Return dict from query functions

Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi

* gn3/db/traits.py: return dicts rather than tuples/list
* tests/unit/db/test_traits.py: Update tests

  Return dicts with the key-value pairs set up so as to ease with the data
  manipulation down the pipeline.
  This is also useful to help with the retrieval of all other extra
  information that was left out in the first iteration.

  This commit also updates the tests by ensuring they expect dicts rather than
  tuples.

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