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
Description
This test whether linkouts work properly when the data are loaded from a local file.
Launch IGB but do NOT choose a species. Save the attached file to desktop, then drag into in IGB (See Tools > Attachments at right.)Click Load Data. Right-click a gene model. You should see an option at the bottom of the popup menu that says: "Get more info" with a Google.
Clicking the google link should bring you to the google search results for that gene.
Results
Sept 21 2010 - Alyssa Gulledge
Version 6.3.1 (6884) The link to Genbank worked fine.
Sept 9 2010 - Ann Loraine
Works for me.
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 |
|---|---|---|
| Status | Open [ 1 ] | Resolved [ 5 ] |
| Resolution | Fixed [ 1 ] |
| Status | Resolved [ 5 ] | Closed [ 6 ] |
| Resolution | Fixed [ 1 ] | |
| Status | Closed [ 6 ] | Reopened [ 4 ] |
Attachment missing...
| Assignee | Afshan Jalali [ afshan ] | Alyssa Gulledge [ alyssa ] |
| Description |
This test whether linkouts work properly when the data are loaded from a local file. Launch IGB and clear preferences (File > Preferences > Other Options > Reset all Preferences to defaults) Choose species Apis mellifera and genome version A_mellifera_Jan_2005 Open the attached file in IGB (See Tools > Attachments at right.) Click Load Mode to Whole Genome to trigger loading of the data New tracks should appear called all_est (one is below the axis, the other above it) Zoom in and right-click a skinny line connecting blocks. You should see an option at the bottom of the popup menu that says: "Genbank" Select it - it should open a page at NCBI describing the selected item, which is an EST alignment. Note that anything that looks like gb|XX123345 (two letters followed by one or more digits) should get linked out to NCBI. This pattern appears in the igb_default_prefs.xml file: <annotation_url annot_id_regex="^gb\|.*$" name="Genbank" url="http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=$$" /> Results Sept 21 2010 - Alyssa Gulledge Version 6.3.1 (6884) The link to Genbank worked fine. Sept 9 2010 - Ann Loraine Works for me. |
This test whether linkouts work properly when the data are loaded from a local file. Launch IGB and clear preferences (File > Preferences > Other Options > Reset all Preferences to defaults) Choose species Apis mellifera and genome version A_mellifera_Jan_2005. Open the BioViz DAS2, select Api Gene models and load. Open the attached file in IGB (See Tools > Attachments at right.) Click Load Mode to Whole Genome to trigger loading of the data New tracks should appear called all_est (one is below the axis, the other above it) Zoom in and right-click a skinny line connecting blocks. You should see an option at the bottom of the popup menu that says: "Genbank" Select it - it should open a page at NCBI describing the selected item, which is an EST alignment. Note that anything that looks like gb|XX123345 (two letters followed by one or more digits) should get linked out to NCBI. This pattern appears in the igb_default_prefs.xml file: <annotation_url annot_id_regex="^gb\|.*$" name="Genbank" url="http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=$$" /> Results Sept 21 2010 - Alyssa Gulledge Version 6.3.1 (6884) The link to Genbank worked fine. Sept 9 2010 - Ann Loraine Works for me. |
Do you have this file somewhere, Ann... I don't know what the original file was and I do not have it on my computer...
| Assignee | Alyssa Gulledge [ alyssa ] | Ann Loraine [ aloraine ] |
| Assignee | Ann Loraine [ aloraine ] | Alyssa Gulledge [ alyssa ] |
| Status | Reopened [ 4 ] | Resolved [ 5 ] |
| Assignee | Alyssa Gulledge [ alyssa ] | |
| Resolution | Fixed [ 1 ] |
| Assignee | Katharine Kubiak [ kkubiak ] |
| Resolution | Fixed [ 1 ] | |
| Status | Resolved [ 5 ] | Reopened [ 4 ] |
| Assignee | Katharine Kubiak [ kkubiak ] | Alyssa Gulledge [ alyssa ] |
| Description |
This test whether linkouts work properly when the data are loaded from a local file. Launch IGB and clear preferences (File > Preferences > Other Options > Reset all Preferences to defaults) Choose species Apis mellifera and genome version A_mellifera_Jan_2005. Open the BioViz DAS2, select Api Gene models and load. Open the attached file in IGB (See Tools > Attachments at right.) Click Load Mode to Whole Genome to trigger loading of the data New tracks should appear called all_est (one is below the axis, the other above it) Zoom in and right-click a skinny line connecting blocks. You should see an option at the bottom of the popup menu that says: "Genbank" Select it - it should open a page at NCBI describing the selected item, which is an EST alignment. Note that anything that looks like gb|XX123345 (two letters followed by one or more digits) should get linked out to NCBI. This pattern appears in the igb_default_prefs.xml file: <annotation_url annot_id_regex="^gb\|.*$" name="Genbank" url="http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=$$" /> Results Sept 21 2010 - Alyssa Gulledge Version 6.3.1 (6884) The link to Genbank worked fine. Sept 9 2010 - Ann Loraine Works for me. |
This test whether linkouts work properly when the data are loaded from a local file. Launch IGB but do NOT choose a species. Save the attached file to desktop, then drag into in IGB (See Tools > Attachments at right.)Click Load Data. Right-click a gene model. You should see an option at the bottom of the popup menu that says: "Get more info" with a Google and a NetAffx option. Clicking the google link should bring you to the google search results for that gene. Clicking the NetAffx link brings you to netAffx login. Results Sept 21 2010 - Alyssa Gulledge Version 6.3.1 (6884) The link to Genbank worked fine. Sept 9 2010 - Ann Loraine Works for me. |
Test case updated. Passed Mac on v. 9804.
| Assignee | Alyssa Gulledge [ alyssa ] | Katharine Kubiak [ kkubiak ] |
| Comment |
[ Not sure how to open this file. "Tools > Attachments at right" is no longer available. When I click "Configure Web Links" I can see the link that you had provided at the bottom of the description, but not sure if I can open it from here. I attempted to "File > Open URL" the link http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=$$ And received this error in the console: "SEVERE: no handler for file type fcgi?val=$$" A new track loaded in the Data Management Table, but no data loaded in the viewer. ] |
Passed v9871 Windows
| Assignee | Katharine Kubiak [ kkubiak ] | Anuj Puram [ anuj ] |
Passed 6.7.0 (9891) on Mac
| Assignee | Anuj Puram [ anuj ] | Alyssa Gulledge [ alyssa ] |
| Status | Reopened [ 4 ] | Resolved [ 5 ] |
| Assignee | Alyssa Gulledge [ alyssa ] | |
| Resolution | Fixed [ 1 ] |
| Status | Resolved [ 5 ] | Closed [ 6 ] |
Attachment missing...
| Resolution | Fixed [ 1 ] | |
| Status | Closed [ 6 ] | Reopened [ 4 ] |
| Assignee | Alyssa Gulledge [ alyssa ] |
| Attachment | RT_U34.link.psl.gz [ 11084 ] | |
| Description |
This test whether linkouts work properly when the data are loaded from a local file. Launch IGB but do NOT choose a species. Save the attached file to desktop, then drag into in IGB (See Tools > Attachments at right.)Click Load Data. Right-click a gene model. You should see an option at the bottom of the popup menu that says: "Get more info" with a Google and a NetAffx option. Clicking the google link should bring you to the google search results for that gene. Clicking the NetAffx link brings you to netAffx login. Results Sept 21 2010 - Alyssa Gulledge Version 6.3.1 (6884) The link to Genbank worked fine. Sept 9 2010 - Ann Loraine Works for me. |
This test whether linkouts work properly when the data are loaded from a local file. Launch IGB but do NOT choose a species. Save the attached file to desktop, then drag into in IGB (See Tools > Attachments at right.)Click Load Data. Right-click a gene model. You should see an option at the bottom of the popup menu that says: "Get more info" with a Google. Clicking the google link should bring you to the google search results for that gene. Results Sept 21 2010 - Alyssa Gulledge Version 6.3.1 (6884) The link to Genbank worked fine. Sept 9 2010 - Ann Loraine Works for me. |
| 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 | Darius Bost [ darius ] |
| Status | Reopened [ 4 ] | Resolved [ 5 ] |
| Assignee | Darius Bost [ darius ] | |
| Resolution | Fixed [ 1 ] |
| Comment | [ Passed 7.0.0 (11974) ] |
| Status | Resolved [ 5 ] | Closed [ 6 ] |
| Resolution | Fixed [ 1 ] | |
| Status | Closed [ 6 ] | Reopened [ 4 ] |
| Status | Reopened [ 4 ] | Closed [ 6 ] |
| Resolution | Fixed [ 1 ] |
version: 6.5 (7717)