diff --git a/src/reports/biospecimen-data/configInclude.ts b/src/reports/biospecimen-data/configInclude.ts index 59923a4..e9b2106 100644 --- a/src/reports/biospecimen-data/configInclude.ts +++ b/src/reports/biospecimen-data/configInclude.ts @@ -5,12 +5,14 @@ const biospecimens: SheetConfig = { root: null, columns: [ { field: 'participant.participant_id', header: 'Participant ID' }, + { field: 'participant.external_id', header: 'External Participant ID' }, { field: 'collection_sample_id', header: 'Collection ID' }, { field: 'collection_sample_type', header: 'Collection Sample Type' }, - { field: 'sample_id', header: 'Sample Id' }, - { field: 'container_id', header: 'Container Id' }, + { field: 'sample_id', header: 'Sample ID' }, + { field: 'container_id', header: 'Container ID' }, + { field: 'external_sample_id', header: 'External Sample ID' }, { field: 'sample_type', header: 'Sample Type' }, - { field: 'parent_sample_id', header: 'Parent Sample Id' }, + { field: 'parent_sample_id', header: 'Parent Sample ID' }, { field: 'parent_sample_type', header: 'Parent Sample Type' }, { field: 'study.study_id', header: 'Study Code' }, { field: 'age_at_biospecimen_collection', header: 'Age At Biospecimen Collection (Days)' }, diff --git a/src/reports/clinical-data/configInclude.ts b/src/reports/clinical-data/configInclude.ts index b9fffeb..ac87bef 100644 --- a/src/reports/clinical-data/configInclude.ts +++ b/src/reports/clinical-data/configInclude.ts @@ -4,8 +4,8 @@ const participants: SheetConfig = { sheetName: 'Participants', root: null, columns: [ - { field: 'participant_id' }, - { field: 'external_id' }, + { field: 'participant_id', header: 'Participant ID' }, + { field: 'external_id', header: 'External Participant ID' }, { field: 'family.family_id', header: 'Family ID' }, { field: 'family_type', header: 'Family Unit' }, { field: 'study.study_name', header: 'Study Name' }, @@ -14,7 +14,7 @@ const participants: SheetConfig = { { field: 'race' }, { field: 'ethnicity' }, { field: 'down_syndrome_status' }, - { field: 'outcomes.vital_status' }, + { field: 'outcomes.vital_status', header: 'Vital Status' }, { field: 'outcomes.age_at_event_days.value', header: 'Age at the Last Vital Status (Days)', @@ -38,8 +38,8 @@ const phenotypes: SheetConfig = { sheetName: 'Phenotypes', root: 'phenotype', columns: [ - { field: 'participant_id' }, - { field: 'external_id' }, + { field: 'participant_id', header: 'Participant ID' }, + { field: 'external_id', header: 'External Participant ID' }, { field: 'phenotype.hpo_phenotype_observed', additionalFields: ['phenotype.hpo_phenotype_not_observed'], @@ -53,12 +53,12 @@ const phenotypes: SheetConfig = { }, { field: 'phenotype.source_text', - header: 'Phenotype (Source Text)' + header: 'Condition (Source Text)', }, { field: 'phenotype.hpo_phenotype_observed', header: 'Interpretation', - transform: (value, row) => (value ? 'Observed' : 'Not Observed'), + transform: (value, _) => (value ? 'Observed' : 'Not Observed'), }, { field: 'phenotype.age_at_event_days', @@ -72,22 +72,14 @@ const diagnoses: SheetConfig = { sheetName: 'Diagnoses', root: 'diagnosis', columns: [ - { field: 'participant_id' }, - { field: 'external_id' }, - { - field: 'fhir_id', - header: 'Diagnosis Type', - transform: () => 'Clinical', - }, + { field: 'participant_id', header: 'Participant ID' }, + { field: 'external_id', header: 'External Participant ID' }, { 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.source_text', header: 'Condition (Source Text)' }, { field: 'diagnosis.age_at_event_days', header: 'Age at Diagnosis (Days)', }, - { field: 'diagnosis.source_text_tumor_location' }, ], sort: [{ fhir_id: 'asc' }], }; @@ -119,7 +111,7 @@ const familyRelationship: SheetConfig = { sheetName: 'Family Relationship', root: 'family.family_relations', columns: [ - { field: 'participant_id' }, + { field: 'participant_id', header: 'Participant ID' }, { field: 'family.family_relations', header: 'Family Members ID', @@ -127,7 +119,7 @@ const familyRelationship: SheetConfig = { }, { field: 'family.family_relations', - header: 'Relationship', + header: 'Family Member Relationship', transform: (value, row) => (row.family ? row.family.family_relations.relation : ''), }, ], diff --git a/src/reports/family-clinical-data/configInclude.ts b/src/reports/family-clinical-data/configInclude.ts index b513826..e73b744 100644 --- a/src/reports/family-clinical-data/configInclude.ts +++ b/src/reports/family-clinical-data/configInclude.ts @@ -4,20 +4,20 @@ const participants: SheetConfig = { sheetName: 'Participants', root: null, columns: [ - { field: 'participant_id' }, - { field: 'external_id' }, + { field: 'participant_id', header: 'Participant ID' }, + { field: 'external_id', header: 'External Participant ID' }, { field: 'families_id', header: 'Family ID' }, { field: 'family_type', header: 'Family Unit' }, { field: 'family.father_id', header: 'Father ID' }, { field: 'family.mother_id', header: 'Mother ID' }, - { field: 'family.family_relations.relation', header: 'Family Relationship' }, + { field: 'family.family_relations.relation', header: 'Family Member Relationship' }, { field: 'study.study_name', header: 'Study Name' }, { field: 'study.study_id', header: 'Study Code' }, { field: 'sex' }, { field: 'race' }, { field: 'ethnicity' }, { field: 'down_syndrome_status' }, - { field: 'outcomes.vital_status' }, + { field: 'outcomes.vital_status', header: 'Vital Status' }, { field: 'outcomes.age_at_event_days.value', header: 'Age at the Last Vital Status (Days)', @@ -41,8 +41,8 @@ const phenotypes: SheetConfig = { sheetName: 'Phenotypes', root: 'phenotype', columns: [ - { field: 'participant_id' }, - { field: 'external_id' }, + { field: 'participant_id', header: 'Participant ID' }, + { field: 'external_id', header: 'External Participant ID' }, { field: 'families_id', header: 'Family ID' }, { field: 'phenotype.hpo_phenotype_observed', @@ -57,12 +57,12 @@ const phenotypes: SheetConfig = { }, { field: 'phenotype.source_text', - header: 'Phenotype (Source Text)', + header: 'Condition (Source Text)', }, { field: 'phenotype.hpo_phenotype_observed', header: 'Interpretation', - transform: (value, row) => (value ? 'Observed' : 'Not Observed'), + transform: (value, _) => (value ? 'Observed' : 'Not Observed'), }, { field: 'phenotype.age_at_event_days', @@ -76,23 +76,15 @@ const diagnoses: SheetConfig = { sheetName: 'Diagnoses', root: 'diagnosis', columns: [ - { field: 'participant_id' }, - { field: 'external_id' }, + { field: 'participant_id', header: 'Participant ID' }, + { field: 'external_id', header: 'External Participant ID' }, { field: 'families_id', header: 'Family ID' }, - { - field: 'fhir_id', - header: 'Diagnosis Type', - transform: () => 'Clinical', - }, { 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.source_text', header: 'Condition (Source Text)' }, { field: 'diagnosis.age_at_event_days', header: 'Age at Diagnosis (Days)', }, - { field: 'diagnoses.source_text_tumor_location' }, ], sort: [{ families_id: 'asc' }, { participant_id: 'asc' }], };