Merge pull request #535 from bento-platform/chore/remove-opa

chore!: clear out old CanDIG code

chord_metadata_service/metadata/settings.py

@@ -14,7 +14,6 @@
 import sys
 import logging
 import json
-from os.path import exists
 
 from bento_lib.service_info.types import GA4GHServiceType
 from urllib.parse import quote, urlparse
@@ -129,16 +128,6 @@
 NGINX_INTERNAL_SOCKET = quote(os.environ.get("NGINX_INTERNAL_SOCKET", "/chord/tmp/nginx_internal.sock"), safe="")
 DRS_URL = os.environ.get("DRS_URL", f"http+unix://{NGINX_INTERNAL_SOCKET}/api/drs").strip().rstrip("/")
 
-# Candig-specific settings
-
-CANDIG_AUTHORIZATION = os.getenv("CANDIG_AUTHORIZATION", "")
-CANDIG_OPA_URL = os.getenv("CANDIG_OPA_URL", "")
-CANDIG_OPA_SECRET = os.getenv("CANDIG_OPA_SECRET", "my-secret-beacon-token")
-CANDIG_OPA_SITE_ADMIN_KEY = os.getenv("CANDIG_OPA_SITE_ADMIN_KEY", "site-admin")
-if exists("/run/secrets/opa-root-token"):
-    with open("/run/secrets/opa-root-token", "r") as f:
-        CANDIG_OPA_SECRET = f.read()
-
 # Application definition
 
 INSTALLED_APPS = (['daphne'] if os.environ.get('BENTO_CONTAINER_LOCAL') else []) + [
@@ -180,11 +169,6 @@
     'django.middleware.clickjacking.XFrameOptionsMiddleware',
 ]
 
-# This middlewares are specific to the CANDIG service
-if os.getenv('INSIDE_CANDIG', ''):
-    MIDDLEWARE.append('chord_metadata_service.restapi.preflight_req_middleware.PreflightRequestMiddleware')
-    MIDDLEWARE.append('chord_metadata_service.restapi.candig_authz_middleware.CandigAuthzMiddleware')
-
 CORS_ALLOWED_ORIGINS = [orig.strip() for orig in os.environ.get("CORS_ORIGINS", "").split(";") if orig.strip()]
 CORS_ALLOW_CREDENTIALS = True
 

chord_metadata_service/metadata/test_settings.py

@@ -1,8 +1,5 @@
 from .settings import *  # noqa: F403, F401
 
-# This allowed to run the tests without keycloak running and we cannot get the token from keycloak
-# If we figure out to do the integration tests, we can remove this
-CANDIG_AUTHORIZATION = ''
 # Tests are run locally with the Django dev server. Adding a sub-path which
 # is managed by the gateway in production, creates wrong references and breaks
 # almost every test. This resets the setting for when an environment variable

chord_metadata_service/restapi/argo_utils.py

@@ -30,130 +30,3 @@ def argo_donor(obj):
             if i in obj["extra_properties"]:
                 donor[i] = obj["extra_properties"][i]
     return donor
-
-
-def argo_specimen(obj):
-    """
-    Convert Genetic Specimen to ARGO Specimen.
-    Takes Katsu genetic specimen object and converts its fields to ARGO according to the mapping.
-    """
-    specimen = {
-        "submitter_specimen_id": obj["id"],
-        "specimen_type": obj["specimen_type"]
-    }
-    for argo_field, mcode_field in zip(
-            ("specimen_tissue_source", "specimen_laterality"),
-            ("collection_body", "laterality")
-    ):
-        if mcode_field in obj:
-            specimen[argo_field] = obj[mcode_field]
-    return specimen
-
-
-def argo_primary_diagnosis(obj):
-    """
-    Convert Cancer Condition to ARGO Primary Diagnosis.
-    Takes Katsu cancer condition object and converts its fields to ARGO according to the mapping.
-    """
-    primary_diagnosis = {
-        "submitter_primary_diagnosis_id": obj["id"],
-        "cancer_type_code": obj["code"]
-    }
-    if "tnm_staging" in obj and obj["tnm_staging"]:
-        primary_diagnosis["specimen"] = {}
-        for item in obj["tnm_staging"]:
-            # tnm_staging clinical is mapped to PrimaryDiagnosis fields
-            if item["tnm_type"] == "clinical":
-                for mcode_field, argo_field in zip(
-                        ["stage_group", "primary_tumor_category",
-                         "regional_nodes_category", "distant_metastases_category"],
-                        ["clinical_stage_group", "clinical_t_category",
-                         "clinical_n_category", "clinical_m_category"]
-                ):
-                    if mcode_field in item and item[mcode_field]:
-                        if argo_field in primary_diagnosis and primary_diagnosis[argo_field]:
-                            primary_diagnosis[argo_field].append(item[mcode_field]["data_value"])
-                        else:
-                            primary_diagnosis[argo_field] = [item[mcode_field]["data_value"]]
-
-            # tnm_staging pathologic is mapped to Specimen fields
-            else:
-                # need to instanciate a local specimen object here
-                for mcode_field, argo_field in zip(
-                        ["stage_group", "primary_tumor_category",
-                         "regional_nodes_category", "distant_metastases_category"],
-                        ["pathological_stage_group", "pathological_t_category",
-                         "pathological_n_category", "pathological_m_category"]
-                ):
-                    if mcode_field in item and item[mcode_field]:
-                        if argo_field in primary_diagnosis["specimen"] and primary_diagnosis["specimen"][argo_field]:
-                            primary_diagnosis["specimen"][argo_field].append(item[mcode_field]["data_value"])
-                        else:
-                            primary_diagnosis["specimen"][argo_field] = [item[mcode_field]["data_value"]]
-        # if no pathologic tnm staging delete specimen
-        if not primary_diagnosis["specimen"]:
-            del primary_diagnosis["specimen"]
-
-    # check for not mapped fields in extra_properties
-    if "extra_properties" in obj and obj["extra_properties"]:
-        for i in ["age_at_diagnosis", "lymph_nodes_examined_status",
-                  "number_lymph_nodes_positive", "clinical_tumour_staging_system"]:
-            if i in obj["extra_properties"]:
-                primary_diagnosis[i] = obj["extra_properties"][i]
-
-    return primary_diagnosis
-
-
-# a dict to map mCODE procedure type to ARGO treatment types
-PROCEDUR_TYPE_TO_TREATMENT_TYPE = {
-    "radiation": "Radiation therapy",
-    "surgical": "Surgery"
-}
-
-
-def argo_treatment(obj):
-    """
-    Convert Cancer Related Procedure to ARGO Treatment.
-    Takes Katsu cancer related procedure object and converts its fields to ARGO according to the mapping.
-    """
-    treatment = {
-        "submitter_treatment_id": obj["id"],
-        "treatment_type": PROCEDUR_TYPE_TO_TREATMENT_TYPE[obj["procedure_type"]]
-    }
-    if "treatment_intent" in obj and obj["treatment_intent"]:
-        treatment["treatment_intent"] = obj["treatment_intent"]
-    # only radiation treatment fields
-    if obj["procedure_type"] == "radiation":
-        for mcode_field, argo_field in zip(
-                ["code", "body_site"],
-                ["radiation_therapy_modality", "anatomical_site_irradiated"]
-        ):
-            if mcode_field in obj and obj[mcode_field]:
-                treatment[argo_field] = obj[mcode_field]
-    return treatment
-
-
-def argo_therapy(obj):
-    """
-    Convert Medication statement to ARGO Immunotherapy, Chemotherapy, Hormone Therapy.
-    Takes Katsu medication statement object and converts its fields to ARGO according to the mapping.
-    """
-    therapy = {
-        "submitter_treatment_id": obj["id"],
-        "drug_rxnormcui": obj["medication_code"]
-    }
-    return therapy
-
-
-def argo_composition_object(obj):
-    """
-    Returns all Mcodepacket related objects converted to their ARGO element according to the mapping.
-    """
-    composition_object = {
-        "donor": argo_donor(obj["subject"]),
-        "primary_diagnoses": [argo_primary_diagnosis(obj["cancer_condition"])],
-        "treatments": [argo_treatment(crp) for crp in obj["cancer_related_procedures"]],
-        # the name doesn't look nice but there is no therapy type field in mcode
-        "immunotherapies_chemotherapies_hormone_therapies": [argo_therapy(ms) for ms in obj["medication_statement"]]
-    }
-    return composition_object