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  1. IGB
  2. IGBF-2804

Output species.txt in the Quickload Saver app

    Details

    • Type: Improvement
    • Status: Closed (View Workflow)
    • Priority: Major
    • Resolution: Done
    • Affects Version/s: None
    • Fix Version/s: None
    • Labels:
      None
    • Story Points:
      4
    • Sprint:
      Winter 6 Mar 8 - Mar 19, Spring 1 2021 Mar 22 - Apr 2, Spring 2 2021 Apr 5 - Apr 16, Spring 3 2021 Apr 19 - Apr 30

      Description

      Situation: The Quickload Saver app outputs an IGB Quickload. It does not currently include the optional species.txt file.

      Task: Output the species.txt file when using the Quickload Saver app.

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            Hide
            inaylor Irvin Naylor added a comment -

            Pasted from log after no files were saved to new quickload folder from blank optional fields:

            10:57:56.542 INFO c.a.igb.view.load.GeneralLoadUtils - Loaded E_unicornis_Jul_2043.bed.gz in 37.22 ms
            Exception in thread "AWT-EventQueue-0" java.lang.ArrayIndexOutOfBoundsException: 1
            at org.lorainelab.igb.menuoption.CreateQuickloadAction.createQuickload(CreateQuickloadAction.java:133)
            at org.lorainelab.igb.menuoption.CreateQuickloadAction.showFileChooser(CreateQuickloadAction.java:104)
            at org.lorainelab.igb.menuoption.CreateQuickloadAction.actionPerformed(CreateQuickloadAction.java:75)
            at org.lorainelab.igb.menuoption.CreateQuickloadAction.lambda$getMenuItems$0(CreateQuickloadAction.java:301)
            at org.lorainelab.igb.menu.api.util.MenuUtils$1.actionPerformed(MenuUtils.java:26)
            at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
            at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
            at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
            at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
            at javax.swing.AbstractButton.doClick(Unknown Source)
            at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
            at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source)
            at java.awt.Component.processMouseEvent(Unknown Source)
            at javax.swing.JComponent.processMouseEvent(Unknown Source)
            at java.awt.Component.processEvent(Unknown Source)
            at java.awt.Container.processEvent(Unknown Source)
            at java.awt.Component.dispatchEventImpl(Unknown Source)
            at java.awt.Container.dispatchEventImpl(Unknown Source)
            at java.awt.Component.dispatchEvent(Unknown Source)
            at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
            at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
            at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
            at java.awt.Container.dispatchEventImpl(Unknown Source)
            at java.awt.Window.dispatchEventImpl(Unknown Source)
            at java.awt.Component.dispatchEvent(Unknown Source)
            at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
            at java.awt.EventQueue.access$500(Unknown Source)
            at java.awt.EventQueue$3.run(Unknown Source)
            at java.awt.EventQueue$3.run(Unknown Source)
            at java.security.AccessController.doPrivileged(Native Method)
            at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
            at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
            at java.awt.EventQueue$4.run(Unknown Source)
            at java.awt.EventQueue$4.run(Unknown Source)
            at java.security.AccessController.doPrivileged(Native Method)
            at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
            at java.awt.EventQueue.dispatchEvent(Unknown Source)
            at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
            at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
            at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
            at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
            at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
            at java.awt.EventDispatchThread.run(Unknown Source)

            Show
            inaylor Irvin Naylor added a comment - Pasted from log after no files were saved to new quickload folder from blank optional fields: 10:57:56.542 INFO c.a.igb.view.load.GeneralLoadUtils - Loaded E_unicornis_Jul_2043.bed.gz in 37.22 ms Exception in thread "AWT-EventQueue-0" java.lang.ArrayIndexOutOfBoundsException: 1 at org.lorainelab.igb.menuoption.CreateQuickloadAction.createQuickload(CreateQuickloadAction.java:133) at org.lorainelab.igb.menuoption.CreateQuickloadAction.showFileChooser(CreateQuickloadAction.java:104) at org.lorainelab.igb.menuoption.CreateQuickloadAction.actionPerformed(CreateQuickloadAction.java:75) at org.lorainelab.igb.menuoption.CreateQuickloadAction.lambda$getMenuItems$0(CreateQuickloadAction.java:301) at org.lorainelab.igb.menu.api.util.MenuUtils$1.actionPerformed(MenuUtils.java:26) at javax.swing.AbstractButton.fireActionPerformed(Unknown Source) at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source) at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source) at javax.swing.DefaultButtonModel.setPressed(Unknown Source) at javax.swing.AbstractButton.doClick(Unknown Source) at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source) at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source) at java.awt.Component.processMouseEvent(Unknown Source) at javax.swing.JComponent.processMouseEvent(Unknown Source) at java.awt.Component.processEvent(Unknown Source) at java.awt.Container.processEvent(Unknown Source) at java.awt.Component.dispatchEventImpl(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Window.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source)
            Hide
            nfreese Nowlan Freese added a comment -

            Three issues:
            Quickload Saver index out of bounds
            Quickload Saver not saving foreground color
            Quickload Saver extra tab in species.txt

            Show
            nfreese Nowlan Freese added a comment - Three issues: Quickload Saver index out of bounds Quickload Saver not saving foreground color Quickload Saver extra tab in species.txt
            Hide
            rweidenh Rachel Weidenhammer (Inactive) added a comment -

            Extra tab is removed from species.txt
            Index out of bounds exception no longer present and files are created appropriately.

            If the user opens a new genome from file and enters no data, the species.txt file will show:
            Custom Species 1 (TAB) (TAB) Custom Genome 1

            Working on foreground color saving now.

            Show
            rweidenh Rachel Weidenhammer (Inactive) added a comment - Extra tab is removed from species.txt Index out of bounds exception no longer present and files are created appropriately. If the user opens a new genome from file and enters no data, the species.txt file will show: Custom Species 1 (TAB) (TAB) Custom Genome 1 Working on foreground color saving now.
            Hide
            nfreese Nowlan Freese added a comment -

            Rachel Weidenhammer - I fixed the foreground color, it was related to the change I made to the URI encoding.

            Show
            nfreese Nowlan Freese added a comment - Rachel Weidenhammer - I fixed the foreground color, it was related to the change I made to the URI encoding.
            Hide
            nfreese Nowlan Freese added a comment -

            Rachel and I tested on Windows and Mac. Working correctly.

            Closing issue.

            Show
            nfreese Nowlan Freese added a comment - Rachel and I tested on Windows and Mac. Working correctly. Closing issue.

              People

              • Assignee:
                rweidenh Rachel Weidenhammer (Inactive)
                Reporter:
                nfreese Nowlan Freese
              • Votes:
                0 Vote for this issue
                Watchers:
                4 Start watching this issue

                Dates

                • Created:
                  Updated:
                  Resolved: