[galaxy-dev] How to escape % characters in tool parameters?
Hi folks, I'm working on a tool that queries a database based on user input, where this user input is a text parameter. The wildcard for the database is the percent (%) character. The user input, which is ultimately translated into the query, should be able to contain a % character. For example, one input field lets the user indicate which cancer cohort he or she is interested in, in a table of available cohorts, and the user should be able to give input like 'TCGA% to indicate all TCGA cohorts. The problem I'm having is that when % is given in the input field, it's translated (to X) by the time it reaches my tool's python script. I haven't been able to figure out the right way to escape the input so that % is not translated. So, how do I escape this? Thanks! Melissa ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] How to escape % characters in tool parameters?
Funny - I just exchanged an e-mail with someone about this tool this morning, the Galaxy-P dbbuilder tool escapes exactly this santizing. Here is the relevant portion: param name=url value= type=text label=URL (http, ftp) sanitizer valid add value=%/ /valid /sanitizer /param The full tool is on the tool shed. https://toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder Hope this helps. -John On Tue, Sep 9, 2014 at 10:08 PM, Melissa Cline cl...@soe.ucsc.edu wrote: Hi folks, I'm working on a tool that queries a database based on user input, where this user input is a text parameter. The wildcard for the database is the percent (%) character. The user input, which is ultimately translated into the query, should be able to contain a % character. For example, one input field lets the user indicate which cancer cohort he or she is interested in, in a table of available cohorts, and the user should be able to give input like 'TCGA% to indicate all TCGA cohorts. The problem I'm having is that when % is given in the input field, it's translated (to X) by the time it reaches my tool's python script. I haven't been able to figure out the right way to escape the input so that % is not translated. So, how do I escape this? Thanks! Melissa ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] How to escape % characters in tool parameters?
Awesome! Thank you, John - I'd actually glanced at the sanitizer and wondered if it was what I needed, but having a working example makes all the difference! On Tue, Sep 9, 2014 at 7:26 PM, John Chilton jmchil...@gmail.com wrote: Funny - I just exchanged an e-mail with someone about this tool this morning, the Galaxy-P dbbuilder tool escapes exactly this santizing. Here is the relevant portion: param name=url value= type=text label=URL (http, ftp) sanitizer valid add value=%/ /valid /sanitizer /param The full tool is on the tool shed. https://toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder Hope this helps. -John On Tue, Sep 9, 2014 at 10:08 PM, Melissa Cline cl...@soe.ucsc.edu wrote: Hi folks, I'm working on a tool that queries a database based on user input, where this user input is a text parameter. The wildcard for the database is the percent (%) character. The user input, which is ultimately translated into the query, should be able to contain a % character. For example, one input field lets the user indicate which cancer cohort he or she is interested in, in a table of available cohorts, and the user should be able to give input like 'TCGA% to indicate all TCGA cohorts. The problem I'm having is that when % is given in the input field, it's translated (to X) by the time it reaches my tool's python script. I haven't been able to figure out the right way to escape the input so that % is not translated. So, how do I escape this? Thanks! Melissa ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
