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Fix logging in export_history.py, fix Azure and S3 tests #19542

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Fix logging in export_history.py, fix Azure and S3 tests #19542

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4 changes: 1 addition & 3 deletions lib/galaxy/model/store/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,6 @@
TYPE_CHECKING,
Union,
)
from urllib.parse import urlparse

from bdbag import bdbag_api as bdb
from boltons.iterutils import remap
Expand Down Expand Up @@ -2659,11 +2658,10 @@ def _finalize(self):
# upload output file to file source
if not self.file_sources:
raise Exception(f"Need self.file_sources but {type(self)} is missing it: {self.file_sources}.")
file_source_uri = urlparse(str(self.file_source_uri))
file_source_path = self.file_sources.get_file_source_path(self.file_source_uri)
file_source = file_source_path.file_source
assert os.path.exists(self.out_file)
self.file_source_uri = f"{file_source_uri.scheme}://{file_source_uri.netloc}" + file_source.write_from(
self.file_source_uri = f"{file_source.get_scheme()}://{file_source.get_prefix()}" + file_source.write_from(
file_source_path.path, self.out_file, user_context=self.user_context
Comment on lines -2662 to 2665
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Shouldn't have any effect.

)
shutil.rmtree(self.temp_output_dir)
Expand Down
4 changes: 3 additions & 1 deletion lib/galaxy/tools/imp_exp/export_history.py
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Original file line number Diff line number Diff line change
Expand Up @@ -67,7 +67,9 @@ def _write_to_destination(file_sources_path: str, out_file: str, destination_uri
file_source_path = file_sources.get_file_source_path(destination_uri)
file_source = file_source_path.file_source
assert os.path.exists(out_file)
return file_source.write_from(file_source_path.path, out_file)
return f"{file_source.get_scheme()}://{file_source.get_prefix()}" + file_source.write_from(
file_source_path.path, out_file
)


def get_file_sources(file_sources_path: str) -> ConfiguredFileSources:
Expand Down
5 changes: 4 additions & 1 deletion test/unit/files/_util.py
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Original file line number Diff line number Diff line change
Expand Up @@ -151,10 +151,13 @@ def write_from(
user_context: OptionalUserContext = None,
) -> str:
file_source_path = file_sources.get_file_source_path(uri)
file_source = file_source_path.file_source
with tempfile.NamedTemporaryFile(mode="w") as f:
f.write(content)
f.flush()
return file_source_path.file_source.write_from(file_source_path.path, f.name, user_context=user_context)
return f"{file_source.get_scheme()}://{file_source.get_prefix()}" + file_source.write_from(
file_source_path.path, f.name, user_context=user_context
)


def configured_file_sources(conf_file, file_sources_config: Optional[FileSourcePluginsConfig] = None):
Expand Down
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