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authorMuriithi Frederick Muriuki2021-07-28 12:32:43 +0300
committerMuriithi Frederick Muriuki2021-07-28 12:32:43 +0300
commitcdf5887506a0b035f5a51f9538815ff77cb71cdc (patch)
treeac01a98f56742599988347271b0d786b2f53eb5c
parent9b66f428f341bc047030126ba1e4cc405a34570c (diff)
downloadgenenetwork3-cdf5887506a0b035f5a51f9538815ff77cb71cdc.tar.gz
Retrieve trait information
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/db/traits.py: add functions to retrieve traits information * tests/unit/db/test_traits.py: add tests for new function Add functions to retrieve traits information as is done in genenetwork1 https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L397-L456 At this point, the data retrieval functions are probably incomplete, as there is more of the `retrieveInfo` function in GN1 that has not been considered as of this commit.
-rw-r--r--gn3/db/traits.py133
-rw-r--r--tests/unit/db/test_traits.py92
2 files changed, 218 insertions, 7 deletions
diff --git a/gn3/db/traits.py b/gn3/db/traits.py
index fddb8be..3c62df8 100644
--- a/gn3/db/traits.py
+++ b/gn3/db/traits.py
@@ -91,7 +91,7 @@ def insert_publication(pubmed_id: int, publication: Optional[Dict],
with conn.cursor() as cursor:
cursor.execute(insert_query, tuple(publication.values()))
-def retrieve_type_trait_name(trait_type, threshold, name, connection):
+def retrieve_trait_dataset_name(trait_type, threshold, name, connection):
"""
Retrieve the name of a trait given the trait's name
@@ -112,3 +112,134 @@ def retrieve_type_trait_name(trait_type, threshold, name, connection):
with connection.cursor() as cursor:
cursor.execute(query, {"threshold": threshold, "name": name})
return cursor.fetchone()
+
+PUBLISH_TRAIT_INFO_QUERY = (
+ "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")
+
+def retrieve_publish_trait_info(trait_data_source, conn):
+ """Retrieve trait information for type `Publish` traits.
+
+ https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L399-L421"""
+ with conn.cursor() as cursor:
+ cursor.execute(
+ PUBLISH_TRAIT_INFO_QUERY,
+ {
+ k:v for k, v in trait_data_source.items()
+ if k in ["trait_name", "trait_dataset_id"]
+ })
+ return cursor.fetchone()
+
+PROBESET_TRAIT_INFO_QUERY = (
+ "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")
+
+def retrieve_probeset_trait_info(trait_data_source, conn):
+ """Retrieve trait information for type `ProbeSet` traits.
+
+ https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L424-L435"""
+ with conn.cursor() as cursor:
+ cursor.execute(
+ PROBESET_TRAIT_INFO_QUERY,
+ {
+ k:v for k, v in trait_data_source.items()
+ if k in ["trait_name", "trait_dataset_name"]
+ })
+ return cursor.fetchone()
+
+GENO_TRAIT_INFO_QUERY = (
+ "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")
+
+def retrieve_geno_trait_info(trait_data_source, conn):
+ """Retrieve trait information for type `Geno` traits.
+
+ https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L438-L449"""
+ with conn.cursor() as cursor:
+ cursor.execute(
+ GENO_TRAIT_INFO_QUERY,
+ {
+ k:v for k, v in trait_data_source.items()
+ if k in ["trait_name", "trait_dataset_name"]
+ })
+ return cursor.fetchone()
+
+TEMP_TRAIT_INFO_QUERY = (
+ "SELECT name, description FROM Temp "
+ "WHERE Name = %(trait_name)s")
+
+def retrieve_temp_trait_info(trait_data_source, conn):
+ """Retrieve trait information for type `Temp` traits.
+
+ https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L450-452"""
+ with conn.cursor() as cursor:
+ cursor.execute(
+ TEMP_TRAIT_INFO_QUERY,
+ {
+ k:v for k, v in trait_data_source.items()
+ if k in ["trait_name"]
+ })
+ return cursor.fetchone()
+
+def retrieve_trait_info(
+ trait_type, trait_name, trait_dataset_id, trait_dataset_name, conn):
+ """Retrieves the trait information.
+
+ https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L397-L456
+
+ This function, or the dependent functions, might be incomplete as they are
+ currently."""
+ trait_info_function_table = {
+ "Publish": retrieve_publish_trait_info,
+ "ProbeSet": retrieve_probeset_trait_info,
+ "Geno": retrieve_geno_trait_info,
+ "Temp": retrieve_temp_trait_info
+ }
+ return trait_info_function_table[trait_type](
+ {
+ "trait_name": trait_name,
+ "trait_dataset_id": trait_dataset_id,
+ "trait_dataset_name":trait_dataset_name
+ },
+ conn)
diff --git a/tests/unit/db/test_traits.py b/tests/unit/db/test_traits.py
index 95c5b27..e3c5c28 100644
--- a/tests/unit/db/test_traits.py
+++ b/tests/unit/db/test_traits.py
@@ -1,13 +1,24 @@
"""Tests for gn3/db/traits.py"""
from unittest import mock, TestCase
-from gn3.db.traits import retrieve_type_trait_name
+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,
+ retrieve_trait_dataset_name,
+ retrieve_publish_trait_info,
+ retrieve_probeset_trait_info)
class TestTraitsDBFunctions(TestCase):
"Test cases for traits functions"
- def test_retrieve_probeset_trait_name(self):
+ def test_retrieve_trait_dataset_name(self):
"""Test that the function is called correctly."""
- for trait_type, thresh, trait_name, columns in [
+ for trait_type, thresh, trait_dataset_name, columns in [
["ProbeSet", 9, "testName",
"Id, Name, FullName, ShortName, DataScale"],
["Geno", 3, "genoTraitName", "Id, Name, FullName, ShortName"],
@@ -21,8 +32,8 @@ class TestTraitsDBFunctions(TestCase):
"testName", "testNameFull", "testNameShort",
"dataScale")
self.assertEqual(
- retrieve_type_trait_name(
- trait_type, thresh, trait_name, db_mock),
+ retrieve_trait_dataset_name(
+ trait_type, thresh, trait_dataset_name, db_mock),
("testName", "testNameFull", "testNameShort",
"dataScale"))
cursor.execute.assert_called_once_with(
@@ -31,4 +42,73 @@ class TestTraitsDBFunctions(TestCase):
"WHERE public > %(threshold)s AND "
"(Name = %(name)s OR FullName = %(name)s OR ShortName = %(name)s)".format(
cols=columns, ttype=trait_type),
- {"threshold": thresh, "name": trait_name})
+ {"threshold": thresh, "name": trait_dataset_name})
+
+ def test_retrieve_publish_trait_info(self):
+ """Test retrieval of type `Publish` traits."""
+ db_mock = mock.MagicMock()
+ with db_mock.cursor() as cursor:
+ cursor.fetchone.return_value = tuple()
+ trait_source = {
+ "trait_name": "PublishTraitName", "trait_dataset_id": 1}
+ self.assertEqual(
+ retrieve_publish_trait_info(
+ trait_source,
+ db_mock),
+ tuple())
+ cursor.execute.assert_called_once_with(
+ PUBLISH_TRAIT_INFO_QUERY, trait_source)
+
+ def test_retrieve_probeset_trait_info(self):
+ """Test retrieval of type `Probeset` traits."""
+ db_mock = mock.MagicMock()
+ with db_mock.cursor() as cursor:
+ cursor.fetchone.return_value = tuple()
+ trait_source = {
+ "trait_name": "ProbeSetTraitName",
+ "trait_dataset_name": "ProbeSetDatasetTraitName"}
+ self.assertEqual(
+ retrieve_probeset_trait_info(trait_source, db_mock), tuple())
+ cursor.execute.assert_called_once_with(
+ PROBESET_TRAIT_INFO_QUERY, trait_source)
+
+ def test_retrieve_geno_trait_info(self):
+ """Test retrieval of type `Geno` traits."""
+ db_mock = mock.MagicMock()
+ with db_mock.cursor() as cursor:
+ cursor.fetchone.return_value = tuple()
+ trait_source = {
+ "trait_name": "GenoTraitName",
+ "trait_dataset_name": "GenoDatasetTraitName"}
+ self.assertEqual(
+ retrieve_geno_trait_info(trait_source, db_mock), tuple())
+ cursor.execute.assert_called_once_with(
+ GENO_TRAIT_INFO_QUERY, trait_source)
+
+ def test_retrieve_temp_trait_info(self):
+ """Test retrieval of type `Temp` traits."""
+ db_mock = mock.MagicMock()
+ with db_mock.cursor() as cursor:
+ cursor.fetchone.return_value = tuple()
+ trait_source = {"trait_name": "TempTraitName"}
+ self.assertEqual(
+ retrieve_temp_trait_info(trait_source, db_mock), tuple())
+ cursor.execute.assert_called_once_with(
+ TEMP_TRAIT_INFO_QUERY, trait_source)
+
+ def test_retrieve_trait_info(self):
+ """Test that information on traits is retrieved as appropriate."""
+ for trait_type, trait_name, trait_dataset_id, trait_dataset_name, in [
+ ["Publish", "PublishTraitName", 1, "PublishDatasetTraitName"],
+ ["ProbeSet", "ProbeSetTraitName", 2, "ProbeSetDatasetTraitName"],
+ ["Geno", "GenoTraitName", 3, "GenoDatasetTraitName"],
+ ["Temp", "TempTraitName", 4, "TempDatasetTraitName"]]:
+ db_mock = mock.MagicMock()
+ with self.subTest(trait_type=trait_type):
+ with db_mock.cursor() as cursor:
+ cursor.fetchone.return_value = tuple()
+ self.assertEqual(
+ retrieve_trait_info(
+ trait_type, trait_name, trait_dataset_id,
+ trait_dataset_name, db_mock),
+ tuple())