }) {
chipText={dataTypesMap.affected_pathway}
request={request}
entity={entity}
- renderDescription={() => (
-
- )}
+ renderDescription={() => }
renderBody={({ disease }) => {
const { rows } = disease.CrisprScreenSummary;
return (
@@ -236,6 +220,8 @@ function Body({ id, label, entity }) {
noWrap={false}
noWrapHeader={false}
rowsPerPageOptions={defaultRowsPerPageOptions}
+ query={CRISPR_QUERY.loc.source.body}
+ variables={variables}
/>
);
}}
diff --git a/packages/sections/src/evidence/CRISPRScreen/CrisprScreenQuery.gql b/packages/sections/src/evidence/CRISPRScreen/CrisprScreenQuery.gql
index 96917a43b..61a9c8d1d 100644
--- a/packages/sections/src/evidence/CRISPRScreen/CrisprScreenQuery.gql
+++ b/packages/sections/src/evidence/CRISPRScreen/CrisprScreenQuery.gql
@@ -1,31 +1,14 @@
-query CrisprScreenQuery($ensemblId: String!, $efoId: String!) {
+query CrisprScreenQuery($ensemblId: String!, $efoId: String!, $size: Int!) {
disease(efoId: $efoId) {
id
CrisprScreenSummary: evidences(
ensemblIds: [$ensemblId]
enableIndirect: true
datasourceIds: ["crispr_screen"]
+ size: $size
) {
count
rows {
- # disease {
- # id
- # name
- # }
- # projectId
- # contrast
- # studyOverview
- # cellType
- # cellLineBackground
- # crisprScreenLibrary
- # statisticalTestTail
- # resourceScore
- # log2FoldChangeValue
- # diseaseCellLines {
- # name
- # }
- # releaseVersion
-
studyId
datatypeId
datasourceId
diff --git a/packages/sections/src/evidence/CancerBiomarkers/Body.jsx b/packages/sections/src/evidence/CancerBiomarkers/Body.jsx
index af5f1d7d8..9dc70ca53 100644
--- a/packages/sections/src/evidence/CancerBiomarkers/Body.jsx
+++ b/packages/sections/src/evidence/CancerBiomarkers/Body.jsx
@@ -1,16 +1,9 @@
import { useQuery } from "@apollo/client";
import { Typography } from "@mui/material";
-import {
- Link,
- Tooltip,
- SectionItem,
- PublicationsDrawer,
- DataTable,
- TableDrawer,
-} from "ui";
+import { Link, Tooltip, SectionItem, PublicationsDrawer, DataTable, TableDrawer } from "ui";
import { naLabel } from "ui/src/constants";
-import { defaultRowsPerPageOptions } from "../../constants";
+import { defaultRowsPerPageOptions, sectionsBaseSizeQuery } from "../../constants";
import { epmcUrl } from "../../utils/urls";
import Description from "./Description";
import BiomarkersDrawer from "./BiomarkersDrawer";
@@ -18,7 +11,7 @@ import { definition } from ".";
import CANCER_BIOMARKERS_EVIDENCE_QUERY from "./CancerBiomarkersEvidence.gql";
-const getColumns = (label) => [
+const getColumns = label => [
{
id: "disease.name",
label: "Disease",
@@ -52,16 +45,13 @@ const getColumns = (label) => [
label: "Reported drug",
renderCell: ({ drug, drugFromSource }) =>
drug ? {drug.name} : drugFromSource,
- filterValue: ({ drug, drugFromSource }) =>
- drug ? drug.name : drugFromSource,
+ filterValue: ({ drug, drugFromSource }) => (drug ? drug.name : drugFromSource),
},
{
id: "drugResponse.name",
label: "Drug response",
renderCell: ({ drugResponse }) =>
- (drugResponse && (
- {drugResponse.name}
- )) ||
+ (drugResponse && {drugResponse.name}) ||
naLabel,
},
{
@@ -69,7 +59,7 @@ const getColumns = (label) => [
label: "Source",
renderCell: ({ confidence, urls }) => {
const entries = urls
- ? urls.map((url) => ({
+ ? urls.map(url => ({
url: url.url,
name: url.niceName,
group: "Sources",
@@ -83,20 +73,14 @@ const getColumns = (label) => [
label: "Literature",
renderCell: ({ literature }) => {
const entries = literature
- ? literature.map((id) => ({
+ ? literature.map(id => ({
name: id,
url: epmcUrl(id),
group: "literature",
}))
: [];
- return (
-
- );
+ return ;
},
},
];
@@ -107,6 +91,7 @@ function Body({ id, label, entity }) {
const variables = {
ensemblId: ensgId,
efoId,
+ size: sectionsBaseSizeQuery,
};
const request = useQuery(CANCER_BIOMARKERS_EVIDENCE_QUERY, {
@@ -121,9 +106,7 @@ function Body({ id, label, entity }) {
chipText={definition.dataType}
request={request}
entity={entity}
- renderDescription={() => (
-
- )}
+ renderDescription={() => }
renderBody={({ disease }) => {
const { rows } = disease.cancerBiomarkersSummary;
return (
diff --git a/packages/sections/src/evidence/CancerBiomarkers/CancerBiomarkersEvidence.gql b/packages/sections/src/evidence/CancerBiomarkers/CancerBiomarkersEvidence.gql
index d39a49a2e..a8cf62021 100644
--- a/packages/sections/src/evidence/CancerBiomarkers/CancerBiomarkersEvidence.gql
+++ b/packages/sections/src/evidence/CancerBiomarkers/CancerBiomarkersEvidence.gql
@@ -1,10 +1,11 @@
-query CancerBiomarkersQuery($ensemblId: String!, $efoId: String!) {
+query CancerBiomarkersQuery($ensemblId: String!, $efoId: String!, $size: Int!) {
disease(efoId: $efoId) {
id
cancerBiomarkersSummary: evidences(
ensemblIds: [$ensemblId]
enableIndirect: true
datasourceIds: ["cancer_biomarkers"]
+ size: $size
) {
count
rows {
diff --git a/packages/sections/src/evidence/CancerGeneCensus/Body.jsx b/packages/sections/src/evidence/CancerGeneCensus/Body.jsx
index d26ebdcf8..6ac8c12a3 100644
--- a/packages/sections/src/evidence/CancerGeneCensus/Body.jsx
+++ b/packages/sections/src/evidence/CancerGeneCensus/Body.jsx
@@ -5,7 +5,7 @@ import { v1 } from "uuid";
import { ChipList, Link, SectionItem, PublicationsDrawer, DataTable } from "ui";
-import { naLabel, defaultRowsPerPageOptions } from "../../constants";
+import { naLabel, defaultRowsPerPageOptions, sectionsBaseSizeQuery } from "../../constants";
import { dataTypesMap } from "../../dataTypes";
import Description from "./Description";
import { epmcUrl } from "../../utils/urls";
@@ -15,19 +15,15 @@ import { definition } from ".";
import CANCER_GENE_CENSUS_QUERY from "./sectionQuery.gql";
-const samplePercent = (item) =>
- (item.numberSamplesWithMutationType / item.numberSamplesTested) * 100;
+const samplePercent = item => (item.numberSamplesWithMutationType / item.numberSamplesTested) * 100;
-const getMaxPercent = (row) =>
- Math.max(...row.mutatedSamples.map((item) => samplePercent(item)));
+const getMaxPercent = row => Math.max(...row.mutatedSamples.map(item => samplePercent(item)));
-const getColumns = (label) => [
+const getColumns = label => [
{
id: "disease.name",
label: "Disease/phenotype",
- renderCell: ({ disease }) => (
- {disease.name}
- ),
+ renderCell: ({ disease }) => {disease.name},
},
{
id: "mutationType",
@@ -40,17 +36,11 @@ const getColumns = (label) => [
.sort((a, b) => samplePercent(b) - samplePercent(a));
return (
- {sortedMutatedSamples.map((mutatedSample) => (
-
+ {sortedMutatedSamples.map(mutatedSample => (
+
{sentenceCase(mutatedSample.functionalConsequence.label)}
@@ -61,9 +51,7 @@ const getColumns = (label) => [
},
filterValue: ({ mutatedSamples }) =>
(mutatedSamples || [])
- .map((mutatedSample) =>
- sentenceCase(mutatedSample.functionalConsequence.label)
- )
+ .map(mutatedSample => sentenceCase(mutatedSample.functionalConsequence.label))
.join(),
},
{
@@ -77,18 +65,14 @@ const getColumns = (label) => [
.sort((a, b) => samplePercent(b) - samplePercent(a));
return (
- {sortedMutatedSamples.map((item) => {
+ {sortedMutatedSamples.map(item => {
const percent = samplePercent(item);
return (
- {percent < 5
- ? parseFloat(percent.toFixed(2)).toString()
- : Math.round(percent)}
- %
+ {percent < 5 ? parseFloat(percent.toFixed(2)).toString() : Math.round(percent)}%
- ({item.numberSamplesWithMutationType}/
- {item.numberSamplesTested})
+ ({item.numberSamplesWithMutationType}/{item.numberSamplesTested})
);
@@ -116,11 +100,7 @@ const getColumns = (label) => [
}, []) || [];
return (
-
+
);
},
},
@@ -142,6 +122,7 @@ function Body({ id, label, entity }) {
const variables = {
ensemblId: ensgId,
efoId,
+ size: sectionsBaseSizeQuery,
};
const request = useQuery(CANCER_GENE_CENSUS_QUERY, {
@@ -156,9 +137,7 @@ function Body({ id, label, entity }) {
chipText={dataTypesMap.somatic_mutation}
request={request}
entity={entity}
- renderDescription={() => (
-
- )}
+ renderDescription={() => }
renderBody={({
disease: {
cancerGeneCensusSummary: { rows },
@@ -168,8 +147,8 @@ function Body({ id, label, entity }) {
const roleInCancerItems =
hallmarks && hallmarks.attributes.length > 0
? hallmarks.attributes
- .filter((attribute) => attribute.name === "role in cancer")
- .map((attribute) => ({
+ .filter(attribute => attribute.name === "role in cancer")
+ .map(attribute => ({
label: attribute.description,
url: epmcUrl(attribute.pmid),
}))
diff --git a/packages/sections/src/evidence/CancerGeneCensus/sectionQuery.gql b/packages/sections/src/evidence/CancerGeneCensus/sectionQuery.gql
index 337c211a2..f29268e0f 100644
--- a/packages/sections/src/evidence/CancerGeneCensus/sectionQuery.gql
+++ b/packages/sections/src/evidence/CancerGeneCensus/sectionQuery.gql
@@ -1,10 +1,11 @@
-query CancerGeneCensusQuery($ensemblId: String!, $efoId: String!) {
+query CancerGeneCensusQuery($ensemblId: String!, $efoId: String!, $size: Int!) {
disease(efoId: $efoId) {
id
cancerGeneCensusSummary: evidences(
ensemblIds: [$ensemblId]
enableIndirect: true
datasourceIds: ["cancer_gene_census"]
+ size: $size
) {
count
rows {
diff --git a/packages/sections/src/evidence/ClinGen/Body.jsx b/packages/sections/src/evidence/ClinGen/Body.jsx
index 7d9283325..80bac0377 100644
--- a/packages/sections/src/evidence/ClinGen/Body.jsx
+++ b/packages/sections/src/evidence/ClinGen/Body.jsx
@@ -1,7 +1,7 @@
import { useQuery } from "@apollo/client";
import { Typography } from "@mui/material";
import { Link, Tooltip, SectionItem, DataTable } from "ui";
-import { defaultRowsPerPageOptions, naLabel } from "../../constants";
+import { defaultRowsPerPageOptions, naLabel, sectionsBaseSizeQuery } from "../../constants";
import { dataTypesMap } from "../../dataTypes";
import Description from "./Description";
import { definition } from ".";
@@ -45,7 +45,7 @@ const columns = [
listStyle: "none",
}}
>
- {allelicRequirements.map((allelicRequirement) => (
+ {allelicRequirements.map(allelicRequirement => (
{allelicRequirement}
))}
@@ -62,10 +62,7 @@ const columns = [
title={
As defined by the{" "}
-
+
GenCC Guidelines
@@ -90,6 +87,7 @@ function Body({ id, label, entity }) {
const variables = {
ensemblId: ensgId,
efoId,
+ size: sectionsBaseSizeQuery,
};
const request = useQuery(CLINGEN_QUERY, {
@@ -102,9 +100,7 @@ function Body({ id, label, entity }) {
entity={entity}
chipText={dataTypesMap.genetic_association}
request={request}
- renderDescription={() => (
-
- )}
+ renderDescription={() => }
renderBody={({ disease }) => {
const { rows } = disease.clingenSummary;
return (
diff --git a/packages/sections/src/evidence/ClinGen/ClingenQuery.gql b/packages/sections/src/evidence/ClinGen/ClingenQuery.gql
index 1f32a4535..b07bc5033 100644
--- a/packages/sections/src/evidence/ClinGen/ClingenQuery.gql
+++ b/packages/sections/src/evidence/ClinGen/ClingenQuery.gql
@@ -1,10 +1,11 @@
-query ClingenQuery($ensemblId: String!, $efoId: String!) {
+query ClingenQuery($ensemblId: String!, $efoId: String!, $size: Int!) {
disease(efoId: $efoId) {
id
clingenSummary: evidences(
ensemblIds: [$ensemblId]
enableIndirect: true
datasourceIds: ["clingen"]
+ size: $size
) {
count
rows {
diff --git a/packages/sections/src/evidence/ExpressionAtlas/Body.jsx b/packages/sections/src/evidence/ExpressionAtlas/Body.jsx
index 1992658da..7f414c51a 100644
--- a/packages/sections/src/evidence/ExpressionAtlas/Body.jsx
+++ b/packages/sections/src/evidence/ExpressionAtlas/Body.jsx
@@ -10,6 +10,7 @@ import { sentenceCase } from "../../utils/global";
import EXPRESSION_ATLAS_QUERY from "./ExpressionAtlasQuery.gql";
import { definition } from ".";
+import { sectionsBaseSizeQuery } from "../../constants";
const columns = [
{
@@ -93,9 +94,7 @@ const columns = [
p-value
>
),
- renderCell: ({ resourceScore }) => (
-
- ),
+ renderCell: ({ resourceScore }) => ,
numeric: true,
sortable: true,
},
@@ -106,6 +105,7 @@ function Body({ id, label, entity }) {
const variables = {
ensemblId: ensgId,
efoId,
+ size: sectionsBaseSizeQuery,
};
const request = useQuery(EXPRESSION_ATLAS_QUERY, {
@@ -118,9 +118,7 @@ function Body({ id, label, entity }) {
chipText={dataTypesMap.rna_expression}
request={request}
entity={entity}
- renderDescription={() => (
-
- )}
+ renderDescription={() => }
renderBody={({ disease }) => {
const { rows } = disease.expressionAtlasSummary;
return (
diff --git a/packages/sections/src/evidence/ExpressionAtlas/ExpressionAtlasQuery.gql b/packages/sections/src/evidence/ExpressionAtlas/ExpressionAtlasQuery.gql
index 7c9e3e552..59739687e 100644
--- a/packages/sections/src/evidence/ExpressionAtlas/ExpressionAtlasQuery.gql
+++ b/packages/sections/src/evidence/ExpressionAtlas/ExpressionAtlasQuery.gql
@@ -1,10 +1,11 @@
-query ExpressionAtlasQuery($ensemblId: String!, $efoId: String!) {
+query ExpressionAtlasQuery($ensemblId: String!, $efoId: String!, $size: Int!) {
disease(efoId: $efoId) {
id
expressionAtlasSummary: evidences(
ensemblIds: [$ensemblId]
enableIndirect: true
datasourceIds: ["expression_atlas"]
+ size: $size
) {
count
rows {
diff --git a/packages/sections/src/evidence/Gene2Phenotype/Body.jsx b/packages/sections/src/evidence/Gene2Phenotype/Body.jsx
index fb8940ffa..2cf895e2f 100644
--- a/packages/sections/src/evidence/Gene2Phenotype/Body.jsx
+++ b/packages/sections/src/evidence/Gene2Phenotype/Body.jsx
@@ -3,7 +3,7 @@ import { useQuery } from "@apollo/client";
import { v1 } from "uuid";
import { SectionItem, Tooltip, Link, PublicationsDrawer, DataTable } from "ui";
-import { defaultRowsPerPageOptions, naLabel } from "../../constants";
+import { defaultRowsPerPageOptions, naLabel, sectionsBaseSizeQuery } from "../../constants";
import Description from "./Description";
import { epmcUrl } from "../../utils/urls";
import { dataTypesMap } from "../../dataTypes";
@@ -14,7 +14,7 @@ import { definition } from ".";
const g2pUrl = (studyId, symbol) =>
`https://www.ebi.ac.uk/gene2phenotype/search?panel=${studyId}&search_term=${symbol}`;
-const getColumns = (label) => [
+const getColumns = label => [
{
id: "disease.name",
label: "Disease/phenotype",
@@ -60,7 +60,7 @@ const getColumns = (label) => [
if (allelicRequirements && allelicRequirements.length > 1) {
return (
- {allelicRequirements.map((item) => (
+ {allelicRequirements.map(item => (
{item}
))}
@@ -92,10 +92,7 @@ const getColumns = (label) => [
title={
As defined by the{" "}
-
+
GenCC Guidelines
@@ -113,25 +110,19 @@ const getColumns = (label) => [
label: "Literature",
renderCell: ({ literature }) => {
const entries = literature
- ? literature.map((id) => ({
+ ? literature.map(id => ({
name: id,
url: epmcUrl(id),
group: "literature",
}))
: [];
- return (
-
- );
+ return ;
},
},
];
function Body({ id: { ensgId, efoId }, label: { symbol, name }, entity }) {
- const variables = { ensemblId: ensgId, efoId };
+ const variables = { ensemblId: ensgId, efoId, size: sectionsBaseSizeQuery };
const request = useQuery(OPEN_TARGETS_GENETICS_QUERY, {
variables,
@@ -146,7 +137,7 @@ function Body({ id: { ensgId, efoId }, label: { symbol, name }, entity }) {
request={request}
entity={entity}
renderDescription={() => }
- renderBody={(data) => (
+ renderBody={data => (
{
};
const getSourceLink = (project, targetId) => {
- if (project === "Epi25 collaborative")
- return `https://epi25.broadinstitute.org/gene/${targetId}`;
+ if (project === "Epi25 collaborative") return `https://epi25.broadinstitute.org/gene/${targetId}`;
if (project === "Autism Sequencing Consortiuml")
return `https://asc.broadinstitute.org/gene/${targetId}`;
- if (project === "SCHEMA consortium")
- return `https://schema.broadinstitute.org/gene/${targetId}`;
+ if (project === "SCHEMA consortium") return `https://schema.broadinstitute.org/gene/${targetId}`;
if (project === "Genebass")
return `https://app.genebass.org/gene/${targetId}?burdenSet=pLoF&phewasOpts=1&resultLayout=full`;
if (project === "AstraZeneca PheWAS Portal") return `https://azphewas.com`;
return "";
};
-const getColumns = (label) => [
+const getColumns = label => [
{
id: "disease.name",
label: "Disease/phenotype",
@@ -145,9 +136,7 @@ const getColumns = (label) => [
numeric: true,
sortable: true,
renderCell: ({ studySampleSize }) =>
- studySampleSize
- ? parseInt(studySampleSize, 10).toLocaleString()
- : naLabel,
+ studySampleSize ? parseInt(studySampleSize, 10).toLocaleString() : naLabel,
},
{
id: "oddsRatio",
@@ -161,9 +150,9 @@ const getColumns = (label) => [
}) => {
const ci =
oddsRatioConfidenceIntervalLower && oddsRatioConfidenceIntervalUpper
- ? `(${parseFloat(
- oddsRatioConfidenceIntervalLower.toFixed(3)
- )}, ${parseFloat(oddsRatioConfidenceIntervalUpper.toFixed(3))})`
+ ? `(${parseFloat(oddsRatioConfidenceIntervalLower.toFixed(3))}, ${parseFloat(
+ oddsRatioConfidenceIntervalUpper.toFixed(3)
+ )})`
: "";
return oddsRatio ? `${parseFloat(oddsRatio.toFixed(3))} ${ci}` : naLabel;
},
@@ -179,24 +168,16 @@ const getColumns = (label) => [
label: "Beta (CI 95%)",
numeric: true,
sortable: true,
- renderCell: ({
- beta,
- betaConfidenceIntervalLower,
- betaConfidenceIntervalUpper,
- }) => {
+ renderCell: ({ beta, betaConfidenceIntervalLower, betaConfidenceIntervalUpper }) => {
const ci =
betaConfidenceIntervalLower && betaConfidenceIntervalUpper
- ? `(${parseFloat(
- betaConfidenceIntervalLower.toFixed(3)
- )}, ${parseFloat(betaConfidenceIntervalUpper.toFixed(3))})`
+ ? `(${parseFloat(betaConfidenceIntervalLower.toFixed(3))}, ${parseFloat(
+ betaConfidenceIntervalUpper.toFixed(3)
+ )})`
: "";
return beta ? `${parseFloat(beta.toFixed(3))} ${ci}` : naLabel;
},
- filterValue: ({
- beta,
- betaConfidenceIntervalLower,
- betaConfidenceIntervalUpper,
- }) =>
+ filterValue: ({ beta, betaConfidenceIntervalLower, betaConfidenceIntervalUpper }) =>
`${beta} ${betaConfidenceIntervalLower} ${betaConfidenceIntervalUpper} ${naLabel}`,
},
{
@@ -211,33 +192,24 @@ const getColumns = (label) => [
renderCell: ({ pValueMantissa, pValueExponent }) => (
),
- filterValue: ({ pValueMantissa, pValueExponent }) =>
- `${pValueMantissa} ${pValueExponent}`,
- exportValue: ({ pValueMantissa, pValueExponent }) =>
- `${pValueMantissa}x10${pValueExponent}`,
+ filterValue: ({ pValueMantissa, pValueExponent }) => `${pValueMantissa} ${pValueExponent}`,
+ exportValue: ({ pValueMantissa, pValueExponent }) => `${pValueMantissa}x10${pValueExponent}`,
comparator: (a, b) =>
- a.pValueMantissa * 10 ** a.pValueExponent -
- b.pValueMantissa * 10 ** b.pValueExponent,
+ a.pValueMantissa * 10 ** a.pValueExponent - b.pValueMantissa * 10 ** b.pValueExponent,
},
{
id: "literature",
label: "Literature",
renderCell: ({ literature }) => {
const entries = literature
- ? literature.map((id) => ({
+ ? literature.map(id => ({
name: id,
url: epmcUrl(id),
group: "literature",
}))
: [];
- return (
-
- );
+ return ;
},
},
];
@@ -247,6 +219,7 @@ export function Body({ id, label, entity }) {
const variables = {
ensemblId: ensgId,
efoId,
+ size: sectionsBaseSizeQuery,
};
const request = useQuery(GENE_BURDEN_QUERY, {
@@ -261,9 +234,7 @@ export function Body({ id, label, entity }) {
chipText={dataTypesMap.genetic_association}
entity={entity}
request={request}
- renderDescription={() => (
-
- )}
+ renderDescription={() => }
renderBody={({ disease }) => {
const { rows } = disease.geneBurdenSummary;
return (
diff --git a/packages/sections/src/evidence/GeneBurden/GeneBurdenQuery.gql b/packages/sections/src/evidence/GeneBurden/GeneBurdenQuery.gql
index bc1a8b87e..504db65c3 100644
--- a/packages/sections/src/evidence/GeneBurden/GeneBurdenQuery.gql
+++ b/packages/sections/src/evidence/GeneBurden/GeneBurdenQuery.gql
@@ -1,10 +1,11 @@
-query GeneBurdenQuery($ensemblId: String!, $efoId: String!) {
+query GeneBurdenQuery($ensemblId: String!, $efoId: String!, $size: Int!) {
disease(efoId: $efoId) {
id
geneBurdenSummary: evidences(
ensemblIds: [$ensemblId]
enableIndirect: true
datasourceIds: ["gene_burden"]
+ size: $size
) {
count
rows {
diff --git a/packages/sections/src/evidence/GenomicsEngland/Body.jsx b/packages/sections/src/evidence/GenomicsEngland/Body.jsx
index d57f9ab23..6cbcb5a44 100644
--- a/packages/sections/src/evidence/GenomicsEngland/Body.jsx
+++ b/packages/sections/src/evidence/GenomicsEngland/Body.jsx
@@ -1,15 +1,12 @@
import { useQuery } from "@apollo/client";
-import {
- faCheckSquare,
- faExclamationTriangle,
-} from "@fortawesome/free-solid-svg-icons";
+import { faCheckSquare, faExclamationTriangle } from "@fortawesome/free-solid-svg-icons";
import { FontAwesomeIcon } from "@fortawesome/react-fontawesome";
import { Typography } from "@mui/material";
import { v1 } from "uuid";
import { Tooltip, SectionItem, Link, PublicationsDrawer, DataTable } from "ui";
import { definition } from ".";
-import { defaultRowsPerPageOptions, naLabel } from "../../constants";
+import { defaultRowsPerPageOptions, naLabel, sectionsBaseSizeQuery } from "../../constants";
import Description from "./Description";
import { epmcUrl } from "../../utils/urls";
import { sentenceCase } from "../../utils/global";
@@ -20,40 +17,35 @@ import GENOMICS_ENGLAND_QUERY from "./sectionQuery.gql";
const geUrl = (id, approvedSymbol) =>
`https://panelapp.genomicsengland.co.uk/panels/${id}/gene/${approvedSymbol}`;
-const confidenceCaption = (confidence) =>
+const confidenceCaption = confidence =>
({
green: (
- {" "}
- {sentenceCase(confidence)}
+ {sentenceCase(confidence)}
),
amber: (
- {" "}
- {sentenceCase(confidence)}
+ {sentenceCase(confidence)}
),
}[confidence]);
-const confidenceMap = (confidence) =>
+const confidenceMap = confidence =>
({
green: 20,
amber: 10,
}[confidence.toLowerCase()] || 0);
-const allelicRequirementsCaption = (allelicRequirements) => {
- const caption = sentenceCase(
- allelicRequirements.split(" ", 1)[0].replace(/[;:,]*/g, "")
- );
+const allelicRequirementsCaption = allelicRequirements => {
+ const caption = sentenceCase(allelicRequirements.split(" ", 1)[0].replace(/[;:,]*/g, ""));
const description =
- allelicRequirements.split(" ").slice(1).join(" ") ||
- "No more information available";
+ allelicRequirements.split(" ").slice(1).join(" ") || "No more information available";
return [caption, description];
};
-const getColumns = (label) => [
+const getColumns = label => [
{
id: "disease",
label: "Disease/phenotype",
@@ -64,12 +56,7 @@ const getColumns = (label) => [
Reported disease or phenotype:
-
+
{sentenceCase(diseaseFromSource)}
@@ -79,7 +66,7 @@ const getColumns = (label) => [
All reported phenotypes:
- {cohortPhenotypes.map((cp) => (
+ {cohortPhenotypes.map(cp => (
{cp}
))}
@@ -94,24 +81,18 @@ const getColumns = (label) => [
{disease.name}
),
- filterValue: ({ disease, diseaseFromSource }) =>
- [disease.name, diseaseFromSource].join(),
+ filterValue: ({ disease, diseaseFromSource }) => [disease.name, diseaseFromSource].join(),
},
{
id: "allelicRequirements",
label: "Allelic Requirement",
renderCell: ({ allelicRequirements }) =>
allelicRequirements
- ? allelicRequirements.map((item) => {
+ ? allelicRequirements.map(item => {
const [caption, description] = allelicRequirementsCaption(item);
return (
-
+
{caption}
);
@@ -139,10 +120,7 @@ const getColumns = (label) => [
title={
As defined by the{" "}
-
+
Panel App Guidelines
@@ -152,8 +130,7 @@ const getColumns = (label) => [
{confidenceCaption(confidence)}
),
- comparator: (a, b) =>
- confidenceMap(a.confidence) - confidenceMap(b.confidence),
+ comparator: (a, b) => confidenceMap(a.confidence) - confidenceMap(b.confidence),
},
{
id: "literature",
@@ -173,11 +150,7 @@ const getColumns = (label) => [
}, []) || [];
return (
-
+
);
},
},
@@ -188,6 +161,7 @@ export function Body({ id, label, entity }) {
const variables = {
ensemblId: ensgId,
efoId,
+ size: sectionsBaseSizeQuery,
};
const request = useQuery(GENOMICS_ENGLAND_QUERY, {
@@ -202,10 +176,8 @@ export function Body({ id, label, entity }) {
chipText={dataTypesMap.genetic_association}
request={request}
entity={entity}
- renderDescription={() => (
-
- )}
- renderBody={(data) => (
+ renderDescription={() => }
+ renderBody={data => (
`https://www.intogen.org/search?gene=${approvedSymbol}&cohort=${id}`;
-const samplePercent = (item) =>
- (item.numberMutatedSamples / item.numberSamplesTested) * 100;
+const samplePercent = item => (item.numberMutatedSamples / item.numberSamplesTested) * 100;
const columns = [
{
@@ -47,8 +39,7 @@ const columns = [
{disease.name}
),
- filterValue: ({ disease, diseaseFromSource }) =>
- [disease.name, diseaseFromSource].join(),
+ filterValue: ({ disease, diseaseFromSource }) => [disease.name, diseaseFromSource].join(),
},
{
id: "mutatedSamples",
@@ -58,15 +49,12 @@ const columns = [
{mutatedSamples
.sort((a, b) => samplePercent(b) - samplePercent(a))
- .map((item) => {
+ .map(item => {
const percent = samplePercent(item);
return (
- {percent < 5
- ? parseFloat(percent.toFixed(2)).toString()
- : Math.round(percent)}
- %
+ {percent < 5 ? parseFloat(percent.toFixed(2)).toString() : Math.round(percent)}%
({item.numberMutatedSamples}/{item.numberSamplesTested})
@@ -95,20 +83,17 @@ const columns = [
),
numeric: true,
sortable: true,
- renderCell: ({ resourceScore }) => (
-
- ),
+ renderCell: ({ resourceScore }) => ,
},
{
id: "significantDriverMethods",
label: "Cancer driver methods",
tooltip: (
<>
- The current version of the intOGen pipeline uses seven methods to
- identify cancer driver genes from somatic point mutations - HotMAPS,
- dNDScv, smRegions, CBaSE, FML, MutPanning, and CLUSTL. The pipeline also
- uses a combination of methods. For further information on the methods,
- please{" "}
+ The current version of the intOGen pipeline uses seven methods to identify cancer driver
+ genes from somatic point mutations - HotMAPS, dNDScv, smRegions, CBaSE, FML, MutPanning, and
+ CLUSTL. The pipeline also uses a combination of methods. For further information on the
+ methods, please{" "}
click here
{" "}
@@ -118,7 +103,7 @@ const columns = [
renderCell: ({ significantDriverMethods }) =>
significantDriverMethods ? (
({
+ items={significantDriverMethods.map(am => ({
label: am,
tooltip: (methods[am] || {}).description,
}))}
@@ -126,18 +111,12 @@ const columns = [
) : (
naLabel
),
- filterValue: ({ significantDriverMethods }) =>
- significantDriverMethods.map((am) => am).join(),
+ filterValue: ({ significantDriverMethods }) => significantDriverMethods.map(am => am).join(),
},
{
id: "cohortShortName",
label: "Cohort Information",
- renderCell: ({
- cohortId,
- cohortShortName,
- cohortDescription,
- target: { approvedSymbol },
- }) =>
+ renderCell: ({ cohortId, cohortShortName, cohortDescription, target: { approvedSymbol } }) =>
cohortShortName && cohortDescription ? (
<>
@@ -169,6 +148,7 @@ function Body({ id, label, entity }) {
const variables = {
ensemblId: ensgId,
efoId,
+ size: sectionsBaseSizeQuery,
};
const request = useQuery(INTOGEN_QUERY, {
@@ -181,9 +161,7 @@ function Body({ id, label, entity }) {
chipText={dataTypesMap.somatic_mutation}
request={request}
entity={entity}
- renderDescription={() => (
-
- )}
+ renderDescription={() => }
renderBody={({
disease: {
intOgen: { rows },
@@ -193,8 +171,8 @@ function Body({ id, label, entity }) {
const roleInCancerItems =
hallmarks && hallmarks.attributes.length > 0
? hallmarks.attributes
- .filter((attribute) => attribute.name === "role in cancer")
- .map((attribute) => ({
+ .filter(attribute => attribute.name === "role in cancer")
+ .map(attribute => ({
label: attribute.description,
url: epmcUrl(attribute.pmid),
}))
diff --git a/packages/sections/src/evidence/IntOgen/sectionQuery.gql b/packages/sections/src/evidence/IntOgen/sectionQuery.gql
index 933c759a0..0667bf59a 100644
--- a/packages/sections/src/evidence/IntOgen/sectionQuery.gql
+++ b/packages/sections/src/evidence/IntOgen/sectionQuery.gql
@@ -1,10 +1,11 @@
-query IntOgenQuery($ensemblId: String!, $efoId: String!) {
+query IntOgenQuery($ensemblId: String!, $efoId: String!, $size: Int!) {
disease(efoId: $efoId) {
id
intOgen: evidences(
ensemblIds: [$ensemblId]
enableIndirect: true
datasourceIds: ["intogen"]
+ size: $size
) {
count
rows {
diff --git a/packages/sections/src/evidence/OTGenetics/Body.jsx b/packages/sections/src/evidence/OTGenetics/Body.jsx
index 21d6207ec..598cf7675 100644
--- a/packages/sections/src/evidence/OTGenetics/Body.jsx
+++ b/packages/sections/src/evidence/OTGenetics/Body.jsx
@@ -12,6 +12,7 @@ import {
import {
defaultRowsPerPageOptions,
naLabel,
+ sectionsBaseSizeQuery,
studySourceMap,
variantConsequenceSource,
} from "../../constants";
@@ -27,9 +28,7 @@ function getColumns(label) {
{
id: "disease",
label: "Disease/phenotype",
- renderCell: ({ disease }) => (
- {disease.name}
- ),
+ renderCell: ({ disease }) => {disease.name},
filterValue: ({ disease }) => disease.name,
},
{
@@ -97,8 +96,7 @@ function getColumns(label) {
) : null}
>
),
- filterValue: ({ variantId, variantRsId }) =>
- `${variantId} ${variantRsId}`,
+ filterValue: ({ variantId, variantRsId }) => `${variantId} ${variantRsId}`,
},
{
id: "variantConsequence",
@@ -116,22 +114,14 @@ function getColumns(label) {
label={variantConsequenceSource.VEP.label}
value={sentenceCase(variantFunctionalConsequence.label)}
tooltip={variantConsequenceSource.VEP.tooltip}
- to={identifiersOrgLink(
- "SO",
- variantFunctionalConsequence.id.slice(3)
- )}
+ to={identifiersOrgLink("SO", variantFunctionalConsequence.id.slice(3))}
/>
)}
{variantFunctionalConsequenceFromQtlId && (
)}
@@ -160,8 +150,7 @@ function getColumns(label) {
),
comparator: (a, b) =>
- a.pValueMantissa * 10 ** a.pValueExponent -
- b.pValueMantissa * 10 ** b.pValueExponent,
+ a.pValueMantissa * 10 ** a.pValueExponent - b.pValueMantissa * 10 ** b.pValueExponent,
},
{
id: "studySampleSize",
@@ -169,9 +158,7 @@ function getColumns(label) {
numeric: true,
sortable: true,
renderCell: ({ studySampleSize }) =>
- studySampleSize
- ? parseInt(studySampleSize, 10).toLocaleString()
- : naLabel,
+ studySampleSize ? parseInt(studySampleSize, 10).toLocaleString() : naLabel,
},
{
id: "oddsRatio",
@@ -184,29 +171,23 @@ function getColumns(label) {
}) => {
const ci =
oddsRatioConfidenceIntervalLower && oddsRatioConfidenceIntervalUpper
- ? `(${parseFloat(
- oddsRatioConfidenceIntervalLower.toFixed(3)
- )}, ${parseFloat(oddsRatioConfidenceIntervalUpper.toFixed(3))})`
+ ? `(${parseFloat(oddsRatioConfidenceIntervalLower.toFixed(3))}, ${parseFloat(
+ oddsRatioConfidenceIntervalUpper.toFixed(3)
+ )})`
: "";
- return oddsRatio
- ? `${parseFloat(oddsRatio.toFixed(3))} ${ci}`
- : naLabel;
+ return oddsRatio ? `${parseFloat(oddsRatio.toFixed(3))} ${ci}` : naLabel;
},
},
{
id: "betaConfidenceInterval",
label: "Beta (CI 95%)",
numeric: true,
- renderCell: ({
- beta,
- betaConfidenceIntervalLower,
- betaConfidenceIntervalUpper,
- }) => {
+ renderCell: ({ beta, betaConfidenceIntervalLower, betaConfidenceIntervalUpper }) => {
const ci =
betaConfidenceIntervalLower && betaConfidenceIntervalUpper
- ? `(${parseFloat(
- betaConfidenceIntervalLower.toFixed(3)
- )}, ${parseFloat(betaConfidenceIntervalUpper.toFixed(3))})`
+ ? `(${parseFloat(betaConfidenceIntervalLower.toFixed(3))}, ${parseFloat(
+ betaConfidenceIntervalUpper.toFixed(3)
+ )})`
: "";
return beta ? `${parseFloat(beta.toFixed(3))} ${ci}` : naLabel;
},
@@ -235,7 +216,7 @@ function getColumns(label) {
function Body({ id, label, entity }) {
const { ensgId, efoId } = id;
- const variables = { ensemblId: ensgId, efoId };
+ const variables = { ensemblId: ensgId, efoId, size: sectionsBaseSizeQuery };
const columns = getColumns(label);
const request = useQuery(OPEN_TARGETS_GENETICS_QUERY, {
@@ -248,10 +229,8 @@ function Body({ id, label, entity }) {
chipText={dataTypesMap.genetic_association}
request={request}
entity={entity}
- renderDescription={() => (
-
- )}
- renderBody={(data) => (
+ renderDescription={() => }
+ renderBody={data => (
[
+const getColumns = label => [
{
id: "disease.name",
label: "Disease/phenotype",
@@ -88,11 +88,7 @@ const getColumns = (label) => [
}, []) || [];
return (
-
+
);
},
},
@@ -101,43 +97,43 @@ const getColumns = (label) => [
const exportColumns = [
{
label: "Disease",
- exportValue: (row) => row.disease.name,
+ exportValue: row => row.disease.name,
},
{
label: "Disease ID",
- exportValue: (row) => row.disease.id,
+ exportValue: row => row.disease.id,
},
{
label: "Disease from source",
- exportValue: (row) => row.diseaseFromSource,
+ exportValue: row => row.diseaseFromSource,
},
{
label: "Target from source",
- exportValue: (row) => row.targetFromSource,
+ exportValue: row => row.targetFromSource,
},
{
label: "Target from source ID",
- exportValue: (row) => row.targetFromSourceId,
+ exportValue: row => row.targetFromSourceId,
},
{
label: "Allele origins",
- exportValue: (row) => row.alleleOrigins.join("; "),
+ exportValue: row => row.alleleOrigins.join("; "),
},
{
label: "Functional consequence",
- exportValue: (row) => sentenceCase(row.variantFunctionalConsequence.label),
+ exportValue: row => sentenceCase(row.variantFunctionalConsequence.label),
},
{
label: "Functional consequence ID",
- exportValue: (row) => row.variantFunctionalConsequence.id,
+ exportValue: row => row.variantFunctionalConsequence.id,
},
{
label: "Confidence",
- exportValue: (row) => row.confidence,
+ exportValue: row => row.confidence,
},
{
label: "Publication IDs",
- exportValue: (row) => row.literature.join(", "),
+ exportValue: row => row.literature.join(", "),
},
];
@@ -147,6 +143,7 @@ function Body({ id, label, entity }) {
const variables = {
ensemblId: ensgId,
efoId,
+ size: sectionsBaseSizeQuery,
};
const request = useQuery(ORPHANET_QUERY, {
@@ -161,9 +158,7 @@ function Body({ id, label, entity }) {
chipText={dataTypesMap.genetic_association}
request={request}
entity={entity}
- renderDescription={() => (
-
- )}
+ renderDescription={() => }
renderBody={({ disease }) => {
const { rows } = disease.orphanetSummary;
return (
diff --git a/packages/sections/src/evidence/Orphanet/OrphanetQuery.gql b/packages/sections/src/evidence/Orphanet/OrphanetQuery.gql
index 3ad31c22d..fbd6d03d8 100644
--- a/packages/sections/src/evidence/Orphanet/OrphanetQuery.gql
+++ b/packages/sections/src/evidence/Orphanet/OrphanetQuery.gql
@@ -1,4 +1,4 @@
-query OrphanetQuery($ensemblId: String!, $efoId: String!) {
+query OrphanetQuery($ensemblId: String!, $efoId: String!, $size: Int!) {
target(ensemblId: $ensemblId) {
approvedSymbol
}
@@ -8,6 +8,7 @@ query OrphanetQuery($ensemblId: String!, $efoId: String!) {
ensemblIds: [$ensemblId]
enableIndirect: true
datasourceIds: ["orphanet"]
+ size: $size
) {
count
rows {
diff --git a/packages/sections/src/evidence/Progeny/Body.jsx b/packages/sections/src/evidence/Progeny/Body.jsx
index b4a72e028..ee672ec89 100644
--- a/packages/sections/src/evidence/Progeny/Body.jsx
+++ b/packages/sections/src/evidence/Progeny/Body.jsx
@@ -7,9 +7,9 @@ import Description from "./Description";
import PROGENY_QUERY from "./sectionQuery.gql";
import { dataTypesMap } from "../../dataTypes";
import { sentenceCase } from "../../utils/global";
-import { defaultRowsPerPageOptions, naLabel } from "../../constants";
+import { defaultRowsPerPageOptions, naLabel, sectionsBaseSizeQuery } from "../../constants";
-const reactomeUrl = (id) => `https://identifiers.org/reactome:${id}`;
+const reactomeUrl = id => `https://identifiers.org/reactome:${id}`;
const columns = [
{
@@ -32,8 +32,7 @@ const columns = [
{disease.name}
),
- filterValue: ({ disease, diseaseFromSource }) =>
- [disease.name, diseaseFromSource].join(),
+ filterValue: ({ disease, diseaseFromSource }) => [disease.name, diseaseFromSource].join(),
},
{
id: "pathwayName",
@@ -56,9 +55,7 @@ const columns = [
),
numeric: true,
sortable: true,
- renderCell: ({ resourceScore }) => (
-
- ),
+ renderCell: ({ resourceScore }) => ,
},
];
@@ -68,6 +65,7 @@ function Body({ id, label, entity }) {
const variables = {
ensemblId: ensgId,
efoId,
+ size: sectionsBaseSizeQuery,
};
const request = useQuery(PROGENY_QUERY, {
@@ -80,10 +78,8 @@ function Body({ id, label, entity }) {
chipText={dataTypesMap.affected_pathway}
request={request}
entity={entity}
- renderDescription={() => (
-
- )}
- renderBody={(data) => (
+ renderDescription={() => }
+ renderBody={data => (
[
+const getColumns = label => [
{
id: "disease.name",
label: "Disease / phenotype",
@@ -52,15 +52,12 @@ const getColumns = (label) => [
}
if (pathways.length === 1) {
return (
-
+
{pathways[0].name}
);
}
- const refs = pathways.map((p) => ({
+ const refs = pathways.map(p => ({
url: `http://www.reactome.org/PathwayBrowser/#${p.id}`,
name: p.name,
group: "Pathways",
@@ -83,10 +80,7 @@ const getColumns = (label) => [
id: "targetFromSourceId",
label: "Reported target",
renderCell: ({ targetFromSourceId }) => (
-
+
{targetFromSourceId}
),
@@ -96,18 +90,14 @@ const getColumns = (label) => [
id: "targetModulation",
label: "Target modulation",
renderCell: ({ targetModulation }) =>
- targetModulation ? (
- {sentenceCase(targetModulation)}
- ) : (
- naLabel
- ),
+ targetModulation ? {sentenceCase(targetModulation)} : naLabel,
filterValue: ({ targetModulation }) => sentenceCase(targetModulation),
width: "12%",
},
{
filterValue: ({ variantAminoacidDescriptions }) =>
variantAminoacidDescriptions
- ?.map((variantAminoacidDescription) => variantAminoacidDescription)
+ ?.map(variantAminoacidDescription => variantAminoacidDescription)
.join(),
label: "Amino acid variation",
renderCell: ({ variantAminoacidDescriptions }) => {
@@ -117,7 +107,7 @@ const getColumns = (label) => [
if (variantAminoacidDescriptions?.length > 1) {
return (
({
+ entries={variantAminoacidDescriptions.map(d => ({
name: d,
group: "Amino acid variation",
}))}
@@ -133,7 +123,7 @@ const getColumns = (label) => [
label: "Literature",
renderCell: ({ literature = [] }) => {
const literatureList = [];
- literature?.forEach((id) => {
+ literature?.forEach(id => {
if (id !== "NA") {
literatureList.push({
name: id,
@@ -143,11 +133,7 @@ const getColumns = (label) => [
}
});
return (
-
+
);
},
width: "12%",
@@ -160,6 +146,7 @@ function Body({ id, label, entity }) {
const variables = {
ensemblId: ensgId,
efoId,
+ size: sectionsBaseSizeQuery,
};
const request = useQuery(REACTOME_QUERY, {
@@ -174,9 +161,7 @@ function Body({ id, label, entity }) {
chipText={dataTypesMap.affected_pathway}
request={request}
entity={entity}
- renderDescription={() => (
-
- )}
+ renderDescription={() => }
renderBody={({ disease }) => {
const { rows } = disease.reactomeSummary;
return (
diff --git a/packages/sections/src/evidence/Reactome/sectionQuery.gql b/packages/sections/src/evidence/Reactome/sectionQuery.gql
index b4c195b78..3dcc47d62 100644
--- a/packages/sections/src/evidence/Reactome/sectionQuery.gql
+++ b/packages/sections/src/evidence/Reactome/sectionQuery.gql
@@ -1,4 +1,4 @@
-query reactomeQuery($ensemblId: String!, $efoId: String!) {
+query reactomeQuery($ensemblId: String!, $efoId: String!, $size: Int!) {
target(ensemblId: $ensemblId) {
approvedSymbol
}
@@ -8,6 +8,7 @@ query reactomeQuery($ensemblId: String!, $efoId: String!) {
ensemblIds: [$ensemblId]
enableIndirect: true
datasourceIds: ["reactome"]
+ size: $size
) {
count
rows {
diff --git a/packages/sections/src/evidence/SlapEnrich/Body.jsx b/packages/sections/src/evidence/SlapEnrich/Body.jsx
index afa80f7c5..4ba922f61 100644
--- a/packages/sections/src/evidence/SlapEnrich/Body.jsx
+++ b/packages/sections/src/evidence/SlapEnrich/Body.jsx
@@ -7,9 +7,9 @@ import Description from "./Description";
import { dataTypesMap } from "../../dataTypes";
import SLAPENRICH_QUERY from "./sectionQuery.gql";
import { sentenceCase } from "../../utils/global";
-import { defaultRowsPerPageOptions, naLabel } from "../../constants";
+import { defaultRowsPerPageOptions, naLabel, sectionsBaseSizeQuery } from "../../constants";
-const reactomeUrl = (id) => `https://identifiers.org/reactome:${id}`;
+const reactomeUrl = id => `https://identifiers.org/reactome:${id}`;
const columns = [
{
@@ -32,8 +32,7 @@ const columns = [
{disease.name}
),
- filterValue: ({ disease, diseaseFromSource }) =>
- [disease.name, diseaseFromSource].join(),
+ filterValue: ({ disease, diseaseFromSource }) => [disease.name, diseaseFromSource].join(),
},
{
id: "pathwayName",
@@ -56,9 +55,7 @@ const columns = [
),
numeric: true,
sortable: true,
- renderCell: ({ resourceScore }) => (
-
- ),
+ renderCell: ({ resourceScore }) => ,
},
];
@@ -67,6 +64,7 @@ function Body({ id, label, entity }) {
const variables = {
ensemblId: ensgId,
efoId,
+ size: sectionsBaseSizeQuery,
};
const request = useQuery(SLAPENRICH_QUERY, {
@@ -79,10 +77,8 @@ function Body({ id, label, entity }) {
entity={entity}
chipText={dataTypesMap.affected_pathway}
request={request}
- renderDescription={() => (
-
- )}
- renderBody={(data) => (
+ renderDescription={() => }
+ renderBody={data => (
[
+const getColumns = label => [
{
id: "disease",
label: "Disease/phenotype",
- renderCell: ({ disease }) => (
- {disease.name}
- ),
+ renderCell: ({ disease }) => {disease.name},
filterValue: ({ disease }) => disease.name,
},
{
@@ -49,11 +47,7 @@ const getColumns = (label) => [
return acc;
}, []) || [];
return (
-
+
);
},
},
@@ -65,6 +59,7 @@ function Body({ id, label, entity }) {
const variables = {
ensemblId: ensgId,
efoId,
+ size: sectionsBaseSizeQuery,
};
const request = useQuery(SYSBIO_QUERY, {
@@ -79,10 +74,8 @@ function Body({ id, label, entity }) {
chipText={dataTypesMap.affected_pathway}
request={request}
entity={entity}
- renderDescription={() => (
-
- )}
- renderBody={(data) => (
+ renderDescription={() => }
+ renderBody={data => (
[
+const getcolumns = label => [
{
id: "disease.name",
label: "Disease/phenotype",
@@ -62,11 +62,7 @@ const getcolumns = (label) => [
}, []) || [];
return (
-
+
);
},
},
@@ -78,6 +74,7 @@ function Body({ id, label, entity }) {
const variables = {
ensemblId: ensgId,
efoId,
+ size: sectionsBaseSizeQuery,
};
const request = useQuery(UNIPROT_LITERATURE_QUERY, {
@@ -92,9 +89,7 @@ function Body({ id, label, entity }) {
chipText={dataTypesMap.genetic_association}
request={request}
entity={entity}
- renderDescription={() => (
-
- )}
+ renderDescription={() => }
renderBody={({ disease }) => {
const { rows } = disease.uniprotLiteratureSummary;
return (
diff --git a/packages/sections/src/evidence/UniProtLiterature/UniprotLiteratureQuery.gql b/packages/sections/src/evidence/UniProtLiterature/UniprotLiteratureQuery.gql
index 07d9cf501..f1bf484ad 100644
--- a/packages/sections/src/evidence/UniProtLiterature/UniprotLiteratureQuery.gql
+++ b/packages/sections/src/evidence/UniProtLiterature/UniprotLiteratureQuery.gql
@@ -1,4 +1,4 @@
-query UniprotLiteratureQuery($ensemblId: String!, $efoId: String!) {
+query UniprotLiteratureQuery($ensemblId: String!, $efoId: String!, $size: Int!) {
target(ensemblId: $ensemblId) {
approvedSymbol
}
@@ -8,6 +8,7 @@ query UniprotLiteratureQuery($ensemblId: String!, $efoId: String!) {
ensemblIds: [$ensemblId]
enableIndirect: true
datasourceIds: ["uniprot_literature"]
+ size: $size
) {
count
rows {
diff --git a/packages/sections/src/evidence/UniProtVariants/Body.jsx b/packages/sections/src/evidence/UniProtVariants/Body.jsx
index 5b8ffe00d..d426f4da8 100644
--- a/packages/sections/src/evidence/UniProtVariants/Body.jsx
+++ b/packages/sections/src/evidence/UniProtVariants/Body.jsx
@@ -1,13 +1,6 @@
import { useQuery } from "@apollo/client";
import { Typography } from "@mui/material";
-import {
- Link,
- SectionItem,
- Tooltip,
- PublicationsDrawer,
- LabelChip,
- DataTable,
-} from "ui";
+import { Link, SectionItem, Tooltip, PublicationsDrawer, LabelChip, DataTable } from "ui";
import { definition } from ".";
@@ -18,6 +11,7 @@ import { identifiersOrgLink } from "../../utils/global";
import {
defaultRowsPerPageOptions,
variantConsequenceSource,
+ sectionsBaseSizeQuery,
} from "../../constants";
import UNIPROT_VARIANTS_QUERY from "./UniprotVariantsQuery.gql";
@@ -98,11 +92,7 @@ function getColumns(label) {
}, []) || [];
return (
-
+
);
},
},
@@ -115,6 +105,7 @@ export function Body({ id, label, entity }) {
const variables = {
ensemblId: ensgId,
efoId,
+ size: sectionsBaseSizeQuery,
};
const columns = getColumns(label);
@@ -128,9 +119,7 @@ export function Body({ id, label, entity }) {
chipText={dataTypesMap.genetic_association}
request={request}
entity={entity}
- renderDescription={() => (
-
- )}
+ renderDescription={() => }
renderBody={({ disease }) => {
const { rows } = disease.uniprotVariantsSummary;
return (
diff --git a/packages/sections/src/evidence/UniProtVariants/UniprotVariantsQuery.gql b/packages/sections/src/evidence/UniProtVariants/UniprotVariantsQuery.gql
index bd82ce17f..f4682456b 100644
--- a/packages/sections/src/evidence/UniProtVariants/UniprotVariantsQuery.gql
+++ b/packages/sections/src/evidence/UniProtVariants/UniprotVariantsQuery.gql
@@ -1,4 +1,4 @@
-query UniprotVariantsQuery($ensemblId: String!, $efoId: String!) {
+query UniprotVariantsQuery($ensemblId: String!, $efoId: String!, $size: Int!) {
target(ensemblId: $ensemblId) {
approvedSymbol
}
@@ -8,6 +8,7 @@ query UniprotVariantsQuery($ensemblId: String!, $efoId: String!) {
ensemblIds: [$ensemblId]
enableIndirect: true
datasourceIds: ["uniprot_variants"]
+ size: $size
) {
count
rows {