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mathieulemieux wants to merge 7 commits into from
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Task/devsu 2797 mlemieux #96

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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
fc0c6cd
More black linting, using v26.1.0
mathieulemieux Feb 3, 2026
b5481b3
Removing support for python v3.9
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 @@ -16,7 +16,7 @@ jobs:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ['3.9', '3.10', '3.11', '3.12']
python-version: ['3.10', '3.11', '3.12']

steps:
- uses: actions/checkout@v3
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5 changes: 5 additions & 0 deletions pori_python/graphkb/util.py
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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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6 changes: 2 additions & 4 deletions pori_python/ipr/summary.py
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Expand Up @@ -305,16 +305,14 @@ def create_section_html(
description = ". ".join(genes[0]["description"].split(". ")[:2]) # type: ignore
sourceId = genes[0].get("sourceId", "")

output.append(
f"""
output.append(f"""
<blockquote class="entrez_description" cite="{ENTREZ_GENE_URL}/{sourceId}">
{description}.
</blockquote>
<p>
{variants_text}
</p>
"""
)
""")

sentences_used: Set[str] = set()

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