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📝 Fix missing fiels for specimens #3831

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merged 1 commit into from
Oct 26, 2023
Merged

📝 Fix missing fiels for specimens #3831

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2 changes: 1 addition & 1 deletion src/components/OutcomesAgeCells/index.tsx
View file
Original file line number Diff line number Diff line change
@@ -20,7 +20,7 @@ const OutcomesAgeCells = ({ outcomes }: OwnProps) => {
? outcomeAges.map((age: number, index: number) => (
<AgeCell key={`${index}-${age}`} ageInDays={age} />
))
: { TABLE_EMPTY_PLACE_HOLDER }}
: TABLE_EMPTY_PLACE_HOLDER}
</>
);
};
1 change: 1 addition & 0 deletions src/graphql/participants/queries.ts
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Original file line number Diff line number Diff line change
@@ -169,6 +169,7 @@ export const GET_PARTICIPANT_ENTITY = gql`
fhir_id
laboratory_procedure
collection_ncit_anatomy_site_id
collection_method_of_sample_procurement
# TODO ncit_id_tissue_type
parent_sample_id
parent_sample_type
7 changes: 5 additions & 2 deletions src/locales/en.ts
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Original file line number Diff line number Diff line change
@@ -1191,8 +1191,9 @@ const en = {
status: 'Sample Availability',
age_at_biospecimen_collection: 'Age at Biospec. Collection (days)',
bio_repository: 'Biorepository',
collection_ncit_anatomy_site_id: 'Collection Anatomical Site (NCIT)',
collection_anatomy_site: 'Collection Anatomical Site (Source Text)',
collection_ncit_anatomy_site_id: 'Anatomical Site (NCIT)',
collection_anatomy_site: 'Anatomical Site (Source Text)',
collection_method_of_sample_procurement: 'Method Of Sample Procurement',
dbgap_consent_code: 'dbGaP Consent Code',
diagnosis_mondo: 'Histological Diagnosis (MONDO)',
diagnosis_ncit: 'Histological Diagnosis (NCIT)',
@@ -1477,6 +1478,8 @@ const en = {
tissue_type: 'Tissue Type (Source Text)',
volume: 'Volume',
volume_unit: 'Volume Unit',
collection_method_of_sample_procurement: 'Method Of Sample Procurement',
tissue_type_source_text: 'Tissue Type (Source Text)',
},
participant: {
age: 'Age',
5 changes: 3 additions & 2 deletions src/utils/translation.ts
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Original file line number Diff line number Diff line change
@@ -304,8 +304,9 @@ export const getFacetsDictionary = () => ({
family_type: 'Family Composition',
age_at_biospecimen_collection: 'Age at Biospec. Collection (days)',
status: 'Sample Availability',
collection_ncit_anatomy_site_id: 'Collection Anatomical Site (NCIT)',
collection_anatomy_site: 'Collection Anatomical Site (Source Text)',
collection_ncit_anatomy_site_id: 'Anatomical Site (NCIT)',
collection_anatomy_site: 'Anatomical Site (Source Text)',
collection_method_of_sample_procurement: 'Method Of Sample Procurement',
dbgap_consent_code: 'dbGaP Consent Code',
diagnosis_mondo: 'Histological Diagnosis (MONDO)',
diagnosis_ncit: 'Histological Diagnosis (NCIT)',
74 changes: 38 additions & 36 deletions src/views/DataExploration/components/PageContent/tabs/Biospecimens/index.tsx
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
import { useEffect, useState } from 'react';
import intl from 'react-intl-universal';
import { useDispatch } from 'react-redux';
import { Link } from 'react-router-dom';
import { DownloadOutlined } from '@ant-design/icons';
@@ -186,34 +187,35 @@ const getDefaultColumns = (): ProColumnType<any>[] => [
render: (participant: IParticipantEntity) =>
participant?.external_id || TABLE_EMPTY_PLACE_HOLDER,
},
// {
// key: 'ncit_anatomy_site_id',
// title: 'Anatomical Site (NCIT)',
// dataIndex: 'ncit_anatomy_site_id',
// defaultHidden: true,
// render: (ncit_anatomy_site_id) => ncit_anatomy_site_id || TABLE_EMPTY_PLACE_HOLDER,
// },
// {
// key: 'anatomy_site',
// title: 'Anatomical Site (Source Text)',
// dataIndex: 'anatomy_site',
// defaultHidden: true,
// render: (anatomy_site) => anatomy_site || TABLE_EMPTY_PLACE_HOLDER,
// },
// {
// key: 'ncit_id_tissue_type',
// title: 'Tissue Type (NCIT)',
// dataIndex: 'ncit_id_tissue_type',
// defaultHidden: true,
// render: (ncit_id_tissue_type) => ncit_id_tissue_type || TABLE_EMPTY_PLACE_HOLDER,
// },
// {
// key: 'tissue_type_source_text',
// title: 'Tissue Type (Source Text)',
// dataIndex: 'tissue_type_source_text',
// defaultHidden: true,
// render: (tissue_type_source_text) => tissue_type_source_text || TABLE_EMPTY_PLACE_HOLDER,
// },
{
key: 'collection_ncit_anatomy_site_id',
title: intl.get('entities.biospecimen.anatomical_site_NCIT'),
dataIndex: 'collection_ncit_anatomy_site_id',
defaultHidden: true,
render: (collection_ncit_anatomy_site_id) =>
collection_ncit_anatomy_site_id || TABLE_EMPTY_PLACE_HOLDER,
},
{
key: 'collection_anatomy_site',
title: intl.get('entities.biospecimen.anatomical_site'),
dataIndex: 'collection_anatomy_site',
defaultHidden: true,
render: (anatomy_site) => anatomy_site || TABLE_EMPTY_PLACE_HOLDER,
},
{
key: 'ncit_id_tissue_type',
title: intl.get('entities.biospecimen.tissue_type_NCIT'),
dataIndex: 'ncit_id_tissue_type',
defaultHidden: true,
render: (ncit_id_tissue_type) => ncit_id_tissue_type || TABLE_EMPTY_PLACE_HOLDER,
},
{
key: 'tissue_type_source_text',
title: intl.get('entities.biospecimen.tissue_type_source_text'),
dataIndex: 'tissue_type_source_text',
defaultHidden: true,
render: (tissue_type_source_text) => tissue_type_source_text || TABLE_EMPTY_PLACE_HOLDER,
},
{
key: 'dbgap_consent_code',
title: 'dbGaP Consent Code',
@@ -228,14 +230,14 @@ const getDefaultColumns = (): ProColumnType<any>[] => [
defaultHidden: true,
render: (consent_type) => consent_type || TABLE_EMPTY_PLACE_HOLDER,
},
// {
// key: 'method_of_sample_procurement',
// title: 'Method of Sample Procurement',
// dataIndex: 'method_of_sample_procurement',
// defaultHidden: true,
// render: (method_of_sample_procurement) =>
// method_of_sample_procurement || TABLE_EMPTY_PLACE_HOLDER,
// },
{
key: 'method_of_sample_procurement',
title: intl.get('entities.biospecimen.collection_method_of_sample_procurement'),
dataIndex: 'collection_method_of_sample_procurement',
defaultHidden: true,
render: (collection_method_of_sample_procurement) =>
collection_method_of_sample_procurement || TABLE_EMPTY_PLACE_HOLDER,
},
{
key: 'volume',
title: 'Volume',
16 changes: 8 additions & 8 deletions src/views/DataExploration/index.tsx
View file
Original file line number Diff line number Diff line change
@@ -122,17 +122,17 @@ const filterGroups: {
'collection_sample_type',
'age_at_biospecimen_collection',
'status',
// 'ncit_anatomy_site_id',
// 'anatomy_site',
'collection_ncit_anatomy_site_id',
'collection_anatomy_site',
'consent_type',
'dbgap_consent_code',
// 'diagnosis_mondo',
// 'diagnosis_ncit',
// 'source_text',
'diagnosis_mondo',
'diagnosis_ncit',
'source_text',
'source_text_tumor_location',
// 'method_of_sample_procurement',
// 'ncit_id_tissue_type',
// 'tissue_type_source_text',
'collection_method_of_sample_procurement',
'ncit_id_tissue_type',
'tissue_type_source_text',
],
},
],
63 changes: 35 additions & 28 deletions src/views/ParticipantEntity/utils/biospecimens.tsx
View file
Original file line number Diff line number Diff line change
@@ -45,34 +45,41 @@ export const getBiospecimensDefaultColumns = (): ProColumnType[] => [
<AgeCell ageInDays={biospecimen?.age_at_biospecimen_collection} />
),
},
// {
// key: 'ncit_anatomy_site_id',
// title: intl.get('entities.biospecimen.anatomical_site_NCIT'),
// defaultHidden: true,
// render: (biospecimen: IBiospecimenEntity) =>
// biospecimen?.ncit_anatomy_site_id || TABLE_EMPTY_PLACE_HOLDER,
// },
// {
// key: 'anatomy_site',
// title: intl.get('entities.biospecimen.anatomical_site'),
// defaultHidden: true,
// render: (biospecimen: IBiospecimenEntity) =>
// biospecimen?.anatomy_site || TABLE_EMPTY_PLACE_HOLDER,
// },
// {
// key: 'ncit_id_tissue_type',
// title: intl.get('entities.biospecimen.tissue_type_NCIT'),
// defaultHidden: true,
// render: (biospecimen: IBiospecimenEntity) =>
// biospecimen?.ncit_id_tissue_type || TABLE_EMPTY_PLACE_HOLDER,
// },
// {
// key: 'tissue_type_source_text',
// title: intl.get('entities.biospecimen.tissue_type'),
// defaultHidden: true,
// render: (biospecimen: IBiospecimenEntity) =>
// biospecimen?.tissue_type_source_text || TABLE_EMPTY_PLACE_HOLDER,
// },
{
key: 'collection_ncit_anatomy_site_id',
title: intl.get('entities.biospecimen.anatomical_site_NCIT'),
defaultHidden: true,
render: (biospecimen: IBiospecimenEntity) =>
biospecimen?.collection_ncit_anatomy_site_id || TABLE_EMPTY_PLACE_HOLDER,
},
{
key: 'collection_anatomy_site',
title: intl.get('entities.biospecimen.anatomical_site'),
defaultHidden: true,
render: (biospecimen: IBiospecimenEntity) =>
biospecimen?.collection_anatomy_site || TABLE_EMPTY_PLACE_HOLDER,
},
{
key: 'collection_method_of_sample_procurement',
title: intl.get('entities.biospecimen.collection_method_of_sample_procurement'),
defaultHidden: true,
render: (biospecimen: IBiospecimenEntity) =>
biospecimen?.collection_method_of_sample_procurement || TABLE_EMPTY_PLACE_HOLDER,
},
{
key: 'ncit_id_tissue_type',
title: intl.get('entities.biospecimen.tissue_type_NCIT'),
defaultHidden: true,
render: (biospecimen: IBiospecimenEntity) =>
biospecimen?.ncit_id_tissue_type || TABLE_EMPTY_PLACE_HOLDER,
},
{
key: 'tissue_type_source_text',
title: intl.get('entities.biospecimen.tissue_type_source_text'),
defaultHidden: true,
render: (biospecimen: IBiospecimenEntity) =>
biospecimen?.tissue_type_source_text || TABLE_EMPTY_PLACE_HOLDER,
},
{
key: 'source_text_tumor_location',
title: intl.get('entities.biospecimen.source_text_tumor_location'),