Appion/Leginon 2.2¶

Appion/Leginon 2.2 will focus on the Extensibility of Appion.
The goal is to make it easy for outside labs to add new processing modules to the Image Pipeline.

View the current 2.2 Deliverable status

1. Complete Appion Wrapper (#692 #675 #676)
    
2. Automated testing #1005 (Amber) (2 weeks)
   1. Develop test scripts where possible #1007
   2. Establish a permanent test data set in Data00
       
3. Expand Auto-Installer #1015 (Amber)
   1. add processing packages to installer (spider, frealign, eman)
       
4. Add modules to pipeline
   1. Add Protomo2 (Amber, Eric) #1026
   2. Add new version of Chimera to existing code to learn what is involved #82 #25
   3. Chose other modules to add after code changes
   4. See if StokesLabProcedure will integrate their stuff as a Beta test
   5. Arne adding XMIPP reconstruction
   6. Lauren adding Phoelix
   7. Dmitry adding multi-model refine
       
5. Refactor Reconstruction code
   1. Identify trouble spots
   2. Focus on readability and modularity
      1. Reduce terminology overloading
      2. Work toward a plugin architecture (look for generalizations, api)
          
6. Create a developers tutorial #1022
   1. Add a developers tab to the appion website with links to all the resources available #1021
   2. Define coding standards (#10)
      1. python doc string viewer/editor (#162)
      2. Edit several key files (such as often copied ones) to use standards rigorously as samples #1012
      3. PHP standards doc #1013
      4. python standards doc #231
          
7. Features for public cluster (release with 2.1.1)
   1. Users need to be able to run imageuploader remotely. (#274)
   2. Need to be able to define max number of procs per node for each processing host - Advanced version (#366)
   3. Add single user sign-on functionality for SDSC roll-out (#1010)
   4. Investigate how data will move between AMI and SDSC (#1011)
   5. Having a different password for the imageviewer login and the cluster login is confusing. #364
   6. Create Appion job submit agent server #1023 (Eric)
      1. One central job submit point and user (optional).
      2. Detail report time, user, status, for each job.
          
          

Moved to low priority:¶

1. PHP_MRC (#669 #680 #314) (Jim)
    
2. Expand Auto-Installer #1015 (Christopher)
   1. multiple servers #1016
   2. multiple platforms #1017 - Mac (highest priority), Fedora, Suse, Ubuntu
   3. more options (Advanced vs Novice user) #1018
   4. yum, rpm ? #1019
       
3. Automated testing #1005 (Amber) (4 weeks)
   1. Develop unit tests where applicable #1006
   2. Look into automated GUI test apps #1008
   3. Static testing for code standards? #1009
       
4. Better error reporting
   1. Biggest problem is jobs management which could be helped with an agent
   2. Show jobs that are errors (#603)
   3. Create an error log (#75)
   4. Remote cluster recons should not return as done if job failed (#531)
       
5. Improve help tools
   1. Add links to redmine wiki help pages to appion pages (#666)
   2. Add pop up dialogs to report pages as well (#516)
   3. Image viewer tool tips
       
6. Create or use an object-relational mapping for PHP #1020
   1. Look into Zend library
      1. example
          
7. Discuss a strategy to modify database schema without effect external developers.
   1. we will wait and address this when someone is ready to make a change.
       
8. clean up web interface
   1. Remove inconsistencies in web interface (#41 #670)
   2. Add session name to window so that window are not reloaded from another session (#512)
   3. Remove select project box in getproject page. (#14)
   4. Implement sorting algorithm into project management tool. (#13)
   5. Job Status updates missing on some tools (#994)
   6. Reorganize the last column in the view project page. (#15)
       
9. Leginon
   1. Feature to measure focus change in a random direction. (#226)
   2. import preset by searching for session that uses an application (#654)
   3. Allow averaging of multiple focus measurements (#225)
   4. Leginon image viewer should cache the FFT images as well. (#217)
   5. target queue editor (#214)
       
10. misc
    1. Data Location tool-find data and push it to external drive (#954)
    2. Snapshots of projection views for uploaded models. (#857)
    3. Put variables from config.php into the database (#699)

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