Appion

h1. 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|need tilt pairs|X||||

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

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

|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||X||||

|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)||