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Appion/Leginon 2.1.0

closed

10/28/2010

Minor feature additions to 2.0.0

99%

119 issues   (118 closed — 1 open)

Appion/Leginon 2.1

Major Goals:

Establish a cohesive interface to the world

  1. Complete User Guides
    #40 #625 #622 #621 #617 #614 #613 #637 #622 #621 #613 #669 #655 #668
     
  2. Establish forum in Redmine
     
    1. Leginon forum migration #626
       
    2. Forum sharing in redmine #627
       
  3. Move components of ami website to redmine
     
  4. Establish mailing list #44

Streamline installation on CentOS

  1. Error Checking in the Setup Wizard #569
     
  2. Troubleshooting tools #38
     
  3. A single interactive setup.py script for CentOS that does everything. #597
     
  4. Change method for running scripts to appion wrapper #319, #661, #662, #675, #676

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Time tracking
Estimated time 0.00 hour
Spent time 26.50 hours
Issues by
Bug

76/77
Feature

35/35
Support

2/2
Task

5/5
Related issues
Leginon - Bug #26: move by image shift should base on the matrix of the preset acquiring the data not the parent Actions
Bug #399: handedness flip in prepFrealign Actions
Leginon - Bug #419: image of the first target moved by multiple navigator move is out of focus and beam shift is off Actions
Bug #428: Hard links that require login get passed to access deny Actions
Bug #446: createmodel.php (EMAN common lines bugs) Actions
Leginon - Bug #447: Connecting to T2 Actions
Leginon - Bug #448: select and submit targets on old image will submit done targets as new as well Actions
Bug #483: Crashed jobs are reported as being completed jobs. Actions
Bug #528: upon a new project I find one complete frealign and one complete Imagic angular reconstitution flag Actions
Bug #529: create Template stack has no effect Actions
Bug #549: Centali webpage does not allow editing of output directory Actions
Bug #573: Need to be able to upload defocal pairs (series) into appion Actions
Leginon - Bug #586: Manual Acquisition camera settings does not revert correctly after manual focusing Actions
Bug #632: particle flipped upside down after running through Beam Tilt corrected subStack.py Actions
Bug #647: Do not let non-admin users create a new Group Actions
Bug #650: matlab Xvfb error Actions
Bug #656: Add MRC2ANY to config.php wizard Actions
Leginon - Bug #685: notes to myself on missing docs Actions
Bug #704: maximum-likelihood alignment page not saving checkboxes / selections Actions
Bug #705: Unable to create a new stack from a stack with a different preset Actions
Bug #709: apDefocalPairs getShiftFromImage should not take params as input Actions
Bug #715: Uploaded stacks missing boxsize info Actions
Bug #728: Topology Alignment does not work on python 2.4 Actions
Bug #729: unqualified names used for shell commands. Actions
Bug #730: emanJobGen.php gives garbage output directory name when the rawdata is archived Actions
Leginon - Bug #739: When RCT will collects a zero degree image it sets targets to complete and does not collect other tilts Actions
Leginon - Bug #741: If angle is less than 28.7 degrees, RCT will collect a zero degree image Actions
Bug #746: multi reference alignment not switching number of particles upon change (javascript issue) Actions
Leginon - Bug #776: addinstrument.php can not access the function is_logged() without Login_Enabled Actions
Leginon - Bug #778: All logged in users can still access various administrator pages by typing in its complete url Actions
Bug #783: schema-r14077.py gives an error message when no appion database is not assigned Actions
Bug #784: lack of GroupData entry causes schema-r12857.py to fail Actions
Bug #796: Do not cache Images if image is not exist Actions
Bug #802: update project or add new project does not dispaly right result. Actions
Bug #818: Clean php warning when there is no session in the database Actions
Bug #826: upload image is not working Actions
Bug #827: When viewing the checkAppionJob.php page, the menu bar items are not selectable Actions
Bug #830: links in menuprocessing.inc do not work when navigating within specific pages Actions
Bug #832: bug fix #871 breaks upgrade for those with processingdb table in projectdb Actions
Bug #833: compare_eulers.php broken Actions
Bug #834: Is authconfig.inc.php.template no longer used? Actions
Bug #835: cannot launch jobs from stackhierarchy.php page Actions
Bug #836: modelFromEMDB.py not working when low-pass filter value not specified Actions
Bug #837: modelFromEMDB.py not working when XML file does not contain mass info Actions
Bug #840: uploadimage.php is redirected to index.php page when coming from an project when login is on Actions
Bug #844: Change the word (incomplete) that is listed under features that are under development to (may be buggy) or (buggy?) Actions
Bug #847: Last finished iteration does not display in checkRefineJobs.php with iteration number Actions
Bug #854: command variable table parses description wrong Actions
Bug #858: Can't upload alignment Actions
Bug #864: uploadimage.php of a new session does not work with cluster submitAppioJob function Actions
Bug #866: new session uploadimage.php does not behaves properly in form-reload and in login/logout Actions
Leginon - Bug #875: myamiImages needs write permission Actions
Leginon - Bug #876: getproject.php SAMPLE_TRACK added in r14661 are removed in r14702 Actions
Bug #878: Project web pages Actions
Bug #881: Troubleshooter needs to correctly identify an extra line at end of Config.php Actions
Bug #885: When using manualpicker.py to edit labeled old pick, the label option must be on and contains the old labels. Actions
Bug #886: tomoreport give error on empty movie Actions
Bug #890: tomosummary page have an array_merge error due to a failed ApClusteringRunData query Actions
Leginon - Bug #899: imageviewer targets on rectangular images are stretched on resampled images Actions
Leginon - Bug #902: scale display in fft display is incorrect in the map and not displayed in the viewer views Actions
Leginon - Bug #903: particle display is on while displaying fft Actions
Bug #907: makestack2.py "print" statements Actions
Bug #909: imod is not included in /ami/sw/bin/appion Actions
Bug #911: webcaller.py Actions
Bug #939: AcquisitionImageTargetData table need to exist to diplay pixelsize in viewer Actions
Leginon - Bug #942: LaunchedApplicationData timestamp is not initialized to not null Actions
Leginon - Bug #951: BeamTiltCalibrator settings missing Actions
Leginon - Bug #960: CameraPanel does not fit in settings windows with the new longer format Actions
Bug #961: Auto-installer db error access denied to root user, using password: NO Actions
Leginon - Bug #962: beam tilt value from some version of tecnai or TEM scripting is not in radian Actions
Bug #964: Myamiweb setup wizard does not work first time through Actions
Bug #973: coran & spider Actions
Bug #975: emancoran fix Actions
Leginon - Bug #980: Key error when Leginon is launched through auto installation script Actions
Bug #982: keep-all option Actions
Bug #983: spaces in testfilename Actions
Leginon - Bug #1166: energy filter property not found with Gatan Camera Actions
Feature #38: Create tools for troubleshooting Appion Install Actions
Feature #139: topologyAlignment.py Actions
Leginon - Feature #224: Re-activate Saxton scheme for electron tomography data collection Actions
Feature #230: add particle labels to pipeline Actions
Feature #513: Make download icon more obvious Actions
Feature #535: Display Error Message from myamiweb/index.php if config.php is missing Actions
Feature #552: Add student's T-distribution option to maxlike alignments Actions
Feature #556: Add the Evil garibaldi users script into pipeline Actions
Feature #557: Create a runAppionJob.php.template for designing a PHP function. Actions
Feature #569: User inputs violation checking in Wizard Actions
Feature #597: Provide an Appion auto-installer for CentOS Actions
Feature #643: viewstack.php remove particles button Actions
Feature #661: Add use_appion wrapper and path to appion wrapper to config.php Actions
Feature #662: Pass all command line results from "Just Show Command" to a common function Actions
Feature #677: Add enable caching in the setup wizard. Actions
Feature #696: Are we using phpami in subversion? Can we delete it? Actions
Feature #698: Add HIDE_MATLAB flag for non-MATLAB installs Actions
Feature #702: Fix duration and num images for summary.php and getproject.php Actions
Feature #719: Add helical fill to manual picker Actions
Feature #722: Add SMTP validation to the setup wizard. Actions
Feature #751: Add anonymous user to the login page. Actions
Feature #752: Add download links to processing/index.php Actions
Feature #765: Login page need to remember the redirect "get" variable's values Actions
Feature #772: bad box sizes Actions
Feature #811: Need a tool to automatic create leginondb and projectdb database schema with default values Actions
Feature #812: Create cluster config file during the centos auto installation. Actions
Feature #828: Add Appion Wrapper to commands - show and run Actions
Feature #842: Make sure the wrapper is disabled for outside installations for v2.1 Actions
Feature #845: It is too confusing to allow image upload to a real Leginon session Actions
Feature #898: Add troubleshooter tool to test dataset page in appion/leginon tools Actions
Feature #900: Proposed change in binning behavior for fft display in webviewers, Let me know if you object. Actions
Feature #940: imagic Refs Actions
Feature #1259: holder info in summary Actions
Feature #1260: ACE graph scales Actions
Feature #1261: ctfreport shows confidence over time Actions
Support #882: !!!! IMPORTANT !!!! Myami Code Freeze in effect until further notice Actions
Support #1068: install appion to Arne's contact computer Actions
Task #544: Create wiki page with all appion citations Actions
Task #697: Subversion reorganization Actions
Task #895: make login input centered on the page and login_header not show home tage when it is at home Actions
Task #950: Document makegoodaverages.py Actions
Leginon - Task #953: Document 2.1 Upgrade procedure Actions