Source code for tvb.storage.h5.file.xml_metadata_handlers

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"""
This module contains logic for meta-data handling.

It handles read/write operations in XML files for retrieving/storing meta-data.
More specific: it contains XML Reader/Writer Utility, for generic metadata dictionary.

.. moduleauthor:: Ionel Ortelecan <ionel.ortelecan@codemart.ro>
.. moduleauthor:: Lia Domide <lia.domide@codemart.ro>

"""

import json
import xml.dom.minidom
from xml.dom.minidom import Node, Document

from tvb.basic.profile import TvbProfile
from tvb.basic.logger.builder import get_logger


[docs] class XMLReader(object): """ Reader for XML with meta-data on generic entities (e.g. Project, Operation). """ def __init__(self, xml_path): self.logger = get_logger(self.__class__.__module__) self.xml_path = xml_path
[docs] def read_metadata_from_xml(self): """ Return a dictionary, filled with data read from XML file. """ self.logger.debug("Starting to parse XML file " + self.xml_path) root_node = self._find_root() # Parse all nodes, and read text content. result_data = self._parse_xml_node_to_dict(root_node) return result_data
[docs] @staticmethod def get_node_text(node): """ From XMl node, read string content. """ for text_child in node.childNodes: if text_child.nodeType == Node.TEXT_NODE: return str(text_child.data).lstrip().rstrip() return ''
####### PRIVATE METHODS Start Here ####################################### def _find_root(self): """ From given file path, get XML root node. """ doc_xml = xml.dom.minidom.parse(self.xml_path) for child_node in doc_xml.childNodes: if child_node.nodeType == Node.ELEMENT_NODE: return child_node return None def _parse_xml_node_to_dict(self, root_node): """ Parse a given input XML node, and return the dictionary of text attributes. The dictionary can have multiple levels of deepness, but when child-nodes are encountered, text value of the node is ignored. """ result = {} for node in root_node.childNodes: if node.nodeType == Node.ELEMENT_NODE: result[node.nodeName] = self.get_node_text(node) result_meta = self._parse_xml_node_to_dict(node) if list(result_meta) is not None and len(list(result_meta)) > 0: result[node.nodeName] = result_meta return result
[docs] class XMLWriter(object): """ Writer for XML with meta-data on generic entities (e.g. Project, Operation). """ ELEM_ROOT = "tvb_data" FILE_EXTENSION = ".xml" def __init__(self, entity): """ :param entity: a dictionary that contains generic metadata to be written """ self.entity = entity self.logger = get_logger(self.__class__.__module__)
[docs] def write_metadata_in_xml(self, final_path): """ From a meta-data dictionary for an entity, create the XML file. """ doc = Document() root_node = doc.createElement(self.ELEM_ROOT) # Add information about version of the stored data root_node.setAttribute(TvbProfile.current.version.DATA_VERSION_ATTRIBUTE, str(TvbProfile.current.version.DATA_VERSION)) # Add each generic metadata attribute as XML node-elements. for att_name, att_value in self.entity.items(): node = doc.createElement(att_name) if isinstance(att_value, list): att_value = json.dumps(att_value) node.appendChild(doc.createTextNode(str(att_value))) root_node.appendChild(node) doc.appendChild(root_node) # Now dump the XML content into a file. with open(final_path, 'wt') as file_obj: doc.writexml(file_obj, addindent="\t", newl="\n")