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  1. Testing
  2. TEST-1

Quickload: genome.txt

          Details

          • Type: Task
          • Status: Open (View Workflow)
          • Priority: Major
          • Resolution: Unresolved
          • Affects Version/s: None
          • Fix Version/s: None
          • Labels:
            None

            Description

            Background:

            genome.txt is a tab-delimited file IGB reads and uses to populate the Current Genome tab. When a user selects a species and genome version, IGB reads the genome.txt file.

            When users select rows in the table, IGB should display the corresponding chromosome/sequence in the main view.

            Example genome.txt file: http://igbquickload.org/quickload/A_thaliana_Jun_2009/genome.txt

            Do the following tests. Report results of each test in a separate comment. Attach files used for testing.

            For each test:

            • select chromosomes and observe IGB behavior
            • view console and report any exceptions

            Tests:

            • test what happens if a chromosome name contains a space
            • test what happens if there is a duplicate line in genome.txt
            • test what happens if the same chromosome name is listed twice but with different sizes
            • test what happens if there is a trailing space after the length column
            • test what happens if a non-ASCII (Unicode) character is used in a chromosome name

            Across servers:

            • test what happens if the same genome version is available at two different QuickLoad sites but they report different sizes for the same chromosome name
            • test what happens if the same genome version is available at two different QuickLoad sites but they report different chromosome names
            • test what happens if the same genome version is available at two different QuickLoad sites, the chromsome names and sizes are the same, but the order is different

              Attachments

                Issue Links

                is blocked by

                Task - A task that needs to be done. TEST-16 genome.txt cross QuickLoad different names

                • Minor - Minor loss of function, or other problem where easy workaround is present.
                • Open
                relates to

                Task - A task that needs to be done. TEST-9 genome.txt: chromosome name contains a space test duplicate line and reload in IGB

                • Major - Major loss of function.
                • Open

                Task - A task that needs to be done. TEST-11 genome.txt trailing space on line

                • Major - Major loss of function.
                • Open

                Task - A task that needs to be done. TEST-12 genome.txt trailing tab on line

                • Major - Major loss of function.
                • Open

                Task - A task that needs to be done. TEST-8 genome.txt chromosome name contains a space

                • Minor - Minor loss of function, or other problem where easy workaround is present.
                • Open

                Task - A task that needs to be done. TEST-10 genome.txt duplicate line in genome.txt

                • Minor - Minor loss of function, or other problem where easy workaround is present.
                • Open

                Task - A task that needs to be done. TEST-13 genome.txt extended ASCII test

                • Minor - Minor loss of function, or other problem where easy workaround is present.
                • Open

                Task - A task that needs to be done. TEST-14 genome.txt Unicode test

                • Minor - Minor loss of function, or other problem where easy workaround is present.
                • Open

                Task - A task that needs to be done. TEST-15 genome.txt cross QuickLoad different sizes

                • Minor - Minor loss of function, or other problem where easy workaround is present.
                • Open

                Task - A task that needs to be done. TEST-17 genome.txt cross QuickLoad different sorting

                • Minor - Minor loss of function, or other problem where easy workaround is present.
                • Open

                  Activity

                  Ascending order - Click to sort in descending order
                  kyle Kyle Suttlemyre (Inactive) created issue -
                  hiralv Hiral Vora (Inactive) made changes -
                  Field Original Value New Value
                  Project IGB 8 [ 10240 ] IGB 8.1 [ 10640 ]
                  Key IGBD-300 IGBE-27
                  ann.loraine Ann Loraine made changes -
                  Project IGB 8.1 [ 10640 ] Testing [ 10741 ]
                  Key IGBE-27 TEST-1
                  ann.loraine Ann Loraine made changes -
                  Description ____Explanation_____
                  Tab delimited file with chromosome and length

                  _____Tests_____
                  Control: http://igbquickload.org/quickload/A_thaliana_Jun_2009/genome.txt


                  Create a mod_chromInfo.txt and see if anything is read from there.


                  Naming errors:
                  -Replace tabs with spaces
                  -Reverse name and length
                  -Put an alpha character in the length
                  -use two tabs instead of one
                  -Replace underscore with space
                  -Alternate capitalization
                  -Duplicate a line
                  -Duplicate a line change col1
                  -Duplicate a line change col2
                  -Remove a length but keep chrom
                  -Remove a chrom but keep length
                  -Remove a whole line
                  -Sort differently
                  -Add extra column
                  -Add spaces to chrom name
                  -Add unicode char

                  Across servers:
                  -All of above across servers as well.
                  -Create name collision on titles across servers
                  -Create file name collision across servers
                  -Name collision on both columns (Title and file name) but different data



                  		 ____Explanation_____
                  Tab delimited file with chromosome and length

                  _____Tests_____
                  Control: http://igbquickload.org/quickload/A_thaliana_Jun_2009/genome.txt


                  Create a mod_chromInfo.txt and see if anything is read from there.

                  Format errors:
                  -Replace tabs with spaces
                  -Reverse name and length
                  -Put an alpha character in the length
                  -Use two tabs instead of one
                  -Remove a length but keep chrom
                  -Remove a chrom but keep length

                  Data errors:
                  -Duplicate a line (redundant data)
                  -Duplicate a line change col1 (conflicting data)
                  -Duplicate a line change col2
                  -Add spaces to chrom name
                  -What happens if you have trailing spaces after the length column?
                  -Add unicode char

                  Across servers:
                  -Remove a whole line (Two sites have the same genome version but one genome.txt is missing a line present in the other)
                  -Sort differently (Two sites with differently sorted genome.txt files)
                  -All of above across servers as well. (???)
                  ann.loraine Ann Loraine made changes -
                  Assignee Kyle Suttlemyre [ kyle ]
                  ann.loraine Ann Loraine made changes -
                  Description ____Explanation_____
                  Tab delimited file with chromosome and length

                  _____Tests_____
                  Control: http://igbquickload.org/quickload/A_thaliana_Jun_2009/genome.txt


                  Create a mod_chromInfo.txt and see if anything is read from there.

                  Format errors:
                  -Replace tabs with spaces
                  -Reverse name and length
                  -Put an alpha character in the length
                  -Use two tabs instead of one
                  -Remove a length but keep chrom
                  -Remove a chrom but keep length

                  Data errors:
                  -Duplicate a line (redundant data)
                  -Duplicate a line change col1 (conflicting data)
                  -Duplicate a line change col2
                  -Add spaces to chrom name
                  -What happens if you have trailing spaces after the length column?
                  -Add unicode char

                  Across servers:
                  -Remove a whole line (Two sites have the same genome version but one genome.txt is missing a line present in the other)
                  -Sort differently (Two sites with differently sorted genome.txt files)
                  -All of above across servers as well. (???)
                  Background:

                  genome.txt is a tab-delimited file IGB reads and uses to populate the Current Genome tab. When a user selects a species and genome version, IGB reads the genome.txt file.

                  When users select rows in the table, IGB should display the corresponding chromosome/sequence in the main view.

                  Example genome.txt file: http://igbquickload.org/quickload/A_thaliana_Jun_2009/genome.txt

                  Do the following tests. Report results of each test in a separate comment. Attach files used for testing.

                  For each test:

                  - select chromosomes and observe IGB behavior
                  - view console and report any exceptions

                  Tests:

                  - test what happens if a chromosome name contains a space
                  - test what happens if there is a duplicate line in contents.txt
                  - test what happens if the same chromosome name is listed twice but with different sizes
                  - test what happens if there is a trailing space after the length column
                  - test what happens if a non-ASCII (Unicode) character is used in a chromosome name

                  Across servers:
                  - test what happens if the same genome version is available at two different QuickLoad sites but they report different sizes for the same chromosome name
                  - test what happens if the same genome version is available at two different QuickLoad sites but they report different chromosome names
                  - test what happens if the same genome version is available at two different QuickLoad sites, the chromsome names and sizes are the same, but the order is different
                  ann.loraine Ann Loraine made changes -
                  Assignee Kyle Suttlemyre [ kyle ]
                  ann.loraine Ann Loraine made changes -
                  Description
                  Background:

                  genome.txt is a tab-delimited file IGB reads and uses to populate the Current Genome tab. When a user selects a species and genome version, IGB reads the genome.txt file.

                  When users select rows in the table, IGB should display the corresponding chromosome/sequence in the main view.

                  Example genome.txt file: http://igbquickload.org/quickload/A_thaliana_Jun_2009/genome.txt

                  Do the following tests. Report results of each test in a separate comment. Attach files used for testing.

                  For each test:

                  - select chromosomes and observe IGB behavior
                  - view console and report any exceptions

                  Tests:

                  - test what happens if a chromosome name contains a space
                  - test what happens if there is a duplicate line in contents.txt
                  - test what happens if the same chromosome name is listed twice but with different sizes
                  - test what happens if there is a trailing space after the length column
                  - test what happens if a non-ASCII (Unicode) character is used in a chromosome name

                  Across servers:
                  - test what happens if the same genome version is available at two different QuickLoad sites but they report different sizes for the same chromosome name
                  - test what happens if the same genome version is available at two different QuickLoad sites but they report different chromosome names
                  - test what happens if the same genome version is available at two different QuickLoad sites, the chromsome names and sizes are the same, but the order is different
                  		 Background:

                  genome.txt is a tab-delimited file IGB reads and uses to populate the Current Genome tab. When a user selects a species and genome version, IGB reads the genome.txt file.

                  When users select rows in the table, IGB should display the corresponding chromosome/sequence in the main view.

                  Example genome.txt file: http://igbquickload.org/quickload/A_thaliana_Jun_2009/genome.txt

                  Do the following tests. Report results of each test in a separate comment. Attach files used for testing.

                  For each test:

                  - select chromosomes and observe IGB behavior
                  - view console and report any exceptions

                  Tests:

                  - test what happens if a chromosome name contains a space
                  - test what happens if there is a duplicate line in genome.txt
                  - test what happens if the same chromosome name is listed twice but with different sizes
                  - test what happens if there is a trailing space after the length column
                  - test what happens if a non-ASCII (Unicode) character is used in a chromosome name

                  Across servers:
                  - test what happens if the same genome version is available at two different QuickLoad sites but they report different sizes for the same chromosome name
                  - test what happens if the same genome version is available at two different QuickLoad sites but they report different chromosome names
                  - test what happens if the same genome version is available at two different QuickLoad sites, the chromsome names and sizes are the same, but the order is different
                  Hide
                  Permalink
                  kyle Kyle Suttlemyre (Inactive) added a comment -

                  Notes:

                  • genome.txt will be merged between QuickLoad sites. If one contains an extra chromosome that will be added to the chromosome table.
                  • when sites are added/removed genome.txt update chromosome if the file has changed but will not remove chromosomes from removed QuickLoad sites.
                  • Attempting to test a clone of A_thaliana_2009 caused issues with polluting of chromosome ranges with the igbquickload.org QuickLoad site. So previous tests are now across servers.
                  • Attempting to rename clone of A_thaliana_2009 to K_suttlemyre_2014 caused issues with data integrity. Aborted this approach.

                  Tests Across Servers:

                  • If a chromosome name contains a space and user attempts to view that chromosome IGB will not display this track nor any other tracks from any other site (since they probably do not have chromosomes with that name)
                  • Exact duplicate line does nothing.
                  Show
                  kyle Kyle Suttlemyre (Inactive) added a comment - Notes: genome.txt will be merged between QuickLoad sites. If one contains an extra chromosome that will be added to the chromosome table. when sites are added/removed genome.txt update chromosome if the file has changed but will not remove chromosomes from removed QuickLoad sites. Attempting to test a clone of A_thaliana_2009 caused issues with polluting of chromosome ranges with the igbquickload.org QuickLoad site. So previous tests are now across servers. Attempting to rename clone of A_thaliana_2009 to K_suttlemyre_2014 caused issues with data integrity. Aborted this approach. Tests Across Servers: If a chromosome name contains a space and user attempts to view that chromosome IGB will not display this track nor any other tracks from any other site (since they probably do not have chromosomes with that name) Exact duplicate line does nothing.
                  Hide
                  Permalink
                  kyle Kyle Suttlemyre (Inactive) added a comment -

                  Tests:
                  Test(A) - will show up in genome table on GUI but when selected will not load any information "Load Data" button inactive and "Load Sequence" does nothing

                  Transition bug (A.5) Going from Test(A) to Test(B) causes the following bug:
                  1) a space in a chromosome then view in IGB.(make sure to select chromosome too)
                  2) go back to server and updating genome.txt to remove the space
                  3) Duplicate the line
                  4) go back to IGB and refresh the server
                  Observe: Species is now set to '-- Unknown – A_thaliana_2009' and exception is thrown
                  Mar 05, 2014 4:50:34 PM com.affymetrix.igb.view.load.GeneralLoadUtils$3 runInBackground
                  INFO: Loaded TAIR10 mRNA in 2.927 secs
                  Mar 05, 2014 4:51:04 PM com.affymetrix.igb.view.load.GeneralLoadUtils$3 runInBackground
                  INFO: Loaded TAIR10 mRNA in 1.895 secs
                  Mar 05, 2014 4:51:39 PM com.affymetrix.igb.view.load.GeneralLoadUtils$3 runInBackground
                  INFO: Loaded TAIR10 mRNA in 1.677 secs
                  java.lang.NullPointerException
                  at com.affymetrix.igb.view.SeqGroupView.valueChanged(SeqGroupView.java:344)
                  at javax.swing.DefaultListSelectionModel.fireValueChanged(DefaultListSelectionModel.java:184)
                  at javax.swing.DefaultListSelectionModel.fireValueChanged(DefaultListSelectionModel.java:154)
                  at javax.swing.DefaultListSelectionModel.setValueIsAdjusting(DefaultListSelectionModel.java:685)
                  at com.jidesoft.grid.JideTable$24.setValueIsAdjusting(Unknown Source)
                  at com.jidesoft.grid.TableUtils.loadSelection(Unknown Source)
                  at com.jidesoft.grid.TableUtils.loadSelection(Unknown Source)
                  at com.jidesoft.grid.JideTable.tableChanged(Unknown Source)
                  at javax.swing.table.AbstractTableModel.fireTableChanged(AbstractTableModel.java:296)
                  at javax.swing.table.AbstractTableModel.fireTableDataChanged(AbstractTableModel.java:198)
                  at com.affymetrix.igb.view.SeqGroupView.genericServerInit(SeqGroupView.java:610)
                  at com.affymetrix.igb.general.ServerList.fireServerInitEvent(ServerList.java:527)
                  at com.affymetrix.igb.view.load.GeneralLoadUtils.discoverServer(GeneralLoadUtils.java:296)
                  at com.affymetrix.igb.view.load.GeneralLoadUtils.addServer(GeneralLoadUtils.java:180)
                  at com.affymetrix.igb.prefs.ServerPrefsView.addDataSource(ServerPrefsView.java:237)
                  at com.affymetrix.igb.prefs.DataLoadPrefsView.updateSource(DataLoadPrefsView.java:381)
                  at com.affymetrix.igb.prefs.SourceTableModel.setValueAt(SourceTableModel.java:141)
                  at javax.swing.JTable.setValueAt(JTable.java:2741)
                  at com.jidesoft.grid.JideTable.editingStopped(Unknown Source)
                  at javax.swing.AbstractCellEditor.fireEditingStopped(AbstractCellEditor.java:141)
                  at com.affymetrix.genoviz.swing.ButtonTableCellEditor.actionPerformed(ButtonTableCellEditor.java:61)
                  at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2018)
                  at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2341)
                  at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
                  at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
                  at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:252)
                  at java.awt.Component.processMouseEvent(Component.java:6505)
                  at javax.swing.JComponent.processMouseEvent(JComponent.java:3320)
                  at java.awt.Component.processEvent(Component.java:6270)
                  at java.awt.Container.processEvent(Container.java:2229)
                  at java.awt.Component.dispatchEventImpl(Component.java:4861)
                  at java.awt.Container.dispatchEventImpl(Container.java:2287)
                  at java.awt.Component.dispatchEvent(Component.java:4687)
                  at javax.swing.plaf.basic.BasicTableUI$Handler.repostEvent(BasicTableUI.java:948)
                  at javax.swing.plaf.basic.BasicTableUI$Handler.mouseReleased(BasicTableUI.java:1164)
                  at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:290)
                  at java.awt.Component.processMouseEvent(Component.java:6505)
                  at javax.swing.JComponent.processMouseEvent(JComponent.java:3320)
                  at java.awt.Component.processEvent(Component.java:6270)
                  at java.awt.Container.processEvent(Container.java:2229)
                  at java.awt.Component.dispatchEventImpl(Component.java:4861)
                  at java.awt.Container.dispatchEventImpl(Container.java:2287)
                  at java.awt.Component.dispatchEvent(Component.java:4687)
                  at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4832)
                  at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4492)
                  at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4422)
                  at java.awt.Container.dispatchEventImpl(Container.java:2273)
                  at java.awt.Window.dispatchEventImpl(Window.java:2719)
                  at java.awt.Component.dispatchEvent(Component.java:4687)
                  at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:735)
                  at java.awt.EventQueue.access$200(EventQueue.java:103)
                  at java.awt.EventQueue$3.run(EventQueue.java:694)
                  at java.awt.EventQueue$3.run(EventQueue.java:692)
                  at java.security.AccessController.doPrivileged(Native Method)
                  at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
                  at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:87)
                  at java.awt.EventQueue$4.run(EventQueue.java:708)
                  at java.awt.EventQueue$4.run(EventQueue.java:706)
                  at java.security.AccessController.doPrivileged(Native Method)
                  at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
                  at java.awt.EventQueue.dispatchEvent(EventQueue.java:705)
                  at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242)
                  at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161)
                  at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150)
                  at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146)
                  at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138)
                  at java.awt.EventDispatchThread.run(EventDispatchThread.java:91)

                  Test(B) - No effect
                  Test(C) - preceding line overwritten by second instance
                  Test(D) - Chromosome is not listed!!!
                  Console message:
                  INFO: Loaded TAIR10 mRNA in 2.816 secs
                  WARNING: chromInfo line does not match. Ignoring: chr3 23459830
                  Hoever: trailing tab throws exception!

                  ar 05, 2014 5:04:28 PM com.affymetrix.igb.view.load.GeneralLoadUtils$3 runInBackground
                  INFO: Loaded TAIR10 mRNA in 1.028 secs
                  java.lang.NullPointerException
                  at com.affymetrix.igb.view.SeqGroupView.valueChanged(SeqGroupView.java:344)
                  at javax.swing.DefaultListSelectionModel.fireValueChanged(DefaultListSelectionModel.java:184)
                  at javax.swing.DefaultListSelectionModel.fireValueChanged(DefaultListSelectionModel.java:154)
                  at javax.swing.DefaultListSelectionModel.setValueIsAdjusting(DefaultListSelectionModel.java:685)
                  at com.jidesoft.grid.JideTable$24.setValueIsAdjusting(Unknown Source)
                  at com.jidesoft.grid.TableUtils.loadSelection(Unknown Source)
                  at com.jidesoft.grid.TableUtils.loadSelection(Unknown Source)
                  at com.jidesoft.grid.JideTable.tableChanged(Unknown Source)
                  at javax.swing.table.AbstractTableModel.fireTableChanged(AbstractTableModel.java:296)
                  at javax.swing.table.AbstractTableModel.fireTableDataChanged(AbstractTableModel.java:198)
                  at com.affymetrix.igb.view.SeqGroupView.genericServerInit(SeqGroupView.java:610)
                  at com.affymetrix.igb.general.ServerList.fireServerInitEvent(ServerList.java:527)
                  at com.affymetrix.igb.view.load.GeneralLoadUtils.discoverServer(GeneralLoadUtils.java:296)
                  at com.affymetrix.igb.view.load.GeneralLoadUtils.addServer(GeneralLoadUtils.java:180)
                  at com.affymetrix.igb.prefs.ServerPrefsView.addDataSource(ServerPrefsView.java:237)
                  at com.affymetrix.igb.prefs.DataLoadPrefsView.updateSource(DataLoadPrefsView.java:381)
                  at com.affymetrix.igb.prefs.SourceTableModel.setValueAt(SourceTableModel.java:141)
                  at javax.swing.JTable.setValueAt(JTable.java:2741)
                  at com.jidesoft.grid.JideTable.editingStopped(Unknown Source)
                  at javax.swing.AbstractCellEditor.fireEditingStopped(AbstractCellEditor.java:141)
                  at com.affymetrix.genoviz.swing.ButtonTableCellEditor.actionPerformed(ButtonTableCellEditor.java:61)
                  at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2018)
                  at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2341)
                  at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
                  at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
                  at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:252)
                  at java.awt.Component.processMouseEvent(Component.java:6505)
                  at javax.swing.JComponent.processMouseEvent(JComponent.java:3320)
                  at java.awt.Component.processEvent(Component.java:6270)
                  at java.awt.Container.processEvent(Container.java:2229)
                  at java.awt.Component.dispatchEventImpl(Component.java:4861)
                  at java.awt.Container.dispatchEventImpl(Container.java:2287)
                  at java.awt.Component.dispatchEvent(Component.java:4687)
                  at javax.swing.plaf.basic.BasicTableUI$Handler.repostEvent(BasicTableUI.java:948)
                  at javax.swing.plaf.basic.BasicTableUI$Handler.mouseReleased(BasicTableUI.java:1164)
                  at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:290)
                  at java.awt.Component.processMouseEvent(Component.java:6505)
                  at javax.swing.JComponent.processMouseEvent(JComponent.java:3320)
                  at java.awt.Component.processEvent(Component.java:6270)
                  at java.awt.Container.processEvent(Container.java:2229)
                  at java.awt.Component.dispatchEventImpl(Component.java:4861)
                  at java.awt.Container.dispatchEventImpl(Container.java:2287)
                  at java.awt.Component.dispatchEvent(Component.java:4687)
                  at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4832)
                  at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4492)
                  at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4422)
                  at java.awt.Container.dispatchEventImpl(Container.java:2273)
                  at java.awt.Window.dispatchEventImpl(Window.java:2719)
                  at java.awt.Component.dispatchEvent(Component.java:4687)
                  at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:735)
                  at java.awt.EventQueue.access$200(EventQueue.java:103)
                  at java.awt.EventQueue$3.run(EventQueue.java:694)
                  at java.awt.EventQueue$3.run(EventQueue.java:692)
                  at java.security.AccessController.doPrivileged(Native Method)
                  at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
                  at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:87)
                  at java.awt.EventQueue$4.run(EventQueue.java:708)
                  at java.awt.EventQueue$4.run(EventQueue.java:706)
                  at java.security.AccessController.doPrivileged(Native Method)
                  at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
                  at java.awt.EventQueue.dispatchEvent(EventQueue.java:705)
                  at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242)
                  at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161)
                  at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150)
                  at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146)
                  at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138)
                  at java.awt.EventDispatchThread.run(EventDispatchThread.java:91)
                  Test(E) - First testing for ASCII extended

                  For these tests refer to attached text file since extended ascii characters causes jira to crash. They will be noted as tags ex: <special1>

                  Changed 'chr3' to <special1> (got most consulted ascii characters from http://www.theasciicode.com.ar/)
                  characters do not show up in Chromosome table (weird diamond question marks appear) and data does not load.

                  Unicode:
                  character source: http://en.wikipedia.org/wiki/List_of_Unicode_characters
                  Chose last character of 'Latin Extended-B' <special2>
                  Changed 'chr3' to 'ch<special2>r3'
                  Shows odd question mark characters in table and will not allow user to view data.
                  Special note:
                  If an entry was already in the table it will cause load time to increase significantly and modifies length of previous entry to be 200,000,000. Does not throw an error

                  Show
                  kyle Kyle Suttlemyre (Inactive) added a comment - Tests: Test(A) - will show up in genome table on GUI but when selected will not load any information "Load Data" button inactive and "Load Sequence" does nothing Transition bug (A.5) Going from Test(A) to Test(B) causes the following bug: 1) a space in a chromosome then view in IGB.(make sure to select chromosome too) 2) go back to server and updating genome.txt to remove the space 3) Duplicate the line 4) go back to IGB and refresh the server Observe: Species is now set to '-- Unknown – A_thaliana_2009' and exception is thrown Mar 05, 2014 4:50:34 PM com.affymetrix.igb.view.load.GeneralLoadUtils$3 runInBackground INFO: Loaded TAIR10 mRNA in 2.927 secs Mar 05, 2014 4:51:04 PM com.affymetrix.igb.view.load.GeneralLoadUtils$3 runInBackground INFO: Loaded TAIR10 mRNA in 1.895 secs Mar 05, 2014 4:51:39 PM com.affymetrix.igb.view.load.GeneralLoadUtils$3 runInBackground INFO: Loaded TAIR10 mRNA in 1.677 secs java.lang.NullPointerException at com.affymetrix.igb.view.SeqGroupView.valueChanged(SeqGroupView.java:344) at javax.swing.DefaultListSelectionModel.fireValueChanged(DefaultListSelectionModel.java:184) at javax.swing.DefaultListSelectionModel.fireValueChanged(DefaultListSelectionModel.java:154) at javax.swing.DefaultListSelectionModel.setValueIsAdjusting(DefaultListSelectionModel.java:685) at com.jidesoft.grid.JideTable$24.setValueIsAdjusting(Unknown Source) at com.jidesoft.grid.TableUtils.loadSelection(Unknown Source) at com.jidesoft.grid.TableUtils.loadSelection(Unknown Source) at com.jidesoft.grid.JideTable.tableChanged(Unknown Source) at javax.swing.table.AbstractTableModel.fireTableChanged(AbstractTableModel.java:296) at javax.swing.table.AbstractTableModel.fireTableDataChanged(AbstractTableModel.java:198) at com.affymetrix.igb.view.SeqGroupView.genericServerInit(SeqGroupView.java:610) at com.affymetrix.igb.general.ServerList.fireServerInitEvent(ServerList.java:527) at com.affymetrix.igb.view.load.GeneralLoadUtils.discoverServer(GeneralLoadUtils.java:296) at com.affymetrix.igb.view.load.GeneralLoadUtils.addServer(GeneralLoadUtils.java:180) at com.affymetrix.igb.prefs.ServerPrefsView.addDataSource(ServerPrefsView.java:237) at com.affymetrix.igb.prefs.DataLoadPrefsView.updateSource(DataLoadPrefsView.java:381) at com.affymetrix.igb.prefs.SourceTableModel.setValueAt(SourceTableModel.java:141) at javax.swing.JTable.setValueAt(JTable.java:2741) at com.jidesoft.grid.JideTable.editingStopped(Unknown Source) at javax.swing.AbstractCellEditor.fireEditingStopped(AbstractCellEditor.java:141) at com.affymetrix.genoviz.swing.ButtonTableCellEditor.actionPerformed(ButtonTableCellEditor.java:61) at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2018) at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2341) at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402) at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259) at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:252) at java.awt.Component.processMouseEvent(Component.java:6505) at javax.swing.JComponent.processMouseEvent(JComponent.java:3320) at java.awt.Component.processEvent(Component.java:6270) at java.awt.Container.processEvent(Container.java:2229) at java.awt.Component.dispatchEventImpl(Component.java:4861) at java.awt.Container.dispatchEventImpl(Container.java:2287) at java.awt.Component.dispatchEvent(Component.java:4687) at javax.swing.plaf.basic.BasicTableUI$Handler.repostEvent(BasicTableUI.java:948) at javax.swing.plaf.basic.BasicTableUI$Handler.mouseReleased(BasicTableUI.java:1164) at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:290) at java.awt.Component.processMouseEvent(Component.java:6505) at javax.swing.JComponent.processMouseEvent(JComponent.java:3320) at java.awt.Component.processEvent(Component.java:6270) at java.awt.Container.processEvent(Container.java:2229) at java.awt.Component.dispatchEventImpl(Component.java:4861) at java.awt.Container.dispatchEventImpl(Container.java:2287) at java.awt.Component.dispatchEvent(Component.java:4687) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4832) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4492) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4422) at java.awt.Container.dispatchEventImpl(Container.java:2273) at java.awt.Window.dispatchEventImpl(Window.java:2719) at java.awt.Component.dispatchEvent(Component.java:4687) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:735) at java.awt.EventQueue.access$200(EventQueue.java:103) at java.awt.EventQueue$3.run(EventQueue.java:694) at java.awt.EventQueue$3.run(EventQueue.java:692) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:87) at java.awt.EventQueue$4.run(EventQueue.java:708) at java.awt.EventQueue$4.run(EventQueue.java:706) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:705) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138) at java.awt.EventDispatchThread.run(EventDispatchThread.java:91) Test(B) - No effect Test(C) - preceding line overwritten by second instance Test(D) - Chromosome is not listed!!! Console message: INFO: Loaded TAIR10 mRNA in 2.816 secs WARNING: chromInfo line does not match. Ignoring: chr3 23459830 Hoever: trailing tab throws exception! ar 05, 2014 5:04:28 PM com.affymetrix.igb.view.load.GeneralLoadUtils$3 runInBackground INFO: Loaded TAIR10 mRNA in 1.028 secs java.lang.NullPointerException at com.affymetrix.igb.view.SeqGroupView.valueChanged(SeqGroupView.java:344) at javax.swing.DefaultListSelectionModel.fireValueChanged(DefaultListSelectionModel.java:184) at javax.swing.DefaultListSelectionModel.fireValueChanged(DefaultListSelectionModel.java:154) at javax.swing.DefaultListSelectionModel.setValueIsAdjusting(DefaultListSelectionModel.java:685) at com.jidesoft.grid.JideTable$24.setValueIsAdjusting(Unknown Source) at com.jidesoft.grid.TableUtils.loadSelection(Unknown Source) at com.jidesoft.grid.TableUtils.loadSelection(Unknown Source) at com.jidesoft.grid.JideTable.tableChanged(Unknown Source) at javax.swing.table.AbstractTableModel.fireTableChanged(AbstractTableModel.java:296) at javax.swing.table.AbstractTableModel.fireTableDataChanged(AbstractTableModel.java:198) at com.affymetrix.igb.view.SeqGroupView.genericServerInit(SeqGroupView.java:610) at com.affymetrix.igb.general.ServerList.fireServerInitEvent(ServerList.java:527) at com.affymetrix.igb.view.load.GeneralLoadUtils.discoverServer(GeneralLoadUtils.java:296) at com.affymetrix.igb.view.load.GeneralLoadUtils.addServer(GeneralLoadUtils.java:180) at com.affymetrix.igb.prefs.ServerPrefsView.addDataSource(ServerPrefsView.java:237) at com.affymetrix.igb.prefs.DataLoadPrefsView.updateSource(DataLoadPrefsView.java:381) at com.affymetrix.igb.prefs.SourceTableModel.setValueAt(SourceTableModel.java:141) at javax.swing.JTable.setValueAt(JTable.java:2741) at com.jidesoft.grid.JideTable.editingStopped(Unknown Source) at javax.swing.AbstractCellEditor.fireEditingStopped(AbstractCellEditor.java:141) at com.affymetrix.genoviz.swing.ButtonTableCellEditor.actionPerformed(ButtonTableCellEditor.java:61) at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2018) at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2341) at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402) at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259) at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:252) at java.awt.Component.processMouseEvent(Component.java:6505) at javax.swing.JComponent.processMouseEvent(JComponent.java:3320) at java.awt.Component.processEvent(Component.java:6270) at java.awt.Container.processEvent(Container.java:2229) at java.awt.Component.dispatchEventImpl(Component.java:4861) at java.awt.Container.dispatchEventImpl(Container.java:2287) at java.awt.Component.dispatchEvent(Component.java:4687) at javax.swing.plaf.basic.BasicTableUI$Handler.repostEvent(BasicTableUI.java:948) at javax.swing.plaf.basic.BasicTableUI$Handler.mouseReleased(BasicTableUI.java:1164) at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:290) at java.awt.Component.processMouseEvent(Component.java:6505) at javax.swing.JComponent.processMouseEvent(JComponent.java:3320) at java.awt.Component.processEvent(Component.java:6270) at java.awt.Container.processEvent(Container.java:2229) at java.awt.Component.dispatchEventImpl(Component.java:4861) at java.awt.Container.dispatchEventImpl(Container.java:2287) at java.awt.Component.dispatchEvent(Component.java:4687) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4832) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4492) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4422) at java.awt.Container.dispatchEventImpl(Container.java:2273) at java.awt.Window.dispatchEventImpl(Window.java:2719) at java.awt.Component.dispatchEvent(Component.java:4687) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:735) at java.awt.EventQueue.access$200(EventQueue.java:103) at java.awt.EventQueue$3.run(EventQueue.java:694) at java.awt.EventQueue$3.run(EventQueue.java:692) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:87) at java.awt.EventQueue$4.run(EventQueue.java:708) at java.awt.EventQueue$4.run(EventQueue.java:706) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:705) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138) at java.awt.EventDispatchThread.run(EventDispatchThread.java:91) Test(E) - First testing for ASCII extended For these tests refer to attached text file since extended ascii characters causes jira to crash. They will be noted as tags ex: <special1> Changed 'chr3' to <special1> (got most consulted ascii characters from http://www.theasciicode.com.ar/ ) characters do not show up in Chromosome table (weird diamond question marks appear) and data does not load. Unicode: character source: http://en.wikipedia.org/wiki/List_of_Unicode_characters Chose last character of 'Latin Extended-B' <special2> Changed 'chr3' to 'ch<special2>r3' Shows odd question mark characters in table and will not allow user to view data. Special note: If an entry was already in the table it will cause load time to increase significantly and modifies length of previous entry to be 200,000,000. Does not throw an error
                  kyle Kyle Suttlemyre (Inactive) made changes -
                  Attachment specialChars.txt [ 12362 ]
                  Hide
                  Permalink
                  kyle Kyle Suttlemyre (Inactive) added a comment -

                  Cross site errors
                  Test (A) Difficult to repeat has to do possibly with starting from initial load having one load before the other or order of appearance in "Data Sources" list

                  WARNING: Found a feature with null style
                  Mar 06, 2014 5:10:06 PM com.affymetrix.igb.view.load.GeneralLoadUtils$3 runInBackground
                  INFO: Loaded TAIR10 mRNA in 4.199 secs
                  Mar 06, 2014 5:10:09 PM com.affymetrix.igb.view.load.GeneralLoadUtils$3 runInBackground
                  INFO: Loaded TAIR10 mRNA in 0.001 secs
                  java.lang.ArrayIndexOutOfBoundsException
                  at java.lang.System.arraycopy(Native Method)
                  at sun.security.provider.DigestBase.engineUpdate(DigestBase.java:127)
                  at java.security.MessageDigest$Delegate.engineUpdate(MessageDigest.java:568)
                  at java.security.MessageDigest.update(MessageDigest.java:323)
                  at java.security.MessageDigest.digest(MessageDigest.java:398)
                  at com.affymetrix.genometryImpl.util.UrlToFileName.toMd5(UrlToFileName.java:107)
                  at com.affymetrix.genometryImpl.util.PreferenceUtils.shortNodeName(PreferenceUtils.java:636)
                  at com.affymetrix.genometryImpl.util.PreferenceUtils.getSubnode(PreferenceUtils.java:657)
                  at com.affymetrix.genometryImpl.util.PreferenceUtils.getSubnode(PreferenceUtils.java:650)
                  at com.affymetrix.igb.tiers.TrackStyle.<init>(TrackStyle.java:139)
                  at com.affymetrix.igb.tiers.IGBStateProvider.getAnnotStyle(IGBStateProvider.java:61)
                  at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.setStyle(QuickLoadSymLoader.java:207)
                  at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadAndAddSymmetries(QuickLoadSymLoader.java:146)
                  at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadSymmetriesThread(QuickLoadSymLoader.java:129)
                  at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadFeatures(QuickLoadSymLoader.java:109)
                  at com.affymetrix.genometryImpl.quickload.QuickloadServerType.loadFeatures(QuickloadServerType.java:354)
                  at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:941)
                  at com.affymetrix.igb.view.load.GeneralLoadUtils$3.loadOnSequence(GeneralLoadUtils.java:847)
                  at com.affymetrix.igb.view.load.GeneralLoadUtils$3.access$400(GeneralLoadUtils.java:713)
                  at com.affymetrix.igb.view.load.GeneralLoadUtils$3$3.run(GeneralLoadUtils.java:788)
                  at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
                  at java.util.concurrent.FutureTask.run(FutureTask.java:262)
                  at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
                  at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
                  at java.lang.Thread.run(Thread.java:744)

                  Test (B) Renamed chromosome does not show anything.

                  Test (C) used command $ sort -t $'\t' -k 2,2 -V genome.txt -o genome.txt
                  no issues but loading the small one first seems to cause noticeable loading (not longer or shorter just graphically noticeable)

                  Show
                  kyle Kyle Suttlemyre (Inactive) added a comment - Cross site errors Test (A) Difficult to repeat has to do possibly with starting from initial load having one load before the other or order of appearance in "Data Sources" list WARNING: Found a feature with null style Mar 06, 2014 5:10:06 PM com.affymetrix.igb.view.load.GeneralLoadUtils$3 runInBackground INFO: Loaded TAIR10 mRNA in 4.199 secs Mar 06, 2014 5:10:09 PM com.affymetrix.igb.view.load.GeneralLoadUtils$3 runInBackground INFO: Loaded TAIR10 mRNA in 0.001 secs java.lang.ArrayIndexOutOfBoundsException at java.lang.System.arraycopy(Native Method) at sun.security.provider.DigestBase.engineUpdate(DigestBase.java:127) at java.security.MessageDigest$Delegate.engineUpdate(MessageDigest.java:568) at java.security.MessageDigest.update(MessageDigest.java:323) at java.security.MessageDigest.digest(MessageDigest.java:398) at com.affymetrix.genometryImpl.util.UrlToFileName.toMd5(UrlToFileName.java:107) at com.affymetrix.genometryImpl.util.PreferenceUtils.shortNodeName(PreferenceUtils.java:636) at com.affymetrix.genometryImpl.util.PreferenceUtils.getSubnode(PreferenceUtils.java:657) at com.affymetrix.genometryImpl.util.PreferenceUtils.getSubnode(PreferenceUtils.java:650) at com.affymetrix.igb.tiers.TrackStyle.<init>(TrackStyle.java:139) at com.affymetrix.igb.tiers.IGBStateProvider.getAnnotStyle(IGBStateProvider.java:61) at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.setStyle(QuickLoadSymLoader.java:207) at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadAndAddSymmetries(QuickLoadSymLoader.java:146) at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadSymmetriesThread(QuickLoadSymLoader.java:129) at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadFeatures(QuickLoadSymLoader.java:109) at com.affymetrix.genometryImpl.quickload.QuickloadServerType.loadFeatures(QuickloadServerType.java:354) at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:941) at com.affymetrix.igb.view.load.GeneralLoadUtils$3.loadOnSequence(GeneralLoadUtils.java:847) at com.affymetrix.igb.view.load.GeneralLoadUtils$3.access$400(GeneralLoadUtils.java:713) at com.affymetrix.igb.view.load.GeneralLoadUtils$3$3.run(GeneralLoadUtils.java:788) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471) at java.util.concurrent.FutureTask.run(FutureTask.java:262) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) at java.lang.Thread.run(Thread.java:744) Test (B) Renamed chromosome does not show anything. Test (C) used command $ sort -t $'\t' -k 2,2 -V genome.txt -o genome.txt no issues but loading the small one first seems to cause noticeable loading (not longer or shorter just graphically noticeable)
                  kyle Kyle Suttlemyre (Inactive) made changes -
                  Link This issue relates to TEST-8 [ TEST-8 ]
                  kyle Kyle Suttlemyre (Inactive) made changes -
                  Link This issue relates to TEST-9 [ TEST-9 ]
                  kyle Kyle Suttlemyre (Inactive) made changes -
                  Link This issue relates to TEST-10 [ TEST-10 ]
                  kyle Kyle Suttlemyre (Inactive) made changes -
                  Link This issue relates to TEST-11 [ TEST-11 ]
                  kyle Kyle Suttlemyre (Inactive) made changes -
                  Link This issue relates to TEST-12 [ TEST-12 ]
                  kyle Kyle Suttlemyre (Inactive) made changes -
                  Link This issue relates to TEST-13 [ TEST-13 ]
                  kyle Kyle Suttlemyre (Inactive) made changes -
                  Link This issue relates to TEST-14 [ TEST-14 ]
                  kyle Kyle Suttlemyre (Inactive) made changes -
                  Link This issue relates to TEST-15 [ TEST-15 ]
                  kyle Kyle Suttlemyre (Inactive) made changes -
                  Link This issue is blocked by TEST-16 [ TEST-16 ]
                  kyle Kyle Suttlemyre (Inactive) made changes -
                  Link This issue relates to TEST-17 [ TEST-17 ]
                  kyle Kyle Suttlemyre (Inactive) made changes -
                  Assignee Kyle Suttlemyre [ kyle ] Ann Loraine [ aloraine ]

                    People

                    • Assignee:
                      ann.loraine Ann Loraine
                      Reporter:
                      kyle Kyle Suttlemyre (Inactive)
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                      Dates

                      • Created:
                        Updated: