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Bug #1074

closed

default appion outdir becomes appiontest/appiondata if the image path for leginon is leginontest/leginondata

Added by Anchi Cheng over 13 years ago. Updated over 13 years ago.

Status:
Closed
Priority:
Urgent
Assignee:
Eric Hou
Category:
-
Target version:
Appion/Leginon 2.1.1
Start date:
12/08/2010
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 2.1.0
Show in known bugs:
No
Workaround:

Description

This does not happen at NRAMM but at UCLA and possibly other outside sites. Ideally it should use some kind of config file to determine where the sister paths should be between leginon and appion but the config file solution would not work if the data is moved from one disk to another.

At UCLA, [Images] module in their leginon.cfg is assigned to /data/leginon/leginon. While it is odd from our point of view. it is a natural decision on their site because it works better for their file mounting system
to create a mount point at /data/leginon that allows write access to their general users.

To fix this bug, many php scripts in myamiweb/processing need to be changed to substitute only the last "leginon" string found, not all as ereg_replace would do in php. Also, the python script appionloop need to be changed together.

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 #1

Updated by Anchi Cheng over 13 years ago

  • Assignee changed from Anchi Cheng to Eric Hou

r15126 fixed the python side in appion directory
r15127 fix uploadimage.php by replacing the rawdata part since it needs to use the leginon base path, not appion. However, upload image to a new session will not use outdir as shown in the php page. It is a separate bug.
r15128 fix the rest of the php scripts.

Testing:

I have created a simulated leginon session that has an image path of /ami/data00/leginon/testleginondata/10dec08anchitestA7/rawdata. It can be used for testing:

For php pages that show default outdir, it should show as /ami/data00/leginon/testappiondata/10dec08anchitestA7/_jobtype_

If pasting the resulting command without --rundir defined, appion script should set rundir
correctly, too.

if not testing all, do one for upload type of job such as uploadtemplate, and one that uses appionLoop2.py

This unfortunately need to be in branch 2.1 so UCLA can have it.

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 #2

Updated by Eric Hou over 13 years ago

  • Status changed from Assigned to In Test
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 #3

Updated by Eric Hou over 13 years ago

  • Status changed from In Test to Closed

tested and verified with Anchi.

Thanks.

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