Feature #828
closed
Add Appion Wrapper to commands - show and run
Added by Amber Herold over 14 years ago.
Updated about 14 years ago.
Description
The flags for the appion wrapper were added in #661. Now we need to use the flags in the code that shows commands for copy and paste as well as where commands are run.
r14691 Adds the Appion Wrapper flag to justShowCommandTable() and submitAppionJob().
This will prepend the path to the appion wrapper, in AMI's case this is /opt/myamisnap/bin/appion. So commands will look something like "/opt/myamisnap/bin/appion prepFrealign.py --stackid=1337 --modelid=22 ..." when the Appion Wrapper is enabled. For Just show command to have the wrapper, the code associated with the command must be refactored to use the new function showOrSubmitCommand() created in #692. Many commands have not yeat had these changes made, so the wrapper path will be prepended to Run commands but not to Just Show Commands.
To test:
- make sure the appion wrapper flag is flase in config.php
- Run a function that does not use the wrapper, like dog picking.
- Confirm that both just show command and Run Command do not prepend the wrapper path and are correctly formatted commands.
- Repeat this with a function that does use the wrapper, like prepare frealign.
- Now change config.php to use the wrapper.
- Repeat the above tests and notice that Just show command for dog picking should not have the wrapper path prepended, but all the others should have it.
SEE TEST MATRIX: Wrapper Testing
- Status changed from In Code Review to In Test
- Assignee changed from Eric Hou to Dmitry Lyumkis
- Status changed from In Test to Assigned
- Assignee changed from Dmitry Lyumkis to Amber Herold
I just tested dog picking with run command and it did not prepend the path as expected. I'm going to take another look at it.
All is Ok.
Since the path to the wrapper is added in the submitAppionJob() function, and because Dog Picking is not using the new showOrSubmitCommand() function, the executed command is being displayed from runDogPicker.php with no knowlede of the fact that the path has been added. To verify that the correct command is being executed, you can set $showDebug = true; in myamiweb/inc/ssh.inc and see the executed command in its full glory...that is if you are testing with your own sandbox.
SO, for testing, here is a link to a test matrix to track which files have been tested:
Wrapper Testing
- Status changed from Assigned to In Test
- Assignee changed from Amber Herold to Dmitry Lyumkis
- Status changed from In Test to Closed
tested according to procedure:
imagicMSA.php and runMaxLikeAlign.php (which use the new function) prepend the wrapper when set "true" and do not when set to "false."
runUploadMaxLike.php (which uses old function) prepend the wrapper when set to "true" and when submitting from webpage, but does not display the prepended wrapper when clicking on "just show command." ... This is confusing, but it works. It does not prepend the wrapper when set to "false."
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