feat: migration from attrs to pydantic (#49) (#65)

Makefile

@@ -33,3 +33,7 @@ lint: flake8 isort-check black-check
 .PHONY: test
 test:
 	TZ=UTC LC_ALL=C pytest .
+
+.PHONY: test-update-snapshots
+test-update-snapshots:
+	TZ=UTC LC_ALL=C pytest --snapshot-update .

requirements/base.txt

@@ -1,12 +1,9 @@
 # Base requirements
 
-# Attrs, helpful for removing boilerplate, cattr is for serialization/deserializaton.
-attrs >=21.2.0
-cattrs >=1.7.1
 # Easy date parsing (e.g., from API).
 python-dateutil >=2.8.1,<3.0
 
-# pydantic: typed models and validation 
+# pydantic: typed models and validation
 pydantic >=2,<3
 
 # toml parsing if python <3.11

requirements/test.txt

@@ -1,7 +1,8 @@
 -r base.txt
 
-# Multi-environment testing
-tox ==4.11.3
+# While pydantic is great in the production code, for just bundling
+# things, attrs is still better.
+attrs >=23
 
 # Wonderful py.test for testing
 pytest >=3.6.0

tests/cli/snapshots/test_cases/test_case_retrieve/result_output

@@ -30,8 +30,8 @@
   ],
   "sodar_uuid": "0b96111f-00c9-4ed2-a4a2-ec2ec3322066",
   "owner": null,
-  "date_created": "2023-06-26T17:15:13+00:00",
-  "date_modified": "2023-08-02T14:34:05+00:00",
+  "date_created": "2023-06-26T17:15:13+02:00",
+  "date_modified": "2023-08-02T14:34:05+02:00",
   "project": "062b8838-453f-4cf3-817d-a5ec76546462",
   "case": null,
   "state": "draft",

tests/cli/snapshots/test_projects/test_project_list_two_elements/result_output

@@ -4,7 +4,7 @@
     "parent": null,
     "title": "Test Category",
     "type": "CATEGORY",
-    "description": "None",
+    "description": null,
     "readme": "",
     "public_guest_access": false,
     "archive": false
@@ -14,7 +14,7 @@
     "parent": "4071c7f5769447f69dd9d2834d4b0164",
     "title": "Test Project",
     "type": "PROJECT",
-    "description": "None",
+    "description": null,
     "readme": "",
     "public_guest_access": false,
     "archive": false

tests/cli/snapshots/test_projects/test_project_retrieve/result_output

@@ -3,7 +3,7 @@
   "parent": null,
   "title": "Test Category",
   "type": "CATEGORY",
-  "description": "None",
+  "description": null,
   "readme": "",
   "public_guest_access": false,
   "archive": false

tests/cli/snapshots/test_varannos/test_varannoset_create/result_output

@@ -1,8 +1,8 @@
 {'sodar_uuid': 'e211747f-2a50-4a65-b192-c96bc2e111fa', 'date_created': '2023-10-31T08:15:15+01:00', 'date_modified': '2023-10-31T08:15:15+01:00', 'project': '062b8838-453f-4cf3-817d-a5ec76546462', 'title': 'my title', 'description': 'None', 'release': 'GRCh37', 'fields': ['pathogenicity', 'notes']}
 {
   "sodar_uuid": "e211747f-2a50-4a65-b192-c96bc2e111fa",
-  "date_created": "2023-10-31T08:15:15+00:00",
-  "date_modified": "2023-10-31T08:15:15+00:00",
+  "date_created": "2023-10-31T08:15:15+01:00",
+  "date_modified": "2023-10-31T08:15:15+01:00",
   "project": "062b8838-453f-4cf3-817d-a5ec76546462",
   "title": "my title",
   "description": "None",

tests/cli/snapshots/test_varannos/test_varannoset_retrieve/result_output

@@ -1,7 +1,7 @@
 {
   "sodar_uuid": "e211747f-2a50-4a65-b192-c96bc2e111fa",
-  "date_created": "2023-10-31T08:15:15+00:00",
-  "date_modified": "2023-10-31T08:15:15+00:00",
+  "date_created": "2023-10-31T08:15:15+01:00",
+  "date_modified": "2023-10-31T08:15:15+01:00",
   "project": "062b8838-453f-4cf3-817d-a5ec76546462",
   "title": "my title",
   "description": "None",

tests/cli/snapshots/test_varannos/test_varannoset_update/result_output

@@ -1,7 +1,7 @@
 {
   "sodar_uuid": "e211747f-2a50-4a65-b192-c96bc2e111fa",
-  "date_created": "2023-10-31T08:15:15+00:00",
-  "date_modified": "2023-10-31T08:15:15+00:00",
+  "date_created": "2023-10-31T08:15:15+01:00",
+  "date_modified": "2023-10-31T08:15:15+01:00",
   "project": "062b8838-453f-4cf3-817d-a5ec76546462",
   "title": "my title",
   "description": "None",

tests/cli/snapshots/test_varannos/test_varannosetentry_create/result_output

@@ -1,7 +1,7 @@
 {
   "sodar_uuid": "4a3a96ae-ddd8-4e9f-897f-5fbbadfedad5",
-  "date_created": "2023-10-31T09:02:26+00:00",
-  "date_modified": "2023-10-31T09:02:26+00:00",
+  "date_created": "2023-10-31T09:02:26+01:00",
+  "date_modified": "2023-10-31T09:02:26+01:00",
   "varannoset": "0a30d59b-7257-43d1-8964-2a2ac50af7f2",
   "release": "GRCh37",
   "chromosome": "1",

tests/cli/snapshots/test_varannos/test_varannosetentry_retrieve/result_output

@@ -1,7 +1,7 @@
 {
   "sodar_uuid": "4a3a96ae-ddd8-4e9f-897f-5fbbadfedad5",
-  "date_created": "2023-10-31T09:02:26+00:00",
-  "date_modified": "2023-10-31T09:02:26+00:00",
+  "date_created": "2023-10-31T09:02:26+01:00",
+  "date_modified": "2023-10-31T09:02:26+01:00",
   "varannoset": "0a30d59b-7257-43d1-8964-2a2ac50af7f2",
   "release": "GRCh37",
   "chromosome": "1",

tests/cli/snapshots/test_varannos/test_varannosetentry_update/result_output

@@ -1,7 +1,7 @@
 {
   "sodar_uuid": "4a3a96ae-ddd8-4e9f-897f-5fbbadfedad5",
-  "date_created": "2023-10-31T09:02:26+00:00",
-  "date_modified": "2023-10-31T09:02:26+00:00",
+  "date_created": "2023-10-31T09:02:26+01:00",
+  "date_modified": "2023-10-31T09:02:26+01:00",
   "varannoset": "0a30d59b-7257-43d1-8964-2a2ac50af7f2",
   "release": "GRCh37",
   "chromosome": "1",

tests/cli/test_importer.py

@@ -1,17 +1,22 @@
 """Test CLI for importer API."""
 
+import glob
 import json
+import types
 import typing
 import uuid
 
 import pytest
 from pytest_mock import MockerFixture
 from pytest_snapshot.plugin import Snapshot
+from requests_mock import ANY
 from requests_mock.mocker import Mocker as RequestsMocker
 from typer.testing import CliRunner
 
 from tests.conftest import FakeFs
 from varfish_cli.cli import app
+from varfish_cli.cli.importer import cli_caseimportinfo_create
+from varfish_cli.config import CommonOptions
 
 
 @pytest.fixture
@@ -78,3 +83,95 @@ def test_varannoset_list_one_element(
 
     assert result.exit_code == 0, result.output
     snapshot.assert_match(result.output, "result_output")
+
+
+def test_caseimportinfo_create_raw_func_call(
+    fake_fs_configured: FakeFs,
+    requests_mock: RequestsMocker,
+    fake_conn: typing.Tuple[str, str],
+    caseimportinfo_list_result_two_elements: typing.List[typing.Any],
+    snapshot: Snapshot,
+    mocker: MockerFixture,
+):
+    """Test through function call and not runner.
+
+    We create a stubbed out replay of the requests communication and only check
+    results against snapshots. This is not much more than a smoke test or a
+    change test.
+    """
+    fake_fs_configured.fs.add_real_directory("tests/data/importer")
+
+    mocker.patch("varfish_cli.config.open", fake_fs_configured.open_, create=True)
+    mocker.patch("varfish_cli.config.os", fake_fs_configured.os)
+
+    project_uuid = "5b1d876d-5ea9-426f-9f8f-f82b18830e16"
+    host, token = fake_conn
+    m_any = requests_mock.register_uri(
+        ANY, ANY, request_headers={"Authorization": f"Token {token}"}, json=[]
+    )
+    m_case_import_info = requests_mock.post(
+        f"{host}/importer/api/case-import-info/{project_uuid}/",
+        request_headers={"Authorization": f"Token {token}"},
+        json=caseimportinfo_list_result_two_elements[0],
+    )
+    m_case_bam_qc_file = requests_mock.post(
+        f"{host}/importer/api/bam-qc-file/8adbf84e-adb2-4c5d-9b5a-2a8194307b79/",
+        request_headers={"Authorization": f"Token {token}"},
+        json=caseimportinfo_list_result_two_elements[0]["bam_qc_files"][0],
+    )
+    m_case_variant_set_import_info_create = requests_mock.post(
+        f"{host}/importer/api/variant-set-import-info/8adbf84e-adb2-4c5d-9b5a-2a8194307b79/",
+        request_headers={"Authorization": f"Token {token}"},
+        json=caseimportinfo_list_result_two_elements[0]["variant_sets"][0],
+    )
+    m_case_genotype_file = requests_mock.post(
+        f"{host}/importer/api/genotype-file/104f900b-fa9c-4bd5-a119-35544293fe7f/",
+        request_headers={"Authorization": f"Token {token}"},
+        json=caseimportinfo_list_result_two_elements[0]["variant_sets"][0]["genotype_files"][0],
+    )
+    m_case_db_info_file = requests_mock.post(
+        f"{host}/importer/api/database-info-file/104f900b-fa9c-4bd5-a119-35544293fe7f/",
+        request_headers={"Authorization": f"Token {token}"},
+        json=caseimportinfo_list_result_two_elements[0]["variant_sets"][0]["db_info_files"][0],
+    )
+    m_case_variant_set_import_info_update = requests_mock.put(
+        (
+            f"{host}/importer/api/variant-set-import-info/8adbf84e-adb2-4c5d-9b5a-2a8194307b79/"
+            "104f900b-fa9c-4bd5-a119-35544293fe7f/"
+        ),
+        request_headers={"Authorization": f"Token {token}"},
+        json=caseimportinfo_list_result_two_elements[0]["variant_sets"][0],
+    )
+    m_case_import_info_update = requests_mock.put(
+        (
+            f"{host}/importer/api/case-import-info/5b1d876d-5ea9-426f-9f8f-f82b18830e16/"
+            "8adbf84e-adb2-4c5d-9b5a-2a8194307b79/"
+        ),
+        request_headers={"Authorization": f"Token {token}"},
+        json=caseimportinfo_list_result_two_elements[0],
+    )
+    ctx = types.SimpleNamespace(
+        obj=CommonOptions(
+            verbose=True,
+            verify_ssl=False,
+            config=None,
+            varfish_server_url=host,
+            varfish_api_token=token,
+        )
+    )
+    cli_caseimportinfo_create(
+        ctx=ctx,
+        project_uuid=project_uuid,
+        paths=list(sorted(glob.glob("tests/data/importer/*"))),
+    )
+
+    assert m_any.call_count == 10
+    assert m_case_import_info.call_count == 1
+    assert m_case_bam_qc_file.call_count == 1
+    assert m_case_variant_set_import_info_create.call_count == 2
+    assert m_case_genotype_file.call_count == 2
+    assert m_case_db_info_file.call_count == 2
+    assert m_case_variant_set_import_info_update.call_count == 2
+    assert m_case_import_info_update.call_count == 1
+
+    mocker.stopall()