Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: 10.2.0
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Labels:None
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Story Points:10
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Epic Link:
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Sprint:Fall 1, Fall 2, Fall 3, Fall 4, Fall 5, Fall 6, Fall 7, Fall 8, Fall 9
Description
Currently, users can import a file with SAMtool tags values and corresponding color hex codes in two columns. This ticket is about adding functionality where users can add corresponding cluster information (cluster id/name) for each tag value as well.
For the completion of this task:
- Users must be able to import 2-column or 3-column tsv/csv/txt file
- Importing 2-column files, SAMtools tag value and color, should work exactly as it does right now.
- Anticipate potential user errors while importing and handle it.
- Importing 3-column files, includes cluster id, users should be able to choose between:
- using the feature as it is right now - color by samtools tag values such as cell barcode
- or, color by cluster ids
Attachments
Issue Links
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- Closed
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Activity
Seeing an error when exiting the Edit filter window via the Red X.
Exception in thread "AWT-EventQueue-0" java.lang.ClassCastException: class java.lang.String cannot be cast to class java.lang.Integer (java.lang.String and java.lang.Integer are in module java.base of loader 'bootstrap') at com.affymetrix.igb.util.ConfigureFilters.beginEditing(ConfigureFilters.java:262) at com.affymetrix.igb.util.ConfigureFilters.editButtonActionPerformed(ConfigureFilters.java:158) at java.desktop/javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1972) at java.desktop/javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2314) at java.desktop/javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:407) at java.desktop/javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:262) at java.desktop/javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:279) at java.desktop/java.awt.Component.processMouseEvent(Component.java:6621) at java.desktop/javax.swing.JComponent.processMouseEvent(JComponent.java:3398) at java.desktop/java.awt.Component.processEvent(Component.java:6386) at java.desktop/java.awt.Container.processEvent(Container.java:2266) at java.desktop/java.awt.Component.dispatchEventImpl(Component.java:4996) at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2324) at java.desktop/java.awt.Component.dispatchEvent(Component.java:4828) at java.desktop/java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4948) at java.desktop/java.awt.LightweightDispatcher.processMouseEvent(Container.java:4575) at java.desktop/java.awt.LightweightDispatcher.dispatchEvent(Container.java:4516) at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2310) at java.desktop/java.awt.Window.dispatchEventImpl(Window.java:2780) at java.desktop/java.awt.Component.dispatchEvent(Component.java:4828) at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:775) at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:720) at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:714) at java.base/java.security.AccessController.doPrivileged(AccessController.java:400) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:98) at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:747) at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:745) at java.base/java.security.AccessController.doPrivileged(AccessController.java:400) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87) at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:744) at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203) at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124) at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113) at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109) at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)
I'm not sure if this was a pre-existing issue because I do recall seeing this before but I can't find evidence of that in any related tickets. Otherwise, I am able to see and interact with the Add/Remove/Edit buttons even after adding a long string of values. The issue of those disappearing appears to have been fixed.
UPDATE - moved to IGBF-4375
Found an issue today while doing some secondary testing with Dr. Freese. This issue was not present before the implementation of the JavaFX file finder.
Action: Click Import... Then, without clicking anything in the file finder that comes up, close out both of the SAMtags Color By windows, then close the file finder.
Result: IGB freezes and needs to be force quit.
UPDATE: Created IGBF-4376
Action: Hard to reproduce, but right-click the track and click Color by...
Result: Sometimes, the Color by window will open in the top-left corner of my screen rather than centered on IGB.
UPDATE: Created IGBF-4377
case 6: (check this case)
Action: import file and click save and apply and again Select SamTags from dropdown
now click on ok
Result: reads turned to gray color
UPDATE: It looks like even though the SAMtag colors are added, because the user is changing from SAMtags to something else and then back in the Color By window IGB is forgetting what the SAMtag colors are and defaulting to gray. Karthik and Nowlan discussed this and this is more or less the intended behavior.
case 7: (check this case)
Action: select first row and import file
Result: First row tag value is not visible
UPDATE: This appears to be resolved.
case 8: (check this case)
Action: Enter tag value manually and click import file and import data
Result: Manually entered value got removed.
UPDATE: I think this should be the intended behavior.
case 9: (check this case)
Action: Enter tag value (GAGTTTGTCCCTTCCC-1) and tick the check box
Result : Error Message displayed
UPDATE: Not able to reproduce this issue.
Action: Import data.
Result: The imported data occupies the entire table, there is no way to add additional user-entered tag values at the bottom
UPDATE: This was discussed, and the conclusion we reached was that if the user is importing data they cannot add additional rows to the table.
Action: Enter a manual tag value
Result: The row remains unchecked. If the user clicks Save and Apply they will not see the change. I think the intended behavior should be that if a user adds values to a row, the row should become checked automatically.
UPDATE: Created IGBF-4379
Action: Enter a manual tag and cluster value. Click View by Cluster. Enter a manual cluster and give it a color. Click View by Tags.
Result: The new cluster populates the rest of the table. Would be good to prevent user from manually adding a cluster in the View by Cluster.
UPDATE: Created IGBF-4378
Pushed commit 627d8d6 in IGBF-4295
This commit addresses:
- Importing 2 column or 3 column files in Color by SAMtags function
- Checkboxes for users to check or uncheck rows in the table
Note: I have added a sample txt file to the ticket with 3 columns. The quickload for the BAM file corresponding to the sample file is in here: https://bitbucket.org/KarthikRavee91/quickload_scrna-seq_10xgenomics/src/main/
In IGB, after add this quickload data source, load any pmbc alignments file from H_sapiens_Feb_2009
Ticket was tested on mac using installer. Some minor issues were identified (see previous comments). After discussion we have triaged the issues that should be addressed and have created new tickets.
Closing ticket.