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 |
kysrpex
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| @@ -804,7 +849,7 @@ def _write_from( | |||
| entity_type, entity_id, attachment_id = match.groups() | |||
| entity_type = entity_type.replace("items", "resources") | |||
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| return f"elabftw://{location.netloc}/{entity_type}/{entity_id}/{attachment_id}" | |||
| return f"/{entity_type}/{entity_id}/{attachment_id}" | |||
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Should've been part of #19319 (bugfix).
Support user-defined file sources based on `eLabFTWFilesSource`. Add a file source template for eLabFTW and the required documentation.
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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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