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Feat/devsu 2797 remove gsc defaults dustin #93

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b209e23
DEVSU-2797 - main.ipr_report - allow null ipr_url if ipr_upload = False
dustinbleile Dec 12, 2025
e95203c
DEVSU-2797 - lint isort - unsorted imports
dustinbleile Dec 12, 2025
0f7b2d7
DEVSU-2797 - improve error message logging when graphkb_conn is made …
dustinbleile Dec 12, 2025
ecb9060
bugfix - ipr_report - upload_json immediately returns
dustinbleile Dec 16, 2025
b572f2b
DEVSU-2797 - check os.environ for IPR_URL and GRAPHKB_URL
dustinbleile Dec 16, 2025
9cd51c3
lint - fix fstring
dustinbleile Dec 16, 2025
b051b27
Merge branch 'develop' of https://github.com/bcgsc/pori_python into f…
dustinbleile Jan 7, 2026
e05ec5b
minor type fix - null string instead of None
dustinbleile Jan 7, 2026
57f97f9
minor lint - isort inputs & quotes
dustinbleile Jan 7, 2026
a48b090
test_genes - remove unused import PREFERRED_GENE_SOURCE_NAME
dustinbleile Jan 7, 2026
87cd9ff
raise errors if no graphkb url has been set
dustinbleile Jan 7, 2026
686511d
Error message when no IPR_URL defined
dustinbleile Jan 7, 2026
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13 changes: 10 additions & 3 deletions pori_python/graphkb/util.py
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Original file line number Diff line number Diff line change
Expand Up @@ -98,7 +98,7 @@ def cache_key(request_body) -> str:
class GraphKBConnection:
def __init__(
self,
url: str = os.environ.get("GRAPHKB_URL"),
url: str = os.environ.get("GRAPHKB_URL", ""),
username: str = "",
password: str = "",
use_global_cache: bool = True,
Expand Down Expand Up @@ -143,6 +143,8 @@ def request(self, endpoint: str, method: str = "GET", **kwargs) -> Dict:
Returns:
dict: the json response as a python dict
"""
if not self.url:
raise ValueError("no GraphKBConnection url set - cannot make a login demo")
url = join_url(self.url, endpoint)
self.request_count += 1
connect_timeout = 7
Expand Down Expand Up @@ -222,6 +224,8 @@ def login_demo(self) -> None:
1. get a first token from KeyCloak using username and password; self.login_demo()
2. get a second token from the GraphKB API using keyCloakToken; self.login()
"""
if not self.url:
raise ValueError("no GraphKBConnection url set - cannot make a login demo")
url_parts = urlsplit(self.url)
base_url = f"{url_parts.scheme}://{url_parts.netloc}"

Expand Down Expand Up @@ -250,8 +254,11 @@ def login(self, username: str, password: str, pori_demo: bool = False) -> None:
connect_timeout = 7
read_timeout = 61

# KBDEV-1328. Alt. GraphKB login for GSC's PORI online demo
if pori_demo or "pori-demo" in self.url:
if not self.url:
raise ValueError("no GraphKBConnection url set - cannot login")
elif pori_demo or "pori-demo" in self.url:
# KBDEV-1328. Alt. GraphKB login for GSC's PORI online demo
logger.warning("login demo")
self.login_demo()

# use requests package directly to avoid recursion loop on login failure
Expand Down
2 changes: 1 addition & 1 deletion pori_python/ipr/inputs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -26,8 +26,8 @@
from .constants import (
COSMIC_SIGNATURE_VARIANT_TYPE,
HLA_SIGNATURE_VARIANT_TYPE,
MSI_MAPPING,
HRD_MAPPING,
MSI_MAPPING,
TMB_SIGNATURE,
TMB_SIGNATURE_VARIANT_TYPE,
)
Expand Down
13 changes: 6 additions & 7 deletions pori_python/ipr/ipr.py
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Original file line number Diff line number Diff line change
Expand Up @@ -168,8 +168,7 @@ def convert_statements_to_alterations(
diseases = [c for c in statement["conditions"] if c["@class"] == "Disease"]
disease_match = len(diseases) == 1 and diseases[0]["@rid"] in disease_matches
reference = ";".join([e["displayName"] for e in statement["evidence"]])

if statement['relevance']['name'] == 'eligibility':
if statement["relevance"]["name"] == "eligibility":
reference = ";".join([e["sourceId"] for e in statement["evidence"]])

ipr_section = gkb_statement.categorize_relevance(
Expand Down Expand Up @@ -296,10 +295,10 @@ def create_key_alterations(
counts: Dict[str, Set] = {v: set() for v in type_mapping.values()}
skipped_variant_types = []

included_kbvariant_ids = list(set([item['kbVariantId'] for item in included_kb_matches]))
included_kbvariant_ids = list(set([item["kbVariantId"] for item in included_kb_matches]))

for kb_match in kb_matches:
if kb_match['kbVariantId'] not in included_kbvariant_ids:
if kb_match["kbVariantId"] not in included_kbvariant_ids:
continue
variant_type = kb_match["variantType"]
variant_key = kb_match["variant"]
Expand Down Expand Up @@ -647,13 +646,13 @@ def get_kb_matches_sections(
unique_kb_variant_ids = list(
set(
[
item['kbVariantId']
item["kbVariantId"]
for conditionSet in kb_statement_matched_conditions
for item in conditionSet['matchedConditions']
for item in conditionSet["matchedConditions"]
]
)
)
kb_variants = [item for item in kb_variants if item['kbVariantId'] in unique_kb_variant_ids]
kb_variants = [item for item in kb_variants if item["kbVariantId"] in unique_kb_variant_ids]

return {
"kbMatches": kb_variants,
Expand Down
31 changes: 16 additions & 15 deletions pori_python/ipr/main.py
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Original file line number Diff line number Diff line change
Expand Up @@ -31,8 +31,8 @@
preprocess_cosmic,
preprocess_expression_variants,
preprocess_hla,
preprocess_msi,
preprocess_hrd,
preprocess_msi,
preprocess_signature_variants,
preprocess_small_mutations,
preprocess_structural_variants,
Expand Down Expand Up @@ -294,7 +294,7 @@ def ipr_report(
username: str,
password: str,
content: Dict,
ipr_url: str = '',
ipr_url: str = "",
log_level: str = "info",
output_json_path: str = "",
always_write_output_json: bool = False,
Expand Down Expand Up @@ -363,17 +363,17 @@ def ipr_report(
if ipr_url:
ipr_conn = IprConnection(username, password, ipr_url)
else:
logger.warning("No ipr_url given")
logger.error("No ipr_url given with no IPR_URL environment variable")

if validate_json:
if not ipr_conn:
raise ValueError("ipr_url required to validate json")
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")
raise ValueError("ipr_url required to upload_json")
ipr_result = ipr_conn.upload_report(
content, mins_to_wait, async_upload, ignore_extra_fields
)
Expand Down Expand Up @@ -419,14 +419,15 @@ def ipr_report(
)

# GKB CONNECTION
gkb_user = graphkb_username if graphkb_username else username
gkb_pass = graphkb_password if graphkb_password else password
graphkb_url = graphkb_url if graphkb_url else os.environ.get("GRAPHKB_URL", "")
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() # This will just error on trying to login
raise ValueError("graphkb_url is required")

graphkb_conn.login(gkb_user, gkb_pass)

Expand Down Expand Up @@ -502,7 +503,7 @@ 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,
Expand All @@ -524,7 +525,7 @@ def ipr_report(

# KEY ALTERATIONS
key_alterations, variant_counts = create_key_alterations(
gkb_matches, all_variants, kb_matched_sections['kbMatches']
gkb_matches, all_variants, kb_matched_sections["kbMatches"]
)

# OUTPUT CONTENT
Expand Down Expand Up @@ -563,10 +564,10 @@ def ipr_report(

# if input includes hrdScore field, that is ok to pass to db
# but prefer the 'hrd' field if it exists
if output.get('hrd'):
if output.get('hrd').get('score'):
output['hrdScore'] = output['hrd']['score']
output.pop('hrd') # kbmatches have already been made
if output.get("hrd"):
if output.get("hrd").get("score"):
output["hrdScore"] = output["hrd"]["score"]
output.pop("hrd") # kbmatches have already been made

ipr_result = {}
upload_error = None
Expand Down
4 changes: 2 additions & 2 deletions tests/test_ipr/test_inputs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,8 +7,8 @@

from pori_python.graphkb.match import INPUT_COPY_CATEGORIES
from pori_python.ipr.constants import (
MSI_MAPPING,
HRD_MAPPING,
MSI_MAPPING,
TMB_SIGNATURE,
TMB_SIGNATURE_HIGH_THRESHOLD,
)
Expand All @@ -21,8 +21,8 @@
preprocess_cosmic,
preprocess_expression_variants,
preprocess_hla,
preprocess_msi,
preprocess_hrd,
preprocess_msi,
preprocess_signature_variants,
preprocess_small_mutations,
preprocess_structural_variants,
Expand Down
28 changes: 14 additions & 14 deletions tests/test_ipr/test_ipr.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,13 +5,13 @@
from pori_python.graphkb import vocab as gkb_vocab
from pori_python.ipr.ipr import (
convert_statements_to_alterations,
create_key_alterations,
germline_kb_matches,
get_kb_disease_matches,
get_kb_matched_statements,
get_kb_matches_sections,
get_kb_statement_matched_conditions,
get_kb_variants,
get_kb_matches_sections,
create_key_alterations,
)
from pori_python.types import Statement

Expand Down Expand Up @@ -497,10 +497,10 @@ def test_germline_kb_matches(self):
]

ALL_VARIANTS = [
{"variant": "var1", "key": '1', "variantType": 'mut'},
{"variant": "var2", "key": '2', "variantType": 'mut'},
{"variant": "var3", "key": '3', "variantType": 'mut'},
{"variant": "var4", "key": '4', "variantType": 'mut'},
{"variant": "var1", "key": "1", "variantType": "mut"},
{"variant": "var2", "key": "2", "variantType": "mut"},
{"variant": "var3", "key": "3", "variantType": "mut"},
{"variant": "var4", "key": "4", "variantType": "mut"},
]

BASIC_GKB_MATCH = {
Expand Down Expand Up @@ -709,8 +709,8 @@ def test_partial_matches_omitted(self):
gkb_matches = create_gkb_matches(input_fields)
sections = get_kb_matches_sections(gkb_matches, allow_partial_matches=False)

stmts = sections['kbMatchedStatements']
kbcs = sections['kbStatementMatchedConditions']
stmts = sections["kbMatchedStatements"]
kbcs = sections["kbStatementMatchedConditions"]
assert len(stmts) == 2
assert len(kbcs) == 1 # X only
assert kbcs[0]["kbStatementId"] == "X"
Expand Down Expand Up @@ -796,14 +796,14 @@ def test_kbvariants_removed_from_set_when_not_part_of_full_conditionset_match(se
item["kbVariant"] = "test"
gkb_matches = create_gkb_matches(input_fields)
sections1 = get_kb_matches_sections(gkb_matches, allow_partial_matches=False)
kbcs1 = sections1['kbStatementMatchedConditions']
kbvars1 = sections1['kbMatches']
kbcs1 = sections1["kbStatementMatchedConditions"]
kbvars1 = sections1["kbMatches"]
assert len(kbcs1) == 1 # only fully matched condition sets included
assert len(kbvars1) == 2 # therefore, kbvars associated with stmt X are pruned

sections2 = get_kb_matches_sections(gkb_matches, allow_partial_matches=True)
kbcs2 = sections2['kbStatementMatchedConditions']
kbvars2 = sections2['kbMatches']
kbcs2 = sections2["kbStatementMatchedConditions"]
kbvars2 = sections2["kbMatches"]
assert len(kbcs2) == 2 # all condition sets included
assert len(kbvars2) == 3 # therefore, no pruning

Expand Down Expand Up @@ -844,12 +844,12 @@ def test_create_key_alterations_includes_only_pruned_kbmatches(self):

sections1 = get_kb_matches_sections(gkb_matches, allow_partial_matches=False)
key_alts1, counts1 = create_key_alterations(
gkb_matches, ALL_VARIANTS, sections1['kbMatches']
gkb_matches, ALL_VARIANTS, sections1["kbMatches"]
)

sections2 = get_kb_matches_sections(gkb_matches, allow_partial_matches=True)
key_alts2, counts2 = create_key_alterations(
gkb_matches, ALL_VARIANTS, sections2['kbMatches']
gkb_matches, ALL_VARIANTS, sections2["kbMatches"]
)

# check partial-match-only variants are not included in key alterations when
Expand Down