create_workflow_xml

#!/usr/bin/python

# See file COPYING distributed with the xnnppx package for the copyright 
# and license.

import sys
import os
try:
    import yaml
    have_yaml = True
except:
    have_yaml = False
import xml.dom.minidom

def create_simple_element(doc, name, value):
    element = doc.createElement(name)
    element.appendChild(doc.createTextNode(value))
    return element

base_xml = """<?xml version="1.0" encoding="UTF-8"?>
<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">
</Pipeline>
"""

progname = os.path.basename(sys.argv.pop(0))

if len(sys.argv) == 0 or len(sys.argv) > 2:
    print
    print 'usage: %s <source file> [output file]' % progname
    print
    print 'source file may be python or YAML (if available)'
    print
    sys.exit(1)

in_fname = sys.argv.pop(0)

try:
    data = open(in_fname).read()
except IOError, data:
    sys.stderr.write('%s: %s\n' % (progname, str(data)))
    sys.exit(1)

try:
    info = eval(data)
except SyntaxError:
    if have_yaml:
        try:
            info = yaml.load(data)
        except yaml.scanner.ScannerError:
            sys.stderr.write("%s: couldn't interpret data in %s\n" % (progname, in_fname))
            sys.exit(1)
    else:
        sys.stderr.write("%s: couldn't interpret data in %s\n" % (progname, in_fname))
        sys.exit(1)

doc = xml.dom.minidom.parseString(base_xml)
pn = doc.getElementsByTagName('Pipeline')[0]

pn.appendChild(create_simple_element(doc, 'name', info['name']))
pn.appendChild(create_simple_element(doc, 'location', info['location']))
pn.appendChild(create_simple_element(doc, 'description', info['description']))

documentation = doc.createElement('documentation')
pn.appendChild(documentation)

if info.has_key('authors'):
    authors = doc.createElement('authors')
    for fullname in info['authors']:
        a = doc.createElement('author')
        (lastname, firstname) = fullname.split(',', 1)
        a.appendChild(create_simple_element(doc, 'lastname', lastname))
        a.appendChild(create_simple_element(doc, 'firstname', firstname))
        authors.appendChild(a)
    documentation.appendChild(authors)

if info.has_key('version'):
    documentation.appendChild(create_simple_element(doc, 'version', info['version']))

if info.has_key('input-parameters'):
    input_parameters = doc.createElement('input-parameters')
    for ip_d in info['input-parameters']:
        ip = doc.createElement('parameter')
        ip.appendChild(create_simple_element(doc, 'name', ip_d['name']))
        vals = doc.createElement('values')
        if ip_d['values'][0] == 's':
            vals.appendChild(create_simple_element(doc, 'schemalink', ip_d['values'][1]))
        elif ip_d['values'][0] == 'v':
            vals.appendChild(create_simple_element(doc, 'csv', ip_d['values'][1]))
        else:
            sys.stderr.write('%s: bad value type \"%s\"\n' % (progname, ip_d['values'][0]))
            sys.exit(1)
        ip.appendChild(vals)
        ip.appendChild(create_simple_element(doc, 'description', ip_d['description']))
        input_parameters.appendChild(ip)
    documentation.appendChild(input_parameters)

if info.has_key('appliesTo'):
    applies_to = doc.createElement('xnatInfo')
    applies_to.setAttribute('appliesTo', info['appliesTo'])
    pn.appendChild(applies_to)

parameters = doc.createElement('parameters')
pn.appendChild(parameters)
steps = doc.createElement('steps')
pn.appendChild(steps)
step = doc.createElement('step')
step.setAttribute('id', '0')
step.setAttribute('description', 'bogus step for validation')
steps.appendChild(step)

if sys.argv:
    try:
        fo = open(sys.argv[0], 'w')
        fo.write(doc.toxml())
        fo.close()
    except IOError, data:
        sys.stderr.write('%s: %s\n' % (progname, str(data)))
        sys.exit(1)
else:
    print doc.toxml()

sys.exit(0)

# eof