Details
-
Type: Bug
-
Status: Closed (View Workflow)
-
Priority: Blocker
-
Resolution: Done
-
Affects Version/s: None
-
Fix Version/s: 9.1.0 Major Release
-
Labels:
-
Story Points:1
-
Epic Link:
-
Sprint:Spring 2019 Sprint 5, Fall 2019 Sprint 3, Fall 4 : 30 Sep to 11 Oct, Fall 5 : 14 Oct to 25 Oct
Description
Investigate and determine why this happens.
Find out if it affects released branch 9.0.2 (get from bioviz.org).
Read user's guide Advanced Search documentation as background.
To repeat:
1) Click Advanced Search tab
2) Select PropertySearch, don't enter query string (leave text blank)
3) Click Search icon (magnifying glass button on right of text entry)
Observe exception:
14:51:37.494 ERROR c.a.genometry.thread.CThreadWorker - Comparison method violates its general contract!
java.lang.IllegalArgumentException: Comparison method violates its general contract!
at java.util.TimSort.mergeHi(TimSort.java:899) ~[na:1.8.0_192]
at java.util.TimSort.mergeAt(TimSort.java:516) ~[na:1.8.0_192]
at java.util.TimSort.mergeCollapse(TimSort.java:441) ~[na:1.8.0_192]
at java.util.TimSort.sort(TimSort.java:245) ~[na:1.8.0_192]
at java.util.Arrays.sort(Arrays.java:1512) ~[na:1.8.0_192]
at java.util.ArrayList.sort(ArrayList.java:1462) ~[na:1.8.0_192]
at java.util.Collections.sort(Collections.java:175) ~[na:1.8.0_192]
at com.affymetrix.igb.searchmodeidorprops.SearchModeIDOrProps.findLocalSyms(SearchModeIDOrProps.java:180) ~[na:na]
at com.affymetrix.igb.searchmodeidorprops.SearchModeIDOrProps.search(SearchModeIDOrProps.java:105) ~[na:na]
at com.affymetrix.igb.searchmodeidorprops.SearchModeID.search(SearchModeID.java:86) ~[na:na]
at com.affymetrix.igb.keywordsearch.KeyWordSearch.search(KeyWordSearch.java:65) ~[na:na]
at com.affymetrix.igb.search.SearchView$SearchAction$1.runInBackground(SearchView.java:175) ~[na:na]
at com.affymetrix.igb.search.SearchView$SearchAction$1.runInBackground(SearchView.java:155) ~[na:na]
at com.affymetrix.genometry.thread.CThreadWorker.doInBackground(CThreadWorker.java:73) ~[na:na]
at javax.swing.SwingWorker$1.call(SwingWorker.java:295) [na:1.8.0_192]
at java.util.concurrent.FutureTask.run(FutureTask.java:266) [na:1.8.0_192]
at javax.swing.SwingWorker.run(SwingWorker.java:334) [na:1.8.0_192]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [na:1.8.0_192]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [na:1.8.0_192]
at java.lang.Thread.run(Thread.java:748) [na:1.8.0_192]
Attachments
Issue Links
Activity
To reproduce:
- Start (or re-start) IGB
- Select human genome (click Mona Lisa image)
- Select "Data Access" tab
- Open RNA-Seq > 20 tissues SRP056969 > Reads > Adrenal gland alignments in "Available Data" (check the checkbox to add a new empty track to IGB)
- Zoom to a region and click Load Data to load some data from above data set
- Select Advanced Search tab
- Choose "Keyword" in "genome" (Note: "Properties" is the default setting - you need to change to keyword to observe the bug")
- Enter a search string (anything is fine)
- Observe error in Console tab
For reference, here is the commit:
https://bitbucket.org/lorainelab/integrated-genome-browser/commits/e3aec2f3b29eb070b0f7edb481552d12337e8bbf