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: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:
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Epic Link:
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Sprint:Sprint 27
Description
Some IPS result spans may have labels that are cut off (ex: "Span 1 of").
To examine this problem you may want to look at a gene id "NM_001144822" under the human genome (Chr1).
View the attached screenshots to help visualize the problem.
To reproduce:
1) Start ProtAnnot for the gene outlined above (NM_001144822).
2) Run "TMHMM" under InterProScan.
*Observe:
Some of the spans (as seen in the screenshots) just say "Span 1 of".
Attachments
Issue Links
- relates to
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DB-119 Add labels for gene models and ips result spans
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-594 [ 15667 ] |
| Description |
Some IPS result spans may have labels that are cut off (ex: "Span 1 of").
To examine this problem you may want to look at a gene id "NM_001144822" under the human genome (Chr1). View the attached screenshots to help visualize the problem. To reproduce: 1) Start ProtAnnot for the gene outlined above (NM_001144822). 2) Run "TMHMM" under InterProScan. *Observe: Some of the spans (as seen in the screenshots) just say "Span 1 of". |
| Attachment | Span1of.PNG [ 13162 ] | |
| Attachment | Span1ofProblem.PNG [ 13163 ] |
| Rank | Ranked higher |
| Rank | Ranked lower |
| Rank | Ranked higher |
| Sprint | Backlog Grooming Meeting [ 34 ] | Backlog Grooming Meeting 2 [ 35 ] |
| Rank | Ranked higher |
| Sprint | Backlog Grooming Meeting 2 [ 35 ] | Sprint 26 [ 34 ] |
| Rank | Ranked higher |
| Status | Open [ 1 ] | Needs Testing [ 10002 ] |
| Status | Needs Testing [ 10002 ] | Testing In Progress [ 10003 ] |
| Link | This issue relates to IGBF-922 [ IGBF-922 ] |
| Labels | ProtAnnot |
This issue should not be tested until issue IGBF-922 is also ready for testing since they touch the same parts of the code.
| Status | Testing In Progress [ 10003 ] | Needs Testing [ 10002 ] |
| Rank | Ranked lower |
| Status | Needs Testing [ 10002 ] | Testing Blocked [ 10201 ] |
| Status | Testing Blocked [ 10201 ] | Testing In Progress [ 10003 ] |
| Assignee | Mason Meyer [ mason ] |
It seems that there is still a case where a span may be missing label information. The team will discuss this to find a solution for this problem.
| Status | Testing In Progress [ 10003 ] | Testing Blocked [ 10201 ] |
From Ann:
This is one of the most important signature libraries in InterPro – and so it is great that you're looking into this.
For cases like this where is no name field in the XML, use the "ac" field. If there is no value in the "ac" field, then use the "library" attribute in the signature-library-release fields.
This issue will be reassigned to John so that he can make changes as requested by Ann.
| Assignee | Mason Meyer [ mason ] | John Eckstein [ jeckstein ] |
| Status | Testing Blocked [ 10201 ] | Open [ 1 ] |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs Testing [ 10002 ] |
| Status | Needs Testing [ 10002 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs Testing [ 10002 ] |
| Assignee | John Eckstein [ jeckstein ] | Mason Meyer [ mason ] |
| Status | Needs Testing [ 10002 ] | Testing In Progress [ 10003 ] |
| Sprint | Sprint 26 [ 34 ] |
| Sprint | Sprint 27 [ 35 ] |
| Rank | Ranked higher |
Testing for this issue included:
1) Verifying that "Span 1 of" is removed for spans that do not contain a full statement.
2) Verify that the label reads the correct name of the span based on the XML file or it uses the "ac" field if no name is given.
3) Verifying that no other label information was affected when fixing this issue.
Since this issue is resolved it will now be closed.
| Resolution | Done [ 10000 ] | |
| Status | Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Workflow | Loraine Lab Workflow [ 16308 ] | Fall 2019 Workflow Update [ 19630 ] |
| Workflow | Fall 2019 Workflow Update [ 19630 ] | Revised Fall 2019 Workflow Update [ 21749 ] |
It has been decided that the "of" in "Span 1 of" should be removed for IPS result spans that do not contain a full statement, as described in the description of this story.