Project

General

Profile

Wrapper Testing » History » Version 40

Amber Herold, 03/01/2011 04:25 PM

1 1 Amber Herold
h1. Wrapper Testing
2
3 2 Amber Herold
Issue #828
4
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:
6
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.
8
2. Commands using submitAppionJob should pre-pend the path when Run Command is selected.
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. 
10
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/
14
15 1 Amber Herold
16 4 Amber Herold
|_.Filename|_.uses new showOrSubmitCommand()|_.uses old submitAppionJob()|_.Show Command (pass/fail)|_.Submit Command (pass/fail)|
17 17 Anchi Cheng
|alignSubStack.php|X||pass||
18 1 Amber Herold
|applyJunkCutoff.php|X||||
19
|bootstrappedAngularReconstitution.php|X||||
20
|centerStack.php|X||||
21
|coranSubStack.php|X||||
22
|createmodel.php|X||||
23
|createSyntheticDataset.php|X||||
24
|emdb2density.php|X||||
25 9 Dmitry Lyumkis
|imagicMSA.php|X||pass|pass|
26 1 Amber Herold
|jumpSubStack.php|X||||
27
|makegoodavg.php|X||||
28
|multiReferenceAlignment.php|X||||
29
|pdb2density.php|X||||
30 12 Dmitry Lyumkis
|postproc.php|X||FAIL (adding "appionlib" to Appion_Lib_Dir var in wrapper fixes this|FAIL (same issue)|
31 3 Amber Herold
|prepareFrealign.php|X||pass|pass|
32 1 Amber Herold
|runAppionScript.php.template|X||||
33 17 Anchi Cheng
|runMaskMaker.php|X||pass|pass|
34 8 Dmitry Lyumkis
|runMaxLikeAlign.php|X||pass|pass|
35 1 Amber Herold
|sortJunk.php|X||||
36 14 Anchi Cheng
|subStack.php|X||pass||
37 1 Amber Herold
|uploadFrealign.php|X||||
38
|uploadmodel.php|X||||
39
|uploadParticles.php|X||||
40 16 Anchi Cheng
|uploadrecon.php|X||pass|pass|
41 1 Amber Herold
|uploadstack.php|X||||
42
|uploadtemplate.php|X||||
43
|uploadTemplateStack.php|X||||
44 17 Anchi Cheng
|uploadtomo.php|X||pass||
45 1 Amber Herold
|uploadXmippRecon.php|X||||
46
|imagic3d0.php||X|||
47
|imagic3dRefine.php||X|||
48 23 Amber Herold
|manualMaskMaker.php|r15438||pass|n/a|
49 20 Amber Herold
|runAce2.php|r15424||||
50 24 Amber Herold
|runAffinityProp.php|r15439||||
51 17 Anchi Cheng
|runClusterCoran.php||X|pass||
52 25 Amber Herold
|runCombineStacks.php|r15440||||
53 17 Anchi Cheng
|runCoranClassify.php||X|pass||
54 21 Amber Herold
|runCtfEstimate.php|r15431||||
55 19 Amber Herold
|runDogPicker.php|r15423||pass|pass|
56 26 Amber Herold
|runEdIterAlignment.php|r15441||getting a file error|getting a file error|
57 1 Amber Herold
|runEmanRefine2d.php||X|||
58 28 Amber Herold
|runImgRejector.php|r15444||||
59 29 Amber Herold
|runJpgMaker.php|uses test image|X|||
60 30 Amber Herold
|runKerDenSom.php|r15445||pass||
61 31 Amber Herold
|runLoopAgain.php|r15446||||
62 22 Amber Herold
|runMakeStack2.php|r15435||pass|pass|
63 33 Amber Herold
|runOtrVolume.php|need tilt pairs|X|||
64 34 Amber Herold
|runPyAce.php|r15447||has errors with matlab stuff||
65 1 Amber Herold
|runRctVolume.php||X|||
66 39 Amber Herold
|runRefBasedAlignment.php|r15451||||
67 40 Amber Herold
|runRefBasedMaxlikeAlign.php|r15452||||
68 35 Amber Herold
|runRotKerDenSom.php|r15448||||
69 32 Amber Herold
|runSignature.php|uses test image|X|||
70 36 Amber Herold
|runSpiderNoRefAlignment.php|r15449||||
71 37 Amber Herold
|runStackIntoPicks.php|r15450||||
72 17 Anchi Cheng
|runSubTomogram.php||X|pass||
73 38 Amber Herold
|runTemplateCorrelator.php|uses test image|X|||
74 1 Amber Herold
|runTiltAligner.php||X|||
75
|runTiltAutoAligner.php||X|||
76 18 Anchi Cheng
|runTomoAligner.php|r15275||pass||
77 17 Anchi Cheng
|runTomoAverage.php||X|pass||
78
|runTomoMaker.php||X|pass||
79 1 Amber Herold
|runTopolAlign.php||X|||
80 10 Dmitry Lyumkis
|runUploadMaxLike.php||X|pass|pass|
81 15 Anchi Cheng
|uploadimage.php|X||pass|pass if from expt;fail if from project (disabled, see #864)|