[galaxy-dev] percent and pipe sign in text input fields
Hello all, I have a tool based on blastdbcmd that contains a param tag of type text. I want to be able to use the % sign in that text field users can enter (%g is for instance the field identifier for gi). However, if I do for instance %f or %f it returns Xf or Xf in the the variable. For single field lines I solved it to remove the % from the argument and only add it at command line, but in this case it can contain % signs anywhere... For instance %g|%a|%t should return by the tool gi..|accno|title. However the variable returned by the tool xml is XgXXaXXt. So it also masks the | (pipe) sign... How to solve this? Thanks for any help. Alex ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Percent and pipe sign in text input fields
Hello all, I have a tool based on blastdbcmd that contains a param tag of type text. I want to be able to use the % sign in that text field users can enter (%g is for instance the field identifier for gi). However, if I do for instance %f or %f it returns Xf or Xf in the the variable. For single field lines I solved it to remove the % from the argument and only add it at command line, but in this case it can contain % signs anywhere... For instance %g|%a|%t should return by the tool gi..|accno|title. However the variable returned by the tool xml is XgXXaXXt. So it also masks the | (pipe) sign... How to solve this? Thanks for any help. Alex ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] percent and pipe sign in text input fields
Hi Alex, Have a look at the 'sanititzer tag set' on the http://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax page. Caution is urged when modifying these options. Please let us know if you encounter difficulty. Thanks for using Galaxy, Dan On Feb 16, 2011, at 5:22 AM, Bossers, Alex wrote: Hello all, I have a tool based on blastdbcmd that contains a param tag of type text. I want to be able to use the % sign in that text field users can enter (%g is for instance the field identifier for gi). However, if I do for instance %f or %f it returns Xf or Xf in the the variable. For single field lines I solved it to remove the % from the argument and only add it at command line, but in this case it can contain % signs anywhere... For instance %g|%a|%t should return by the tool gi..|accno|title. However the variable returned by the tool xml is XgXXaXXt. So it also masks the | (pipe) sign... How to solve this? Thanks for any help. Alex ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Percent and pipe sign in text input fields
Hi Alex, Galaxy sanitizes the params to remove unsafe characters. It's a security feature. From a previous post some time ago: If you trust your users you can add the option name to NEVER_SANITIZE in lib/galaxy/utils/_init_.py You can also have a look at that *.py file and lib/galaxy/tools/parameters/sanitize.py to see what gets sanitized. AFAIK this is not well documented on the Wiki... Cheers, Pi On Feb 16, 2011, at 1:23 PM, Bossers, Alex wrote: Hello all, I have a tool based on blastdbcmd that contains a param tag of type text. I want to be able to use the % sign in that text field users can enter (%g is for instance the field identifier for gi). However, if I do for instance %f or %f it returns Xf or Xf in the the variable. For single field lines I solved it to remove the % from the argument and only add it at command line, but in this case it can contain % signs anywhere... For instance %g|%a|%t should return by the tool gi..|accno|title. However the variable returned by the tool xml is XgXXaXXt. So it also masks the | (pipe) sign... How to solve this? Thanks for any help. Alex ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ - mobile: +31 6 143 66 783 e-mail: pieter.neeri...@gmail.com skype: pieter.online - ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Percent and pipe sign in text input fields
On Feb 16, 2011, at 3:44 PM, Pieter Neerincx wrote: Hi Alex, Galaxy sanitizes the params to remove unsafe characters. It's a security feature. From a previous post some time ago: If you trust your users you can add the option name to NEVER_SANITIZE in lib/galaxy/utils/_init_.py You can also have a look at that *.py file and lib/galaxy/tools/parameters/sanitize.py to see what gets sanitized. AFAIK this is not well documented on the Wiki... Eh, Google was not my friend, but it is actually documented: have a look at the sanititzer tag set... Cheers, Pi On Feb 16, 2011, at 1:23 PM, Bossers, Alex wrote: Hello all, I have a tool based on blastdbcmd that contains a param tag of type text. I want to be able to use the % sign in that text field users can enter (%g is for instance the field identifier for gi). However, if I do for instance %f or %f it returns Xf or Xf in the the variable. For single field lines I solved it to remove the % from the argument and only add it at command line, but in this case it can contain % signs anywhere... For instance %g|%a|%t should return by the tool gi..|accno|title. However the variable returned by the tool xml is XgXXaXXt. So it also masks the | (pipe) sign... How to solve this? Thanks for any help. Alex ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ - mobile: +31 6 143 66 783 e-mail: pieter.neeri...@gmail.com skype: pieter.online - - mobile: +31 6 143 66 783 e-mail: pieter.neeri...@gmail.com skype: pieter.online - ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Percent and pipe sign in text input fields
Daniel/Pieter, thanks for the hints. I solved it using the santizer tags. Even though it was quite cryptic what to do... but below is what I added to the param text tag and now it allows the chars I want. Now I will fiddle around somewhat to use the default inital allowed characters and just add the % and | characters to it Thanks Alex sanitizer valid initial=string.printable remove value=apos;/ /valid mapping initial=none add source=apos; target=/ /mapping /sanitizer Van: Pieter Neerincx [pieter.neeri...@gmail.com] Verzonden: woensdag 16 februari 2011 15:44 Aan: Bossers, Alex CC: galaxy-...@bx.psu.edu Onderwerp: Re: [galaxy-dev] Percent and pipe sign in text input fields Hi Alex, Galaxy sanitizes the params to remove unsafe characters. It's a security feature. From a previous post some time ago: If you trust your users you can add the option name to NEVER_SANITIZE in lib/galaxy/utils/_init_.py You can also have a look at that *.py file and lib/galaxy/tools/parameters/sanitize.py to see what gets sanitized. AFAIK this is not well documented on the Wiki... Cheers, Pi On Feb 16, 2011, at 1:23 PM, Bossers, Alex wrote: Hello all, I have a tool based on blastdbcmd that contains a param tag of type text. I want to be able to use the % sign in that text field users can enter (%g is for instance the field identifier for gi). However, if I do for instance %f or %f it returns Xf or Xf in the the variable. For single field lines I solved it to remove the % from the argument and only add it at command line, but in this case it can contain % signs anywhere... For instance %g|%a|%t should return by the tool gi..|accno|title. However the variable returned by the tool xml is XgXXaXXt. So it also masks the | (pipe) sign... How to solve this? Thanks for any help. Alex ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ - mobile: +31 6 143 66 783 e-mail: pieter.neeri...@gmail.com skype: pieter.online - ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
