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authorlist_dblayer.py
0ca2e106953biugw2017

authorlist_dblayer.py
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			## This file is part of Invenio.
			## Copyright (C) 2011, 2012, 2013 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
			import invenio.authorlist_config as cfg

			from invenio.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

R3600/modules/webauthorlist/lib/authorlist_dblayer.py0ca2e106953biugw2017

authorlist_dblayer.pyView Options

R3600/modules/webauthorlist/lib/authorlist_dblayer.py
0ca2e106953biugw2017

authorlist_dblayer.py
View Options