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Merged
mathieulemieux merged 7 commits into from
Feb 3, 2026
Merged

Task/devsu 2797 mlemieux #97

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dfcf87e
Add login demo warning in GraphKBConnection
mathieulemieux Feb 2, 2026
8a3d29d
Fix error msg typo in ipr_report()
mathieulemieux Feb 2, 2026
8516832
Add empty url check to GraphKBConnection
mathieulemieux Feb 3, 2026
02bb7c8
Update GraphKB connection in ipr_report()
mathieulemieux Feb 3, 2026
e667d5e
Black linting
mathieulemieux Feb 3, 2026
318f6b0
Set black to v25.11.0
mathieulemieux Feb 3, 2026
01e64fa
Set black to v25.11.0 in pytests.yml
mathieulemieux Feb 3, 2026
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2 changes: 1 addition & 1 deletion .github/workflows/pytest.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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: |
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2 changes: 1 addition & 1 deletion .github/workflows/quick-pytest.yml
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Expand Up @@ -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
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5 changes: 5 additions & 0 deletions pori_python/graphkb/util.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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:
Expand Down Expand Up @@ -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
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17 changes: 7 additions & 10 deletions pori_python/ipr/main.py
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Expand Up @@ -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
Expand Down Expand Up @@ -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,
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2 changes: 1 addition & 1 deletion setup.cfg
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Expand Up @@ -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
Expand Down