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  1. IGB
  2. IGBF-2944

Update annots.xml url validation and filetype determination for trackhubs

        Details

          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

              Task - A task that needs to be done. IGBF-2936 Update main branch to 9.1.10

              • Major - Major loss of function.
              • Closed
              relates to

              Bug - A problem which impairs or prevents the functions of the product. IGBF-2953 Sanitize annots.xml trackhub data source file URLs for use in IGB 9.1.8

              • Major - Major loss of function.
              • Closed

              Bug - A problem which impairs or prevents the functions of the product. IGBF-2910 Investigate: ENCODE RNA track hub does not appear after added to IGB

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-2954 Investigate: why is loading bb (bigbed) and bigwig (bw) files so slow?

              • Major - Major loss of function.
              • Closed

                Activity

                  People

                  • Assignee:
                    pbadzuh Philip Badzuh (Inactive)
                    Reporter:
                    pbadzuh Philip Badzuh (Inactive)
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                    3 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: