Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Minor
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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:None
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Story Points:0.5
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Epic Link:
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Sprint:Fall 6 : 28 Oct to 8 Nov, Fall 7 : 11 Nov to 22 Nov
Description
Situation: Data for testing various file formats when preparing to release new versions of IGB are stored at http://igbquickload.org/smokeTestingQuickload/. However, only Dr. Loraine can update/add additional files to this Quickload.
Task: To make it simpler to update smoke testing data, files should be moved to S3. These changes will need to be reflected in the IGB release documentation
Attachments
Issue Links
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Activity
Text has been updated in the IGB Release Documentation: https://wiki.transvar.org/display/ITD/General+Smoke+Testing
| Field | Original Value | New Value |
|---|---|---|
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
To test:
Add https://quickload-testing.s3.amazonaws.com/smokeTestingQuickload/ as a quickload in the Data Access tab.
Open the human genome.
In Available Data, open the various files contained within the quickload and make sure that the files load in IGB.
| Assignee | Nowlan Freese [ nfreese ] |
| Assignee | Philip Badzuh [ pbadzuh ] |
| Sprint | Fall 6 : 28 Oct to 8 Nov [ 77 ] | Fall 6 : 28 Oct to 8 Nov, Fall 7 : 11 Nov to 22 Nov [ 77, 78 ] |
| Rank | Ranked higher |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
Everything looks good in the docs. The data can be loaded into IGB, but access via browser is denied - is this part of the design?
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Philip Badzuh [ pbadzuh ] | Nowlan Freese [ nfreese ] |
As far as I can tell there is not a way to view the files in a directory structure through S3: https://www.reddit.com/r/aws/comments/5stycu/s3_bucket_want_to_view_bucket_like_a_directory/
If anyone else knows more about this that would be great, as it would be useful to see the directory structure and files.
I would probably change the URL from an embedded link back to the full URL in the documentation. It may be confusing for us when we smoketest if people expect something to happen when they click on that link, versus copying and pasting the full URL into IGB.
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
That makes sense. I've made the URL change.
I found an interesting way to get show S3 directory structure in a browser here: https://github.com/rufuspollock/s3-bucket-listing, but that would require running a web server dedicated just for this task.
Cool – I have seen this too.
This reminds me to set up an AWS account for you so that that you can view the contents using the AWS S3 contents browser. I will do that shortly. Philip Badzuh
| Epic Link | IGBF-1531 [ 17617 ] |
Data have been moved to https://quickload-testing.s3.amazonaws.com/smokeTestingQuickload/ and can be added as a data source in IGB.