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Amber Herold, 11/17/2010 07:22 AM

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.

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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Updated by Amber Herold almost 14 years ago · 8 revisions