Fix SodarAPI implementation & add tests

src/cubi_tk/sodar_api.py

@@ -90,7 +90,7 @@ def _api_call(
         # afterward remove the final trailing slash from the joined URL
         base_url_parts = [
             part if part.endswith("/") else f"{part}/"
-            for part in (self.sodar_url, "project", self.project_uuid, api, action)
+            for part in (self.sodar_url, api, "api", action, self.project_uuid)
         ]
         url = reduce(urlparse.urljoin, base_url_parts)[:-1]
         if params:

tests/conftest.py

@@ -65,6 +65,17 @@ def germline_trio_sheet_object(germline_trio_sheet_tsv):
         sheet=read_germline_tsv_sheet(germline_sheet_io, naming_scheme=NAMING_ONLY_SECONDARY_ID)
     )
 
+@pytest.fixture
+def mock_toml_config():
+    return textwrap.dedent(
+        """
+        [global]
+        sodar_server_url = "https://sodar.bihealth.org/"
+        sodar_api_token = "token123"
+        """
+    ).lstrip()
+
+
 
 def my_exists(self):
     """Method is used to patch pathlib.Path.exists"""

tests/test_sodar_api.py

@@ -0,0 +1,114 @@
+import os
+import pytest
+from unittest.mock import patch, MagicMock
+
+from cubi_tk import sodar_api
+from cubi_tk.common import GLOBAL_CONFIG_PATHS
+from cubi_tk.exceptions import ParameterException, SodarAPIException
+
+
+@pytest.fixture
+def sodar_api_args():
+    return {
+        "sodar_url": "https://sodar.bihealth.org/",
+        "sodar_api_token": "token123",
+        "project_uuid": "123e4567-e89b-12d3-a456-426655440000",
+    }
+
+@pytest.fixture
+def sodar_api_instance(sodar_api_args):
+    return sodar_api.SodarAPI(**sodar_api_args)
+
+def test_sodar_api_check_args(sodar_api_args, mock_toml_config, fs):
+    # Check args is automatically called in __init__, so we only need to create instances for testing
+    args = sodar_api_args.copy()
+
+    # Successful baseline creation
+    sodar_api.SodarAPI(**sodar_api_args)
+
+    # No toml config available, fail if any value is not given, or malformed
+    args["sodar_url"] = ""
+    with pytest.raises(ParameterException):
+        sodar_api.SodarAPI(**args)
+    args["sodar_url"] = "https://sodar.bihealth.org/"
+    args["sodar_api_token"] = ""
+    with pytest.raises(ParameterException):
+        sodar_api.SodarAPI(**args)
+    args["sodar_api_token"] = "token"
+    args["project_uuid"] = "not a uuid"
+    with pytest.raises(ParameterException):
+        sodar_api.SodarAPI(**args)
+
+    # With toml config available, only project_uuid is required
+    fs.create_file(os.path.expanduser(GLOBAL_CONFIG_PATHS[0]), contents=mock_toml_config)
+    sodar_api.SodarAPI(sodar_url='', sodar_api_token='', project_uuid='123e4567-e89b-12d3-a456-426655440000')
+
+
+@patch("cubi_tk.sodar_api.requests.get")
+@patch("cubi_tk.sodar_api.requests.post")
+def test_sodar_api_api_call(mock_post, mock_get, sodar_api_instance):
+
+    mock_get.return_value.status_code = 200
+    mock_get.return_value.json = MagicMock(return_value={"test": "test"})
+
+    # Test simple request
+    out = sodar_api_instance._api_call("samplesheet", "test")
+    mock_get.assert_called_with(
+        "https://sodar.bihealth.org/samplesheet/api/test/123e4567-e89b-12d3-a456-426655440000",
+        headers={"Authorization": "token token123"},
+    )
+    assert out == {"test": "test"}
+
+    # Test request with params
+    #FIXME: also test proper URL encoding of params?
+    out = sodar_api_instance._api_call("samplesheet", "test", params={'test': 'test'})
+    mock_get.assert_called_with(
+        "https://sodar.bihealth.org/samplesheet/api/test/123e4567-e89b-12d3-a456-426655440000?test=test",
+        headers={"Authorization": "token token123"},
+    )
+
+    # Test request with error
+    mock_get.return_value.status_code = 123
+    with pytest.raises(SodarAPIException):
+        out = sodar_api_instance._api_call("samplesheet", "test/action")
+
+    # Test post request with extra data
+    mock_post.return_value.status_code = 200
+    out = sodar_api_instance._api_call(
+        "landingzones", "fake/upload", method="post", data={'test': 'test2'}
+    )
+    mock_post.assert_called_once_with(
+        "https://sodar.bihealth.org/landingzones/api/fake/upload/123e4567-e89b-12d3-a456-426655440000",
+        headers={"Authorization": "token token123"},
+        files=None, data={'test': 'test2'}
+    )
+
+
+@patch("cubi_tk.sodar_api.SodarAPI._api_call")
+def test_sodar_api_get_ISA_samplesheet(mock_api_call, sodar_api_instance):
+
+    mock_api_call.return_value = {
+        "investigation": {"path": "i_Investigation.txt", "tsv": ""},
+        "studies": {"s_Study_0.txt": {"tsv": ""}},
+        "assays": {"a_name_0": {"tsv": ""}},
+        'date_modified': '2021-09-01T12:00:00Z',
+    }
+    expected = {
+        "investigation": {"filename": "i_Investigation.txt", "content": ""},
+        "study": {"filename": "s_Study_0.txt", "content": ""},
+        "assay": {"filename": "a_name_0", "content": ""},
+    }
+    assert expected == sodar_api_instance.get_ISA_samplesheet()
+
+
+    mock_api_call.return_value = {
+        "investigation": {"path": "i_Investigation.txt", "tsv": ""},
+        "studies": {"s_Study_0.txt": {"tsv": ""}, "s_Study_1.txt": {"tsv": ""}},
+        "assays": {"a_name_0": {"tsv": ""}, "a_name_1": {"tsv": ""}},
+        'date_modified': '2021-09-01T12:00:00Z',
+    }
+    with pytest.raises(NotImplementedError):
+        sodar_api_instance.get_ISA_samplesheet()
+
+
+