Feature #219: Create Frealign web interface - Appion - Electron Microscopy Group

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Feature #219

closed

Create Frealign web interface

Added by Neil Voss over 14 years ago. Updated over 14 years ago.

Status:

Closed

Priority:

Normal

Assignee:

Neil Voss

Category:

Web interface

Target version:

Start date:

03/17/2010

Due date:

% Done:

50%

Estimated time:

Description

Create Frealign web interface. There are many steps involved:

Current state:

Prepare Frealign (interface)
1. Click Frealign Refinement from the menu
2. Select Model and Stack
3. Set Frealign parameters
4. Launch prepFrealign.py script
Prepare Frealign (background)
1. Create shell script for each node
2. Package tar file for transfer to garibaldi
3. Create entry into ApFrealignPrepareData
Lanuch Frealign Job (interface)
1. Menu shows frealign jobs are prepare (from ApFrealignPrepareData query)
2. Click on menu shows list of prepared jobs
3. Select a prepared job and use this job
4. Set Wall and CPU time, cluster directory and click show job file
5. Review job file, (copy files to DMF?), and click submit job to cluster
6. Job runs on Garibaldi

Needed:

Method to review progress of job
Method to flag prepared job as running and/or complere
Method to (copy data from DMF? and) launch uploadFrealign jobs

Related issues 2 (0 open — 2 closed)

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Updated by Neil Voss over 14 years ago

Method to flag prepared job as running and/or complere

We could do a query, because the garibaldi job in ApClusterJobData and the prepared frealign job in ApFrealignPrepareData share the same path. So, prepared jobs that share a path with a cluster job of type runfrealign are no longer prepared.

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Updated by Neil Voss over 14 years ago

I went with a much simpler method, looking at the job types in ApClusterJobData. One drawback is that the number can get out of whack. But it makes it much simpler.

Prepared = prepfrealign(done) - runfrealign(all)
Run (Ready to Upload) = runfrealign(done) - uploadfrealign(all)
Uploaded = uploadfrealign(done)

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Updated by Neil Voss over 14 years ago

The prepareFrealign script will use the method from note 1 to determine if a specific prepared job has already been run.

Neil Voss wrote:

Method to flag prepared job as running and/or complere

We could do a query, because the garibaldi job in ApClusterJobData and the prepared frealign job in ApFrealignPrepareData share the same path. So, prepared jobs that share a path with a cluster job of type runfrealign are no longer prepared.

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