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Don't look for BAMs on HDFS #865

Merged
merged 6 commits into from
Dec 18, 2015
Merged

Don't look for BAMs on HDFS #865

merged 6 commits into from
Dec 18, 2015

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ihodes
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@ihodes ihodes commented Dec 16, 2015

Instead, BAM URLs are now just HTTP(s) URLs pointing anywhere.

Addresses #791

If we don't want to break links on the deployed Cycledash when we push this change, we'll need to add http://hammerlab-dev3.hpc.mssm.edu:9876 in front of all our existing BAM URIs.

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Instead, BAM URLs are now just HTTP(s) URLs pointing anywhere.
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danvk commented Dec 16, 2015

Review status: 0 of 12 files reviewed at latest revision, 3 unresolved discussions, some commit checks failed.


API.md, line 33 [r1] (raw file):
URI or URL? (The field name is one but the documentation is the other.)


cycledash/api/bams.py, line 70 [r1] (raw file):
This can't be true if the BAM is just available via HTTP...


cycledash/templates/about.html, line 35 [r1] (raw file):
not implemented yet?


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ihodes commented Dec 17, 2015

Review status: 0 of 13 files reviewed at latest revision, 1 unresolved discussion.


API.md, line 33 [r1] (raw file):
It's a URL now; previously it was a URI (just the path on HDFS). A URI is a subset of a URL, so I figured I'd keep it the same on the backend http://stackoverflow.com/questions/176264/what-is-the-difference-between-a-uri-a-url-and-a-urn


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danvk commented Dec 18, 2015

LGTM


Review status: 0 of 13 files reviewed at latest revision, 2 unresolved discussions, some commit checks failed.


cycledash/api/bams.py, line 84 [r1] (raw file):
How about deleting this worker, too?


Comments from the review on Reviewable.io

ihodes added a commit that referenced this pull request Dec 18, 2015
Don't look for BAMs on HDFS
@ihodes ihodes merged commit a436c4f into master Dec 18, 2015
@ihodes ihodes deleted the nfs_bams branch December 23, 2015 16:53
@hammer hammer unassigned danvk Feb 8, 2016
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2 participants