Delete Sequencing Run script #156
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* fixed bash script not finding python startup file when executing from outside base directory (#54) * fixed bash script not finding python startup file when executing from outside base directory * bump version to 0.3.1 * fix travis and readthedocs builds for new irida dev * update travis ci configg * Testing java 11 in dev tests noted in changelog * fix strings and wording * fixed iseq runs to work with the miniseq parser * add gui close message boxes * changed gui close to only prompt mid upload * log crash stack trace to logging directory on crash * fix readthedocs link not pointing to stable build * Fixed irida disconnect hard crash * fix gui hard exit on first launch * added notes about new crash logging to changelog and docs * cleaned up code flow * Updated config tests to match new functionality * python 3.5 compatibility fix * updated other RTD links in Readme to point to stable * fixed wording in closeEvent comment block * fix formatting issues * fixed crash case found during crash log testing * fixed parsing thread not catching all errors * add note to changelog about parsing crash bugfix * fix crash log catching to use excepthook override instead of try/catch * added link to tutorials to readme and docs
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Diff Coverage details (click to unfold)iridauploader/init.py
iridauploader/api/api_calls.py
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What does this PR do and why?
This adds a script
scripts/delete_sequencing_run.shthat accepts a config file and a run directory, and deletes the associated sequencing run from IRIDA.This is needed because sometimes high throughput users upload to the wrong project, and the data needs to be quickly removed and reuploaded.
Screenshots or screen recordings
How to set up and validate locally
a. Pull this branch
b.
make guic.
./scripts/gui.shd. open Configuration Settings and enter client/user/url details
e. Upload some data, the example data in
examples/will work for thisf. Verify on IRIDA that the data exists in the project
e. Verify the Sequencing Run exists in the Admin panel
./scripts/delete_sequencing_run.sh./scripts/delete_sequencing_run.sh --version./scripts/delete_sequencing_run.sh --helpa. default config file directory is
-c ~/.config/irida-uploader/config.confb. directory should be the directory you uploaded, ex: `-d examples/miseq_run
examples/miseq_run/irida_uploader_status.info, changing"Upload Status": "complete"to"Upload Status": "partial"PR acceptance checklist
Things for the developer to confirm they've done before the PR should be accepted: