[Bioc-devel] ExperimentHub ft resource with password

Mon Feb 10 14:40:21 CET 2025

I know Martin and a collogue worked on trying to get a version of the hubs updated to have a licensing acceptance portion which required substantial efforts/rewrites as the base database of hubs had to migrate/change as well. I can look around to see where that left off.

I think its similar but still distinct.  Right now I'm not sure it's directly possible. And I don't think Robert's suggestion would work as it seems the work around is after the file is downloaded.   I would have to look up if/how httr (and really httr2 since we are in process of converting since httr is no longer maintained) handles this. If httr2 allows this with a config or argument it should be possible to allow with additional argument in the hubs.

Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Robert Castelo via Bioc-devel <bioc-devel using r-project.org>
Sent: Friday, February 7, 2025 3:08 AM
To: Laurent Gatto <laurent.gatto using uclouvain.be>
Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] ExperimentHub ft resource with password

Hi,

I think this is an analogous question to the one brought up about year
and a half ago by Martin Morgan in this issue:

https://secure-web.cisco.com/1xcashewkbQZcqqHQxelujWJqKSvcxnK9Q2IAvU3vbhmfBx2Xdml8gMETuzBAP7ZpEhIfwLJmT6SO9OKNpWtvG2wzXf_Fh4zW6h6k7zM6RVns6ZuRQx64J3urCBY0ejs5z5ixQWIGjLp3d11jzUmSzLrpOJNBbIQy31ZOKSL-5pJIMcE-nVD3S1x83KhdHpD0zEEbtQ-DB06X63QzzpjT8zkf1XNIjAaoOaBavuIrYULe5ULp1NSXzsPLJQtG5RnLB3-OyHKDvGEtnU8Jvnpk480oy5uGGDkI0F6UKYZMmvWxeLHqRBkDBPF1m2q73KZE/https%3A%2F%2Fgithub.com%2FBioconductor%2FAnnotationHub%2Fissues%2F45

on how could we ask the user to accept a license before downloading the
corresponding AlphaMissense data from the AnnotationHub.

In GenomicScores, which also provides access to AlphaMissense data, I
implemented a temporary solution until we have a general solution for
all AH resources, by which if the resource metadata (that I created
myself) included a license, this is displayed to the user, who must
accept it to use the data:

 > library(GenomicScores)

 > am <- getGScores("AlphaMissense.v2023.hg38")
snapshotDate(): 2024-10-28
loading from cache
These data is shared under the license CC BY-NC-SA 4.0 (see
https://secure-web.cisco.com/1awrcjsDj2PlvUmP4fTefz87hWNdc25ltWYt0_UJeCffi7WMKL1tjMmYhilWIDEQUcyL_7ji0PdLaRzv3pL110Lsl8FzFpJqv1p-5tQnJMCYA_hsCJivnDWZouXzHAjl_UqlfYisvakPB0UlWDDrQCd4656j5Lrk2MyPnkZRn1vyb3g0wZ1zJaZLx1U9PUv4T2OpIW4ir5bX3MYoh58HxDtVQlPjEwvL1Dd0Q7pYFNWORSUWV3bKOVqpOBTvtJCu-MOnVA5YjKEmvTok_58U6LjgXwlZpt05U6SYIeahj2bURwmsq0SeGsGuutWyDcvJt/https%3A%2F%2Fcreativecommons.org%2Flicenses%2Fby-nc-sa%2F4.0), do you accept it?
[y/n]: y
 > am
GScores object
# organism: Homo sapiens (UCSC, hg38)
# provider: Google DeepMind
# provider version: v2023
# download date: Oct 10, 2023
# loaded sequences: chr1
# maximum abs. error: 0.005
# license: CC BY-NC-SA 4.0, see
https://secure-web.cisco.com/1awrcjsDj2PlvUmP4fTefz87hWNdc25ltWYt0_UJeCffi7WMKL1tjMmYhilWIDEQUcyL_7ji0PdLaRzv3pL110Lsl8FzFpJqv1p-5tQnJMCYA_hsCJivnDWZouXzHAjl_UqlfYisvakPB0UlWDDrQCd4656j5Lrk2MyPnkZRn1vyb3g0wZ1zJaZLx1U9PUv4T2OpIW4ir5bX3MYoh58HxDtVQlPjEwvL1Dd0Q7pYFNWORSUWV3bKOVqpOBTvtJCu-MOnVA5YjKEmvTok_58U6LjgXwlZpt05U6SYIeahj2bURwmsq0SeGsGuutWyDcvJt/https%3A%2F%2Fcreativecommons.org%2Flicenses%2Fby-nc-sa%2F4.0
# use 'citation()' to cite these data in publications

so, I guess a similar strategy could be applied, but requiring a
password instead of accepting a license. this of course implies
implementing a hub package that handles this, as GenomicScores is doing.

cheers,

robert.

On 6/2/25 10:53, Laurent Gatto via Bioc-devel wrote:
> Dear hub developers, dear Lori,
>
> Section 7.1 'Hosting Data on a Publicly Accessible Site' from the 'Creating A Hub Package' vignette (HubPub package) [1] describes how to define resources stored on ftp servers. Is there a way to specify a password to download such a resource?
>
> The data I would like to share as a hub resource needs a password. The password is public (it's spelled out in the associated publication). I imagine that at some point, the data will become accessible without password, but that can be a bit of a hit and miss situation. I would prefer avoiding re-sharing the files elsewhere or to have to wait until the data becomes accessible without password.
>
> Thank you in advance.
>
> Laurent
>
> [1]https://secure-web.cisco.com/1SbkOz9UzHSZM3BbImwZCSskaJYUD5YrKL9HLpIyVSlGNAcb_jmsZga2QHnaUyECf0TDry2JyjhmkIIWN40aBT158yemkEpCk8MyF_pytj8ort-zmB2N7cPnBXRepgP2QzQzI6XGLZFLr1W9PQHdx7zqnr49fnjy8MWrB6J08_sDtHm3w0O-UHrQSTIBx6SgQgX7VVsSBs089pmJT1U1ouSZzdzYsJrWG8uojcyUjVwliT5waEwa2b2ayB8VRFLtc7Q1aPFBOlhQUVlIBhgBe54l6YXXMmSNeSvCrOB-qAdbVWhpLxhDs46Pq1Bj-jmIj/https%3A%2F%2Fbioconductor.org%2Fpackages%2F3.20%2Fbioc%2Fvignettes%2FHubPub%2Finst%2Fdoc%2FCreateAHubPackage.html%23storage-of-data-files
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://secure-web.cisco.com/1fpqrJlFU7GKXGW_B5iI6_r4obI_vVzK8MPxnMN0AahPvpT-Zg0Bgayg_BQ_tT1kvrv14_8RzScfdMUB50P82Gy3kli0_EfsQJN0qpzskNwt3d6uEZQ25hRdrDg0UdNl9PqfAbZ1HRX6-vCcWiiSQWTWPreb5A3eCoLqdzO5UZXeQCnZW-_uyZDwDs4CWLTViQpI4s2Ql7VI2C2ibvHN52ULL89uMfLyuYF68BKfoINYlUprU4KGIAJsrxyPMmaaD6F4gQLyAYw3Mt3mpInDNJCWNwq6otv956htbOTXoBpTVe_gWO_05ohqwWjnNGCV0/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel

--
Robert Castelo, PhD
Associate Professor
Dept. of Medicine and Life Sciences
Universitat Pompeu Fabra (UPF)
Barcelona Biomedical Research Park (PRBB)
Dr Aiguader 88
E-08003 Barcelona, Spain
telf: +34.933.160.514

        [[alternative HTML version deleted]]

_______________________________________________
Bioc-devel using r-project.org mailing list
https://secure-web.cisco.com/1fpqrJlFU7GKXGW_B5iI6_r4obI_vVzK8MPxnMN0AahPvpT-Zg0Bgayg_BQ_tT1kvrv14_8RzScfdMUB50P82Gy3kli0_EfsQJN0qpzskNwt3d6uEZQ25hRdrDg0UdNl9PqfAbZ1HRX6-vCcWiiSQWTWPreb5A3eCoLqdzO5UZXeQCnZW-_uyZDwDs4CWLTViQpI4s2Ql7VI2C2ibvHN52ULL89uMfLyuYF68BKfoINYlUprU4KGIAJsrxyPMmaaD6F4gQLyAYw3Mt3mpInDNJCWNwq6otv956htbOTXoBpTVe_gWO_05ohqwWjnNGCV0/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel

This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
	[[alternative HTML version deleted]]