Add eLabFTW file source from file source templates #19493
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| def get_prefix(self) -> Optional[str]: | ||
| return None | ||
| def get_prefix(self, user_context: OptionalUserContext = None) -> Optional[str]: | ||
| endpoint: ParseResult = self._get_endpoint(user_context=user_context) | ||
| return self.id if self.scheme not in {"elabftw", DEFAULT_SCHEME} else (endpoint.netloc or None) | ||
| # it would make better sense to return | ||
| # `self.id if self.scheme == USER_FILE_SOURCES_SCHEME else (endpoint.netloc or None)`, where | ||
| # `USER_FILE_SOURCES_SCHEME` comes from `galaxy.managers.file_source_instances`; however, that would lead to a | ||
| # circular import (maybe `USER_FILE_SOURCES_SCHEME` should be moved to a module in a layer deeper than | ||
| # `galaxy.managers`) | ||
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| def get_scheme(self) -> str: | ||
| return "elabftw" | ||
| return self.scheme if self.scheme and self.scheme != DEFAULT_SCHEME else "elabftw" | ||
| # it would make better sense to return `self.scheme if self.scheme == USER_FILE_SOURCES_SCHEME else "elabftw"`, | ||
| # but the same circular import issue as above arises |
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If this ended up being so weird there must be something I am not getting about the scheme... Where are schemes other than "gxfiles" and "gxuserfiles" coming from? The design intended in #19319 with a URI that only depends on the configured endpoint is not how things are supposed to work, right?
File sources reference files via a URI, while eLabFTW uses auto-incrementing positive integers. For more details read #18665 [5]. This leads to the need to declare a mapping between said identifiers and Galaxy URIs.
Those take the form
elabftw://demo.elabftw.net/entity_type/entity_id attachment_id, where:
entity_typeis either 'experiments' or 'resources'entity_idis the id (an integer in string form) of an experiment or resourceattachment_idis the id (an integer in string form) of an attachmentFor the user-defined file sources use case (when users configure one or more instances of the FilesSource via a file source template), Galaxy URIs have a different scheme and authority, taking the form
gxuserfiles://file_source_id/entity_type/entity_id/attachment_id, where:
file_source_idis the file source identifier assigned by Galaxy
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FYI @bgruening |
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Thanks @davelopez for realizing that |
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Support user-defined file sources based on `eLabFTWFilesSource`. Add a file source template for eLabFTW and the required documentation.
Let users choose whether Galaxy should be allowed to export data to eLabFTW or they only need to import data to Galaxy.
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Test failures seem unrelated |
ahmedhamidawan
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Support user-defined file sources based on
eLabFTWFilesSource. Add a file source template for eLabFTW and the required documentation.How to test the changes?
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