diff --git a/README.md b/README.md index 208f0b891..406c6a049 100644 --- a/README.md +++ b/README.md @@ -46,25 +46,22 @@ CANARIE funded initial development of the Katsu Metadata service under the CHORD Katsu Metadata Service is a service to store epigenomic metadata. 1. Patients service handles anonymized individual’s data (individual id, sex, age or date of birth) - * Data model: aggregated profile from GA4GH Phenopackets Individual, FHIR Patient and mCODE Patient. + * Data model: aggregated profile from GA4GH Phenopackets Individual, and FHIR Patient. 2. Phenopackets service handles phenotypic and clinical data * Data model: [GA4GH Phenopackets schema](https://github.com/phenopackets/phenopacket-schema) -3. mCode service handles patient's oncology related data. - * Data model: [mCODE data elements](https://mcodeinitiative.org/) - -4. Experiments service handles experiment related data. +3. Experiments service handles experiment related data. * Data model: derived from [IHEC Metadata Experiment](https://github.com/IHEC/ihec-ecosystems/blob/master/docs/metadata/2.0/Ihec_metadata_specification.md#experiments) -5. Resources service handles metadata about ontologies used for data annotation. +4. Resources service handles metadata about ontologies used for data annotation. * Data model: derived from Phenopackets Resource profile -6. CHORD service handles metadata about dataset, has relation to phenopackets (one dataset can have many phenopackets) +5. CHORD service handles metadata about dataset, has relation to phenopackets (one dataset can have many phenopackets) * Data model: [DATS](https://github.com/datatagsuite) + [GA4GH DUO](https://github.com/EBISPOT/DUO) -7. Rest api service handles all generic functionality shared among other services +6. Rest api service handles all generic functionality shared among other services ## REST API highlights diff --git a/chord_metadata_service/chord/data_types.py b/chord_metadata_service/chord/data_types.py index ccdc6ea97..97ea46629 100644 --- a/chord_metadata_service/chord/data_types.py +++ b/chord_metadata_service/chord/data_types.py @@ -2,14 +2,12 @@ from chord_metadata_service.experiments.search_schemas import EXPERIMENT_SEARCH_SCHEMA from chord_metadata_service.phenopackets.search_schemas import PHENOPACKET_SEARCH_SCHEMA -# from chord_metadata_service.mcode.schemas import MCODE_SCHEMA from chord_metadata_service.experiments.schemas import EXPERIMENT_RESULT_SCHEMA __all__ = [ "DATA_TYPE_EXPERIMENT", "DATA_TYPE_EXPERIMENT_RESULT", "DATA_TYPE_PHENOPACKET", - "DATA_TYPE_MCODEPACKET", "DATA_TYPE_READSET", "DATA_TYPES", ] @@ -18,7 +16,6 @@ DATA_TYPE_EXPERIMENT = "experiment" DATA_TYPE_EXPERIMENT_RESULT = "experiment_result" DATA_TYPE_PHENOPACKET = "phenopacket" -DATA_TYPE_MCODEPACKET = "mcodepacket" DATA_TYPE_READSET = "readset" DATA_TYPES = { @@ -38,13 +35,6 @@ "type": "object", # TODO }, }, - # De-listed 2022-12-08 - David L - # DATA_TYPE_MCODEPACKET: { - # "schema": MCODE_SCHEMA, - # "metadata_schema": { - # "type": "object", # TODO - # } - # }, DATA_TYPE_READSET: { "label": "Readsets", "queryable": False, diff --git a/chord_metadata_service/chord/ingest/__init__.py b/chord_metadata_service/chord/ingest/__init__.py index 6c8f30dcc..cbcd8511a 100644 --- a/chord_metadata_service/chord/ingest/__init__.py +++ b/chord_metadata_service/chord/ingest/__init__.py @@ -2,7 +2,6 @@ from .experiments import ingest_experiments_workflow, ingest_maf_derived_from_vcf_workflow from .fhir import ingest_fhir_workflow -from .mcode import ingest_mcode_fhir_workflow, ingest_mcode_workflow from .phenopackets import ingest_phenopacket_workflow from .readsets import ingest_readset_workflow @@ -16,8 +15,6 @@ wm.WORKFLOW_EXPERIMENTS_JSON: ingest_experiments_workflow, wm.WORKFLOW_PHENOPACKETS_JSON: ingest_phenopacket_workflow, wm.WORKFLOW_FHIR_JSON: ingest_fhir_workflow, - wm.WORKFLOW_MCODE_FHIR_JSON: ingest_mcode_fhir_workflow, - wm.WORKFLOW_MCODE_JSON: ingest_mcode_workflow, wm.WORKFLOW_READSET: ingest_readset_workflow, wm.WORKFLOW_MAF_DERIVED_FROM_VCF_JSON: ingest_maf_derived_from_vcf_workflow, } diff --git a/chord_metadata_service/chord/ingest/phenopackets.py b/chord_metadata_service/chord/ingest/phenopackets.py index 690160c87..d5b5f34e9 100644 --- a/chord_metadata_service/chord/ingest/phenopackets.py +++ b/chord_metadata_service/chord/ingest/phenopackets.py @@ -103,8 +103,6 @@ def update_or_create_subject(subject: dict) -> pm.Individual: id=subject["id"], # if left out/null, karyotypic_sex defaults to UNKNOWN_KARYOTYPE karyotypic_sex=subject.get("karyotypic_sex") or KaryotypicSex.UNKNOWN_KARYOTYPE, - race=subject.get("race", ""), - ethnicity=subject.get("ethnicity", ""), age_numeric=age_numeric_value, age_unit=age_unit_value if age_unit_value else "", extra_properties=existing_extra_properties, diff --git a/chord_metadata_service/chord/migrations/0006_remove_tableownership_dataset.py b/chord_metadata_service/chord/migrations/0006_remove_tableownership_dataset.py deleted file mode 100644 index 43f38409f..000000000 --- a/chord_metadata_service/chord/migrations/0006_remove_tableownership_dataset.py +++ /dev/null @@ -1,17 +0,0 @@ -# Generated by Django 4.2.1 on 2023-06-13 18:28 - -from django.db import migrations - - -class Migration(migrations.Migration): - - dependencies = [ - ('chord', '0005_v3_0_0'), - ] - - operations = [ - migrations.RemoveField( - model_name='tableownership', - name='dataset', - ), - ] diff --git a/chord_metadata_service/chord/migrations/0006_v4_0_0.py b/chord_metadata_service/chord/migrations/0006_v4_0_0.py index 64ad738b6..f8233c91f 100644 --- a/chord_metadata_service/chord/migrations/0006_v4_0_0.py +++ b/chord_metadata_service/chord/migrations/0006_v4_0_0.py @@ -5,8 +5,6 @@ class Migration(migrations.Migration): - replaces = [('chord', '0006_remove_tableownership_dataset'), ('chord', '0007_delete_table_delete_tableownership')] - dependencies = [ ('phenopackets', '0005_v4_0_0'), ('chord', '0005_v3_0_0'), diff --git a/chord_metadata_service/chord/migrations/0007_delete_table_delete_tableownership.py b/chord_metadata_service/chord/migrations/0007_delete_table_delete_tableownership.py deleted file mode 100644 index 8fc9a5c80..000000000 --- a/chord_metadata_service/chord/migrations/0007_delete_table_delete_tableownership.py +++ /dev/null @@ -1,22 +0,0 @@ -# Generated by Django 4.2.1 on 2023-06-13 18:32 - -from django.db import migrations - - -class Migration(migrations.Migration): - - dependencies = [ - ('mcode', '__latest__'), - ('experiments', '__latest__'), - ('phenopackets', '__latest__'), - ('chord', '0006_remove_tableownership_dataset'), - ] - - operations = [ - migrations.DeleteModel( - name='Table', - ), - migrations.DeleteModel( - name='TableOwnership', - ), - ] diff --git a/chord_metadata_service/chord/tests/test_api_data_types.py b/chord_metadata_service/chord/tests/test_api_data_types.py index ca62d9276..44a1b0aa6 100644 --- a/chord_metadata_service/chord/tests/test_api_data_types.py +++ b/chord_metadata_service/chord/tests/test_api_data_types.py @@ -24,7 +24,6 @@ def test_data_type_list(self): self.assertEqual(len(c), len(DATA_TYPES)) ids = [dt["id"] for dt in c] self.assertIn(DATA_TYPE_EXPERIMENT, ids) - # self.assertIn(DATA_TYPE_MCODEPACKET, ids) self.assertIn(DATA_TYPE_PHENOPACKET, ids) self.assertIn(DATA_TYPE_READSET, ids) self.assertIn(DATA_TYPE_EXPERIMENT_RESULT, ids) diff --git a/chord_metadata_service/chord/views_data_types.py b/chord_metadata_service/chord/views_data_types.py index 155087bb1..16430e34f 100644 --- a/chord_metadata_service/chord/views_data_types.py +++ b/chord_metadata_service/chord/views_data_types.py @@ -16,14 +16,12 @@ from chord_metadata_service.cleanup import run_all_cleanup from chord_metadata_service.experiments.models import Experiment, ExperimentResult from chord_metadata_service.logger import logger -from chord_metadata_service.mcode.models import MCodePacket from chord_metadata_service.phenopackets.models import Phenopacket from . import data_types as dt QUERYSET_FN: Dict[str, Callable] = { dt.DATA_TYPE_EXPERIMENT: lambda dataset_id: Experiment.objects.filter(dataset_id=dataset_id), - dt.DATA_TYPE_MCODEPACKET: lambda dataset_id: MCodePacket.objects.filter(dataset_id=dataset_id), dt.DATA_TYPE_PHENOPACKET: lambda dataset_id: Phenopacket.objects.filter(dataset_id=dataset_id), dt.DATA_TYPE_EXPERIMENT_RESULT: lambda dataset_id: ExperimentResult.objects.filter( experiment__dataset_id=dataset_id), diff --git a/chord_metadata_service/chord/views_search.py b/chord_metadata_service/chord/views_search.py index e703222dc..6fa4a4a5f 100644 --- a/chord_metadata_service/chord/views_search.py +++ b/chord_metadata_service/chord/views_search.py @@ -29,8 +29,6 @@ from chord_metadata_service.experiments.models import Experiment from chord_metadata_service.experiments.serializers import ExperimentSerializer -from chord_metadata_service.mcode.models import MCodePacket -from chord_metadata_service.mcode.serializers import MCodePacketSerializer from chord_metadata_service.metadata.elastic import es @@ -40,7 +38,7 @@ from chord_metadata_service.phenopackets.models import Phenopacket, Biosample, Variant from chord_metadata_service.phenopackets.serializers import PhenopacketSerializer -from .data_types import DATA_TYPE_EXPERIMENT, DATA_TYPE_MCODEPACKET, DATA_TYPE_PHENOPACKET, DATA_TYPES +from .data_types import DATA_TYPE_EXPERIMENT, DATA_TYPE_PHENOPACKET, DATA_TYPES from .models import Dataset from collections import defaultdict @@ -59,15 +57,6 @@ def experiment_dataset_summary(dataset): } -def mcodepacket_dataset_summary(dataset): - mcodepackets = MCodePacket.objects.filter(dataset=dataset) # TODO - - return { - "count": mcodepackets.count(), - "data_type_specific": {}, # TODO - } - - def variant_dataset_summary(dataset): variants = Variant.objects.filter(dataset=dataset) @@ -158,20 +147,6 @@ def experiment_query_results(query, params, options=None): .prefetch_related(*EXPERIMENT_PREFETCH) -def mcodepacket_query_results(query, params, options=None): - # TODO: possibly a quite inefficient way of doing things... - # TODO: select_related / prefetch_related for instant performance boost! - queryset = MCodePacket.objects.filter( - id__in=data_type_results(query, params, "id") - ) - - output_format = options.get("output") if options else None - if output_format == OUTPUT_FORMAT_VALUES_LIST: - return get_values_list(queryset, options) - - return queryset - - def get_biosamples_with_experiment_details(subject_ids): """ The function returns a queryset where each entry represents a biosample obtained from a subject, along with @@ -244,13 +219,11 @@ def phenopacket_query_results(query, params, options=None): QUERY_RESULTS_FN: Dict[str, Callable] = { DATA_TYPE_EXPERIMENT: experiment_query_results, - DATA_TYPE_MCODEPACKET: mcodepacket_query_results, DATA_TYPE_PHENOPACKET: phenopacket_query_results, } QUERY_RESULT_SERIALIZERS = { DATA_TYPE_EXPERIMENT: ExperimentSerializer, - DATA_TYPE_MCODEPACKET: MCodePacketSerializer, DATA_TYPE_PHENOPACKET: PhenopacketSerializer, } @@ -260,7 +233,7 @@ def search(request, internal_data=False): Generic function that takes a request object containing the following parameters: - query: a Bento specific string representation of a query. e.g. ["#eq", ["#resolve", "experiment_results", "[item]", "file_format"], "VCF"] - - data_type: one of "experiment", "mcode", "phenopacket" + - data_type: one of "experiment", "phenopacket" If internal_data is False, this function returns the tables id where matches are found. If internal_data is True, this function returns matches grouped by their @@ -361,7 +334,7 @@ def chord_private_search(request): - query: a Bento specific object representing a query e.g.: ["#eq", ["#resolve", "experiment_results", "[item]", "file_format"], "VCF"] Note: for GET method, it must be encoded as a JSON string. - - data_type: one of "phenopackets"/"experiments"/"mcodepackets" + - data_type: one of "phenopackets"/"experiments" - optional parameters: see chord_private_table_search @@ -489,7 +462,7 @@ def get_chord_search_parameters(request, data_type=None): - request: DRF Request object. See `chord_private_table_search` for a detail of the possible values. Note that the "output" parameter is not implemented for this search. - - data_type: optional argument. Can be "experiment"/"phenopacket"/"mcodepacket" + - data_type: optional argument. Can be "experiment"/"phenopacket" This value is provided for the chord searches that are restricted to a specific table (values inferred from the table properties) - returns: @@ -622,5 +595,4 @@ def dataset_summary(request: HttpRequest, dataset_id: str): return Response({ DATA_TYPE_PHENOPACKET: phenopacket_dataset_summary(dataset=dataset), DATA_TYPE_EXPERIMENT: experiment_dataset_summary(dataset=dataset), - DATA_TYPE_MCODEPACKET: mcodepacket_dataset_summary(dataset=dataset), }) diff --git a/chord_metadata_service/chord/workflows/metadata.py b/chord_metadata_service/chord/workflows/metadata.py index 3e2ac6f89..a7eb8db39 100644 --- a/chord_metadata_service/chord/workflows/metadata.py +++ b/chord_metadata_service/chord/workflows/metadata.py @@ -4,8 +4,6 @@ "WORKFLOW_PHENOPACKETS_JSON", "WORKFLOW_EXPERIMENTS_JSON", "WORKFLOW_FHIR_JSON", - "WORKFLOW_MCODE_FHIR_JSON", - "WORKFLOW_MCODE_JSON", "WORKFLOW_READSET", "WORKFLOW_MAF_DERIVED_FROM_VCF_JSON", "WORKFLOW_VCF2MAF", @@ -22,7 +20,6 @@ DATA_TYPE_EXPERIMENT, DATA_TYPE_EXPERIMENT_RESULT, DATA_TYPE_PHENOPACKET, - DATA_TYPE_MCODEPACKET, DATA_TYPE_READSET, ) @@ -31,8 +28,6 @@ WORKFLOW_PHENOPACKETS_JSON = "phenopackets_json" WORKFLOW_EXPERIMENTS_JSON = "experiments_json" WORKFLOW_FHIR_JSON = "fhir_json" -WORKFLOW_MCODE_FHIR_JSON = "mcode_fhir_json" -WORKFLOW_MCODE_JSON = "mcode_json" WORKFLOW_READSET = "readset" WORKFLOW_MAF_DERIVED_FROM_VCF_JSON = "maf_derived_from_vcf_json" WORKFLOW_VCF2MAF = "vcf2maf" @@ -130,25 +125,6 @@ def json_file_output(id_: str, output_name: Optional[str] = None): ] }, - WORKFLOW_MCODE_FHIR_JSON: { - "name": "MCODE FHIR Resources JSON", - "description": "This ingestion workflow will validate and import a mCODE FHIR 4.0. schema-compatible " - "JSON document, and convert it to the Bento metadata service's internal mCODE-based " - "data model.", - "data_type": DATA_TYPE_MCODEPACKET, - "file": "mcode_fhir_json.wdl", - "inputs": [KATSU_URL_INPUT, json_file_input("json_document")], - "outputs": [json_file_output("json_document", "ingest.json")], - }, - WORKFLOW_MCODE_JSON: { - "name": "MCODE Resources JSON", - "description": "This ingestion workflow will validate and import the Bento metadata service's " - "internal mCODE-based JSON document", - "data_type": DATA_TYPE_MCODEPACKET, - "file": "mcode_json.wdl", - "inputs": [KATSU_URL_INPUT, json_file_input("json_document")], - "outputs": [json_file_output("json_document", "ingest.json")], - }, WORKFLOW_READSET: { "name": "Readset", "description": "This workflow will copy readset files over to DRS.", diff --git a/chord_metadata_service/chord/workflows/wdls/mcode_fhir_json.wdl b/chord_metadata_service/chord/workflows/wdls/mcode_fhir_json.wdl deleted file mode 100644 index 29004d02f..000000000 --- a/chord_metadata_service/chord/workflows/wdls/mcode_fhir_json.wdl +++ /dev/null @@ -1,21 +0,0 @@ -workflow mcode_fhir_json { - File json_document - - call copy_task { - input: json_document_in = json_document - } - - output { - File json_document_out = copy_task.json_document - } -} - -task copy_task { - File json_document_in - command { - cp "${json_document_in}" ingest.json - } - output { - File json_document = "ingest.json" - } -} diff --git a/chord_metadata_service/chord/workflows/wdls/mcode_json.wdl b/chord_metadata_service/chord/workflows/wdls/mcode_json.wdl deleted file mode 100644 index 91d0193ed..000000000 --- a/chord_metadata_service/chord/workflows/wdls/mcode_json.wdl +++ /dev/null @@ -1,21 +0,0 @@ -workflow mcode_json { - File json_document - - call copy_task { - input: json_document_in = json_document - } - - output { - File json_document_out = copy_task.json_document - } -} - -task copy_task { - File json_document_in - command { - cp "${json_document_in}" ingest.json - } - output { - File json_document = "ingest.json" - } -} diff --git a/chord_metadata_service/mcode/admin.py b/chord_metadata_service/mcode/admin.py index 78355dfcb..e69de29bb 100644 --- a/chord_metadata_service/mcode/admin.py +++ b/chord_metadata_service/mcode/admin.py @@ -1,52 +0,0 @@ -from django.contrib import admin -from . import models as m - - -@admin.register(m.GeneticSpecimen) -class GeneticSpecimenAdmin(admin.ModelAdmin): - pass - - -@admin.register(m.CancerGeneticVariant) -class CancerGeneticVariantAdmin(admin.ModelAdmin): - pass - - -@admin.register(m.GenomicRegionStudied) -class GenomicRegionStudiedAdmin(admin.ModelAdmin): - pass - - -@admin.register(m.GenomicsReport) -class GenomicsReportAdmin(admin.ModelAdmin): - pass - - -@admin.register(m.LabsVital) -class LabsVitalAdmin(admin.ModelAdmin): - pass - - -@admin.register(m.CancerCondition) -class CancerConditionAdmin(admin.ModelAdmin): - pass - - -@admin.register(m.TNMStaging) -class TNMStagingAdmin(admin.ModelAdmin): - pass - - -@admin.register(m.CancerRelatedProcedure) -class CancerRelatedProcedureAdmin(admin.ModelAdmin): - pass - - -@admin.register(m.MedicationStatement) -class MedicationStatementAdmin(admin.ModelAdmin): - pass - - -@admin.register(m.MCodePacket) -class MCodePacketAdmin(admin.ModelAdmin): - pass diff --git a/chord_metadata_service/mcode/migrations/0007_remove_cancergeneticvariant_gene_studied_and_more.py b/chord_metadata_service/mcode/migrations/0007_remove_cancergeneticvariant_gene_studied_and_more.py new file mode 100644 index 000000000..7d9705a78 --- /dev/null +++ b/chord_metadata_service/mcode/migrations/0007_remove_cancergeneticvariant_gene_studied_and_more.py @@ -0,0 +1,99 @@ +# Generated by Django 4.2.5 on 2023-10-23 19:04 + +from django.db import migrations + + +class Migration(migrations.Migration): + + dependencies = [ + ('mcode', '0006_v4_0_0'), + ] + + operations = [ + migrations.RemoveField( + model_name='cancergeneticvariant', + name='gene_studied', + ), + migrations.RemoveField( + model_name='cancerrelatedprocedure', + name='reason_reference', + ), + migrations.RemoveField( + model_name='genomicsreport', + name='genetic_specimen', + ), + migrations.RemoveField( + model_name='genomicsreport', + name='genetic_variant', + ), + migrations.RemoveField( + model_name='genomicsreport', + name='genomic_region_studied', + ), + migrations.RemoveField( + model_name='labsvital', + name='individual', + ), + migrations.RemoveField( + model_name='mcodepacket', + name='cancer_condition', + ), + migrations.RemoveField( + model_name='mcodepacket', + name='cancer_related_procedures', + ), + migrations.RemoveField( + model_name='mcodepacket', + name='dataset', + ), + migrations.RemoveField( + model_name='mcodepacket', + name='genomics_report', + ), + migrations.RemoveField( + model_name='mcodepacket', + name='medication_statement', + ), + migrations.RemoveField( + model_name='mcodepacket', + name='subject', + ), + migrations.RemoveField( + model_name='mcodepacket', + name='tumor_marker', + ), + migrations.RemoveField( + model_name='tnmstaging', + name='cancer_condition', + ), + migrations.DeleteModel( + name='CancerCondition', + ), + migrations.DeleteModel( + name='CancerGeneticVariant', + ), + migrations.DeleteModel( + name='CancerRelatedProcedure', + ), + migrations.DeleteModel( + name='GeneticSpecimen', + ), + migrations.DeleteModel( + name='GenomicRegionStudied', + ), + migrations.DeleteModel( + name='GenomicsReport', + ), + migrations.DeleteModel( + name='LabsVital', + ), + migrations.DeleteModel( + name='MCodePacket', + ), + migrations.DeleteModel( + name='MedicationStatement', + ), + migrations.DeleteModel( + name='TNMStaging', + ), + ] diff --git a/chord_metadata_service/mcode/models.py b/chord_metadata_service/mcode/models.py index f8c0bbe6f..e69de29bb 100644 --- a/chord_metadata_service/mcode/models.py +++ b/chord_metadata_service/mcode/models.py @@ -1,342 +0,0 @@ -from django.utils import timezone -from django.db import models -from django.db.models import JSONField -from django.contrib.postgres.fields import ArrayField -from chord_metadata_service.restapi.models import IndexableMixin -from chord_metadata_service.phenopackets.models import Gene -from chord_metadata_service.patients.models import Individual -from chord_metadata_service.restapi.description_utils import rec_help -import chord_metadata_service.mcode.descriptions as d -from chord_metadata_service.restapi.validators import ontology_validator, ontology_list_validator -from .validators import ( - tumor_marker_data_value_validator, - complex_ontology_validator -) - - -class GeneticSpecimen(models.Model, IndexableMixin): - """ - Class to describe a biosample used for genomics testing or analysis. - """ - id = models.CharField(primary_key=True, max_length=200, help_text=rec_help(d.GENETIC_SPECIMEN, "id")) - specimen_type = JSONField(validators=[ontology_validator], help_text=rec_help(d.GENETIC_SPECIMEN, "specimen_type")) - collection_body = JSONField(blank=True, null=True, validators=[ontology_validator], - help_text=rec_help(d.GENETIC_SPECIMEN, "collection_body")) - laterality = JSONField(blank=True, null=True, validators=[ontology_validator], - help_text=rec_help(d.GENETIC_SPECIMEN, "laterality")) - extra_properties = JSONField(blank=True, null=True, - help_text=rec_help(d.GENETIC_SPECIMEN, "extra_properties")) - created = models.DateTimeField(auto_now=True) - updated = models.DateTimeField(auto_now_add=True) - - class Meta: - ordering = ['id'] - - def __str__(self): - return str(self.id) - - -class CancerGeneticVariant(models.Model, IndexableMixin): - """ - Class to record an alteration in DNA. - """ - id = models.CharField(primary_key=True, max_length=200, help_text=rec_help(d.CANCER_GENETIC_VARIANT, "id")) - data_value = JSONField(blank=True, null=True, validators=[ontology_validator], - help_text=rec_help(d.CANCER_GENETIC_VARIANT, "data_value")) - method = JSONField(blank=True, null=True, validators=[ontology_validator], - help_text=rec_help(d.CANCER_GENETIC_VARIANT, "method")) - amino_acid_change = JSONField(blank=True, null=True, validators=[ontology_validator], - help_text=rec_help(d.CANCER_GENETIC_VARIANT, "amino_acid_change")) - amino_acid_change_type = JSONField(blank=True, null=True, validators=[ontology_validator], - help_text=rec_help(d.CANCER_GENETIC_VARIANT, "amino_acid_change_type")) - cytogenetic_location = JSONField(blank=True, null=True, - help_text=rec_help(d.CANCER_GENETIC_VARIANT, "cytogenetic_location")) - cytogenetic_nomenclature = JSONField(blank=True, null=True, validators=[ontology_validator], - help_text=rec_help(d.CANCER_GENETIC_VARIANT, "cytogenetic_nomenclature")) - gene_studied = models.ManyToManyField(Gene, blank=True, - help_text=rec_help(d.CANCER_GENETIC_VARIANT, "gene_studied")) - genomic_dna_change = JSONField(blank=True, null=True, validators=[ontology_validator], - help_text=rec_help(d.CANCER_GENETIC_VARIANT, "genomic_dna_change")) - genomic_source_class = JSONField(blank=True, null=True, validators=[ontology_validator], - help_text=rec_help(d.CANCER_GENETIC_VARIANT, "genomic_source_class")) - variation_code = JSONField(blank=True, null=True, validators=[ontology_list_validator], - help_text=rec_help(d.CANCER_GENETIC_VARIANT, "variation_code")) - extra_properties = JSONField(blank=True, null=True, - help_text=rec_help(d.CANCER_GENETIC_VARIANT, "extra_properties")) - created = models.DateTimeField(auto_now=True) - updated = models.DateTimeField(auto_now_add=True) - - class Meta: - ordering = ['id'] - - def __str__(self): - return str(self.id) - - -class GenomicRegionStudied(models.Model, IndexableMixin): - """ - Class to describe the area of the genome region referenced in testing for variants. - """ - id = models.CharField(primary_key=True, max_length=200, help_text=rec_help(d.GENOMIC_REGION_STUDIED, "id")) - # TODO schema Range list - dna_ranges_examined = JSONField(blank=True, null=True, validators=[ontology_list_validator], - help_text=rec_help(d.GENOMIC_REGION_STUDIED, "dna_ranges_examined")) - dna_region_description = ArrayField(models.CharField(max_length=100, - help_text=rec_help(d.GENOMIC_REGION_STUDIED, - 'dna_region_description')), - blank=True, default=list) - gene_mutation = JSONField(blank=True, null=True, validators=[ontology_list_validator], - help_text=rec_help(d.GENOMIC_REGION_STUDIED, "gene_mutation")) - # TODO check: thisis not a Reference in mcode data dictionary why not? - gene_studied = JSONField(blank=True, null=True, validators=[ontology_list_validator], - help_text=rec_help(d.GENOMIC_REGION_STUDIED, "gene_studied")) - genomic_reference_sequence_id = JSONField(blank=True, null=True, - help_text=rec_help(d.GENOMIC_REGION_STUDIED, - "genomic_reference_sequence_id")) - genomic_region_coordinate_system = JSONField(blank=True, null=True, validators=[ontology_validator], - help_text=rec_help(d.GENOMIC_REGION_STUDIED, - "genomic_region_coordinate_system")) - extra_properties = JSONField(blank=True, null=True, - help_text=rec_help(d.GENOMIC_REGION_STUDIED, "extra_properties")) - created = models.DateTimeField(auto_now=True) - updated = models.DateTimeField(auto_now_add=True) - - class Meta: - ordering = ['id'] - - def __str__(self): - return str(self.id) - - -class GenomicsReport(models.Model, IndexableMixin): - """ - Genetic Analysis Summary. - """ - - id = models.CharField(primary_key=True, max_length=200, help_text=rec_help(d.GENOMICS_REPORT, "id")) - code = JSONField(validators=[ontology_validator], help_text=rec_help(d.GENOMICS_REPORT, "code")) - performing_organization_name = models.CharField( - max_length=200, blank=True, help_text=rec_help(d.GENOMICS_REPORT, "performing_organization_name")) - issued = models.DateTimeField(default=timezone.now, help_text=rec_help(d.GENOMICS_REPORT, "issued")) - genetic_specimen = models.ManyToManyField(GeneticSpecimen, blank=True, - help_text=rec_help(d.GENOMICS_REPORT, "genetic_specimen")) - genetic_variant = models.ForeignKey(CancerGeneticVariant, blank=True, null=True, on_delete=models.SET_NULL, - help_text=rec_help(d.GENOMICS_REPORT, "genetic_variant")) - genomic_region_studied = models.ForeignKey(GenomicRegionStudied, blank=True, null=True, on_delete=models.SET_NULL, - help_text=rec_help(d.GENOMICS_REPORT, "genomic_region_studied")) - extra_properties = JSONField(blank=True, null=True, - help_text=rec_help(d.GENOMICS_REPORT, "extra_properties")) - created = models.DateTimeField(auto_now=True) - updated = models.DateTimeField(auto_now_add=True) - - class Meta: - ordering = ['id'] - - def __str__(self): - return str(self.id) - - -# ================================ Labs/Vital ================================ - - -class LabsVital(models.Model, IndexableMixin): - """ - Class to record tests performed on patient. - """ - # TODO Should this class be a part of Patients app? patient related metadata - id = models.CharField(primary_key=True, max_length=200, - help_text=rec_help(d.LABS_VITAL, "id")) - individual = models.ForeignKey(Individual, on_delete=models.CASCADE, - help_text=rec_help(d.LABS_VITAL, "individual")) - # TODO Change CodeableConcept to Ontology class - tumor_marker_code = JSONField(validators=[ontology_validator], - help_text=rec_help(d.LABS_VITAL, "tumor_marker_code")) - tumor_marker_data_value = JSONField(blank=True, null=True, validators=[tumor_marker_data_value_validator], - help_text=rec_help(d.LABS_VITAL, "tumor_marker_data_value")) - extra_properties = JSONField(blank=True, null=True, - help_text=rec_help(d.LABS_VITAL, "extra_properties")) - created = models.DateTimeField(auto_now=True) - updated = models.DateTimeField(auto_now_add=True) - - class Meta: - ordering = ['id'] - - def __str__(self): - return str(self.id) - - -# ================================== Disease ================================== - -class CancerCondition(models.Model, IndexableMixin): - """ - Class to record the history of primary or secondary cancer conditions. - """ - CANCER_CONDITION_TYPE = ( - ('primary', 'primary'), - ('secondary', 'secondary') - ) - id = models.CharField(primary_key=True, max_length=200, help_text=rec_help(d.CANCER_CONDITION, "id")) - condition_type = models.CharField(choices=CANCER_CONDITION_TYPE, max_length=200, - help_text=rec_help(d.CANCER_CONDITION, "condition_type")) - body_site = JSONField(null=True, validators=[ontology_list_validator], - help_text=rec_help(d.CANCER_CONDITION, 'body_site')) - laterality = JSONField(blank=True, null=True, validators=[ontology_validator], - help_text=rec_help(d.CANCER_CONDITION, "laterality")) - clinical_status = JSONField(blank=True, null=True, validators=[ontology_validator], - help_text=rec_help(d.CANCER_CONDITION, "clinical_status")) - code = JSONField(validators=[ontology_validator], - help_text=rec_help(d.CANCER_CONDITION, "code")) - date_of_diagnosis = models.DateTimeField(blank=True, null=True, - help_text=rec_help(d.CANCER_CONDITION, "date_of_diagnosis")) - histology_morphology_behavior = JSONField(blank=True, null=True, validators=[ontology_validator], - help_text=rec_help(d.CANCER_CONDITION, "histology_morphology_behavior")) - verification_status = JSONField(blank=True, null=True, validators=[ontology_validator], - help_text=rec_help(d.CANCER_CONDITION, "verification_status")) - extra_properties = JSONField(blank=True, null=True, - help_text=rec_help(d.CANCER_CONDITION, "extra_properties")) - created = models.DateTimeField(auto_now=True) - updated = models.DateTimeField(auto_now_add=True) - - class Meta: - ordering = ['id'] - - def __str__(self): - return str(self.id) - - -class TNMStaging(models.Model, IndexableMixin): - """ - Class to describe the spread of cancer in a patient’s body. - """ - - TNM_TYPES = ( - ('clinical', 'clinical'), - ('pathologic', 'pathologic') - ) - id = models.CharField(primary_key=True, max_length=200, help_text=rec_help(d.TNM_STAGING, "id")) - tnm_type = models.CharField(choices=TNM_TYPES, max_length=200, help_text=rec_help(d.TNM_STAGING, "tnm_type")) - stage_group = JSONField(validators=[complex_ontology_validator], help_text=rec_help(d.TNM_STAGING, "stage_group")) - primary_tumor_category = JSONField(validators=[complex_ontology_validator], - help_text=rec_help(d.TNM_STAGING, "primary_tumor_category")) - regional_nodes_category = JSONField(validators=[complex_ontology_validator], - help_text=rec_help(d.TNM_STAGING, "regional_nodes_category")) - distant_metastases_category = JSONField(validators=[complex_ontology_validator], - help_text=rec_help(d.TNM_STAGING, "distant_metastases_category")) - # TODO check if one cancer condition has many TNM Staging - cancer_condition = models.ForeignKey(CancerCondition, on_delete=models.CASCADE, - help_text=rec_help(d.TNM_STAGING, "cancer_condition")) - extra_properties = JSONField(blank=True, null=True, - help_text=rec_help(d.TNM_STAGING, "extra_properties")) - created = models.DateTimeField(auto_now=True) - updated = models.DateTimeField(auto_now_add=True) - - class Meta: - ordering = ['id'] - - def __str__(self): - return str(self.id) - - -# ================================= Treatment ================================= - -# ==== Procedure ==== - -class CancerRelatedProcedure(models.Model, IndexableMixin): - """ - Class to represent radiological treatment or surgical action addressing a cancer condition. - """ - - PROCEDURE_TYPES = ( - ('radiation', 'radiation'), - ('surgical', 'surgical') - ) - id = models.CharField(primary_key=True, max_length=200, help_text=rec_help(d.CANCER_RELATED_PROCEDURE, "id")) - procedure_type = models.CharField(choices=PROCEDURE_TYPES, max_length=200, - help_text=rec_help(d.CANCER_RELATED_PROCEDURE, "procedure_type")) - code = JSONField(validators=[ontology_validator], help_text=rec_help(d.CANCER_RELATED_PROCEDURE, "code")) - body_site = JSONField(null=True, validators=[ontology_list_validator], - help_text=rec_help(d.CANCER_RELATED_PROCEDURE, 'body_site')) - laterality = JSONField(blank=True, null=True, validators=[ontology_validator], - help_text=rec_help(d.CANCER_RELATED_PROCEDURE, "laterality")) - treatment_intent = JSONField(blank=True, null=True, validators=[ontology_validator], - help_text=rec_help(d.CANCER_RELATED_PROCEDURE, "treatment_intent")) - # Only for Surgical Procedure - # TODO CHANGE to ontology list validator - reason_code = JSONField(blank=True, null=True, validators=[ontology_validator], - help_text=rec_help(d.CANCER_RELATED_PROCEDURE, "reason_code")) - reason_reference = models.ManyToManyField(CancerCondition, blank=True, - help_text=rec_help(d.CANCER_RELATED_PROCEDURE, "reason_reference")) - extra_properties = JSONField(blank=True, null=True, - help_text=rec_help(d.CANCER_RELATED_PROCEDURE, "extra_properties")) - created = models.DateTimeField(auto_now=True) - updated = models.DateTimeField(auto_now_add=True) - - class Meta: - ordering = ['id'] - - def __str__(self): - return str(self.id) - - -# ==== Medication Statement ==== - - -class MedicationStatement(models.Model, IndexableMixin): - """ - Class to record the use of a medication. - """ - - id = models.CharField(primary_key=True, max_length=200, help_text=rec_help(d.MEDICATION_STATEMENT, "id")) - # list http://hl7.org/fhir/us/core/STU3.1/ValueSet-us-core-medication-codes.html - medication_code = JSONField(validators=[ontology_validator], - help_text=rec_help(d.MEDICATION_STATEMENT, "medication_code")) - termination_reason = JSONField(null=True, validators=[ontology_list_validator], - help_text=rec_help(d.MEDICATION_STATEMENT, 'termination_reason')) - treatment_intent = JSONField(blank=True, null=True, validators=[ontology_validator], - help_text=rec_help(d.MEDICATION_STATEMENT, "treatment_intent")) - start_date = models.DateTimeField(blank=True, null=True, help_text=rec_help(d.MEDICATION_STATEMENT, "start_date")) - end_date = models.DateTimeField(blank=True, null=True, help_text=rec_help(d.MEDICATION_STATEMENT, "end_date")) - extra_properties = JSONField(blank=True, null=True, - help_text=rec_help(d.MEDICATION_STATEMENT, "extra_properties")) - created = models.DateTimeField(auto_now=True) - updated = models.DateTimeField(auto_now_add=True) - - class Meta: - ordering = ['id'] - - def __str__(self): - return str(self.id) - - -class MCodePacket(models.Model, IndexableMixin): - """ - Class to aggregate Individual's cancer related metadata - """ - - id = models.CharField(primary_key=True, max_length=200, help_text=rec_help(d.MCODEPACKET, "id")) - subject = models.ForeignKey(Individual, on_delete=models.CASCADE, - help_text=rec_help(d.MCODEPACKET, "subject")) - genomics_report = models.ForeignKey(GenomicsReport, blank=True, null=True, on_delete=models.SET_NULL, - help_text=rec_help(d.MCODEPACKET, "genomics_report")) - cancer_condition = models.ForeignKey(CancerCondition, blank=True, null=True, on_delete=models.SET_NULL, - help_text=rec_help(d.MCODEPACKET, "cancer_condition")) - cancer_related_procedures = models.ManyToManyField(CancerRelatedProcedure, blank=True, - help_text=rec_help(d.MCODEPACKET, "cancer_related_procedures")) - medication_statement = models.ManyToManyField(MedicationStatement, blank=True, - help_text=rec_help(d.MCODEPACKET, "medication_statement")) - date_of_death = models.CharField(max_length=200, blank=True, help_text=rec_help(d.MCODEPACKET, "date_of_death")) - cancer_disease_status = JSONField(blank=True, null=True, validators=[ontology_validator], - help_text=rec_help(d.MCODEPACKET, "cancer_disease_status")) - tumor_marker = models.ManyToManyField(LabsVital, blank=True, help_text=rec_help(d.MCODEPACKET, "tumor_marker")) - # link to dataset via the table - dataset = models.ForeignKey("chord.Dataset", on_delete=models.CASCADE, blank=True, null=True) # TODO: Help text - - extra_properties = JSONField(blank=True, null=True, help_text=rec_help(d.MCODEPACKET, "extra_properties")) - created = models.DateTimeField(auto_now=True) - updated = models.DateTimeField(auto_now_add=True) - - class Meta: - ordering = ['id'] - - def __str__(self): - return str(self.id) diff --git a/chord_metadata_service/mcode/tests/__init__.py b/chord_metadata_service/mcode/tests/__init__.py deleted file mode 100644 index e69de29bb..000000000 diff --git a/chord_metadata_service/mcode/tests/example_mcode_fhir.json b/chord_metadata_service/mcode/tests/example_mcode_fhir.json deleted file mode 100644 index e47970f42..000000000 --- a/chord_metadata_service/mcode/tests/example_mcode_fhir.json +++ /dev/null @@ -1,170189 +0,0 @@ -{ - "resourceType": "Bundle", - "type": "transaction", - "entry": [ - { - "fullUrl": "urn:uuid:6fcf56ed-8ad8-4395-a966-9ebee3822656", - "resource": { - "resourceType": "Patient", - "id": "6fcf56ed-8ad8-4395-a966-9ebee3822656", - "meta": { - "profile": [ - "http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-cancer-patient", - "http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient" - ] - }, - "text": { - "status": "generated", - "div": "
Generated by Synthea.Version identifier: v2.5.0-340-gabc9fc4a\n . Person seed: -8566645817921759208 Population seed: 1586171921878
" - }, - "extension": [ - { - "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-race", - "extension": [ - { - "url": "ombCategory", - "valueCoding": { - "system": "urn:oid:2.16.840.1.113883.6.238", - "code": "2106-3", - "display": "White" - } - }, - { - "url": "text", - "valueString": "White" - } - ] - }, - { - "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity", - "extension": [ - { - "url": "ombCategory", - "valueCoding": { - "system": "urn:oid:2.16.840.1.113883.6.238", - "code": "2186-5", - "display": "Not Hispanic or Latino" - } - }, - { - "url": "text", - "valueString": "Not Hispanic or Latino" - } - ] - }, - { - "url": "http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName", - "valueString": "Meryl421 Hintz995" - }, - { - "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex", - "valueCode": "F" - }, - { - "url": "http://hl7.org/fhir/StructureDefinition/patient-birthPlace", - "valueAddress": { - "city": "Waltham", - "state": "Massachusetts", - "country": "US" - } - }, - { - "url": "http://synthetichealth.github.io/synthea/disability-adjusted-life-years", - "valueDecimal": 4.846071127966769 - }, - { - "url": "http://synthetichealth.github.io/synthea/quality-adjusted-life-years", - "valueDecimal": 73.15392887203323 - } - ], - "identifier": [ - { - "system": "https://github.com/synthetichealth/synthea", - "value": "6fcf56ed-8ad8-4395-a966-9ebee3822656" - }, - { - "type": { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/v2-0203", - "code": "MR", - "display": "Medical Record Number" - } - ], - "text": "Medical Record Number" - }, - "system": "http://hospital.smarthealthit.org", - "value": "6fcf56ed-8ad8-4395-a966-9ebee3822656" - }, - { - "type": { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/v2-0203", - "code": "SS", - "display": "Social Security Number" - } - ], - "text": "Social Security Number" - }, - "system": "http://hl7.org/fhir/sid/us-ssn", - "value": "999-57-5876" - }, - { - "type": { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/v2-0203", - "code": "DL", - "display": "Driver's License" - } - ], - "text": "Driver's License" - }, - "system": "urn:oid:2.16.840.1.113883.4.3.25", - "value": "S99952488" - }, - { - "type": { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/v2-0203", - "code": "PPN", - "display": "Passport Number" - } - ], - "text": "Passport Number" - }, - "system": "http://standardhealthrecord.org/fhir/StructureDefinition/passportNumber", - "value": "X12533214X" - } - ], - "name": [ - { - "use": "official", - "family": "Boyer713", - "given": [ - "Adrianna470" - ], - "prefix": [ - "Mrs." - ] - }, - { - "use": "maiden", - "family": "Shanahan202", - "given": [ - "Adrianna470" - ], - "prefix": [ - "Mrs." - ] - } - ], - "telecom": [ - { - "system": "phone", - "value": "555-933-3429", - "use": "home" - } - ], - "gender": "female", - "birthDate": "1941-03-21", - "address": [ - { - "extension": [ - { - "url": "http://hl7.org/fhir/StructureDefinition/geolocation", - "extension": [ - { - "url": "latitude", - "valueDecimal": 41.9227657482067 - }, - { - "url": "longitude", - "valueDecimal": -70.74295008010517 - } - ] - } - ], - "line": [ - "917 Pfeffer Tunnel" - ], - "city": "Carver", - "state": "MA", - "country": "US" - } - ], - "maritalStatus": { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/v3-MaritalStatus", - "code": "M", - "display": "M" - } - ], - "text": "M" - }, - "multipleBirthBoolean": false, - "communication": [ - { - "language": { - "coding": [ - { - "system": "urn:ietf:bcp:47", - "code": "en-US", - "display": "English" - } - ], - "text": "English" - } - } - ] - }, - "request": { - "method": "POST", - "url": "Patient" - } - }, - { - "fullUrl": "urn:uuid:b4be02ea-a3a7-4210-9bcd-ae445355cc0a", - "resource": { - "resourceType": "Location", - "id": "b4be02ea-a3a7-4210-9bcd-ae445355cc0a", - "meta": { - "profile": [ - "http://hl7.org/fhir/us/core/StructureDefinition/us-core-location" - ] - }, - "status": "active", - "name": "MINUTECLINIC DIAGNOSTIC OF MASSACHUSETTS, LLC", - "telecom": [ - { - "system": "phone", - "value": "866-389-2727" - } - ], - "address": { - "line": [ - "100 DN MAIN ST" - ], - "city": "CARVER", - "state": "MA", - "postalCode": "02330-1046", - "country": "US" - }, - "position": { - "longitude": -70.74671500000001, - "latitude": 41.875178999999996 - }, - "managingOrganization": { - "reference": "urn:uuid:fa39b515-ef6d-3b4f-80cb-55d6c482aadc", - "display": "MINUTECLINIC DIAGNOSTIC OF MASSACHUSETTS, LLC" - } - }, - "request": { - "method": "POST", - "url": "Location" - } - }, - { - "fullUrl": "urn:uuid:fa39b515-ef6d-3b4f-80cb-55d6c482aadc", - "resource": { - "resourceType": "Organization", - "id": "fa39b515-ef6d-3b4f-80cb-55d6c482aadc", - "meta": { - "profile": [ - "http://hl7.org/fhir/us/core/StructureDefinition/us-core-organization" - ] - }, - "identifier": [ - { - "system": "https://github.com/synthetichealth/synthea", - "value": "fa39b515-ef6d-3b4f-80cb-55d6c482aadc" - } - ], - "active": true, - "type": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/organization-type", - "code": "prov", - "display": "Healthcare Provider" - } - ], - "text": "Healthcare Provider" - } - ], - "name": "MINUTECLINIC DIAGNOSTIC OF MASSACHUSETTS, LLC", - "telecom": [ - { - "system": "phone", - "value": "866-389-2727" - } - ], - "address": [ - { - "line": [ - "100 DN MAIN ST" - ], - "city": "CARVER", - "state": "MA", - "postalCode": "02330-1046", - "country": "US" - } - ] - }, - "request": { - "method": "POST", - "url": "Organization" - } - }, - { - "fullUrl": "urn:uuid:cad93b5f-d9b3-3916-a9b1-05b43dd66b95", - "resource": { - "resourceType": "Practitioner", - "id": "cad93b5f-d9b3-3916-a9b1-05b43dd66b95", - "meta": { - "profile": [ - "http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitioner" - ] - }, - "identifier": [ - { - "system": "http://hl7.org/fhir/sid/us-npi", - "value": "9999921109" - } - ], - "active": true, - "name": [ - { - "family": "Grady603", - 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} - }, - "cancer_disease_status": { - "id": "http://snomed.info/sct:268910001", - "label": "Patient's condition improved" - }, - "medication_statement": [ - { - "id": "fd5416ee-78ad-41ea-b847-dcc3e975dec5", - "medication_code": { - "id": "http://www.nlm.nih.gov/research/umls/rxnorm:198240", - "label": "tamoxifen citrate 10 MG Oral Tablet" - } - } - ], - "tumor_marker": [ - { - "id": "9f785640-bdd2-4afe-93e2-3959b8994569", - "tumor_marker_code": { - "id": "http://loinc.org:48676-1", - "label": "HER2 [Interpretation] in Tissue" - }, - "tumor_marker_data_value": { - "id": "http://snomed.info/sct:260385009", - "label": "Negative (qualifier value)" - }, - "individual": "ind:HG00096" - }, - { - "id": "deeb6699-867b-4260-9d52-18b302bc42de", - "tumor_marker_code": { - "id": "http://loinc.org:48676-1", - "label": "HER2 [Interpretation] in Tissue" - }, - "tumor_marker_data_value": { - "id": "http://snomed.info/sct:260385009", - "label": "Negative (qualifier value)" - }, - "individual": "ind:HG00096" - }, - { - "id": "61f262ea-d3e9-4657-99c3-420d4b0f5283", - "tumor_marker_code": { - "id": "http://loinc.org:16112-5", - "label": "Estrogen receptor [Interpretation] in Tissue" - }, - "tumor_marker_data_value": { - "id": "http://snomed.info/sct:10828004", - "label": "Positive (qualifier value)" - }, - "individual": "ind:HG00096" - } - ], - "cancer_related_procedures": [ - { - "id": "910dba95-2870-4e83-9f0f-b16da9c39295", - "code": { - "id": "http://snomed.info/sct:69031006", - "label": "Excision of breast tissue (procedure)" - }, - "reason_reference": [ - "5f2395f3-3271-441d-841a-af276c238eb2" - ], - "procedure_type": "surgical" - } - ] - } -] \ No newline at end of file diff --git a/chord_metadata_service/mcode/tests/test_api.py b/chord_metadata_service/mcode/tests/test_api.py deleted file mode 100644 index 23aa631fe..000000000 --- a/chord_metadata_service/mcode/tests/test_api.py +++ /dev/null @@ -1,80 +0,0 @@ -from rest_framework import status -from rest_framework.test import APITestCase - -from chord_metadata_service.chord.models import Project, Dataset -# noinspection PyProtectedMember -from chord_metadata_service.chord.ingest import WORKFLOW_INGEST_FUNCTION_MAP -from chord_metadata_service.chord.workflows.metadata import WORKFLOW_MCODE_JSON -from chord_metadata_service.chord.tests.constants import VALID_DATA_USE_1 -from chord_metadata_service.restapi.tests.utils import load_local_json - -EXAMPLE_INGEST_OUTPUTS_MCODE_JSON = load_local_json("example_mcode_json.json") - - -class GetMcodeApiTest(APITestCase): - """ - Test that we can retrieve mcodepackets with valid dataset titles or without dataset title. - """ - - def setUp(self) -> None: - """ - Set up 1 dataset and ingest 1 mcodepacket. - """ - p = Project.objects.create(title="Project 1", description="") - self.d = Dataset.objects.create(title="Dataset 1", description="Some dataset", data_use=VALID_DATA_USE_1, - project=p) - WORKFLOW_INGEST_FUNCTION_MAP[WORKFLOW_MCODE_JSON](EXAMPLE_INGEST_OUTPUTS_MCODE_JSON, self.d.identifier) - - def test_get_mcodepackets(self): - """ - Test that we can get 1 mcodepacket without a dataset title. - """ - response = self.client.get('/api/mcodepackets') - self.assertEqual(response.status_code, status.HTTP_200_OK) - response_data = response.json() - self.assertEqual(len(response_data["results"]), 1) - - def test_get_mcodepackets_with_valid_dataset(self): - """ - Test that we can get 1 mcodepacket with a valid dataset title. - """ - response = self.client.get('/api/mcodepackets?datasets=Dataset+1') - self.assertEqual(response.status_code, status.HTTP_200_OK) - response_data = response.json() - self.assertEqual(len(response_data["results"]), 1) - - def test_get_mcodepackets_with_invalid_dataset(self): - """ - Test that we cannot get mcodepackets with invalid dataset titles. - """ - response = self.client.get('/api/mcodepackets?datasets=notADataset') - self.assertEqual(response.status_code, status.HTTP_200_OK) - response_data = response.json() - self.assertEqual(len(response_data["results"]), 0) - - def test_get_mcodepackets_with_authz_dataset_1(self): - """ - Test that we can get 1 mcodepacket with 1 authorized dataset. - """ - response = self.client.get('/api/mcodepackets?authorized_datasets=Dataset+1') - self.assertEqual(response.status_code, status.HTTP_200_OK) - response_data = response.json() - self.assertEqual(len(response_data["results"]), 1) - - def test_get_mcodepackets_with_authz_dataset_2(self): - """ - Test that we can get 0 mcodepacket with 0 authorized dataset. - """ - response = self.client.get('/api/mcodepackets?authorized_datasets=NO_DATASETS_AUTHORIZED') - self.assertEqual(response.status_code, status.HTTP_200_OK) - response_data = response.json() - self.assertEqual(len(response_data["results"]), 0) - - def test_get_mcodepackets_with_authz_dataset_3(self): - """ - Test that we can get 0 phenopackets with 0 authorized datasets. - """ - response = self.client.get('/api/mcodepackets?authorized_datasets=fakeDataset') - self.assertEqual(response.status_code, status.HTTP_200_OK) - response_data = response.json() - self.assertEqual(len(response_data["results"]), 0) diff --git a/chord_metadata_service/mcode/tests/test_ingest.py b/chord_metadata_service/mcode/tests/test_ingest.py deleted file mode 100644 index 3b4e744b7..000000000 --- a/chord_metadata_service/mcode/tests/test_ingest.py +++ /dev/null @@ -1,137 +0,0 @@ -from django.test import TestCase - -from chord_metadata_service.chord.models import Project, Dataset -from chord_metadata_service.patients.models import Individual -from chord_metadata_service.phenopackets.models import Gene -from chord_metadata_service.chord.ingest import WORKFLOW_INGEST_FUNCTION_MAP -from chord_metadata_service.chord.workflows.metadata import WORKFLOW_MCODE_JSON -from chord_metadata_service.chord.tests.constants import VALID_DATA_USE_1 -from chord_metadata_service.restapi.tests.utils import load_local_json - -from ..models import ( - MCodePacket, CancerCondition, MedicationStatement, - CancerRelatedProcedure, GenomicsReport, GeneticSpecimen, - CancerGeneticVariant, GenomicRegionStudied, TNMStaging, -) - -EXAMPLE_INGEST_MCODE_JSON = load_local_json("example_mcode_json.json") - - -class IngestMcodeJsonTest(TestCase): - - def setUp(self) -> None: - p = Project.objects.create(title="Project 1", description="") - self.d = Dataset.objects.create(title="Dataset 1", description="Some dataset", - data_use=VALID_DATA_USE_1, - project=p) - - def test_ingest_mcodepacket_json(self): - WORKFLOW_INGEST_FUNCTION_MAP[WORKFLOW_MCODE_JSON](EXAMPLE_INGEST_MCODE_JSON, self.d.identifier) - self.assertEqual(len(MCodePacket.objects.all()), 1) - self.assertEqual(len(Individual.objects.all()), 1) - individual = Individual.objects.get(id="ind:HG00096") - self.assertEqual(individual.sex, "FEMALE") - self.assertIsNotNone(individual.date_of_birth) - self.assertIsNotNone(individual.age) - self.assertEqual(individual.karyotypic_sex, "XX") - self.assertIsNotNone(individual.taxonomy) - self.assertEqual(individual.active, True) - self.assertEqual(individual.deceased, False) - self.assertIsNotNone(individual.comorbid_condition) - self.assertIsInstance(individual.comorbid_condition, dict) - self.assertIn("clinical_status", individual.comorbid_condition.keys()) - self.assertIn("code", individual.comorbid_condition.keys()) - self.assertIsInstance(individual.ecog_performance_status, dict) - self.assertEqual(individual.ecog_performance_status["label"], "Fully active") - self.assertEqual(individual.ecog_performance_status["id"], "0") - self.assertIsInstance(individual.karnofsky, dict) - self.assertEqual(individual.karnofsky["label"], "Normal, no complaints; no evidence of disease") - self.assertEqual(individual.karnofsky["id"], "100") - self.assertEqual(individual.race, "Unknown") - self.assertEqual(individual.ethnicity, "Unknown") - # cancer condition - self.assertEqual(len(CancerCondition.objects.all()), 1) - cancer_condition = CancerCondition.objects.filter(condition_type="primary")[0] - self.assertEqual("active", cancer_condition.clinical_status["label"]) - self.assertEqual("SNOMED:24028007", cancer_condition.laterality["id"]) - self.assertIsInstance(cancer_condition.body_site, list) - self.assertEqual("SNOMED:253035009", cancer_condition.histology_morphology_behavior["id"]) - # cancer condition tnm staging - self.assertEqual(len(TNMStaging.objects.all()), 2) - for tnm_staging in TNMStaging.objects.all(): - self.assertIsNotNone(tnm_staging.tnm_type) - for field in ["stage_group", "primary_tumor_category", - "regional_nodes_category", "distant_metastases_category"]: - self.assertIsNotNone(tnm_staging.__dict__[field]) - self.assertIsInstance(tnm_staging.__dict__[field], dict) - - # mcodepacket - self.assertEqual(len(MCodePacket.objects.all()), 1) - mcodepacket = MCodePacket.objects.all()[0] - self.assertEqual(mcodepacket.cancer_disease_status["label"], "Patient's condition improved") - # medication statement - self.assertEqual(len(MedicationStatement.objects.all()), 1) - # tumor marker - self.assertEqual(len(CancerRelatedProcedure.objects.all()), 1) - # genomics report - self.assertEqual(len(GenomicsReport.objects.all()), 1) - genomics_report = GenomicsReport.objects.get(id="3000") - self.assertIn("DNA double strand", genomics_report.code["label"]) - self.assertIn("Cancer Centre", genomics_report.performing_organization_name) - self.assertIsNotNone(genomics_report.issued) - # genetic specimen - self.assertEqual(len(GeneticSpecimen.objects.all()), 3) - # 1 - genetic_specimen_1 = GeneticSpecimen.objects.get(id="3000-0") - self.assertEqual("SNOMED:2855004", genetic_specimen_1.collection_body["id"]) - self.assertIn("cephalic vein", genetic_specimen_1.collection_body["label"]) - self.assertEqual("BLD", genetic_specimen_1.specimen_type["id"]) - self.assertIn("blood", genetic_specimen_1.specimen_type["label"]) - self.assertEqual("SNOMED:24028007", genetic_specimen_1.laterality["id"]) - self.assertEqual("Right (qualifier value)", genetic_specimen_1.laterality["label"]) - # 2 - genetic_specimen_2 = GeneticSpecimen.objects.get(id="3000-1") - self.assertEqual("SNOMED:9568000", genetic_specimen_2.collection_body["id"]) - self.assertIn("areola", genetic_specimen_2.collection_body["label"]) - self.assertEqual("TUMOR", genetic_specimen_2.specimen_type["id"]) - self.assertIn("Tumor", genetic_specimen_2.specimen_type["label"]) - # 3 - genetic_specimen_3 = GeneticSpecimen.objects.get(id="3000-2") - self.assertEqual("SNOMED:9568000", genetic_specimen_3.collection_body["id"]) - self.assertIn("areola", genetic_specimen_3.collection_body["label"]) - self.assertEqual("TISS", genetic_specimen_3.specimen_type["id"]) - self.assertIn("Tissue", genetic_specimen_3.specimen_type["label"]) - # genetic variant - self.assertEqual(len(CancerGeneticVariant.objects.all()), 1) - genetic_variant = CancerGeneticVariant.objects.get(id="3000") - self.assertIsInstance(genetic_variant.data_value, dict) - self.assertEqual("LOINC:LA4489-6", genetic_variant.data_value["id"]) - self.assertEqual("Unknown", genetic_variant.data_value["label"]) - for field in ["method", "amino_acid_change", "amino_acid_change_type", "cytogenetic_location", - "cytogenetic_nomenclature", "genomic_dna_change", "genomic_source_class"]: - self.assertEqual("SNOMED:261665006", genetic_variant.__dict__[field]["id"]) - self.assertEqual("Unknown", genetic_variant.__dict__[field]["label"]) - self.assertIsNotNone(genetic_variant.extra_properties) - # gene studied in genetic variant - self.assertEqual(len(Gene.objects.all()), 1) - gene = Gene.objects.get(id="HGNC:7989") - self.assertEqual(gene.symbol, "NRAS") - # genomic region studied - self.assertEqual(len(GenomicRegionStudied.objects.all()), 1) - genomic_region_studied = GenomicRegionStudied.objects.get(id="3000") - for field in ["genomic_reference_sequence_id", "genomic_region_coordinate_system"]: - self.assertEqual("SNOMED:261665006", genomic_region_studied.__dict__[field]["id"]) - self.assertEqual("Unknown", genomic_region_studied.__dict__[field]["label"]) - self.assertIsNotNone(genomic_region_studied.extra_properties) - self.assertIsInstance(genomic_region_studied.dna_region_description, list) - self.assertEqual(len(genomic_region_studied.dna_ranges_examined), 1) - # gene mutation in genomic region studied - self.assertIsInstance(genomic_region_studied.gene_mutation, list) - self.assertEqual(len(genomic_region_studied.gene_mutation), 1) - self.assertEqual(genomic_region_studied.gene_mutation[0]["id"], "HGVS:40488") - self.assertIn("NM_002834.5", genomic_region_studied.gene_mutation[0]["label"]) - # gene studied in genomic region studied - self.assertIsInstance(genomic_region_studied.gene_studied, list) - self.assertEqual(len(genomic_region_studied.gene_studied), 1) - self.assertEqual(genomic_region_studied.gene_studied[0]["id"], "HGNC:7989") - self.assertEqual("NRAS", genomic_region_studied.gene_studied[0]["label"]) diff --git a/chord_metadata_service/mcode/tests/test_models.py b/chord_metadata_service/mcode/tests/test_models.py deleted file mode 100644 index 291e4a484..000000000 --- a/chord_metadata_service/mcode/tests/test_models.py +++ /dev/null @@ -1,155 +0,0 @@ -import datetime -from django.test import TestCase -from chord_metadata_service.patients.models import Individual -from .. import models as m -from . import constants as c -from rest_framework import serializers - - -class GenomicsReportTest(TestCase): - """ Test module for Genomics Report model """ - - def setUp(self): - self.genomics_report = m.GenomicsReport.objects.create(**c.valid_genetic_report()) - - def test_genomics_report(self): - genomics_report = m.GenomicsReport.objects.get(id='genomics_report:01') - self.assertEqual(genomics_report.code['id'], 'GTR000567625.2') - - -class LabsVitalTest(TestCase): - """ Test module for LabsVital model """ - - def setUp(self): - self.individual = Individual.objects.create(**c.VALID_INDIVIDUAL) - self.labs_vital = m.LabsVital.objects.create(**c.valid_labs_vital(self.individual)) - - def test_labs_vital(self): - labs_vital = m.LabsVital.objects.get(id='labs_vital:01') - self.assertIsInstance(labs_vital.tumor_marker_code, dict) - - def test_validation(self): - invalid_obj = c.valid_labs_vital(self.individual) - invalid_obj["id"] = "labs_vital:02" - invalid_obj["tumor_marker_code"] = { - "coding": [ - { - "code": "50610-5", - "display": "Alpha-1-Fetoprotein", - "system": "loinc.org" - } - ] - } - invalid = m.LabsVital.objects.create(**invalid_obj) - with self.assertRaises(serializers.ValidationError): - invalid.full_clean() - - -class CancerConditionTest(TestCase): - """ Test module for CancerCondition model """ - - def setUp(self): - self.cancer_condition = m.CancerCondition.objects.create(**c.valid_cancer_condition()) - - def test_cancer_condition(self): - cancer_condition = m.CancerCondition.objects.get(id='cancer_condition:01') - self.assertEqual(cancer_condition.condition_type, 'primary') - self.assertIsInstance(cancer_condition.body_site, list) - self.assertEqual(cancer_condition.body_site[0]['id'], '442083009') - self.assertEqual(cancer_condition.clinical_status['id'], 'active') - code_keys = [key for key in cancer_condition.code.keys()] - self.assertEqual(code_keys, ['id', 'label']) - self.assertEqual(cancer_condition.histology_morphology_behavior['id'], '372147008') - - -class TNMStagingTest(TestCase): - """ Test module for TNMstaging model """ - - # TODO URI syntax examples for tests https://tools.ietf.org/html/rfc3986 - - def setUp(self): - self.cancer_condition = m.CancerCondition.objects.create(**c.valid_cancer_condition()) - self.tnm_staging = m.TNMStaging.objects.create(**c.invalid_tnm_staging(self.cancer_condition)) - - def test_tnm_staging(self): - tnm_staging = m.TNMStaging.objects.get(id='tnm_staging:01') - self.assertEqual(tnm_staging.tnm_type, 'clinical') - # this should fails in validation below - self.assertIsInstance(tnm_staging.stage_group['data_value']['coding'], list) - - def test_validation(self): - invalid_obj = c.invalid_tnm_staging(self.cancer_condition) - invalid_obj["id"] = "tnm_staging:02" - invalid = m.TNMStaging.objects.create(**invalid_obj) - with self.assertRaises(serializers.ValidationError): - invalid.full_clean() - - -class CancerRelatedProcedureTest(TestCase): - """ Test module for CancerRelatedProcedure model """ - - def setUp(self): - self.cancer_related_procedure = m.CancerRelatedProcedure.objects.create( - **c.valid_cancer_related_procedure() - ) - - def test_cancer_related_procedure(self): - cancer_related_procedure = m.CancerRelatedProcedure.objects.get(id='cancer_related_procedure:01') - self.assertEqual(cancer_related_procedure.procedure_type, 'radiation') - self.assertEqual(cancer_related_procedure.code['id'], '33356009') - self.assertIsInstance(cancer_related_procedure.body_site, list) - self.assertEqual(cancer_related_procedure.treatment_intent['label'], 'Curative - procedure intent') - - -class MedicationStatementTest(TestCase): - """ Test module for MedicationStatement model """ - - def setUp(self): - self.medication_statement = m.MedicationStatement.objects.create( - **c.valid_medication_statement() - ) - - def test_cancer_related_procedure(self): - medication_statement = m.MedicationStatement.objects.get(id='medication_statement:01') - self.assertEqual(medication_statement.medication_code['id'], '92052') - self.assertIsInstance(medication_statement.termination_reason, list) - self.assertEqual(medication_statement.treatment_intent['label'], 'Curative - procedure intent') - for date in [medication_statement.start_date, medication_statement.end_date]: - self.assertIsInstance(date, datetime.datetime) - - -class McodePacketTest(TestCase): - """ Test module for MCodePacket model """ - - def setUp(self): - self.individual = Individual.objects.create(**c.VALID_INDIVIDUAL) - self.labs_vital = m.LabsVital.objects.create(**c.valid_labs_vital(self.individual)) - self.genomics_report = m.GenomicsReport.objects.create(**c.valid_genetic_report()) - self.cancer_condition = m.CancerCondition.objects.create(**c.valid_cancer_condition()) - self.tnm_staging = m.TNMStaging.objects.create(**c.invalid_tnm_staging(self.cancer_condition)) - self.cancer_related_procedure = m.CancerRelatedProcedure.objects.create( - **c.valid_cancer_related_procedure() - ) - self.medication_statement = m.MedicationStatement.objects.create(**c.valid_medication_statement()) - self.mcodepacket = m.MCodePacket.objects.create( - id="mcodepacket:01", - subject=self.individual, - genomics_report=self.genomics_report, - cancer_disease_status={ - "id": "TEST:01", - "label": "Patient's condition improved" - }, - cancer_condition=self.cancer_condition - ) - self.mcodepacket.cancer_related_procedures.set([self.cancer_related_procedure]) - self.mcodepacket.medication_statement.set([self.medication_statement]) - - def test_mcodepacket(self): - mcodepacket = m.MCodePacket.objects.get(id="mcodepacket:01") - self.assertEqual(mcodepacket.subject.id, "patient:1") - self.assertIsInstance(mcodepacket.cancer_disease_status, dict) - self.assertEqual(mcodepacket.cancer_disease_status["label"], "Patient's condition improved") - self.assertEqual(mcodepacket.cancer_condition.id, "cancer_condition:01") - self.assertEqual(len(mcodepacket.cancer_related_procedures.all()), 1) - self.assertEqual(mcodepacket.genomics_report.id, "genomics_report:01") - self.assertEqual(len(mcodepacket.medication_statement.all()), 1) diff --git a/chord_metadata_service/patients/api_views.py b/chord_metadata_service/patients/api_views.py index 200f8066d..48ab2fedc 100644 --- a/chord_metadata_service/patients/api_views.py +++ b/chord_metadata_service/patients/api_views.py @@ -63,7 +63,7 @@ class IndividualViewSet(viewsets.ModelViewSet): filter_backends = [DjangoFilterBackend, filters.OrderingFilter] filterset_class = IndividualFilter ordering_fields = ["id"] - search_fields = ["sex", "ethnicity"] + search_fields = ["sex"] queryset = Individual.objects.all().prefetch_related( *(f"biosamples__{p}" for p in BIOSAMPLE_PREFETCH), *(f"phenopackets__{p}" for p in PHENOPACKET_PREFETCH if p != "subject"), diff --git a/chord_metadata_service/patients/cleanup.py b/chord_metadata_service/patients/cleanup.py index 400bacb5b..0f3d00425 100644 --- a/chord_metadata_service/patients/cleanup.py +++ b/chord_metadata_service/patients/cleanup.py @@ -1,4 +1,3 @@ -import chord_metadata_service.mcode.models as mm import chord_metadata_service.phenopackets.models as pm from chord_metadata_service.cleanup.remove import remove_not_referenced @@ -18,10 +17,6 @@ async def clean_individuals() -> int: individuals_referenced = set() - # Collect references to individuals from MCode - individuals_referenced |= await build_id_set_from_model(mm.LabsVital, "individual_id") - individuals_referenced |= await build_id_set_from_model(mm.MCodePacket, "subject_id") - # Collect references to individuals from Phenopackets individuals_referenced |= await build_id_set_from_model(pm.Biosample, "individual_id") individuals_referenced |= await build_id_set_from_model(pm.Phenopacket, "subject_id") diff --git a/chord_metadata_service/patients/descriptions.py b/chord_metadata_service/patients/descriptions.py index f66bdf961..22713695d 100644 --- a/chord_metadata_service/patients/descriptions.py +++ b/chord_metadata_service/patients/descriptions.py @@ -28,27 +28,6 @@ "help": "FHIR-specific property." }, - # mCode-specific - "race": { - "description": "A code for a person's race (mCode).", - "help": "mCode-specific property." - }, - "ethnicity": { - "description": "A code for a person's ethnicity (mCode).", - "help": "mCode-specific property." - }, - "comorbid_condition": { - "description": "One or more conditions that occur with primary condition.", - "help": "mCode-specific property." - }, - "ecog_performance_status": { - "description": "Value representing the Eastern Cooperative Oncology Group performance status.", - "help": "mCode-specific property." - }, - "karnofsky": { - "description": "Value representing the Karnofsky Performance status.", - "help": "mCode-specific property." - }, **EXTRA_PROPERTIES } } diff --git a/chord_metadata_service/patients/filters.py b/chord_metadata_service/patients/filters.py index 27d66a544..9e4bd3fb3 100644 --- a/chord_metadata_service/patients/filters.py +++ b/chord_metadata_service/patients/filters.py @@ -11,8 +11,6 @@ class IndividualFilter(django_filters.rest_framework.FilterSet): alternate_ids = django_filters.CharFilter(lookup_expr="icontains") sex = django_filters.CharFilter(lookup_expr="iexact") karyotypic_sex = django_filters.CharFilter(lookup_expr="iexact") - ethnicity = django_filters.CharFilter(lookup_expr="icontains") - race = django_filters.CharFilter(lookup_expr="icontains") disease = django_filters.CharFilter( method="filter_disease", field_name="phenopackets__diseases", label="Disease" @@ -46,14 +44,6 @@ def filter_found_phenotypic_feature(self, qs, name, value): ).distinct() return qs - def filter_on_cancer_condition_name(self, qs, name, value): - qs = qs.filter(mcodepacket__cancer_condition__body_site__icontains=value).distinct() - return qs - - def filter_on_treatment_name(self, qs, name, value): - qs = qs.filter(mcodepacket__cancer_related_procedures__code__icontains=value).distinct() - return qs - def filter_disease(self, qs, name, value): qs = qs.filter( Q(phenopackets__diseases__term__id__icontains=value) | @@ -71,10 +61,6 @@ def filter_search(self, qs, name, value): Cast("age", TextField()), "sex", "karyotypic_sex", Cast("taxonomy", TextField()), - Cast("comorbid_condition", TextField()), - Cast("ecog_performance_status", TextField()), - Cast("karnofsky", TextField()), - "ethnicity", "race", Cast("extra_properties", TextField()), # Phenotypic feature fields diff --git a/chord_metadata_service/patients/migrations/0005_remove_individual_comorbid_condition_and_more.py b/chord_metadata_service/patients/migrations/0005_remove_individual_comorbid_condition_and_more.py new file mode 100644 index 000000000..12dd02013 --- /dev/null +++ b/chord_metadata_service/patients/migrations/0005_remove_individual_comorbid_condition_and_more.py @@ -0,0 +1,35 @@ +# Generated by Django 4.2.5 on 2023-10-23 19:04 + +from django.db import migrations + + +class Migration(migrations.Migration): + + dependencies = [ + ('patients', '0004_v2_18_0'), + ] + + # TODO: data migration of removed fields to extra_properties + + operations = [ + migrations.RemoveField( + model_name='individual', + name='comorbid_condition', + ), + migrations.RemoveField( + model_name='individual', + name='ecog_performance_status', + ), + migrations.RemoveField( + model_name='individual', + name='ethnicity', + ), + migrations.RemoveField( + model_name='individual', + name='karnofsky', + ), + migrations.RemoveField( + model_name='individual', + name='race', + ), + ] diff --git a/chord_metadata_service/patients/models.py b/chord_metadata_service/patients/models.py index 8ec3d3076..f328197b8 100644 --- a/chord_metadata_service/patients/models.py +++ b/chord_metadata_service/patients/models.py @@ -6,7 +6,6 @@ from chord_metadata_service.restapi.models import IndexableMixin, SchemaType, BaseExtraProperties from chord_metadata_service.restapi.validators import ontology_validator, age_or_age_range_validator from .values import Sex, KaryotypicSex -from .validators import comorbid_condition_validator class Individual(BaseExtraProperties, IndexableMixin): @@ -50,20 +49,7 @@ def get_project_id(self) -> Optional[str]: # FHIR specific active = models.BooleanField(default=False, help_text='Whether this patient\'s record is in active use.') deceased = models.BooleanField(default=False, help_text='Indicates if the individual is deceased or not.') - # mCode specific - # this field should be complex Ontology - clinical status and code - two Codeable concept - single, cl status has - # enum list of values - # TODO add these fields to FHIR converter ? - comorbid_condition = JSONField(blank=True, null=True, validators=[comorbid_condition_validator], - help_text='One or more conditions that occur with primary condition.') - # TODO decide use ONTOLOGY_CLASS vs. CODEABLE_CONCEPT - currently Ontology class - ecog_performance_status = JSONField(blank=True, null=True, validators=[ontology_validator], - help_text='Value representing the Eastern Cooperative ' - 'Oncology Group performance status.') - karnofsky = JSONField(blank=True, null=True, validators=[ontology_validator], - help_text='Value representing the Karnofsky Performance status.') - race = models.CharField(max_length=200, blank=True, help_text='A code for the person\'s race.') - ethnicity = models.CharField(max_length=200, blank=True, help_text='A code for the person\'s ethnicity.') + # extra extra_properties = JSONField(blank=True, null=True, help_text='Extra properties that are not supported by current schema') diff --git a/chord_metadata_service/patients/schemas.py b/chord_metadata_service/patients/schemas.py index 0dee1e0e2..e8d4684c9 100644 --- a/chord_metadata_service/patients/schemas.py +++ b/chord_metadata_service/patients/schemas.py @@ -5,17 +5,6 @@ from .values import Sex, KaryotypicSex -COMORBID_CONDITION = customize_schema( - first_typeof=ONTOLOGY_CLASS, - second_typeof=ONTOLOGY_CLASS, - first_property="clinical_status", - second_property="code", - schema_id="katsu:comorbid_condition_schema", - title="Comorbid Condition schema", - description="Comorbid condition schema." -) - - INDIVIDUAL_SCHEMA = tag_ids_and_describe({ "$schema": "http://json-schema.org/draft-07/schema#", "$id": "katsu:patients:individual", @@ -54,15 +43,6 @@ "deceased": { "type": "boolean" }, - "race": { - "type": "string" - }, - "ethnicity": { - "type": "string" - }, - "comorbid_condition": COMORBID_CONDITION, - "ecog_performance_status": ONTOLOGY_CLASS, - "karnofsky": ONTOLOGY_CLASS, "extra_properties": EXTRA_PROPERTIES_SCHEMA, }, "required": ["id"] diff --git a/chord_metadata_service/patients/tests/constants.py b/chord_metadata_service/patients/tests/constants.py index 8dd1576d2..8510a6443 100644 --- a/chord_metadata_service/patients/tests/constants.py +++ b/chord_metadata_service/patients/tests/constants.py @@ -65,9 +65,9 @@ def generate_random_date(years_from: int, years_to: int): "active": True } -CSV_HEADER = "Id,Sex,Date of birth,Taxonomy,Karyotypic sex,Race,Ethnicity,Age,Diseases,Created,Updated" -INDIVIDUAL_1_CSV = "patient:1,FEMALE,1960-01-01,human,UNKNOWN_KARYOTYPE,,,P45Y - P49Y,,--IGNORE--,--IGNORE--" -INDIVIDUAL_2_CSV = "patient:2,MALE,1967-01-01,human,UNKNOWN_KARYOTYPE,,,P55Y,,--IGNORE--,--IGNORE--" +CSV_HEADER = "Id,Sex,Date of birth,Taxonomy,Karyotypic sex,Age,Diseases,Created,Updated" +INDIVIDUAL_1_CSV = "patient:1,FEMALE,1960-01-01,human,UNKNOWN_KARYOTYPE,P45Y - P49Y,,--IGNORE--,--IGNORE--" +INDIVIDUAL_2_CSV = "patient:2,MALE,1967-01-01,human,UNKNOWN_KARYOTYPE,P55Y,,--IGNORE--,--IGNORE--" def generate_valid_individual(): diff --git a/chord_metadata_service/patients/tests/test_api.py b/chord_metadata_service/patients/tests/test_api.py index 2d8c548c1..265d74644 100644 --- a/chord_metadata_service/patients/tests/test_api.py +++ b/chord_metadata_service/patients/tests/test_api.py @@ -6,6 +6,7 @@ from django.conf import settings from django.urls import reverse from django.test import override_settings +from datetime import datetime from rest_framework import status from rest_framework.test import APITestCase from chord_metadata_service.patients.models import Individual @@ -150,7 +151,7 @@ def test_csv_export(self): self.assertEqual(body[1][1], c.VALID_INDIVIDUAL['sex']) headers = body.pop(0) for column in ['id', 'sex', 'date of birth', 'taxonomy', 'karyotypic sex', - 'race', 'ethnicity', 'age', 'diseases', 'created', 'updated']: + 'age', 'diseases', 'created', 'updated']: self.assertIn(column, [column_name.lower() for column_name in headers]) @@ -561,13 +562,15 @@ def test_public_filtering_extra_properties_multiple_ranges_1(self): @override_settings(CONFIG_PUBLIC=CONFIG_PUBLIC_TEST) def test_public_filtering_extra_properties_date_range_1(self): # extra_properties date range search (only after or before, single value) + # Testing with a date of consent from 1 year ago + year_of_consent = datetime.now().year - 1 response = self.client.get( - '/api/public?date_of_consent=Mar 2021' + f'/api/public?date_of_consent=Mar {year_of_consent}' ) self.assertEqual(response.status_code, status.HTTP_200_OK) response_obj = response.json() range_parameters = { - "extra_properties__date_of_consent__startswith": "2021-03" + "extra_properties__date_of_consent__startswith": f"{year_of_consent}-03" } db_count = Individual.objects.filter(**range_parameters).count() self.assertIn(self.response_threshold_check(response_obj), [db_count, settings.INSUFFICIENT_DATA_AVAILABLE]) @@ -579,13 +582,15 @@ def test_public_filtering_extra_properties_date_range_1(self): @override_settings(CONFIG_PUBLIC=CONFIG_PUBLIC_TEST) def test_public_filtering_extra_properties_date_range_and_other_range(self): # extra_properties date range search (both after and before, single value) and other number range search + # Testing with a date of consent from 2 years ago + year_of_consent = datetime.now().year - 1 response = self.client.get( - '/api/public?date_of_consent=Mar 2021&lab_test_result_value=< 200' + f'/api/public?date_of_consent=Mar {year_of_consent}&lab_test_result_value=< 200' ) self.assertEqual(response.status_code, status.HTTP_200_OK) response_obj = response.json() range_parameters = { - "extra_properties__date_of_consent__startswith": "2021-03", + "extra_properties__date_of_consent__startswith": f"{year_of_consent}-03", "extra_properties__lab_test_result_value__gte": 0, "extra_properties__lab_test_result_value__lt": 200, } diff --git a/chord_metadata_service/patients/validators.py b/chord_metadata_service/patients/validators.py deleted file mode 100644 index 5f22ad29d..000000000 --- a/chord_metadata_service/patients/validators.py +++ /dev/null @@ -1,5 +0,0 @@ -from chord_metadata_service.restapi.validators import JsonSchemaValidator -from .schemas import COMORBID_CONDITION - - -comorbid_condition_validator = JsonSchemaValidator(COMORBID_CONDITION) diff --git a/chord_metadata_service/restapi/api_renderers.py b/chord_metadata_service/restapi/api_renderers.py index 53d448048..d04ceebde 100644 --- a/chord_metadata_service/restapi/api_renderers.py +++ b/chord_metadata_service/restapi/api_renderers.py @@ -132,8 +132,6 @@ def render(self, data, media_type=None, renderer_context=None): 'date_of_birth': individual.get('date_of_birth', None), 'taxonomy': None, 'karyotypic_sex': individual['karyotypic_sex'], - 'race': individual.get('race', None), - 'ethnicity': individual.get('ethnicity', None), 'age': None, 'diseases': None, 'created': individual['created'], diff --git a/chord_metadata_service/restapi/api_views.py b/chord_metadata_service/restapi/api_views.py index 6be37f377..f1b5dbb12 100644 --- a/chord_metadata_service/restapi/api_views.py +++ b/chord_metadata_service/restapi/api_views.py @@ -23,10 +23,8 @@ from chord_metadata_service.metadata.service_info import SERVICE_INFO from chord_metadata_service.chord import models as chord_models from chord_metadata_service.phenopackets import models as pheno_models -from chord_metadata_service.mcode import models as mcode_models from chord_metadata_service.patients import models as patients_models from chord_metadata_service.experiments import models as experiments_models -from chord_metadata_service.mcode.api_views import MCODEPACKET_PREFETCH, MCODEPACKET_SELECT from chord_metadata_service.restapi.models import SchemaType from drf_spectacular.utils import extend_schema, inline_serializer from rest_framework import serializers @@ -108,7 +106,6 @@ def overview(_request): }, "taxonomy": stats_for_field(patients_models.Individual, "taxonomy__label"), "age": individuals_age, - "ethnicity": stats_for_field(patients_models.Individual, "ethnicity"), }, "phenotypic_features": { # count is a number of unique phenotypic feature types (not all pfs in the database) @@ -206,100 +203,6 @@ def search_overview(request): return Response(r) -@extend_schema( - description="Overview of all mCode data in the database", - responses={ - 200: inline_serializer( - name='mcode_overview_response', - fields={ - 'mcodepackets': serializers.IntegerField(), - 'data_type_specific': serializers.JSONField(), - } - ) - } -) -# Cache page for the requested url for 2 hours -@cache_page(60 * 60 * 2) -@api_view(["GET"]) -@permission_classes([OverrideOrSuperUserOnly]) -def mcode_overview(_request): - """ - get: - Overview of all mCode data in the database - """ - mcodepackets = mcode_models.MCodePacket.objects.all()\ - .prefetch_related(*MCODEPACKET_PREFETCH)\ - .select_related(*MCODEPACKET_SELECT) - - # cancer condition code - cancer_condition_counter = Counter() - # cancer related procedure type - radiation vs. surgical - cancer_related_procedure_type_counter = Counter() - # cancer related procedure code - cancer_related_procedure_counter = Counter() - # cancer disease status - cancer_disease_status_counter = Counter() - - individuals_set = set() - individuals_sex = Counter() - individuals_k_sex = Counter() - individuals_taxonomy = Counter() - individuals_age = Counter() - individuals_ethnicity = Counter() - - for mcodepacket in mcodepackets: - # subject/individual - individual = mcodepacket.subject - individuals_set.add(individual.id) - individuals_sex.update((individual.sex,)) - individuals_k_sex.update((individual.karyotypic_sex,)) - if individual.ethnicity != "": - individuals_ethnicity.update((individual.ethnicity,)) - if individual.age is not None: - individuals_age.update((parse_individual_age(individual.age),)) - if individual.taxonomy is not None: - individuals_taxonomy.update((individual.taxonomy["label"],)) - if mcodepacket.cancer_condition is not None: - cancer_condition_counter.update((mcodepacket.cancer_condition.condition_type,)) - for cancer_related_procedure in mcodepacket.cancer_related_procedures.all(): - cancer_related_procedure_type_counter.update((cancer_related_procedure.procedure_type,)) - cancer_related_procedure_counter.update((cancer_related_procedure.code["label"],)) - if mcodepacket.cancer_disease_status is not None: - cancer_disease_status_counter.update((mcodepacket.cancer_disease_status["label"],)) - - return Response({ - "mcodepackets": mcodepackets.count(), - "data_type_specific": { - "cancer_conditions": { - "count": len(cancer_condition_counter.keys()), - "term": dict(cancer_condition_counter) - }, - "cancer_related_procedure_types": { - "count": len(cancer_related_procedure_type_counter.keys()), - "term": dict(cancer_related_procedure_type_counter) - }, - "cancer_related_procedures": { - "count": len(cancer_related_procedure_counter.keys()), - "term": dict(cancer_related_procedure_counter) - }, - "cancer_disease_status": { - "count": len(cancer_disease_status_counter.keys()), - "term": dict(cancer_disease_status_counter) - }, - "individuals": { - "count": len(individuals_set), - "sex": {k: individuals_sex[k] for k in (s[0] for s in pheno_models.Individual.SEX)}, - "karyotypic_sex": { - k: individuals_k_sex[k] for k in (s[0] for s in pheno_models.Individual.KARYOTYPIC_SEX) - }, - "taxonomy": dict(individuals_taxonomy), - "age": dict(individuals_age), - "ethnicity": dict(individuals_ethnicity) - }, - } - }) - - @extend_schema( description="Public search fields with their configuration", responses={ @@ -449,7 +352,6 @@ def public_dataset(_request): DT_QUERYSETS = { dt.DATA_TYPE_EXPERIMENT: experiments_models.Experiment.objects.all(), dt.DATA_TYPE_EXPERIMENT_RESULT: experiments_models.ExperimentResult.objects.all(), - dt.DATA_TYPE_MCODEPACKET: mcode_models.MCodePacket.objects.all(), dt.DATA_TYPE_PHENOPACKET: pheno_models.Phenopacket.objects.all(), # dt.DATA_TYPE_READSET: None, } diff --git a/chord_metadata_service/restapi/candig_authz_middleware.py b/chord_metadata_service/restapi/candig_authz_middleware.py index e5696c1f8..786a436df 100644 --- a/chord_metadata_service/restapi/candig_authz_middleware.py +++ b/chord_metadata_service/restapi/candig_authz_middleware.py @@ -63,7 +63,6 @@ def is_authorized_get(self, request): "^/api/genes/?.*", "^/api/genomicinterpretations/?.*", "^/api/htsfiles/?.*", "^/api/individuals/?.*", "^/api/interpretations/?.*", "^/api/metadata/?.*", "^/api/phenopackets/?.*", "^/api/phenotypicfeatures/?.*", "^/api/procedures/?.*", "^/api/variants/?.*", "^/api/biosamples/?.*", "^/api/labsvital/?.*", - "^/api/mcodepackets/?.*", "^/api/medicationstatements/?.*", "^/api/geneticspecimens/?.*", "^/api/cancergeneticvariants/?.*", "^/api/genomicregionsstudied/?.*", "^/api/genomicsreports/?.*", "^/api/cancerconditions/?.*", "^/api/tnmstaging/?.*", "^/api/cancerrelatedprocedures/?.*" ] diff --git a/chord_metadata_service/restapi/tests/test_api.py b/chord_metadata_service/restapi/tests/test_api.py index a10b83672..6938485a8 100644 --- a/chord_metadata_service/restapi/tests/test_api.py +++ b/chord_metadata_service/restapi/tests/test_api.py @@ -15,8 +15,6 @@ from chord_metadata_service.phenopackets.tests import constants as ph_c from chord_metadata_service.experiments import models as exp_m from chord_metadata_service.experiments.tests import constants as exp_c -from chord_metadata_service.mcode import models as mcode_m -from chord_metadata_service.mcode.tests import constants as mcode_c from .constants import ( CONFIG_PUBLIC_TEST, @@ -131,56 +129,6 @@ def test_search_overview(self): self.assertIn(ph_c.VALID_DISEASE_1['term']['label'], response_obj['diseases']['term']) -class McodeOverviewTest(APITestCase): - # create 2 mcodepackets for 2 individuals - def setUp(self) -> None: - self.individual = ph_m.Individual.objects.create(**mcode_c.VALID_INDIVIDUAL) - self.individual_2 = ph_m.Individual.objects.create(**ph_c.VALID_INDIVIDUAL_2) - self.labs_vital = mcode_m.LabsVital.objects.create(**mcode_c.valid_labs_vital(self.individual)) - self.genomics_report = mcode_m.GenomicsReport.objects.create(**mcode_c.valid_genetic_report()) - self.cancer_condition = mcode_m.CancerCondition.objects.create(**mcode_c.valid_cancer_condition()) - self.cancer_condition_2 = mcode_m.CancerCondition.objects.create(**mcode_c.VALID_CANCER_CONDITION) - self.tnm_staging = mcode_m.TNMStaging.objects.create(**mcode_c.invalid_tnm_staging(self.cancer_condition)) - self.cancer_related_procedure = mcode_m.CancerRelatedProcedure.objects.create( - **mcode_c.valid_cancer_related_procedure() - ) - self.medication_statement = mcode_m.MedicationStatement.objects.create(**mcode_c.valid_medication_statement()) - self.mcodepacket_1 = mcode_m.MCodePacket.objects.create( - id="mcodepacket:01", - subject=self.individual, - genomics_report=self.genomics_report, - cancer_disease_status={ - "id": "SNOMED:268910001", - "label": "Patient's condition improved" - }, - cancer_condition=self.cancer_condition - ) - self.mcodepacket_1.cancer_related_procedures.set([self.cancer_related_procedure]) - self.mcodepacket_1.medication_statement.set([self.medication_statement]) - self.mcodepacket_2 = mcode_m.MCodePacket.objects.create( - id="mcodepacket:02", - subject=self.individual_2, - cancer_disease_status={ - "id": "SNOMED:359746009", - "label": "Patient's condition stable" - }, - cancer_condition=self.cancer_condition_2 - ) - - def test_mcode_overview(self): - response = self.client.get("/api/mcode_overview") - response_obj = response.json() - self.assertEqual(response.status_code, status.HTTP_200_OK) - self.assertIsInstance(response_obj, dict) - # mcodepackets - self.assertEqual(response_obj["mcodepackets"], 2) - self.assertEqual(response_obj["data_type_specific"]["cancer_conditions"]["count"], 2) - self.assertEqual(response_obj["data_type_specific"]["cancer_related_procedure_types"]["count"], 1) - self.assertEqual(response_obj["data_type_specific"]["cancer_related_procedures"]["count"], 1) - self.assertEqual(response_obj["data_type_specific"]["cancer_disease_status"]["count"], 2) - self.assertEqual(response_obj["data_type_specific"]["individuals"]["count"], 2) - - class PublicSearchFieldsTest(APITestCase): def setUp(self) -> None: diff --git a/chord_metadata_service/restapi/tests/test_argo.py b/chord_metadata_service/restapi/tests/test_argo.py deleted file mode 100644 index 0363ab298..000000000 --- a/chord_metadata_service/restapi/tests/test_argo.py +++ /dev/null @@ -1,293 +0,0 @@ -from copy import deepcopy - -from django.db.models import Q -from rest_framework import status -from rest_framework.test import APITestCase - -from chord_metadata_service.patients.models import Individual -from chord_metadata_service.patients.tests.constants import VALID_INDIVIDUAL -from chord_metadata_service.mcode.models import ( - CancerCondition, - TNMStaging, - CancerRelatedProcedure, - MedicationStatement, - MCodePacket -) -from chord_metadata_service.mcode.tests.constants import ( - valid_cancer_condition, - invalid_tnm_staging, - valid_cancer_related_procedure, - valid_medication_statement, - valid_genetic_specimen, -) -from chord_metadata_service.restapi.argo_utils import argo_administrative_gender -from chord_metadata_service.restapi.tests.utils import get_response - - -class ARGOMcodepacketTest(APITestCase): - """ Test module for testing conversion of mcodepacket to argo fields.""" - - def setUp(self) -> None: - self.subject = Individual.objects.create(**VALID_INDIVIDUAL) - self.cancer_condition = CancerCondition.objects.create(**valid_cancer_condition()) - cancer_condition_2 = valid_cancer_condition() - cancer_condition_2["id"] = "cancer_condition:02" - cancer_condition_2["extra_properties"] = { - "lymph_nodes_examined_status": "Cannot be determined", - "age_at_diagnosis": 47 - } - self.cancer_condition_2 = CancerCondition.objects.create(**cancer_condition_2) - # make tnm staging valid - # tnm staging 1 clinical - tnm_staging = invalid_tnm_staging(self.cancer_condition_2) - for item in ["stage_group", "primary_tumor_category", "regional_nodes_category", "distant_metastases_category"]: - tnm_staging[item] = { - "data_value": { - "id": "001", - "label": "test stage group" - } - } - self.tnm_staging = TNMStaging.objects.create(**tnm_staging) - # tnm staging 2 pathologic - tnm_staging_2 = deepcopy(tnm_staging) - tnm_staging_2["id"] = "tnm_staging:02" - tnm_staging_2["tnm_type"] = "pathologic" - self.tnm_staging_2 = TNMStaging.objects.create(**tnm_staging_2) - # tnm staging 3 clinical - tnm_staging_3 = deepcopy(tnm_staging) - tnm_staging_3["id"] = "tnm_staging:03" - self.tnm_staging_3 = TNMStaging.objects.create(**tnm_staging_3) - # tnm staging 4 pathologic - tnm_staging_4 = deepcopy(tnm_staging) - tnm_staging_4["id"] = "tnm_staging:04" - tnm_staging_4["tnm_type"] = "pathologic" - for item in ["stage_group", "primary_tumor_category", "regional_nodes_category", "distant_metastases_category"]: - tnm_staging_4[item] = { - "data_value": { - "id": "002", - "label": "test stage group 002" - } - } - self.tnm_staging_4 = TNMStaging.objects.create(**tnm_staging_4) - - self.cancer_related_procedure = CancerRelatedProcedure.objects.create(**valid_cancer_related_procedure()) - self.medication_statement = MedicationStatement.objects.create(**valid_medication_statement()) - self.mcodepacket = MCodePacket.objects.create( - id="mcodepacket:01", - subject=self.subject, - cancer_disease_status={ - "id": "001", - "label": "patient's condition improved" - }, - cancer_condition=self.cancer_condition - ) - self.mcodepacket.cancer_related_procedures.set([self.cancer_related_procedure]) - self.mcodepacket.medication_statement.set([self.medication_statement]) - - def test_get_argo(self): - get_resp = self.client.get("/api/mcodepackets?format=argo") - self.assertEqual(get_resp.status_code, status.HTTP_200_OK) - get_resp_obj = get_resp.json() - # donor - self.assertEqual(get_resp_obj["composition_objects"][0]["donor"]["submitter_donor_id"], "patient:1") - self.assertEqual(get_resp_obj["composition_objects"][0]["donor"]["gender"], "Female") - # primary_diagnoses - self.assertIn("Carcinosarcoma", - get_resp_obj["composition_objects"][0]["primary_diagnoses"][0]["cancer_type_code"]["label"]) - # ===================== DISABLED ASSERTIONS ==================== - # The following assertions have been disabled when the mCode cancer condition format - # has been moved from a list to a single value. - # >>>>>>>>>>>>>>>>>>>>>>>> - # tnm staging clinical - # second primary diagnosis (cancer condition 2) has two clinical tnm stagings - # for field in ["clinical_stage_group", "clinical_t_category", - # "clinical_n_category", "clinical_m_category"]: - # self.assertIsInstance(get_resp_obj["composition_objects"][0]["primary_diagnoses"][1][field], - # list) - # self.assertEqual(len(get_resp_obj["composition_objects"][0]["primary_diagnoses"][1][field]), 2) - # <<<<<<<<<<<<<<<<<<<<<<<<< - # tnm staging pathlogical - self.assertEqual(len(TNMStaging.objects.all()), 4) - self.assertEqual(TNMStaging.objects.filter(tnm_type="pathologic").count(), 2) - self.assertEqual(TNMStaging.objects.filter(cancer_condition__id="cancer_condition:02").count(), 4) - self.assertEqual(TNMStaging.objects.filter - (Q(cancer_condition__id="cancer_condition:02") & Q(tnm_type="pathologic")).count(), 2) - # ===================== DISABLED ASSERTIONS ==================== - # The following assertions have been disabled when the mCode cancer condition format - # has been moved from a list to a single value. - # `primary_diagnoses` is composed from the cancer_condition field - # >>>>>>>>>>>>>>>>>>>>>>>> - # for field in ["pathological_stage_group", "pathological_t_category", - # "pathological_n_category", "pathological_m_category"]: - # self.assertIsInstance(get_resp_obj["composition_objects"][0]["primary_diagnoses"][1]["specimen"][field], - # list) - # self.assertEqual( - # len(get_resp_obj["composition_objects"][0]["primary_diagnoses"][1]["specimen"][field]), 2 - # ) - # <<<<<<<<<<<<<<<<<<<<<<<<<< - # treatments - self.assertEqual("Radiation therapy", - get_resp_obj["composition_objects"][0]["treatments"][0]["treatment_type"]) - self.assertIn("Betatron teleradiotherapy", - get_resp_obj["composition_objects"][0]["treatments"][0]["radiation_therapy_modality"]["label"]) - self.assertEqual("Mammary gland sinus", - get_resp_obj["composition_objects"][0]["treatments"][0] - ["anatomical_site_irradiated"][0]["label"]) - self.assertIn("Curative", - get_resp_obj["composition_objects"][0]["treatments"][0]["treatment_intent"]["label"]) - # ===================== DISABLED ASSERTIONS ==================== - # The following assertions have been disabled when the mCode cancer condition format - # has been moved from a list to a single value. - # `primary_diagnoses` is composed from the cancer_condition field - # >>>>>>>>>>>>>>>>>>>>>>>> - # self.assertIsInstance(get_resp_obj["composition_objects"][0]["primary_diagnoses"][1]["specimen"], - # dict) - # <<<<<<<<<<<<<<<<<<<<<<<< - # therapies - self.assertIsInstance( - get_resp_obj["composition_objects"][0]["immunotherapies_chemotherapies_hormone_therapies"], - list - ) - self.assertIn( - "Verapamil", - get_resp_obj["composition_objects"][0]["immunotherapies_chemotherapies_hormone_therapies"][0] - ["drug_rxnormcui"]["label"] - ) - - -class ARGODonorTest(APITestCase): - """ Test module for testing conversion of individual to argo donor.""" - - def setUp(self): - self.donor = VALID_INDIVIDUAL - valid_individual_2 = deepcopy(VALID_INDIVIDUAL) - valid_individual_2["id"] = "patient:2" - valid_individual_2["sex"] = "OTHER_SEX" - # test if argo fields were saved to extra_properties - valid_individual_2["extra_properties"] = { - "cause_of_death": "Unknown", - "survival_time": 2, - "primary_site": "Breast" - } - self.donor_2 = valid_individual_2 - invalid_individual_3 = deepcopy(VALID_INDIVIDUAL) - invalid_individual_3["id"] = "patient:3" - invalid_individual_3["sex"] = "No value" - self.donor_3 = invalid_individual_3 - - def test_get_argo(self): - create_object_response = get_response("individuals-list", self.donor) - self.assertEqual(create_object_response.status_code, status.HTTP_201_CREATED) - get_resp = self.client.get("/api/individuals?format=argo") - self.assertEqual(get_resp.status_code, status.HTTP_200_OK) - get_resp_obj = get_resp.json() - for donor in get_resp_obj["donors"]: - self.assertIsNotNone(donor["gender"]) - self.assertIsNotNone(donor["submitter_donor_id"]) - self.assertIsNotNone(donor["vital_status"]) - - def test_gender_condition_1(self): - create_object_response = get_response("individuals-list", self.donor_2) - self.assertEqual(create_object_response.status_code, status.HTTP_201_CREATED) - get_resp = self.client.get("/api/individuals/patient:2?format=argo") - self.assertEqual(get_resp.status_code, status.HTTP_200_OK) - get_resp_obj = get_resp.json() - self.assertIsNotNone(get_resp_obj["gender"]) - self.assertEqual(get_resp_obj["gender"], "Other") - self.assertEqual(get_resp_obj["submitter_donor_id"], "patient:2") - self.assertEqual(get_resp_obj["cause_of_death"], "Unknown") - self.assertEqual(get_resp_obj["survival_time"], 2) - self.assertEqual(get_resp_obj["primary_site"], "Breast") - - def test_gender_condition_2(self): - create_object_response = get_response("individuals-list", self.donor_3) - self.assertEqual(create_object_response.status_code, status.HTTP_400_BAD_REQUEST) - - def test_value_error(self): - with self.assertRaises(ValueError): - argo_administrative_gender(self.donor_3["sex"]) - - -class ARGOSpecimenTest(APITestCase): - """ Test module for testing conversion of genetic specimen to argo specimen.""" - - def setUp(self): - self.specimen = valid_genetic_specimen("specimen:01") - - def test_get_argo(self): - create_object_response = get_response("geneticspecimens-list", self.specimen) - self.assertEqual(create_object_response.status_code, status.HTTP_201_CREATED) - get_resp = self.client.get("/api/geneticspecimens?format=argo") - self.assertEqual(get_resp.status_code, status.HTTP_200_OK) - get_resp_obj = get_resp.json() - self.assertIsNotNone(get_resp_obj["specimens"][0]["submitter_specimen_id"]) - self.assertIsInstance(get_resp_obj["specimens"][0]["submitter_specimen_id"], str) - self.assertIsNotNone(get_resp_obj["specimens"][0]["specimen_type"]) - self.assertIsInstance(get_resp_obj["specimens"][0]["specimen_type"], dict) - self.assertIsNotNone(get_resp_obj["specimens"][0]["specimen_tissue_source"]) - self.assertIsInstance(get_resp_obj["specimens"][0]["specimen_tissue_source"], dict) - self.assertIsNotNone(get_resp_obj["specimens"][0]["specimen_laterality"]) - self.assertIsInstance(get_resp_obj["specimens"][0]["specimen_laterality"], dict) - - -class ARGOPrimaryDiagnosisTest(APITestCase): - """ Test module for testing conversion of cancer condition to argo primary diagnosis.""" - - def setUp(self): - self.primary_diagnosis = valid_cancer_condition() - - def test_get_argo(self): - create_object_response = get_response("cancerconditions-list", self.primary_diagnosis) - self.assertEqual(create_object_response.status_code, status.HTTP_201_CREATED) - get_resp = self.client.get("/api/cancerconditions?format=argo") - self.assertEqual(get_resp.status_code, status.HTTP_200_OK) - get_resp_obj = get_resp.json() - self.assertIsNotNone(get_resp_obj["primary_diagnoses"][0]["submitter_primary_diagnosis_id"]) - self.assertIsInstance(get_resp_obj["primary_diagnoses"][0]["submitter_primary_diagnosis_id"], str) - self.assertIsNotNone(get_resp_obj["primary_diagnoses"][0]["cancer_type_code"]) - self.assertIsInstance(get_resp_obj["primary_diagnoses"][0]["cancer_type_code"], dict) - - -class ARGOTreatmentTest(APITestCase): - """ Test module for testing conversion of cancer related procedure to argo treatment.""" - - def setUp(self): - self.treatment = valid_cancer_related_procedure() - - def test_get_argo(self): - create_object_response = get_response("cancerrelatedprocedures-list", self.treatment) - self.assertEqual(create_object_response.status_code, status.HTTP_201_CREATED) - get_resp = self.client.get("/api/cancerrelatedprocedures?format=argo") - self.assertEqual(get_resp.status_code, status.HTTP_200_OK) - get_resp_obj = get_resp.json() - self.assertIsNotNone(get_resp_obj["treatments"][0]["submitter_treatment_id"]) - self.assertIsInstance(get_resp_obj["treatments"][0]["submitter_treatment_id"], str) - self.assertIsNotNone(get_resp_obj["treatments"][0]["treatment_type"]) - self.assertIsInstance(get_resp_obj["treatments"][0]["treatment_type"], str) - # radiation procedure only - self.assertEqual(get_resp_obj["treatments"][0]["treatment_type"], "Radiation therapy") - self.assertIsNotNone(get_resp_obj["treatments"][0]["radiation_therapy_modality"]) - self.assertIsInstance(get_resp_obj["treatments"][0]["radiation_therapy_modality"], dict) - self.assertIsNotNone(get_resp_obj["treatments"][0]["anatomical_site_irradiated"]) - # TODO run schema validation on ingest and check type - # self.assertIsInstance(get_resp_obj["treatments"][0]["anatomical_site_irradiated"], dict) - - -class ARGOTherapyTest(APITestCase): - """ Test module for testing conversion of medication statement to argo -therapy.""" - - def setUp(self): - self.therapy = valid_medication_statement() - - def test_get_argo(self): - create_object_response = get_response("medicationstatements-list", self.therapy) - self.assertEqual(create_object_response.status_code, status.HTTP_201_CREATED) - get_resp = self.client.get("/api/medicationstatements?format=argo") - self.assertEqual(get_resp.status_code, status.HTTP_200_OK) - results = get_resp.json()["immunotherapies_chemotherapies_hormone_therapies"] - self.assertIsNotNone(results[0]["submitter_treatment_id"]) - self.assertIsInstance(results[0]["submitter_treatment_id"], str) - self.assertIsNotNone(results[0]["drug_rxnormcui"]) - self.assertIsInstance(results[0]["drug_rxnormcui"], dict) - self.assertIn("label", results[0]["drug_rxnormcui"]) - self.assertIn("id", results[0]["drug_rxnormcui"]) diff --git a/chord_metadata_service/restapi/urls.py b/chord_metadata_service/restapi/urls.py index 5651dacbb..3a37cd4bd 100644 --- a/chord_metadata_service/restapi/urls.py +++ b/chord_metadata_service/restapi/urls.py @@ -3,7 +3,6 @@ from chord_metadata_service.chord import api_views as chord_views from chord_metadata_service.experiments import api_views as experiment_views -from chord_metadata_service.mcode import api_views as mcode_views from chord_metadata_service.patients import api_views as individual_views from chord_metadata_service.phenopackets import api_views as phenopacket_views from chord_metadata_service.phenopackets.autocomplete_views import ( @@ -14,7 +13,6 @@ from chord_metadata_service.resources import api_views as resources_views from .api_views import ( overview, - mcode_overview, public_search_fields, public_overview, public_dataset, @@ -60,19 +58,6 @@ router.register(r'diagnoses', phenopacket_views.DiagnosisViewSet, basename="diagnoses") router.register(r'interpretations', phenopacket_views.InterpretationViewSet, basename="interpretations") -# mCode app urls -router.register(r'geneticspecimens', mcode_views.GeneticSpecimenViewSet, basename="geneticspecimens") -router.register(r'cancergeneticvariants', mcode_views.CancerGeneticVariantViewSet, basename="cancergeneticvariants") -router.register(r'genomicregionsstudied', mcode_views.GenomicRegionStudiedViewSet, basename="genomicregionsstudied") -router.register(r'genomicsreports', mcode_views.GenomicsReportViewSet, basename="genomicsreports") -router.register(r'labsvital', mcode_views.LabsVitalViewSet, basename="labsvital") -router.register(r'cancerconditions', mcode_views.CancerConditionViewSet, basename="cancerconditions") -router.register(r'tnmstaging', mcode_views.TNMStagingViewSet, basename="tnmstaging") -router.register(r'cancerrelatedprocedures', mcode_views.CancerRelatedProcedureViewSet, - basename="cancerrelatedprocedures") -router.register(r'medicationstatements', mcode_views.MedicationStatementViewSet, basename="medicationstatements") -router.register(r'mcodepackets', mcode_views.MCodePacketViewSet, basename="mcodepackets") - # Resources app urls router.register(r'resources', resources_views.ResourceViewSet) @@ -85,15 +70,12 @@ name="chord-phenopacket-schema"), path('experiment_schema', experiment_views.get_experiment_schema, name="experiment-schema"), - path('mcode_schema', mcode_views.get_mcode_schema, - name="mcode-schema"), # extra properties schema types path('extra_properties_schema_types', extra_properties_schema_types, name="extra-properties-schema-types"), # overviews (statistics) path('overview', overview, name="overview"), - path('mcode_overview', mcode_overview, name="mcode-overview"), path('search_overview', search_overview, name="search-overview"), # autocomplete URLs diff --git a/pyproject.toml b/pyproject.toml index 701b3e5f1..8882dc327 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -20,7 +20,6 @@ include = [ "chord_metadata_service/chord/workflows/wdls/*.wdl", "chord_metadata_service/chord/tests/*.json", "chord_metadata_service/dats/*", - "chord_metadata_service/mcode/tests/*.json", "chord_metadata_service/restapi/tests/*.json", ] repository = "https://github.com/bento-platform/katsu" diff --git a/scripts/remove_from_db.py b/scripts/remove_from_db.py index 26ae6b623..9e24a4840 100644 --- a/scripts/remove_from_db.py +++ b/scripts/remove_from_db.py @@ -18,7 +18,6 @@ def main(): script = ( "from chord_metadata_service.chord.models import *;" "from chord_metadata_service.experiments.models import *;" - "from chord_metadata_service.mcode.models import *;" "from chord_metadata_service.patients.models import *;" "from chord_metadata_service.phenopackets.models import *;" "from chord_metadata_service.resources.models import *;" diff --git a/swagger_schema.json b/swagger_schema.json index 9cefb26f5..45d57f916 100644 --- a/swagger_schema.json +++ b/swagger_schema.json @@ -8817,423 +8817,6 @@ ] } }, - "/api/mcode_overview": { - "get": { - "operationId": "api_mcode_overview_list", - "responses": { - "200": { - "description": "" - } - }, - "parameters": [], - "description": "Overview of all mCode data in the database", - "summary": "Overview of all mCode data in the database", - "tags": [ - "api" - ] - } - }, - "/api/mcode_schema": { - "get": { - "operationId": "api_mcode_schema_list", - "responses": { - "200": { - "description": "" - } - }, - "parameters": [], - "description": "Mcodepacket schema", - "summary": "Mcodepacket schema", - "tags": [ - "api" - ] - } - }, - "/api/mcodepackets": { - "get": { - "operationId": "api_mcodepackets_list", - "responses": { - "200": { - "description": "" - } - }, - "parameters": [ - { - "name": "page", - "required": false, - "in": "query", - "description": "A page number within the paginated result set.", - "type": "integer" - }, - { - "name": "page_size", - "required": false, - "in": "query", - "description": "Number of results to return per page.", - "type": "integer" - }, - { - "name": "datasets", - "required": false, - "in": "query", - "description": "", - "type": "string" - }, - { - "name": "authorized_datasets", - "required": false, - "in": "query", - "description": "", - "type": "string" - } - ], - "tags": [ - "api" - ] - }, - "post": { - "operationId": "api_mcodepackets_create", - "responses": { - "201": { - "description": "" - } - }, - "parameters": [ - { - "name": "data", - "in": "body", - "schema": { - "type": "object", - "properties": { - "id": { - "description": "An arbitrary identifier for the mcodepacket.", - "type": "string" - }, - "date_of_death": { - "description": "An indication that the patient is no longer living, given by a date of death or boolean.", - "type": "string" - }, - "cancer_disease_status": { - "description": "A clinician's qualitative judgment on the current trend of the cancer, e.g., whether it is stable, worsening (progressing), or improving (responding).", - "type": "object" - }, - "extra_properties": { - "description": "Extra properties that are not supported by current schema.", - "type": "object" - }, - "subject": { - "description": "An individual who is a subject of mcodepacket.", - "type": "string" - }, - "genomics_report": { - "description": "A genomics report associated with an Individual.", - "type": "string" - }, - "table": { - "description": "", - "type": "string" - }, - "cancer_condition": { - "description": "An Individual's cancer condition.", - "type": "array", - "items": { - "type": "string" - } - }, - "cancer_related_procedures": { - "description": "A radiological or surgical procedures addressing a cancer condition.", - "type": "array", - "items": { - "type": "string" - } - }, - "medication_statement": { - "description": "Medication treatment addressed to an Individual.", - "type": "array", - "items": { - "type": "string" - } - } - }, - "required": [ - "id", - "subject" - ] - } - } - ], - "consumes": [ - "application/json" - ], - "tags": [ - "api" - ] - } - }, - "/api/mcodepackets/{id}": { - "get": { - "operationId": "api_mcodepackets_read", - "responses": { - "200": { - "description": "" - } - }, - "parameters": [ - { - "name": "id", - "required": true, - "in": "path", - "description": "An arbitrary identifier for the mcodepacket.", - "type": "string" - }, - { - "name": "datasets", - "required": false, - "in": "query", - "description": "", - "type": "string" - }, - { - "name": "authorized_datasets", - "required": false, - "in": "query", - "description": "", - "type": "string" - } - ], - "tags": [ - "api" - ] - }, - "put": { - "operationId": "api_mcodepackets_update", - "responses": { - "200": { - "description": "" - } - }, - "parameters": [ - { - "name": "id", - "required": true, - "in": "path", - "description": "An arbitrary identifier for the mcodepacket.", - "type": "string" - }, - { - "name": "datasets", - "required": false, - "in": "query", - "description": "", - "type": "string" - }, - { - "name": "authorized_datasets", - "required": false, - "in": "query", - "description": "", - "type": "string" - }, - { - "name": "data", - "in": "body", - "schema": { - "type": "object", - "properties": { - "id": { - "description": "An arbitrary identifier for the mcodepacket.", - "type": "string" - }, - "date_of_death": { - "description": "An indication that the patient is no longer living, given by a date of death or boolean.", - "type": "string" - }, - "cancer_disease_status": { - "description": "A clinician's qualitative judgment on the current trend of the cancer, e.g., whether it is stable, worsening (progressing), or improving (responding).", - "type": "object" - }, - "extra_properties": { - "description": "Extra properties that are not supported by current schema.", - "type": "object" - }, - "subject": { - "description": "An individual who is a subject of mcodepacket.", - "type": "string" - }, - "genomics_report": { - "description": "A genomics report associated with an Individual.", - "type": "string" - }, - "table": { - "description": "", - "type": "string" - }, - "cancer_condition": { - "description": "An Individual's cancer condition.", - "type": "array", - "items": { - "type": "string" - } - }, - "cancer_related_procedures": { - "description": "A radiological or surgical procedures addressing a cancer condition.", - "type": "array", - "items": { - "type": "string" - } - }, - "medication_statement": { - "description": "Medication treatment addressed to an Individual.", - "type": "array", - "items": { - "type": "string" - } - } - }, - "required": [ - "id", - "subject" - ] - } - } - ], - "consumes": [ - "application/json" - ], - "tags": [ - "api" - ] - }, - "patch": { - "operationId": "api_mcodepackets_partial_update", - "responses": { - "200": { - "description": "" - } - }, - "parameters": [ - { - "name": "id", - "required": true, - "in": "path", - "description": "An arbitrary identifier for the mcodepacket.", - "type": "string" - }, - { - "name": "datasets", - "required": false, - "in": "query", - "description": "", - "type": "string" - }, - { - "name": "authorized_datasets", - "required": false, - "in": "query", - "description": "", - "type": "string" - }, - { - "name": "data", - "in": "body", - "schema": { - "type": "object", - "properties": { - "id": { - "description": "An arbitrary identifier for the mcodepacket.", - "type": "string" - }, - "date_of_death": { - "description": "An indication that the patient is no longer living, given by a date of death or boolean.", - "type": "string" - }, - "cancer_disease_status": { - "description": "A clinician's qualitative judgment on the current trend of the cancer, e.g., whether it is stable, worsening (progressing), or improving (responding).", - "type": "object" - }, - "extra_properties": { - "description": "Extra properties that are not supported by current schema.", - "type": "object" - }, - "subject": { - "description": "An individual who is a subject of mcodepacket.", - "type": "string" - }, - "genomics_report": { - "description": "A genomics report associated with an Individual.", - "type": "string" - }, - "table": { - "description": "", - "type": "string" - }, - "cancer_condition": { - "description": "An Individual's cancer condition.", - "type": "array", - "items": { - "type": "string" - } - }, - "cancer_related_procedures": { - "description": "A radiological or surgical procedures addressing a cancer condition.", - "type": "array", - "items": { - "type": "string" - } - }, - "medication_statement": { - "description": "Medication treatment addressed to an Individual.", - "type": "array", - "items": { - "type": "string" - } - } - } - } - } - ], - "consumes": [ - "application/json" - ], - "tags": [ - "api" - ] - }, - "delete": { - "operationId": "api_mcodepackets_delete", - "responses": { - "204": { - "description": "" - } - }, - "parameters": [ - { - "name": "id", - "required": true, - "in": "path", - "description": "An arbitrary identifier for the mcodepacket.", - "type": "string" - }, - { - "name": "datasets", - "required": false, - "in": "query", - "description": "", - "type": "string" - }, - { - "name": "authorized_datasets", - "required": false, - "in": "query", - "description": "", - "type": "string" - } - ], - "tags": [ - "api" - ] - } - }, "/api/medicationstatements": { "get": { "operationId": "api_medicationstatements_list", @@ -14409,4 +13992,4 @@ "type": "basic" } } -} \ No newline at end of file +}