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: 10.1.0
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Labels:None
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Story Points:2
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Epic Link:
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Sprint:Summer 3, Summer 4, Summer 5, Summer 6, Summer 7
Description
There is a way to link to UCSC track descriptions using this link pattern:
Where "g" is a string identifying a track.
You can also add a "db" parameter to specify the genome version of interest. With this new parameter, the URL pattern is:
- https://genome.ucsc.edu/cgi-bin/hgTrackUi?g=(track name)&db=(ucsc genome version name)
For example:
opens a page at the UCSC genome browser with a page describing track "dbSnp155Composite" in the context of the hg18 genome version.
This page is even an entry-point for the UCSC genome browser interface. The page has a "submit" button. When you click this "submit" button, a new page opens showing a genomic scene for the requested genome version, with the track shown, as well. It's hard to interpret this page if you are not already familiar with the browser, but it provides an entrée for a user to start comparing how the track data look in its native UCSC Genome Browser context with how it looks in IGB.
It would be fantastic if we could provide link-outs going from the IGB UCSC REST data sets shown in IGB's Data Access panel.
Doing this shouldn't be too difficult, and the goal of this task is to determine if it is feasible. If yes, we can include implementation in this ticket as well, as the developer sees fit.
The code would construct the "link out" URLs using this pattern:
or, even better:
- https://genome.ucsc.edu/cgi-bin/hgTrackUi?g=(track name)&db=(ucsc genome name)
Let's call this "option 1" also known as (aka) "direct link into UCSC Web site."
Attachments
Issue Links
- relates to
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- Closed
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Activity
Example for external link from the hg18 human genome and the track set to refGene: https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=refGene
Consensus:
We would like:
- "option 1" also known as "direct link into UCSC Web site."
We need some kind of system to let us know the instant UCSC changes their URL format!
Nowlan Freese and Jaya Sravani Sirigineedi like the idea of adding tests to the build process to alert us to changes.
Developed code to create linkouts for UCSC REST tracks, the code works if I keep the base domain URL as a string in the code but when I introduce a properties file and try to read from it, it's not working and throws an error. Below is the error, investigating this issue currently.
ERROR : bundle igb:10.1.0 (40)[com.affymetrix.igb.prefs.IgbPreferencesLoadingOrchestrator(44)] : The activate method has thrown an exception
java.util.MissingResourceException: Can't find bundle for base name ucsc, locale en_US
at java.base/java.util.ResourceBundle.throwMissingResourceException(ResourceBundle.java:2059)
at java.base/java.util.ResourceBundle.getBundleImpl(ResourceBundle.java:1697)
at java.base/java.util.ResourceBundle.getBundleImpl(ResourceBundle.java:1600)
at java.base/java.util.ResourceBundle.getBundleImpl(ResourceBundle.java:1555)
at java.base/java.util.ResourceBundle.getBundle(ResourceBundle.java:861)
at org.lorainelab.igb.ucsc.rest.api.service.UCSCRestApiDataProvider.<init>(UCSCRestApiDataProvider.java:39)
Nowlan Freese meanwhile if you are free could you help me in building this branch (https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-3807) in your local and let me know if you are also facing the same issue when IGB is starting.
I'm seeing the same error when starting IGB on branch IGBF-3807. It looks like something in OSGi is not happy.
As discussed with Nowlan Freese, Changed the code to use the base domain URL as a string in the code instead of loading it from the properties file for now, as we are facing an issue with that. Also, observed an error log regarding SLf4j while running the tests, currently working on resolving both these issues. Updated code is available at the branch: https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-3807. Please review and let me know if there are any issues.
Tested on Mac using Sravani's branch.
Link outs are working as expected, tested on mouse and human genomes using multiple files in UCSC REST. I was able to build IGB without internet (showing that the test for the link outs can fail without killing the build). But I didn't see anything in the log about the link out failing.
I am seeing is a lot of what look like null pointer exceptions in the log when I mouse over the UCSC REST subfolder names (like genePred) in the Available Data window.
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException: Cannot invoke "java.util.Map.getOrDefault(Object, Object)" because the return value of "com.affymetrix.genometry.general.DataSet.getProperties()" is null at org.lorainelab.igb.ucsc.rest.api.service.UCSCRestApiDataProvider.getDataSetLinkoutUrl(UCSCRestApiDataProvider.java:166) at com.affymetrix.igb.view.load.FeatureTreeView.featureFriendlyURL(FeatureTreeView.java:453) at com.affymetrix.igb.view.load.FeatureTreeView.getURLAt(FeatureTreeView.java:437) at com.affymetrix.igb.view.load.FeatureTreeView$TreeMouseListener.mouseMoved(FeatureTreeView.java:373) at java.desktop/java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:338) at java.desktop/java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:337) at java.desktop/java.awt.Component.processMouseMotionEvent(Component.java:6666) at java.desktop/javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3416) at java.desktop/java.awt.Component.processEvent(Component.java:6390) at java.desktop/java.awt.Container.processEvent(Container.java:2266) at java.desktop/java.awt.Component.dispatchEventImpl(Component.java:4996) at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2324) at java.desktop/java.awt.Component.dispatchEvent(Component.java:4828) at java.desktop/java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4948) at java.desktop/java.awt.LightweightDispatcher.processMouseEvent(Container.java:4588) at java.desktop/java.awt.LightweightDispatcher.dispatchEvent(Container.java:4516) at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2310) at java.desktop/java.awt.Window.dispatchEventImpl(Window.java:2780) at java.desktop/java.awt.Component.dispatchEvent(Component.java:4828) at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:775) at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:720) at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:714) at java.base/java.security.AccessController.doPrivileged(AccessController.java:400) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:98) at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:747) at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:745) at java.base/java.security.AccessController.doPrivileged(AccessController.java:400) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87) at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:744) at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203) at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124) at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113) at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109) at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)
Fixed the exception issue and pushed the updated code to the above-mentioned branch. And for the test case log, I have mentioned a Slf4j error in the comment previously which is the cause for the log to not appear, currently, I am investigating this issue and another error as part of this ticket - https://jira.bioviz.org/browse/IGBF-3813
Just a quick FYI for Jaya Sravani Sirigineedi and Nowlan Freese:
There's no rush from my side. Mentioning this because Nowlan Freese is at a meeting and might not be able to take a look as quickly as usual.
FYI, this feature can be tested along with this https://jira.bioviz.org/browse/IGBF-3813 ticket as that branch includes these changes.
The PR containing the change is merged as part of another ticket. The new code is now available in the "early access" installers available from the BioViz.org Web site.
Ready for testing.
Tested main branch installer on Mac.
Link outs worked correctly for several tested genomes (human, mouse, elephant). No errors in the log.
Closing ticket.
Also:
Idea for UCSC Web Links: Make link out to google search on the UCSC domain - can put site:https://genome.ucsc.edu/ in the search so that only results from UCSC are returned
example)
https://www.google.com/search?q=site%3Ahttps%3A%2F%2Fgenome.ucsc.edu+phastConsElements100way
Nowlan Freese: suggests we could use the above pattern for a Web Links option.