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chaselgrovechaselgrove
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workflow xml creator and example file
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‎create_workflow_xml‎

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#!/usr/bin/python
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# See file COPYING distributed with the xnnppx package for the copyright
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# and license.
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import sys
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import os
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try:
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import yaml
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have_yaml = True
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except:
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have_yaml = False
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import xml.dom.minidom
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def create_simple_element(doc, name, value):
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element = doc.createElement(name)
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element.appendChild(doc.createTextNode(value))
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return element
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base_xml = """<?xml version="1.0" encoding="UTF-8"?>
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<Pipeline xmlns="http://nrg.wustl.edu/pipeline" xmlns:xi="http://www.w3.org/2001/XInclude" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://nrg.wustl.edu/pipeline ..\schema\pipeline.xsd" xmlns:fileUtils="http://www.xnat.org/java/org.nrg.imagingtools.utils.FileUtils">
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</Pipeline>
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"""
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progname = os.path.basename(sys.argv.pop(0))
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if len(sys.argv) == 0 or len(sys.argv) > 2:
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print
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print 'usage: %s <source file> [output file]' % progname
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print
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print 'source file may be python or YAML (if available)'
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print
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sys.exit(1)
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in_fname = sys.argv.pop(0)
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try:
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data = open(in_fname).read()
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except IOError, data:
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sys.stderr.write('%s: %s\n' % (progname, str(data)))
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sys.exit(1)
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try:
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info = eval(data)
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except SyntaxError:
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if have_yaml:
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try:
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info = yaml.load(data)
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except yaml.scanner.ScannerError:
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sys.stderr.write("%s: couldn't interpret data in %s\n" % (progname, in_fname))
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sys.exit(1)
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else:
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sys.stderr.write("%s: couldn't interpret data in %s\n" % (progname, in_fname))
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sys.exit(1)
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doc = xml.dom.minidom.parseString(base_xml)
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pn = doc.getElementsByTagName('Pipeline')[0]
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pn.appendChild(create_simple_element(doc, 'name', info['name']))
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pn.appendChild(create_simple_element(doc, 'location', info['location']))
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pn.appendChild(create_simple_element(doc, 'description', info['description']))
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documentation = doc.createElement('documentation')
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pn.appendChild(documentation)
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if info.has_key('authors'):
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authors = doc.createElement('authors')
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for fullname in info['authors']:
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a = doc.createElement('author')
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(lastname, firstname) = fullname.split(',', 1)
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a.appendChild(create_simple_element(doc, 'lastname', lastname))
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a.appendChild(create_simple_element(doc, 'firstname', firstname))
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authors.appendChild(a)
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documentation.appendChild(authors)
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if info.has_key('version'):
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documentation.appendChild(create_simple_element(doc, 'version', info['version']))
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if info.has_key('input-parameters'):
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input_parameters = doc.createElement('input-parameters')
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for ip_d in info['input-parameters']:
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ip = doc.createElement('parameter')
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ip.appendChild(create_simple_element(doc, 'name', ip_d['name']))
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vals = doc.createElement('values')
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if ip_d['values'][0] == 's':
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vals.appendChild(create_simple_element(doc, 'schemalink', ip_d['values'][1]))
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elif ip_d['values'][0] == 'v':
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vals.appendChild(create_simple_element(doc, 'csv', ip_d['values'][1]))
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else:
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sys.stderr.write('%s: bad value type \"%s\"\n' % (progname, ip_d['values'][0]))
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sys.exit(1)
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ip.appendChild(vals)
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ip.appendChild(create_simple_element(doc, 'description', ip_d['description']))
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input_parameters.appendChild(ip)
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documentation.appendChild(input_parameters)
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if info.has_key('appliesTo'):
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applies_to = doc.createElement('xnatInfo')
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applies_to.setAttribute('appliesTo', info['appliesTo'])
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pn.appendChild(applies_to)
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parameters = doc.createElement('parameters')
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pn.appendChild(parameters)
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steps = doc.createElement('steps')
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pn.appendChild(steps)
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step = doc.createElement('step')
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step.setAttribute('id', '0')
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step.setAttribute('description', 'bogus step for validation')
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steps.appendChild(step)
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if sys.argv:
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try:
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fo = open(sys.argv[0], 'w')
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fo.write(doc.toxml())
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fo.close()
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except IOError, data:
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sys.stderr.write('%s: %s\n' % (progname, str(data)))
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sys.exit(1)
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else:
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print doc.toxml()
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sys.exit(0)
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# eof

‎recon_all.info‎

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{'name': 'recon_all',
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'description': 'freesurfer recon-all',
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'location': '/home/vmuser/xnat/pipeline/catalog/candi-store',
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'authors': ['Haselgrove, Christian'],
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'version': '0.1',
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'appliesTo': 'xnat:mrSessionData',
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'input-parameters': [
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{'name': 'session', 'values': ('s', 'xnat:experimentData/ID'), 'description': 'Experiment ID'},
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{'name': 'sessionLabel', 'values': ('s', 'xnat:experimentData/label'), 'description': 'Session Label'},
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{'name': 'xnat_project', 'values': ('s', 'xnat:experimentData/project'), 'description': 'Project ID'}
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]
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}

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