Wrapper Testing » History » Version 60
Amber Herold, 03/10/2011 02:12 PM
| 1 | 1 | Amber Herold | h1. Wrapper Testing |
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| 3 | 2 | Amber Herold | Issue #828 |
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| 5 | 1 | Amber Herold | 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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| 7 | 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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| 8 | 2. Commands using submitAppionJob should pre-pend the path when Run Command is selected. |
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| 9 | 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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| 11 | 6 | Amber Herold | Appion wrapper path should look like: *"/opt/myamisnap/bin/appion prepFrealign.py --stackid=1337 --modelid=22 ..."* |
| 12 | 5 | Amber Herold | |
| 13 | 7 | Amber Herold | To get to the trunk installation: http://cronus3.scripps.edu/betamyamiweb/ |
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| 15 | 1 | Amber Herold | |
| 16 | 56 | Amber Herold | |_.Filename|_.uses new showOrSubmitCommand()|_.uses old submitAppionJob()|_.Show Command (pass/fail)|_.Submit Command (pass/fail)|_.Notes| |
| 17 | |alignSubStack.php|X||pass||| |
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| 18 | |applyJunkCutoff.php|X||||| |
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| 19 | |bootstrappedAngularReconstitution.php|X||||| |
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| 20 | |centerStack.php|X||||| |
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| 21 | |coranSubStack.php|X||||| |
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| 22 | |createmodel.php|X||||| |
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| 23 | |createSyntheticDataset.php|X||||| |
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| 24 | |emdb2density.php|X||||| |
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| 25 | |imagicMSA.php|X||pass|pass|| |
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| 26 | |jumpSubStack.php|X||||| |
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| 27 | |makegoodavg.php|X||||| |
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| 28 | |multiReferenceAlignment.php|X||||| |
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| 29 | |pdb2density.php|X||||| |
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| 30 | |postproc.php|X||FAIL (adding "appionlib" to Appion_Lib_Dir var in wrapper fixes this|FAIL (same issue)|| |
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| 31 | |prepareFrealign.php|X||pass|pass|| |
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| 32 | |runAppionScript.php.template|X||||| |
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| 33 | |runMaskMaker.php|X||pass|pass|| |
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| 34 | |runMaxLikeAlign.php|X||pass|pass|| |
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| 35 | |sortJunk.php|X||||| |
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| 36 | |subStack.php|X||pass||| |
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| 37 | |uploadFrealign.php|X||||| |
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| 38 | |uploadmodel.php|X||||| |
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| 39 | |uploadParticles.php|X||||| |
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| 40 | |uploadrecon.php|X||pass|pass|| |
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| 41 | |uploadstack.php|X||||| |
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| 42 | |uploadtemplate.php|X||||| |
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| 43 | |uploadTemplateStack.php|X||||| |
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| 44 | |uploadtomo.php|X||pass||| |
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| 45 | |uploadXmippRecon.php|X||||| |
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| 46 | |imagic3d0.php||X(Dmitry wants this left alone)|||not working| |
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| 47 | |imagic3dRefine.php|a bit complicated to test|X (Dmitry wants this left alone)|||not working| |
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| 48 | |manualMaskMaker.php|r15438||pass|n/a|| |
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| 49 | |runAce2.php|r15424||||| |
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| 50 | |runAffinityProp.php|r15439||||| |
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| 51 | |runClusterCoran.php|r15459||||| |
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| 52 | |runCombineStacks.php|r15440||||| |
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| 53 | |runCoranClassify.php|r15461||pass||| |
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| 54 | |runCtfEstimate.php|r15431||||| |
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| 55 | |runDogPicker.php|r15423|Only for just show cmd when testing an image|pass|pass|| |
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| 56 | |runEdIterAlignment.php|r15441||getting a file error|getting a file error|| |
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| 57 | |runEmanRefine2d.php|r15455||||| |
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| 58 | |runImgRejector.php|r15444||||| |
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| 59 | |runJpgMaker.php|r15490||||| |
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| 60 | |runKerDenSom.php|r15445||pass||| |
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| 61 | |runLoopAgain.php|r15446||||| |
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| 62 | |runMakeStack2.php|r15435||pass|pass|| |
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| 63 | 59 | Amber Herold | |runOtrVolume.php|r15492||||need tilt pairs| |
| 64 | 56 | Amber Herold | |runPyAce.php|r15447||has errors with matlab stuff||| |
| 65 | 58 | Amber Herold | |runRctVolume.php|r15493||||need a tilted stack| |
| 66 | 56 | Amber Herold | |runRefBasedAlignment.php|r15451||||| |
| 67 | |runRefBasedMaxlikeAlign.php|r15452||||| |
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| 68 | |runRotKerDenSom.php|r15448||||| |
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| 69 | |runSignature.php|r15491||||| |
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| 70 | |runSpiderNoRefAlignment.php|r15449||||| |
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| 71 | |runStackIntoPicks.php|r15450||||| |
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| 72 | |runSubTomogram.php|r15277||pass|pass|| |
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| 73 | |runTemplateCorrelator.php|r15475|Only for just show cmd when testing an image|||| |
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| 74 | 60 | Amber Herold | |runTiltAligner.php|r15494||||| |
| 75 | 56 | Amber Herold | |runTiltAutoAligner.php||X|||| |
| 76 | |runTomoAligner.php|r15275||pass|pass|| |
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| 77 | |runTomoAverage.php|r15277||pass|pass|| |
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| 78 | |runTomoMaker.php|r15277||pass|pass|| |
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| 79 | |runTopolAlign.php|r15454||||| |
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| 80 | |runUploadMaxLike.php|r15458|||error with database - student key || |
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| 81 | |uploadimage.php|X||pass|pass if from expt;fail if from project (disabled, see #864)|| |