Details
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Type:
Bug
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Status: Closed (View Workflow)
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Priority:
Blocker
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: 9.1.0 Major Release
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Labels:
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Story Points:1
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Epic Link:
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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
The above mentioned error is shown when the keyword entered is empty.
We have not handled empty keyword.
The below function in KeyWordSearch.java always returns null without checking the input string.
public String checkInput(String search_text, BioSeq vseq, String seq)
Mostly we can handle empty/null string condition in this function.
[~aloraine] - Can I fix the issue by following the above solution?
I have a doubt:
Is this addressing the root cause?
How is an empty string getting passed?
In testing, I have entered a value (anything) into the search form.
So I am wondering: How is an empty string getting passed in?
Also, why does the bug only occur after the RNA-Seq data has been loaded but not before?
Noor Zahara: Answering these will probably require a deeper dive into the code. My request: answer as much as you can for now, and then move the ticket back to "To-Do" to work on later - either yourself or another developer.
Is this addressing the root cause? Yes
How is an empty string getting passed? The issue is occurring only if the user enters search without any keyword.
In testing, I have entered a value (anything) into the search form.
So I am wondering: How is an empty string getting passed in? I tested it with random keywords and the exception is not thrown
Also, why does the bug only occur after the RNA-Seq data has been loaded but not before? This is happening with any data not just RNA-Seq data
Original bug report differs from bug 15 Sep comment. In the original report (description), an empty string is entered by user. In 15 Sep comment, a non-empty string is entered.
Sorry – this was very confusing!
I figured out that the bug is in the sorting functionality where we were not handling the case when 2 objects where equal .
The code change can be found : https://bitbucket.org/noorzahara/integrated-genome-browser-local1/branch/IGBF-2011#diff
Please build a branch-specific installer for functional testing and then move to Needs Review.
Regarding building the installer:
Unfortunately there's a bug with the pipeline file that blocks automatic building of the branch specific installer, so you have to run the pipeline manually.
(Bug is being fixed with https://jira.transvar.org/browse/IGBF-2027)
I have manually ran the pipleline.
The IllegalArgumentException no longer occurs.
However, another problem has come up.
When the user fails to enter a search string in the Advanced Search tab and clicks the "run search" (magnifying glass) button, the search proceeds and all items currently in memory get returned.
It looks like the residue search does not have this behavior. If the user tries to search without entering a search string, a dialog appears letting them know that they need to enter a query string to run the search.
Also, if the user enters * (globbing character that ought to match anything), a regular expression error appears.
This UI clearly needs some love to improve usability and predictability. Will create another ticket for that and link to this one.
Recommending PR.
Tested the ticket using branch the installer IGBF-2011. I was able to search without entering any keyword in the search box with no exceptions on run time. Noor Zahara could you please mention a detailed set of instructions for testing so that anyone who has not worked on IGB can easily navigate to advanced search tab just by following those instructions. Also doing it would expedite the process of 9.1.0 release. Moving it to DONE.
Thanks.
For reference, here is the commit:
To reproduce: