Details
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Type:
Sub-task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Fixed
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Labels:None
Description
This feature relates to mirroring IGB QuickLoad.
The annots.xml file tag has attribute "url"
When a data set (file) is displayed in the Available Data treeview, the URL is used to create the hyperlinked 'i' info icon linkout.
Feature request is:
If the url is relative (e.g., looks like foo/bar/baz.html or ./foo/bar/baz.html or /foo/bar/baz.html – anything lacking a protocol prefix such as http://, ftp://, or file://) then IGB should append the relative url path to the QuickLoad URL.
In other words, if it would be a valid link in a Web page, then it should work as an info hyperlink, and the web root should be the address of the QuickLoad site.
For example, if "url" attribute is "M_musculus_Dec_2011" and the server URL is "http://www.igbquickload.org/quickload", then the linkout from the info icon should be "http://www.igbquickload.org/quickload/M_musculus_Dec_2011"
Note that IGB will need to be able to handle url attributes that begin (or don't begin) with a leading slash and also that this will need to be tested with local quickload as well.
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Description |
This feature relates to mirroring IGB QuickLoad. The annots.xml file tag has attribute "url" When a data set (file) is displayed in the Available Data treeview, the URL is used to create the hyperlinked 'i' info icon linkout. Feature request is: If the url is relative (e.g., looks like foo/bar/baz.html or ./foo/bar/baz.html or /foo/bar/baz.html -- in short, anything lacking a protocol a Web browser can support) then IGB should append the relative url path to the QuickLoad URL. For example, if "url" attribute is "M_musculus_Dec_2011" and the server URL is "http://www.igbquickload.org/quickload", then the linkout from the info icon should be "http://www.igbquickload.org/quickload/M_musculus_Dec_2011" Note that IGB will need to be able to handle url attributes that begin (or don't begin) with a leading slash and also that this will need to be tested with local quickload as well. |
This feature relates to mirroring IGB QuickLoad. The annots.xml file tag has attribute "url" When a data set (file) is displayed in the Available Data treeview, the URL is used to create the hyperlinked 'i' info icon linkout. Feature request is: If the url is relative (e.g., looks like foo/bar/baz.html or ./foo/bar/baz.html or /foo/bar/baz.html -- anything lacking a protocol prefix such as http://, ftp://, or file://) then IGB should append the relative url path to the QuickLoad URL. In other words, if it would be a valid link in a Web page, then it should work as an info hyperlink, and the web root should be the address of the QuickLoad site. For example, if "url" attribute is "M_musculus_Dec_2011" and the server URL is "http://www.igbquickload.org/quickload", then the linkout from the info icon should be "http://www.igbquickload.org/quickload/M_musculus_Dec_2011" Note that IGB will need to be able to handle url attributes that begin (or don't begin) with a leading slash and also that this will need to be tested with local quickload as well. |
| Parent |
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| Issue Type | New Feature [ 2 ] | Sub-task [ 5 ] |
| Assignee | Hiral Vora [ hiralv ] | Fuquan Wang [ fwang4 ] |
| Parent |
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| Issue Type | Sub-task [ 5 ] | Bug [ 1 ] |
| Parent |
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| Issue Type | Bug [ 1 ] | Sub-task [ 5 ] |
| Assignee | Fuquan Wang [ fwang4 ] | Alyssa Gulledge [ alyssa ] |
| Status | Open [ 1 ] | Resolved [ 5 ] |
| Assignee | Alyssa Gulledge [ alyssa ] | |
| Resolution | Fixed [ 1 ] |
| Assignee | Fuquan Wang [ fwang4 ] |
The URL in annots.xml is:
/A_thaliana_Jun_2009/sr45a_hs_TH2.0.5_processed
The QuickLoad URL is
file:/Users/pi/src/genomes/lorainelabrnaseq/
However, when I click the "i" button, IGB tries to open the following URL:
/Users/pi/src/genomes/lorainelabrnaseq/A_thaliana_Jun_2009/A_thaliana_Jun_2009/sr45a_hs_TH2.0.5_processed
Why does it include the directory A_thaliana_Jun_2009 twice?
See exception:
Feb 27, 2013 12:35:59 PM com.affymetrix.genometryImpl.util.LocalUrlCacher getUncachedFileStream
INFO: Couldn't find file file:/Users/pi/src/genomes/lorainelabrnaseq/synonyms.txt, but it's optional.
Feb 27, 2013 12:35:59 PM com.affymetrix.genometryImpl.util.LocalUrlCacher getUncachedFileStream
INFO: Couldn't find file file:/Users/pi/src/genomes/lorainelabrnaseq/species.txt, but it's optional.
Feb 27, 2013 12:35:59 PM com.affymetrix.genometryImpl.util.LocalUrlCacher getUncachedFileStream
INFO: Couldn't find file file:/Users/pi/src/genomes/lorainelabrnaseq/preferences.xml, but it's optional.
Feb 27, 2013 12:35:59 PM com.affymetrix.genometryImpl.util.LocalUrlCacher getUncachedFileStream
INFO: Couldn't find file file:/Users/pi/src/genomes/lorainelabrnaseq/A_thaliana_Jun_2009/liftAll.lft, but it's optional.
Exception in thread "AWT-EventQueue-0" java.lang.IllegalArgumentException: The file: /Users/pi/src/genomes/lorainelabrnaseq/A_thaliana_Jun_2009/A_thaliana_Jun_2009/sr45a_hs_TH2.0.5_processed doesn't exist.
at java.awt.Desktop.checkFileValidation(Desktop.java:191)
at java.awt.Desktop.open(Desktop.java:252)
at com.affymetrix.genometryImpl.util.GeneralUtils.browse(GeneralUtils.java:291)
at com.affymetrix.igb.view.load.FeatureTreeView$TreeMouseListener.mouseClicked(FeatureTreeView.java:403)
at java.awt.AWTEventMulticaster.mouseClicked(AWTEventMulticaster.java:253)
at java.awt.Component.processMouseEvent(Component.java:6355)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
at java.awt.Component.processEvent(Component.java:6117)
at java.awt.Container.processEvent(Container.java:2085)
at java.awt.Component.dispatchEventImpl(Component.java:4714)
at java.awt.Container.dispatchEventImpl(Container.java:2143)
at java.awt.Component.dispatchEvent(Component.java:4544)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4621)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4291)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4212)
at java.awt.Container.dispatchEventImpl(Container.java:2129)
at java.awt.Window.dispatchEventImpl(Window.java:2478)
at java.awt.Component.dispatchEvent(Component.java:4544)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:635)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
| Resolution | Fixed [ 1 ] | |
| Status | Resolved [ 5 ] | Reopened [ 4 ] |
| Attachment | quickload.zip [ 11887 ] |
Fixed in 14252.
I attached a simple quickload site with 9 test cases included for X_tropicalis_Nov_2009 (refer to the annots.xml for detail):
1. Relative path to a file starts with ./
2. Relative path to a file starts with /
3. Relative path to a file starts with directory/file directly
4. Relative path to a directory starts with ./
5. Relative path to a directory starts with /
6. Relative path to a directory starts with directory
7. Absolute web address
8. Absolute local address (update the annots.xml to make sure the local address is correct for you)
9. A bad address
There are no actual data set included in this quickload site, so please only test the 'info' icon for each feature.
Please do the test on both local (add a local quickload site) and a http server (if you don't have one on hand, you can use http://128.196.142.66/quickload/)
For the test case #9 it will generate a error message box for local site since the address is not existing (please advise if the words looks fine), but page not found for remote server.
| Assignee | Fuquan Wang [ fwang4 ] | Alyssa Gulledge [ alyssa ] |
1-3 open webpage, 4-6 open "finder", 7 opens bioviz, 8 throws error (as it should - I don't have the file) and 9 throws error (as it should)
Wording for #8,9: I would change it to read "Invalid address or path for information page:"
which covers both URLs and files stored locally.
| Assignee | Alyssa Gulledge [ alyssa ] | Fuquan Wang [ fwang4 ] |
Changed in 14263.
| Assignee | Fuquan Wang [ fwang4 ] | Alyssa Gulledge [ alyssa ] |
| Assignee | Alyssa Gulledge [ alyssa ] | Fuquan Wang [ fwang4 ] |
| Assignee | Fuquan Wang [ fwang4 ] | Alyssa Gulledge [ alyssa ] |
| Assignee | Alyssa Gulledge [ alyssa ] | Fuquan Wang [ fwang4 ] |
| Assignee | Fuquan Wang [ fwang4 ] | Alyssa Gulledge [ alyssa ] |
Resolve this issue as getting failure to re-assign.
| Status | Reopened [ 4 ] | Resolved [ 5 ] |
| Assignee | Alyssa Gulledge [ alyssa ] | |
| Resolution | Fixed [ 1 ] |
| Assignee | Fuquan Wang [ fwang4 ] |
| Assignee | Fuquan Wang [ fwang4 ] |
| Resolution | Fixed [ 1 ] | |
| Status | Resolved [ 5 ] | Reopened [ 4 ] |
Assigning for testing, done in 14263
| Assignee | Fuquan Wang [ fwang4 ] | Alyssa Gulledge [ alyssa ] |
Wording corrected.
| Status | Reopened [ 4 ] | Resolved [ 5 ] |
| Assignee | Alyssa Gulledge [ alyssa ] | |
| Resolution | Fixed [ 1 ] |
| Status | Resolved [ 5 ] | Closed [ 6 ] |
| Resolution | Fixed [ 1 ] | |
| Status | Closed [ 6 ] | Reopened [ 4 ] |
| Assignee | Fuquan Wang [ fwang4 ] |
| Assignee | Fuquan Wang [ fwang4 ] | Alyssa Gulledge [ alyssa ] |
To test,
Add http://bioviz.org/quickload/ Quickload
Go to S_lycopersicum_May_2012 && A_gambiae_Feb_2003
Try to load file from that server and see if everything works.
Data loaded just fine.
| Status | Reopened [ 4 ] | Resolved [ 5 ] |
| Assignee | Alyssa Gulledge [ alyssa ] | |
| Resolution | Fixed [ 1 ] |
| Status | Resolved [ 5 ] | Closed [ 6 ] |
It probably already done. Test it along with backup server test.