about summary refs log tree commit diff
path: root/tests/uploader
diff options
context:
space:
mode:
Diffstat (limited to 'tests/uploader')
-rw-r--r--tests/uploader/phenotypes/__init__.py1
-rw-r--r--tests/uploader/phenotypes/test_misc.py387
-rw-r--r--tests/uploader/publications/__init__.py1
-rw-r--r--tests/uploader/publications/test_misc.py68
-rw-r--r--tests/uploader/test_parse.py3
5 files changed, 459 insertions, 1 deletions
diff --git a/tests/uploader/phenotypes/__init__.py b/tests/uploader/phenotypes/__init__.py
new file mode 100644
index 0000000..1e0a932
--- /dev/null
+++ b/tests/uploader/phenotypes/__init__.py
@@ -0,0 +1 @@
+"""phenotypes tests"""
diff --git a/tests/uploader/phenotypes/test_misc.py b/tests/uploader/phenotypes/test_misc.py
new file mode 100644
index 0000000..cf475ad
--- /dev/null
+++ b/tests/uploader/phenotypes/test_misc.py
@@ -0,0 +1,387 @@
+"""Test miscellaneous phenotypes functions."""
+
+import pytest
+
+from uploader.phenotypes.misc import phenotypes_data_differences
+
+__sample_db_phenotypes_data__ = (
+    {
+        "PhenotypeId": 4,
+        "xref_id": 10001,
+        "DataId": 8967043,
+        "data": {
+            "B6D2F1": {"StrainId": 1, "value": None},
+            "C57BL/6J": {"StrainId": 2, "value": None},
+            "DBA/2J": {"StrainId": 3, "value": None},
+            "BXD1": {"StrainId": 4, "value": 61.4},
+            "BXD2": {"StrainId": 5, "value": 49},
+            "BXD5": {"StrainId": 6, "value": 62.5},
+            "BXD6": {"StrainId": 7, "value": 53.1}
+        }
+    },
+    {
+        "PhenotypeId": 10,
+        "xref_id": 10002,
+        "DataId": 8967044,
+        "data": {
+            "B6D2F1": {"StrainId": 1, "value": None},
+            "C57BL/6J": {"StrainId": 2, "value": None},
+            "DBA/2J": {"StrainId": 3, "value": None},
+            "BXD1": {"StrainId": 4, "value": 54.1},
+            "BXD2": {"StrainId": 5, "value": 50.1},
+            "BXD5": {"StrainId": 6, "value": 53.3},
+            "BXD6": {"StrainId": 7, "value": 55.1}
+        }
+    },
+    {
+        "PhenotypeId": 15,
+        "xref_id": 10003,
+        "DataId": 8967045,
+        "data": {
+            "B6D2F1": {"StrainId": 1, "value": None},
+            "C57BL/6J": {"StrainId": 2, "value": None},
+            "DBA/2J": {"StrainId": 3, "value": None},
+            "BXD1": {"StrainId": 4, "value": 483},
+            "BXD2": {"StrainId": 5, "value": 403},
+            "BXD5": {"StrainId": 6, "value": 501},
+            "BXD6": {"StrainId": 7, "value": 403}
+        }
+    },
+    {
+        "PhenotypeId": 20,
+        "xref_id": 10004,
+        "DataId": 8967046,
+        "data": {
+            "B6D2F1": {"StrainId": 1, "value": None},
+            "C57BL/6J": {"StrainId": 2, "value": None},
+            "DBA/2J": {"StrainId": 3, "value": None},
+            "BXD1": {"StrainId": 4, "value": 49.8},
+            "BXD2": {"StrainId": 5, "value": 45.5},
+            "BXD5": {"StrainId": 6, "value": 62.9},
+            "BXD6": {"StrainId": 7, "value": None}
+        }
+    },
+    {
+        "PhenotypeId": 25,
+        "xref_id": 10005,
+        "DataId": 8967047,
+        "data": {
+            "B6D2F1": {"StrainId": 1, "value": None},
+            "C57BL/6J": {"StrainId": 2, "value": None},
+            "DBA/2J": {"StrainId": 3, "value": None},
+            "BXD1": {"StrainId": 4, "value": 46},
+            "BXD2": {"StrainId": 5, "value": 44.9},
+            "BXD5": {"StrainId": 6, "value": 52.5},
+            "BXD6": {"StrainId": 7, "value": None}
+        }
+    })
+
+
+@pytest.mark.unit_test
+@pytest.mark.parametrize(
+    "filedata,dbdata,expected",
+    ((tuple(), tuple(), tuple()), # No data
+
+     # No data difference
+     (({
+             "phenotype_id": 4,
+             "xref_id": 10001,
+             "data": {
+                 "B6D2F1": None,
+                 "C57BL/6J": None,
+                 "DBA/2J": None,
+                 "BXD1": 61.4,
+                 "BXD2": 49,
+                 "BXD5":62.5,
+                 "BXD6": 53.1
+             }
+     },
+          {
+              "phenotype_id": 10,
+              "xref_id": 10002,
+              "data": {
+                  "B6D2F1": None,
+                  "C57BL/6J": None,
+                  "DBA/2J": None,
+                  "BXD1": 54.1,
+                  "BXD2": 50.1,
+                  "BXD5": 53.3,
+                  "BXD6": 55.1
+              }
+          },
+          {
+              "phenotype_id": 15,
+              "xref_id": 10003,
+              "data": {
+                  "B6D2F1": None,
+                  "C57BL/6J": None,
+                  "DBA/2J": None,
+                  "BXD1": 483,
+                  "BXD2": 403,
+                  "BXD5": 501,
+                  "BXD6": 403
+              }
+          },
+          {
+              "phenotype_id": 20,
+              "xref_id": 10004,
+              "data": {
+                  "B6D2F1": None,
+                  "C57BL/6J": None,
+                  "DBA/2J": None,
+                  "BXD1": 49.8,
+                  "BXD2": 45.5,
+                  "BXD5": 62.9,
+                  "BXD6": None
+              }
+          },
+          {
+              "phenotype_id": 25,
+              "xref_id": 10005,
+              "data": {
+                  "B6D2F1": None,
+                  "C57BL/6J": None,
+                  "DBA/2J": None,
+                  "BXD1": 46,
+                  "BXD2": 44.9,
+                  "BXD5": 52.5,
+                  "BXD6": None
+              }
+          }),
+         __sample_db_phenotypes_data__,
+         tuple()),
+
+     # Change values: No deletions
+     (({
+             "phenotype_id": 4,
+             "xref_id": 10001,
+             "data": {
+                 "B6D2F1": None,
+                 "C57BL/6J": None,
+                 "DBA/2J": None,
+                 "BXD1": 77.2,
+                 "BXD2": 49,
+                 "BXD5":62.5,
+                 "BXD6": 53.1
+             }
+     },
+          {
+              "phenotype_id": 10,
+              "xref_id": 10002,
+              "data": {
+                  "B6D2F1": None,
+                  "C57BL/6J": None,
+                  "DBA/2J": None,
+                  "BXD1": 54.1,
+                  "BXD2": 50.1,
+                  "BXD5": 53.3,
+                  "BXD6": 55.1
+              }
+          },
+          {
+              "phenotype_id": 15,
+              "xref_id": 10003,
+              "data": {
+                  "B6D2F1": None,
+                  "C57BL/6J": None,
+                  "DBA/2J": None,
+                  "BXD1": 483,
+                  "BXD2": 403,
+                  "BXD5": 503,
+                  "BXD6": 903
+              }
+          },
+          {
+              "phenotype_id": 20,
+              "xref_id": 10004,
+              "data": {
+                  "B6D2F1": None,
+                  "C57BL/6J": None,
+                  "DBA/2J": 1,
+                  "BXD1": 8,
+                  "BXD2": 9,
+                  "BXD5": 62.9,
+                  "BXD6": None
+              }
+          },
+          {
+              "phenotype_id": 25,
+              "xref_id": 10005,
+              "data": {
+                  "B6D2F1": None,
+                  "C57BL/6J": None,
+                  "DBA/2J": None,
+                  "BXD1": 46,
+                  "BXD2": 44.9,
+                  "BXD5": 52.5,
+                  "BXD6": None
+              }
+          }),
+         __sample_db_phenotypes_data__,
+      ({
+          "PhenotypeId": 4,
+          "xref_id": 10001,
+          "DataId": 8967043,
+          "StrainId": 4,
+          "StrainName": "BXD1",
+          "value": 77.2
+      },
+       {
+           "PhenotypeId": 15,
+           "xref_id": 10003,
+           "DataId": 8967045,
+           "StrainId": 6,
+           "StrainName": "BXD5",
+           "value": 503
+       },
+       {
+           "PhenotypeId": 15,
+           "xref_id": 10003,
+           "DataId": 8967045,
+           "StrainId": 7,
+           "StrainName": "BXD6",
+           "value": 903
+       },
+       {
+           "PhenotypeId": 20,
+           "xref_id": 10004,
+           "DataId": 8967046,
+           "StrainId": 3,
+           "StrainName": "DBA/2J",
+           "value": 1
+       },
+       {
+           "PhenotypeId": 20,
+           "xref_id": 10004,
+           "DataId": 8967046,
+           "StrainId": 4,
+           "StrainName": "BXD1",
+           "value": 8
+       },
+       {
+           "PhenotypeId": 20,
+           "xref_id": 10004,
+           "DataId": 8967046,
+           "StrainId": 5,
+           "StrainName": "BXD2",
+           "value": 9
+       })),
+
+     # Changes — with deletions
+     (({
+             "phenotype_id": 4,
+             "xref_id": 10001,
+             "data": {
+                 "B6D2F1": None,
+                 "C57BL/6J": None,
+                 "DBA/2J": None,
+                 "BXD1": None,
+                 "BXD2": 49,
+                 "BXD5":62.5,
+                 "BXD6": 53.1
+             }
+     },
+          {
+              "phenotype_id": 10,
+              "xref_id": 10002,
+              "data": {
+                  "B6D2F1": None,
+                  "C57BL/6J": None,
+                  "DBA/2J": None,
+                  "BXD1": 54.1,
+                  "BXD2": 50.1,
+                  "BXD5": 53.3,
+                  "BXD6": 55.1
+              }
+          },
+          {
+              "phenotype_id": 15,
+              "xref_id": 10003,
+              "data": {
+                  "B6D2F1": None,
+                  "C57BL/6J": None,
+                  "DBA/2J": None,
+                  "BXD1": 483,
+                  "BXD2": 403,
+                  "BXD5": None,
+                  "BXD6": None
+              }
+          },
+          {
+              "phenotype_id": 20,
+              "xref_id": 10004,
+              "data": {
+                  "B6D2F1": None,
+                  "C57BL/6J": None,
+                  "DBA/2J": 15,
+                  "BXD1": None,
+                  "BXD2": 24,
+                  "BXD5": 62.9,
+                  "BXD6": None
+              }
+          },
+          {
+              "phenotype_id": 25,
+              "xref_id": 10005,
+              "data": {
+                  "B6D2F1": None,
+                  "C57BL/6J": None,
+                  "DBA/2J": None,
+                  "BXD1": 46,
+                  "BXD2": 44.9,
+                  "BXD5": 52.5,
+                  "BXD6": None
+              }
+          }),
+         __sample_db_phenotypes_data__,
+      ({
+          "PhenotypeId": 4,
+          "xref_id": 10001,
+          "DataId": 8967043,
+          "StrainId": 4,
+          "StrainName": "BXD1",
+          "value": None
+      },
+       {
+           "PhenotypeId": 15,
+           "xref_id": 10003,
+           "DataId": 8967045,
+           "StrainId": 6,
+           "StrainName": "BXD5",
+           "value": None
+       },
+       {
+           "PhenotypeId": 15,
+           "xref_id": 10003,
+           "DataId": 8967045,
+           "StrainId": 7,
+           "StrainName": "BXD6",
+           "value": None
+       },
+       {
+           "PhenotypeId": 20,
+           "xref_id": 10004,
+           "DataId": 8967046,
+           "StrainId": 3,
+           "StrainName": "DBA/2J",
+           "value": 15
+       },
+       {
+           "PhenotypeId": 20,
+           "xref_id": 10004,
+           "DataId": 8967046,
+           "StrainId": 4,
+           "StrainName": "BXD1",
+           "value": None
+       },
+       {
+           "PhenotypeId": 20,
+           "xref_id": 10004,
+           "DataId": 8967046,
+           "StrainId": 5,
+           "StrainName": "BXD2",
+           "value": 24
+       }))))
+def test_phenotypes_data_differences(filedata, dbdata, expected):
+    """Test differences are computed correctly."""
+    assert phenotypes_data_differences(filedata, dbdata) == expected
diff --git a/tests/uploader/publications/__init__.py b/tests/uploader/publications/__init__.py
new file mode 100644
index 0000000..de15e08
--- /dev/null
+++ b/tests/uploader/publications/__init__.py
@@ -0,0 +1 @@
+"""publications tests"""
diff --git a/tests/uploader/publications/test_misc.py b/tests/uploader/publications/test_misc.py
new file mode 100644
index 0000000..8c7e567
--- /dev/null
+++ b/tests/uploader/publications/test_misc.py
@@ -0,0 +1,68 @@
+"""Tests for functions used for bulk editing."""
+import pytest
+
+from uploader.publications.misc import publications_differences
+
+
+@pytest.mark.unit_test
+@pytest.mark.parametrize(
+    "filedata,dbdata,pubmed2pubidmap,expected",
+    (((), (), {}, tuple()), # no data
+
+     # Same Data
+     (({"phenotype_id": 1, "xref_id": 10001, "PubMed_ID": 9999999999999},
+       {"phenotype_id": 1, "xref_id": 10002, "PubMed_ID": 9999999999999},
+       {"phenotype_id": 1, "xref_id": 10003, "PubMed_ID": 9999999999999},
+       {"phenotype_id": 1, "xref_id": 10005, "PubMed_ID": 9999999999999}),
+      ({"PhenotypeId": 1, "xref_id": 10001, "PublicationId": 15,
+        "PubMed_ID": 9999999999999},
+       {"PhenotypeId": 1, "xref_id": 10002, "PublicationId": 15,
+        "PubMed_ID": 9999999999999},
+       {"PhenotypeId": 1, "xref_id": 10003, "PublicationId": 15,
+        "PubMed_ID": 9999999999999},
+       {"PhenotypeId": 1, "xref_id": 10004, "PublicationId": 15,
+        "PubMed_ID": 9999999999999}),
+      {9999999999999: 15},
+      tuple()),
+
+     # Differences: no new pubmeds (all pubmeds in db)
+     (({"phenotype_id": 1, "xref_id": 10001, "PubMed_ID": 9999999999999},
+       {"phenotype_id": 1, "xref_id": 10002, "PubMed_ID": 9999999999998},
+       {"phenotype_id": 1, "xref_id": 10003, "PubMed_ID": 9999999999999},
+       {"phenotype_id": 1, "xref_id": 10004, "PubMed_ID": 9999999999997}),
+      ({"PhenotypeId": 1, "xref_id": 10001, "PublicationId": 15,
+        "PubMed_ID": 9999999999999},
+       {"PhenotypeId": 1, "xref_id": 10002, "PublicationId": 15,
+        "PubMed_ID": 9999999999999},
+       {"PhenotypeId": 1, "xref_id": 10003, "PublicationId": 15,
+        "PubMed_ID": 9999999999999},
+       {"PhenotypeId": 1, "xref_id": 10004, "PublicationId": 15,
+        "PubMed_ID": None}),
+      {9999999999999: 15, 9999999999998: 18, 9999999999997: 12},
+      ({"PhenotypeId": 1, "xref_id": 10002, "PublicationId": 18,
+          "PubMed_ID": 9999999999998},
+       {"PhenotypeId": 1, "xref_id": 10004, "PublicationId": 12,
+        "PubMed_ID": 9999999999997})),
+
+     # Differences: Deletions of pubmeds
+     (({"phenotype_id": 1, "xref_id": 10001, "PubMed_ID": 9999999999999},
+       {"phenotype_id": 1, "xref_id": 10002, "PubMed_ID": None},
+       {"phenotype_id": 1, "xref_id": 10003, "PubMed_ID": 9999999999999},
+       {"phenotype_id": 1, "xref_id": 10004, "PubMed_ID": None}),
+      ({"PhenotypeId": 1, "xref_id": 10001, "PublicationId": 15,
+        "PubMed_ID": 9999999999999},
+       {"PhenotypeId": 1, "xref_id": 10002, "PublicationId": 15,
+        "PubMed_ID": 9999999999999},
+       {"PhenotypeId": 1, "xref_id": 10003, "PublicationId": 15,
+        "PubMed_ID": 9999999999999},
+       {"PhenotypeId": 1, "xref_id": 10004, "PublicationId": 15,
+        "PubMed_ID": 9999999999999}),
+      {9999999999999: 15, 9999999999998: 18, 9999999999997: 12},
+      ({"PhenotypeId": 1, "xref_id": 10002, "PublicationId": None,
+        "PubMed_ID": None},
+       {"PhenotypeId": 1, "xref_id": 10004, "PublicationId": None,
+        "PubMed_ID": None}))))
+def test_publications_differences(filedata, dbdata, pubmed2pubidmap, expected):
+    """Test publication differences — flesh out description…"""
+    assert publications_differences(
+        filedata, dbdata, pubmed2pubidmap) == expected
diff --git a/tests/uploader/test_parse.py b/tests/uploader/test_parse.py
index 076c47c..20c75b7 100644
--- a/tests/uploader/test_parse.py
+++ b/tests/uploader/test_parse.py
@@ -8,7 +8,8 @@ from uploader.jobs import job, jobsnamespace
 
 from tests.conftest import uploadable_file_object
 
-def test_parse_with_existing_uploaded_file(#pylint: disable=[too-many-arguments]
+def test_parse_with_existing_uploaded_file(
+        #pylint: disable=[too-many-arguments,too-many-positional-arguments]
         client,
         db_url,
         redis_url,
generated by cgit-pink 1.4.1 (git 2.36.1) at 2025-11-08 17:31:59 +0000