diff --git a/src/graphql/biospecimens/queries.ts b/src/graphql/biospecimens/queries.ts
index 788323025..8cbe18c1a 100644
--- a/src/graphql/biospecimens/queries.ts
+++ b/src/graphql/biospecimens/queries.ts
@@ -149,6 +149,7 @@ export const CHECK_BIOSPECIMEN_MATCH = gql`
edges {
node {
fhir_id
+ external_sample_id
sample_id
study {
study_id
@@ -169,6 +170,7 @@ export const BIOSPECIMEN_SEARCH_BY_ID_QUERY = gql`
edges {
node {
sample_id
+ external_sample_id
collection_sample_id
}
}
diff --git a/src/graphql/participants/queries.ts b/src/graphql/participants/queries.ts
index 192fb3ec0..57a316b30 100644
--- a/src/graphql/participants/queries.ts
+++ b/src/graphql/participants/queries.ts
@@ -307,6 +307,7 @@ export const PARTICIPANT_SEARCH_BY_ID_QUERY = gql`
edges {
node {
participant_id
+ external_id
}
}
}
diff --git a/src/locales/en.ts b/src/locales/en.ts
index 62f61af4b..22f2afe09 100644
--- a/src/locales/en.ts
+++ b/src/locales/en.ts
@@ -52,6 +52,28 @@ const en = {
title: 'Search by study',
tooltip: 'Search by Study Code, Study Name, dbGaP Accession Number',
},
+ participant: {
+ emptyText: 'No participants found',
+ placeholder: 'e.g. PT_1BCRHQVF, HTP0001',
+ title: 'Search by Participant ID',
+ tooltip: 'Search by Participant ID or External Participant ID',
+ },
+ biospecimen: {
+ emptyText: 'No samples found',
+ placeholder: 'e.g. BS_011DYZ2J, HTP0001B2_Plasma, SSH3953290',
+ title: 'Search by Sample ID',
+ tooltip: 'Search by Sample ID or External Sample ID',
+ collection: {
+ emptyText: 'No collection ID found',
+ placeholder: 'e.g. HTP0001B2_Whole blood, BS_1YEZ2XR4_Saliva',
+ title: 'Search by Collection ID',
+ },
+ },
+ file: {
+ emptyText: 'No files found',
+ placeholder: 'e.g. GF_001CSF26',
+ title: 'Search by File ID',
+ },
},
filters: {
actions: {
@@ -364,6 +386,16 @@ const en = {
inputLabel: 'Copy-paste a list of identifiers or upload a file',
match: 'Matched ({count})',
unmatch: 'Unmatched ({count})',
+ identifiers: {
+ participant: 'Participant ID, External Participant ID',
+ biospecimen: 'Sample ID, External Sample ID',
+ file: 'File ID',
+ },
+ placeholders: {
+ participant: 'e.g. PT_03Y3K025, HTP0001, 10214, HTP0001',
+ biospecimen: 'e.g. HTP0001B2_Whole blood, BS_011DYZ2J_DNA, 238981007, SSH3953290',
+ file: 'e.g. GF_2JAYWYDX, GF_TP6PG8Z0',
+ },
tableMessage:
'{submittedCount} submitted identifiers mapped to {mappedCount} unique system identifiers',
matchTable: {
diff --git a/src/views/DataExploration/components/BiospecimenSearch.tsx b/src/views/DataExploration/components/BiospecimenSearch.tsx
index dadb3e9d9..e7a6629ac 100644
--- a/src/views/DataExploration/components/BiospecimenSearch.tsx
+++ b/src/views/DataExploration/components/BiospecimenSearch.tsx
@@ -1,3 +1,4 @@
+import intl from 'react-intl-universal';
import { ExperimentOutlined } from '@ant-design/icons';
import useQueryBuilderState from '@ferlab/ui/core/components/QueryBuilder/utils/useQueryBuilderState';
import { ISqonGroupFilter } from '@ferlab/ui/core/data/sqon/types';
@@ -18,9 +19,10 @@ const BiospecimenSearch = ({ queryBuilderId }: ICustomSearchProps) => {
<GlobalSearch<IBiospecimenEntity>
queryBuilderId={queryBuilderId}
field="sample_id" // @todo: search_text, see when implemented
+ searchFields={['sample_id', 'external_sample_id']}
index={INDEXES.BIOSPECIMEN}
- placeholder="e.g. BS_011DYZ2J, HTP0001B2_Plasma"
- emptyDescription="No samples found"
+ placeholder={intl.get('global.search.biospecimen.placeholder')}
+ emptyDescription={intl.get('global.search.biospecimen.emptyText')}
query={BIOSPECIMEN_SEARCH_BY_ID_QUERY}
sqon={activeQuery as ISqonGroupFilter}
optionsFormatter={(options, matchRegex, search) =>
@@ -29,12 +31,14 @@ const BiospecimenSearch = ({ queryBuilderId }: ICustomSearchProps) => {
<SelectItem
icon={<ExperimentOutlined />}
title={highlightSearchMatch(option.sample_id, matchRegex, search)}
+ caption={highlightSearchMatch(option.external_sample_id, matchRegex, search)}
/>
),
value: option.sample_id,
}))
}
- title="Search by sample ID"
+ title={intl.get('global.search.biospecimen.title')}
+ tooltipText={intl.get('global.search.biospecimen.tooltip')}
/>
);
};
@@ -47,8 +51,8 @@ const BiospecimenCollectionSearch = ({ queryBuilderId }: ICustomSearchProps) =>
queryBuilderId={queryBuilderId}
field="collection_sample_id" // @todo: search_text, see when implemented
index={INDEXES.BIOSPECIMEN}
- placeholder="e.g. HTP0001B2_Whole blood, BS_1YEZ2XR4_Saliva"
- emptyDescription="No collection ID found"
+ placeholder={intl.get('global.search.biospecimen.collection.placeholder')}
+ emptyDescription={intl.get('global.search.biospecimen.collection.emptyText')}
query={BIOSPECIMEN_SEARCH_BY_ID_QUERY}
sqon={sqon}
optionsFormatter={(options, matchRegex, search) =>
@@ -62,7 +66,7 @@ const BiospecimenCollectionSearch = ({ queryBuilderId }: ICustomSearchProps) =>
value: option.collection_sample_id,
}))
}
- title="Search by collection ID"
+ title={intl.get('global.search.biospecimen.collection.title')}
/>
);
};
diff --git a/src/views/DataExploration/components/FileSearch.tsx b/src/views/DataExploration/components/FileSearch.tsx
index 6333dff61..9ec51230d 100644
--- a/src/views/DataExploration/components/FileSearch.tsx
+++ b/src/views/DataExploration/components/FileSearch.tsx
@@ -1,3 +1,4 @@
+import intl from 'react-intl-universal';
import { FileTextOutlined } from '@ant-design/icons';
import useQueryBuilderState from '@ferlab/ui/core/components/QueryBuilder/utils/useQueryBuilderState';
import { ISqonGroupFilter } from '@ferlab/ui/core/data/sqon/types';
@@ -17,8 +18,8 @@ const FileSearch = ({ queryBuilderId }: ICustomSearchProps) => {
queryBuilderId={queryBuilderId}
field="file_id"
index={INDEXES.FILE}
- placeholder="e.g. GF_001CSF26"
- emptyDescription="No files found"
+ placeholder={intl.get('global.search.file.placeholder')}
+ emptyDescription={intl.get('global.search.file.emptyText')}
query={FILE_SEARCH_BY_ID_QUERY}
sqon={activeQuery as ISqonGroupFilter}
optionsFormatter={(options, matchRegex, search) =>
@@ -32,7 +33,7 @@ const FileSearch = ({ queryBuilderId }: ICustomSearchProps) => {
value: option.file_id,
}))
}
- title="Search by file ID"
+ title={intl.get('global.search.file.title')}
/>
);
};
diff --git a/src/views/DataExploration/components/ParticipantSearch.tsx b/src/views/DataExploration/components/ParticipantSearch.tsx
index 2dddd27c7..955280dcf 100644
--- a/src/views/DataExploration/components/ParticipantSearch.tsx
+++ b/src/views/DataExploration/components/ParticipantSearch.tsx
@@ -1,3 +1,4 @@
+import intl from 'react-intl-universal';
import { UserOutlined } from '@ant-design/icons';
import useQueryBuilderState from '@ferlab/ui/core/components/QueryBuilder/utils/useQueryBuilderState';
import { ISqonGroupFilter } from '@ferlab/ui/core/data/sqon/types';
@@ -16,9 +17,10 @@ const ParticipantSearch = ({ queryBuilderId }: ICustomSearchProps) => {
<GlobalSearch<IParticipantEntity>
queryBuilderId={queryBuilderId}
field="participant_id"
+ searchFields={['participant_id', 'external_id']}
index={INDEXES.PARTICIPANT}
- placeholder="e.g. PT_1BCRHQVF"
- emptyDescription="No participants found"
+ placeholder={intl.get('global.search.participant.placeholder')}
+ emptyDescription={intl.get('global.search.participant.emptyText')}
query={PARTICIPANT_SEARCH_BY_ID_QUERY}
sqon={activeQuery as ISqonGroupFilter}
optionsFormatter={(options, matchRegex, search) =>
@@ -27,12 +29,14 @@ const ParticipantSearch = ({ queryBuilderId }: ICustomSearchProps) => {
<SelectItem
icon={<UserOutlined />}
title={highlightSearchMatch(option.participant_id, matchRegex, search)}
+ caption={highlightSearchMatch(option.external_id, matchRegex, search)}
/>
),
value: option.participant_id,
}))
}
- title="Search by participant ID"
+ title={intl.get('global.search.participant.title')}
+ tooltipText={intl.get('global.search.participant.tooltip')}
/>
);
};
diff --git a/src/views/DataExploration/components/UploadIds/BiospecimenUploadIds.tsx b/src/views/DataExploration/components/UploadIds/BiospecimenUploadIds.tsx
index 6e3776c63..e64b06e96 100644
--- a/src/views/DataExploration/components/UploadIds/BiospecimenUploadIds.tsx
+++ b/src/views/DataExploration/components/UploadIds/BiospecimenUploadIds.tsx
@@ -22,8 +22,8 @@ const BiospecimenUploadIds = ({ queryBuilderId }: OwnProps) => (
<EntityUploadIds
entityId="biospecimen"
entityIdTrans="sample"
- entityIdentifiers="Sample ID"
- placeHolder="e.g. HTP0001B2_Whole blood, BS_011DYZ2J_DNA, 238981007"
+ entityIdentifiers={intl.get('components.uploadIds.modal.identifiers.biospecimen')}
+ placeHolder={intl.get('components.uploadIds.modal.placeholders.biospecimen')}
fetchMatch={async (ids) => {
const response = await ArrangerApi.graphqlRequest({
query: CHECK_BIOSPECIMEN_MATCH.loc?.source.body,
@@ -32,7 +32,7 @@ const BiospecimenUploadIds = ({ queryBuilderId }: OwnProps) => (
offset: 0,
sqon: generateQuery({
operator: BooleanOperators.or,
- newFilters: ['sample_id'].map((field) =>
+ newFilters: ['sample_id', 'external_sample_id'].map((field) =>
generateValueFilter({
field,
value: ids,
@@ -49,7 +49,9 @@ const BiospecimenUploadIds = ({ queryBuilderId }: OwnProps) => (
return biospecimens?.flatMap((biospecimen) => {
const matchedIds: string[] = ids.filter(
- (id: string) => biospecimen.sample_id.toLocaleLowerCase() === id.toLocaleLowerCase(),
+ (id: string) =>
+ biospecimen.sample_id.toLocaleLowerCase() === id.toLocaleLowerCase() ||
+ biospecimen.external_sample_id.toLocaleLowerCase() === id.toLocaleLowerCase(),
);
return matchedIds.map((id, index) => ({
diff --git a/src/views/DataExploration/components/UploadIds/FileUploadIds.tsx b/src/views/DataExploration/components/UploadIds/FileUploadIds.tsx
index 8cacfad01..35d6064ad 100644
--- a/src/views/DataExploration/components/UploadIds/FileUploadIds.tsx
+++ b/src/views/DataExploration/components/UploadIds/FileUploadIds.tsx
@@ -22,8 +22,8 @@ const FileUploadIds = ({ queryBuilderId }: OwnProps) => (
<EntityUploadIds
entityId="file"
entityIdTrans="file"
- entityIdentifiers="File ID"
- placeHolder="e.g. GF_2JAYWYDX, GF_TP6PG8Z0"
+ entityIdentifiers={intl.get('components.uploadIds.modal.identifiers.file')}
+ placeHolder={intl.get('components.uploadIds.modal.placeholders.file')}
fetchMatch={async (ids: string[]) => {
const response = await ArrangerApi.graphqlRequest({
query: CHECK_FILE_MATCH.loc?.source.body,
diff --git a/src/views/DataExploration/components/UploadIds/ParticipantUploadIds.tsx b/src/views/DataExploration/components/UploadIds/ParticipantUploadIds.tsx
index fdcca7618..a231e791b 100644
--- a/src/views/DataExploration/components/UploadIds/ParticipantUploadIds.tsx
+++ b/src/views/DataExploration/components/UploadIds/ParticipantUploadIds.tsx
@@ -22,8 +22,8 @@ const ParticipantUploadIds = ({ queryBuilderId }: OwnProps) => (
<EntityUploadIds
entityId="participant"
entityIdTrans="participant"
- entityIdentifiers="Participant ID"
- placeHolder="e.g. PT_03Y3K025, HTP0001, 10214"
+ entityIdentifiers={intl.get('components.uploadIds.modal.identifiers.participant')}
+ placeHolder={intl.get('components.uploadIds.modal.placeholders.participant')}
fetchMatch={async (ids: string[]) => {
const response = await ArrangerApi.graphqlRequest({
query: CHECK_PARTICIPANT_MATCH.loc?.source.body,
@@ -32,7 +32,7 @@ const ParticipantUploadIds = ({ queryBuilderId }: OwnProps) => (
offset: 0,
sqon: generateQuery({
operator: BooleanOperators.or,
- newFilters: ['participant_id'].map((field) =>
+ newFilters: ['participant_id', 'external_id'].map((field) =>
generateValueFilter({
field,
value: ids,
@@ -49,7 +49,9 @@ const ParticipantUploadIds = ({ queryBuilderId }: OwnProps) => (
return participants?.flatMap((participant) => {
const matchedIds: string[] = ids.filter(
- (id: string) => participant.participant_id.toLocaleLowerCase() === id.toLocaleLowerCase(),
+ (id: string) =>
+ participant.participant_id.toLocaleLowerCase() === id.toLocaleLowerCase() ||
+ participant.external_id.toLocaleLowerCase() === id.toLocaleLowerCase(),
);
return matchedIds.map((id, index) => ({