dblayer.py
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dblayer.py
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	## This file is part of Invenio.
	## Copyright (C) 2011, 2012, 2013, 2014 CERN.
	##
	## Invenio is free software; you can redistribute it and/or
	## modify it under the terms of the GNU General Public License as
	## published by the Free Software Foundation; either version 2 of the
	## License, or (at your option) any later version.
	##
	## Invenio is distributed in the hope that it will be useful, but
	## WITHOUT ANY WARRANTY; without even the implied warranty of
	## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
	## General Public License for more details.
	##
	## You should have received a copy of the GNU General Public License
	## along with Invenio; if not, write to the Free Software Foundation, Inc.,
	## 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA.

	import time
	from invenio.legacy.authorlist import config as cfg

	from invenio.legacy.dbquery import run_sql

	def now():
	"""
	Returns a unix epoch time stamp as integer.
	"""
	return int(time.time())

	def clone(paper_id, user_id):
	"""
	Clones a whole paper data having the given id and returns the paper
	information of the clone as a dictionary. If the paper_id was a falsy value
	(None usually) or the id of the paper to be cloned does not exist in the
	database. The function will create a new empty record, save it and return it
	instead.
	"""
	data = {}
	clone_id = clone_paper(paper_id, user_id)

	if (clone_id == 0):
	data = load(None)
	clone_id = save(None, user_id, data)
	else:
	clone_references(paper_id, clone_id)
	clone_affiliations(paper_id, clone_id)
	clone_authors(paper_id, clone_id)

	load_paper(clone_id, data)
	data[cfg.JSON.PAPER_ID] = clone_id

	return data

	def clone_paper(paper_id, user_id):
	"""
	Clones the general paper information - i.e. title, collaboration and
	experiment number. Furthermore, the last modified timestamp will be set
	to the current time. All of this is only done, if the requested paper id
	was found in the database, otherwise 0 is returned. This function
	should NOT be called alone as long as you are really sure that you want
	to do this. Refer to clone() instead.
	"""
	return run_sql("""INSERT INTO aulPAPERS (id, id_user, title, collaboration,
	experiment_number, last_modified) SELECT %s, id_user, title,
	collaboration, experiment_number, %s FROM aulPAPERS
	WHERE id = %s;""", (None, now(), paper_id,))

	def clone_references(paper_id, clone_id):
	"""
	Clones the references of the paper with the given id and assigns the new
	clone id instead. Returns the clone id again for convenience reasons. The
	function should NOT be used alone as long as you are really sure that you
	want to do this. Have a look on clone() instead.
	"""
	run_sql("""INSERT INTO aulREFERENCES (item, reference, paper_id)
	SELECT item, reference, %s FROM aulREFERENCES
	WHERE paper_id = %s;""", (clone_id, paper_id,))
	return clone_id

	def clone_affiliations(paper_id, clone_id):
	"""
	Clones the affiliations of the given paper id and assigns the clone id
	instead. Returns the clone id for convenience reasons. The function should
	NOT be used alone as long as you are really sure that you want to do this.
	Have a look on clone() instead.
	"""
	run_sql("""INSERT INTO aulAFFILIATIONS (item, acronym, umbrella,
	name_and_address, domain, member, spires_id, paper_id)
	SELECT item, acronym, umbrella, name_and_address,
	domain, member, spires_id, %s FROM aulAFFILIATIONS
	WHERE paper_id = %s;""", (clone_id, paper_id,))
	return clone_id

	def clone_authors(paper_id, clone_id):
	"""
	Clones the authors of the paper with the passed id and assigns the new clone
	id instead. It also invokes the cloning of the affiliations of the authors.
	The clone id will be returned again for convenience reasons. The function
	should NOT be used alone as long as you are really sure that you want to do
	this. Have a look on clone() instead.
	"""
	run_sql("""INSERT INTO aulAUTHORS (item, family_name, given_name,
	name_on_paper, status, paper_id)
	SELECT item, family_name, given_name, name_on_paper,
	status, %s FROM aulAUTHORS
	WHERE paper_id = %s;""", (clone_id, paper_id,))
	clone_author_affiliations(paper_id, clone_id)
	clone_author_identifiers(paper_id, clone_id)
	return clone_id

	def clone_author_affiliations(paper_id, clone_id):
	"""
	Clones the affiliations of the authors of the paper with the given id and
	assigns the new clone id to them. Returns the clone_id again for convenience
	reasons. Should NOT be used alone but only as part of clone() as long as you
	are not really sure what you are doing.
	"""
	run_sql("""INSERT INTO aulAUTHOR_AFFILIATIONS (item, affiliation_acronym,
	affiliation_status, author_item, paper_id)
	SELECT item, affiliation_acronym, affiliation_status,
	author_item, %s FROM aulAUTHOR_AFFILIATIONS
	WHERE paper_id = %s;""", (clone_id, paper_id,))
	return clone_id

	def clone_author_identifiers(paper_id, clone_id):
	"""
	Clones the identifiers of the authors of the paper with the given id and
	assigns the new clone id to them. Returns the clone_id again for convenience
	reasons. Should NOT be used alone but only as part of clone() as long as you
	are not really sure what you are doing.
	"""
	run_sql("""INSERT INTO aulAUTHOR_IDENTIFIERS (item, identifier_number,
	identifier_name, author_item, paper_id)
	SELECT item, identifier_number, identifier_name,
	author_item, %s FROM aulAUTHOR_IDENTIFIERS
	WHERE paper_id = %s;""", (clone_id, paper_id,))
	return clone_id

	def delete(paper_id):
	"""
	Deletes the paper with the given id completely from the database. There is
	no backup copy so better we sure that you want to do this :). Returns the
	id of the deleted paper again for convenience reasons.
	"""
	data = {cfg.JSON.PAPER_ID : paper_id}

	delete_paper(paper_id)
	delete_references(paper_id)
	delete_affiliations(paper_id)
	delete_authors(paper_id)
	delete_author_affiliations(paper_id)
	delete_author_identifiers(paper_id)

	return data

	def delete_paper(paper_id):
	"""
	Deletes the general informations of a paper without making any backup copy
	and safety net for the paper with the given id. Should NOT be used alone
	unless you are sure that you want to do this. Refer to delete() instead.
	Returns the paper_id for convenience reasons.
	"""
	run_sql("""DELETE FROM aulPAPERS WHERE id = %s;""", (paper_id,))
	return paper_id

	def delete_references(paper_id):
	"""
	Deletes the paper references from the database with the given id. It does
	not create any backup copy. Should NOT be used unless you are really sure
	that you want to do this. Refer to delete() instead. Returns the paper_id
	for convenience reasons.
	"""
	run_sql("""DELETE FROM aulREFERENCES WHERE paper_id = %s;""", (paper_id,))
	return paper_id

	def delete_affiliations(paper_id):
	"""
	Deletes the affiliations of the paper with the given paper id completely
	from the database. There is no safety net or backup copy. Should NOT be used
	alone unless you are sure that you want to do this. Refer to delete()
	instead. Returns the paper id for convenience reasons.
	"""
	run_sql("""DELETE FROM aulAFFILIATIONS WHERE paper_id = %s;""", (paper_id,))
	return paper_id

	def delete_authors(paper_id):
	"""
	Deletes the authors of the paper with the given id completely from the
	database. There is no backup copy or safety net, make sure you want to do
	this. This function should NOT be used alone unless you know what you are
	doing. Refer to delete() instead. Returns the paper id for convenience
	reasons.
	"""
	run_sql("""DELETE FROM aulAUTHORS WHERE paper_id = %s;""", (paper_id,))
	return paper_id

	def delete_author_affiliations(paper_id):
	"""
	Deletes the affiliations of each author that is part of the paper of the
	passed id. There is no backup copy or safety net, so make sure you want to
	call this function. This function should NOT be called alone unless you know
	what you are doing. Refer to delete() instead. Returns the paper id for
	convenience reasons.
	"""
	run_sql("""DELETE FROM aulAUTHOR_AFFILIATIONS
	WHERE paper_id = %s;""", (paper_id,))
	return paper_id

	def delete_author_identifiers(paper_id):
	"""
	Deletes the identifiers of each author that is part of the paper of the
	passed id. There is no backup copy or safety net, so make sure you want to
	call this function. This function should NOT be called alone unless you know
	what you are doing. Refer to delete() instead. Returns the paper id for
	convenience reasons.
	"""
	run_sql("""DELETE FROM aulAUTHOR_IDENTIFIERS
	WHERE paper_id = %s;""", (paper_id,))
	return paper_id

	def itemize(id_user):
	"""
	Returns the general information of all papers ordered descending by the last
	modification date. Each items is represented by a dictionary having the keys
	as can be found in the authorlist_config.
	"""
	data = {}
	papers = run_sql("""SELECT id, title, collaboration, experiment_number,
	last_modified FROM aulPAPERS WHERE id_user = %s
	ORDER BY last_modified DESC;""" % (id_user))
	out_papers = data.setdefault('data', [])
	for paper in papers:
	paper_id, title, collaboration, experiment_number, last_modified = paper
	out_papers.append({cfg.JSON.PAPER_ID : paper_id,
	cfg.JSON.PAPER_TITLE : title,
	cfg.JSON.COLLABORATION : collaboration,
	cfg.JSON.EXPERIMENT_NUMBER : experiment_number,
	cfg.JSON.LAST_MODIFIED : last_modified})
	return data

	def load(paper_id):
	"""
	Loads all data of a paper data set with the given paper id. If the paper id
	is a falsy value or is not yet in the database the function will create a
	basic empty paper object and return it including the requested id (a falsy
	value will just be reused without any modification). The returned object is
	a dictionary using the standard keys as defined in authorlist_config.
	"""
	data = {}
	load_id = load_paper(paper_id, data)
	data[cfg.JSON.PAPER_ID] = load_id
	load_references(paper_id, data)
	load_affiliations(paper_id, data)
	load_authors(paper_id, data)

	return data

	def load_paper(paper_id, data):
	"""
	Loads only the general paper information of the given id and adds them to
	the passed data dictionary. Should NOT be used alone as long as you are not
	sure what you are doing. Refer to load() instead. Returns the paper id for
	convenience reasons.
	"""
	paper = run_sql("""SELECT title, collaboration, experiment_number,
	last_modified FROM aulPAPERS
	WHERE id = %s;""", (paper_id,))
	if (not paper):
	# TODO add message here
	data[cfg.JSON.PAPER_TITLE] = ''
	data[cfg.JSON.COLLABORATION] = ''
	data[cfg.JSON.EXPERIMENT_NUMBER] = ''
	data[cfg.JSON.LAST_MODIFIED] = now()

	return paper_id

	title, collaboration, experiment_number, last_modified = paper[ 0 ]
	data[cfg.JSON.PAPER_TITLE] = title
	data[cfg.JSON.COLLABORATION] = collaboration
	data[cfg.JSON.EXPERIMENT_NUMBER] = experiment_number
	data[cfg.JSON.LAST_MODIFIED] = last_modified

	return paper_id

	def load_references(paper_id, data):
	"""
	Lodas only the reference information of the paper with the given id and adds
	them to the passed data dictionary. Should NOT be used alone as long as you
	are not sure what you are doing. Refer to load() instead. Returns the passed
	id for convenience reasons.
	"""
	references = run_sql("""SELECT reference FROM aulREFERENCES
	WHERE paper_id = %s;""", (paper_id,))
	reference_ids = [reference[0] for reference in references]
	data[cfg.JSON.REFERENCE_IDS] = reference_ids

	return paper_id

	def load_affiliations(paper_id, data):
	"""
	Loads only the affiliations information of the paper with the given id and
	adds them to the passed data dictionary. Should NOT be used alone as long as
	you do not know what you are doing. Refer to load() instead. Returns the
	passed id for convenience reasons.
	"""
	result = run_sql("""SELECT item, acronym, umbrella, name_and_address, domain,
	member, spires_id FROM aulAFFILIATIONS
	WHERE paper_id = %s ORDER BY item;""", (paper_id,))
	affiliations = data.setdefault(cfg.JSON.AFFILIATIONS_KEY, [])

	for affiliation in result:
	item, acronym, umbrella, name, domain, member, spires_id = affiliation
	affiliations.append([item + 1, '', acronym, umbrella, name,
	domain, bool(member), spires_id])

	return data

	def load_authors(paper_id, data):
	"""
	Loads the authors information of the paper with the passed id and adds them
	to the passed data dicitionary. This function will automatically also load
	all affiliations of the respective author. Should NOT be used alone as long
	as you do not know what you are doing. Refer to load() instead. Returns the
	passed id for convenience reasons.
	"""
	result = run_sql("""SELECT item, family_name, given_name, name_on_paper,
	status FROM aulAUTHORS
	WHERE paper_id = %s ORDER BY item;""", (paper_id,))
	authors = data.setdefault(cfg.JSON.AUTHORS_KEY, [])

	for author in result:
	item, family_name, given_name, paper_name, status = author
	author_affiliations = load_author_affiliations(paper_id, item)
	author_identifiers = load_author_identifiers(paper_id, item)
	authors.append([item + 1, '', family_name, given_name, paper_name,
	status, author_affiliations, author_identifiers])

	return data

	def load_author_affiliations(paper_id, author_id):
	"""
	Loads the affiliations of the author with the passed id that is part of the
	author lists of the paper with the given id. Should NOT be used alone as
	long as you are not sure what you are doing. Refer to load() instead. In
	this case the paper id is NOT returned but the author affiliations.
	"""
	result = run_sql("""SELECT affiliation_acronym, affiliation_status
	FROM aulAUTHOR_AFFILIATIONS WHERE author_item = %s
	AND paper_id = %s ORDER BY item;""", (author_id, paper_id,))
	author_affiliations = []

	for author_affiliation in result:
	acronym, status = author_affiliation
	author_affiliations.append([acronym, status])

	return author_affiliations

	def load_author_identifiers(paper_id, author_id):
	"""
	Loads the identifiers of the author with the passed id that is part of the
	author lists of the paper with the given id. Should NOT be used alone as
	long as you are not sure what you are doing. Refer to load() instead. In
	this case the paper id is NOT returned but the author affiliations.
	"""
	result = run_sql("""SELECT identifier_number, identifier_name
	FROM aulAUTHOR_IDENTIFIERS WHERE author_item = %s
	AND paper_id = %s ORDER BY item;""", (author_id, paper_id,))
	author_identifiers = []

	for author_identifier in result:
	number, name = author_identifier
	author_identifiers.append([number, name])

	return author_identifiers

	def save(paper_id, user_id, in_data):
	"""
	Saves the passed data dictionary using the standard authorlist_config keys
	in the database using the passed paper_id. If the id is falsy or not yet in
	the database a new data set is created, otherwise the old data set will be
	overwritten. Returns a dictionary the holds the id of the saved data set.
	"""
	out_data = {}

	new_paper_id = save_paper(paper_id, user_id, in_data)
	if (paper_id is None):
	paper_id = new_paper_id
	out_data[cfg.JSON.PAPER_ID] = paper_id

	save_references(paper_id, in_data)
	save_affliations(paper_id, in_data)
	save_authors(paper_id, in_data)

	return out_data

	def save_paper(paper_id, user_id, data):
	"""
	Saves the general paper information from the passed data dictionary using
	the standard authorlist_config keys of the paper with the given id. Updates
	the last modified timestamp. Should NOT be used alone as long as you are not
	sure what you are doing. Refer to save() instead. Returns the paper if of
	the dataset.
	"""
	if (not paper_id):
	paper_id = None
	timestamp = now()
	paper_title = data.get(cfg.JSON.PAPER_TITLE)
	if not paper_title:
	paper_title = 'Untitled paper'

	data_tuple = ( # insert values
	paper_id,
	user_id,
	paper_title,
	data[cfg.JSON.COLLABORATION],
	data[cfg.JSON.EXPERIMENT_NUMBER],
	timestamp,

	# update values
	paper_title,
	data[cfg.JSON.COLLABORATION],
	data[cfg.JSON.EXPERIMENT_NUMBER],
	timestamp)

	return run_sql("""INSERT INTO aulPAPERS (id, id_user, title, collaboration,
	experiment_number, last_modified)
	VALUES (%s, %s, %s, %s, %s, %s)
	ON DUPLICATE KEY UPDATE
	title = %s,
	collaboration = %s,
	experiment_number = %s,
	last_modified = %s;""", data_tuple)

	def save_references(paper_id, data):
	"""
	Saves the references of the passed data dictionary using the standard
	authorlist_config keys of the paper data set with the given id. Should NOT
	be used alone as long as you are not sure what you are doing. Refer to
	save() instead. Returns the paper id.
	"""
	reference_ids = data[cfg.JSON.REFERENCE_IDS]

	# Insert or update old references
	for index, reference in enumerate(reference_ids):
	data_tuple = (# insert values
	index,
	reference,
	paper_id,

	# update values
	reference)

	run_sql("""INSERT INTO
	aulREFERENCES (item, reference, paper_id)
	VALUES (%s, %s, %s)
	ON DUPLICATE KEY UPDATE
	reference = %s;""", data_tuple)

	# Delete old references that are out of bounds - i.e. have a higher index
	# than the length of the reference list
	run_sql("""DELETE FROM aulREFERENCES WHERE item >= %s AND paper_id = %s;""",
	(len(reference_ids), paper_id))

	return paper_id

	def save_affliations(paper_id, data):
	"""
	Saves the affiliations of the passed data dictionary using the standard
	authorlist_config keys to the data set of the paper with the given id.
	Should NOT be used alone as long as you are not sure what you are doing.
	Refer to save() instead. Returns the paper_id for convenience reasons.
	"""
	affiliations = data[cfg.JSON.AFFILIATIONS_KEY]

	for index, affiliation in enumerate(affiliations):
	data_tuple = (# insert values
	index,
	affiliation[cfg.JSON.ACRONYM],
	affiliation[cfg.JSON.UMBRELLA],
	affiliation[cfg.JSON.NAME],
	affiliation[cfg.JSON.DOMAIN],
	affiliation[cfg.JSON.MEMBER],
	affiliation[cfg.JSON.SPIRES_ID],
	paper_id,

	# update values
	affiliation[cfg.JSON.ACRONYM],
	affiliation[cfg.JSON.UMBRELLA],
	affiliation[cfg.JSON.NAME],
	affiliation[cfg.JSON.DOMAIN],
	affiliation[cfg.JSON.MEMBER],
	affiliation[cfg.JSON.SPIRES_ID])

	run_sql("""INSERT INTO
	aulAFFILIATIONS (item, acronym, umbrella, name_and_address,
	domain, member, spires_id, paper_id)
	VALUES(%s, %s, %s, %s, %s, %s, %s, %s)
	ON DUPLICATE KEY UPDATE
	acronym = %s,
	umbrella = %s,
	name_and_address = %s,
	domain = %s,
	member = %s,
	spires_id = %s;""", data_tuple)

	# Delete old affiliations that are out of bounds - i.e. have a higher index
	# than the length of the affiliations list
	run_sql("""DELETE FROM aulAFFILIATIONS WHERE item >= %s AND paper_id = %s;""",
	(len(affiliations), paper_id))

	return paper_id

	def save_authors(paper_id, data):
	"""
	Saves the authors of the passed data dictionary using the standard
	authorlist_config keys in the database of the paper with the given id.
	Should NOT be used alone as long as you do not know what you are doing.
	Refer to save() instead. Returns the paper_id.
	"""
	authors = data[cfg.JSON.AUTHORS_KEY]

	for index, author in enumerate(authors):
	data_tuple = (# insert values
	index,
	author[cfg.JSON.FAMILY_NAME],
	author[cfg.JSON.GIVEN_NAME],
	author[cfg.JSON.PAPER_NAME],
	author[cfg.JSON.STATUS],
	paper_id,

	# update values
	author[cfg.JSON.FAMILY_NAME],
	author[cfg.JSON.GIVEN_NAME],
	author[cfg.JSON.PAPER_NAME],
	author[cfg.JSON.STATUS])

	run_sql("""INSERT INTO
	aulAUTHORS (item, family_name, given_name, name_on_paper,
	status, paper_id)
	VALUES(%s, %s, %s, %s, %s, %s)
	ON DUPLICATE KEY UPDATE
	family_name = %s,
	given_name = %s,
	name_on_paper = %s,
	status = %s;""", data_tuple)

	save_author_affiliations(paper_id, index, len(authors),
	author[cfg.JSON.AFFILIATIONS])
	save_author_identifiers(paper_id, index, len(authors),
	author[cfg.JSON.IDENTIFIERS])

	# Delete old authors that are out of bounds - i.e. have a higher index
	# than the length of the affiliations list
	run_sql("""DELETE FROM aulAUTHORS WHERE item >= %s AND paper_id = %s;""",
	(len(authors), paper_id))

	return paper_id

	def save_author_affiliations(paper_id, author_id, number_of_authors, data):
	"""
	Saves the affiliations of the passed author using the data dictionary and
	the standard authorlist_config keys and the paper id. Deletes also all old
	entries that are 'out of bounds' facilitating the number_of_authors
	paramter. Should NOT be used alone as long as you do not exactly know what
	you are doing. Refer to save() instead. Returns the paper id.
	"""
	for index, affiliation in enumerate(data):
	data_tuple = (# insert values
	index,
	affiliation[cfg.JSON.AFFILIATION_ACRONYM],
	affiliation[cfg.JSON.AFFILIATION_STATUS],
	author_id,
	paper_id,

	# update values
	affiliation[cfg.JSON.AFFILIATION_ACRONYM],
	affiliation[cfg.JSON.AFFILIATION_STATUS])

	run_sql("""INSERT INTO
	aulAUTHOR_AFFILIATIONS (item, affiliation_acronym,
	affiliation_status, author_item,
	paper_id)
	VALUES(%s, %s, %s, %s, %s)
	ON DUPLICATE KEY UPDATE
	affiliation_acronym = %s,
	affiliation_status = %s;""", data_tuple)

	# Delete entries that the author does not have anymore
	run_sql("""DELETE FROM aulAUTHOR_AFFILIATIONS WHERE item >= %s
	AND author_item = %s AND paper_id = %s;""",
	(len(data), author_id, paper_id))

	# Delete entries of non existing author
	run_sql("""DELETE FROM aulAUTHOR_AFFILIATIONS WHERE author_item >= %s
	AND paper_id = %s;""",
	(number_of_authors, paper_id))

	return paper_id

	def save_author_identifiers(paper_id, author_id, number_of_authors, data):
	"""
	Saves the identifiers of the passed author using the data dictionary and
	the standard authorlist_config keys and the paper id. Deletes also all old
	entries that are 'out of bounds' facilitating the number_of_authors
	paramter. Should NOT be used alone as long as you do not exactly know what
	you are doing. Refer to save() instead. Returns the paper id.
	"""
	for index, identifier in enumerate(data):
	data_tuple = (# insert values
	index,
	identifier[cfg.JSON.IDENTIFIER_NUMBER],
	identifier[cfg.JSON.IDENTIFIER_NAME],
	author_id,
	paper_id,

	# update values
	identifier[cfg.JSON.IDENTIFIER_NUMBER],
	identifier[cfg.JSON.IDENTIFIER_NAME])

	run_sql("""INSERT INTO
	aulAUTHOR_IDENTIFIERS (item, identifier_number,
	identifier_name, author_item,
	paper_id)
	VALUES(%s, %s, %s, %s, %s)
	ON DUPLICATE KEY UPDATE
	identifier_number = %s,
	identifier_name = %s;""", data_tuple)

	# Delete entries that the author does not have anymore
	run_sql("""DELETE FROM aulAUTHOR_IDENTIFIERS WHERE item >= %s
	AND author_item = %s AND paper_id = %s;""",
	(len(data), author_id, paper_id))

	# Delete entries of non existing author
	run_sql("""DELETE FROM aulAUTHOR_IDENTIFIERS WHERE author_item >= %s
	AND paper_id = %s;""",
	(number_of_authors, paper_id))

	return paper_id

	def get_owner(paper_id):
	"""Returns the id_user of a paper"""
	result = run_sql("SELECT id_user FROM aulPAPERS WHERE id = %s;" % \
	(paper_id))[0][0]
	if result:
	return result
	return None

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