[IGBF-2944] Update annots.xml url validation and filetype determination for trackhubs - JIRA UNCC

Details

Type: Improvement
Status: Closed (View Workflow)
Priority: Major
Resolution: Done
Affects Version/s: None
Fix Version/s: 9.1.10 Major Release
Labels:
None

Story Points:
1
Epic Link:
Improve IGB for users
Sprint:
Fall 3 2021 Sep 13 - Sep 24

Description

To replicate this exception, add the following data source to IGB, and open the genome hg38.

https://translate.bioviz.org/rest_api/?hubUrl=https://api.wenglab.org/screen_v13/hubs/rna22/hub.txt&fileName=/

Note: You may need to run the trackhub backend locally to ensure you are checkout out at https://bitbucket.org/lorainelab/hub-facade/commits/7c75ef9a6991c932e71724e675315938f5176f35 or earlier, as new changes may prevent this exception from being thrown.

Stack trace:

18:03:48.959 ERROR c.a.genometry.thread.CThreadWorker - sun.net.www.protocol.http.HttpURLConnection cannot be cast to javax.net.ssl.HttpsURLConnection
java.lang.ClassCastException: sun.net.www.protocol.http.HttpURLConnection cannot be cast to javax.net.ssl.HttpsURLConnection
	at org.lorainelab.igb.quickload.util.QuickloadUtils.isValidRepositoryUrl(QuickloadUtils.java:133) ~[na:na]
	at org.lorainelab.igb.quickload.util.QuickloadUtils.getGenomeVersionData(QuickloadUtils.java:160) ~[na:na]
	at org.lorainelab.igb.quickload.QuickloadDataProvider.getAvailableDataSets(QuickloadDataProvider.java:189) ~[na:na]
	at com.affymetrix.igb.view.load.GeneralLoadUtils.initializeDataContainer(GeneralLoadUtils.java:293) ~[na:na]
	at com.affymetrix.igb.view.load.GeneralLoadUtils.lambda$initVersionAndSeq$137(GeneralLoadUtils.java:315) ~[na:na]
	at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184) ~[na:1.8.0_181]
	at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175) ~[na:1.8.0_181]
	at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175) ~[na:1.8.0_181]
	at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1382) ~[na:1.8.0_181]
	at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481) ~[na:1.8.0_181]
	at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471) ~[na:1.8.0_181]
	at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151) ~[na:1.8.0_181]
	at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174) ~[na:1.8.0_181]
	at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234) ~[na:1.8.0_181]
	at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418) ~[na:1.8.0_181]
	at com.affymetrix.igb.view.load.GeneralLoadUtils.initVersionAndSeq(GeneralLoadUtils.java:313) ~[na:na]
	at com.affymetrix.igb.view.SeqGroupView$InitVersionWorker.runInBackground(SeqGroupView.java:680) ~[na:na]
	at com.affymetrix.igb.view.SeqGroupView$InitVersionWorker.runInBackground(SeqGroupView.java:668) ~[na:na]
	at com.affymetrix.genometry.thread.CThreadWorker.doInBackground(CThreadWorker.java:73) ~[na:na]
	at javax.swing.SwingWorker$1.call(SwingWorker.java:295) [na:1.8.0_181]
	at java.util.concurrent.FutureTask.run(FutureTask.java:266) [na:1.8.0_181]
	at javax.swing.SwingWorker.run(SwingWorker.java:334) [na:1.8.0_181]
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [na:1.8.0_181]
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [na:1.8.0_181]
	at java.lang.Thread.run(Thread.java:748) [na:1.8.0_181

Attachments

Issue Links

is blocked by

IGBF-2936 Update main branch to 9.1.10

Closed

relates to

IGBF-2953 Sanitize annots.xml trackhub data source file URLs for use in IGB 9.1.8

Closed

IGBF-2910 Investigate: ENCODE RNA track hub does not appear after added to IGB

Closed

IGBF-2954 Investigate: why is loading bb (bigbed) and bigwig (bw) files so slow?

Closed

Activity

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Philip Badzuh (Inactive) added a comment - 20/Sep/21 9:50 AM

Please see the changes that fix this issue here. These are required to ensure proper validation of trackhub-converted quickload datasource annots.xml URLs. Required for the fix at ~~IGBF-2910~~ to work.

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Philip Badzuh (Inactive) added a comment - 20/Sep/21 9:50 AM Please see the changes that fix this issue here . These are required to ensure proper validation of trackhub-converted quickload datasource annots.xml URLs. Required for the fix at IGBF-2910 to work.

5 older comments

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Philip Badzuh (Inactive) added a comment - 24/Sep/21 10:18 AM

I have rebased and tests are passing. Please see the PR here.

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Philip Badzuh (Inactive) added a comment - 24/Sep/21 10:18 AM I have rebased and tests are passing. Please see the PR here .

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Ann Loraine added a comment - 24/Sep/21 10:36 AM - edited

Merged; main branch installers built and ready for testing.

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Ann Loraine added a comment - 24/Sep/21 10:36 AM - edited Merged; main branch installers built and ready for testing.

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Ann Loraine added a comment - 24/Sep/21 10:49 AM

Request for Nowlan Freese: Could you test the installer for MacOS? Testing could be a bit involved, including testing from a variety of quickload data sources, including from saved quickloads.

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Ann Loraine added a comment - 24/Sep/21 10:49 AM Request for Nowlan Freese : Could you test the installer for MacOS? Testing could be a bit involved, including testing from a variety of quickload data sources, including from saved quickloads.

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Nowlan Freese added a comment - 24/Sep/21 10:53 AM

I can take a look.

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Nowlan Freese added a comment - 24/Sep/21 10:53 AM I can take a look.

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Nowlan Freese added a comment - 24/Sep/21 4:43 PM - edited

Here is what I have tested so far on Mac 11.6 with IGB 9.1.10 (commit: dcc2086b995ef4f49eb8770cb891d372f3ca0022)
Everything has worked so far.

IGB Quickload:

hg38
blacklist
UCSC Das
UCSC tracks folder
genetics folder
giab

TAIR10
chip-seq folder
bar folder
rna-seq folder

blueberry
gene predictions
rna-seq
454

g_max_jan_2014
soyseq

Local Quickload - worked

BioViz Connect
worked on SRR10060911.bam

efp-seq browser
worked on AT2G24270

usegalaxy
worked on https://usegalaxy.org/u/rajeevnepal/h/unnamed-history

Loading BAM file data from a quickload stored on CyVerse worked.

Show

Nowlan Freese added a comment - 24/Sep/21 4:43 PM - edited Here is what I have tested so far on Mac 11.6 with IGB 9.1.10 (commit: dcc2086b995ef4f49eb8770cb891d372f3ca0022) Everything has worked so far. IGB Quickload: hg38 blacklist UCSC Das UCSC tracks folder genetics folder giab TAIR10 chip-seq folder bar folder rna-seq folder blueberry gene predictions rna-seq 454 g_max_jan_2014 soyseq Local Quickload - worked BioViz Connect worked on SRR10060911.bam efp-seq browser worked on AT2G24270 usegalaxy worked on https://usegalaxy.org/u/rajeevnepal/h/unnamed-history Loading BAM file data from a quickload stored on CyVerse worked.

People

Assignee:

Philip Badzuh (Inactive)

Reporter:

Philip Badzuh (Inactive)

Votes:

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Watchers:

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Dates

Created:

15/Sep/21 10:41 AM

Updated:

04/Aug/22 4:41 PM

Resolved:

24/Sep/21 8:17 PM