Uploaded image for project: 'IGB'
  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
        • Epic Link:
        • 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.

            Attachments

              Issue Links

              relates to

              New Plugin - actual specs for new plugin IGBF-510 Create Quickload Saver IGB app

              • Major - Major loss of function.
              • Closed

                Activity

                Ascending order - Click to sort in descending order
                14 older comments
                Hide
                Permalink
                inaylor Irvin Naylor (Inactive) 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 (Inactive) 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
                Permalink
                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
                Permalink
                rweidenh Logan 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 Logan 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
                Permalink
                nfreese Nowlan Freese added a comment -

                Logan 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 - Logan Weidenhammer - I fixed the foreground color, it was related to the change I made to the URI encoding.
                Hide
                Permalink
                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 Logan Weidenhammer (Inactive)
                    Reporter:
                    nfreese Nowlan Freese
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: