Details
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Type:
Task
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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: None
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Labels:None
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Story Points:0.25
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Epic Link:
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Sprint:Fall 4 2022 Oct 10
Description
Situation: While testing IGBF-1075 I ran into the following error when trying to add a new data source (see comment below).
Task: Investigate and if possible fix the problem.
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12:35:19.018 ERROR c.a.genometry.thread.CThreadWorker - sun.net.www.protocol.file.FileURLConnection cannot be cast to java.net.HttpURLConnection
java.lang.ClassCastException: sun.net.www.protocol.file.FileURLConnection cannot be cast to java.net.HttpURLConnection
at com.affymetrix.igb.prefs.AddDataProvider.checkValidAndSetUrl(AddDataProvider.java:371) ~[na:na]
at com.affymetrix.igb.prefs.AddDataProvider$5.runInBackground(AddDataProvider.java:323) ~[na:na]
at com.affymetrix.igb.prefs.AddDataProvider$5.runInBackground(AddDataProvider.java:283) ~[na:na]
at com.affymetrix.genometry.thread.CThreadWorker.doInBackground(CThreadWorker.java:73) ~[na:na]
at javax.swing.SwingWorker$1.call(SwingWorker.java:295) [na:1.8.0_332]
at java.util.concurrent.FutureTask.run(FutureTask.java:266) [na:1.8.0_332]
at javax.swing.SwingWorker.run(SwingWorker.java:334) [na:1.8.0_332]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [na:1.8.0_332]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [na:1.8.0_332]
at java.lang. Thread .run( Thread .java:750) [na:1.8.0_332]
12:35:19.037 ERROR c.a.igb.prefs.AddDataProvider - java.lang.ClassCastException: sun.net.www.protocol.file.FileURLConnection cannot be cast to java.net.HttpURLConnection
java.util.concurrent.ExecutionException: java.lang.ClassCastException: sun.net.www.protocol.file.FileURLConnection cannot be cast to java.net.HttpURLConnection
at java.util.concurrent.FutureTask.report(FutureTask.java:122) ~[na:1.8.0_332]
at java.util.concurrent.FutureTask.get(FutureTask.java:192) ~[na:1.8.0_332]
at javax.swing.SwingWorker.get(SwingWorker.java:602) ~[na:1.8.0_332]
at com.affymetrix.igb.prefs.AddDataProvider$5.finished(AddDataProvider.java:344) ~[na:na]
at com.affymetrix.genometry.thread.CThreadWorker.done(CThreadWorker.java:51) [genometry-9.1.10.jar:na]
at javax.swing.SwingWorker$5.run(SwingWorker.java:737) [na:1.8.0_332]
at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.run(SwingWorker.java:832) [na:1.8.0_332]
at sun.swing.AccumulativeRunnable.run(AccumulativeRunnable.java:112) [na:1.8.0_332]
at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.actionPerformed(SwingWorker.java:842) [na:1.8.0_332]
at javax.swing.Timer.fireActionPerformed(Timer.java:313) [na:1.8.0_332]
at javax.swing.Timer$DoPostEvent.run(Timer.java:245) [na:1.8.0_332]
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) [na:1.8.0_332]
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) [na:1.8.0_332]
at java.awt.EventQueue.access$500(EventQueue.java:97) [na:1.8.0_332]
at java.awt.EventQueue$3.run(EventQueue.java:709) [na:1.8.0_332]
at java.awt.EventQueue$3.run(EventQueue.java:703) [na:1.8.0_332]
at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_332]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74) [na:1.8.0_332]
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) [na:1.8.0_332]
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205) [na:1.8.0_332]
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) [na:1.8.0_332]
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) [na:1.8.0_332]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [na:1.8.0_332]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) [na:1.8.0_332]
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) [na:1.8.0_332]
Caused by: java.lang.ClassCastException: sun.net.www.protocol.file.FileURLConnection cannot be cast to java.net.HttpURLConnection
at com.affymetrix.igb.prefs.AddDataProvider.checkValidAndSetUrl(AddDataProvider.java:371) ~[na:na]
at com.affymetrix.igb.prefs.AddDataProvider$5.runInBackground(AddDataProvider.java:323) ~[na:na]
at com.affymetrix.igb.prefs.AddDataProvider$5.runInBackground(AddDataProvider.java:283) ~[na:na]
at com.affymetrix.genometry.thread.CThreadWorker.doInBackground(CThreadWorker.java:73) [genometry-9.1.10.jar:na]
at javax.swing.SwingWorker$1.call(SwingWorker.java:295) ~[na:1.8.0_332]
at java.util.concurrent.FutureTask.run(FutureTask.java:266) ~[na:1.8.0_332]
at javax.swing.SwingWorker.run(SwingWorker.java:334) ~[na:1.8.0_332]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) ~[na:1.8.0_332]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) ~[na:1.8.0_332]
at java.lang. Thread .run( Thread .java:750) ~[na:1.8.0_332]
To reproduce:
Download the unicorn.zip file from IGBF-1075
Unzip unicorn.zip
Start latest IGB master 9.1.10
Click on Configure in the Data Access tab
Click Add...
Click Choose local folder
Select the unzipped unicorn folder
Click Submit
View the IGB log
I tested this on Mac and came across the same issue. I think it has to do with the way the Quickload Saver app uses the full path to file names. Why this leads to the above error is unclear to me. I think we should do a quick sanity check to make sure everything is working the way it should be for both the recent changes to the checkValidAndSetUrl and for how the Quickload Saver is saving file paths in the annots.xml.