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.
Time Frame ~6 months. Release by June 2011.

1. Open Bug Reduction (Everyone)

|._issue|._descriprion|._lead|._estimated hours| |#965 | Error check for array size in FindEM|lauren|| |#963 | FindEM/Template picking crashing on rectangular images|lauren|| |#957 | Can't choose output directory|lauren|| |#948 | Add note in UploadStack|lauren|| |#839 | Nasty error message when trying to test template finder show command|lauren|| |#1025| appion params['session'] should be replaced by ['sessionname']|dmitry|| |#195| envelope image does not take into account pixel size changes|dmitry|| |#862| Mising help in xmipp maxlike launch page|arne|| |#990| missing image file causes getimg.php to hang|eric|| |#855| data16 used instead of data00 for pdbtoem|eric|| |#612| Normal Stack creation states complete though still running|eric|| |#461| Need to find a way to solve the permission issue|eric|| |#443| postproc.php has hard-coded link to appion directory change to config.php|eric|| |#434| We have both a project.inc and project.inc.php, which should probably merge them.|eric|| |#364| Having a different password for the imageviewer login and the cluster login is confusing.|eric|| |#292| Normal login doesn't work when base_path is the document root. |eric|| |#277| Users that cannot login to cluster CAN login to myamiweb/processing|eric|| |#276| Normal Users that cannot login to web server cannot login to myamiweb/processing|eric|| |#194| Amplitude correction files path is hard coded in the myami code|eric|| |#179| viewstack.php bug|eric||
 

1. Automated testing #1005 (Amber) (6 weeks)
   1. Develop unit tests where applicable #1006
   2. Develop test scripts where possible #1007
   3. Look into automated GUI test apps #1008
   4. Static testing for code standards? #1009
   5. Establish a permanent test data set in Data00
       
2. Expand Auto-Installer #1015 (Christopher, Eric)
   1. multiple servers #1016
   2. multiple platforms #1017 - Mac (highest priority), Fedora, Suse, Ubuntu (Eric)
   3. more options (Advanced vs Novice user) #1018
   4. yum, rpm ? #1019
   5. add processing packages to installer (spider, frealign, eman)
       
3. try adding modules (Amber, Lauren?)
   1. Add new version of Chimera to existing code to learn what is involved #82 #25
   2. Chose other modules to add after code changes
   3. See if StokesLabProcedure will integrate their stuff as a Beta test
       
4. Refactor code (Eric, Amber)
   1. Identify trouble spots
   2. Focus on readability and modularity
      1. Reduce terminology overloading
      2. Work toward a plugin architecture (look for generalizations, api)
          
5. 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
          
6. PHP_MRC (#669 #680 #314) (Jim & Eric)
    
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.
          
          
8. Complete Appion Wrapper (#692 #675 #676)
    
9. 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)
       
10. 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
        

Moved to low priority:¶

1. Create or use an object-relational mapping for PHP #1020 (Eric)
   1. Look into Zend library
      1. example
          
2. 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.
       
3. 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)
       
4. 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)
       
5. 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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