| Previous changeset 9:ce5ec1d989fd (2015-01-14) Next changeset 11:000bb4888c81 (2015-01-15) |
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Commit message:
Uploaded |
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modified:
rgToolFactory2.py |
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| diff -r ce5ec1d989fd -r 8de2b7571d98 rgToolFactory2.py --- a/rgToolFactory2.py Wed Jan 14 19:17:11 2015 -0500 +++ b/rgToolFactory2.py Thu Jan 15 07:35:06 2015 -0500 |
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| b'@@ -7,6 +7,11 @@\n # Licensed under the LGPL\n # suggestions for improvement and bug fixes welcome at https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home\n #\n+# January 2015\n+# in the process of building a complex tool\n+# added ability to choose one of the current toolshed package_r or package_perl or package_python dependencies and source that package\n+# need to add that package to tool_dependencies\n+#\n # sept 2014 added additional params from\n # https://bitbucket.org/mvdbeek/dockertoolfactory/src/d4863bcf7b521532c7e8c61b6333840ba5393f73/DockerToolFactory.py?at=default\n # passing them is complex\n@@ -107,32 +112,6 @@\n \n # if we do html we need these dependencies specified in a tool_dependencies.xml file and referred to in the generated\n # tool xml\n-toolhtmldepskel = """<?xml version="1.0"?>\n-<tool_dependency>\n- <package name="ghostscript" version="9.10">\n- <repository name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" />\n- </package>\n- <package name="graphicsmagick" version="1.3.18">\n- <repository name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" />\n- </package>\n- <readme>\n- %s\n- </readme>\n-</tool_dependency>\n-"""\n-\n-emptytoolhtmldepskel = """<?xml version="1.0"?>\n-<tool_dependency>\n- <readme>\n- %s\n- </readme>\n-</tool_dependency>\n-"""\n-\n-protorequirements = """<requirements>\n- <requirement type="package" version="9.10">ghostscript</requirement>\n- <requirement type="package" version="1.3.18">graphicsmagick</requirement>\n- </requirements>"""\n \n def timenow():\n """return current time as a string\n@@ -188,13 +167,141 @@\n \n class ScriptRunner:\n """class is a wrapper for an arbitrary script\n+ note funky templating. this should all be done proper.\n+ Problem is, this kludge developed quite naturally and seems to work ok with\n+ little overhead...\n+ \n """\n \n+\n def __init__(self,opts=None,treatbashSpecial=True):\n """\n cleanup inputs, setup some outputs\n \n """\n+ \n+ self.toolhtmldepinterpskel = """<?xml version="1.0"?>\n+ <tool_dependency>\n+ <package name="ghostscript" version="9.10">\n+ <repository name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" />\n+ </package>\n+ <package name="graphicsmagick" version="1.3.18">\n+ <repository name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" />\n+ </package>\n+ <package name="%(interpreter)s" version="%(interpreter_version)s">\n+ <repository name="%(interpreter_name)s" owner="%(interpreter_owner)s" prior_installation_required="True" />\n+ </package>\n+ \n+ <readme>\n+ %(readme)s\n+ </readme>\n+ </tool_dependency>\n+ """\n+ \n+ self.toolhtmldepskel = """<?xml version="1.0"?>\n+ <tool_dependency>\n+ <package name="ghostscript" version="9.10">\n+ <repository name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" />\n+ </package>\n+ <package name="graphicsmagick" version="1.3.18">\n+ <repository name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" />\n+ </package>\n+ <readme>\n+ %(readme)s\n+ </readme>\n+ </tool_dependency>\n+ """\n+\n+ self.emptytoolhtmldepskel = """<?xml version="1.0"?>\n+ <tool_dependency>\n+ <readme>\n+ %(readme)s\n+ </readme>\n+ </tool_dependency>\n+ """\n+\n+ self.protorequirements = """<requirements>\n+ <requirement type="package" version="9.10">ghostscript</requirement>\n+ <requirement type="package" version="1.3.18">graphicsmagick</requ'..b'form with default value set to original value\n xdict[\'additionalInputs\'] = \'\\n\'.join([\'<param name="%s" value="%s" label="%s" help="%s" type="%s"/>\' % \\\n (x.split(\',\')[0],html_escape(x.split(\',\')[1]),html_escape(x.split(\',\')[2]),html_escape(x.split(\',\')[3]), x.split(\',\')[4]) for x in self.opts.additional_parameters])\n- xdict[\'additionalParams\'] = \'\\n\'.join([\'<param name="%s" value="%s" />\' % (x.split(\',\')[0],html_escape(x.split(\',\')[1])) for x in self.opts.additional_parameters])\n+ xdict[\'additionalParams\'] = \'\\n\'.join([\'<param name="%s" value="%s" />\' % (x.split(\',\')[0],html_escape(x.split(\',\')[1])) for x in self.opts.additional_parameters])\n+ xdict[\'interpreter_owner\'] = self.interpreter_owner\n+ xdict[\'interpreter_version\'] = self.interpreter_version\n+ xdict[\'interpreter_name\'] = self.interpreter_pack\n xdict[\'requirements\'] = \'\'\n- if self.opts.make_HTML:\n- if self.opts.include_dependencies == "yes":\n- xdict[\'requirements\'] = protorequirements\n+ if self.opts.include_dependencies == "yes":\n+ if self.opts.envshpath <> \'system\':\n+ xdict[\'requirements\'] = self.protorequirements_interpreter % xdict \n+ else: \n+ xdict[\'requirements\'] = self.protorequirements\n xdict[\'tool_version\'] = self.opts.tool_version\n xdict[\'test1HTML\'] = self.test1HTML\n xdict[\'test1Output\'] = self.test1Output\n xdict[\'test1Inputs\'] = self.test1Inputs\n if self.opts.make_HTML and self.opts.output_tab:\n- xdict[\'tooltests\'] = tooltestsBoth % xdict\n+ xdict[\'tooltests\'] = self.tooltestsBoth % xdict\n elif self.opts.make_HTML:\n- xdict[\'tooltests\'] = tooltestsHTMLOnly % xdict\n+ xdict[\'tooltests\'] = self.tooltestsHTMLOnly % xdict\n else:\n- xdict[\'tooltests\'] = tooltestsTabOnly % xdict\n+ xdict[\'tooltests\'] = self.tooltestsTabOnly % xdict\n xdict[\'script\'] = self.escapedScript \n # configfile is least painful way to embed script to avoid external dependencies\n # but requires escaping of <, > and $ to avoid Mako parsing\n@@ -520,7 +579,7 @@\n if self.opts.output_tab:\n xdict[\'command_outputs\'] += \' --output_tab "$output1"\'\n xdict[\'outputs\'] += \' <data format="%s" name="output1" label="${job_name}"/>\\n\' % self.outFormats\n- xdict[\'command\'] = newCommand % xdict\n+ xdict[\'command\'] = self.newCommand % xdict\n if self.opts.citations:\n citationstext = open(self.opts.citations,\'r\').read()\n citation_tuples = parse_citations(citationstext)\n@@ -531,7 +590,7 @@\n xdict[\'citations\'] = citations_xml\n else:\n xdict[\'citations\'] = ""\n- xmls = newXML % xdict\n+ xmls = self.newXML % xdict\n xf = open(self.xmlfile,\'w\')\n xf.write(xmls)\n xf.write(\'\\n\')\n@@ -555,10 +614,15 @@\n hlp = open(self.opts.help_text,\'r\').read()\n else:\n hlp = \'Please ask the tool author for help as none was supplied at tool generation\\n\'\n+ readme_dict = {\'readme\':hlp,\'interpreter\':self.opts.interpreter,\'interpreter_version\':self.interpreter_version,\'interpreter_name\':self.interpreter_pack,\n+ \'interpreter_owner\':self.interpreter_owner}\n if self.opts.include_dependencies == "yes":\n- tooldepcontent = toolhtmldepskel % hlp\n+ if self.opts.envshpath == \'system\':\n+ tooldepcontent = self.toolhtmldepskel % readme_dict\n+ else:\n+ tooldepcontent = self.toolhtmldepinterpskel % readme_dict\n else:\n- tooldepcontent = emptytoolhtmldepskel % hlp\n+ tooldepcontent = self.emptytoolhtmldepskel % readme_dictls -l\n depf = open(os.path.join(tdir,\'tool_dependencies.xml\'),\'w\')\n depf.write(tooldepcontent)\n depf.write(\'\\n\')\n' |