Merge pull request #89 from bcgsc/feat/DEVSU-2797-remove-gsc-defaults

remove default urls and rid

Author: elewis2

.github/workflows/pytest.yml

@@ -46,6 +46,7 @@ jobs:
         IPR_PASS: ${{ secrets.IPR_TEST_PASSWORD }}
         GRAPHKB_USER: ${{ secrets.GKB_TEST_USER }}
         GRAPHKB_PASS: ${{ secrets.GKB_TEST_PASS }}
+        GRAPHKB_URL: ${{ secrets.GKB_TEST_URL }}
         # SDEV-3381 - Turn off integration tests temporarily, till efficiency is increased
         # turn on integration tests for one python version only
         EXCLUDE_INTEGRATION_TESTS: ${{ matrix.python-version != '3.11' }}

.github/workflows/quick-pytest.yml

@@ -39,8 +39,10 @@ jobs:
       env:
         IPR_USER: ${{ secrets.IPR_TEST_USER }}
         IPR_PASS: ${{ secrets.IPR_TEST_PASSWORD }}
+        IPR_URL: ${{ secrets.IPR_TEST_URL }}
         GRAPHKB_USER: ${{ secrets.GKB_TEST_USER }}
         GRAPHKB_PASS: ${{ secrets.GKB_TEST_PASS }}
+        GRAPHKB_URL: ${{ secrets.GKB_TEST_URL }}
         EXCLUDE_INTEGRATION_TESTS: 1
         # EXCLUDE_INTEGRATION_TESTS: ${{ matrix.python-version != '3.11' }}
-      if: github.event_name != 'pull_request'
+      if: github.event_name != 'pull_request'

pori_python/graphkb/__init__.py

@@ -1,2 +1 @@
-from .constants import DEFAULT_URL  # noqa: F401
 from .util import GraphKBConnection, logger  # noqa: F401

pori_python/graphkb/constants.py

@@ -4,12 +4,7 @@
 from pori_python.types import CategoryBaseTermMapping
 
 DEFAULT_LIMIT = 1000
-GKB_BASE_URL = "https://graphkb-api.bcgsc.ca/api"
-GKB_STAGING_URL = "https://graphkbstaging-api.bcgsc.ca/api"
-GKB_DEV_URL = "https://graphkbdev-api.bcgsc.ca/api"
-DEFAULT_URL = GKB_BASE_URL
 
-PREFERRED_GENE_SOURCE = "#39:5"  # HGNC
 PREFERRED_GENE_SOURCE_NAME = "HGNC"
 
 BASE_RETURN_PROPERTIES = ["@rid", "@class"]

pori_python/graphkb/genes.py

@@ -17,7 +17,6 @@
     GSC_PHARMACOGENOMIC_SOURCE_EXCLUDE_LIST,
     ONCOGENE,
     ONCOKB_SOURCE_NAME,
-    PREFERRED_GENE_SOURCE,
     PREFERRED_GENE_SOURCE_NAME,
     RELEVANCE_BASE_TERMS,
     TSO500_SOURCE_NAME,
@@ -267,24 +266,23 @@ def get_cancer_predisposition_info(
 
 
 def get_gene_linked_cancer_predisposition_info(
-    conn: GraphKBConnection, source: str = PREFERRED_GENE_SOURCE
+    conn: GraphKBConnection, source: str = PREFERRED_GENE_SOURCE_NAME
 ) -> Tuple[List[str], Dict[str, Tuple[str, List[str]]]]:
     """
     Return two lists from GraphKB, one of cancer predisposition genes and one of associated variants.
 
     GERO-272 - criteria for what counts as a "cancer predisposition" variant
 
     In short:
-    * Statement 'source' is 'CGL'
+    * Statement 'source' is 'CGL' (not related to the preferred gene source)
     * Statement 'relevance' is 'pathogenic'
     * gene is gotten from any associated 'PositionalVariant' records
 
     Example: https://graphkb.bcgsc.ca/view/Statement/155:11616
 
-
-
     Returns:
         genes: list of cancer predisposition genes
+            (using names from the source specified in this function's arguments)
         variants: dictionary mapping pharmacogenomic variant IDs to variant display names
     """
     genes = set()
@@ -372,7 +370,7 @@ def get_pharmacogenomic_info(
 
 
 def get_gene_linked_pharmacogenomic_info(
-    conn: GraphKBConnection, source: str = PREFERRED_GENE_SOURCE
+    conn: GraphKBConnection, source: str = PREFERRED_GENE_SOURCE_NAME
 ) -> Tuple[List[str], Dict[str, Tuple[str, List[str]]]]:
     """
     Return two lists from GraphKB, one of pharmacogenomic genes and one of associated variants.

pori_python/graphkb/util.py

@@ -14,7 +14,7 @@
 
 from pori_python.types import ParsedVariant, PositionalVariant, Record
 
-from .constants import DEFAULT_LIMIT, DEFAULT_URL, TYPES_TO_NOTATION, AA_3to1_MAPPING
+from .constants import DEFAULT_LIMIT, TYPES_TO_NOTATION, AA_3to1_MAPPING
 
 QUERY_CACHE: Dict[Any, Any] = {}
 
@@ -98,7 +98,7 @@ def cache_key(request_body) -> str:
 class GraphKBConnection:
     def __init__(
         self,
-        url: str = os.environ.get("GRAPHKB_URL", DEFAULT_URL),
+        url: str = os.environ.get("GRAPHKB_URL"),
         username: str = "",
         password: str = "",
         use_global_cache: bool = True,

pori_python/ipr/connection.py

@@ -6,7 +6,6 @@
 import zlib
 from typing import Dict, List
 
-from .constants import DEFAULT_URL
 from .util import logger
 
 IMAGE_MAX = 20  # cannot upload more than 20 images at a time
@@ -17,7 +16,7 @@ def __init__(
         self,
         username: str,
         password: str,
-        url: str = os.environ.get("IPR_URL", DEFAULT_URL),
+        url: str = os.environ.get("IPR_URL"),
     ):
         self.token = None
         self.url = url

pori_python/ipr/constants.py

@@ -1,4 +1,3 @@
-DEFAULT_URL = "https://iprstaging-api.bcgsc.ca/api"
 GERMLINE_BASE_TERMS = ("pharmacogenomic", "cancer predisposition")  # based on graphkb.constants
 VARIANT_CLASSES = {"Variant", "CategoryVariant", "PositionalVariant", "CatalogueVariant"}
 

pori_python/ipr/inputs.py

@@ -25,7 +25,6 @@
 
 from .constants import (
     COSMIC_SIGNATURE_VARIANT_TYPE,
-    DEFAULT_URL,
     HLA_SIGNATURE_VARIANT_TYPE,
     MSI_MAPPING,
     HRD_MAPPING,
@@ -39,7 +38,7 @@
 SPECIFICATION = os.path.join(os.path.dirname(__file__), "content.spec.json")
 
 # content in the local specification should match the values in IPR_API_SPEC_JSON_URL
-IPR_API_SPEC_JSON_URL = f'{os.environ.get("IPR_URL", DEFAULT_URL)}/spec.json'
+IPR_API_SPEC_JSON_URL = f'{os.environ.get("IPR_URL")}/spec.json'
 
 # TODO: GERO-307 - use SPECIFICATION json to derive the variant required and optional details defined below
 

pori_python/ipr/main.py

@@ -23,7 +23,7 @@
 
 from .annotate import annotate_variants
 from .connection import IprConnection
-from .constants import DEFAULT_URL, TMB_SIGNATURE_HIGH_THRESHOLD
+from .constants import TMB_SIGNATURE_HIGH_THRESHOLD
 from .inputs import (
     check_comparators,
     check_variant_links,
@@ -86,7 +86,7 @@ def command_interface() -> None:
         "-c", "--content", required=True, type=file_path, help="Report Content as JSON"
     )
 
-    parser.add_argument("--ipr_url", default=os.environ.get("IPR_URL", DEFAULT_URL))
+    parser.add_argument("--ipr_url", default=os.environ.get("IPR_URL"))
     parser.add_argument(
         "--graphkb_username",
         help="username to use connecting to graphkb if different from ipr",
@@ -294,7 +294,7 @@ def ipr_report(
     username: str,
     password: str,
     content: Dict,
-    ipr_url: str = DEFAULT_URL,
+    ipr_url: str = '',
     log_level: str = "info",
     output_json_path: str = "",
     always_write_output_json: bool = False,
@@ -324,7 +324,7 @@ def ipr_report(
     Args:
         username: the username for connecting to GraphKB and IPR
         password: the password for connecting to GraphKB and IPR
-        ipr_url: base URL to use in connecting to IPR
+        ipr_url: base URL to use in connecting to IPR (eg. https://ipr-api.bcgsc.ca/api)
         log_level: the logging level
         content: report content
         output_json_path: path to a JSON file to output the report upload body.
@@ -358,13 +358,22 @@ def ipr_report(
     )
 
     # IPR CONNECTION
-    ipr_conn = IprConnection(username, password, ipr_url)
+    ipr_url = ipr_url if ipr_url else os.environ.get("IPR_URL", "")
+    ipr_conn = None
+    if ipr_url:
+        ipr_conn = IprConnection(username, password, ipr_url)
+    else:
+        logger.warning("No ipr_url given")
 
     if validate_json:
+        if not ipr_conn:
+            raise ValueError("ipr_url required to validate json")
         ipr_result = ipr_conn.validate_json(content)
         return ipr_result
 
     if upload_json:
+        if not ipr_conn:
+            raise ValueError("ipr_url required to upload json")
         ipr_result = ipr_conn.upload_report(
             content, mins_to_wait, async_upload, ignore_extra_fields
         )
@@ -492,6 +501,8 @@ def ipr_report(
         comments_list.append(graphkb_comments)
 
     if include_ipr_variant_text:
+        if not ipr_conn:
+            raise ValueError("ipr_url required to to include ipr variant text")
         ipr_comments = get_ipr_analyst_comments(
             ipr_conn,
             gkb_matches,
@@ -557,13 +568,16 @@ def ipr_report(
             output['hrdScore'] = output['hrd']['score']
         output.pop('hrd')  # kbmatches have already been made
 
-    ipr_spec = ipr_conn.get_spec()
-    output = clean_unsupported_content(output, ipr_spec)
     ipr_result = {}
     upload_error = None
 
     # UPLOAD TO IPR
+
     if ipr_upload:
+        if not ipr_conn:
+            raise ValueError("ipr_url required to upload report")
+        ipr_spec = ipr_conn.get_spec()
+        output = clean_unsupported_content(output, ipr_spec)
         try:
             logger.info(f"Uploading to IPR {ipr_conn.url}")
             ipr_result = ipr_conn.upload_report(