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Wrapper Testing » History » Version 49

Amber Herold, 03/01/2011 06:56 PM

1 1 Amber Herold 
h1. Wrapper Testing
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Issue #828





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





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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.





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2. Commands using submitAppionJob should pre-pend the path when Run Command is selected.





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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. 





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





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





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|_.Filename|_.uses new showOrSubmitCommand()|_.uses old submitAppionJob()|_.Show Command (pass/fail)|_.Submit Command (pass/fail)|





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|alignSubStack.php|X||pass||





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|applyJunkCutoff.php|X||||





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|bootstrappedAngularReconstitution.php|X||||





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|centerStack.php|X||||





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|coranSubStack.php|X||||





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|createmodel.php|X||||





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|createSyntheticDataset.php|X||||





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|emdb2density.php|X||||





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|imagicMSA.php|X||pass|pass|





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|jumpSubStack.php|X||||





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|makegoodavg.php|X||||





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|multiReferenceAlignment.php|X||||





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|pdb2density.php|X||||





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|postproc.php|X||FAIL (adding "appionlib" to Appion_Lib_Dir var in wrapper fixes this|FAIL (same issue)|





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|prepareFrealign.php|X||pass|pass|





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|runAppionScript.php.template|X||||





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|runMaskMaker.php|X||pass|pass|





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|runMaxLikeAlign.php|X||pass|pass|





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|sortJunk.php|X||||





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|subStack.php|X||pass||





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|uploadFrealign.php|X||||





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|uploadmodel.php|X||||





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|uploadParticles.php|X||||





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|uploadrecon.php|X||pass|pass|





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|uploadstack.php|X||||





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|uploadtemplate.php|X||||





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|uploadTemplateStack.php|X||||





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|uploadtomo.php|X||pass||





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|uploadXmippRecon.php|X||||





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|imagic3d0.php||X|||





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|imagic3dRefine.php|a bit complicated|X|||





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|manualMaskMaker.php|r15438||pass|n/a|





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|runAce2.php|r15424||||





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|runAffinityProp.php|r15439||||





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|runClusterCoran.php|r15459||||





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|runCombineStacks.php|r15440||||





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|runCoranClassify.php|r15461||pass||





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|runCtfEstimate.php|r15431||||





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|runDogPicker.php|r15423||pass|pass|





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|runEdIterAlignment.php|r15441||getting a file error|getting a file error|





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|runEmanRefine2d.php|r15455||||





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|runImgRejector.php|r15444||||





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|runJpgMaker.php|uses test image|X|||





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|runKerDenSom.php|r15445||pass||





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|runLoopAgain.php|r15446||||





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|runMakeStack2.php|r15435||pass|pass|





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|runOtrVolume.php|need tilt pairs|X|||





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|runPyAce.php|r15447||has errors with matlab stuff||





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|runRctVolume.php|need a tilted stack|X|||





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|runRefBasedAlignment.php|r15451||||





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|runRefBasedMaxlikeAlign.php|r15452||||





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|runRotKerDenSom.php|r15448||||





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|runSignature.php|uses test image|X|||





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|runSpiderNoRefAlignment.php|r15449||||





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|runStackIntoPicks.php|r15450||||





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|runSubTomogram.php|need tilt series|X|pass||





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|runTemplateCorrelator.php|uses test image|X|||





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|runTiltAligner.php||X|||





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|runTiltAutoAligner.php||X|||





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|runTomoAligner.php|r15275||pass||





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|runTomoAverage.php||X|pass||





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|runTomoMaker.php||X|pass||





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|runTopolAlign.php|r15454||||





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|runUploadMaxLike.php|r15458|||error with database - student key |





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|uploadimage.php|X||pass|pass if from expt;fail if from project (disabled, see #864)|