Merge pull request #97 from bcgsc/task/DEVSU-2797-mlemieux

Task/devsu 2797 mlemieux

Author: mathieulemieux

.github/workflows/pytest.yml

@@ -35,7 +35,7 @@ jobs:
         flake8 pori_python --count --select=E9,F63,F7,F82 --show-source --statistics
     - name: Check with black
       run: |
-        pip install black
+        pip install black==25.11.0
         black --check -S -l 100 pori_python tests
     - name: Full Tests with pytest
       run: |

.github/workflows/quick-pytest.yml

@@ -32,7 +32,7 @@ jobs:
         flake8 pori_python --count --select=E9,F63,F7,F82 --show-source --statistics
     - name: Check with black
       run: |
-        pip install black
+        pip install black==25.11.0
         black --check -S -l 100 pori_python tests
     - name: Short Tests with pytest
       run: pytest --junitxml=junit/test-results-${{ matrix.python-version }}.xml --cov ipr --cov-report term --cov-report xml

pori_python/graphkb/util.py

@@ -125,6 +125,10 @@ def __init__(
         if username and password:
             self.login(username=username, password=password)
 
+        # URL check
+        if not self.url:
+            raise ValueError("URL to a GraphKB API instance is required")
+
     @property
     def load(self) -> Optional[float]:
         if self.first_request and self.last_request:
@@ -252,6 +256,7 @@ def login(self, username: str, password: str, pori_demo: bool = False) -> None:
 
         # KBDEV-1328. Alt. GraphKB login for GSC's PORI online demo
         if pori_demo or "pori-demo" in self.url:
+            logger.warning("login demo")
             self.login_demo()
 
         # use requests package directly to avoid recursion loop on login failure

pori_python/ipr/main.py

@@ -419,16 +419,13 @@ def ipr_report(
     )
 
     # GKB CONNECTION
-    if graphkb_url:
-        logger.info(f"connecting to graphkb: {graphkb_url}")
-        graphkb_conn = GraphKBConnection(graphkb_url)
-    else:
-        graphkb_conn = GraphKBConnection()
-
-    gkb_user = graphkb_username if graphkb_username else username
-    gkb_pass = graphkb_password if graphkb_password else password
+    graphkb_conn = GraphKBConnection(graphkb_url) if graphkb_url else GraphKBConnection()
+    logger.info(f"connecting to graphkb: {graphkb_conn.url}")
 
-    graphkb_conn.login(gkb_user, gkb_pass)
+    graphkb_conn.login(
+        graphkb_username if graphkb_username else username,
+        graphkb_password if graphkb_password else password,
+    )
 
     # DISEASE
     # Disease term from bioapps; expected OncoTree term
@@ -502,7 +499,7 @@ def ipr_report(
 
     if include_ipr_variant_text:
         if not ipr_conn:
-            raise ValueError("ipr_url required to to include ipr variant text")
+            raise ValueError("ipr_url required to include ipr variant text")
         ipr_comments = get_ipr_analyst_comments(
             ipr_conn,
             gkb_matches,

setup.cfg

@@ -54,7 +54,7 @@ dev =
     mkdocs-redirects
     markdown-refdocs
     flake8
-    black
+    black==25.11.0 # black >25.11 requires python >=3.10
     flake8-annotations
     isort
     mypy