[TEST-1] Quickload: genome.txt - JIRA UNCC

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

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specialChars.txt
0.1 kB
05/Mar/14 12:33 PM

Issue Links

is blocked by

TEST-16 genome.txt cross QuickLoad different names

Open

relates to

TEST-9 genome.txt: chromosome name contains a space test duplicate line and reload in IGB

Open

TEST-11 genome.txt trailing space on line

Open

TEST-12 genome.txt trailing tab on line

Open

TEST-8 genome.txt chromosome name contains a space

Open

TEST-10 genome.txt duplicate line in genome.txt

Open

TEST-13 genome.txt extended ASCII test

Open

TEST-14 genome.txt Unicode test

Open

TEST-15 genome.txt cross QuickLoad different sizes

Open

TEST-17 genome.txt cross QuickLoad different sorting

Open

Show 5 more links (5 relates to)

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Ascending order - Click to sort in descending order

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Kyle Suttlemyre (Inactive) added a comment - 05/Mar/14 11:03 AM

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 Suttlemyre (Inactive) added a comment - 05/Mar/14 11:03 AM 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.

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Kyle Suttlemyre (Inactive) added a comment - 05/Mar/14 12:32 PM

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 Suttlemyre (Inactive) added a comment - 05/Mar/14 12:32 PM 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

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Kyle Suttlemyre (Inactive) added a comment - 06/Mar/14 12:45 PM

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)

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Kyle Suttlemyre (Inactive) added a comment - 06/Mar/14 12:45 PM 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)

Quickload: genome.txt

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