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Wrapper Testing » History » Revision 60

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Amber Herold, 03/10/2011 02:12 PM


Wrapper Testing

Issue #828

The following files contain a call to showOrSubmitCommand() or submitAppionJob(). These function calls need to be executed to verify the following:

1. Commands using showOrSubmitCommand should pre-pend the Appion Wrapper Path defined in the config file when both Show Command and Run Command are selected by the user.
2. Commands using submitAppionJob should pre-pend the path when Run Command is selected.
3. Commands using submitAppionJob should NOT pre-pend the path when Just Show Command is selected. In this case, the user will need to manually modify the command prior to executing it to include the wrapper path.

Appion wrapper path should look like: "/opt/myamisnap/bin/appion prepFrealign.py --stackid=1337 --modelid=22 ..."

To get to the trunk installation: http://cronus3.scripps.edu/betamyamiweb/

Filename uses new showOrSubmitCommand() uses old submitAppionJob() Show Command (pass/fail) Submit Command (pass/fail) Notes
alignSubStack.php X pass
applyJunkCutoff.php X
bootstrappedAngularReconstitution.php X
centerStack.php X
coranSubStack.php X
createmodel.php X
createSyntheticDataset.php X
emdb2density.php X
imagicMSA.php X pass pass
jumpSubStack.php X
makegoodavg.php X
multiReferenceAlignment.php X
pdb2density.php X
postproc.php X FAIL (adding "appionlib" to Appion_Lib_Dir var in wrapper fixes this FAIL (same issue)
prepareFrealign.php X pass pass
runAppionScript.php.template X
runMaskMaker.php X pass pass
runMaxLikeAlign.php X pass pass
sortJunk.php X
subStack.php X pass
uploadFrealign.php X
uploadmodel.php X
uploadParticles.php X
uploadrecon.php X pass pass
uploadstack.php X
uploadtemplate.php X
uploadTemplateStack.php X
uploadtomo.php X pass
uploadXmippRecon.php X
imagic3d0.php X(Dmitry wants this left alone) not working
imagic3dRefine.php a bit complicated to test X (Dmitry wants this left alone) not working
manualMaskMaker.php r15438 pass n/a
runAce2.php r15424
runAffinityProp.php r15439
runClusterCoran.php r15459
runCombineStacks.php r15440
runCoranClassify.php r15461 pass
runCtfEstimate.php r15431
runDogPicker.php r15423 Only for just show cmd when testing an image pass pass
runEdIterAlignment.php r15441 getting a file error getting a file error
runEmanRefine2d.php r15455
runImgRejector.php r15444
runJpgMaker.php r15490
runKerDenSom.php r15445 pass
runLoopAgain.php r15446
runMakeStack2.php r15435 pass pass
runOtrVolume.php r15492 need tilt pairs
runPyAce.php r15447 has errors with matlab stuff
runRctVolume.php r15493 need a tilted stack
runRefBasedAlignment.php r15451
runRefBasedMaxlikeAlign.php r15452
runRotKerDenSom.php r15448
runSignature.php r15491
runSpiderNoRefAlignment.php r15449
runStackIntoPicks.php r15450
runSubTomogram.php r15277 pass pass
runTemplateCorrelator.php r15475 Only for just show cmd when testing an image
runTiltAligner.php r15494
runTiltAutoAligner.php X
runTomoAligner.php r15275 pass pass
runTomoAverage.php r15277 pass pass
runTomoMaker.php r15277 pass pass
runTopolAlign.php r15454
runUploadMaxLike.php r15458 error with database - student key
uploadimage.php X pass pass if from expt;fail if from project (disabled, see #864)

Updated by Amber Herold almost 14 years ago · 60 revisions