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Amber Herold, 03/03/2011 05:25 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) | |
|---|---|---|---|---|---|
| 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 | ||||
| imagic3dRefine.php | a bit complicated | X | |||
| 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 | pass | pass | ||
| runEdIterAlignment.php | r15441 | getting a file error | getting a file error | ||
| runEmanRefine2d.php | r15455 | ||||
| runImgRejector.php | r15444 | ||||
| runJpgMaker.php | uses test image | X | |||
| 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 | uses test image | X | |||
| runSpiderNoRefAlignment.php | r15449 | ||||
| runStackIntoPicks.php | r15450 | ||||
| runSubTomogram.php | need tilt series | r15277 | pass | pass | |
| runTemplateCorrelator.php | r15475 | ||||
| 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) |
Updated by Amber Herold almost 14 years ago · 51 revisions