From 82dfd2d9e7c0bde0bf3aab554804ed7b8dabc802 Mon Sep 17 00:00:00 2001 From: "emmet.obrien@e4a3124a9cf70a33bd02e6cab55d0db0352ce9e1" Date: Thu, 23 May 2019 20:39:29 +0000 Subject: [PATCH] --- ...when_trying_to_cconnect_to_ftp_server.mdwn | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 doc/bugs/__34__Unsupported_url_scheme__34___message_when_trying_to_cconnect_to_ftp_server.mdwn diff --git a/doc/bugs/__34__Unsupported_url_scheme__34___message_when_trying_to_cconnect_to_ftp_server.mdwn b/doc/bugs/__34__Unsupported_url_scheme__34___message_when_trying_to_cconnect_to_ftp_server.mdwn new file mode 100644 index 0000000000..8e8b1bca7f --- /dev/null +++ b/doc/bugs/__34__Unsupported_url_scheme__34___message_when_trying_to_cconnect_to_ftp_server.mdwn @@ -0,0 +1,52 @@ +I am trying to use git-annex as part of a datalad install on an Ubuntu 18.04 VirtualBox VM to set up a repository linking to some datasets at a public ftp server. When I use git-annex version 7.20190219 (installed with apt-get install git-annex-standalone from NeuroDebian) to add the links, I get the following error: + +emmet@emmet-VirtualBox:~/conp-dataset/projects/1KGP-22May2019$ git annex addurl ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr6.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz –file=1KGP_chr6-vcf.gz +addurl ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr6.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz Unsupported url scheme ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr6.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz + +download failed: Unsupported url scheme ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr6.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz +failed +git-annex: addurl: 1 failed + + + +However when I use git-annex v 6.20180227 (installed from the apt repository that came with Ubuntu 18.04) the link is generated correctly: + +emmet@emmet-VirtualBox:~/conp-dataset/projects/1KGP-22May2019$ git annex addurl ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr6.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz --file=1KGP_chr6-vcf.gz +addurl ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr6.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz +ALL.chr6.phase3_shapeit2_mvncall_integrated_ 100%[===========================================================================================>] 953.14M 9.81MB/s in 93s +2019-05-22 16:10:44 URL: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr6.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz [999436830] -> "/home/emmet/conp-dataset/projects/1KGP-22May2019/.git/annex/tmp/URL-s999436830--ftp&c%%ftp.1000genomes.ebi.ac.uk-dda0592051d00d19f6c947a6b3aae6a5" [1] +(to 1KGP_chr6-vcf.gz) ok +(recording state in git...) + + + +Similarly, after publishing the correctly formed links generated with 6.20180227 to github, trying to download them on another Ubuntu VirtualBox VM with git-annex 7.20190219 installed causes the following error: + +emmet@emmet-VirtualBox:~/conp-dataset/projects/1KGP-22May2019$ git annex get 1KGP_chr2-vcf.gz +get 1KGP_chr2-vcf.gz (from web...) +download failed: Unsupported url scheme ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr2.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz + + Unable to access these remotes: web + + Try making some of these repositories available: + 00000000-0000-0000-0000-000000000001 -- web + 2cc9a182-813f-4740-8157-c7a560560238 -- emmet@emmet-VirtualBox:~/conp-dataset/projects/1KGP-22May2019 + + (Note that these git remotes have annex-ignore set: origin) +failed +git-annex: get: 1 failed + + + +but downloading them on that same VM with git-annex v 6.20180227 installed instead works: + +emmet@emmet-VirtualBox:~/conp-dataset/projects/1KGP-22May2019$ git annex get 1KGP_chr2-vcf.gz +get 1KGP_chr2-vcf.gz (from web...) +ALL.chr2.phase3_sha 100%[===================>] 1.22G 6.99MB/s in 3m 11s +2019-05-22 16:25:44 URL: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr2.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz [1312735578] -> "/home/emmet/conp-dataset/projects/1KGP-22May2019/.git/annex/tmp/MD5E-s1312735578--774370621affaf125e6994089f975ed7.gz" [1] +(checksum...) ok +(recording state in git...) + + +Would you know why this is happening? And how I can avoid this failure mode in the more up-to-date version of git-annex? +