PALSE_xml_DB Class Reference

Constructions
def	__init__ (self)
	Default constructor. More...

Internal Methods
def	__len__ (self)
	Number of trees in the database. More...
def	append (self, et)
	Add a etree to the database. More...
def	add_XML_etree (self, my_tree, tree_name)
	Add the given Element tree into the database (at the last position). More...

Load Files
def	load_from_directory (self, input_dir, regex="", subdirs=False)
	Parse the input directory, possibly filter the filenames, and build one ETree for each file retained. More...
def	sort_databases (self, varname, type=str, options_suffix="__options.xml")
	Sorts input databases by looking for each of them its corresponding options.xml file, and sorting following the value of the described option. More...
def	add_pdb_namespaces (self)
	Add all namespaces specific to xml files from PDB. More...
def	add_namespace (self, prefix, uri)
	Add a namespace represented by a URI and its prefix. More...

Boost Archive Identifiers
def	__collect_boost_ids_recursive__ (self, tree, id_dict)
	Collect the ids recursively in a tree, exploring all the subtrees. More...
def	__duplicate_boost_id_reference_recursive__ (self, tree, id_dict)
	In a tree, replace the boost id references for which the id exists in the dictionary. More...
def	duplicate_boost_archive_references (self)
	If any references in a boost archive, replace them by copy of initial objects. More...

Hierarchy of Dataset
def	__get_path_recursive__ (self, tree, path, paths)
	get_path_recursive More...
def	__get_intersection_of_paths__ (self, paths_1, paths_2)
	get_intersection_of_paths More...
def	__make_path_strings_as_list_recursive__ (self, path, paths)
	make_path_strings_as_list_recursive More...
def	__make_path_strings_as_xml_recursive__ (self, deepness, paths)
	make_path_strings_as_xml_recursive More...
def	get_common_hierarchy (self)
	Return the different paths that are common to all XML files in the dataset as a dictionnary. More...
def	get_common_hierarchy_as_xml (self)
	Return the different paths that are common to all XML files in the dataset as a list of paths. More...
def	get_common_hierarchy_as_list (self)
	Return the different paths that are common to all XML files in the dataset as a XML file. More...

Queries
def	convert_prefix_to_uri (self, xpath_query)
	Convert all registered prefixes in the query to their associated URI. More...
def	get_attribute (self, xpath_query)
	Returns the following pair: first, a boolean that is True iff the XPath query points to the attribute of a tag; second, if first is True, it is the attribute. More...
def	get_all_elements_from_root (self, xpath_query, root)
	Retrieves the list of all the elements matching the XPath query from the given root. More...
def	get_all_elements_from_tree (self, xpath_query, my_tree)
	Retrieves the list of all the elements matching the XPath query in the given ETree. More...
def	get_all_elements_from_database (self, xpath_query)
	Retrieves the list of all the elements matching the XPath query in each ETree, and returns them as a list of lists (one list per ETree). More...
def	is_data_value_in_tree (self, xpath_query, my_tree, data_value, type=str)
	Is the given data_value pointed by the given Xpath query. More...
def	get_all_data_values_from_root (self, xpath_query, root, type=str)
	Retrieves the list of all the data_values matching the XPath query from the given root. More...
def	get_all_data_values_from_tree (self, xpath_query, my_tree, type=str)
	Retrieves the list of all the data_values matching the XPath query in the given ETree. More...
def	get_all_data_values_from_database (self, xpath_query, type=str)
	Retrieves the list of all the data_values matching the XPath query in each ETree, and returns them as a list of lists (one list per ETree) More...
def	get_all_data_values_from_elements (self, elements, xpath_query, type=str)
	Retrieves the list of all the data_values matching the XPath query in the given list of elements. More...
def	get_leftmost_data_value_from_tree (self, xpath_query, my_tree, type=str)
	Retrieves the first (leftmost) data_value matching the XPath query in the given ETree. More...
def	get_leftmost_data_values_from_database (self, xpath_query, type=str)
	Retrieves list of leftmost data_values matching the XPath query over all the ETrees of the database (one leftmost data_value per ETree). More...
def	get_rightmost_data_value_from_tree (self, xpath_query, my_tree, type=str)
	Retrieves the last (rightmost) data_value matching the XPath query in the given ETree. More...
def	get_rightmost_data_values_from_database (self, xpath_query, type=str)
	Retrieves list of rightmost data_values matching the XPath query over all the ETrees of the database (one lrightmost data_value per ETree). More...
def	get_data_source_file (self, xpath_query, data_value, type=str)
	Retrieves the filename list of all XML documents having the given data_value pointed by the given XPath query. More...
def	get_filenames (self)
	Returns the list of filenames. More...

Filtering Elements
def	get_all_data_values_from_database_compare_to (self, xpath_query, type, data_value, comp)
	get_all_data_values_from_database_compare_to More...
def	get_all_data_values_from_database_equal_to (self, xpath_query, type, data_value)
	get_all_data_values_from_database_equal_to More...
def	get_all_data_values_from_database_lower_than (self, xpath_query, type, data_value)
	get_all_data_values_from_database_lower_than More...
def	get_all_data_values_from_database_greater_than (self, xpath_query, type, data_value)
	get_all_data_values_from_database_greater_than More...
def	filter_elements_by_data_values_compare_to (self, elements, xpath_query, data_value, comp)
	Filter the input elements and create a list of filtered elements. More...
def	filter_elements_by_data_values_equal_to (self, elements, xpath_query, data_value)
	Same as previous but with the equal comparator. More...
def	filter_elements_by_data_values_lower_than (self, elements, xpath_query, data_value)
	Same as previous but with the less comparator. More...
def	filter_elements_by_data_values_leq_than (self, elements, xpath_query, data_value)
	Same as previous but with the less or equal comparator. More...
def	filter_elements_by_data_values_greater_than (self, elements, xpath_query, data_value)
	Same as previous but with the more comparator. More...
def	filter_elements_by_data_values_geq_than (self, elements, xpath_query, data_value)
	Same as previous but with the more or equal comparator. More...

Detailed Description

A class to represent XML files having the same hierarchical structure.

   This class parses a list of xml files, returns
      one Element Tree (ETree) for each of them, and
      stores these in a DB consistin of a list.
      Furthermore, the class allows selecting
      specific elements common to all trees thanks to
      so-called XPath queries.

Constructor & Destructor Documentation

__init__()

def __init__

(

self

)

Default constructor.

Member Function Documentation

__collect_boost_ids_recursive__()

def __collect_boost_ids_recursive__	(		self,
			tree,
			id_dict
	)

Collect the ids recursively in a tree, exploring all the subtrees.

__duplicate_boost_id_reference_recursive__()

def __duplicate_boost_id_reference_recursive__	(		self,
			tree,
			id_dict
	)

In a tree, replace the boost id references for which the id exists in the dictionary.

__get_intersection_of_paths__()

def __get_intersection_of_paths__	(		self,
			paths_1,
			paths_2
	)

get_intersection_of_paths

__get_path_recursive__()

def __get_path_recursive__	(		self,
			tree,
			path,
			paths
	)

get_path_recursive

__len__()

def __len__

(

self

)

Number of trees in the database.

__make_path_strings_as_list_recursive__()

def __make_path_strings_as_list_recursive__	(		self,
			path,
			paths
	)

make_path_strings_as_list_recursive

__make_path_strings_as_xml_recursive__()

def __make_path_strings_as_xml_recursive__	(		self,
			deepness,
			paths
	)

make_path_strings_as_xml_recursive

add_namespace()

def add_namespace	(		self,
			prefix,
			uri
	)

Add a namespace represented by a URI and its prefix.

add_pdb_namespaces()

def add_pdb_namespaces

(

self

)

Add all namespaces specific to xml files from PDB.

add_XML_etree()

def add_XML_etree	(		self,
			my_tree,
			tree_name
	)

Add the given Element tree into the database (at the last position).

append()

def append	(		self,
			et
	)

Add a etree to the database.

convert_prefix_to_uri()

def convert_prefix_to_uri	(		self,
			xpath_query
	)

Convert all registered prefixes in the query to their associated URI.

duplicate_boost_archive_references()

def duplicate_boost_archive_references

(

self

)

If any references in a boost archive, replace them by copy of initial objects.

filter_elements_by_data_values_compare_to()

def filter_elements_by_data_values_compare_to	(		self,
			elements,
			xpath_query,
			data_value,
			comp
	)

Filter the input elements and create a list of filtered elements.

For each element in the input list, if there exists a child pointed by the xpath query having as text a number positively compared to the input data_value with the imput comparator, it is added to the filtered output. Note that the pointed data_values have to be convertible to float.

filter_elements_by_data_values_equal_to()

def filter_elements_by_data_values_equal_to	(		self,
			elements,
			xpath_query,
			data_value
	)

Same as previous but with the equal comparator.

filter_elements_by_data_values_geq_than()

def filter_elements_by_data_values_geq_than	(		self,
			elements,
			xpath_query,
			data_value
	)

Same as previous but with the more or equal comparator.

filter_elements_by_data_values_greater_than()

def filter_elements_by_data_values_greater_than	(		self,
			elements,
			xpath_query,
			data_value
	)

Same as previous but with the more comparator.

filter_elements_by_data_values_leq_than()

def filter_elements_by_data_values_leq_than	(		self,
			elements,
			xpath_query,
			data_value
	)

Same as previous but with the less or equal comparator.

filter_elements_by_data_values_lower_than()

def filter_elements_by_data_values_lower_than	(		self,
			elements,
			xpath_query,
			data_value
	)

Same as previous but with the less comparator.

get_all_data_values_from_database()

def get_all_data_values_from_database	(		self,
			xpath_query,
			type = str
	)

Retrieves the list of all the data_values matching the XPath query in each ETree, and returns them as a list of lists (one list per ETree)

get_all_data_values_from_database_compare_to()

def get_all_data_values_from_database_compare_to	(		self,
			xpath_query,
			type,
			data_value,
			comp
	)

get_all_data_values_from_database_compare_to

get_all_data_values_from_database_equal_to()

def get_all_data_values_from_database_equal_to	(		self,
			xpath_query,
			type,
			data_value
	)

get_all_data_values_from_database_equal_to

get_all_data_values_from_database_greater_than()

def get_all_data_values_from_database_greater_than	(		self,
			xpath_query,
			type,
			data_value
	)

get_all_data_values_from_database_greater_than

get_all_data_values_from_database_lower_than()

def get_all_data_values_from_database_lower_than	(		self,
			xpath_query,
			type,
			data_value
	)

get_all_data_values_from_database_lower_than

get_all_data_values_from_elements()

def get_all_data_values_from_elements	(		self,
			elements,
			xpath_query,
			type = str
	)

Retrieves the list of all the data_values matching the XPath query in the given list of elements.

get_all_data_values_from_root()

def get_all_data_values_from_root	(		self,
			xpath_query,
			root,
			type = str
	)

Retrieves the list of all the data_values matching the XPath query from the given root.

get_all_data_values_from_tree()

def get_all_data_values_from_tree	(		self,
			xpath_query,
			my_tree,
			type = str
	)

Retrieves the list of all the data_values matching the XPath query in the given ETree.

get_all_elements_from_database()

def get_all_elements_from_database	(		self,
			xpath_query
	)

Retrieves the list of all the elements matching the XPath query in each ETree, and returns them as a list of lists (one list per ETree).

get_all_elements_from_root()

def get_all_elements_from_root	(		self,
			xpath_query,
			root
	)

Retrieves the list of all the elements matching the XPath query from the given root.

get_all_elements_from_tree()

def get_all_elements_from_tree	(		self,
			xpath_query,
			my_tree
	)

Retrieves the list of all the elements matching the XPath query in the given ETree.

get_attribute()

def get_attribute	(		self,
			xpath_query
	)

Returns the following pair: first, a boolean that is True iff the XPath query points to the attribute of a tag; second, if first is True, it is the attribute.

get_common_hierarchy()

def get_common_hierarchy

(

self

)

Return the different paths that are common to all XML files in the dataset as a dictionnary.

Note that only paths that are identical from the root of each XML file are stored.

get_common_hierarchy_as_list()

def get_common_hierarchy_as_list

(

self

)

Return the different paths that are common to all XML files in the dataset as a XML file.

Note that only paths that are identical from the root of each XML file are stored.

get_common_hierarchy_as_xml()

def get_common_hierarchy_as_xml

(

self

)

Return the different paths that are common to all XML files in the dataset as a list of paths.

Note that only paths that are identical from the root of each XML file are stored.

get_data_source_file()

def get_data_source_file	(		self,
			xpath_query,
			data_value,
			type = str
	)

Retrieves the filename list of all XML documents having the given data_value pointed by the given XPath query.

get_filenames()

def get_filenames

(

self

)

Returns the list of filenames.

get_leftmost_data_value_from_tree()

def get_leftmost_data_value_from_tree	(		self,
			xpath_query,
			my_tree,
			type = str
	)

Retrieves the first (leftmost) data_value matching the XPath query in the given ETree.

get_leftmost_data_values_from_database()

def get_leftmost_data_values_from_database	(		self,
			xpath_query,
			type = str
	)

Retrieves list of leftmost data_values matching the XPath query over all the ETrees of the database (one leftmost data_value per ETree).

get_rightmost_data_value_from_tree()

def get_rightmost_data_value_from_tree	(		self,
			xpath_query,
			my_tree,
			type = str
	)

Retrieves the last (rightmost) data_value matching the XPath query in the given ETree.

get_rightmost_data_values_from_database()

def get_rightmost_data_values_from_database	(		self,
			xpath_query,
			type = str
	)

Retrieves list of rightmost data_values matching the XPath query over all the ETrees of the database (one lrightmost data_value per ETree).

is_data_value_in_tree()

def is_data_value_in_tree	(		self,
			xpath_query,
			my_tree,
			data_value,
			type = str
	)

Is the given data_value pointed by the given Xpath query.

load_from_directory()

def load_from_directory	(		self,
			input_dir,
			regex = "",
			subdirs = False
	)

Parse the input directory, possibly filter the filenames, and build one ETree for each file retained.

sort_databases()

def sort_databases	(		self,
			varname,
			type = str,
			options_suffix = "__options.xml"
	)

Sorts input databases by looking for each of them its corresponding options.xml file, and sorting following the value of the described option.