def __init__(self, xml_file, config_file=None):
self.tree = etree.parse(xml_file)
self.cur_form = None
self.doc = None
self.indent_stack = {}
self.logic_parser = LogicParser()
self.to_print = []
if config_file != None:
self.config = ConfigParser()
self.config.read(config_file)
self._indent = True
self.print_const_name=None
def __init__(self, xml_file, config_file=None):
self.tree = etree.parse(xml_file)
self.cur_form = None
self.multiline = True
self.header_box = 'box'
self.all_same_page = False
self.doc = None
self.indent_stack = {}
self.logic_parser = LogicParser()
self.to_print = []
self.print_selected_only = False
if config_file != None:
self.config = ConfigParser()
self.config.read(config_file)
self._indent = True
self.print_const_name = None
class PdfForm(object):
def __init__(self, xml_file, config_file=None):
self.tree = etree.parse(xml_file)
self.cur_form = None
self.multiline = True
self.header_box = 'box'
self.all_same_page = False
self.doc = None
self.indent_stack = {}
self.logic_parser = LogicParser()
self.to_print = []
self.print_selected_only = False
if config_file != None:
self.config = ConfigParser()
self.config.read(config_file)
self._indent = True
self.print_const_name = None
def revert_indent_val(self):
self._indent = not self._indent
def add_constraint_list(self, const_section):
'''If proceessed without running add_constraint_list
then will print all forms and elements in the project.
Arguments:
const_section -- The section in the config_file to use along with
the base seciton
'''
multiline = True
if not self.config:
raise ValueError("self.config is {config}: Please set the config"
" file before adding constraint.".format(config=self.config))
sections = ['base', const_section]
for sec in sections:
if self.config.has_section(sec):
for name, vals in self.config.items(sec):
if name == '__print_name':
#Flag for whether or not the form name should be
#printed at the top of the form
if vals == 'True':
self.print_const_name=const_section
elif name == '__multiline':
# If flase each element is printed on an individual line
# If true as many elements that can fit on a line are
# printed
self.multiline = eval(vals)
elif name == '__all_same_page':
# Print all the forms together on one page
self.all_same_page = eval(vals)
elif name == '__header_box':
#The values to put in the header box
self.header_box = vals
elif name == '__regex_no_print':
# A list of regular expressions. If the regular
# expression match a field name it will not be printed
vals = vals.split(",")
self.logic_parser.add_no_print_regex(vals)
elif name == '__print_selected_only':
# Only print the values that are specified instead of
# all the options
self.print_selected_only = eval(vals)
elif name != '__forms':
# Add parsing Logic constriaints. You designate values
# in the const_* file and only print if conditions are
# met.
self.logic_parser.add_constraint(name, eval(vals))
else:
if sec != 'base':
raise ConstraintError(
'{section} is not in the constraint file.'.format(
section=sec), sec
)
def _get_choices(self, choices):
''' Return a list of valid choices for the current question.
Arguments:
choices -- the string from REDCap data dictionary containing the
choices.
'''
vals = choices.split("\\n")
if len(vals) > 1:
return map(lambda c: c.lstrip(' 0123456789').lstrip(',').strip(' '),
vals)
else:
vals = choices.split("|", 2)
if len(vals) > 1:
return vals
elif len(vals) == 1:
one = re.match("\s?[0-9.-]*\s?,\s?(.*)",vals[0]);
if one:
return [one.group(1)]
return None
def _get_level(self, names):
''' Return the set of all the field names that the current field is
branched under
Arguments:
names -- The branching logic string from the redcap export
'''
vals = re.split(' and | or ', names)
indented_test = []
if vals[0] != '':
for v in vals:
logic = v
long_form = re.search(
'\[([a-z_0-9]*)\](\[[a-z_0-9\(\)]*\][0-9 \'=]*)', v)
if long_form:
v = long_form.group(2)
word = re.search('\[([a-z_0-9\(\)]*)\]([0-9 \'=]*)', v)
if word != None:
val = word.group(2)
logic = word.group(1)
rm_num = re.search('([a-z_0-9]*)\(([0-9]*)\)', logic)
if rm_num != None:
#Pull out the number for checkboxes
logic = rm_num.group(1)
check_num = rm_num.group(2)
indented_test.append(logic)
return set(indented_test)
def _indent_ques(self, logic, cur_field):
''' Indent the left margin as necessary for the field's level.
Arguments:
logic -- The set of fields that the current field is nested under
cur_field -- The current field name.
'''
if self.indent_stack == {}:
if len(logic) > 0:
self.indent_stack[cur_field] = 1
self.doc.start_indent()
self.all_forms.start_indent()
else:
top = sorted(self.indent_stack.values()).pop()
if len(logic) == 0:
for k in self.indent_stack.keys():
self.doc.stop_indent()
self.all_forms.stop_indent()
self.indent_stack = {}
return {}
high = 0
for l in logic:
if self.indent_stack.has_key(l):
if self.indent_stack[l] > high:
high = self.indent_stack[l]
if high == 0:
num = 0
for k in self.indent_stack.keys():
if num > 0:
self.doc.stop_indent()
self.all_forms.stop_indent()
del self.indent_stack[k]
num += 1
self.indent_stack[cur_field] = 1
elif high == top:
self.doc.start_indent()
self.all_forms.start_indent()
self.indent_stack[cur_field] = top + 1
else:
num = 0
for k, v in self.indent_stack.items():
if v > high:
del self.indent_stack[k]
if num > 0:
self.doc.stop_indent()
self.all_forms.stop_indent()
num += 1
self.indent_stack[cur_field] = high + 1
def __reset_indent(self):
if self.indent_stack != {}:
top = sorted(self.indent_stack.values()).pop()
for val in range(top):
self.all_forms.stop_indent()
def _create_form(self, const, form_name):
if const != None:
self.doc = RedcapForm("{constraint}_{form_name}.pdf"
.format(constraint=const, form_name=form_name),
self.multiline, self.header_box
)
else:
self.doc = RedcapForm("{form_name}.pdf".format(
form_name=form_name),self.multiline, self.header_box
)
if self.print_const_name != None:
self.doc.print_const_name(self.print_const_name)
self.all_forms.print_const_name(self.print_const_name)
self.doc.setup()
self.doc.form_name(form_name)
def process(self, const):
''' Parse and create the RedcapForm associated with the REDcap XML data
dictionary.
'''
self.all_forms = RedcapForm('ALL.pdf', self.multiline, self.header_box)
self.all_forms.setup()
try:
iterator = self.tree.iter('item')
except AttributeError:
iterator = self.tree.findall('item')
for item in iterator:
form_name = item.findtext('form_name')
if self.to_print == [] or form_name in self.to_print:
name = form_name.replace('_', " ")
prop_name = string.capwords(name)
if self.cur_form == None:
self._create_form(const, item.findtext('form_name'))
self.all_forms.form_name(prop_name)
self.cur_form = item.findtext('form_name')
elif not self.cur_form == item.findtext('form_name'):
self.doc.render()
self.__reset_indent()
self._create_form(const, item.findtext('form_name'))
self.indent_stack = {}
if self.print_const_name != None:
self.doc.print_const_name(self.print_const_name)
self.all_forms.print_const_name(self.print_const_name)
if not self.all_same_page:
if self.all_forms.form_name_current:
self.all_forms.remove_header_footer(
self.all_forms.form_name_current)
self.all_forms.new_page()
self.all_forms.form_name(prop_name)
self.cur_form = item.findtext('form_name')
redcap_types = {
'number': RedcapForm.number_element,
'integer': RedcapForm.integer_element,
'text': RedcapForm.text_element,
'checkbox': RedcapForm.check_box_element,
'yesno': RedcapForm.yesno_element,
'dropdown': RedcapForm.radio_element,
'date_mdy': RedcapForm.date_element,
'date' : RedcapForm.date_ymd,
'date_dmy' : RedcapForm.date_dmy,
'date_ymd' : RedcapForm.date_ymd,
'truefalse': RedcapForm.truefalse_element,
'notes': RedcapForm.note_element,
'descriptive': RedcapForm.descriptive_element,
'sql': RedcapForm.sql_element,
'radio': RedcapForm.radio_element,
'calc': RedcapForm.calculated_element,
'file' : RedcapForm.no_print,
'time' : RedcapForm.time,
'time_mm_ss' : RedcapForm.time_mm_ss,
'datetime_mdy' : RedcapForm.datetime_mdy,
'datetime_dmy' : RedcapForm.datetime_dmy,
'datetime_ymd' : RedcapForm.datetime_ymd,
'datetime_seconds_dmy' : RedcapForm.datetime_sec_dmy,
'datetime_seconds_mdy' : RedcapForm.datetime_sec_mdy,
'datetime_seconds_ymd' : RedcapForm.datetime_sec_ymd,
'slider' : RedcapForm.slider_element,
}
field_text = clean_html(item.findtext('field_label'))
field_type = item.findtext('field_type')
field_name = item.findtext('field_name')
branching_logic = item.findtext('branching_logic')
if field_type == 'text':
spec = item.findtext(
'text_validation_type_or_show_slider_number')
if spec != '':
field_type = spec
choices = self._get_choices(item.findtext(
'select_choices_or_calculations'))
if (branching_logic =='' or
self.logic_parser.evaluate(field_name, branching_logic)):
if self._indent != '':
logic_vals = self._get_level(branching_logic)
indent_stack = self._indent_ques(logic_vals,
field_name)
if item.findtext('section_header'):
self.doc.section_name(clean_html(item.findtext(
'section_header')))
self.all_forms.section_name(clean_html(item.findtext(
'section_header')))
if choices != None:
if self.print_selected_only:
if self.logic_parser.has_constraint(field_name):
valid_choices = (self.logic_parser
.get_const_vals(field_name))
choice_list=[]
for n in valid_choices:
choice_list.append(choices[n-1])
choices=choice_list
if redcap_types.has_key(field_type):
redcap_types[field_type](
self.doc, field_text, choices)
redcap_types[field_type](
self.all_forms, field_text, choices)
else:
redcap_types['text'](self.doc, field_text)
redcap_types['text'](self.all_forms, field_text)
else:
if redcap_types.has_key(field_type):
redcap_types[field_type](self.doc, field_text)
redcap_types[field_type](self.all_forms, field_text)
else:
redcap_types['text'](self.doc, field_text)
redcap_types['text'](self.all_forms, field_text)
self.all_forms.render()
self.doc.render()
class PdfForm(object):
def __init__(self, xml_file, config_file=None):
self.tree = etree.parse(xml_file)
self.cur_form = None
self.doc = None
self.indent_stack = {}
self.logic_parser = LogicParser()
self.to_print = []
if config_file != None:
self.config = ConfigParser()
self.config.read(config_file)
self._indent = True
self.print_const_name=None
def revert_indent_val(self):
self._indent = not self._indent
def add_constraint_list(self, const_section):
'''If proceessed without running add_constraint_list
then will print all forms and elements in the project.
Arguments:
const_section -- The section in the config_file to use along with
the base seciton
'''
if not self.config:
raise ValueError("self.config is %(self.config)s: Please set the config file before adding constraint." %({'config': self.config,
}))
sections = ['base', const_section]
for sec in sections:
if self.config.has_section(sec):
for name, vals in self.config.items(sec):
if name == '__print_name':
if vals == 'True':
self.print_const_name=const_section
elif name != '__forms':
self.logic_parser.add_constraint(name, eval(vals))
else:
if sec != 'base':
raise ConstraintError('%(sec)s is not in the constraint file.', sec);
def _get_choices(self, choices):
''' Return a list of valid choices for the current question.
Arguments:
choices -- the string from REDCap data dictionary containing the
choices.
'''
vals = choices.split("\\n")
if len(vals) > 1:
return map(lambda c: c.lstrip(' 0123456789').lstrip(',').strip(' '), vals)
else:
vals = choices.split("|", 2)
if len(vals) > 1:
return vals
elif len(vals) == 1:
one = re.match("\s?[0-9.-]*\s?,\s?(.*)",vals[0]);
if one:
return [one.group(1)]
return None
def _get_level(self, names):
''' Return the set of all the field names that the current field is
branched under
Arguments:
names -- The branching logic string from the redcap export
'''
vals = re.split(' and | or ', names)
indented_test = []
if vals[0] != '':
for v in vals:
logic = v
long_form = re.search('\[([a-z_0-9]*)\](\[[a-z_0-9\(\)]*\][0-9 \'=]*)', v)
if long_form:
v = long_form.group(2)
word = re.search('\[([a-z_0-9\(\)]*)\]([0-9 \'=]*)', v)
if word != None:
val = word.group(2)
logic = word.group(1)
rm_num = re.search('([a-z_0-9]*)\(([0-9]*)\)', logic)
if rm_num != None:
#Pull out the number for checkboxes
logic = rm_num.group(1)
check_num = rm_num.group(2)
indented_test.append(logic)
return set(indented_test)
def _indent_ques(self, logic, cur_field):
''' Indent the left margin as necessary for the field's level.
Arguments:
logic -- The set of fields that the current field is nested under
cur_field -- The current field name.
'''
if self.indent_stack == {}:
if len(logic) > 0:
self.indent_stack[cur_field] = 1
self.doc.start_indent()
else:
top = sorted(self.indent_stack.values()).pop()
if len(logic) == 0:
for k in self.indent_stack.keys():
self.doc.stop_indent()
self.indent_stack={}
return {}
high = 0
for l in logic:
if self.indent_stack.has_key(l):
if self.indent_stack[l] > high:
high = self.indent_stack[l]
if high == 0:
num = 0
for k in self.indent_stack.keys():
if num > 0:
self.doc.stop_indent()
del self.indent_stack[k]
num+=1
self.indent_stack[cur_field] = 1
elif high == top:
self.doc.start_indent()
self.indent_stack[cur_field] = top + 1
else:
num = 0
for k, v in self.indent_stack.items():
if v > high:
del self.indent_stack[k]
if num > 0:
self.doc.stop_indent()
num+=1
self.indent_stack[cur_field] = high + 1
def process(self,const):
''' Parse and create the RedcapForm associated with the REDcap XML data
dictionary.
'''
for item in self.tree.iter('item'):
form_name = item.findtext('form_name')
if self.to_print == [] or form_name in self.to_print:
name = form_name.replace('_', " ")
prop_name = string.capwords(name)
if self.cur_form == None:
if const != None:
self.doc = RedcapForm(const + '_' + item.findtext('form_name')+".pdf")
else:
self.doc = RedcapForm(item.findtext('form_name')+".pdf")
if self.print_const_name != None:
self.doc.print_const_name(self.print_const_name)
self.doc.setup()
self.doc.form_name(prop_name)
self.cur_form = item.findtext('form_name')
elif not self.cur_form == item.findtext('form_name'):
self.doc.render()
if const != None:
self.doc = RedcapForm(const + '_' + item.findtext('form_name')+".pdf")
else:
self.doc = RedcapForm(item.findtext('form_name')+".pdf")
self.indent_stack = {}
if self.print_const_name != None:
self.doc.print_const_name(self.print_const_name)
self.doc.setup()
self.doc.form_name(prop_name)
self.cur_form = item.findtext('form_name')
redcap_types = {
'number': RedcapForm.number_element,
'integer': RedcapForm.integer_element,
'text': RedcapForm.text_element,
'checkbox': RedcapForm.check_box_element,
'yesno': RedcapForm.yesno_element,
'dropdown': RedcapForm.radio_element,
'date_mdy': RedcapForm.date_element,
'date' : RedcapForm.date_ymd,
'date_dmy' : RedcapForm.date_dmy,
'date_ymd' : RedcapForm.date_ymd,
'truefalse': RedcapForm.truefalse_element,
'notes': RedcapForm.note_element,
'descriptive': RedcapForm.descriptive_element,
'sql': RedcapForm.sql_element,
'radio': RedcapForm.radio_element,
'calc': RedcapForm.number_element,
'file' : RedcapForm.no_print,
'time' : RedcapForm.time,
'time_mm_ss' : RedcapForm.time_mm_ss,
'datetime_mdy' : RedcapForm.datetime_mdy,
'datetime_dmy' : RedcapForm.datetime_dmy,
'datetime_ymd' : RedcapForm.datetime_ymd,
'datetime_seconds_dmy' : RedcapForm.datetime_sec_dmy,
'datetime_seconds_mdy' : RedcapForm.datetime_sec_mdy,
'datetime_seconds_ymd' : RedcapForm.datetime_sec_ymd,
'slider' : RedcapForm.slider_element,
}
field_text = clean_html(item.findtext('field_label'))
field_type = item.findtext('field_type')
field_name = item.findtext('field_name')
branching_logic = item.findtext('branching_logic')
if field_type == 'text':
spec = item.findtext('text_validation_type_or_show_slider_number')
if spec != '':
field_type = spec
choices = self._get_choices(item.findtext('select_choices_or_calculations'))
if branching_logic =='' or self.logic_parser.evaluate(field_name, branching_logic):
if self._indent != '':
logic_vals = self._get_level(branching_logic)
indent_stack = self._indent_ques(logic_vals, field_name)
if item.findtext('section_header'):
self.doc.section_name(clean_html(item.findtext('section_header')))
if choices != None:
if redcap_types.has_key(field_type):
redcap_types[field_type](self.doc, field_text, choices)
else:
redcap_types['text'](self.doc, field_text)
else:
if redcap_types.has_key(field_type):
redcap_types[field_type](self.doc, field_text)
else:
redcap_types['text'](self.doc, field_text)
return self.doc.render()
