| Previous changeset 6:81198714ac8e (2015-01-11) Next changeset 8:9d58cc32a12d (2015-01-12) |
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Commit message:
Uploaded |
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modified:
rgToolFactory2.py tool_dependencies.xml |
| b |
| diff -r 81198714ac8e -r 61381bad936d rgToolFactory2.py --- a/rgToolFactory2.py Sun Jan 11 23:34:39 2015 -0500 +++ b/rgToolFactory2.py Mon Jan 12 05:01:29 2015 -0500 |
| [ |
| @@ -145,11 +145,16 @@ "<": "<", "$": "\$" } - +html_unescape_table = dict(zip(html_escape_table.values(),html_escape_table.keys())) def html_escape(text): """Produce entities within text.""" return "".join(html_escape_table.get(c,c) for c in text) + +def html_unescape(text): + """Revert entities within text.""" + return "".join(html_unescape_table.get(c,c) for c in text) + def cmd_exists(cmd): return subprocess.call("type " + cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0 @@ -245,8 +250,10 @@ a('--OUTPATH "%s"' % self.opts.output_tab) for p in opts.additional_parameters: p = p.replace('"','') - ps = p.split(',') - a('%s="%s"' % (ps[0],ps[1])) + psplit = p.split(',') + param = html_unescape(psplit[0]) + value = html_unescape(psplit[1]) + a('%s="%s"' % (param,value)) if (self.opts.interpreter == 'Rscript'): # pass params on command line if self.opts.input_tab: @@ -256,8 +263,10 @@ a('OUTPATH="%s"' % self.opts.output_tab) for p in opts.additional_parameters: p = p.replace('"','') - ps = p.split(',') - a('%s="%s"' % (ps[0],ps[1])) + psplit = p.split(',') + param = html_unescape(psplit[0]) + value = html_unescape(psplit[1]) + a('%s="%s"' % (param,value)) if (self.opts.interpreter == 'perl'): # pass params on command line if self.opts.input_tab: @@ -267,9 +276,9 @@ a('%s' % self.opts.output_tab) for p in opts.additional_parameters: p = p.replace('"','') - ps = p.split(',') - param = ps[0] - value = ps[1] + psplit = p.split(',') + param = html_unescape(psplit[0]) + value = html_unescape(psplit[1]) if (value.find(' ') <> -1): a('%s="%s"' % (param,value)) else: @@ -285,16 +294,16 @@ a('OUTPATH=%s' % (self.opts.output_tab)) # sets those environment variables for the script # additional params appear in CL - yes, it's confusing - for i,param in enumerate(opts.additional_parameters): - psplit = param.split(',') - n = psplit[0] - v = psplit[1] - if (v.find(' ') <> -1): - a('%s="%s"' % (n,v)) - self.cl.insert(4+i,'%s="%s"' % (n,v)) + for i,p in enumerate(opts.additional_parameters): + psplit = p.split(',') + param = html_unescape(psplit[0]) + value = html_unescape(psplit[1]) + if (value.find(' ') <> -1): + a('%s="%s"' % (param,value)) + self.cl.insert(4+i,'%s="%s"' % (param,value)) else: - a('%s=%s' % (n,v)) - self.cl.insert(4+i,'%s=%s' % (n,v)) + a('%s=%s' % (param,value)) + self.cl.insert(4+i,'%s=%s' % (param,value)) self.outFormats = opts.output_format |
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| diff -r 81198714ac8e -r 61381bad936d tool_dependencies.xml --- a/tool_dependencies.xml Sun Jan 11 23:34:39 2015 -0500 +++ b/tool_dependencies.xml Mon Jan 12 05:01:29 2015 -0500 |
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| @@ -1,10 +1,10 @@ <?xml version="1.0"?> <tool_dependency> <package name="ghostscript" version="9.10"> - <repository changeset_revision="a285e78179bd" name="package_ghostscript_9_10" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu/" /> + <repository changeset_revision="a285e78179bd" name="package_ghostscript_9_10" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="graphicsmagick" version="1.3.20"> - <repository changeset_revision="d87c457bbbc2" name="package_graphicsmagick_1_3_20" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu/" /> + <repository changeset_revision="d87c457bbbc2" name="package_graphicsmagick_1_3_20" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <readme> Only Admins can use this tool generator but please do NOT install on a public facing Galaxy as it exposes unrestricted scripting as your Galaxy user |