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Used to report and track bioCADDIE prototype issues
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[LINCS] accessURL #279

Open chung88 opened 7 years ago

chung88 commented 7 years ago

The accessURL in here is not correct:

accessURL: http://lincsportal.ccs.miami.edu/dcic/api/download?path=LINCS_Data/HMS_LINCS&file=LDS-1354.tar.gz

https://datamed.org/display-item.php?repository=0004&id=5833650a5152c608d984a415&query=

How did you get this value field?

yul129 commented 7 years ago

@chung88 , what do you think should be a correct access url for this record? can you give more details about this issue?

chung88 commented 7 years ago

LINCS Dataset ID LDS-1354, is from NeuroLINCS, as described in the BioCaddie landing page. On the accessURL: http://lincsportal.ccs.miami.edu/dcic/api/download?path=LINCS_Data/HMS_LINCS&file=LDS-1354.tar.gz (download 1)

I see HMS LINCS, which is Harvard.

The correct access URL to download the package should be http://lincsportal.ccs.miami.edu/dcic/api/download?path=LINCS_Data/NeuroLINCS&file=LDS-1354.tar.gz (download 2)

The file size difference between [download 1] 0 GB and [download 2] 138 MB. The first download puts an empty file in the user download directory.

yul129 commented 7 years ago

Thank you for the information, i have updated the code for LINCS and the new index will be pushed to production before next week.

From: Caty Chung [notifications@github.com] Sent: Wednesday, August 02, 2017 10:15 AM To: biocaddie/prototype_issues Cc: Yueling Li; Comment Subject: Re: [biocaddie/prototype_issues] [LINCS] accessURL (#279)

LINCS Dataset ID LDS-1354, is from NeuroLINCS, as described in the BioCaddie landing page. On the accessURL: http://lincsportal.ccs.miami.edu/dcic/api/download?path=LINCS_Data/HMS_LINCS&file=LDS-1354.tar.gz (download 1)

I see HMS LINCS, which is Harvard.

The correct access URL to download the package should be http://lincsportal.ccs.miami.edu/dcic/api/download?path=LINCS_Data/NeuroLINCS&file=LDS-1354.tar.gz (download 2)

The file size difference between [download 1] 0 GB and [download 2] 138 MB. The first download puts an empty file in the user download directory.

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/biocaddie/prototype_issues/issues/279#issuecomment-319738454, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ALPhs2mWRoesBFc9I2nh0Jk8ggb3IM2Nks5sUK7BgaJpZM4Oq-GS.

ianfore commented 6 years ago

The wrong URL is still visible today. When do we expect the corrected version?

yul129 commented 6 years ago

The transformation file has been updated to the new URL and re-indexed by Burak, not sure what next step will be.

From: Ian Fore [notifications@github.com] Sent: Friday, September 15, 2017 9:49 AM To: biocaddie/prototype_issues Cc: Yueling Li; Comment Subject: Re: [biocaddie/prototype_issues] [LINCS] accessURL (#279)

The wrong URL is still visible today. When do we expect the corrected version?

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/biocaddie/prototype_issues/issues/279#issuecomment-329837216, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ALPhs6tDYIaD0kBv8zLjv5gNHMgXk9cCks5siqqRgaJpZM4Oq-GS.

jgrethe commented 6 years ago

Is this just deployed on development?

chung88 commented 6 years ago

Ian, LINCS uses identifiers.orghttp://identifiers.org PURL, where did you get the URL? Caty

On Sep 18, 2017, at 10:44 AM, yul129 notifications@github.com<mailto:notifications@github.com> wrote:

The transformation file has been updated to the new URL and re-indexed by Burak, not sure what next step will be.

From: Ian Fore [notifications@github.commailto:notifications@github.com] Sent: Friday, September 15, 2017 9:49 AM To: biocaddie/prototype_issues Cc: Yueling Li; Comment Subject: Re: [biocaddie/prototype_issues] [LINCS] accessURL (#279)

The wrong URL is still visible today. When do we expect the corrected version?

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/biocaddie/prototype_issues/issues/279#issuecomment-329837216, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ALPhs6tDYIaD0kBv8zLjv5gNHMgXk9cCks5siqqRgaJpZM4Oq-GS.

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bozyurt commented 6 years ago

LINCS is reindexed and available at

http://biocaddie.scicrunch.io/lincs_20170918/dataset

Burak On 09/18/2017 10:44 AM, yul129 wrote:

The transformation file has been updated to the new URL and re-indexed by Burak, not sure what next step will be.

From: Ian Fore [notifications@github.com] Sent: Friday, September 15, 2017 9:49 AM To: biocaddie/prototype_issues Cc: Yueling Li; Comment Subject: Re: [biocaddie/prototype_issues] [LINCS] accessURL (#279)

The wrong URL is still visible today. When do we expect the corrected version?

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/biocaddie/prototype_issues/issues/279#issuecomment-329837216, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ALPhs6tDYIaD0kBv8zLjv5gNHMgXk9cCks5siqqRgaJpZM4Oq-GS.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/biocaddie/prototype_issues/issues/279#issuecomment-330299524, or mute the thread https://github.com/notifications/unsubscribe-auth/AHLczDB35YIraeR1A9keynuwjTPZeB-Xks5sjqvwgaJpZM4Oq-GS.

-- I. Burak Ozyurt PhD Project Scientist University of California, San Diego 9500 Gilman Drive, M/C 0608 La Jolla, CA 92093-0608

ianfore commented 6 years ago

Caty - I was referring to the URL shown on the page you referenced (https://datamed.org/display-item.php?repository=0004&id=5833650a5152c608d984a415&query= ) is still a HMS_LINCS url and not the NeuroLINCS link that you had indicated was the correct one. The file downloaded is still zero bytes.

Though the dialog in this thread suggest this has been fixed the original problem you mentioned is still there. I was just asking what remains to be done to propagate the correction all the way through.

chung88 commented 6 years ago

On the pasted image, the highlight is the difference in the download path for the same dataset.

https://datamed.org/display-item.php?repository=0004&id=5833650a5152c608d984a3f2&query=LINCS image

http://lincsportal.ccs.miami.edu/dcic/api/download?path=LINCS_Data/BroadT_LINCS&file=LDS-1293.tar.gz