How to use deid - 10 common examples

def parse_group_action(section, line, config, section_name):
    """parse a group action, either FIELD or SPLIT, which must belong to
       either a fields or values section.

       Parameters
       =========
       section: a valid section name from the deid config file
       line: the line content to parse for the section/action
       config: the growing/current config dictionary
       section_name: optionally, a section name
    """
    if not line.upper().startswith(group_actions):
        bot.exit("%s is not a valid group action." % line)

    if not line.upper().startswith("FIELD") and section == "fields":
        bot.exit("%fields only supports FIELD actions.")

    # We may have to deal with cases of spaces
    bot.debug("%s: adding %s" % (section, line))
    parts = line.split(" ")
    action = parts.pop(0).replace(" ", "")

    # Both require some parts
    if not parts:
        bot.exit("%s action %s requires additional arguments" % (section, action))

    # For both, the second is always a field or field expander
    field = parts.pop(0)

    # Fields supports one or more fields with expanders (no third arguments)
    if section == "fields":
        config[section][section_name].append({"action": action, "field": field})

# Default values for split are length 1 and character empty space
            bot.debug("Parsing action %s" % action)
            split_by = " "
            minlength = 1

            if "value" in action:
                for param in action["value"].split(";"):
                    param_name, param_val = param.split("=")
                    param_name = param_name.strip()
                    param_val = param_val.strip()

                    # Set a custom parameter legnth
                    if param_name == "minlength":
                        minlength = int(param_val)
                        bot.debug("Minimum length set to %s" % minlength)
                    elif param_name == "by":
                        split_by = param_val.strip("'").strip('"')
                        bot.debug("Splitting value set to %s" % split_by)

            for uid, field in subset.items():
                new_values = (str(field.element.value) or "").split(split_by)
                for new_value in new_values:
                    if len(new_value) >= minlength:
                        values.add(new_value)

        else:
            bot.warning(
                "Unrecognized action %s for values list extraction." % action["action"]
            )

    return list(values)

"""
    # A default deid will be loaded if all else fails
    default_deid = os.path.join(get_installdir(), "data", "deid.dicom")

    if path is None:
        path = os.getcwd()

    # The user has provided a directory
    if os.path.isdir(path):
        contenders = [
            "%s/%s" % (path, x) for x in os.listdir(path) if x.startswith("deid")
        ]

        if len(contenders) == 0:
            bot.warning(
                "No deid settings files found in %s, will use default dicom.deid."
                % path
            )
            contenders.append(default_deid)

        elif len(contenders) > 1:
            bot.warning("Multiple deid files found in %s, will use first." % (path))

        path = contenders[0]

    # We have a file path at this point
    if not os.path.exists(path):
        bot.exit("Cannot find deid file %s, exiting." % (path))

    return path

def parse_value(item,value):
    '''parse_value will parse the value field of an action,
    either returning the string, or a variable looked up
    in the case of var:FieldName
    '''
    # Does the user want a custom value?
    if re.search('[:]',value):
        value_type,value_option = value.split(':') 
        if value_type.lower() == "var": 

            # If selected variable not provided, skip
            if value_option not in item:
                return None
            return item[value_option]
        bot.warning('%s is not a valid value type, skipping.' %(value_type))
        return None
    return value

# Does the user want a custom value?
    if re.search("[:]", value):
        value_type, value_option = value.split(":", 1)
        if value_type.lower() == "var":

            # If selected variable not provided, skip
            if value_option not in item:
                return None
            return item[value_option]

        # The user is providing a specific function
        elif value_type.lower() == "func":

            if value_option not in item:
                bot.warning("%s not found in item lookup." % (value_option))
                return None

            # item is the lookup, value from the recipe, and field
            # The field is an entire dicom element object
            return item[value_option](dicom=dicom, value=value, field=field, item=item)

        bot.warning("%s is not a valid value type, skipping." % (value_type))
        return None
    return value

# The user has provided a directory
    if os.path.isdir(path):
        contenders = [
            "%s/%s" % (path, x) for x in os.listdir(path) if x.startswith("deid")
        ]

        if len(contenders) == 0:
            bot.warning(
                "No deid settings files found in %s, will use default dicom.deid."
                % path
            )
            contenders.append(default_deid)

        elif len(contenders) > 1:
            bot.warning("Multiple deid files found in %s, will use first." % (path))

        path = contenders[0]

    # We have a file path at this point
    if not os.path.exists(path):
        bot.exit("Cannot find deid file %s, exiting." % (path))

    return path

Parameters
       ==========
       tag: the text that comes after deid to indicate the tag of the file in deid/data
       exit_on_fail: if None is an acceptable return value, this should be set to False
                     (default is True).
       quiet: Default False. If None is acceptable, quiet can be set to True
       load: also load the deid, if resulting path (from path or tag) is not None

    """
    # no tag/path means load default
    if tag is None:
        tag = "dicom"

    # If it's already loaded
    if isinstance(tag, dict):
        bot.debug("deid is already loaded.")
        return tag

    # If it's a path, get full path
    if os.path.exists(tag):
        deid = os.path.abspath(tag)
    else:
        deid = "%s/deid.%s" % (data_base, tag)

    if not os.path.exists(deid):
        if quiet is False:
            bot.error("Cannot find %s" % (deid))
        if exit_on_fail is True:
            sys.exit(1)
        else:
            return None

bot.exit("%s is not a valid action line." % line)

    # We may have to deal with cases of spaces
    parts = line.split(" ")
    action = parts.pop(0).replace(" ", "")

    # What field is the action for?
    if len(parts) < 1:
        bot.exit("%s requires a FIELD value, but not found." % action)

    field = parts.pop(0)

    # Actions that require a value
    if action in ["ADD", "REPLACE", "JITTER"]:
        if len(parts) == 0:
            bot.exit("%s requires a VALUE, but not found" % action)

        value = _remove_comments(parts)
        bot.debug("%s: adding %s" % (section, line))
        config[section].append({"action": action, "field": field, "value": value})

    # Actions that can optionally have a value
    elif action in ["REMOVE"]:
        bot.debug("%s: adding %s" % (section, line))

        # Case 1: removing without any criteria
        if len(parts) == 0:
            config[section].append({"action": action, "field": field})

        # Case 2: REMOVE can have a func:is_thing to return boolean
        else:
            value = _remove_comments(parts)

"""add section will add a section (and optionally)
       section name to a config

       Parameters
       ==========
       config: the config (dict) parsed thus far
       section: the section name to add
       section_name: an optional name, added as a level

    """

    if section is None:
        bot.exit("You must define a section (e.g. %header) before any action.")

    if section in ["filter", "values", "fields"] and section_name is None:
        bot.exit("You must provide a name for a filter section.")

    if section not in sections:
        bot.exit("%s is not a valid section." % section)

    if section not in config:

        # If a section is named, we have more one level (dict)
        if section_name is not None:
            config[section] = OrderedDict()
            config[section][section_name] = []
            bot.debug("Adding section %s %s" % (section, section_name))
        else:
            config[section] = []
            bot.debug("Adding section %s" % section)
        return config

def add_section(config, section, section_name=None):
    """add section will add a section (and optionally)
       section name to a config

       Parameters
       ==========
       config: the config (dict) parsed thus far
       section: the section name to add
       section_name: an optional name, added as a level

    """

    if section is None:
        bot.exit("You must define a section (e.g. %header) before any action.")

    if section in ["filter", "values", "fields"] and section_name is None:
        bot.exit("You must provide a name for a filter section.")

    if section not in sections:
        bot.exit("%s is not a valid section." % section)

    if section not in config:

        # If a section is named, we have more one level (dict)
        if section_name is not None:
            config[section] = OrderedDict()
            config[section][section_name] = []
            bot.debug("Adding section %s %s" % (section, section_name))
        else:
            config[section] = []