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-rw-r--r--tests/unit/db/test_traits.py83
1 files changed, 65 insertions, 18 deletions
diff --git a/tests/unit/db/test_traits.py b/tests/unit/db/test_traits.py
index c8f28b5..393983d 100644
--- a/tests/unit/db/test_traits.py
+++ b/tests/unit/db/test_traits.py
@@ -1,11 +1,6 @@
"""Tests for gn3/db/traits.py"""
from unittest import mock, TestCase
from gn3.db.traits import (
- GENO_TRAIT_INFO_QUERY,
- TEMP_TRAIT_INFO_QUERY,
- PUBLISH_TRAIT_INFO_QUERY,
- PROBESET_TRAIT_INFO_QUERY)
-from gn3.db.traits import (
retrieve_trait_info,
retrieve_geno_trait_info,
retrieve_temp_trait_info,
@@ -14,7 +9,6 @@ from gn3.db.traits import (
retrieve_probeset_trait_info,
update_sample_data)
-
class TestTraitsDBFunctions(TestCase):
"Test cases for traits functions"
@@ -54,12 +48,32 @@ class TestTraitsDBFunctions(TestCase):
trait_source = {
"trait_name": "PublishTraitName", "trait_dataset_id": 1}
self.assertEqual(
- retrieve_publish_trait_info(
- trait_source,
- db_mock),
- tuple())
+ retrieve_publish_trait_info(trait_source, db_mock), {})
cursor.execute.assert_called_once_with(
- PUBLISH_TRAIT_INFO_QUERY, trait_source)
+ ("SELECT "
+ "PublishXRef.Id, Publication.PubMed_ID,"
+ " Phenotype.Pre_publication_description,"
+ " Phenotype.Post_publication_description,"
+ " Phenotype.Original_description,"
+ " Phenotype.Pre_publication_abbreviation,"
+ " Phenotype.Post_publication_abbreviation,"
+ " Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner,"
+ " Phenotype.Authorized_Users,"
+ " CAST(Publication.Authors AS BINARY),"
+ " Publication.Title, Publication.Abstract,"
+ " Publication.Journal,"
+ " Publication.Volume, Publication.Pages, Publication.Month,"
+ " Publication.Year, PublishXRef.Sequence, Phenotype.Units,"
+ " PublishXRef.comments"
+ " FROM"
+ " PublishXRef, Publication, Phenotype, PublishFreeze"
+ " WHERE"
+ " PublishXRef.Id = %(trait_name)s "
+ " AND Phenotype.Id = PublishXRef.PhenotypeId"
+ " AND Publication.Id = PublishXRef.PublicationId"
+ " AND PublishXRef.InbredSetId = PublishFreeze.InbredSetId"
+ " AND PublishFreeze.Id =%(trait_dataset_id)s"),
+ trait_source)
def test_retrieve_probeset_trait_info(self):
"""Test retrieval of type `Probeset` traits."""
@@ -70,9 +84,31 @@ class TestTraitsDBFunctions(TestCase):
"trait_name": "ProbeSetTraitName",
"trait_dataset_name": "ProbeSetDatasetTraitName"}
self.assertEqual(
- retrieve_probeset_trait_info(trait_source, db_mock), tuple())
+ retrieve_probeset_trait_info(trait_source, db_mock), {})
cursor.execute.assert_called_once_with(
- PROBESET_TRAIT_INFO_QUERY, trait_source)
+ (
+ "SELECT "
+ "ProbeSet.name, ProbeSet.symbol, ProbeSet.description, "
+ "ProbeSet.probe_target_description, ProbeSet.chr, "
+ "ProbeSet.mb, ProbeSet.alias, ProbeSet.geneid, "
+ "ProbeSet.genbankid, ProbeSet.unigeneid, ProbeSet.omim, "
+ "ProbeSet.refseq_transcriptid, ProbeSet.blatseq, "
+ "ProbeSet.targetseq, ProbeSet.chipid, ProbeSet.comments, "
+ "ProbeSet.strand_probe, ProbeSet.strand_gene, "
+ "ProbeSet.probe_set_target_region, ProbeSet.proteinid, "
+ "ProbeSet.probe_set_specificity, "
+ "ProbeSet.probe_set_blat_score, "
+ "ProbeSet.probe_set_blat_mb_start, "
+ "ProbeSet.probe_set_blat_mb_end, "
+ "ProbeSet.probe_set_strand, ProbeSet.probe_set_note_by_rw, "
+ "ProbeSet.flag "
+ "FROM "
+ "ProbeSet, ProbeSetFreeze, ProbeSetXRef "
+ "WHERE "
+ "ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id "
+ "AND ProbeSetXRef.ProbeSetId = ProbeSet.Id "
+ "AND ProbeSetFreeze.Name = %(trait_dataset_name)s "
+ "AND ProbeSet.Name = %(trait_name)s"), trait_source)
def test_retrieve_geno_trait_info(self):
"""Test retrieval of type `Geno` traits."""
@@ -83,9 +119,19 @@ class TestTraitsDBFunctions(TestCase):
"trait_name": "GenoTraitName",
"trait_dataset_name": "GenoDatasetTraitName"}
self.assertEqual(
- retrieve_geno_trait_info(trait_source, db_mock), tuple())
+ retrieve_geno_trait_info(trait_source, db_mock), {})
cursor.execute.assert_called_once_with(
- GENO_TRAIT_INFO_QUERY, trait_source)
+ (
+ "SELECT "
+ "Geno.name, Geno.chr, Geno.mb, Geno.source2, Geno.sequence "
+ "FROM "
+ "Geno, GenoFreeze, GenoXRef "
+ "WHERE "
+ "GenoXRef.GenoFreezeId = GenoFreeze.Id "
+ "AND GenoXRef.GenoId = Geno.Id "
+ "AND GenoFreeze.Name = %(trait_dataset_name)s "
+ "AND Geno.Name = %(trait_name)s"),
+ trait_source)
def test_retrieve_temp_trait_info(self):
"""Test retrieval of type `Temp` traits."""
@@ -94,9 +140,10 @@ class TestTraitsDBFunctions(TestCase):
cursor.fetchone.return_value = tuple()
trait_source = {"trait_name": "TempTraitName"}
self.assertEqual(
- retrieve_temp_trait_info(trait_source, db_mock), tuple())
+ retrieve_temp_trait_info(trait_source, db_mock), {})
cursor.execute.assert_called_once_with(
- TEMP_TRAIT_INFO_QUERY, trait_source)
+ "SELECT name, description FROM Temp WHERE Name = %(trait_name)s",
+ trait_source)
def test_retrieve_trait_info(self):
"""Test that information on traits is retrieved as appropriate."""
@@ -113,7 +160,7 @@ class TestTraitsDBFunctions(TestCase):
retrieve_trait_info(
trait_type, trait_name, trait_dataset_id,
trait_dataset_name, db_mock),
- tuple())
+ {})
def test_update_sample_data(self):
"""Test that the SQL queries when calling update_sample_data are called with