how do I pass the URL of the input and output files to my tool wrapper?
Anyone know if it possible to pass the url (shown in the eye ball) to a tool wrapper? Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: ichorny@illumina.com<mailto:ichorny@illumina.com> Website: www.illumina.com<http://www.illumina.com>
Excerpts from Chorny, Ilya's message of 2011-10-14 23:46:25 +0000:
Anyone know if it possible to pass the url (shown in the eye ball) to a tool wrapper?
Ilya, this isn't currently supported because it breaks the abstraction between the web interface and tools (tools shouldn't know they are being invoked by a web application). What are you trying to achieve with this? Is this for a tool generating an HTML report? -- James Taylor, Assistant Professor, Biology / Computer Science, Emory University
PDF report. Sent from my iPhone On Oct 15, 2011, at 7:36 PM, "James Taylor" <james@jamestaylor.org> wrote:
Excerpts from Chorny, Ilya's message of 2011-10-14 23:46:25 +0000:
Anyone know if it possible to pass the url (shown in the eye ball) to a tool wrapper?
Ilya, this isn't currently supported because it breaks the abstraction between the web interface and tools (tools shouldn't know they are being invoked by a web application). What are you trying to achieve with this? Is this for a tool generating an HTML report? -- James Taylor, Assistant Professor, Biology / Computer Science, Emory University ___________________________________________________________ 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:
Would it be difficult to add the url as an attribute of the input and output parameters ($param.url)? If you point me to where these values are set, I can try to make the changes to the code. Thanks, Ilya -----Original Message----- From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Chorny, Ilya Sent: Sunday, October 16, 2011 7:36 AM To: James Taylor Cc: galaxy-dev Subject: Re: [galaxy-dev] how do I pass the URL of the input and output files to my tool wrapper? PDF report. Sent from my iPhone On Oct 15, 2011, at 7:36 PM, "James Taylor" <james@jamestaylor.org> wrote:
Excerpts from Chorny, Ilya's message of 2011-10-14 23:46:25 +0000:
Anyone know if it possible to pass the url (shown in the eye ball) to a tool wrapper?
Ilya, this isn't currently supported because it breaks the abstraction between the web interface and tools (tools shouldn't know they are being invoked by a web application). What are you trying to achieve with this? Is this for a tool generating an HTML report? -- James Taylor, Assistant Professor, Biology / Computer Science, Emory University ___________________________________________________________ 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:
___________________________________________________________ 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: http://lists.bx.psu.edu/
So we came up with a work around and I wouldn't mind getting your opinion on it. Specifically with respect to passing cookie_path. I could not figure out how to get the proxy prefix from the universe_wsgi.ini file via the $__app__ call. Also you mention in the wiki the the $__app__ may get deprecated. Thanks, Ilya We copied the encryption code (i.e) def encode_id(dataset_id,id_secret): id_cipher = Blowfish.new(id_secret) s = dataset_id s = ( "!" * ( 8 - len(s) % 8 ) ) + s encrypted_id = id_cipher.encrypt( s ).encode( 'hex' ) return encrypted_id and we passed to the too wrapperl: -i input -i $input.dataset.id as well as --id_secret=$__app__.config.id_secret --cookie_path=$__app__.config.cookie_path -----Original Message----- From: Chorny, Ilya Sent: Monday, October 17, 2011 11:10 AM To: Chorny, Ilya; James Taylor Cc: galaxy-dev Subject: RE: [galaxy-dev] how do I pass the URL of the input and output files to my tool wrapper? Would it be difficult to add the url as an attribute of the input and output parameters ($param.url)? If you point me to where these values are set, I can try to make the changes to the code. Thanks, Ilya -----Original Message----- From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Chorny, Ilya Sent: Sunday, October 16, 2011 7:36 AM To: James Taylor Cc: galaxy-dev Subject: Re: [galaxy-dev] how do I pass the URL of the input and output files to my tool wrapper? PDF report. Sent from my iPhone On Oct 15, 2011, at 7:36 PM, "James Taylor" <james@jamestaylor.org> wrote:
Excerpts from Chorny, Ilya's message of 2011-10-14 23:46:25 +0000:
Anyone know if it possible to pass the url (shown in the eye ball) to a tool wrapper?
Ilya, this isn't currently supported because it breaks the abstraction between the web interface and tools (tools shouldn't know they are being invoked by a web application). What are you trying to achieve with this? Is this for a tool generating an HTML report? -- James Taylor, Assistant Professor, Biology / Computer Science, Emory University ___________________________________________________________ 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:
___________________________________________________________ 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: http://lists.bx.psu.edu/
participants (2)
-
Chorny, Ilya -
James Taylor