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update wrapper to specify the html file paths for cluster HTML output - #395
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amyjaynethompson wants to merge 2 commits into
Open
amyjaynethompson wants to merge 2 commits into
amyjaynethompson wants to merge 2 commits into
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pblowey
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Oct 23, 2026
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| # Step 3.5: Ammend paths in HTML for synchweb interactivity | ||
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| for attachment in attachments: | ||
| html_path = pathlib.Path(attachment["file_path"]) / attachment["file_name"] | ||
| # pipeline-final is in file_path, but we want the /processed for data processing | ||
| parts = list(html_path.parts) | ||
| if "pipeline-final" in parts: | ||
| parts.remove("pipeline-final") | ||
| desired_path = pathlib.Path(*parts) | ||
| if attachment["file_name"] == "xia2.multiplex.html": | ||
| path_to_insert = desired_path.parent / "xia2-multiplex-working.phil" | ||
| self.fix_paths_in_html_output(html_path, path_to_insert) | ||
| elif attachment["file_name"] == "xia2.multiplex_clustering.html": | ||
| path_to_insert = ( | ||
| desired_path.parent.parent / "xia2-multiplex-working.phil" | ||
| ) | ||
| self.fix_paths_in_html_output(html_path, path_to_insert) | ||
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This seems to be a long-winded way of getting to a file path, which I think will always be results_directory / xia2-multiplex-working.phil
I think it would be better to just have some logic when you are constructing the attachments list in the first place to look out for the two html files of interest and fix the paths then using results_directory / xia2-multiplex-working.phil
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I agree it was a bit long-winded - have simplified significantly in the recent commit.
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The xia2.multiplex html output files (
xia2.multiplex.htmlandxia2.multiplex_clustering.html) contain within them a function that assembles a command that a user can copy-paste into a terminal to reprocess custom sub-groups. This happens when the user selects custom subgroups in either of these html files. The HTML derives this path from looking at the location of the file - this breaks down when using attachments on SynchWeb and the following results:In xia2 PR #953 , a variable was added to this HTML file that could overwrite the logic and specify a custom file path. In this PR, the multiplex wrapper edits this variable to point to the data in the processed directory. This means that the user could interact with these files on SynchWeb while remotely connected to Diamond, and copy paste the file path for reprocessing.