Hi all, Using either the legacy upload tool, or the new upload widget, the following FTP URL *appears* to load into Galaxy correctly giving a green history entry.
However, on closer inspection it is an empty file with this peep text: Unable to fetch ftp://ftp.sanger.ac.uk/pub/pathogens/Bursaphelenchus/xylophilus/Assembly-v1.2/BurXv1.2.supercontigs.fa.gz [Errno ftp error] 550 pathogens: No such file or directory Clearly this should have been treated as a failure (red history entry). Should I file this as a bug on Trello? It seems there is a problem with the Sanger folder permissions which trips up Galaxy and curl (but does not bother Firefox and wget): $ curl -O ftp://ftp.sanger.ac.uk/pub/pathogens/Bursaphelenchus/xylophilus/Assembly-v1.2/BurXv1.2.supercontigs.fa.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 curl: (9) Server denied you to change to the given directory Using curl -v for verbose mode it tries to walk the path (as per the https://www.ietf.org/rfc/rfc1738.txt standard) and fails with the command "CWD pathogens" matching the Galaxy error. The alternative curl FTP methods work: $ curl -O ftp://ftp.sanger.ac.uk/pub/pathogens/Bursaphelenchus/xylophilus/Assembly-v1.2/BurXv1.2.supercontigs.fa.gz --ftp-method nocwd % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 21.8M 100 21.8M 0 0 7656k 0 0:00:02 0:00:02 --:--:-- 7654k and: $ curl -O ftp://ftp.sanger.ac.uk/pub/pathogens/Bursaphelenchus/xylophilus/Assembly-v1.2/BurXv1.2.supercontigs.fa.gz --ftp-method singlecwd % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 21.8M 100 21.8M 0 0 7767k 0 0:00:02 0:00:02 --:--:-- 7766k You can also trick curl by replacing (some of the) slashes with the escaped version %2f which has the result of combining the CWD commands, e.g. $ curl -O ftp://ftp.sanger.ac.uk/pub%2fpathogens%2fBursaphelenchus%2fxylophilus%2fAssembly-v1.2/BurXv1.2.supercontigs.fa.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 21.8M 100 21.8M 0 0 6827k 0 0:00:03 0:00:03 --:--:-- 6829k This encoding trick does not seem to work within Galaxy. I plan to report this to Sanger tomorrow. Should they fix this quickly additional test cases might be useful (does Galaxy have an FTP server which might be used for testing data importing like this?). Is this a common issue? Should Galaxy automatically use an FTP CWD workaround in this situation? Regards, Peter ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
