def get_form():
"""
@return: the body of a form
"""
# define the default tree string
tree = NewickIO.parse(g_default_string, FelTree.NewickTree)
formatted_tree_string = NewickIO.get_narrow_newick_string(tree, 60)
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree', formatted_tree_string),
Form.RadioGroup('matrix', 'nodes used for the distance matrix', [
RadioItem('standard', 'tips only', True),
RadioItem('augmented', 'all nodes'),
RadioItem('named', 'all named nodes')
]),
Form.CheckGroup('output_options', 'output options', [
CheckItem('show_split', 'exact criterion partition', True),
CheckItem('show_value', 'exact criterion value', True),
CheckItem('show_value_minus_trace',
'exact criterion value minus trace', True),
CheckItem('show_fiedler_split', 'show the spectral sign partition',
True),
CheckItem('show_fiedler_eigenvector',
'show the eigenvector of interest', True),
CheckItem('show_labels', 'ordered labels', True),
CheckItem('show_distance_matrix', 'distance matrix', True),
CheckItem('show_M_matrix', 'M matrix', True)
])
]
return form_objects
def get_presets():
presets = [
Form.Preset('a puzzle from the internet', {'sudoku': g_grid_hard}),
Form.Preset('a 17 clue puzzle', {'sudoku': g_grid_min_1}),
Form.Preset('tricky by Arto Inkala', {'sudoku': g_grid_arto_inkala}),
]
return presets
def get_form():
"""
@return: the body of a form
"""
# define the default newick tree
tree_string = '((((a:.05, b:.05)L1:.15, c:.2)L2:.8, x:1)L3:.5, (((m:.05, n:.05)R1:.15, p:.2)R2:.8, y:1)R3:.5)root;'
tree = Newick.parse(tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# define the default rate matrix and its ordered states
R = np.array([[-.3, .1, .1, .1], [.1, -.3, .1, .1], [.1, .1, -.3, .1],
[.1, .1, .1, -.3]])
ordered_states = list('ACGT')
# define the default leaf state assigments
leaf_assignment_lines = [
'a : A', 'b : A', 'c : A', 'x : A', 'm : C', 'n : C', 'p : C', 'y : C'
]
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree with branch lengths',
formatted_tree_string),
Form.Matrix('rate_matrix', 'rate matrix', R,
MatrixUtil.assert_rate_matrix),
Form.MultiLine('states', 'ordered states', '\n'.join(ordered_states)),
Form.MultiLine('assignments', 'leaf states',
'\n'.join(leaf_assignment_lines))
]
return form_objects
def main():
if len(sys.argv) < 2:
raise UsageError('not enough args')
script_name, module_name = sys.argv[:2]
if not re.match(g_module_name_pattern, module_name):
raise UsageError('expected the first arg to be a module name')
usermod = __import__(module_name, globals(), locals(), [], -1)
form_objects = usermod.get_form()
if '--help' in sys.argv:
print usermod.__doc__
print Form.get_help_string(form_objects)
return
else:
d_in = argv_to_dict(sys.argv)
d_out = {}
for obj in form_objects:
if not obj.web_only():
obj.process_cmdline_dict(d_in, d_out)
args = dict_to_args(d_out)
args.submit = 'download'
if hasattr(usermod, 'get_response_content'):
content = usermod.get_response_content(args)
else:
deprecated_header_pairs, content = usermod.get_response(args)
output_filename_for_galaxy = get_output_filename_for_galaxy(sys.argv)
if output_filename_for_galaxy:
with open(output_filename_for_galaxy, 'w') as fout:
fout.write(content)
elif '--write_to_file_for_mobyle' in sys.argv:
form_out = usermod.get_form_out()
filename = form_out.get_filename(args)
with open(filename, 'w') as fout:
fout.write(content)
else:
sys.stdout.write(content)
def get_form():
"""
@return: the body of a form
"""
# define some default data
column_info_list = (ColumnData('TMEM195', 279, 'F',
'L'), ColumnData('SHANK3', 552, 'R', 'W'),
ColumnData('ARHGAP6', 76, 'G',
'D'), ColumnData('GRPR', 261, 'R', 'L'),
ColumnData('DRP2', 203, 'T',
'M'), ColumnData('PLXNB3', 981, 'R', 'H'))
data_lines = [str(info) for info in column_info_list]
# define the default wild and mutant amino acids
wild_string = ''.join(info.wild for info in column_info_list)
mutant_string = ''.join(info.mutant for info in column_info_list)
# define the form objects
form_objects = [
Form.MultiLine('mapp', 'MAPP output', g_mapp_output.strip()),
Form.MultiLine('headers', 'alignment column headers',
'\n'.join(data_lines)),
Form.SingleLine('wild', 'wild type amino acids', wild_string),
Form.SingleLine('mutant', 'mutant amino acids', mutant_string),
Form.ImageFormat()
]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# format the default tree string
tree = Newick.parse(g_default_tree, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# make a real distance matrix
D_s = [line.split() for line in g_default_D_lines]
D_default = np.array([[float(x) for x in row] for row in D_s])
# define the form objects
form_objects = [
Form.MultiLine('test_tree', 'harmonic extension tree',
formatted_tree_string),
Form.Matrix('D', 'leaf distance matrix', D_default,
MatrixUtil.assert_symmetric),
Form.MultiLine('names', 'ordered leaf names',
'\n'.join(g_default_leaf_names)),
Form.Float('scale',
'scale the image of the tree by this factor',
200.0,
low_exclusive=0.0),
Form.ImageFormat()
]
return form_objects
def get_presets():
return [
Form.Preset(
'a mutation probably happened', {
'ngenerations': '10',
'selection_param': '2.0',
'mutation_param': '0.0001',
'recombination_param': '0.001',
'initial_state': '1111\n0000\n',
'final_state': '0101\n0101\n'
}),
Form.Preset(
'a mutation must have happened', {
'ngenerations': '10',
'selection_param': '2.0',
'mutation_param': '0.0001',
'recombination_param': '0.001',
'initial_state': '1111\n0001\n',
'final_state': '1100\n0011\n'
}),
Form.Preset(
'identical endpoints', {
'ngenerations': '10',
'selection_param': '2.0',
'mutation_param': '0.0001',
'recombination_param': '0.001',
'initial_state': '1111\n1111\n',
'final_state': '1111\n1111\n'
}),
]
def main():
if len(sys.argv) < 2:
raise UsageError('not enough args')
script_name, module_name = sys.argv[:2]
if not re.match(g_module_name_pattern, module_name):
raise UsageError('expected the first arg to be a module name')
usermod = __import__(module_name, globals(), locals(), [], -1)
form_objects = usermod.get_form()
if '--help' in sys.argv:
print usermod.__doc__
print Form.get_help_string(form_objects)
return
else:
d_in = argv_to_dict(sys.argv)
d_out = {}
for obj in form_objects:
if not obj.web_only():
obj.process_cmdline_dict(d_in, d_out)
args = dict_to_args(d_out)
args.submit = 'download'
if hasattr(usermod, 'get_response_content'):
content = usermod.get_response_content(args)
else:
deprecated_header_pairs, content = usermod.get_response(args)
output_filename_for_galaxy = get_output_filename_for_galaxy(sys.argv)
if output_filename_for_galaxy:
with open(output_filename_for_galaxy, 'w') as fout:
fout.write(content)
elif '--write_to_file_for_mobyle' in sys.argv:
form_out = usermod.get_form_out()
filename = form_out.get_filename(args)
with open(filename, 'w') as fout:
fout.write(content)
else:
sys.stdout.write(content)
def get_form():
"""
@return: the body of a form
"""
form_objects = [
Form.Float('plot_width',
'plot width in tikz units',
'4',
low_exclusive=0,
high_exclusive=20),
Form.Float('plot_height',
'plot height in tikz units',
'6',
low_exclusive=0,
high_exclusive=20),
Form.Float('t_max', 'max time', '5', low_exclusive=0),
Form.FloatInterval('p_low',
'p_high',
'proportion interval',
'0.6',
'0.8',
low_exclusive=0.25,
high_exclusive=1),
Form.TikzFormat()
]
return form_objects
def _render_content(self):
txt = "<h1>General Settings</h1>"
txt += "<h2>Networking</h2>"
table = TableProps()
self.AddPropEntry(table, 'Port', 'server!port', NOTE_PORT)
self.AddPropEntry(table, 'Port TLS', 'server!port_tls', NOTE_PORT_TLS)
self.AddPropCheck(table, 'IPv6', 'server!ipv6', True, NOTE_IPV6)
self.AddPropEntry(table, 'Listen', 'server!listen', NOTE_LISTEN)
txt += self.Indent(table)
txt += "<h2>Basic Behavior</h2>"
table = TableProps()
self.AddPropEntry(table, 'Timeout (<i>secs</i>)', 'server!timeout',
NOTE_TIMEOUT)
self.AddPropOptions_Reload(table, 'Server Tokens',
'server!server_tokens', PRODUCT_TOKENS,
NOTE_TOKENS)
txt += self.Indent(table)
txt += "<h2>Server Permissions</h2>"
table = TableProps()
self.AddPropEntry(table, 'User', 'server!user', NOTE_USER)
self.AddPropEntry(table, 'Group', 'server!group', NOTE_GROUP)
self.AddPropEntry(table, 'Chroot', 'server!chroot', NOTE_CHROOT)
txt += self.Indent(table)
form = Form("/%s" % (self._id), add_submit=False)
return form.Render(txt, DEFAULT_SUBMIT_VALUE)
def get_form():
"""
@return: the body of a form
"""
form_objects = [
Form.RadioGroup('leaf_options', 'number of leaves', [
RadioItem('six_leaves', '6', True),
RadioItem('seven_leaves', '7')]),
Form.CheckGroup('requirements', 'requirements', [
CheckItem('invalid_dendrogram',
'the topology of the naive dendrogram must be incorrect',
True),
CheckItem('informative_children',
'splits of the child trees must be informative',
True),
CheckItem('force_difference',
'full graph split must differ from Schur graph split',
False),
CheckItem('informative_full_split',
'full graph split must be informative', False)]),
Form.CheckGroup('sampling_options', 'branch length sampling', [
CheckItem('allow_integers',
'allow single digit integer branch lengths', True),
CheckItem('allow_reciprocals',
'allow reciprocal single digit integer branch lengths',
False)])]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# define the tree string
tree = Newick.parse(g_tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# define the default tip data lines
default_tip_data_lines = [
'a : A',
'b : A',
'c : C',
'd : T',
'e : T',
'f : T']
# define the default rate matrix lines
R = np.array([
[-1, 1/3.0, 1/3.0, 1/3.0],
[1/3.0, -1, 1/3.0, 1/3.0],
[1/3.0, 1/3.0, -1, 1/3.0],
[1/3.0, 1/3.0, 1/3.0, -1]])
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree', formatted_tree_string),
Form.MultiLine('column', 'tip data',
'\n'.join(default_tip_data_lines)),
Form.Matrix('matrix', 'rate matrix',
R, MatrixUtil.assert_rate_matrix),
Form.ImageFormat()]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# define the default tree string
tree_string = Newick.brown_example_tree
tree = Newick.parse(tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# define the default alignment string
default_alignment_string = Fasta.brown_example_alignment.strip()
# define the default nucleotide distribution weights
default_nt_lines = ['A : 1', 'C : 1', 'G : 1', 'T : 1']
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree', formatted_tree_string),
Form.MultiLine('alignment', 'nucleotide alignment',
default_alignment_string),
Form.MultiLine('weights', 'nucleotide weights',
'\n'.join(default_nt_lines)),
Form.Float('kappa',
'transition transversion rate ratio',
2,
low_inclusive=0)
]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# define the default tree lines
default_tree_lines = [
'(((a:0.05, b:0.05):0.15, c:0.2):0.8, x:1.0, (((m:0.05, n:0.05):0.15, p:0.2):0.8, y:1.0):1.0);',
'(a:1.062, c:0.190, (d:1.080, b:2.30):2.112);',
'((d:0.083, b:0.614):0.150, e:0.581, (c:1.290, a:0.359):1.070);',
'((b:1.749, d:0.523):0.107, e:1.703, (a:0.746, c:0.070):4.025);'
]
# define the list of form objects
form_objects = [
Form.MultiLine('trees', 'newick trees (one tree per line)',
'\n'.join(default_tree_lines)),
Form.Float('epsilon', 'non-negligible eigenvalue', '1e-9'),
Form.CheckGroup('options', 'show these tree sets', [
CheckItem('show_all', 'all reconstructed trees', True),
CheckItem('show_incomplete',
'incompletely resolved reconstructed trees', True),
CheckItem('show_conflicting', 'conflicting reconstructed trees',
True),
CheckItem('show_negligible',
'trees with potentially informative but small loadings',
True)
])
]
return form_objects
def get_presets():
return [
Form.Preset(
'fig 1',
{
'N_diploid' : '100',
'nmutants' : '20',
's_values' : ('0', '2.5', '5'),
'h_values' : ('-3', '0', '1', '2'),
}),
Form.Preset(
'fig 2',
{
'N_diploid' : '100',
'nmutants' : '160',
's_values' : ('-1', '0', '1'),
'h_values' : ('2', '3', '5', '7'),
}),
Form.Preset(
'check confounding',
{
'N_diploid' : '200',
'nmutants' : '1',
's_values' : ('1', '2', '4'),
'h_values' : ('0.5', '0.25'),
}),
]
def main():
app = QApplication()
app.setApplicationDisplayName("Function Plotter")
app.setStyle("fusion")
form = Form()
form.show()
sys.exit(app.exec_())
def get_form():
"""
@return: the body of a form
"""
return [
Form.Float('blink_birth', 'tolerance birth rate', '0.01'),
Form.Float('blink_death', 'tolerance death rate', '0.02'),
]
def get_form():
form_objects = [
Form.Integer('nstates', 'number of states', 4, low=2, high=10),
Form.CheckGroup(
'partition_options', 'partition options',
[Form.CheckItem('bipartitioned', 'bipartitioned', True)]),
]
return form_objects
def get_form():
"""
@return: a list of form objects
"""
# sample some points to use as the defaults
M = np.array(list(SpiralSampler.gen_points(200, .01)))
# define the form objects
form_objects = [Form.Matrix('points', 'points', M), Form.ImageFormat()]
return form_objects
def get_form():
"""
@return: the body of a form
"""
form_objects = [
Form.MultiLine('table', 'table', '\n'.join(g_lines)),
Form.ImageFormat()
]
return form_objects
def _render_content(self):
polling_methods = []
for name, desc in POLL_METHODS:
if ((not name) or \
cherokee_has_polling_method (name)):
polling_methods.append((name, desc))
txt = "<h1>Advanced configuration</h1>"
txt += self.Dialog(WARNING, 'warning')
txt += "<h2>Connections management</h2>"
table = TableProps()
self.AddPropCheck(table, 'Keep Alive', 'server!keepalive', True,
NOTE_KEEPALIVE)
self.AddPropEntry(table, 'Max keepalive reqs',
'server!keepalive_max_requests', NOTE_KEEPALIVE_RS)
self.AddPropCheck(table, 'Chunked Encoding', 'server!chunked_encoding',
True, NOTE_CHUNKED)
txt += self.Indent(table)
txt += "<h2>System tweaking</h2>"
table = TableProps()
self.AddPropEntry(table, 'Thread Number', 'server!thread_number',
NOTE_THREAD_NUM)
self.AddPropOptions_Reload(table, 'Thread Policy',
'server!thread_policy', THREAD_POLICY,
NOTE_THREAD)
self.AddPropEntry(table, 'File descriptors', 'server!fdlimit',
NOTE_FD_NUM)
txt += self.Indent(table)
txt += "<h2>Server tweaking</h2>"
table = TableProps()
self.AddPropOptions_Reload(table, 'Polling Method',
'server!poll_method', polling_methods,
NOTE_POLLING)
self.AddPropEntry(table, 'Sendfile min size', 'server!sendfile_min',
NOTE_SENDFILE_MIN)
self.AddPropEntry(table, 'Sendfile max size', 'server!sendfile_max',
NOTE_SENDFILE_MAX)
self.AddPropEntry(table, 'Panic action', 'server!panic_action',
NOTE_PANIC_ACTION)
self.AddPropEntry(table, 'PID file', 'server!pid_file', NOTE_PID_FILE)
txt += self.Indent(table)
txt += "<h2>Server behavior</h2>"
table = TableProps()
self.AddPropEntry(table, 'Listening queue length',
'server!listen_queue', NOTE_LISTEN_Q)
self.AddPropEntry(table, 'Reuse connections',
'server!max_connection_reuse', NOTE_REUSE_CONNS)
self.AddPropEntry(table, 'Log flush time', 'server!log_flush_elapse',
NOTE_FLUSH_TIME)
txt += self.Indent(table)
form = Form("/%s" % (self._id), add_submit=False)
return form.Render(txt, DEFAULT_SUBMIT_VALUE)
def get_form():
"""
@return: the body of a form
"""
form_objects = [
Form.Float('scaling_factor', 'scaling factor', 1.0, low_exclusive=0),
Form.LatexFormat()
]
return form_objects
def get_form():
"""
@return: the body of a form
"""
form_objects = [
Form.MultiLine('table_a', 'first .hud table', '\n'.join(g_a_lines)),
Form.MultiLine('table_b', 'second .hud table', '\n'.join(g_b_lines))
]
return form_objects
def __init__(self):
Form.RadioGroup.__init__(
self, 'kmeans_init', 'cluster center initialization', [
Form.RadioItem('init_choice',
'center on randomly chosen observed points', True),
Form.RadioItem('init_cluster',
'use centroids of a random partition'),
Form.RadioItem('init_range',
'choose centers uniformly in the observed range')])
def get_form():
"""
@return: the body of a form
"""
return [
Form.RadioGroup('mattype', 'predefined rate matrix', [
Form.RadioItem('plain', 'plain 4x4 integer rate matrix', True),
Form.RadioItem('rand', 'random rate matrix'),
]),
]
def get_form():
form_objects = [
Form.IntegerInterval(
'start_pos', 'stop_pos', 'alignment interval',
1, 4263, low=1, high=4263),
Form.Integer('nsteps', 'MCMC steps', 8000, low=1),
Form.SingleLine('alignment_id', 'alignment id', 'alignment'),
Form.SingleLine('mcmc_id', 'mcmc id', 'mcmc'),
]
return form_objects
def get_form():
"""
@return: a list of form objects
"""
# define the form objects
form_objects = [
Form.MultiLine('tree_string', 'newick tree', g_tree_string),
Form.Integer('N', 'tip duplication factor', 10)
]
return form_objects
def get_form():
"""
@return: a list of form objects
"""
# define the form objects
form_objects = [
Form.MultiLine('tree_string', 'newick tree', g_tree_string),
Form.Float('strength', 'duplicate node pair connection strength', 100)
]
return form_objects
def get_form():
"""
@return: the body of a form
"""
return [
Form.Float('theta', 'mutation rate 4*N*mu', '1.0',
low_inclusive=0.001),
Form.Float('Nr', 'recombination rate N*r', '5.0', low_inclusive=0),
Form.Float('Ns', 'selection N*s', '1.0', low_inclusive=0),
]
def get_form():
"""
@return: the body of a form
"""
form_objects = [
Form.Float('ref_length', 'length of the reference branch',
'0.1', low_inclusive=0.0),
Form.Float('child_length', 'length of each child branch',
'0.1', low_inclusive=0.0)]
return form_objects
def get_form():
"""
@return: the body of a form
"""
return [
Form.Integer('nB', 'number of B alleles', 1, low=0),
Form.Integer('nb', 'number of b alleles', 400, low=0),
Form.Float('s', 'positive when B is more fit', 0.01,
low_exclusive=-1),
]
def process_module_name(module_name, bad_modules):
"""
@param module_name: name of the snippet module to try to run
@param bad_modules: a collection of disallowed module names
@return: module, success
"""
module = None
try:
requested_methods = [
'__doc__',
'get_form',
'get_response',
'get_response_content']
module = __import__(module_name, globals(), locals(),
requested_methods)
except Exception as e:
raise SnippetTestError('error importing the snippet: ' + str(e))
if any(hasattr(module, x) for x in bad_modules):
raise SnippetTestError(
'skipping because the snippet imports a disallowed module')
try:
response = module.get_form()
form_body = Form.get_html_string(response)
form_html = '<form>' + form_body + '</form>'
except Exception as e:
raise SnippetTestError('get form: ' + str(e))
# parse the default html parameters from the html string
document = ht.fragment_fromstring(form_html)
html_form = document.forms[0]
html_inputs = html_form.inputs
# create an object that looks like a FieldStorage object
mock_field_storage = MockFieldStorage(html_inputs)
# parse the field storage data according to the form data
try:
for form_item in response:
form_item.process_fieldstorage(mock_field_storage)
except Form.FormError as e:
raise SnippetTestError('default error: ' + str(e))
# get the result of calling the function
# using the default parameter values
if hasattr(module, 'get_response_content'):
try:
response = module.get_response_content(mock_field_storage)
if response is None:
raise SnippetTestError('no response')
except Exception as e:
raise SnippetTestError('get response content: ' + str(e))
else:
return module, True
elif hasattr(module, 'get_response'):
try:
module.get_response(mock_field_storage)
except Exception as e:
raise SnippetTestError('get response: ' + str(e))
else:
return module, True
return module, False
def testmem(sa):
import titlefield
import textbox
import slider
import multiline
while 1:
F = Form(name="Testing")
w = F.add_widget(titlefield.TitleText)
str = "useable space = %s, %s; my height and width is: %s, %s" % (F.useable_space()[0], F.useable_space()[1], w.height, w.width)
w.value = str
w2 = F.add_widget(textbox.Textfield)
str2 = "useable space = %s, %s; my height and width is: %s, %s" % (F.useable_space()[0], F.useable_space()[1], w2.height, w2.width)
w2.value = str2
w3 = F.add_widget(slider.Slider)
#w4 = F.add_widget(multiline.MultiLine, height=5)
F.display()
def _get_cat_4_text(form_objects, presets):
# this complicatedness helps to deal with integer and float intervals
label_object_pairs = []
for obj in form_objects:
obj_items = None
try:
obj_items = obj._get_temp_items()
except AttributeError as e:
pass
if obj_items is None:
obj_items = [obj]
label_object_pairs.extend([(x.label, x) for x in obj_items])
label_to_form_object = dict(label_object_pairs)
# write the javascript using horrific typechecking
out = StringIO()
print >> out, '<!-- these are hardcoded presets -->'
print >> out, '<script type="text/javascript">'
default_preset = Form.get_default_preset(form_objects)
for i, preset in enumerate([default_preset] + presets):
print >> out, 'function on_wsf_preset%d() {' % i
for k, v in preset.d.items():
# check the form object corresponding to this item
# FIXME this is horrible typechecking that is not pythonic
form_object = label_to_form_object[k]
if isinstance(form_object, Form.RadioGroup):
print >> out, 'wsfSetRadio("%s", "%s");' % (k, v)
elif isinstance(form_object, Form.CheckGroup):
js_literal = _collection_to_javascript_literal(v)
print >> out, 'wsfSetChecks("%s", %s);' % (k, js_literal)
elif isinstance(form_object, Form.Sequence):
print >> out, 'wsfSetInner("%s", "%s");' % (k, '\\n'.join(v))
elif isinstance(form_object, Form.MultiLine):
contents = '\\n'.join(v.splitlines())
print >> out, 'wsfSetInner("%s", "%s");' % (k, contents)
elif any([
isinstance(form_object, Form.Integer),
isinstance(form_object, Form.Float),
isinstance(form_object, Form.SingleLine)]):
print >> out, 'wsfSetValue("%s", "%s");' % (k, v)
else:
# assume we want to set the inner html
print >> out, 'wsfSetInner("%s", "%s");' % (k, v)
print >> out, '}'
print >> out, '</script>'
return out.getvalue().rstrip()
def initialize( context ):
import Document
initializeProduct(context, this_module, globals(),
document_module = Document,
document_classes = document_classes,
object_classes = object_classes,
portal_tools = portal_tools,
content_constructors = content_constructors,
content_classes = content_classes)
# Initialise ERP5Form Formulator
FieldRegistry.registerField(ProxyField.ProxyField,
'www/StringField.gif')
FieldRegistry.registerField(DurationField.DurationField,
'www/StringField.gif')
FieldRegistry.registerField(EditorField.EditorField,
'www/TextAreaField.gif')
FieldRegistry.registerField(FormBox.FormBox,
'www/StringField.gif')
FieldRegistry.registerField(POSBox.POSBox,
'www/StringField.gif')
FieldRegistry.registerField(ListBox.ListBox,
'www/StringField.gif')
FieldRegistry.registerField(ReportBox.ReportBox,
'www/StringField.gif')
FieldRegistry.registerField(PlanningBox.PlanningBox,
'www/StringField.gif')
FieldRegistry.registerField(MatrixBox.MatrixBox,
'www/StringField.gif')
FieldRegistry.registerField(RelationField.RelationStringField,
'www/StringField.gif')
FieldRegistry.registerField(MultiRelationField.MultiRelationStringField,
'www/StringField.gif')
FieldRegistry.registerField(ImageField.ImageField,
'www/StringField.gif')
FieldRegistry.registerField(StandardFields.StringField,
'www/StringField.gif')
FieldRegistry.registerField(StandardFields.CheckBoxField,
'www/CheckBoxField.gif')
FieldRegistry.registerField(StandardFields.IntegerField,
'www/IntegerField.gif')
FieldRegistry.registerField(StandardFields.TextAreaField,
'www/TextAreaField.gif')
FieldRegistry.registerField(StandardFields.RawTextAreaField,
'www/TextAreaField.gif')
FieldRegistry.registerField(StandardFields.LinesField,
'www/LinesField.gif')
FieldRegistry.registerField(StandardFields.ListField,
'www/ListField.gif')
FieldRegistry.registerField(StandardFields.MultiListField,
'www/MultiListField.gif')
FieldRegistry.registerField(ParallelListField.ParallelListField,
'www/MultiListField.gif')
FieldRegistry.registerField(StandardFields.RadioField,
'www/RadioField.gif')
FieldRegistry.registerField(StandardFields.MultiCheckBoxField,
'www/MultiCheckBoxField.gif')
FieldRegistry.registerField(StandardFields.PasswordField,
'www/PasswordField.gif')
FieldRegistry.registerField(StandardFields.EmailField,
'www/EmailField.gif')
FieldRegistry.registerField(StandardFields.PatternField,
'www/PatternField.gif')
FieldRegistry.registerField(StandardFields.FloatField,
'www/FloatField.gif')
FieldRegistry.registerField(StandardFields.DateTimeField,
'www/DateTimeField.gif')
FieldRegistry.registerField(StandardFields.FileField,
'www/FileField.gif')
FieldRegistry.registerField(StandardFields.LinkField,
'www/LinkField.gif')
FieldRegistry.registerField(StandardFields.LabelField,
'www/LabelField.gif')
FieldRegistry.registerField(MultiLinkField.MultiLinkField,
'www/LinkField.gif')
FieldRegistry.registerField(InputButtonField.InputButtonField,
'www/StringField.gif')
FieldRegistry.registerField(OOoChart.OOoChart,
'www/StringField.gif')
FieldRegistry.registerField(CaptchaField.CaptchaField,
'www/StringField.gif')
# some helper fields
FieldRegistry.registerField(HelperFields.ListTextAreaField)
FieldRegistry.registerField(HelperFields.MethodField)
FieldRegistry.registerField(HelperFields.TALESField)
import HyperLinkField
FieldRegistry.registerField(HyperLinkField.HyperLinkField,
'www/LinkField.gif')
import VideoField
FieldRegistry.registerField(VideoField.VideoField,
'www/StringField.gif')
import AudioField
FieldRegistry.registerField(AudioField.AudioField,
'www/StringField.gif')
# register help for the product
context.registerHelp()
# register field help for all fields
FieldRegistry.registerFieldHelp(context)
# make Dummy Fields into real fields
FieldRegistry.initializeFields()
# do initialization of Form class to make fields addable
Form.initializeForm(FieldRegistry)
Form.initializeForm(FieldRegistry, form_class=Report.ERP5Report)
# Register FSPDFTemplate icon
registerIcon(PDFTemplate.FSPDFTemplate,
'www/PDF.png', globals())
# Register ProxyField icon
registerIcon(ProxyField.ProxyField,
'www/ProxyField.png', globals())
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 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 initialize(context):
"""Initialize the Formulator product.
"""
# register field classes
FieldRegistry.registerField(StandardFields.StringField,
'www/StringField.gif')
FieldRegistry.registerField(StandardFields.CheckBoxField,
'www/CheckBoxField.gif')
FieldRegistry.registerField(StandardFields.IntegerField,
'www/IntegerField.gif')
FieldRegistry.registerField(StandardFields.TextAreaField,
'www/TextAreaField.gif')
FieldRegistry.registerField(StandardFields.RawTextAreaField,
'www/TextAreaField.gif')
FieldRegistry.registerField(StandardFields.LinesField,
'www/LinesField.gif')
FieldRegistry.registerField(StandardFields.ListField,
'www/ListField.gif')
FieldRegistry.registerField(StandardFields.MultiListField,
'www/MultiListField.gif')
FieldRegistry.registerField(StandardFields.RadioField,
'www/RadioField.gif')
FieldRegistry.registerField(StandardFields.MultiCheckBoxField,
'www/MultiCheckBoxField.gif')
FieldRegistry.registerField(StandardFields.PasswordField,
'www/PasswordField.gif')
FieldRegistry.registerField(StandardFields.EmailField,
'www/EmailField.gif')
FieldRegistry.registerField(StandardFields.PatternField,
'www/PatternField.gif')
FieldRegistry.registerField(StandardFields.FloatField,
'www/FloatField.gif')
FieldRegistry.registerField(StandardFields.DateTimeField,
'www/DateTimeField.gif')
FieldRegistry.registerField(StandardFields.FileField,
'www/FileField.gif')
FieldRegistry.registerField(StandardFields.LinkField,
'www/LinkField.gif')
FieldRegistry.registerField(StandardFields.LabelField,
'www/LabelField.gif')
# some helper fields
FieldRegistry.registerField(HelperFields.ListTextAreaField)
FieldRegistry.registerField(HelperFields.MethodField)
FieldRegistry.registerField(HelperFields.TALESField)
# obsolete field (same as helper; useable but not addable)
FieldRegistry.registerField(StandardFields.RangedIntegerField,
'www/RangedIntegerField.gif')
# register help for the product
context.registerHelp()
# register field help for all fields
FieldRegistry.registerFieldHelp(context)
# register the form itself
context.registerClass(
Form.ZMIForm,
constructors = (Form.manage_addForm,
Form.manage_add),
icon = 'www/Form.gif')
# make Dummy Fields into real fields
FieldRegistry.initializeFields()
# do initialization of Form class to make fields addable
Form.initializeForm(FieldRegistry)
crawler = Crawler.Crawler(start,opener1) print "Scanning..." try: #for each url in queue while crawler.hasNext(): url = crawler.next() print url #display current url soup=crawler.process(root) if not soup: continue; # Process page's forms # i=0 for m in Form.getAllForms(soup): #take all forms wich have action attribute action = uri.buildAction(url,m['action']) if not action in actionDone and action!='': try: formResults=form.prepareFormInputs(m) #get inputs for form m r1 = request(url,action,formResults,opener1) #send request with user1 formResults=form.prepareFormInputs(m) #regenerate data r2 = request(url,action,formResults,opener2) #send same request with user 2 if(len(csrf)>0): if not re.search(csrf, r2): #We got a CSRF! try: print '=CSRF='+"\n\t"+'Name: '+m['name']+"\n\t"+'Action: '+m['action']+"\n\t"+'From: '+url+"\n" except KeyError: print '=CSRF='+"\n\t"+'Action: '+m['action']+"\n\t"+'From: '+url print "\t"+urllib.urlencode(formResults)
