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  1. IGB
  2. IGBF-1245

command socket refuses connect

        Details

        • 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)

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              Activity

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              ann.loraine Ann Loraine made changes -
              Workflow Fall 2019 Workflow Update [ 19858 ] Revised Fall 2019 Workflow Update [ 21977 ]
              ann.loraine Ann Loraine made changes -
              Workflow Loraine Lab Workflow [ 17936 ] Fall 2019 Workflow Update [ 19858 ]
              ieclabau Ivory Blakley (Inactive) made changes -
              Resolution Done [ 10000 ]
              Status Testing In Progress [ 10003 ] Closed [ 6 ]
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              ieclabau Ivory Blakley (Inactive) added a comment -

              I tested this with an installer.
              The script works without any errors and the images are created in the specified folder.

              All good.
              : )

              Show
              ieclabau Ivory Blakley (Inactive) added a comment - I tested this with an installer. The script works without any errors and the images are created in the specified folder. All good. : )
              ieclabau Ivory Blakley (Inactive) made changes -
              Status Needs Testing [ 10002 ] Testing In Progress [ 10003 ]
              ieclabau Ivory Blakley (Inactive) made changes -
              Status Testing In Progress [ 10003 ] Needs Testing [ 10002 ]
              ieclabau Ivory Blakley (Inactive) made changes -
              Assignee Ivory Blakley [ ieclabau ]
              ieclabau Ivory Blakley (Inactive) made changes -
              Status Needs Testing [ 10002 ] Testing In Progress [ 10003 ]
              ann.loraine Ann Loraine made changes -
              Assignee Ann Loraine [ aloraine ]
              ann.loraine Ann Loraine made changes -
              Status Open [ 1 ] Needs Testing [ 10002 ]
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              ann.loraine Ann Loraine added a comment -

              Added to release-9.0.1

              Show
              ann.loraine Ann Loraine added a comment - Added to release-9.0.1
              ann.loraine Ann Loraine made changes -
              Status Needs Testing [ 10002 ] Open [ 1 ]
              ann.loraine Ann Loraine made changes -
              Assignee Kiran Korey [ kkorey ] Ann Loraine [ aloraine ]
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              ann.loraine Ann Loraine added a comment -

              Merge to 9.0.1 branch.

              Show
              ann.loraine Ann Loraine added a comment - Merge to 9.0.1 branch.
              ann.loraine Ann Loraine made changes -
              Comment [ Follow-up: Does bug affect 9.0.0 ? ]
              kkorey Kiran Korey (Inactive) made changes -
              Fix Version/s 9.0.1 Minor Release [ 10500 ]
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              kkorey Kiran Korey (Inactive) added a comment -

              The issue exists in 9.0.0 as well.

              Show
              kkorey Kiran Korey (Inactive) added a comment - The issue exists in 9.0.0 as well.
              ann.loraine Ann Loraine made changes -
              Assignee Kiran Korey [ kkorey ]
              ann.loraine Ann Loraine made changes -
              Assignee Kiran Korey [ kkorey ]
              ann.loraine Ann Loraine made changes -
              Status Pull Request Submitted [ 10101 ] Needs Testing [ 10002 ]
              kkorey Kiran Korey (Inactive) made changes -
              Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
              ann.loraine Ann Loraine made changes -
              Status Reviewing [ 10301 ] Ready for Pull Request [ 10304 ]
              ann.loraine Ann Loraine made changes -
              Status Ready for Pull Request [ 10304 ] Reviewing [ 10301 ]
              ann.loraine Ann Loraine made changes -
              Status Needs 1st Level Review [ 10005 ] Ready for Pull Request [ 10304 ]
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              kkorey Kiran Korey (Inactive) added a comment -

              Yes, when I run the script 3 IGB image files gets created in the specified location.

              Show
              kkorey Kiran Korey (Inactive) added a comment - Yes, when I run the script 3 IGB image files gets created in the specified location.
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              ann.loraine Ann Loraine added a comment - - edited

              When you run the script, do 3 IGB image files get created in /tmp ?

              (One for 3 locations of interest.)

              Script:

              https://bitbucket.org/lorainelab/integrated-genome-browser/src/master/optionalPlugins/igb-command-socket/README.md

              Show
              ann.loraine Ann Loraine added a comment - - edited When you run the script, do 3 IGB image files get created in /tmp ? (One for 3 locations of interest.) Script: https://bitbucket.org/lorainelab/integrated-genome-browser/src/master/optionalPlugins/igb-command-socket/README.md
              kkorey Kiran Korey (Inactive) made changes -
              Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
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              kkorey Kiran Korey (Inactive) added a comment -

              Need a review for the branch

              https://bitbucket.org/kkorey/kkorey-igb/branch/IGBF-1245-CommandSocket

              Thanks

              Show
              kkorey Kiran Korey (Inactive) added a comment - Need a review for the branch https://bitbucket.org/kkorey/kkorey-igb/branch/IGBF-1245-CommandSocket Thanks
              kkorey Kiran Korey (Inactive) made changes -
              Sprint B - Summer 2018 [ 48 ]
              kkorey Kiran Korey (Inactive) made changes -
              Status Open [ 1 ] In Progress [ 3 ]
              kkorey Kiran Korey (Inactive) made changes -
              Assignee Kiran Korey [ kkorey ]
              ann.loraine Ann Loraine made changes -
              Sprint B - Summer 2018 [ 48 ]
              ann.loraine Ann Loraine made changes -
              Assignee Ann Loraine [ aloraine ]
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              ann.loraine Ann Loraine added a comment -

              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.

              Show
              ann.loraine Ann Loraine added a comment - 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.
              ieclabau Ivory Blakley (Inactive) made changes -
              Field Original Value New Value
              Sprint B - Summer 2018 [ 48 ]
              ieclabau Ivory Blakley (Inactive) created issue -

                People

                • Assignee:
                  ieclabau Ivory Blakley (Inactive)
                  Reporter:
                  ieclabau Ivory Blakley (Inactive)
                • Votes:
                  0 Vote for this issue
                  Watchers:
                  3 Start watching this issue

                  Dates

                  • Created:
                    Updated:
                    Resolved: