Details
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Type:
Bug
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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
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Environment:
Integrated Genome Browser, version: 6.5 (8017)
Description
There are two problems: First, two "Genbank" options appear for Arabidopsis ESTs. They are the same, and both lead to error pages at NCBI. (See attached.)
To repeat:
(1) Launch IGB
(2) Choose A_thaliana_Jun_2009
(3) Choose BioViz (DAS2) -> EST (spliced, single map)
(4) Zoom in to about 5-7 genes. Load data
(5) Right click one loaded EST
(6) Select 'Get more info' and NCBI and Google as options.
(7) Follow both links and be sure that they bring up both pages properly.
Attachments
Issue Links
- relates to
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BUG-674 Weblinks
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Assignee | Ann Loraine [ aloraine ] | Alyssa Gulledge [ alyssa ] |
| Assignee | Alyssa Gulledge [ alyssa ] | Nick Ren [ imnick ] |
After right click a loaded EST, I don't have an option "Get more info".
Is there anything wrong here?
| Assignee | Nick Ren [ imnick ] | Alyssa Gulledge [ alyssa ] |
| Project | IGB 6.5.1 [ 10032 ] | IGB6.5 [ 10010 ] |
| Key |
|
|
the menu does not offer 'get more information' but rather offers a 'web search' icon next to the actual site containing the data (NCBI, TAIR, etc.) For Arabidopsis, the linkout is TAIR.
| Assignee | Alyssa Gulledge [ alyssa ] | Nick Ren [ imnick ] |
I follow the repeat step provided by Dr. Loraine.
After right click a loaded EST, the 'web search' icon does not display.
| Assignee | Nick Ren [ imnick ] | Hiral Vora [ hiralv ] |
Seems to be fixed in r8259.
| Assignee | Hiral Vora [ hiralv ] | Ann Loraine [ aloraine ] |
Linkouts are fixed current version.
| Assignee | Ann Loraine [ aloraine ] | Alyssa Gulledge [ alyssa ] |
| Status | Open [ 1 ] | Resolved [ 5 ] |
| Assignee | Alyssa Gulledge [ alyssa ] | |
| Resolution | Fixed [ 1 ] |
| Status | Resolved [ 5 ] | Closed [ 6 ] |
| Resolution | Fixed [ 1 ] | |
| Status | Closed [ 6 ] | Reopened [ 4 ] |
| Assignee | Katharine Kubiak [ kkubiak ] |
Passed v9804 Windows
Get more info > Google or NCBI
Both links work.
| Assignee | Katharine Kubiak [ kkubiak ] | Anuj Puram [ anuj ] |
6.7.0 (9824) on Mac
There is no get more info link
instead it has a link to Google directly and that works fine
| Assignee | Anuj Puram [ anuj ] | Alyssa Gulledge [ alyssa ] |
| 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 | Vineeth Mylapur [ smylapur ] |
| Assignee | Vineeth Mylapur [ smylapur ] | Alyssa Gulledge [ alyssa ] |
Passes both google and ncbi link outs.
| Comment |
[ unable to do Choose BioViz (DAS2) -> EST (spliced, single map) and Refresh data. Heap Out of memory exception. 7.0 (11928) on windows. ] |
| Description |
There are two problems: First, two "Genbank" options appear for Arabidopsis ESTs. They are the same, and both lead to error pages at NCBI. (See attached.) To repeat: (1) Launch IGB (2) Choose A_thaliana_Jun_2009 (3) Choose BioViz (DAS2) -> EST (spliced, single map) (4) Refresh data (5) Right click a loaded EST (6) Observe 2 GenBank links, follow each in turn (7) Observe the link is broken Ideas for a solution: Ann will re-run the EST alignments pipeline and fix the ids. The EST pattern should be changed to precisely match the title of each data set. IGB should be modified to not report two linkouts with the same name. |
There are two problems: First, two "Genbank" options appear for Arabidopsis ESTs. They are the same, and both lead to error pages at NCBI. (See attached.) To repeat: (1) Launch IGB (2) Choose A_thaliana_Jun_2009 (3) Choose BioViz (DAS2) -> EST (spliced, single map) (4) Zoom in to about 5-7 genes. Load data (5) Right click one loaded EST (6) Select 'Get more info' and NCBI and Google as options. (7) Follow both links and be sure that they bring up both pages properly. |
| 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 ] |
Passed on 7.0.0 (11945) Mac.
Both links works.
| Status | Reopened [ 4 ] | Resolved [ 5 ] |
| Assignee | Fuquan Wang [ fwang4 ] | |
| Resolution | Fixed [ 1 ] |
| Resolution | Fixed [ 1 ] | |
| Status | Resolved [ 5 ] | Reopened [ 4 ] |
| Assigned Group | [jira-developers] |
| Assignee | Richard Linchangco [ richard ] |
Passed V.13839, Mac, Java 1.7.0_10
There are links to Google and NCBI when selecting any EST of A. thaliana.
Examples are:
Google displays two results:
http://www.metalife.com/UniGene/At%2015526_382586
http://signal.salk.edu/cgi-bin/atta?JOB=TEXT&TYPE=GENE&QUERY=At1g32410
NCBI links directly to:
http://www.ncbi.nlm.nih.gov/nucest/DR291694.1
All links correlate to the correct, selected EST from the IGB main viewer.
| Status | Reopened [ 4 ] | Resolved [ 5 ] |
| Assignee | Richard Linchangco [ richard ] | |
| Resolution | Fixed [ 1 ] |
| Status | Resolved [ 5 ] | Closed [ 6 ] |
Please check or assign to Nick.