Merge pull request #103 from c3g/mcode

Mcode app

chord_metadata_service/mcode/admin.py

@@ -0,0 +1,44 @@
+from django.contrib import admin
+from .models import *
+
+
+@admin.register(GeneticVariantTested)
+class GeneticVariantTestedAdmin(admin.ModelAdmin):
+    pass
+
+
+@admin.register(GeneticVariantFound)
+class GeneticVariantFoundAdmin(admin.ModelAdmin):
+    pass
+
+
+@admin.register(GenomicsReport)
+class GenomicsReportAdmin(admin.ModelAdmin):
+    pass
+
+
+@admin.register(LabsVital)
+class LabsVitalAdmin(admin.ModelAdmin):
+    pass
+
+
+@admin.register(CancerCondition)
+class CancerConditionAdmin(admin.ModelAdmin):
+    pass
+
+
+@admin.register(TNMStaging)
+class TNMStagingAdmin(admin.ModelAdmin):
+    pass
+
+
+@admin.register(CancerRelatedProcedure)
+class CancerRelatedProcedureAdmin(admin.ModelAdmin):
+    pass
+
+
+@admin.register(MedicationStatement)
+class MedicationStatementAdmin(admin.ModelAdmin):
+    pass
+
+

chord_metadata_service/mcode/api_views.py

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+from rest_framework import viewsets
+from rest_framework.settings import api_settings
+from .serializers import *
+from chord_metadata_service.restapi.api_renderers import (
+    PhenopacketsRenderer
+)
+from chord_metadata_service.restapi.pagination import LargeResultsSetPagination
+
+
+class McodeModelViewSet(viewsets.ModelViewSet):
+    pagination_class = LargeResultsSetPagination
+    renderer_classes = (*api_settings.DEFAULT_RENDERER_CLASSES, PhenopacketsRenderer)
+
+
+class GeneticVariantTestedViewSet(McodeModelViewSet):
+    queryset = GeneticVariantTested.objects.all()
+    serializer_class = GeneticVariantTestedSerializer
+
+
+class GeneticVariantFoundViewSet(McodeModelViewSet):
+    queryset = GeneticVariantFound.objects.all()
+    serializer_class = GeneticVariantFoundSerializer
+
+
+class GenomicsReportViewSet(McodeModelViewSet):
+    queryset = GenomicsReport.objects.all()
+    serializer_class = GenomicsReportSerializer
+
+
+class LabsVitalViewSet(McodeModelViewSet):
+    queryset = LabsVital.objects.all()
+    serializer_class = LabsVitalSerializer
+
+
+class CancerConditionViewSet(McodeModelViewSet):
+    queryset = CancerCondition.objects.all()
+    serializer_class = CancerConditionSerializer
+
+
+class TNMStagingViewSet(McodeModelViewSet):
+    queryset = TNMStaging.objects.all()
+    serializer_class = TNMStagingSerializer
+
+
+class CancerRelatedProcedureViewSet(McodeModelViewSet):
+    queryset = CancerRelatedProcedure.objects.all()
+    serializer_class = CancerRelatedProcedureSerializer
+
+
+class MedicationStatementViewSet(McodeModelViewSet):
+    queryset = MedicationStatement.objects.all()
+    serializer_class = MedicationStatementSerializer
+
+
+class MCodePacketViewSet(McodeModelViewSet):
+    queryset = MCodePacket.objects.all()
+    serializer_class = MCodePacketSerializer

chord_metadata_service/mcode/apps.py

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+from django.apps import AppConfig
+
+
+class McodeConfig(AppConfig):
+    name = 'chord_metadata_service.mcode'

chord_metadata_service/mcode/descriptions.py

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+# Most parts of this text are taken from the mCODE:Minimal Common Oncology Data Elements Data Dictionary.
+# The mCODE is made available under the Creative Commons 0 "No Rights Reserved" license https://creativecommons.org/share-your-work/public-domain/cc0/
+
+# Portions of this text copyright (c) 2019-2020 the Canadian Centre for Computational Genomics; licensed under the
+# GNU Lesser General Public License version 3.
+
+from chord_metadata_service.restapi.description_utils import EXTRA_PROPERTIES
+
+GENETIC_VARIANT_TESTED = {
+    "description": "A description of an alteration in the most common DNA nucleotide sequence.",
+    "properties": {
+        "id": "An arbitrary identifier for the genetic variant tested.",
+        "gene_studied": "A gene targeted for mutation analysis, identified in HUGO Gene Nomenclature Committee "
+                        "(HGNC) notation.",
+        "method": "An ontology or controlled vocabulary term to identify the method used to perform the genetic test. "
+                  "Accepted value set: NCIT.",
+        "variant_tested_identifier": "The variation ID assigned by HGVS, for example, 360448 is the identifier for "
+                                     "NM_005228.4(EGFR):c.-237A>G (single nucleotide variant in EGFR).",
+        "variant_tested_hgvs_name": "Symbolic representation of the variant used in HGVS, for example, "
+                                    "NM_005228.4(EGFR):c.-237A>G for HVGS variation ID 360448.",
+        "variant_tested_description": "Description of the variant.",
+        "data_value": "An ontology or controlled vocabulary term to identify positive or negative value for"
+                      "the mutation. Accepted value set: SNOMED CT.",
+        **EXTRA_PROPERTIES
+    }
+}
+
+GENETIC_VARIANT_FOUND = {
+    "description": "Description of single discrete variant tested.",
+    "properties": {
+        "id": "An arbitrary identifier for the genetic variant found.",
+        "method": "An ontology or controlled vocabulary term to identify the method used to perform the genetic test. "
+                  "Accepted value set: NCIT.",
+        "variant_found_identifier": "The variation ID assigned by HGVS, for example, 360448 is the identifier for "
+                                    "NM_005228.4(EGFR):c.-237A>G (single nucleotide variant in EGFR). "
+                                    "Accepted value set: ClinVar.",
+        "variant_found_hgvs_name": "Symbolic representation of the variant used in HGVS, for example, "
+                                   "NM_005228.4(EGFR):c.-237A>G for HVGS variation ID 360448.",
+        "variant_found_description": "Description of the variant.",
+        "genomic_source_class": "An ontology or controlled vocabulary term to identify the genomic class of the "
+                                "specimen being analyzed.",
+        **EXTRA_PROPERTIES
+    }
+}
+
+GENOMICS_REPORT = {
+    "description": "Genetic Analysis Summary.",
+    "properties": {
+        "id": "An arbitrary identifier for the genetics report.",
+        "test_name": "An ontology or controlled vocabulary term to identify the laboratory test. "
+                     "Accepted value sets: LOINC, GTR.",
+        "performing_organization_name": "The name of the organization  producing the genomics report.",
+        "specimen_type": "An ontology or controlled vocabulary term to identify the type of material the specimen "
+                         "contains or consists of. Accepted value set: HL7 Version 2 and Specimen Type.",
+        "genetic_variant_tested": "A test for a specific mutation on a particular gene.",
+        "genetic_variant_found": "Records an alteration in the most common DNA nucleotide sequence.",
+        **EXTRA_PROPERTIES
+    }
+}
+
+LABS_VITAL = {
+    "description": "A description of tests performed on patient.",
+    "properties": {
+        "id": "An arbitrary identifier for the labs/vital tests.",
+        "individual": "The individual who is the subject of the tests.",
+        "body_height": "The patient\'s height.",
+        "body_weight": "The patient\'s weight.",
+        "cbc_with_auto_differential_panel": "Reference to a laboratory observation in the CBC with Auto Differential"
+                                            "Panel test.",
+        "comprehensive_metabolic_2000": "Reference to a laboratory observation in the CMP 2000 test.",
+        "blood_pressure_diastolic": "The blood pressure after the contraction of the heart while the chambers of "
+                                    "the heart refill with blood, when the pressure is lowest.",
+        "blood_pressure_systolic": "The blood pressure during the contraction of the left ventricle of the heart, "
+                                   "when blood pressure is at its highest.",
+        "tumor_marker_test": "An ontology or controlled vocabulary term to identify tumor marker test.",
+        **EXTRA_PROPERTIES
+    }
+}
+
+CANCER_CONDITION = {
+    "description": "A description of history of primary or secondary cancer conditions.",
+    "properties": {
+        "id": "An arbitrary identifier for the cancer condition.",
+        "condition_type": "Cancer condition type: primary or secondary.",
+        "body_location_code": "Code for the body location, optionally pre-coordinating laterality or direction. "
+                              "Accepted ontologies: SNOMED CT, ICD-O-3 and others.",
+        "clinical_status": "A flag indicating whether the condition is active or inactive, recurring, in remission, "
+                           "or resolved (as of the last update of the Condition). Accepted code system: "
+                           "http://terminology.hl7.org/CodeSystem/condition-clinical",
+        "condition_code": "A code describing the type of primary or secondary malignant neoplastic disease.",
+        "date_of_diagnosis": "The date the disease was first clinically recognized with sufficient certainty, "
+                             "regardless of whether it was fully characterized at that time.",
+        "histology_morphology_behavior": "A description of the morphologic and behavioral characteristics of "
+                                         "the cancer. Accepted ontologies: SNOMED CT, ICD-O-3 and others.",
+        **EXTRA_PROPERTIES
+    }
+}
+
+TNM_STAGING = {
+    "description": "A description of the cancer spread in a patient's body.",
+    "properties": {
+        "id": "An arbitrary identifier for the TNM staging.",
+        "tnm_type": "TNM type: clinical or pathological.",
+        "stage_group": "The extent of the cancer in the body, according to the TNM classification system."
+                       "Accepted ontologies: SNOMED CT, AJCC and others.",
+        "primary_tumor_category": "Category of the primary tumor, based on its size and extent. "
+                                  "Accepted ontologies: SNOMED CT, AJCC and others.",
+        "regional_nodes_category": "Category of the presence or absence of metastases in regional lymph nodes. "
+                                   "Accepted ontologies: SNOMED CT, AJCC and others.",
+        "distant_metastases_category": "Category describing the presence or absence of metastases in remote "
+                                       "anatomical locations. Accepted ontologies: SNOMED CT, AJCC and others.",
+        "cancer_condition": "Cancer condition.",
+        **EXTRA_PROPERTIES
+    }
+}
+
+CANCER_RELATED_PROCEDURE = {
+    "description": "Description of radiological treatment or surgical action addressing a cancer condition.",
+    "properties": {
+        "id": "An arbitrary identifier for the procedure.",
+        "procedure_type": "Type of cancer related procedure: radion or surgical.",
+        "code": "Code for the procedure performed.",
+        "occurence_time_or_period": "The date/time that a procedure was performed.",
+        "target_body_site": "The body location(s) where the procedure was performed.",
+        "treatment_intent": "The purpose of a treatment.",
+        **EXTRA_PROPERTIES
+    }
+}
+
+MEDICATION_STATEMENT = {
+    "description": "Description of medication use.",
+    "properties": {
+        "id": "An arbitrary identifier for the medication statement.",
+        "medication_code": "A code for medication. Accepted code systems: Medication Clinical Drug (RxNorm) and other.",
+        "termination_reason": "A code explaining unplanned or premature termination of a course of medication. "
+                              "Accepted ontologies: SNOMED CT.",
+        "treatment_intent": "The purpose of a treatment. Accepted ontologies: SNOMED CT.",
+        "start_date": "The start date/time of the medication.",
+        "end_date": "The end date/time of the medication.",
+        "date_time": "The date/time the medication was administered.",
+        **EXTRA_PROPERTIES
+    }
+}
+
+MCODEPACKET = {
+    "description": "Collection of cancer related metadata.",
+    "properties": {
+        "id": "An arbitrary identifier for the mcodepacket.",
+        "subject": "An individual who is a subject of mcodepacket.",
+        "genomics_report": "A genomics report associated with an Individual.",
+        "cancer_condition": "An Individual's cancer condition.",
+        "cancer_related_procedures": "A radiological or surgical procedures addressing a cancer condition.",
+        "medication_statement": "Medication treatment addressed to an Individual.",
+        **EXTRA_PROPERTIES
+    }
+}