Details
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Type:
Improvement
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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: 8.5.0 Major Release
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Labels:
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Story Points:0.5
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Epic Link:
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Sprint:Sprint 29
Description
Cloud storage providers like Dropbox typically make it possible for users to create links to files and then share the links. However, paths exposed in links don't correspond to physical storage, which means that IGB can't make assumptions about the location of index files for BAM, tabix, or other indexed, random access formats.
Let's add a new optional attribute ("index") to the QuickLoad "file" tag where "index" indicates the location of the index file. Same rules about defining file locations should apply.
Attachments
Issue Links
- relates to
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REL-15 Create example BAM/BAI Quickloads
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- Testing Complete
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Rank | Ranked higher |
| Rank | Ranked lower |
| Epic Link | IGBF-440 [ 15498 ] |
| Rank | Ranked lower |
| Rank | Ranked higher |
| Summary | new attribute for file tag | index attribute for file tag |
| Story Points | 0.5 |
| Summary | index attribute for file tag | index attribute for file tag in annots.xml |
| Sprint | Sprint 19 [ 24 ] |
| Rank | Ranked lower |
| Sprint | Sprint 19 [ 24 ] |
| Rank | Ranked higher |
| Rank | Ranked higher |
| Sprint | Sprint 27 [ 35 ] |
| Rank | Ranked lower |
| Assignee | David Norris [ dcnorris ] | John Eckstein [ jeckstein ] |
| Status | Open [ 1 ] | 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 ] |
Testing for this issue included:
-Verifying that annots.xml files with an index tag use the index in the specified location (verified on Mac and Windows).
-Verifying that the index file specified in the index tag overrides any index file in the folder with the file needing indexing.
-I removed the index attribute for bam files to verify that the bam would not load.
-I tested loading of bam files with an index file in the same directory and with an index file specified in the annots.xml to test differences and see which one gets used if both are present (annots.xml overrides an index in same directory).
While testing I noticed that the index attribute in the annots.xml file is being ignored for local Quickloads.
We should look into this to see if this can be fixed for local Quickloads.
Reassigning to John to take a look at this issue.
| Assignee | Mason Meyer [ mason ] | John Eckstein [ jeckstein ] |
| Status | Testing In Progress [ 10003 ] | Open [ 1 ] |
Yes, we definitely will want to fix this, as people might think they can put indexes in other places besides the same directory as the target (indexed) file.
| Sprint | Sprint 27 [ 35 ] |
| Sprint | Sprint 28 [ 36 ] |
| Rank | Ranked higher |
| Assignee | John Eckstein [ jeckstein ] | Tarun Mall [ tmall ] |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs Testing [ 10002 ] |
| Status | Needs Testing [ 10002 ] | Pull Request Submitted [ 10101 ] |
| Sprint | Sprint 28 [ 36 ] |
| Sprint | Sprint 29 [ 37 ] |
| Rank | Ranked higher |
| Assignee | Tarun Mall [ tmall ] | John Eckstein [ jeckstein ] |
| Status | Pull Request Submitted [ 10101 ] | Needs Testing [ 10002 ] |
| Assignee | John Eckstein [ jeckstein ] | Mason Meyer [ mason ] |
| Status | Needs Testing [ 10002 ] | Testing In Progress [ 10003 ] |
Testing for this issue included:
-Verifying that annots.xml files with an index tag use the index in the specified location (verified on Mac and Windows).
-Verifying that the index file specified in the index tag overrides any index file in the folder with the file needing indexing.
-I removed the index attribute for bam files to verify that the bam would not load.
-I tested loading of bam files with an index file in the same directory and with an index file specified in the annots.xml to test differences and see which one gets used if both are present (annots.xml overrides an index in same directory).
-Verifying that the index attribute in the annots.xml for local Quickloads is not being ignored.
Since this story is resolved it will now be closed.
| Resolution | Done [ 10000 ] | |
| Status | Testing In Progress [ 10003 ] | Closed [ 6 ] |
This comment sounds wrong:
"I removed the index attribute for bam files to verify that the bam would not load."
If you remove the index attribute, then the file should STILL load if the index is in the same directory as the BAM file.
The index attribute is optional, not required. If the index file attribute is not present in the annots.xml file, then IGB should attempt to retrieve the index file from the same directory (context root) where the BAM file is located.
| Resolution | Done [ 10000 ] | |
| Status | Closed [ 6 ] | Open [ 1 ] |
| Fix Version/s | 8.5.0 Major Release [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Open [ 1 ] | Closed [ 6 ] |
| Resolution | Done [ 10000 ] | |
| Status | Closed [ 6 ] | Open [ 1 ] |
| Labels | Data_Provider |
| Resolution | Done [ 10000 ] | |
| Status | Open [ 1 ] | Closed [ 6 ] |
| Workflow | Loraine Lab Workflow [ 15707 ] | Fall 2019 Workflow Update [ 19382 ] |
| Workflow | Fall 2019 Workflow Update [ 19382 ] | Revised Fall 2019 Workflow Update [ 21499 ] |
http://test.bioviz.org/quickload/