Details
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Type:
Bug
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: 9.0.1 Minor Release
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Labels:None
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Sprint:B - Summer 2018
Description
We tested the command socket (in v9.0.0 and v9.0.1):
- install the Command Socket plugin
- Copy the example script text into a script (make it executable)
- Run the script.
The terminal (where you run the script) says each ncat call was met with "Connection refused".
The IGB console (in IGB, *Help > Show Console* shows the following error:
Exception in thread "Thread-26" java.lang.NullPointerException
at java.net.URLDecoder.decode(URLDecoder.java:136)
at com.gene.igbscript.IGBScriptEngine.eval(IGBScriptEngine.java:108)
at com.gene.igbscript.IGBScriptEngine.eval(IGBScriptEngine.java:102)
at com.affymetrix.igb.swing.script.ScriptManager.runScriptString(ScriptManager.java:128)
at org.lorainelab.igbr.CommandProcessor.recieveIgbCommand(CommandProcessor.java:38)
at org.lorainelab.igbr.CommandProcessor.run(CommandProcessor.java:48)
at org.lorainelab.igbr.SocketCommandListener.run(SocketCommandListener.java:41)
at java.lang.Thread.run(Thread.java:745)
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Sprint | B - Summer 2018 [ 48 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Sprint | B - Summer 2018 [ 48 ] |
| Assignee | Kiran Korey [ kkorey ] |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Sprint | B - Summer 2018 [ 48 ] |
Need a review for the branch
https://bitbucket.org/kkorey/kkorey-igb/branch/IGBF-1245-CommandSocket
Thanks
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
When you run the script, do 3 IGB image files get created in /tmp ?
(One for 3 locations of interest.)
Script:
Yes, when I run the script 3 IGB image files gets created in the specified location.
| Status | Needs 1st Level Review [ 10005 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Reviewing [ 10301 ] |
| Status | Reviewing [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Needs Testing [ 10002 ] |
| Assignee | Kiran Korey [ kkorey ] |
| Assignee | Kiran Korey [ kkorey ] |
The issue exists in 9.0.0 as well.
| Fix Version/s | 9.0.1 Minor Release [ 10500 ] |
| Comment | [ Follow-up: Does bug affect 9.0.0 ? ] |
Merge to 9.0.1 branch.
| Assignee | Kiran Korey [ kkorey ] | Ann Loraine [ aloraine ] |
| Status | Needs Testing [ 10002 ] | Open [ 1 ] |
Added to release-9.0.1
| Status | Open [ 1 ] | Needs Testing [ 10002 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Status | Needs Testing [ 10002 ] | Testing In Progress [ 10003 ] |
| Assignee | Ivory Blakley [ ieclabau ] |
| Status | Testing In Progress [ 10003 ] | Needs Testing [ 10002 ] |
| Status | Needs Testing [ 10002 ] | Testing In Progress [ 10003 ] |
I tested this with an installer.
The script works without any errors and the images are created in the specified folder.
All good.
: )
| Resolution | Done [ 10000 ] | |
| Status | Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Workflow | Loraine Lab Workflow [ 17936 ] | Fall 2019 Workflow Update [ 19858 ] |
| Workflow | Fall 2019 Workflow Update [ 19858 ] | Revised Fall 2019 Workflow Update [ 21977 ] |
Re-test on 9.0.0 after removing all bundles from 9.0.0 bundle cache.
May relate to:
https://jira.transvar.org/browse/IGBF-1182
This bug may be a side effect of imposition of file filter that restricts script file name extensions. Was introduced in https://jira.transvar.org/browse/IGBF-1182
See:
https://bitbucket.org/lorainelab/integrated-genome-browser/src/master/core/igb-swing-ext/src/main/java/com/affymetrix/igb/swing/script/ScriptManager.java?fileviewer=file-view-default (master)
https://bitbucket.org/lorainelab/integrated-genome-browser/src/release-9.0.1/core/igb-swing-ext/src/main/java/com/affymetrix/igb/swing/script/ScriptManager.java?fileviewer=file-view-default (release-9.0.1)
FYI:
See https://confluence.atlassian.com/bitbucket/hyperlinking-to-source-code-in-bitbucket-824476709.html#HyperlinkingtosourcecodeinBitbucket-SourceviewURL for how to link directly to latest version of source code on a particular branch.