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Version220 » History » Revision 7

Revision 6 (Amber Herold, 11/17/2010 07:20 AM) → Revision 7/21 (Amber Herold, 11/17/2010 07:21 AM)

h1. 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 |._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|| 

   
 # *Automated testing* #1005 (Amber) (6 weeks) 
 ## Develop unit tests where applicable #1006 
 ## Develop test scripts where possible #1007 
 ## Look into automated GUI test apps #1008 
 ## Static testing for code standards? #1009 
 ## Establish a permanent test data set in Data00 
   
 # *Expand Auto-Installer* #1015 (Christopher, Eric) 
 ## multiple servers #1016 
 ## multiple platforms #1017 - Mac (highest priority), Fedora, Suse, Ubuntu (Eric) 
 ## more options (Advanced vs Novice user) #1018 
 ## yum, rpm ? #1019 
 ## add processing packages to installer (spider, frealign, eman) 
   
 # *try adding modules* (Amber, Lauren?) 
 ## Add new version of Chimera to existing code to learn what is involved #82 #25 
 ## Chose other modules to add after code changes 
 ## See if StokesLabProcedure will integrate their stuff as a Beta test 
   
 # *Refactor code* (Eric, Amber) 
 ## Identify trouble spots  
 ## Focus on readability and modularity 
 ### Reduce terminology overloading 
 ### Work toward a plugin architecture (look for generalizations, api) 
   
 # *Create a developers tutorial* #1022 
 ## Add a developers tab to the appion website with links to all the resources available #1021 
 ## Define coding standards (#10) 
 ### python doc string viewer/editor (#162) 
 ### Edit several key files (such as often copied ones) to use standards rigorously as samples #1012 
 ### PHP standards doc #1013 
 ### python standards doc #231 
   
 # *PHP_MRC* (#669 #680 #314) (Jim & Eric) 
   
 # *Features for public cluster* (release with 2.1.1) 
 ## Users need to be able to run imageuploader remotely. (#274) 
 ## Need to be able to define max number of procs per node for each processing host - Advanced version (#366) 
 ## Add single user sign-on functionality for SDSC roll-out (#1010) 
 ## Investigate how data will move between AMI and SDSC (#1011) 
 ## Having a different password for the imageviewer login and the cluster login is confusing. #364 
 ## Create Appion job submit agent server #1023 (Eric) 
 ### One central job submit point and user (optional). 
 ### Detail report time, user, status, for each job. 
   
   
 # *Complete Appion Wrapper* (#692 #675 #676) 
   
 # *Better error reporting*  
 ## Biggest problem is jobs management which could be helped with an agent 
 ## Show jobs that are errors (#603) 
 ## Create an error log (#75) 
 ## Remote cluster recons should not return as done if job failed (#531) 
   
 # *Improve help tools* 
 ## Add links to redmine wiki help pages to appion pages (#666) 
 ## Add pop up dialogs to report pages as well (#516) 
 ## Image viewer tool tips 
   


 h3. Moved to low priority: 

 # *Create or use an object-relational mapping for PHP* #1020 (Eric) 
 ## Look into Zend library 
 ### "example":http://framework.zend.com/manual/en/zend.db.select.html 
   
 # *Discuss a strategy to modify database schema without effect external developers.* 
 ## we will wait and address this when someone is ready to make a change. 
   
 # *clean up web interface* 
 ## Remove inconsistencies in web interface (#41 #670) 
 ## Add session name to window so that window are not reloaded from another session (#512) 
 ## Remove select project box in getproject page. (#14) 
 ## Implement sorting algorithm into project management tool. (#13) 
 ## Job Status updates missing on some tools (#994) 
 ## Reorganize the last column in the view project page. (#15) 
   
 # *Leginon* 
 ## Feature to measure focus change in a random direction. (#226) 
 ## import preset by searching for session that uses an application (#654) 
 ## Allow averaging of multiple focus measurements (#225) 
 ## Leginon image viewer should cache the FFT images as well. (#217) 
 ## target queue editor (#214) 
   
 # *misc* 
 ## Data Location tool-find data and push it to external drive (#954) 
 ## Snapshots of projection views for uploaded models. (#857) 
 ## Put variables from config.php into the database (#699) 



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