black reformat

tests/test_absolutize.py

@@ -17,24 +17,28 @@ def get_test_data_file(filename):
     return os.path.join(tests_dir, "test_data", filename)
 
 
-class TestAbsolutizePaths: #(unittest.TestCase):
+class TestAbsolutizePaths:  # (unittest.TestCase):
     # NOTE: ids can not be found, like 634, or forbidden, like 678
     @pytest.mark.parametrize("workflow_id", [41, 552])
     def test_make_paths_absolute(self, workflow_id):
-
         with patch_rdflib_urlopen(get_test_data_file):
-            with open(get_test_data_file(f"{workflow_id}_ro-crate-metadata.json"), "r") as f:
+            with open(
+                get_test_data_file(f"{workflow_id}_ro-crate-metadata.json"), "r"
+            ) as f:
                 json_data = json.load(f)
 
-            assert not is_all_absolute(rdflib.Graph().parse(data=json.dumps(json_data), format="json-ld"))
+            assert not is_all_absolute(
+                rdflib.Graph().parse(data=json.dumps(json_data), format="json-ld")
+            )
 
             json_data_abs_paths = make_paths_absolute(json_data, BASE_URL, 41)
 
-            G = rdflib.Graph().parse(data=json.dumps(json_data_abs_paths), format="json-ld")
+            G = rdflib.Graph().parse(
+                data=json.dumps(json_data_abs_paths), format="json-ld"
+            )
 
             assert is_all_absolute(G)
 
-
     def test_merged(self):
         G = merge_all_files("data/*21*.json")
         assert is_all_absolute(G)

tests/test_source_crates.py

@@ -141,4 +141,4 @@ def test_process_workflow_ids(
 
         with open(expected_file_path, "rb") as f:
             content = f.read()
-            assert content == b'{"name": "test"}'
+            assert content == b'{"name": "test"}'

workflowhub_graph/absolutize.py

@@ -14,8 +14,10 @@ def is_all_absolute(G: rdflib.Graph) -> bool:
 
                 # we accept file:// with a netloc, even if netloc is not a FQDN,
                 # see https://github.com/workflowhub-eu/workflowhub-graph/issues/1#issuecomment-2127351752
-                if netloc == '':
-                    print(f"found non-absolute path <{item}> {netloc}, {urlparse(item)}")
+                if netloc == "":
+                    print(
+                        f"found non-absolute path <{item}> {netloc}, {urlparse(item)}"
+                    )
                     return False
                 else:
                     print("this path is absolute", item, urlparse(item))

workflowhub_graph/cachedurlopen.py

@@ -1,21 +1,19 @@
-
-
 from unittest.mock import patch, MagicMock
 from contextlib import contextmanager
 import io
 
 
 cached_urls = {
-        "https://w3id.org/ro/crate/1.0/context": "ro-crate-context-1.0.json",
-        "https://w3id.org/ro/crate/1.1/context": "ro-crate-context-1.1.json",
-    }
+    "https://w3id.org/ro/crate/1.0/context": "ro-crate-context-1.0.json",
+    "https://w3id.org/ro/crate/1.1/context": "ro-crate-context-1.1.json",
+}
 
 
 @contextmanager
-def patch_rdflib_urlopen(file_locator):    
+def patch_rdflib_urlopen(file_locator):
     def cached_urlopen(request):
         url = request.get_full_url()
-        
+
         if url not in cached_urls:
             # TODO: store and use cache
             raise ValueError(f"URL {url} not in cache, have: {cached_urls.keys()}")
@@ -26,14 +24,13 @@ class Response(io.StringIO):
 
             def info(self):
                 return self.headers
-            
+
             def geturl(self):
                 return url
-            
+
         content = open(file_locator(cached_urls[url]), "rt").read()
 
         return Response(content)
-    
+
     with patch("rdflib.parser.urlopen", cached_urlopen):
         yield
-

workflowhub_graph/constants.py

@@ -18,4 +18,3 @@
 ZIP_ENDPOINT = "/workflows/{w_id}/ro_crate?version={w_version}"
 
 TARGET_FILE_NAME = "ro-crate-metadata.json"
-

workflowhub_graph/merge.py

@@ -1,4 +1,3 @@
-
 import argparse
 import glob
 import json
@@ -29,17 +28,21 @@ def merge_all_files(pattern="data/*.json") -> rdflib.Graph:
             json_data = make_paths_absolute(json_data, BASE_URL, w_id)
 
             # TODO: make this actual caching, and pre-populate in the test
-            with patch_rdflib_urlopen(lambda x: "tests/test_data/ro-crate-context-1.0.json"):
+            with patch_rdflib_urlopen(
+                lambda x: "tests/test_data/ro-crate-context-1.0.json"
+            ):
                 G.parse(data=json_data, format="json-ld")
-            
+
     # TODO: set a total version
-    return G    
+    return G
 
 
 if __name__ == "__main__":
     argparser = argparse.ArgumentParser()
-    argparser.add_argument("output_filename", help="The output filename.", default="merged.ttl")
+    argparser.add_argument(
+        "output_filename", help="The output filename.", default="merged.ttl"
+    )
     args = argparser.parse_args()
 
     G = merge_all_files()
-    G.serialize(args.output_filename, format="ttl")
+    G.serialize(args.output_filename, format="ttl")