Details
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Type:
New Feature
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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: 8.4.4 Minor Release, 8.5.0 Major Release
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Labels:
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Story Points:3
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Epic Link:
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Sprint:Sprint 24
Description
This affects IGB 8.5, possibly 8.4 as well.
If I edit an annots.xml file, rename a data set by editing its "title" attribute, and then click the refresh icon in the Data Sources table under the "Data Sources" Preference tab, IGB removes the data set from the main view and replaces it with the new one, but then the message notifying me of the removal at the bottom left of the window never goes away. I noticed this when editing the title for the A lyrata reference genes.
See attached.
Problem:
To repeat:
1) Set
Attachments
Issue Links
- relates to
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IGBF-839 Prepare IGB 8.4.2 Minor Release
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-439 [ 15497 ] |
| Fix Version/s | 8.4.2 Minor Release [ 10004 ] |
| Rank | Ranked higher |
| Rank | Ranked higher |
| Sprint | Sprint 24 [ 31 ] | Backlog Grooming Meeting [ 32 ] |
| Summary | data never removed upon QuickLoad refresh | Greatly improve propagation of error handling of quickload meta data parsing issues |
| Summary | Greatly improve propagation of error handling of quickload meta data parsing issues | Greatly improve propagation of error handling of quickload meta data parsing issues. |
| Issue Type | Bug [ 1 ] | New Feature [ 2 ] |
| Sprint | Backlog Grooming Meeting [ 32 ] | Sprint 24 [ 31 ] |
| Story Points | 1 | 3 |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs Testing [ 10002 ] |
| Status | Needs Testing [ 10002 ] | Testing In Progress [ 10003 ] |
| Assignee | David Norris [ dcnorris ] | Mason Meyer [ mason ] |
| Rank | Ranked higher |
I have tested David's broken quickload sites and verify that IGB is handling these broken quickload sites as expected, except for when an annots.xml is missing. In this case I am seeing a null pointer exception:
16:17:29.778 ERROR c.l.quickload.util.QuickloadUtils - Missing required annots.xml file for genome version A_thaliana_Jun_2009, skipping this genome version for quickload site http://igbquickload.org/brokenQuickloads/missingAnnotsXml/A_thaliana_Jun_2009/
java.io.IOException: null
at com.affymetrix.genometry.util.UriUtils.checkIsValidRequest(UriUtils.java:86) ~[genometry-8.4.2.jar:na]
at com.affymetrix.genometry.util.UriUtils.getInputStream(UriUtils.java:58) ~[genometry-8.4.2.jar:na]
at com.lorainelab.quickload.util.QuickloadUtils.getGenomeVersionData(QuickloadUtils.java:126) ~[quickload-8.4.2.jar:na]
at com.lorainelab.quickload.QuickloadDataProvider.getAvailableDataSets(QuickloadDataProvider.java:154) [quickload-8.4.2.jar:na]
at com.affymetrix.igb.view.load.GeneralLoadUtils.initializeDataContainer(GeneralLoadUtils.java:296) [igb-8.4.2.jar:na]
at com.affymetrix.igb.view.load.GeneralLoadUtils.lambda$initVersionAndSeq$40(GeneralLoadUtils.java:318) [igb-8.4.2.jar:na]
at com.affymetrix.igb.view.load.GeneralLoadUtils$$Lambda$267/2037209653.accept(Unknown Source) [igb-8.4.2.jar:na]
at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184) [na:1.8.0_51]
at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175) [na:1.8.0_51]
at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175) [na:1.8.0_51]
at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1374) [na:1.8.0_51]
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:512) [na:1.8.0_51]
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:502) [na:1.8.0_51]
at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151) [na:1.8.0_51]
at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174) [na:1.8.0_51]
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234) [na:1.8.0_51]
at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418) [na:1.8.0_51]
at com.affymetrix.igb.view.load.GeneralLoadUtils.initVersionAndSeq(GeneralLoadUtils.java:316) [igb-8.4.2.jar:na]
at com.affymetrix.igb.view.SeqGroupView$InitVersionWorker.runInBackground(SeqGroupView.java:697) [igb-8.4.2.jar:na]
at com.affymetrix.igb.view.SeqGroupView$InitVersionWorker.runInBackground(SeqGroupView.java:685) [igb-8.4.2.jar:na]
at com.affymetrix.genometry.thread.CThreadWorker.doInBackground(CThreadWorker.java:73) [genometry-8.4.2.jar:na]
at javax.swing.SwingWorker$1.call(SwingWorker.java:295) [na:1.8.0_51]
at java.util.concurrent.FutureTask.run(FutureTask.java:266) [na:1.8.0_51]
at javax.swing.SwingWorker.run(SwingWorker.java:334) [na:1.8.0_51]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [na:1.8.0_51]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [na:1.8.0_51]
at java.lang.Thread.run(Thread.java:745) [na:1.8.0_51]
| Assignee | Mason Meyer [ mason ] |
| Rank | Ranked lower |
David has fixed the issue noted in the comment above. IGB is now handling the broken quickload sites as expected. This issue still needs to be tested on 8.5.0. before closing.
| Status | Testing In Progress [ 10003 ] | Needs Testing [ 10002 ] |
| Status | Needs Testing [ 10002 ] | Testing In Progress [ 10003 ] |
| Status | Testing In Progress [ 10003 ] | Needs Testing [ 10002 ] |
| Assignee | Mason Meyer [ mason ] |
| Status | Needs Testing [ 10002 ] | Testing In Progress [ 10003 ] |
| Labels | Data_Provider |
| Resolution | Done [ 10000 ] | |
| Status | Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Resolution | Done [ 10000 ] | |
| Status | Closed [ 6 ] | Open [ 1 ] |
| Fix Version/s | 8.5.0 Major Release [ 10003 ] | |
| Fix Version/s | 8.4.2 Minor Release [ 10004 ] |
| Fix Version/s | 8.4.4 Minor Release [ 10101 ] |
| Resolution | Done [ 10000 ] | |
| Status | Open [ 1 ] | Closed [ 6 ] |
| Workflow | Loraine Lab Workflow [ 16115 ] | Fall 2019 Workflow Update [ 19587 ] |
| Workflow | Fall 2019 Workflow Update [ 19587 ] | Revised Fall 2019 Workflow Update [ 21706 ] |
Setup several broken quickload sites which are designed to be broken in specific ways. Document the way each site is broken and keep these sites around for future regression testing.