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 I would have to look up if/how httr (and really httr2 since we are in process of converting since httr is no longer maintained) handles this.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. 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