Details
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Type:
Bug
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Fixed
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Labels:None
Description
Launch IGB, choose Arabidopsis thaliana genome version A_thaliana_Jun_2009
Open Bioviz (DAS2) > AtTile1R > GSE9646 > Untreated and 10_drought; check each of the boxes.
Use Search to zoom to AT1G07350. Load Data button to load the tiling array data sets
Click Graph Adjuster tab and click Select All Graphs. Click Delete Selected Graphs. Scroll and zoom to a different region (doesn't matter where) and click Load Data again
Note that IGB appears to load more data from the server (the application pauses and a message to this effect appears in the lower left corner) however nothing appears on the screen.
If the user deletes a graph and if the Data Access Load Model table still shows that data set, it would be good if IGB would go ahead and display the data.
Testing Results:
November 8, 2010 - Alyssa Gulledge
version 6.4 (7141). Tested as above and works fine. Also tried deleting some graph files then refreshing in a different location. It works exactly like it should.
Attachments
Issue Links
- is blocked by
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BUG-638 Graph files
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Status | Open [ 1 ] | Closed [ 6 ] |
| Resolution | Fixed [ 1 ] |
| Resolution | Fixed [ 1 ] | |
| Status | Closed [ 6 ] | Reopened [ 4 ] |
| Assignee | Afshan Jalali [ afshan ] | Hiral Vora [ hiralv ] |
I am not able to reproduce it.
I had added fix for exact same exception.
| Assignee | Hiral Vora [ hiralv ] | Alyssa Gulledge [ alyssa ] |
Its either fixed or something else I did yesterday i'm unaware of had an effect on its reproduction.
Bug update: There is still a weird bug associated with this.
Zoom into a gene, before you load these graphs, so only 1 gene/region is showing. Load. Using graph adjuster tab, select all, then delete all. Now try reload - this region does NOT reload and the console says:
"Sep 2, 2011 12:48:27 PM com.affymetrix.igb.view.load.GeneralLoadUtils loadFeaturesForSym
INFO: All of new query covered by previous queries for feature AtTile1R/GSE9646/10h_drought/GSM243701
Sep 2, 2011 12:48:27 PM com.affymetrix.igb.view.load.GeneralLoadUtils loadFeaturesForSym
INFO: All of new query covered by previous queries for feature AtTile1R/GSE9646/10h_drought/GSM243702
Sep 2, 2011 12:48:27 PM com.affymetrix.igb.view.load.GeneralLoadUtils loadFeaturesForSym
INFO: All of new query covered by previous queries for feature AtTile1R/GSE9646/10h_drought/GSM243703"
Now expand the view/zoom, so that there are new genes on either side of the previous one. NOW hit reload. The graphs reload, leaving a gap of the delete material in the middle. This affects all graph types
| Assignee | Alyssa Gulledge [ alyssa ] | Hiral Vora [ hiralv ] |
Fixed in r8826.
| Assignee | Hiral Vora [ hiralv ] | Alyssa Gulledge [ alyssa ] |
| Status | Reopened [ 4 ] | Resolved [ 5 ] |
| Resolution | Fixed [ 1 ] |
| Status | Resolved [ 5 ] | Closed [ 6 ] |
| Assignee | Alyssa Gulledge [ alyssa ] |
| Resolution | Fixed [ 1 ] | |
| Status | Closed [ 6 ] | Reopened [ 4 ] |
| Assignee | Katharine Kubiak [ kkubiak ] |
| Assignee | Katharine Kubiak [ kkubiak ] | Alyssa Gulledge [ alyssa ] |
| Description |
1. Launch IGB, choose Arabidopsis thaliana genome version A_thaliana_Jun_2009 2. Open Bioviz (Quickload) and click TAIR9 mRNA and choose Whole Genome load mode 3. Under Data Access tab, click Configure. 4. Add DAS2 site http://demodas.transvar.org/das2/genome (to get some tiling array data sets) 5. Choose Arabidopsis thaliana genome version A_thaliana_Jun_2009 6. Open AtTile1R->GSE9646->Untreated and check each of the boxes. 7. Open AtTile1R->GSE9646->10h_drought and check each of the boxes. 8. Use Search tab to search for AT1G61520.1. 9. Click the table cell to zoom/scroll to region of AT1G61520.1 10. Click Refresh Data button to load the tiling array data sets 11. Click Graph Adjuster tab and click Select All Graphs 12. Click Delete Selected Graphs 13. Scroll and zoom to a different region (doesn't matter where) and click Refresh Data again 14. Note that IGB appears to load more data from the server (the application pauses and a message to this effect appears in the lower left corner) 15. Note that even though IGB appears to have loaded data from the server, nothing appears on the screen. 16. No matter how many times you click Refresh Data, the graphs data will not show up. The graph data should show up on refreshing data. 17. If the user deletes a graph and if the Data Access Load Model table still shows that data set, it would be good if IGB would go ahead and display the data. Testing Results: November 8, 2010 - Alyssa Gulledge version 6.4 (7141). Tested as above and works fine. Also tried deleting some graph files then refreshing in a different location. It works exactly like it should. |
Launch IGB, choose Arabidopsis thaliana genome version A_thaliana_Jun_2009 Open Bioviz (DAS2) > AtTile1R > GSE9646 > Untreated and 10_drought; check each of the boxes. Use Search for AT1G61520.1. Load Data button to load the tiling array data sets Click Graph Adjuster tab and click Select All Graphs. Click Delete Selected Graphs. Scroll and zoom to a different region (doesn't matter where) and click Load Data again Note that IGB appears to load more data from the server (the application pauses and a message to this effect appears in the lower left corner) however nothing appears on the screen. If the user deletes a graph and if the Data Access Load Model table still shows that data set, it would be good if IGB would go ahead and display the data. Testing Results: November 8, 2010 - Alyssa Gulledge version 6.4 (7141). Tested as above and works fine. Also tried deleting some graph files then refreshing in a different location. It works exactly like it should. |
Test case sequence updated for 6.7. Passes Mac.
| Description |
Launch IGB, choose Arabidopsis thaliana genome version A_thaliana_Jun_2009 Open Bioviz (DAS2) > AtTile1R > GSE9646 > Untreated and 10_drought; check each of the boxes. Use Search for AT1G61520.1. Load Data button to load the tiling array data sets Click Graph Adjuster tab and click Select All Graphs. Click Delete Selected Graphs. Scroll and zoom to a different region (doesn't matter where) and click Load Data again Note that IGB appears to load more data from the server (the application pauses and a message to this effect appears in the lower left corner) however nothing appears on the screen. If the user deletes a graph and if the Data Access Load Model table still shows that data set, it would be good if IGB would go ahead and display the data. Testing Results: November 8, 2010 - Alyssa Gulledge version 6.4 (7141). Tested as above and works fine. Also tried deleting some graph files then refreshing in a different location. It works exactly like it should. |
Launch IGB, choose Arabidopsis thaliana genome version A_thaliana_Jun_2009 Open Bioviz (DAS2) > AtTile1R > GSE9646 > Untreated and 10_drought; check each of the boxes. Use Search to zoom to AT1G07350. Load Data button to load the tiling array data sets Click Graph Adjuster tab and click Select All Graphs. Click Delete Selected Graphs. Scroll and zoom to a different region (doesn't matter where) and click Load Data again Note that IGB appears to load more data from the server (the application pauses and a message to this effect appears in the lower left corner) however nothing appears on the screen. If the user deletes a graph and if the Data Access Load Model table still shows that data set, it would be good if IGB would go ahead and display the data. Testing Results: November 8, 2010 - Alyssa Gulledge version 6.4 (7141). Tested as above and works fine. Also tried deleting some graph files then refreshing in a different location. It works exactly like it should. |
| Assignee | Alyssa Gulledge [ alyssa ] | Katharine Kubiak [ kkubiak ] |
| Comment | [ Cannot connect to server "DAS2 site http://demodas.transvar.org/das2/genome" from step 4. ] |
Passed v9804 Windows
| Assignee | Katharine Kubiak [ kkubiak ] | Alyssa Gulledge [ alyssa ] |
| Status | Reopened [ 4 ] | Resolved [ 5 ] |
| Assignee | Alyssa Gulledge [ alyssa ] | |
| Resolution | Fixed [ 1 ] |
| Status | Resolved [ 5 ] | Closed [ 6 ] |
| Resolution | Fixed [ 1 ] | |
| Status | Closed [ 6 ] | Reopened [ 4 ] |
| Assignee | Vineeth Mylapur [ smylapur ] |
Passed 7.0 (11892) on Windows
-No select all button in Track Adjuster. Instead I tried shift+ click on all.Deleted the selected Graph.
| Status | Reopened [ 4 ] | Resolved [ 5 ] |
| Assignee | Vineeth Mylapur [ smylapur ] | |
| Resolution | Fixed [ 1 ] |
| Resolution | Fixed [ 1 ] | |
| Status | Resolved [ 5 ] | Reopened [ 4 ] |
Passed V.13740, Mac, Java 1.6.0_33
When 'Delete Graph' is selected, all graphs are deleted from the main viewer as well as under the 'Data Management Table' under the 'Data Access' Tab. Selecting the same data again to display worked without any issues.
| Status | Reopened [ 4 ] | Resolved [ 5 ] |
| Assignee | Alyssa Gulledge [ alyssa ] | |
| Resolution | Fixed [ 1 ] |
| Status | Resolved [ 5 ] | Closed [ 6 ] |
| Assignee | Alyssa Gulledge [ alyssa ] |
This bug does appear to be fixed; however, this exception is thrown when following these exact steps on step 12. After further testing I have discovered this exception is thrown every time the "delete selected" button is used from the graph adjuster tab.
Exception in thread "AWT-EventQueue-0" java.lang.IllegalArgumentException: must remove item from previous map before adding it to new map
at com.affymetrix.genoviz.widget.NeoMap.addItem(NeoMap.java:1305)
at com.affymetrix.igb.tiers.AffyTieredMap.addTier(AffyTieredMap.java:130)
at com.affymetrix.igb.tiers.AffyLabelledTierMap.addTier(AffyLabelledTierMap.java:160)
at com.affymetrix.igb.tiers.AffyTieredMap.addTier(AffyTieredMap.java:116)
at com.affymetrix.igb.view.TrackView.getGraphTrack(TrackView.java:169)
at com.affymetrix.igb.view.SeqMapView.getGraphTrack(SeqMapView.java:1847)
at com.affymetrix.igb.glyph.GenericGraphGlyphFactory.displayGraphSym(GenericGraphGlyphFactory.java:154)
at com.affymetrix.igb.glyph.GenericGraphGlyphFactory.displayGraph(GenericGraphGlyphFactory.java:111)
at com.affymetrix.igb.glyph.GenericGraphGlyphFactory.createGlyph(GenericGraphGlyphFactory.java:44)
at com.affymetrix.igb.view.TrackView.addAnnotationGlyphs(TrackView.java:231)
at com.affymetrix.igb.view.TrackView.addTracks(TrackView.java:201)
at com.affymetrix.igb.view.SeqMapView.addAnnotationTracks(SeqMapView.java:988)
at com.affymetrix.igb.view.SeqMapView.addGlyphs(SeqMapView.java:829)
at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:711)
at com.affymetrix.igb.view.AltSpliceSeqMapView.setAnnotatedSeq(AltSpliceSeqMapView.java:277)
at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:638)
at com.affymetrix.igb.view.AltSpliceSeqMapView.setAnnotatedSeq(AltSpliceSeqMapView.java:56)
at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:626)
at com.affymetrix.igb.view.AltSpliceSeqMapView.sliceAndDiceNow(AltSpliceSeqMapView.java:250)
at com.affymetrix.igb.view.AltSpliceSeqMapView.dataRemoved(AltSpliceSeqMapView.java:169)
at com.affymetrix.igb.view.SeqMapView.dataRemoved(SeqMapView.java:620)
at com.affymetrix.igb.IGBServiceImpl.deleteGlyph(IGBServiceImpl.java:286)
at com.affymetrix.igb.graph.SimpleGraphTab.deleteGraph(SimpleGraphTab.java:1088)
at com.affymetrix.igb.graph.SimpleGraphTab.deleteGraphs(SimpleGraphTab.java:1050)
at com.affymetrix.igb.graph.SimpleGraphTab.access$200(SimpleGraphTab.java:67)
at com.affymetrix.igb.graph.SimpleGraphTab$2.actionPerformed(SimpleGraphTab.java:110)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028)
at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236)
at java.awt.Component.processMouseEvent(Component.java:6374)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
at java.awt.Component.processEvent(Component.java:6139)
at java.awt.Container.processEvent(Container.java:2085)
at java.awt.Component.dispatchEventImpl(Component.java:4736)
at java.awt.Container.dispatchEventImpl(Container.java:2143)
at java.awt.Component.dispatchEvent(Component.java:4566)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4621)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4282)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4212)
at java.awt.Container.dispatchEventImpl(Container.java:2129)
at java.awt.Window.dispatchEventImpl(Window.java:2478)
at java.awt.Component.dispatchEvent(Component.java:4566)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:680)
at java.awt.EventQueue.access$000(EventQueue.java:86)
at java.awt.EventQueue$1.run(EventQueue.java:639)
at java.awt.EventQueue$1.run(EventQueue.java:637)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)
at java.awt.EventQueue$2.run(EventQueue.java:653)
at java.awt.EventQueue$2.run(EventQueue.java:651)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:650)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)