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-rw-r--r--tests/integration/conftest.py24
-rw-r--r--tests/integration/test_data/pcorrs_data.json1039
-rw-r--r--tests/integration/test_partial_correlations.py5
3 files changed, 1066 insertions, 2 deletions
diff --git a/tests/integration/conftest.py b/tests/integration/conftest.py
index 4274233..90cf985 100644
--- a/tests/integration/conftest.py
+++ b/tests/integration/conftest.py
@@ -78,3 +78,27 @@ def db_conn():
#
# b.) Delete the test database
db_cursor.execute(f"DROP DATABASE IF EXISTS {test_db_name}")
+
+@pytest.fixture(scope="function")
+def db_conn_with_pcorrs_data(db_conn):
+ """Fixture with data for partial correlations tests"""
+ with open(
+ "tests/integration/test_data/pcorrs_data.json",
+ encoding="utf8") as data_file:
+ data = json.loads(data_file.read())
+ with db_conn.cursor() as cursor:
+ for item in data:
+ row_keys = item["rows"][0].keys()
+ query = (
+ f"INSERT INTO {item['dbtable']}({', '.join(row_keys)}) "
+ f"VALUES ({', '.join(['%s' for key in row_keys])})")
+ cursor.executemany(
+ query,
+ tuple(
+ tuple(row[key] for key in row_keys)
+ for row in item["rows"]))
+
+ yield db_conn
+
+ for item in data:
+ cursor.execute(f"DELETE FROM {item['dbtable']}")
diff --git a/tests/integration/test_data/pcorrs_data.json b/tests/integration/test_data/pcorrs_data.json
new file mode 100644
index 0000000..8f748fc
--- /dev/null
+++ b/tests/integration/test_data/pcorrs_data.json
@@ -0,0 +1,1039 @@
+[
+ {
+ "dbtable": "Phenotype",
+ "rows": [
+ {
+ "Id": 16472,
+ "Pre_publication_description": "Central nervous system, be ...",
+ "Post_publication_description": "Central nervous system, ...",
+ "Original_description": "Original post publication descrip ...",
+ "Units": "Unknown",
+ "Pre_publication_abbreviation": "Learning3",
+ "Post_publication_abbreviation": "Touches_N",
+ "Lab_code": null,
+ "Submitter": "synomehbp",
+ "Owner": null,
+ "Authorized_Users": "synomehbp"
+ },
+ {
+ "Id": 16475,
+ "Pre_publication_description": "Central nervous system, be ...",
+ "Post_publication_description": "Central nervous system, b ...",
+ "Original_description": "Original post publication descrip ...",
+ "Units": "Unknown",
+ "Pre_publication_abbreviation": "Learning6",
+ "Post_publication_abbreviation": "Final_Pretrain_Blank_Latency_S",
+ "Lab_code": null,
+ "Submitter": "synomehbp",
+ "Owner": null,
+ "Authorized_Users": "synomehbp"
+ }]
+ },
+ {
+ "dbtable": "InbredSet",
+ "rows": [
+ {
+ "Id": 1,
+ "InbredSetId": 1,
+ "InbredSetName": "BXD",
+ "Name": "BXD",
+ "SpeciesId": 1,
+ "FullName": "BXD Family",
+ "public": 2,
+ "MappingMethodId": 1,
+ "GeneticType": "riset",
+ "Family": "Reference Populations",
+ "FamilyOrder": 1,
+ "MenuOrderId": 0,
+ "InbredSetCode": "BXD"
+ }]
+ },
+ {
+ "dbtable": "PublishXRef",
+ "rows": [
+ {
+ "Id": 17937,
+ "InbredSetId": 1,
+ "PhenotypeId": 16472,
+ "PublicationId": 13554,
+ "DataId": 41005366,
+ "mean": 229.93754196166992,
+ "Locus": "16p_no_data",
+ "LRS": 23.7705104960664,
+ "additive": -46.0108582181818,
+ "Sequence": 1,
+ "comments": "a publish trait"
+ },
+ {
+ "Id": 17940,
+ "InbredSetId": 1,
+ "PhenotypeId": 16475,
+ "PublicationId": 13557,
+ "DataId": 41005369,
+ "mean": 8.97237495581309,
+ "Locus": "rs30305830",
+ "LRS": 18.3037843139756,
+ "additive": -1.79666089108911,
+ "Sequence": 1,
+ "comments": "a publish trait"
+ }]
+ },
+ {
+ "dbtable": "Publication",
+ "rows": [
+ {
+ "Id": 13554,
+ "PubMed_ID": null,
+ "Abstract": "SYNOME (Partner 97). Since April 2014, when ...",
+ "Authors": "Horner A, Kopanitsa M, McLaren R, Human Brain Project Task 1.1.7",
+ "Title": "HBP MAPGENCO BXD study",
+ "Journal": null,
+ "Volume": null,
+ "Pages": null,
+ "Month": null,
+ "Year": 2015
+ },
+ {
+ "Id": 13557,
+ "PubMed_ID": null,
+ "Abstract": "SYNOME (Partner 97). Since April 2014, when ...",
+ "Authors": "Horner A, Kopanitsa M, McLaren R, Human Brain Project Task 1.1.7",
+ "Title": "HBP MAPGENCO BXD study",
+ "Journal": null,
+ "Volume": null,
+ "Pages": null,
+ "Month": null,
+ "Year": 2015
+ }]
+ },
+ {
+ "dbtable": "PublishFreeze",
+ "rows": [
+ {
+ "Id": 1,
+ "Name": "BXDPublish",
+ "FullName": "BXD Published Phenotypes",
+ "ShortName": "BXDPublish",
+ "CreateTime": "2004-07-17",
+ "public": 2,
+ "InbredSetId": 1,
+ "confidentiality": 0,
+ "AuthorisedUsers": null
+ }
+ ]
+ },
+ {
+ "dbtable": "ProbeSet",
+ "rows": [
+ {
+ "Id": 162363,
+ "ChipId":7,
+ "Name": "ILM105290026",
+ "TargetId": "GI_38090455-S",
+ "Symbol": "Gm1151",
+ "description": "gene model 1151, (NCBI)",
+ "Chr": 10,
+ "Mb":36.833229,
+ "Chr_2016": 10,
+ "Mb_2016": 36.553035,
+ "alias": "",
+ "GeneId": 382362,
+ "GenbankId": null,
+ "SNP": null,
+ "BlatSeq": "GATGGTGACCGTCTTATCACAGAACCTCTGCCGGAACTACAGCTGGTGGA",
+ "TargetSeq": "",
+ "UniGeneId": null,
+ "Strand_Probe": "+",
+ "Strand_Gene": null,
+ "OMIM": "",
+ "comments": "",
+ "Probe_set_target_region": null,
+ "Probe_set_specificity": 5,
+ "Probe_set_BLAT_score": 50,
+ "Probe_set_Blat_Mb_start": 36.833229,
+ "Probe_set_Blat_Mb_end": 36.833279,
+ "Probe_set_Blat_Mb_start_2016": 36.553035,
+ "Probe_set_Blat_Mb_end_2016": 36.553085,
+ "Probe_set_strand": "+",
+ "Probe_set_Note_by_RW": null,
+ "flag": 0,
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+ },
+ {
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+ "Probe_set_Blat_Mb_start_mm8": "110.599097",
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+ "SecondaryNames": null,
+ "PeptideSequence": null
+ },
+ {
+ "Id": "162365",
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+ "alias": "2810028N01Rik; DKFZp667L1817; FLJ10484; KIAA1008; MGC33035; RP11-342J4.3; RRP44; bA555G22.1; dis3p",
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+ "TargetSeq": "CAGAACATCCAAAGACTCAACAGCAACAAAATGGAGAGCATACTTACAGACTCCTGTGCGATAGCTACTT",
+ "UniGeneId": "Mm.163339",
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+ "SecondaryNames": null,
+ "PeptideSequence": null
+ },
+ {
+ "Id": "162369",
+ "ChipId": "7",
+ "Name": "ILM870181",
+ "TargetId": "scl056379.2_58-S",
+ "Symbol": "Kcnj1",
+ "description": "potassium inwardly-rectifying channel, subfamily J, member 1",
+ "Chr": "9",
+ "Mb": "32.398853",
+ "Chr_2016": "9",
+ "Mb_2016": "32.206438",
+ "alias": "KIR1.1; Kir1.1; ROMK; ROMK-2; ROMK1; Romk2",
+ "GeneId": "56379",
+ "GenbankId": "BC020525|AF012834|",
+ "SNP": null,
+ "BlatSeq": "CCTGGAGTGTGTATGATGCTAACACCGAATGGTTCTTGTGTTTCTCTGCC",
+ "TargetSeq": "CAGCCTGGAGTGTGTATGATGCTAACACCGAATGGTTCTTGTGTTTCTCTGCCTAGTGGTTGAACTGCAA",
+ "UniGeneId": "Mm.390168",
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diff --git a/tests/integration/test_partial_correlations.py b/tests/integration/test_partial_correlations.py
index d249b42..e047e3d 100644
--- a/tests/integration/test_partial_correlations.py
+++ b/tests/integration/test_partial_correlations.py
@@ -213,7 +213,7 @@ def test_partial_correlation_api_with_non_existent_control_traits(client, post_d
# traits data set to something we are in control of
)
def test_part_corr_api_with_mix_of_existing_and_non_existing_control_traits(
- db_conn, primary, controls, method, target):
+ db_conn_with_pcorrs_data, primary, controls, method, target):
"""
Check that calling the function with a mix of existing and missing control
traits raises an warning.
@@ -221,4 +221,5 @@ def test_part_corr_api_with_mix_of_existing_and_non_existing_control_traits(
criteria = 10
with pytest.warns(UserWarning):
partial_correlations_entry(
- db_conn, primary, controls, method, criteria, target)
+ db_conn_with_pcorrs_data, primary, controls, method, criteria,
+ target)
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-18 17:27:06 +0000