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Merged
avikdatta merged 7 commits into from
Feb 19, 2026
Merged

Hot fix cosmx registration feb26 #159

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ac23dbe
fix for metadata sync call
avikdatta Feb 18, 2026
172ef94
adding user category as required metadata
avikdatta Feb 18, 2026
5400ae5
minor format change
avikdatta Feb 18, 2026
70eb99d
updated unittest
avikdatta Feb 18, 2026
f4e9d2f
more fixes
avikdatta Feb 18, 2026
b5e1e90
fixed tests
avikdatta Feb 19, 2026
805c0b5
added more fixes
avikdatta Feb 19, 2026
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20 changes: 14 additions & 6 deletions igf_data/process/seqrun_processing/unified_metadata_registration.py
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Original file line number Diff line number Diff line change
Expand Up @@ -55,7 +55,7 @@ def __init__(
table_columns: dict[str, list[Any]] = {
"project": ["project_igf_id", "deliverable"],
"project_user": ["project_igf_id", "email_id"],
"user": ["name", "email_id", "username"],
"user": ["name", "email_id", "username", "category"],
"sample": ["sample_igf_id", "project_igf_id"]},
error_list: list[str] = []
) -> None:
Expand Down Expand Up @@ -318,16 +318,24 @@ def _split_metadata(
for table_name, table_column_list in table_columns.items():
if table_name == 'project':
project_metadata_list.extend(
metadata_df[table_column_list].to_dict(orient='records'))
metadata_df[table_column_list]
.to_dict(orient='records')
)
elif table_name == 'sample' and samples_required:
sample_metadata_list.extend(
metadata_df[table_column_list].to_dict(orient='records'))
metadata_df[table_column_list]
.to_dict(orient='records')
)
elif table_name == 'user':
user_metadata_list.extend(
metadata_df[table_column_list].to_dict(orient='records'))
metadata_df[table_column_list]
.to_dict(orient='records')
)
elif table_name == 'project_user':
project_user_metadata.extend(
metadata_df[table_column_list].to_dict(orient='records'))
metadata_df[table_column_list]
.to_dict(orient='records')
)
return (
project_metadata_list,
user_metadata_list,
Expand Down Expand Up @@ -692,7 +700,7 @@ def execute(self, metadata_context: MetadataContext) -> None:
_ = get_data_from_portal(
url_suffix=metadata_url,
portal_config_file=portal_config_file,
request_mode='post'
request_mode='get'
)
synced_metadata_dict.update({
metadata_id: True}
Expand Down
31 changes: 17 additions & 14 deletions test/process/unified_metadata_registration_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -253,8 +253,8 @@ def test_CheckRawMetadataColumnsCommand_execute(self):
# '"username": "D", "sample_igf_id": "E"}]'
# }
metadata_context.raw_metadata_dict = {
"A": "project_igf_id,deliverable,name,email_id,username,sample_igf_id\n" +
"A,FASTQ,B,C,D,E"
"A": "project_igf_id,deliverable,name,email_id,username,category,sample_igf_id\n" +
"A,FASTQ,B,C,D,HPC_USER,E"
}
metadata_context.samples_required = True
CheckRawMetadataColumnsCommand().execute(
Expand Down Expand Up @@ -284,8 +284,8 @@ def test_CheckRawMetadataColumnsCommand_execute(self):
default_project_user_email='c@c.com',
metadata_fetched=True,
raw_metadata_dict={"A": "project_igf_id,deliverable,name," +
"email_id,username\n" +
"A,FASTQ,B,C,D"
"email_id,username,category\n" +
"A,FASTQ,B,C,D,HPC_USER"
},
samples_required=False)
CheckRawMetadataColumnsCommand().execute(
Expand All @@ -308,24 +308,24 @@ def test_ValidateMetadataCommand_validate_metadata(self):
validate = ValidateMetadataCommand()
errors = validate._validate_metadata(
metadata_entry="project_igf_id,deliverable,name," +
"email_id,username,sample_igf_id\n" +
"IGF001,COSMX,Ba Da,c@d.com,aaa,IGF001",
"email_id,username,category,sample_igf_id\n" +
"IGF001,COSMX,Ba Da,c@d.com,aaa,HPC_USER,IGF001",
metadata_validation_schema=self.metadata_validation_schema,
metadata_id="A"
)
self.assertEqual(len(errors), 0)
errors = validate._validate_metadata(
metadata_entry="project_igf_id,deliverable,name," +
"email_id,username\n" +
"IGF001,COSMX,Ba Da,c@d.com,aaa",
"email_id,username,category\n" +
"IGF001,COSMX,Ba Da,c@d.com,aaa,HPC_USER",
metadata_validation_schema=self.metadata_validation_schema,
metadata_id="A"
)
self.assertEqual(len(errors), 0)
errors = validate._validate_metadata(
metadata_entry="project_igf_id,deliverable,name," +
"email_id,username\n" +
"IGF001,COSMX,Ba Da,c-d.com,aaa",
"email_id,username,category\n" +
"IGF001,COSMX,Ba Da,c-d.com,aaa,HPC_USER",
metadata_validation_schema=self.metadata_validation_schema,
metadata_id=1
)
Expand All @@ -343,8 +343,8 @@ def test_ValidateMetadataCommand_execute(self):
default_project_user_email='c@c.com',
error_list=[],
raw_metadata_dict={
"A": "project_igf_id,deliverable,name,email_id,username\n" +
"IGF001,COSMX,Ba Da,c-d.com,aaa"
"A": "project_igf_id,deliverable,name,email_id,username,category\n" +
"IGF001,COSMX,Ba Da,c-d.com,aaa,HPC_USER"
},
checked_required_column_dict={"A": True})
with self.assertRaises(Exception):
Expand Down Expand Up @@ -373,6 +373,7 @@ def test_CheckAndRegisterMetadataCommand_split_metadata(self):
"name": "Ga Ga",
"email_id": "g@g.com",
"username": "ggg",
"category": "HPC_USER",
"sample_igf_id": "AAA"}])
.to_csv(index=False)
},
Expand Down Expand Up @@ -640,12 +641,14 @@ def test_CheckAndRegisterMetadataCommand_execute(self):
"deliverable": "COSMX",
"name": "Ga Ga",
"email_id": "g@g.com",
"category": "HPC_USER",
"username": "ggg"}])
.to_csv(index=False),
2: pd.DataFrame([{
"project_igf_id": "IGF001",
"deliverable": "COSMX",
"name": "Ba Da",
"category": "HPC_USER",
"username": "aaa"}])
.to_csv(index=False)},
validated_metadata_dict={1: True, 2: False})
Expand Down Expand Up @@ -787,8 +790,8 @@ def tearDown(self):
@patch(
"igf_data.process.seqrun_processing.unified_metadata_registration.get_data_from_portal",
return_value={"A": "project_igf_id,deliverable,name," +
"email_id,username\n" +
"IGF001,COSMX,Ba Da,c@d.com,aaa"}
"email_id,username,category\n" +
"IGF001,COSMX,Ba Da,c@d.com,aaa,HPC_USER"}
)
def test_UnifiedMetadataRegistration_execute(self, *args):
metadata_registration = UnifiedMetadataRegistration(
Expand Down