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protomo2aligner myamiweb form need to default to commit results #3910

Open leginonbot opened 5 months ago

leginonbot commented 5 months ago

Author Name: Anchi Cheng (@anchi2c) Original Redmine Issue: 3910, https://emg.nysbc.org/redmine/issues/3910 Original Date: 2016-01-27 Original Assignee: Alex Noble

Without it, the users don't see the results even if its is run to completion.

leginonbot commented 5 months ago

Original Redmine Comment Author Name: Alex Noble (@alexjnoble) Original Date: 2016-01-27T18:56:11Z

Hi Anchi,

Yes this is an annoyance. Currently the method of revisiting a run is to click on Align Tilt-Series on the left, fill in the correct outdir and runname, and choose the corresponding tilt-series from the list. Then click Just Show Command. On the next page click the link to the Coarse Alignment Summary page. Your results should be there if your run finished properly. You can continue on to the Refinement, Reconstruction, and Batch processing pages from here.

The user-interface could definitely be improved with a commit to the database, and you and I set up a lot of the database-call pseudo workflow during the last hackathon, but it hasn't been implemented yet primarily due to me not having time. In the protomo2aligner.py script I have in place a giant function that is meant to deal with all of the parameters, but that function is not in use yet.

The current PHP-based setup uses sessions to keep track of which run summary is displayed. The session variables are either manually reset by going to the Align Tilt-Series main page, or by variable timeout, which is dependent on some PHP configuration stuff I don't yet understand. This all works, but the user has to keep track of the paths to their alignments.

I'm currently trying to finish up a couple projects and write and defend my PhD thesis, so I really don't know when I will get the time to put database insertion into my scripts.