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Fix/sjip 157 clinical data fixes (#52)
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* fix: #SJIP-157 various column fixes for include

* fix biospecimens tab

* fix desired columns
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@adipaul1981
adipaul1981 committed Mar 11, 2022
1 parent 6414b76 commit b8f5ebc
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Showing 3 changed files with 78 additions and 132 deletions.
33 changes: 17 additions & 16 deletions src/reports/biospecimen-data/configInclude.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -2,26 +2,27 @@ import { QueryConfig, ReportConfig, SheetConfig } from '../types';

const biospecimens: SheetConfig = {
sheetName: 'Biospecimens',
root: 'biospecimens',
root: 'files.biospecimens',
columns: [
{ field: 'fhir_id' },
{ field: 'external_id' },
{ field: 'files.biospecimens.biospecimen_id', header: 'Biospecimens Biospecimens Id' },
{
field: 'files.biospecimens.age_at_biospecimen_collection',
header: 'Biospecimens Age At Biospecimen Collection',
},
{ field: 'files.biospecimens.bio_repository', header: 'Biospecimens Bio Repository' },
{ field: 'files.biospecimens.biospecimen_type', header: 'Biospecimens Biospecimen Type' },
{ field: 'files.biospecimens.derived_sample_id', header: 'Biospecimens Derived Sample Id' },
{ field: 'files.biospecimens.derived_sample_type', header: 'Biospecimens Derived Sample Type' },
{ field: 'files.biospecimens.ncit_id_tissue_type', header: 'Biospecimens NCIT Id Tissue Type' },
{ field: 'files.biospecimens.sample_id', header: 'Biospecimens Sample Id' },
{ field: 'files.biospecimens.sample_type', header: 'Biospecimens Sample Type' },
{ field: 'participant_id', header: 'Participant ID' },
{ field: 'files.biospecimens.collection_sample_id', header: 'Collection ID' },
{ field: 'files.biospecimens.collection_sample_type', header: 'Collection Sample Type' },
{ field: 'files.biospecimens.sample_id', header: 'Sample Id' },
{ field: 'files.biospecimens.container_id', header: 'Container Id' },
{ field: 'files.biospecimens.sample_type', header: 'Sample Type' },
{ field: 'files.biospecimens.parent_sample_id', header: 'Parent Sample Id' },
{ field: 'files.biospecimens.parent_sample_type', header: 'Parent Sample Type' },
{ field: 'study.study_code', header: 'Study Code' },
{ field: 'files.biospecimens.age_at_biospecimen_collection', header: 'Age At Biospecimen Collection (Days)' },
{ field: 'files.biospecimens.status', header: 'Sample Availability' },
{ field: 'files.biospecimens.volume_ul', header: 'Volume' },
{ field: 'files.biospecimens.volume_unit', header: 'Volume Unit' },
{ field: 'files.biospecimens.laboratory_procedure', header: 'Laboratory Procedure' },
{ field: 'files.biospecimens.biospecimen_storage', header: 'Biospecimen Storage' },
],
sort: [
{
'files.biospecimens.biospecimen_id': {
'files.biospecimens.sample_id': {
order: 'asc',
},
},
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152 changes: 55 additions & 97 deletions src/reports/clinical-data/configInclude.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -4,25 +4,21 @@ const participants: SheetConfig = {
sheetName: 'Participants',
root: null,
columns: [
{ field: 'fhir_id' },
{ field: 'participant_id' },
{ field: 'external_id' },
{ field: 'families_id' },
{ field: 'family.family_id', header: 'Family ID' },
{ field: 'family_type' },
{ field: 'is_proband' },
{ field: 'study.study_name' },
{ field: 'families.family_members.exploded_member_entity' },
{ field: 'study.study_name', header: 'Study Name' },
{ field: 'study.study_code', header: 'Study Code' },
{ field: 'sex' },
{ field: 'race' },
{ field: 'ethnicity' },
{ field: 'karyotype' },
{ field: 'down_syndrome_diagnosis' },
// { field: 'outcomes.vital_status' }, //TODO TBD
// {
// field: 'outcomes.age_at_event_days',
// header: 'Age at the Last Vital Status (Days)',
// }, //TODO TBD
// { field: 'outcome.disease_related' }, //TODO TBD
// { field: 'affected_status' }, //TODO TBD
{ field: 'down_syndrome_status' },
{ field: 'outcomes.vital_status' },
{
field: 'outcomes.age_at_event_days.value',
header: 'Age at the Last Vital Status (Days)',
},
],
sort: [
{
Expand All @@ -44,41 +40,26 @@ const phenotypes: SheetConfig = {
columns: [
{ field: 'fhir_id' },
{ field: 'external_id' },
{ field: 'is_proband' },
{
field: 'phenotype.observed',
additionalFields: ['phenotype.hpo_phenotype_observed', 'phenotype.hpo_phenotype_not_observed'],
field: 'phenotype.hpo_phenotype_observed',
additionalFields: ['phenotype.hpo_phenotype_not_observed'],
header: 'Phenotype (HPO)',
transform: (observed, row) => {
transform: (value, row) => {
if (!row.phenotype) {
return;
}
return observed ? row.phenotype.hpo_phenotype_observed : row.phenotype.hpo_phenotype_not_observed;
return value || row.phenotype.hpo_phenotype_not_observed;
},
},
// {
// field: 'phenotype.observed',
// additionalFields: ['phenotype.snomed_phenotype_observed', 'phenotype.snomed_phenotype_not_observed'],
// header: 'Phenotype (SNOMED)',
// transform: (observed, row) => {
// if (!row.phenotype) {
// return;
// }
// return observed ? row.phenotype.snomed_phenotype_observed : row.phenotype.snomed_phenotype_not_observed;
// },
// }, //TODO TBD
{ field: 'phenotype.source_text_phenotype' },
{
field: 'phenotype.observed',
additionalFields: ['phenotype.hpo_phenotype_observed_text', 'phenotype.hpo_phenotype_not_observed_text'],
header: 'Phenotype Source Text',
transform: (observed, row) => {
field: 'phenotype.hpo_phenotype_observed_text',
additionalFields: ['phenotype.hpo_phenotype_not_observed_text'],
header: 'Phenotype (Source Text)',
transform: (value, row) => {
if (!row.phenotype) {
return;
}
return observed
? row.phenotype.hpo_phenotype_observed_text
: row.phenotype.hpo_phenotype_not_observed_text;
return value || row.phenotype.hpo_phenotype_not_observed_text;
},
},
{
Expand All @@ -96,20 +77,19 @@ const phenotypes: SheetConfig = {

const diagnoses: SheetConfig = {
sheetName: 'Diagnoses',
root: 'diagnoses',
root: 'diagnosis',
columns: [
{ field: 'fhir_id' },
{ field: 'external_id' },
{ field: 'is_proband' },
{
field: 'fhir_id',
header: 'Diagnosis Type',
transform: () => 'Clinical',
},
{ field: 'diagnosis.mondo_id_diagnosis' },
{ field: 'diagnosis.ncit_id_diagnosis' },
{ field: 'diagnosis.icd_id_diagnosis' },
{ field: 'diagnosis.source_text' },
{ field: 'diagnosis.mondo_id_diagnosis', header: ' Diagnosis (MONDO)' },
{ field: 'diagnosis.ncit_id_diagnosis', header: 'Diagnosis (NCIT)' },
{ field: 'diagnosis.icd_id_diagnosis', header: 'Diagnosis (ICD)' },
{ field: 'diagnosis.source_text', header: 'Diagnosis (Source Text)' },
{
field: 'diagnosis.age_at_event_days',
header: 'Age at Diagnosis (Days)',
Expand All @@ -121,66 +101,44 @@ const diagnoses: SheetConfig = {

const histologicalDiagnoses: SheetConfig = {
sheetName: 'Histological Diagnoses',
root: 'biospecimens.diagnoses',
root: 'files.biospecimens',
columns: [
{ field: 'fhir_id' },
{ field: 'external_id' }, //TODO TBD biospecimen fields
// { field: 'biospecimens.kf_id' },
// { field: 'biospecimens.external_sample_id' },
// { field: 'biospecimens.external_aliquot_id' },
// { field: 'is_proband' },
// {
// // This allows to do a cell with a static value.
// // The value will be formatted like the value of `field` would have.
// field: 'kf_id',
// header: 'Diagnosis Type',
// transform: () => 'Histological',
// },
// { field: 'biospecimens.diagnoses.diagnosis_category' },
// { field: 'biospecimens.diagnoses.mondo_id_diagnosis' },
// { field: 'biospecimens.diagnoses.ncit_id_diagnosis' },
// { field: 'biospecimens.diagnoses.source_text_diagnosis' },
// {
// field: 'biospecimens.diagnoses.age_at_event_days',
// header: 'Age at Diagnosis (Days)',
// },
// { field: 'biospecimens.diagnoses.source_text_tumor_location' },
// { field: 'biospecimens.source_text_anatomical_site' },
// { field: 'biospecimens.ncit_id_tissue_type' },
// { field: 'biospecimens.source_text_tissue_type' },
// { field: 'biospecimens.composition' },
// { field: 'biospecimens.method_of_sample_procurement' },
// { field: 'biospecimens.analyte_type' },
],
sort: [
{ fhir_id: 'asc' },
{
'biospecimens.diagnoses.age_at_event_days': {
order: 'desc',
nested: {
path: 'biospecimens',
nested: {
path: 'biospecimens.diagnoses',
},
},
},
},
{ field: 'participant_id', header: 'Participant ID' },
{ field: 'files.biospecimens.collection_sample_id', header: 'Collection ID' },
{ field: 'files.biospecimens.collection_sample_type', header: 'Collection Sample Type' },
{ field: 'files.biospecimens.sample_id', header: 'Sample Id' },
{ field: 'files.biospecimens.container_id', header: 'Container Id' },
{ field: 'files.biospecimens.sample_type', header: 'Sample Type' },
{ field: 'files.biospecimens.parent_sample_id', header: 'Parent Sample Id' },
{ field: 'files.biospecimens.parent_sample_type', header: 'Parent Sample Type' },
{ field: 'study.study_code', header: 'Study Code' },
{ field: 'files.biospecimens.age_at_biospecimen_collection', header: 'Age At Biospecimen Collection (Days)' },
{ field: 'files.biospecimens.status', header: 'Sample Availability' },
{ field: 'files.biospecimens.volume_ul', header: 'Volume' },
{ field: 'files.biospecimens.volume_unit', header: 'Volume Unit' },
{ field: 'files.biospecimens.laboratory_procedure', header: 'Laboratory Procedure' },
{ field: 'files.biospecimens.biospecimen_storage', header: 'Biospecimen Storage' },
],
sort: [{ fhir_id: 'asc' }],
};

const familyRelationship: SheetConfig = {
sheetName: 'Family Relationship',
root: 'families',
root: 'family.family_relations',
columns: [
{ field: 'fhir_id' },
{ field: 'family.family_members_id' },
// {
// field: 'family.family_compositions.family_members.relationship',
// header: 'Relationship',
// transform: value => value || 'self',
// }, //TODO TBD
{ field: 'participant_id' },
{
field: 'family.family_relations',
header: 'Family Members ID',
transform: (value, row) => (row.family ? row.family.family_relations.related_participant_id : ''),
},
{
field: 'family.family_relations',
header: 'Relationship',
transform: (value, row) => (row.family ? row.family.family_relations.relation : ''),
},
],
sort: [{ fhir_id: 'asc' }],
sort: [{ participant_id: 'asc' }],
};

export const queryConfigs: QueryConfig = {
Expand All @@ -192,7 +150,7 @@ export const sheetConfigs: SheetConfig[] = [
participants,
phenotypes,
diagnoses,
// histologicalDiagnoses, //TODO TBD missing biospecimen
// histologicalDiagnoses,
familyRelationship,
];

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25 changes: 6 additions & 19 deletions src/reports/family-clinical-data/configInclude.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -9,19 +9,17 @@ const participants: SheetConfig = {
{ field: 'families_id' },
{ field: 'is_proband' },
{ field: 'study.study_name' },
// { field: 'family.family_compositions.composition' }, //TODO TBD
{ field: 'family_type' },
{ field: 'sex' },
{ field: 'race' },
{ field: 'ethnicity' },
{ field: 'down_syndrome_diagnosis' },
{ field: 'karyotype' },
// { field: 'outcome.vital_status' }, //TODO TBD
// {
// field: 'outcome.age_at_event_days',
// header: 'Age at the Last Vital Status (Days)',
// }, //TODO TBD
// { field: 'outcome.disease_related' }, //TODO TBD
// { field: 'affected_status' }, //TODO TBD
{ field: 'outcome.vital_status' },
{
field: 'outcome.age_at_event_days',
header: 'Age at the Last Vital Status (Days)',
},
],
sort: [
{
Expand Down Expand Up @@ -49,17 +47,6 @@ const phenotypes: SheetConfig = {
field: 'phenotype.hpo_phenotype_observed_text',
header: 'Phenotype (HPO)',
},
// {
// field: 'phenotype.observed',
// additionalFields: ['phenotype.snomed_phenotype_observed', 'phenotype.snomed_phenotype_not_observed'],
// header: 'Phenotype (SNOMED)',
// transform: (observed, row) => {
// if (!row.phenotype) {
// return;
// }
// return observed ? row.phenotype.snomed_phenotype_observed : row.phenotype.snomed_phenotype_not_observed;
// },
// }, //TODO TBD
{
field: 'phenotype.observed',
additionalFields: ['phenotype.hpo_phenotype_observed_text', 'phenotype.hpo_phenotype_not_observed_text'],
Expand Down

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