def do_cgi():
"""
This is called when the script is run as a cgi script.
"""
# get the fields sent by the browser
fs = cgi.FieldStorage()
# start writing a response
out = StringIO()
# initialize the header dictionary
header_dict = {}
# get some environment variables from the cgi
document_root = os.getenv('DOCUMENT_ROOT')
script_filename = os.getenv('SCRIPT_FILENAME')
# try to generate some useful data to send to the user
try:
if not list(fs):
# if the page was called with no arguments then show a directory html page
doc_directory = os.path.join(document_root, 'phydoc')
header_dict['Content-Type'] = 'text/html'
write_directory_html(script_directory, doc_directory, out)
else:
# the page was called with arguments so get a response from the module
scriptid = fs.getfirst('myscript')
if not scriptid:
raise DispatchError('no script snippet was specified')
if not re.match(r'^\d{8}[a-zA-Z]$', scriptid):
raise DispatchError(
'the specified script name did not meet the format requirements'
)
try:
module = __import__(
scriptid, globals(), locals(),
['__doc__', 'handler', 'get_form', 'get_response'])
except ImportError:
raise DispatchError('the script could not be imported')
# process the module differently depending on its type
if hasattr(module, 'get_form') and hasattr(module, 'get_response'):
# This is the more advanced dispatch method.
# Determine whether we are asking for a form or for a response.
if len(fs.keys()) == 1:
# send a form
form_html = module.get_form()
header_dict['Content-Type'] = 'text/html'
print >> out, '<html>'
title = SnippetUtil.docstring_to_title(module.__doc__)
if title:
print >> out, '<head>'
print >> out, '<title>'
print >> out, title
print >> out, '</title>'
print >> out, '</head>'
print >> out, '<body>'
print >> out, SnippetUtil.docstring_to_html(module.__doc__)
print >> out, '<br/><br/>'
print >> out, '<form method="post">'
print >> out, '<input type="hidden" name="myscript" value="%s"/>' % scriptid
print >> out, form_html
print >> out, '<br/><br/>'
print >> out, '<input type="submit" name="mysubmit" value="Submit"/><br/>'
print >> out, '</form>'
print >> out, '</body>'
print >> out, '</html>'
else:
content_info, content_text = module.get_response(fs)
header_dict.update(content_info)
out.write(content_text)
else:
raise DispatchError(
'no web interface was found for this script')
except (DirectoryError, DispatchError, HandlingError), e:
header_dict['Content-Type'] = 'text/plain'
print >> out, 'Error:', e
print >> out, 'S:'
print >> out, S
print >> out
print >> out, 'pseudoinverse of S:'
print >> out, S_pinv
print >> out
return out.getvalue().strip()
def get_response_content(fs):
return process(fs.ntaxa) + '\n'
def get_ordered_ids(tree):
"""
Maybe I could use postorder here instead.
@param tree: a tree
@return: a list of ids beginning with the leaves
"""
ordered_ids = []
ordered_ids.extend(id(node) for node in tree.gen_tips())
ordered_ids.extend(id(node) for node in tree.gen_internal_nodes())
return ordered_ids
def main(args):
print process(args.ntaxa)
if __name__ == '__main__':
parser = argparse.ArgumentParser(description=SnippetUtil.docstring_to_title(__doc__))
parser.add_argument('--ntaxa', type=int, default=5, help='number of taxa in the tree')
args = parser.parse_args()
main(args)
def handler(req):
"""
If no arguments were provided then display the directory of scripts.
Otherwise if a valid myscript identifier was provided then dispatch the request to the script.
Otherwise show an error message.
"""
try:
field_storage = mod_python.util.FieldStorage(req)
scriptid = field_storage.getfirst('myscript')
if not req.args:
# if the page was called with no arguments then show a directory html page
try:
script_directory = get_script_directory(req)
doc_directory = os.path.join(get_doc_root(req), 'phydoc')
except DirectoryError as e:
req.content_type = "text/plain"
print >> req, 'Error:', e
else:
req.content_type = "text/html"
page_buffer = StringIO()
write_directory_html(script_directory, doc_directory,
page_buffer)
req.write(page_buffer.getvalue())
else:
# the page was called with arguments so get a response from the module
if not scriptid:
raise DispatchError('no script snippet was specified')
if not re.match(r'^\d{8}[a-zA-Z]$', scriptid):
raise DispatchError(
'the specified script name did not meet the format requirements'
)
try:
module = __import__(
scriptid, globals(), locals(),
['__doc__', 'handler', 'get_form', 'get_response'])
except ImportError:
raise DispatchError('the script could not be imported')
# process the module differently depending on its type
if hasattr(module, 'get_form') and hasattr(module, 'get_response'):
# This is the more advanced dispatch method.
# Determine whether we are asking for a form or for a response.
if len(field_storage.keys()) == 1:
# send a form
form_html = module.get_form()
req.content_type = "text/html"
print >> req, '<html>'
title = SnippetUtil.docstring_to_title(module.__doc__)
if title:
print >> req, '<head>'
print >> req, '<title>'
print >> req, title
print >> req, '</title>'
print >> req, '</head>'
print >> req, '<body>'
print >> req, SnippetUtil.docstring_to_html(module.__doc__)
print >> req, '<br/><br/>'
print >> req, '<form method="post">'
print >> req, '<input type="hidden" name="myscript" value="%s"/>' % scriptid
print >> req, form_html
print >> req, '<br/><br/>'
print >> req, '<input type="submit" name="mysubmit" value="Submit"/><br/>'
print >> req, '</form>'
print >> req, '</body>'
print >> req, '</html>'
else:
content_info, content_text = module.get_response(
field_storage)
for key, value in content_info:
if key == 'Content-Type':
req.content_type = value
else:
req.headers_out[key] = value
req.write(content_text)
else:
raise DispatchError(
'no web interface was found for this script')
except DispatchError as e:
req.content_type = "text/plain"
print >> req, 'Error:', e
except HandlingError as e:
req.content_type = "text/plain"
print >> req, 'Error:', e
# pretend everything is OK
return mod_python.apache.OK
def index(self):
out = StringIO()
self._init_form()
form_html = Form.get_html_string(self.form_objects)
print >> out, '<html>'
print >> out, '<head>'
title = SnippetUtil.docstring_to_title(self.module.__doc__)
if title:
print >> out, '<title>'
print >> out, title
print >> out, '</title>'
print >> out, FormHeaderJs.get_header_script_text(
self.form_objects, self.form_presets)
print >> out, '</head>'
print >> out, '<body>'
lines = smallutil.get_stripped_lines(StringIO(self.module.__doc__))
if lines:
print >> out, lines[0]
else:
print >> out, gray_span('untitled')
print >> out, '<br/>'
print >> out, '<code>',
if self.source_link:
relative_link = '../' + self.source_link
print >> out, '<a href="%s">source code</a>' % relative_link
else:
print >> out, gray_span('source code')
print >> out, '</code>'
print >> out, '<br/><br/>'
print >> out
if len(lines) > 1:
print >> out, '<!-- long description -->'
for line in lines[1:]:
print >> out, line
print >> out, '<br/><br/>'
else:
print >> out, '<!-- no long description available -->'
print >> out
print >> out, '<!-- main form -->'
print >> out, '<div style="float: left;">'
print >> out, '<form id="mainform" action="process" method="post">'
if form_html:
print >> out, form_html
print >> out, '<br/><br/>'
print >> out, '<input type="submit" name="submit" value="view"/>'
print >> out, '<input type="submit" name="submit" value="download"/>'
print >> out, '<br/>'
print >> out, '</form>'
print >> out, '</div>'
print >> out
if self.form_presets:
print >> out, '<!-- preset configurations -->'
print >> out, '<div style="float: left;">'
print >> out, '<fieldset>'
print >> out, '<legend>preset configurations</legend>'
button_tags = []
default_preset = Form.get_default_preset(self.form_objects)
for i, preset in enumerate([default_preset] + self.form_presets):
tag = get_preset_button_tag(i, preset.description)
button_tags.append(tag)
print >> out, '<br/>\n'.join(button_tags)
print >> out, '</fieldset>'
print >> out, '</div>'
print >> out
print >> out, '</body>'
print >> out, '</html>'
return out.getvalue().rstrip()
def index(self):
out = StringIO()
self._init_form()
form_html = Form.get_html_string(self.form_objects)
print >> out, '<html>'
print >> out, '<head>'
title = SnippetUtil.docstring_to_title(self.module.__doc__)
if title:
print >> out, '<title>'
print >> out, title
print >> out, '</title>'
print >> out, FormHeaderJs.get_header_script_text(
self.form_objects,
self.form_presets)
print >> out, '</head>'
print >> out, '<body>'
lines = smallutil.get_stripped_lines(StringIO(self.module.__doc__))
if lines:
print >> out, lines[0]
else:
print >> out, gray_span('untitled')
print >> out, '<br/>'
print >> out, '<code>',
if self.source_link:
relative_link = '../' + self.source_link
print >> out, '<a href="%s">source code</a>' % relative_link
else:
print >> out, gray_span('source code')
print >> out, '</code>'
print >> out, '<br/><br/>'
print >> out
if len(lines) > 1:
print >> out, '<!-- long description -->'
for line in lines[1:]:
print >> out, line
print >> out, '<br/><br/>'
else:
print >> out, '<!-- no long description available -->'
print >> out
print >> out, '<!-- main form -->'
print >> out, '<div style="float: left;">'
print >> out, '<form id="mainform" action="process" method="post">'
if form_html:
print >> out, form_html
print >> out, '<br/><br/>'
print >> out, '<input type="submit" name="submit" value="view"/>'
print >> out, '<input type="submit" name="submit" value="download"/>'
print >> out, '<br/>'
print >> out, '</form>'
print >> out, '</div>'
print >> out
if self.form_presets:
print >> out, '<!-- preset configurations -->'
print >> out, '<div style="float: left;">'
print >> out, '<fieldset>'
print >> out, '<legend>preset configurations</legend>'
button_tags = []
default_preset = Form.get_default_preset(self.form_objects)
for i, preset in enumerate([default_preset] + self.form_presets):
tag = get_preset_button_tag(i, preset.description)
button_tags.append(tag)
print >> out, '<br/>\n'.join(button_tags)
print >> out, '</fieldset>'
print >> out, '</div>'
print >> out
print >> out, '</body>'
print >> out, '</html>'
return out.getvalue().rstrip()
def handler(req):
"""
If no arguments were provided then display the directory of scripts.
Otherwise if a valid myscript identifier was provided then dispatch the request to the script.
Otherwise show an error message.
"""
import mod_python
# redirect to the code page if no args were passed
if not req.args:
req.content_type = "text/html"
print >> req, '<head>'
print >> req, '<meta HTTP-EQUIV="REFRESH" content="0; url=/code">'
print >> req, '</head>'
print >> req, '<body></body>'
return mod_python.apache.OK
try:
field_storage = mod_python.util.FieldStorage(req)
scriptid = field_storage.getfirst('myscript')
if not scriptid:
raise DispatchError('no script snippet was specified')
if not re.match(r'^\d{8}[a-zA-Z]$', scriptid):
raise DispatchError(
'the specified script name did not meet the format requirements'
)
try:
module = __import__(
scriptid, globals(), locals(),
['__doc__', 'handler', 'get_form', 'get_response'])
except ImportError:
raise DispatchError('the script could not be imported')
# process the module differently depending on its type
if hasattr(module, 'get_form') and hasattr(module, 'get_response'):
# This is the more advanced dispatch method.
# Get the form data.
form_data = module.get_form()
# Determine whether we are asking for a form or for a response.
if len(field_storage.keys()) == 1:
# the form from the module is either a string or a list of form objects
if type(form_data) is str:
form_html = form_data
else:
form_html = Form.get_html_string(form_data)
req.content_type = str('text/html')
print >> req, '<html>'
title = SnippetUtil.docstring_to_title(module.__doc__)
if title:
print >> req, '<head>'
print >> req, '<title>'
print >> req, title
print >> req, '</title>'
print >> req, '</head>'
print >> req, '<body>'
print >> req, SnippetUtil.docstring_to_html(module.__doc__)
print >> req, '<br/><br/>'
print >> req, '<form method="post">'
print >> req, '<input type="hidden" name="myscript" value="%s"/>' % scriptid
print >> req, form_html
print >> req, '<br/><br/>'
print >> req, '<input type="submit" name="mysubmit" value="Submit"/><br/>'
print >> req, '</form>'
print >> req, '</body>'
print >> req, '</html>'
else:
# possibly parse the field storage data according to the form data
if type(form_data) is not str:
for form_item in form_data:
form_item.process_fieldstorage(field_storage)
# get the response
content_info, content_text = module.get_response(field_storage)
for key, value in content_info:
if key == 'Content-Type':
req.content_type = value
else:
req.headers_out[key] = value
req.write(content_text)
else:
raise DispatchError('no web interface was found for this script')
except ImportError as e:
req.content_type = "text/plain"
print >> req, 'Uncaught ImportError:', e
except DispatchError as e:
req.content_type = "text/plain"
print >> req, 'Error:', e
except HandlingError as e:
req.content_type = "text/plain"
print >> req, 'Error:', e
except Form.FormError as e:
req.content_type = "text/plain"
print >> req, 'Form validation error:', e
# pretend everything is OK
return mod_python.apache.OK
def get_ordered_ids(tree):
"""
Maybe I could use postorder here instead.
@param tree: a tree
@return: a list of ids beginning with the leaves
"""
ordered_ids = []
ordered_ids.extend(id(node) for node in tree.gen_tips())
ordered_ids.extend(id(node) for node in tree.gen_internal_nodes())
return ordered_ids
def main(args):
print process(args.ntaxa, args.nseconds)
if __name__ == '__main__':
parser = argparse.ArgumentParser(
description=SnippetUtil.docstring_to_title(__doc__))
parser.add_argument('--nseconds',
type=int,
default=0,
help='seconds to run or 0 to run until ctrl-c')
parser.add_argument('--ntaxa',
type=int,
default=5,
help='number of taxa in each sampled tree topology')
args = parser.parse_args()
main(args)
def handler(req):
"""
If no arguments were provided then display the directory of scripts.
Otherwise if a valid myscript identifier was provided then dispatch the request to the script.
Otherwise show an error message.
"""
import mod_python
# redirect to the code page if no args were passed
if not req.args:
req.content_type = "text/html"
print >> req, '<head>'
print >> req, '<meta HTTP-EQUIV="REFRESH" content="0; url=/code">'
print >> req, '</head>'
print >> req, '<body></body>'
return mod_python.apache.OK
try:
field_storage = mod_python.util.FieldStorage(req)
scriptid = field_storage.getfirst('myscript')
if not scriptid:
raise DispatchError('no script snippet was specified')
if not re.match(r'^\d{8}[a-zA-Z]$', scriptid):
raise DispatchError('the specified script name did not meet the format requirements')
try:
module = __import__(scriptid, globals(), locals(), ['__doc__', 'handler', 'get_form', 'get_response'])
except ImportError:
raise DispatchError('the script could not be imported')
# process the module differently depending on its type
if hasattr(module, 'get_form') and hasattr(module, 'get_response'):
# This is the more advanced dispatch method.
# Get the form data.
form_data = module.get_form()
# Determine whether we are asking for a form or for a response.
if len(field_storage.keys()) == 1:
# the form from the module is either a string or a list of form objects
if type(form_data) is str:
form_html = form_data
else:
form_html = Form.get_html_string(form_data)
req.content_type = str('text/html')
print >> req, '<html>'
title = SnippetUtil.docstring_to_title(module.__doc__)
if title:
print >> req, '<head>'
print >> req, '<title>'
print >> req, title
print >> req, '</title>'
print >> req, '</head>'
print >> req, '<body>'
print >> req, SnippetUtil.docstring_to_html(module.__doc__)
print >> req, '<br/><br/>'
print >> req, '<form method="post">'
print >> req, '<input type="hidden" name="myscript" value="%s"/>' % scriptid
print >> req, form_html
print >> req, '<br/><br/>'
print >> req, '<input type="submit" name="mysubmit" value="Submit"/><br/>'
print >> req, '</form>'
print >> req, '</body>'
print >> req, '</html>'
else:
# possibly parse the field storage data according to the form data
if type(form_data) is not str:
for form_item in form_data:
form_item.process_fieldstorage(field_storage)
# get the response
content_info, content_text = module.get_response(field_storage)
for key, value in content_info:
if key == 'Content-Type':
req.content_type = value
else:
req.headers_out[key] = value
req.write(content_text)
else:
raise DispatchError('no web interface was found for this script')
except ImportError as e:
req.content_type = "text/plain"
print >> req, 'Uncaught ImportError:', e
except DispatchError as e:
req.content_type = "text/plain"
print >> req, 'Error:', e
except HandlingError as e:
req.content_type = "text/plain"
print >> req, 'Error:', e
except Form.FormError as e:
req.content_type = "text/plain"
print >> req, 'Form validation error:', e
# pretend everything is OK
return mod_python.apache.OK
def do_cgi():
"""
This is called when the script is run as a cgi script.
"""
# get the fields sent by the browser
fs = cgi.FieldStorage()
# start writing a response
out = StringIO()
# initialize the header dictionary
header_dict = {}
# get some environment variables from the cgi
document_root = os.getenv('DOCUMENT_ROOT')
script_filename = os.getenv('SCRIPT_FILENAME')
# try to generate some useful data to send to the user
try:
if not list(fs):
# if the page was called with no arguments then show a directory html page
doc_directory = os.path.join(document_root, 'phydoc')
header_dict['Content-Type'] = 'text/html'
write_directory_html(script_directory, doc_directory, out)
else:
# the page was called with arguments so get a response from the module
scriptid = fs.getfirst('myscript')
if not scriptid:
raise DispatchError('no script snippet was specified')
if not re.match(r'^\d{8}[a-zA-Z]$', scriptid):
raise DispatchError('the specified script name did not meet the format requirements')
try:
module = __import__(scriptid, globals(), locals(), ['__doc__', 'handler', 'get_form', 'get_response'])
except ImportError:
raise DispatchError('the script could not be imported')
# process the module differently depending on its type
if hasattr(module, 'get_form') and hasattr(module, 'get_response'):
# This is the more advanced dispatch method.
# Determine whether we are asking for a form or for a response.
if len(fs.keys()) == 1:
# send a form
form_html = module.get_form()
header_dict['Content-Type'] = 'text/html'
print >> out, '<html>'
title = SnippetUtil.docstring_to_title(module.__doc__)
if title:
print >> out, '<head>'
print >> out, '<title>'
print >> out, title
print >> out, '</title>'
print >> out, '</head>'
print >> out, '<body>'
print >> out, SnippetUtil.docstring_to_html(module.__doc__)
print >> out, '<br/><br/>'
print >> out, '<form method="post">'
print >> out, '<input type="hidden" name="myscript" value="%s"/>' % scriptid
print >> out, form_html
print >> out, '<br/><br/>'
print >> out, '<input type="submit" name="mysubmit" value="Submit"/><br/>'
print >> out, '</form>'
print >> out, '</body>'
print >> out, '</html>'
else:
content_info, content_text = module.get_response(fs)
header_dict.update(content_info)
out.write(content_text)
else:
raise DispatchError('no web interface was found for this script')
except (DirectoryError, DispatchError, HandlingError), e:
header_dict['Content-Type'] = 'text/plain'
print >> out, 'Error:', e
def handler(req):
"""
If no arguments were provided then display the directory of scripts.
Otherwise if a valid myscript identifier was provided then dispatch the request to the script.
Otherwise show an error message.
"""
try:
field_storage = mod_python.util.FieldStorage(req)
scriptid = field_storage.getfirst('myscript')
if not req.args:
# if the page was called with no arguments then show a directory html page
try:
script_directory = get_script_directory(req)
doc_directory = os.path.join(get_doc_root(req), 'phydoc')
except DirectoryError as e:
req.content_type = "text/plain"
print >> req, 'Error:', e
else:
req.content_type = "text/html"
page_buffer = StringIO()
write_directory_html(script_directory, doc_directory, page_buffer)
req.write(page_buffer.getvalue())
else:
# the page was called with arguments so get a response from the module
if not scriptid:
raise DispatchError('no script snippet was specified')
if not re.match(r'^\d{8}[a-zA-Z]$', scriptid):
raise DispatchError('the specified script name did not meet the format requirements')
try:
module = __import__(scriptid, globals(), locals(), ['__doc__', 'handler', 'get_form', 'get_response'])
except ImportError:
raise DispatchError('the script could not be imported')
# process the module differently depending on its type
if hasattr(module, 'get_form') and hasattr(module, 'get_response'):
# This is the more advanced dispatch method.
# Determine whether we are asking for a form or for a response.
if len(field_storage.keys()) == 1:
# send a form
form_html = module.get_form()
req.content_type = "text/html"
print >> req, '<html>'
title = SnippetUtil.docstring_to_title(module.__doc__)
if title:
print >> req, '<head>'
print >> req, '<title>'
print >> req, title
print >> req, '</title>'
print >> req, '</head>'
print >> req, '<body>'
print >> req, SnippetUtil.docstring_to_html(module.__doc__)
print >> req, '<br/><br/>'
print >> req, '<form method="post">'
print >> req, '<input type="hidden" name="myscript" value="%s"/>' % scriptid
print >> req, form_html
print >> req, '<br/><br/>'
print >> req, '<input type="submit" name="mysubmit" value="Submit"/><br/>'
print >> req, '</form>'
print >> req, '</body>'
print >> req, '</html>'
else:
content_info, content_text = module.get_response(field_storage)
for key, value in content_info:
if key == 'Content-Type':
req.content_type = value
else:
req.headers_out[key] = value
req.write(content_text)
else:
raise DispatchError('no web interface was found for this script')
except DispatchError as e:
req.content_type = "text/plain"
print >> req, 'Error:', e
except HandlingError as e:
req.content_type = "text/plain"
print >> req, 'Error:', e
# pretend everything is OK
return mod_python.apache.OK
