CLI support for Documents Portal #210
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polyatail
requested review from
audy and
boydgreenfield
and removed request for
boydgreenfield
onecodex/cli.py
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| if not doc_obj: | ||
| log.error('Could not find document {} (404 status code)'.format(file)) | ||
| return |
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replace with quit(-1) so scripts wrapping this executable will know something went wrong?
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(or however you have to exit so that Sentry still records something)
onecodex/lib/upload.py
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| ------- | ||
| `list` of `string`s containing document UUIDs of newly uploaded files. | ||
| """ | ||
| if threads is None: |
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default to threads=1 in function definition?
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Oooh this is leftover from when we were using DEFAULT_UPLOAD_THREADS.
| # handle inside the thread to prevent the exception message from leaking out | ||
| wrapped_args[-1].value = '{}'.format(e) | ||
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| if log: |
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I noticed this pattern being used a lot. When is log not defined? I noticed that it's often defined at the top of modules making it global so that you don't have to put if log everywhere.
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I don't think it's available when these methods (which are on the document models) are executed from, e.g., within a jupyter notebook.
onecodex/models/misc.py
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| if path is None: | ||
| path = os.path.join(os.getcwd(), self.filename) | ||
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| if os.path.exists(path): |
polyatail
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polyatail
added
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This PR addresses the following issues, related to the new documents portal:
OneCodexDocumentExporterOneCodexHTMLExporternbconvert entry point for exporting reports as HTML, in addition to PDF