Appion

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 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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