I’d suggest adding these ideas as issues to AnnotationHub: https://github.com/Bioconductor/AnnotationHub
(or ExperimentHub, depending on the perceived best fit for the data). Even if there is not yet consensus on development priorities, it will be helpful to have a catalog of additional use cases and requirements. Sean From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Mike Smith <grimbo...@gmail.com> Date: Tuesday, February 11, 2025 at 8:03 AM To: bioc-devel@r-project.org <bioc-devel@r-project.org> Subject: Re: [Bioc-devel] ExperimentHub ft resource with password This might require significant work on the Hub backend, but might it be possible to support getting data from an S3 bucket, and then requiring a permissions key to actually get access? Something like paws.storage could be used in an analogous way to httr2 inside AnnotationHub to actually obtain the data. In Laurent's original scenario the key would be publicly known, and the supporting package could have it stored and ready to use for any access request, so downloading would be seamless to a user. Of course this doesn't actually help with password protecting an FTP site. Cheers, Mike On Mon, 10 Feb 2025 at 14:40, Kern, Lori via Bioc-devel < bioc-devel@r-project.org> wrote: > 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 since httr is no longer maintained) handles this.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-boun...@r-project.org> on behalf of Robert > Castelo via Bioc-devel <bioc-devel@r-project.org> > Sent: Friday, February 7, 2025 3:08 AM > To: Laurent Gatto <laurent.ga...@uclouvain.be> > Cc: bioc-devel@r-project.org <bioc-devel@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@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@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]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
