diff gd_composite.py @ 0:2c498d40ecde

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gd_composite.py	Mon Apr 09 12:03:06 2012 -0400
@@ -0,0 +1,128 @@
+#!/usr/bin/env python
+
+from galaxy import eggs
+import pkg_resources
+pkg_resources.require( "Cheetah" )
+from Cheetah.Template import Template
+
+import errno
+import os
+from datetime import datetime
+
+################################################################################
+
+def die(message):
+    print >> sys.stderr, message
+    sys.exit(1)
+
+def mkdir_p(path):
+    try:
+        os.makedirs(path)
+    except OSError, e:
+        if e.errno <> errno.EEXIST:
+            raise
+
+################################################################################
+
+class Display(object):
+    def display(self, parameter):
+        print parameter
+
+class DisplayFile(Display):
+    def display(self, parameter):
+        return '<a href="{0}">{1}</a>'.format(parameter.value, parameter.name)
+
+class DisplayValue(Display):
+    def display(self, parameter):
+        if parameter.value is not None:
+            return '{0}: {1}'.format(parameter.description, parameter.value)
+        else:
+            return '{0}'.format(parameter.description)
+
+class DisplayTagList(Display):
+    def display(self, parameter):
+        rv = []
+        if parameter.name:
+            rv.append(parameter.name)
+        rv.append('<ol>')
+        for tag in parameter.value:
+            col, individual_name = tag.split(':')
+            rv.append('<li>{0}</li>'.format(individual_name))
+        rv.append('</ol>')
+        return '\n'.join(rv)
+
+class DisplayPopulationList(Display):
+    def display(self, parameter):
+        rv = []
+        rv.append('Populations')
+        rv.append('<ul>')
+        for population in parameter.value:
+            rv.append('<li>')
+            if population.name is not None:
+                rv.append(population.name)
+            rv.append('<ol>')
+            for name in population.individual_names():
+                rv.append('<li>{0}</li>'.format(name))
+            rv.append('</ol>')
+            rv.append('</li>')
+        rv.append('</ul>')
+        return '\n'.join(rv)
+
+#    def display(self, parameter, name=''):
+#        print '<ul> {0}'.format(name)
+#        for individual_name in parameter.individual_names():
+#            print '<li>{0}>/li>'.format(individual_name)
+#        print '</ul>'
+        
+        
+class Parameter(object):
+    def __init__(self, name=None, value=None, description=None, display_type=None):
+        self.name = name
+        self.value = value
+        self.description = description
+        if display_type is None:
+            self.display_type = Display()
+        else:
+            self.display_type = display_type
+
+    def display(self):
+        return self.display_type.display(self)
+
+class InfoPage(object):
+    _realpath = os.path.realpath(__file__)
+    _script_dir = os.path.dirname(_realpath)
+    template_file = os.path.join(_script_dir, 'gd_composite_template.html')
+    def __init__(self):
+        self.timestamp = datetime.now().strftime('%Y-%m-%d %I:%M:%S %p')
+        self.title = 'Genome Diversity Composite Dataset'
+        self.inputs = []
+        self.outputs = []
+        self.misc = ''
+        self.template = self.load_template()
+
+    def load_template(self):
+        with open(self.template_file) as f:
+            return f.read().rstrip('\r\n')
+
+    def set_title(self, title):
+        self.title = title
+
+    def add_input_parameter(self, parameter):
+        self.inputs.append(parameter)
+
+    def add_output_parameter(self, parameter):
+        self.outputs.append(parameter)
+
+    def add_misc(self, misc):
+        self.misc = misc
+
+    def render(self):
+        return Template(self.template, searchList=[{'tool': self}])
+        
+
+            
+
+
+
+
+