Fix linting and typing errors

lib/galaxy/files/sources/__init__.py

@@ -185,15 +185,11 @@ class BaseFilesSource(FilesSource):
         else:
             return ctime.strftime("%m/%d/%Y %I:%M:%S %p")
 
+    @abc.abstractmethod
     def _serialization_props(self, user_context=None):
         """Serialize properties needed to recover plugin configuration.
-
         Used in to_dict method if for_serialization is True.
         """
-        effective_props = {}
-        for key, val in self._props.items():
-            effective_props[key] = self._evaluate_prop(val, user_context=user_context)
-        return effective_props
 
     def list(self, path="/", recursive=False, user_context=None, **kwargs):
         self._check_user_access(user_context)

lib/galaxy/files/sources/_pyfilesystem2.py

@@ -79,3 +79,9 @@ class PyFilesystem2FilesSource(BaseFilesSource):
                 "uri": uri,
                 "path": path,
             }
+
+    def _serialization_props(self, user_context=None):
+        effective_props = {}
+        for key, val in self._props.items():
+            effective_props[key] = self._evaluate_prop(val, user_context=user_context)
+        return effective_props

lib/galaxy/files/sources/anvil.py

@@ -10,7 +10,7 @@ class AnVILFilesSource(PyFilesystem2FilesSource):
     required_module = AnVILFS
     required_package = "fs.anvilfs"
 
-    def _open_fs(self, user_context, extra_props=None):
+    def _open_fs(self, user_context, kwargs=None):
         props = self._serialization_props(user_context)
         extra_props = kwargs.get("extra_props") or {}
         handle = AnVILFS(**{**props, **extra_props})

lib/galaxy/files/sources/base64.py

@@ -34,5 +34,11 @@ class Base64FilesSource(BaseFilesSource):
         else:
             return 0
 
+    def _serialization_props(self, user_context=None):
+        effective_props = {}
+        for key, val in self._props.items():
+            effective_props[key] = self._evaluate_prop(val, user_context=user_context)
+        return effective_props
+
 
 __all__ = ("Base64FilesSource",)

lib/galaxy/files/sources/drs.py

@@ -35,5 +35,11 @@ class DRSFilesSource(BaseFilesSource):
         else:
             return 0
 
+    def _serialization_props(self, user_context=None):
+        effective_props = {}
+        for key, val in self._props.items():
+            effective_props[key] = self._evaluate_prop(val, user_context=user_context)
+        return effective_props
+
 
 __all__ = ("DRSFilesSource",)

lib/galaxy/files/sources/http.py

@@ -44,7 +44,9 @@ class HTTPFilesSource(BaseFilesSource):
         raise NotImplementedError()
 
     def _serialization_props(self, user_context=None):
-        effective_props = super()._serialization_props(user_context=user_context)
+        effective_props = {}
+        for key, val in self._props.items():
+            effective_props[key] = self._evaluate_prop(val, user_context=user_context)
         effective_props["url_regex"] = self._url_regex_str
         return effective_props
 

lib/galaxy/files/sources/s3fs.py

@@ -86,7 +86,9 @@ class S3FsFilesSource(BaseFilesSource):
             }
 
     def _serialization_props(self, user_context=None):
-        effective_props = super()._serialization_props(user_context=user_context)
+        effective_props = {}
+        for key, val in self._props.items():
+            effective_props[key] = self._evaluate_prop(val, user_context=user_context)
         effective_props["bucket"] = self._bucket
         return effective_props
 

lib/galaxy/files/uris.py

@@ -46,7 +46,7 @@ def stream_url_to_file(
     target_path: Optional[str] = None,
     **kwargs: dict
 ) -> str:
-    if not file_sources:
+    if file_sources is None:
         file_sources = ConfiguredFileSources.from_dict(None, load_stock_plugins=True)
     file_source, rel_path = file_sources.get_file_source_path(url)
     if file_source:

test/unit/files/test_drs.py

@@ -2,6 +2,7 @@ import io
 import json
 import os
 import urllib
+from typing import Any
 from unittest import mock
 
 import responses
@@ -43,7 +44,7 @@ def test_file_source_drs_http():
     def check_specific_header(request, **kwargs):
         assert request.full_url == "https://my.respository.org/myfile.txt"
         assert request.headers["Authorization"] == "Basic Z2E0Z2g6ZHJz"
-        response = io.StringIO("hello drs world")
+        response: Any = io.StringIO("hello drs world")
         response.headers = {}
         return response
 

test/unit/files/test_ftp.py

@@ -1,9 +1,6 @@
-import io
 import os
-import urllib
-from unittest import mock
 
-from ._util import configured_file_sources, user_context_fixture, assert_realizes_as, assert_realizes_contains
+from ._util import configured_file_sources, user_context_fixture, assert_realizes_contains
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
 FILE_SOURCES_CONF = os.path.join(SCRIPT_DIRECTORY, "ftp_file_sources_conf.yml")

test/unit/files/test_http.py

@@ -1,6 +1,7 @@
 import io
 import os
 import urllib
+from typing import Any
 from unittest import mock
 
 from ._util import configured_file_sources, user_context_fixture, assert_realizes_as, assert_realizes_contains
@@ -13,7 +14,7 @@ def test_file_source_http_specific():
 
     def check_specific_header(request, **kwargs):
         assert request.headers["Authorization"] == "Bearer IBearTokens"
-        response = io.StringIO('hello specific world')
+        response: Any = io.StringIO('hello specific world')
         response.headers = {}
         return response
 
@@ -33,7 +34,7 @@ def test_file_source_another_http_specific():
 
     def check_another_header(request, **kwargs):
         assert request.headers["Another_header"] == "found"
-        response = io.StringIO('hello another world')
+        response: Any = io.StringIO('hello another world')
         response.headers = {}
         return response
 
@@ -53,7 +54,7 @@ def test_file_source_http_generic():
 
     def check_generic_headers(request, **kwargs):
         assert not request.headers
-        response = io.StringIO('hello generic world')
+        response: Any = io.StringIO('hello generic world')
         response.headers = {}
         return response
 
@@ -73,7 +74,7 @@ def test_file_source_ftp_url():
 
     def check_generic_headers(request, **kwargs):
         assert not request.headers
-        response = io.StringIO('This is ftp.gnu.org, the FTP server of the the GNU project.')
+        response: Any = io.StringIO('This is ftp.gnu.org, the FTP server of the the GNU project.')
         response.headers = {}
         return response
 

test/unit/files/test_s3.py

@@ -21,6 +21,7 @@ def test_file_source():
         contains=True,
     )
 
+
 def test_file_source_generic():
     file_url = "s3://ga4gh-demo-data/phenopackets/Cao-2018-TGFBR2-Patient_4.json"
     user_context = user_context_fixture()
@@ -34,6 +35,7 @@ def test_file_source_generic():
         file_sources, file_url, "PMID:30101859-Cao-2018-TGFBR2-Patient_4", user_context=user_context
     )
 
+
 def test_file_source_specific():
     file_url = "s3://genomeark/data_use_policies.txt"
     user_context = user_context_fixture()
@@ -43,6 +45,4 @@ def test_file_source_specific():
     assert file_source_pair.path == file_url
     assert file_source_pair.file_source.id == "test1"
 
-    assert_realizes_contains(
-        file_sources, file_url, "DATA USE POLICIES", user_context=user_context
-    )
+    assert_realizes_contains(file_sources, file_url, "DATA USE POLICIES", user_context=user_context)