📝 Add data to specimen tables (#3838)

kids-first · Nov 6, 2023 · dc78e4f · dc78e4f
1 parent c2a75c6
commit dc78e4f
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Showing 8 changed files with 130 additions and 33 deletions.
diff --git a/src/graphql/biospecimens/models.ts b/src/graphql/biospecimens/models.ts
@@ -44,4 +44,8 @@ export interface IBiospecimenEntity {
   consent_type: string;
   collection_method_of_sample_procurement: string;
   external_sample_id: string;
+  source_text_tumor_descriptor: string;
+  diagnosis_ncit: string;
+  source_text: string;
+  diagnosis_mondo: string;
 }
diff --git a/src/graphql/biospecimens/queries.ts b/src/graphql/biospecimens/queries.ts
@@ -30,12 +30,16 @@ export const SEARCH_BIOSPECIMEN_QUERY = gql`
             nb_files
             collection_sample_id
             collection_sample_type
+            diagnosis_ncit
             status
             dbgap_consent_code
             collection_method_of_sample_procurement
             volume
             volume_unit
             external_sample_id
+            source_text_tumor_descriptor
+            source_text_tumor_location
+            source_text
             study {
               study_code
             }
@@ -82,15 +86,22 @@ export const GET_PARTICIPANT_BIOSPECIMENS = gql`
             parent_sample_id
             age_at_biospecimen_collection
             collection_ncit_anatomy_site_id
+            tissue_type_source_text
             collection_anatomy_site
             ncit_id_tissue_type
             tissue_type_source_text
             consent_type
-
+            collection_sample_id
+            collection_sample_type
             participant {
               participant_id
             }
-
+            source_text_tumor_descriptor
+            source_text_tumor_location
+            dbgap_consent_code
+            volume_unit
+            volume
+            status
             parent_0 {
               sample_id
             }

diff --git a/src/graphql/participants/queries.ts b/src/graphql/participants/queries.ts
@@ -159,22 +159,23 @@ export const GET_PARTICIPANT_ENTITY = gql`
                         edges {
                           node {
                             age_at_biospecimen_collection
-                            collection_anatomy_site
                             biospecimen_storage
+                            collection_anatomy_site
+                            collection_method_of_sample_procurement
+                            collection_ncit_anatomy_site_id
+                            collection_ncit_id_tissue_type
                             collection_sample_id
                             collection_sample_type
                             consent_type
                             container_id
                             dbgap_consent_code
                             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
                             sample_id
                             sample_type
+                            source_text_tumor_descriptor
                             source_text_tumor_location
                             status
                             tissue_type_source_text

diff --git a/src/locales/en.ts b/src/locales/en.ts
@@ -1202,7 +1202,10 @@ const en = {
     source_text_tumor_location: 'Tumor Location (Source Text)',
     tissue_type_source_text: 'Tissue Type (Source Text)',
     sample_id: 'Sample ID',
-
+    source_text_tumor_descriptor: 'Tumor Descriptor (Source Text)',
+    age_at_event: {
+      value: 'Age at Histological Diagnosis (days)',
+    },
     // File
     files: filesFacets,
     ...filesFacets,
@@ -1481,6 +1484,13 @@ const en = {
       volume_unit: 'Volume Unit',
       collection_method_of_sample_procurement: 'Method Of Sample Procurement',
       tissue_type_source_text: 'Tissue Type (Source Text)',
+      ncit_id_tissue_type: 'Tissue Type (NCIT)',
+      source_text_tumor_descriptor: 'Tumor Descriptor (Source Text)',
+      external_sample_id: 'External Sample ID',
+      external_pt_id: 'External Participant ID',
+      source_text: 'Histological Diagnosis (Source Text)',
+      diagnosis_ncit: 'Histological Diagnosis (NCIT)',
+      diagnosis_mondo: 'Histological Diagnosis (MONDO)',
     },
     participant: {
       age: 'Age',

diff --git a/src/utils/translation.ts b/src/utils/translation.ts
@@ -314,6 +314,9 @@ export const getFacetsDictionary = () => ({
   source_text_tumor_location: 'Tumor Location (Source Text)',
   ncit_id_tissue_type: 'Tissue Type (NCIT)',
   tissue_type_source_text: 'Tissue Type (Source Text)',
+  age_at_event: {
+    value: 'Age at Histological Diagnosis (days)'
+  },
   clinvar: {
     clin_sig: 'ClinVar',
   },

diff --git a/src/views/DataExploration/components/PageContent/tabs/Biospecimens/index.tsx b/src/views/DataExploration/components/PageContent/tabs/Biospecimens/index.tsx
@@ -53,7 +53,7 @@ interface OwnProps {
 const getDefaultColumns = (): ProColumnType<any>[] => [
   {
     key: 'sample_id',
-    title: 'Sample ID',
+    title: intl.get('entities.biospecimen.sample_id'),
     sorter: { multiple: 1 },
     render: (record: IBiospecimenEntity) => record?.sample_id || TABLE_EMPTY_PLACE_HOLDER,
   },
@@ -66,21 +66,21 @@ const getDefaultColumns = (): ProColumnType<any>[] => [
   },
   {
     key: 'sample_type',
-    title: 'Sample Type',
+    title: intl.get('entities.biospecimen.sample_type'),
     dataIndex: 'sample_type',
     sorter: { multiple: 1 },
     render: (sample_type: string) => sample_type || TABLE_EMPTY_PLACE_HOLDER,
   },
   {
     key: 'parent_sample_id',
-    title: 'Parent Sample ID',
+    title: intl.get('entities.biospecimen.parent_sample_id'),
     dataIndex: 'parent_sample_id',
     sorter: { multiple: 1 },
     render: (parent_sample_id) => parent_sample_id || TABLE_EMPTY_PLACE_HOLDER,
   },
   {
     key: 'parent_sample_type',
-    title: 'Parent Sample Type',
+    title: intl.get('entities.biospecimen.parent_sample_type'),
     dataIndex: 'parent_sample_type',
     sorter: { multiple: 1 },
     render: (parent_sample_type) => parent_sample_type || TABLE_EMPTY_PLACE_HOLDER,
@@ -100,7 +100,7 @@ const getDefaultColumns = (): ProColumnType<any>[] => [
   },
   {
     key: 'collection_sample_id',
-    title: 'Collection ID',
+    title: intl.get('entities.biospecimen.collection_id'),
     dataIndex: 'collection_sample_id',
     render: (collection_sample_id) =>
       collection_sample_id ? (
@@ -111,19 +111,25 @@ const getDefaultColumns = (): ProColumnType<any>[] => [
   },
   {
     key: 'collection_sample_type',
-    title: 'Collection Sample Type',
+    title: intl.get('entities.biospecimen.collection_sample_type'),
     dataIndex: 'collection_sample_type',
     render: (collection_sample_type) => collection_sample_type || TABLE_EMPTY_PLACE_HOLDER,
   },
   {
     key: 'age_at_biospecimen_collection',
-    title: 'Age',
-    tooltip: 'Age at Biospecimen Collection (days)',
+    title: intl.get('entities.participant.age'),
+    tooltip: intl.get('entities.biospecimen.age_tooltip'),
     dataIndex: 'age_at_biospecimen_collection',
     render: (age_at_biospecimen_collection) => (
       <AgeCell ageInDays={age_at_biospecimen_collection} />
     ),
   },
+  {
+    key: 'diagnosis_mondo',
+    title: intl.get('entities.biospecimen.diagnosis_mondo'),
+    dataIndex: 'diagnosis_mondo',
+    render: (diagnosis_mondo) => diagnosis_mondo || TABLE_EMPTY_PLACE_HOLDER,
+  },
   // TODO back implementation needed
   // {
   //   key: 'diagnosis.mondo_id_diagnosis',
@@ -142,7 +148,7 @@ const getDefaultColumns = (): ProColumnType<any>[] => [
   // },
   {
     key: 'status',
-    title: 'Sample Availability',
+    title: intl.get('entities.biospecimen.sample_availabilty'),
     dataIndex: 'status',
     render: (status) => status || TABLE_EMPTY_PLACE_HOLDER,
   },
@@ -179,14 +185,6 @@ const getDefaultColumns = (): ProColumnType<any>[] => [
       );
     },
   },
-  {
-    key: 'participant.external_id',
-    title: 'External Participant ID',
-    dataIndex: 'participant',
-    defaultHidden: true,
-    render: (participant: IParticipantEntity) =>
-      participant?.external_id || TABLE_EMPTY_PLACE_HOLDER,
-  },
   {
     key: 'collection_ncit_anatomy_site_id',
     title: intl.get('entities.biospecimen.anatomical_site_NCIT'),
@@ -202,16 +200,51 @@ const getDefaultColumns = (): ProColumnType<any>[] => [
     defaultHidden: true,
     render: (anatomy_site) => anatomy_site || TABLE_EMPTY_PLACE_HOLDER,
   },
+  {
+    key: 'ncit_id_tissue_type',
+    title: intl.get('entities.biospecimen.ncit_id_tissue_type'),
+    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: 'diagnosis_ncit',
+    title: intl.get('entities.biospecimen.diagnosis_ncit'),
+    dataIndex: 'diagnosis_ncit',
+    defaultHidden: true,
+    render: (diagnosis_ncit) => diagnosis_ncit || TABLE_EMPTY_PLACE_HOLDER,
+  },
+  {
+    key: 'source_text',
+    title: intl.get('entities.biospecimen.source_text'),
+    dataIndex: 'source_text',
+    defaultHidden: true,
+    render: (source_text) => source_text || TABLE_EMPTY_PLACE_HOLDER,
+  },
+  {
+    key: 'source_text_tumor_location',
+    title: intl.get('entities.biospecimen.source_text_tumor_location'),
+    dataIndex: 'source_text_tumor_location',
+    defaultHidden: true,
+    render: (source_text_tumor_location) => source_text_tumor_location || TABLE_EMPTY_PLACE_HOLDER,
+  },
   {
     key: 'dbgap_consent_code',
-    title: 'dbGaP Consent Code',
+    title: intl.get('entities.biospecimen.dbgap_consent_code'),
     dataIndex: 'dbgap_consent_code',
     defaultHidden: true,
     render: (dbgap_consent_code) => dbgap_consent_code || TABLE_EMPTY_PLACE_HOLDER,
   },
   {
     key: 'consent_type',
-    title: 'Consent Type',
+    title: intl.get('entities.biospecimen.consent_type'),
     dataIndex: 'consent_type',
     defaultHidden: true,
     render: (consent_type) => consent_type || TABLE_EMPTY_PLACE_HOLDER,
@@ -224,23 +257,39 @@ const getDefaultColumns = (): ProColumnType<any>[] => [
     render: (collection_method_of_sample_procurement) =>
       collection_method_of_sample_procurement || TABLE_EMPTY_PLACE_HOLDER,
   },
+  {
+    key: 'source_text_tumor_descriptor',
+    title: intl.get('entities.biospecimen.source_text_tumor_descriptor'),
+    dataIndex: 'source_text_tumor_descriptor',
+    defaultHidden: true,
+    render: (source_text_tumor_descriptor) =>
+      source_text_tumor_descriptor || TABLE_EMPTY_PLACE_HOLDER,
+  },
   {
     key: 'volume',
-    title: 'Volume',
+    title: intl.get('entities.biospecimen.volume'),
     dataIndex: 'volume',
     defaultHidden: true,
     render: (volume) => volume || TABLE_EMPTY_PLACE_HOLDER,
   },
   {
     key: 'volume_unit',
-    title: 'Volume Unit',
+    title: intl.get('entities.biospecimen.volume_unit'),
     dataIndex: 'volume_unit',
     defaultHidden: true,
     render: (volume_unit) => volume_unit || TABLE_EMPTY_PLACE_HOLDER,
   },
+  {
+    key: 'participant.external_id',
+    title: intl.get('entities.biospecimen.external_pt_id'),
+    dataIndex: 'participant',
+    defaultHidden: true,
+    render: (participant: IParticipantEntity) =>
+      participant?.external_id || TABLE_EMPTY_PLACE_HOLDER,
+  },
   {
     key: 'external_sample_id',
-    title: 'External Sample ID',
+    title: intl.get('entities.biospecimen.external_sample_id'),
     dataIndex: 'external_sample_id',
     defaultHidden: true,
     render: (external_sample_id) => external_sample_id || TABLE_EMPTY_PLACE_HOLDER,

diff --git a/src/views/DataExploration/index.tsx b/src/views/DataExploration/index.tsx
@@ -121,6 +121,7 @@ const filterGroups: {
           'sample_type',
           'collection_sample_type',
           'age_at_biospecimen_collection',
+          'age_at_event__value',
           'status',
           'collection_ncit_anatomy_site_id',
           'collection_anatomy_site',
@@ -131,6 +132,9 @@ const filterGroups: {
           'source_text',
           'source_text_tumor_location',
           'collection_method_of_sample_procurement',
+          'ncit_id_tissue_type',
+          'tissue_type_source_text',
+          'source_text_tumor_descriptor',
         ],
       },
     ],

diff --git a/src/views/ParticipantEntity/utils/biospecimens.tsx b/src/views/ParticipantEntity/utils/biospecimens.tsx
@@ -60,11 +60,26 @@ export const getBiospecimensDefaultColumns = (): ProColumnType[] => [
       biospecimen?.collection_anatomy_site || TABLE_EMPTY_PLACE_HOLDER,
   },
   {
-    key: 'collection_method_of_sample_procurement',
-    title: intl.get('entities.biospecimen.collection_method_of_sample_procurement'),
+    key: 'collection_ncit_id_tissue_type',
+    title: intl.get('entities.biospecimen.ncit_id_tissue_type'),
+    dataIndex: 'collection_ncit_id_tissue_type',
     defaultHidden: true,
-    render: (biospecimen: IBiospecimenEntity) =>
-      biospecimen?.collection_method_of_sample_procurement || TABLE_EMPTY_PLACE_HOLDER,
+    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: 'source_text_tumor_descriptor',
+    title: intl.get('entities.biospecimen.source_text_tumor_descriptor'),
+    dataIndex: 'source_text_tumor_descriptor',
+    defaultHidden: true,
+    render: (source_text_tumor_descriptor) =>
+      source_text_tumor_descriptor || TABLE_EMPTY_PLACE_HOLDER,
   },
   {
     key: 'source_text_tumor_location',