Пример #1
0
def get_dictionary(dictionary_string, state_name, value_name, required_states):
    """
    This high level function returns a mapping from states to floating point values.
    Each required state is expected to have exactly one floating point value.
    @param dictionary_string: a string of lines of text that each look something like 'A : 0.245'
    @param state_name: something like 'amino acid'
    @param value_name: something like 'energy'
    @param required_states: a set of required states
    @return: a dictionary mapping each state to a value
    """
    # convert the multi-line string to a list of non-empty lines
    lines = smallutil.get_stripped_lines(StringIO(dictionary_string))
    # make sure that at least one line is non-empty
    if not lines:
        raise HandlingError('no %s to %s mapping was specified' %
                            (key_name, value_name))
    d = {}
    for line in lines:
        state, value_string = get_state_value_pair(line)
        if state not in required_states:
            raise HandlingError('invalid %s: %s' % (state_name, state))
        try:
            value = float(value_string)
        except ValueError:
            raise HandlingError(
                'this %s could not be interpreted as a number: %s' %
                (value_name, value_string))
        d[state] = value
    # assert that each state was assigned a value
    if len(d) < len(required_states):
        raise HandlingError('one or more %s was not assigned a %s' %
                            (state_name, value_name))
    return d
Пример #2
0
def docstring_to_title(docstring):
    """
    @param docstring: something like __doc__
    @return: the first line of the docstring as a title, or None
    """
    # get lines of text without whitespace between lines
    lines = smallutil.get_stripped_lines(StringIO(docstring))
    if lines:
        return lines[0]
    else:
        return None
Пример #3
0
def docstring_to_html(docstring):
    """
    Convert the docstring to an html header.
    @param docstring: something like __doc__
    """
    # get lines of text without whitespace between lines
    lines = smallutil.get_stripped_lines(StringIO(docstring))
    # no docstring
    if not lines:
        return ''
    # a single line docstring
    if len(lines) == 1:
        return lines[0]
    # multiple lines
    # the first line will be separated by an empty line
    arr = []
    arr.append(lines[0])
    arr.append('<br/><br/>')
    arr.extend(lines[1:])
    return '\n'.join(arr)
Пример #4
0
 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()
Пример #5
0
 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()