Version220 » History » Revision 5
Revision 4 (Amber Herold, 06/25/2010 04:01 PM) → Revision 5/21 (Amber Herold, 11/17/2010 07:20 AM)
h1. Appion/Leginon 2.2 Appion/Leginon 2.2 version:"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| *Extensibility* |#965 | Error check for array size in FindEM|lauren|| ## Define coding standards (#10) |#963 | FindEM/Template picking crashing on rectangular images|lauren|| ## Establish Code review procedure |#957 | Can't choose output directory|lauren|| ## Refactor code for readability |#948 | Add note in UploadStack|lauren|| ### Reduce terminology overloading |#839 | Nasty error message when trying to test template finder show command|lauren|| ## Refactor code for Modularity |#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 ### Remove inconsistencies in xmipp maxlike launch page|arne|| web interface |#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 ### Work toward a way to solve the permission issue|eric|| plugin arhcitecture |#443| postproc.php has hard-coded link to appion directory change to config.php|eric|| |#434| We have both ## Create a project.inc and project.inc.php, which should probably merge them.|eric|| |#364| Having a different password tutorial for working with 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 software as well as an in depth paper on the myami code|eric|| subject |#179| viewstack.php bug|eric|| # *Automated testing* #1005 (Amber) (6 weeks) ## Develop unit tests where applicable #1006 Create or use and object-relational mapping for PHP ## Develop test scripts where possible #1007 ## ### Look into automated GUI test apps #1008 Zend library ## 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 try adding modules* (Amber, Lauren?) modules ## ### 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 Automated testing ### Reduce terminology overloading Develop unit tests where applicable ### Work toward a plugin architecture (look for generalizations, api) Develop test scripts where possible # *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) automated GUI test apps [[appion:Version220|<Edit this page>]]