Clean up

mutalyzer_retriever/retriever.py

@@ -69,7 +69,7 @@ def _fetch_unknown_source(reference_id, reference_type, reference_source, size_o
     else:
         status["lrg"]["errors"].append(
             ValueError(
-                "Lrg fetch does not support '{}' reference type.".format(reference_type)
+                f"Lrg fetch does not support '{reference_type}' reference type."
             )
         )
 

mutalyzer_retriever/sources/ensembl.py

@@ -52,7 +52,9 @@ def fetch_gff3(feature_id, api_base, timeout=1):
 def _get_tark_versions(reference_id, api_base, timeout=1):
     endpoint = "transcript"
     params = {"stable_id": reference_id}
-    tark_req = json.loads(request(url=f"{api_base}/{endpoint}", params=params, timeout=timeout))
+    tark_req = json.loads(
+        request(url=f"{api_base}/{endpoint}", params=params, timeout=timeout)
+    )
     tark_versions_38 = []
     tark_versions_37 = []
     if tark_req["results"]:
@@ -99,7 +101,9 @@ def fetch_json(reference_id, reference_version, api_base, assembly="GRCh38", tim
         "stable_id_version": reference_version,
         "expand": "translations, genes, exons",
     }
-    req = requests.request(method="get", url=f"{api_base}/{endpoint}", params=params, timeout=timeout)
+    req = requests.request(
+        method="get", url=f"{api_base}/{endpoint}", params=params, timeout=timeout
+    )
     return req.json()
 
 
@@ -150,4 +154,6 @@ def fetch(reference_id, reference_type=None, reference_source=None, timeout=1):
     elif reference_type == "genbank":
         return None, "genbank"
 
-    raise ValueError(f"{reference_source} fetch does not support {reference_type} reference type.")
+    raise ValueError(
+        f"{reference_source} fetch does not support {reference_type} reference type."
+    )

tests/commons.py

@@ -1,14 +1,12 @@
 import json
 from pathlib import Path
-
 import pytest
-
 from mutalyzer_retriever.retriever import NoReferenceError
 
 
 @pytest.fixture(autouse=True)
 def patch_retriever(monkeypatch):
-    '''retrieve all monkeypath'''
+    """retrieve all monkeypath"""
     from .test_fetch import (
         _fetch_gff3,
         _fetch_json,
@@ -26,11 +24,6 @@ def patch_retriever(monkeypatch):
     )
     monkeypatch.setattr("mutalyzer_retriever.sources.ensembl.fetch_json", _fetch_json)
     monkeypatch.setattr("mutalyzer_retriever.retriever.retrieve_raw", _retrieve_raw)
-
-
-
-
-
 
 
 def _get_content(relative_location):
@@ -56,7 +49,11 @@ def _retrieve_raw(
     elif r_id.startswith("LRG_"):
         return _get_content("data/" + r_id + ".lrg"), "lrg", "lrg"
     elif r_type == "json":
-        return (json.loads(_get_content("data/" + r_id + ".tark_raw.json")),"json","ensembl_tark")
+        return (
+            json.loads(_get_content("data/" + r_id + ".tark_raw.json")),
+            "json",
+            "ensembl_tark",
+        )
     else:
         return _get_content("data/" + r_id + ".gff3"), "gff3", "ncbi"
 
@@ -94,7 +91,7 @@ def _retrieve_raw(
             "ENSG00000198899",
         ]
     },
-    "ensembl_tark":{
+    "ensembl_tark": {
         "json": [
             "ENST00000383925.1",
             "ENST00000383925",

tests/test_fetch.py

@@ -1,8 +1,6 @@
 import pytest
-
 from mutalyzer_retriever.configuration import settings
 from mutalyzer_retriever.sources.ensembl import fetch
-
 from .commons import _get_content, patch_retriever
 
 API_BASE = settings["ENSEMBL_API"]

tests/test_model_validation.py

@@ -10,9 +10,8 @@
 from .commons import references, patch_retriever
 
 
-
 def get_references_content(references):
-    '''read raw response from tests data folder'''
+    """Read raw response from tests data folder"""
     r_contents = []
     for r_source in references.keys():
         for r_type in references[r_source]:
@@ -25,11 +24,7 @@ def get_references_content(references):
                     )
                     r_content = json.loads(path_gb.open().read())
                 else:
-                    path_gb = (
-                        Path(Path(__file__).parent)
-                        / "data"
-                        / f"{r_id}.{r_type}"
-                    )
+                    path_gb = Path(Path(__file__).parent) / "data" / f"{r_id}.{r_type}"
                     with path_gb.open() as f:
                         r_content = f.read()
                 r_contents.append(
@@ -44,20 +39,18 @@ def get_references_content(references):
     return r_contents
 
 
-@pytest.mark.parametrize(
-    "r_source, r_type, r_content, r_id",
-    get_references_content(references),
-)
+@pytest.mark.parametrize("r_source, r_type, r_content, r_id", get_references_content(references))
 def test_schema_validation(r_source, r_type, r_content, r_id, monkeypatch: pytest.MonkeyPatch):
-    '''parse raw response and check its output schema'''
-    monkeypatch.setattr("mutalyzer_retriever.parsers.json_ensembl._seq_from_rest", 
-                        lambda _0,_1, _2, _3, _4: _seq_from_rest(r_id))
+    """Parse raw response and check its output schema"""
+    monkeypatch.setattr(
+        "mutalyzer_retriever.parsers.json_ensembl._seq_from_rest",
+        lambda _0, _1, _2, _3, _4: _seq_from_rest(r_id),
+    )
     r_model = parser.parse(
         reference_content=r_content,
         reference_type=r_type,
         reference_source=r_source,
     )
-
     if r_source in ["ensembl_tark", "lrg"]:
         assert validate(r_model["annotations"]) is None
     else:

tests/test_retriever_model.py

@@ -2,9 +2,9 @@
 from pathlib import Path
 
 import pytest
+from mutalyzer_retriever import retrieve_model
 from .commons import references, _retrieve_raw, patch_retriever, _get_content
 
-from mutalyzer_retriever import retrieve_model
 
 
 def get_tests(references):
@@ -15,19 +15,22 @@ def get_tests(references):
         for r_type in references[r_source].keys():
             for r_id in references[r_source][r_type]:
                 if r_type == "json":
-                    p = Path(Path(__file__).parent) / "data" / str(r_id + ".tark.model.json")
+                    p = (
+                        Path(Path(__file__).parent)
+                        / "data"
+                        / str(r_id + ".tark.model.json")
+                    )
                 else:
                     p = Path(Path(__file__).parent) / "data" / str(r_id + ".model.json")
                 with p.open() as f:
                     r_model = json.loads(f.read())
-
                 tests.append(
                     pytest.param(
                         r_id,
                         r_source,
                         r_type,
                         r_model,
-                        id="{}-{}-{}".format(r_source, r_type, r_id),
+                        id=f"{r_source}-{r_type}-{r_id}",
                     )
                 )
 
@@ -38,10 +41,10 @@ def _seq_from_rest(r_id):
     return _get_content("data/" + str(r_id) + ".sequence")
 
 
-
-@pytest.mark.parametrize("r_id, r_source, r_type, expected_model",get_tests(references))
+@pytest.mark.parametrize("r_id, r_source, r_type, expected_model", get_tests(references))
 def test_model(r_id, r_source, r_type, expected_model, monkeypatch: pytest.MonkeyPatch):
-    monkeypatch.setattr("mutalyzer_retriever.parsers.json_ensembl._seq_from_rest", 
-                        lambda _0, _1, _2, _3, _4: _seq_from_rest(r_id))
-    assert retrieve_model(r_id, r_source,r_type) == expected_model
-
+    monkeypatch.setattr(
+        "mutalyzer_retriever.parsers.json_ensembl._seq_from_rest",
+        lambda _0, _1, _2, _3, _4: _seq_from_rest(r_id),
+    )
+    assert retrieve_model(r_id, r_source, r_type) == expected_model