From N.Schurch@dundee.ac.uk Fri Aug 21 10:24:04 2009 From: Nick Schurch To: galaxy-user@lists.galaxyproject.org Subject: [galaxy-user] Problems with links in webpage output... Date: Fri, 21 Aug 2009 15:23:40 +0100 Message-ID: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============2262986515459696722==" --===============2262986515459696722== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: 7bit Dear Galaxy-gurus, I have a tool I've written myself which runs successfully and generates an HTML file as its output. Included in the webpage are several links for downloading other files produced by the script. I've tried to follow the instructions I found on the wiki -- http://g2.trac.bx.psu.edu/wiki/AddingToolsFAQ -- which gives some (rather vague) instructions about where to put the files and how to reference them in the output webpage, but I'm not having much luck. The script successfully puts the files in the directory where (I think) they are supposed to be: i.e /homes/www-galaxy/galaxy_devel/database/files/000/{myoutputfile}.files_path, and the output links to them very simply with download file - as per the wikipage... But when I view the output webpage from a test run and try and download the links all I get is a page saying: "The resource could not be found. File Not Found (myfilename.txt)." The link itself is pointing to: /datasets/XXX/display/myfilename.txt Is this the right place? Once again, any help would be greatly appreciated! -- Cheers, Nick Schurch Data Analysis Group (The Barton Group), School of Life Sciences, University of Dundee, Dow St, Dundee, DD1 5EH, Scotland, UK Tel: +44 1382 388707 Fax: +44 1382 345 893 --===============2262986515459696722== Content-Type: text/html Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename="attachment.htm" MIME-Version: 1.0 RGVhciBHYWxheHktZ3VydXMsPGJyPjxicj5JIGhhdmUgYSB0b29sIEkmIzM5O3ZlIHdyaXR0ZW4g bXlzZWxmIHdoaWNoIHJ1bnMgc3VjY2Vzc2Z1bGx5IGFuZCBnZW5lcmF0ZXMgYW4gSFRNTCBmaWxl IGFzIGl0cyBvdXRwdXQuIEluY2x1ZGVkIGluIHRoZSB3ZWJwYWdlIGFyZSBzZXZlcmFsIGxpbmtz IGZvciBkb3dubG9hZGluZyBvdGhlciBmaWxlcyBwcm9kdWNlZCBieSB0aGUgc2NyaXB0LiBJJiMz OTt2ZSB0cmllZCB0byBmb2xsb3cgdGhlIGluc3RydWN0aW9ucyBJIGZvdW5kIG9uIHRoZSB3aWtp IC0tIDxhIGhyZWY9Imh0dHA6Ly9nMi50cmFjLmJ4LnBzdS5lZHUvd2lraS9BZGRpbmdUb29sc0ZB USI+aHR0cDovL2cyLnRyYWMuYngucHN1LmVkdS93aWtpL0FkZGluZ1Rvb2xzRkFRPC9hPiAtLSB3 aGljaCBnaXZlcyBzb21lIChyYXRoZXIgdmFndWUpIGluc3RydWN0aW9ucyBhYm91dCB3aGVyZSB0 byBwdXQgdGhlIGZpbGVzIGFuZCBob3cgdG8gcmVmZXJlbmNlIHRoZW0gaW4gdGhlIG91dHB1dCB3 ZWJwYWdlLCBidXQgSSYjMzk7bSBub3QgaGF2aW5nIG11Y2ggbHVjay48YnI+Cgo8YnI+VGhlIHNj cmlwdCBzdWNjZXNzZnVsbHkgcHV0cyB0aGUgZmlsZXMgaW4gdGhlIGRpcmVjdG9yeSB3aGVyZSAo SSB0aGluaykgdGhleSBhcmUgc3VwcG9zZWQgdG8gYmU6IGkuZaAgL2hvbWVzL3d3dy1nYWxheHkv Z2FsYXh5X2RldmVsL2RhdGFiYXNlL2ZpbGVzLzAwMC97bXlvdXRwdXRmaWxlfS5maWxlc19wYXRo LCBhbmQgdGhlIG91dHB1dCBsaW5rcyB0byB0aGVtIHZlcnkgc2ltcGx5IHdpdGggJmx0O2EgaHJl Zj0mcXVvdDtteWZpbGVuYW1lLnR4dCZxdW90OyZndDtkb3dubG9hZCBmaWxlJmx0Oy9hJmd0OyAt IGFzIHBlciB0aGUgd2lraXBhZ2UuLi48YnI+Cgo8YnI+QnV0IHdoZW4gSSB2aWV3IHRoZSBvdXRw dXQgd2VicGFnZSBmcm9tIGEgdGVzdCBydW4gYW5kIHRyeSBhbmQgZG93bmxvYWQgdGhlIGxpbmtz IGFsbCBJIGdldCBpcyBhIHBhZ2Ugc2F5aW5nOjxicj48YnI+JnF1b3Q7VGhlIHJlc291cmNlIGNv dWxkIG5vdCBiZSBmb3VuZC4KPGJyPkZpbGUgTm90IEZvdW5kIChteWZpbGVuYW1lLnR4dCkuJnF1 b3Q7PGJyPjxicj5UaGUgbGluayBpdHNlbGYgaXMgcG9pbnRpbmcgdG86ICZsdDtteSBnYWxheHkg VVJMJmd0Oy9kYXRhc2V0cy9YWFgvZGlzcGxheS9teWZpbGVuYW1lLnR4dDxicj48YnI+SXMgdGhp cyB0aGUgcmlnaHQgcGxhY2U/IE9uY2UgYWdhaW4sIGFueSBoZWxwIHdvdWxkIGJlIGdyZWF0bHkg YXBwcmVjaWF0ZWQhPGJyPgoKPGJyPi0tIDxicj5DaGVlcnMsPGJyPjxicj5OaWNrIFNjaHVyY2g8 YnI+PGJyPkRhdGEgQW5hbHlzaXMgR3JvdXAgKFRoZSBCYXJ0b24gR3JvdXApLDxicj5TY2hvb2wg b2YgTGlmZSBTY2llbmNlcyw8YnI+VW5pdmVyc2l0eSBvZiBEdW5kZWUsPGJyPkRvdyBTdCw8YnI+ RHVuZGVlLDxicj5ERDEgNUVILDxicj5TY290bGFuZCw8YnI+VUs8YnI+PGJyPlRlbDogKzQ0IDEz ODIgMzg4NzA3PGJyPgoKRmF4OiArNDQgMTM4MiAzNDUgODkzIDxicj4K --===============2262986515459696722==-- From dan@bx.psu.edu Fri Aug 21 11:09:26 2009 From: Daniel Blankenberg To: galaxy-user@lists.galaxyproject.org Subject: Re: [galaxy-user] Problems with links in webpage output... Date: Fri, 21 Aug 2009 11:09:24 -0400 Message-ID: <50837.128.118.201.71.1250867364.squirrel@webmail.bx.psu.edu> In-Reply-To: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============6890728424071749023==" --===============6890728424071749023== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: 7bit Hi Nick, If your command is like this: some_command $input1 $output1 $output1.files_path Your script 'some_command' needs to create the directory specified by '$output1.files_path' and then place your additional files in that directory. These files can then be accessed by relative links in your html file (output1). Let us know if you need further assistance, Dan > Dear Galaxy-gurus, > > I have a tool I've written myself which runs successfully and generates an > HTML file as its output. Included in the webpage are several links for > downloading other files produced by the script. I've tried to follow the > instructions I found on the wiki -- > http://g2.trac.bx.psu.edu/wiki/AddingToolsFAQ -- which gives some (rather > vague) instructions about where to put the files and how to reference them > in the output webpage, but I'm not having much luck. > > The script successfully puts the files in the directory where (I think) > they > are supposed to be: i.e > /homes/www-galaxy/galaxy_devel/database/files/000/{myoutputfile}.files_path, > and the output links to them very simply with href="myfilename.txt">download file - as per the wikipage... > > But when I view the output webpage from a test run and try and download > the > links all I get is a page saying: > > "The resource could not be found. > File Not Found (myfilename.txt)." > > The link itself is pointing to: URL>/datasets/XXX/display/myfilename.txt > > Is this the right place? Once again, any help would be greatly > appreciated! > > -- > Cheers, > > Nick Schurch > > Data Analysis Group (The Barton Group), > School of Life Sciences, > University of Dundee, > Dow St, > Dundee, > DD1 5EH, > Scotland, > UK > > Tel: +44 1382 388707 > Fax: +44 1382 345 893 > _______________________________________________ > galaxy-user mailing list > galaxy-user(a)bx.psu.edu > http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user > --===============6890728424071749023==--