From 77e4f110f1e70494b9d37f764cdfb5fcafafc905 Mon Sep 17 00:00:00 2001
From: SanjeevLakhwani <lakhwani.sanjeev691@gmail.com>
Date: Thu, 30 Jan 2025 08:39:27 -0500
Subject: [PATCH] Split up individual.ts

Split up individual.ts
---
 src/js/features/reference/types.ts      |   2 +-
 src/js/types/clinphen/experiments.ts    |  37 ++++++
 src/js/types/{ => clinphen}/ontology.ts |   0
 src/js/types/clinphen/phenopackets.ts   |  31 +++++
 src/js/types/clinphen/resources.ts      |  97 +++++++++++++++
 src/js/types/individual.ts              | 156 +-----------------------
 6 files changed, 169 insertions(+), 154 deletions(-)
 create mode 100644 src/js/types/clinphen/experiments.ts
 rename src/js/types/{ => clinphen}/ontology.ts (100%)
 create mode 100644 src/js/types/clinphen/phenopackets.ts
 create mode 100644 src/js/types/clinphen/resources.ts

diff --git a/src/js/features/reference/types.ts b/src/js/features/reference/types.ts
index 656957a2..6b3e7a8d 100644
--- a/src/js/features/reference/types.ts
+++ b/src/js/features/reference/types.ts
@@ -1,4 +1,4 @@
-import type { OntologyTerm } from '@/types/ontology';
+import type { OntologyTerm } from '@/types/clinphen/ontology';
 
 // See also: https://github.com/bento-platform/bento_reference_service/blob/main/bento_reference_service/models.py
 
diff --git a/src/js/types/clinphen/experiments.ts b/src/js/types/clinphen/experiments.ts
new file mode 100644
index 00000000..e88d98ac
--- /dev/null
+++ b/src/js/types/clinphen/experiments.ts
@@ -0,0 +1,37 @@
+import type { OntologyTerm } from '@/types/clinphen/ontology';
+import type { Instrument } from '@/types/clinphen/resources';
+
+type ExperimentResult = {
+  id: number;
+  identifier: string;
+  description: string;
+  filename: string;
+  url: string;
+  genome_assembly_id: string;
+  file_format: string;
+  data_output_type: string;
+  creation_date: string;
+  created: string;
+  updated: string;
+};
+
+export type Experiment = {
+  id: string;
+  experiment_results?: ExperimentResult[];
+  instrument: Instrument;
+  biosample_individual: {
+    id: string;
+  };
+  study_type: string;
+  experiment_type: string;
+  experiment_ontology: OntologyTerm[];
+  molecule?: string;
+  molecule_ontology?: OntologyTerm[];
+  library_strategy?: string;
+  library_source?: string;
+  library_selection?: string;
+  created: string;
+  updated: string;
+  biosample: string;
+  dataset: string;
+};
diff --git a/src/js/types/ontology.ts b/src/js/types/clinphen/ontology.ts
similarity index 100%
rename from src/js/types/ontology.ts
rename to src/js/types/clinphen/ontology.ts
diff --git a/src/js/types/clinphen/phenopackets.ts b/src/js/types/clinphen/phenopackets.ts
new file mode 100644
index 00000000..29f5433b
--- /dev/null
+++ b/src/js/types/clinphen/phenopackets.ts
@@ -0,0 +1,31 @@
+import type { OntologyTerm } from '@/types/clinphen/ontology';
+import type {
+  Biosample,
+  Disease,
+  Interpretation,
+  Measurement,
+  MedicalAction,
+  MetaData,
+} from '@/types/clinphen/resources';
+
+type PhenotypicFeature = {
+  type: OntologyTerm;
+  created: string;
+  updated: string;
+  excluded: boolean;
+  phenopacket: string;
+};
+
+export type Phenopacket = {
+  id: string;
+  phenotypic_features?: PhenotypicFeature[];
+  interpretations?: Interpretation[];
+  diseases?: Disease[];
+  created: string;
+  updated: string;
+  measurements?: Measurement[];
+  medical_actions?: MedicalAction[];
+  meta_data: MetaData;
+  dataset: string;
+  biosamples?: Biosample[];
+};
diff --git a/src/js/types/clinphen/resources.ts b/src/js/types/clinphen/resources.ts
new file mode 100644
index 00000000..a57df589
--- /dev/null
+++ b/src/js/types/clinphen/resources.ts
@@ -0,0 +1,97 @@
+import type { Experiment } from '@/types/clinphen/experiments';
+import type { OntologyTerm } from '@/types/clinphen/ontology';
+
+export type Instrument = {
+  id: number;
+  identifier: string;
+  created: string;
+  updated: string;
+};
+
+export type Biosample = {
+  id: string;
+  experiments?: Experiment[];
+  created: string;
+  updated: string;
+  sampled_tissue?: {
+    id: string;
+    label: string;
+  };
+  procedure?: {
+    code: OntologyTerm;
+  };
+};
+
+export type Diagnosis = {
+  id: string;
+  genomic_interpretations: unknown[];
+  disease: unknown | null;
+  extra_properties: unknown | null;
+};
+
+export type Interpretation = {
+  id: string;
+  created: string;
+  updated: string;
+  progress_status: string;
+  summary: string;
+  diagnosis: Diagnosis;
+};
+
+export type Disease = {
+  id: number;
+  created: string;
+  updated: string;
+  term: OntologyTerm;
+  excluded: boolean;
+};
+
+export type MeasurementValue = {
+  quantity?: {
+    unit: OntologyTerm;
+    value: number;
+  };
+  complex_value?: {
+    typed_quantities: {
+      type: OntologyTerm;
+      quantity: {
+        unit: OntologyTerm;
+        value: number;
+      };
+    }[];
+  };
+};
+
+export type Measurement = {
+  assay: OntologyTerm;
+  value?: MeasurementValue;
+};
+
+export type Treatment = {
+  agent: OntologyTerm;
+};
+
+export type MedicalAction = {
+  treatment?: Treatment;
+  adverse_events?: OntologyTerm[];
+  treatment_target?: OntologyTerm;
+};
+
+export type MetaDataResource = {
+  id: string;
+  name: string;
+  namespace_prefix: string;
+  url: string;
+  version: string;
+  iri_prefix: string;
+  created: string;
+  updated: string;
+};
+
+export type MetaData = {
+  resources: MetaDataResource[];
+  created: string;
+  updated: string;
+  created_by: string;
+  phenopacket_schema_version: string;
+};
diff --git a/src/js/types/individual.ts b/src/js/types/individual.ts
index 0a3b3e76..d23e880a 100644
--- a/src/js/types/individual.ts
+++ b/src/js/types/individual.ts
@@ -1,156 +1,6 @@
-import type { OntologyTerm } from './ontology';
-
-type ExperimentResult = {
-  id: number;
-  identifier: string;
-  description: string;
-  filename: string;
-  url: string;
-  genome_assembly_id: string;
-  file_format: string;
-  data_output_type: string;
-  creation_date: string;
-  created: string;
-  updated: string;
-};
-
-type Instrument = {
-  id: number;
-  identifier: string;
-  created: string;
-  updated: string;
-};
-
-type Experiment = {
-  id: string;
-  experiment_results?: ExperimentResult[];
-  instrument: Instrument;
-  biosample_individual: {
-    id: string;
-  };
-  study_type: string;
-  experiment_type: string;
-  experiment_ontology: OntologyTerm[];
-  molecule?: string;
-  molecule_ontology?: OntologyTerm[];
-  library_strategy?: string;
-  library_source?: string;
-  library_selection?: string;
-  created: string;
-  updated: string;
-  biosample: string;
-  dataset: string;
-};
-
-type Biosample = {
-  id: string;
-  experiments?: Experiment[];
-  created: string;
-  updated: string;
-  sampled_tissue?: {
-    id: string;
-    label: string;
-  };
-  procedure?: {
-    code: OntologyTerm;
-  };
-};
-
-type PhenotypicFeature = {
-  type: OntologyTerm;
-  created: string;
-  updated: string;
-  excluded: boolean;
-  phenopacket: string;
-};
-
-type Diagnosis = {
-  id: string;
-  genomic_interpretations: unknown[];
-  disease: unknown | null;
-  extra_properties: unknown | null;
-};
-
-type Interpretation = {
-  id: string;
-  created: string;
-  updated: string;
-  progress_status: string;
-  summary: string;
-  diagnosis: Diagnosis;
-};
-
-type Disease = {
-  id: number;
-  created: string;
-  updated: string;
-  term: OntologyTerm;
-  excluded: boolean;
-};
-
-type MeasurementValue = {
-  quantity?: {
-    unit: OntologyTerm;
-    value: number;
-  };
-  complex_value?: {
-    typed_quantities: {
-      type: OntologyTerm;
-      quantity: {
-        unit: OntologyTerm;
-        value: number;
-      };
-    }[];
-  };
-};
-
-type Measurement = {
-  assay: OntologyTerm;
-  value?: MeasurementValue;
-};
-
-type Treatment = {
-  agent: OntologyTerm;
-};
-
-type MedicalAction = {
-  treatment?: Treatment;
-  adverse_events?: OntologyTerm[];
-  treatment_target?: OntologyTerm;
-};
-
-type MetaDataResource = {
-  id: string;
-  name: string;
-  namespace_prefix: string;
-  url: string;
-  version: string;
-  iri_prefix: string;
-  created: string;
-  updated: string;
-};
-
-type MetaData = {
-  resources: MetaDataResource[];
-  created: string;
-  updated: string;
-  created_by: string;
-  phenopacket_schema_version: string;
-};
-
-type Phenopacket = {
-  id: string;
-  phenotypic_features?: PhenotypicFeature[];
-  interpretations?: Interpretation[];
-  diseases?: Disease[];
-  created: string;
-  updated: string;
-  measurements?: Measurement[];
-  medical_actions?: MedicalAction[];
-  meta_data: MetaData;
-  dataset: string;
-  biosamples?: Biosample[];
-};
+import type { OntologyTerm } from './clinphen/ontology';
+import type { Biosample } from './clinphen/resources';
+import type { Phenopacket } from '@/types/clinphen/phenopackets';
 
 export type IndividualRootObject = {
   id: string;