def update_virtualauthor_record(va_id, tag, value):
    '''
    Change the value associated to the given tag for a certain virtual author

    @param va_id: ID of the virtual author
    @type va_id: int
    @param tag: tag to be updated
    @type tag: string
    @param value: value to be written for the tag
    @type value: string
    '''
    current_tag_value = [row for row in dat.VIRTUALAUTHOR_DATA
                         if ((row['virtualauthorid'] == va_id)
                             and (row['tag'] == tag))]

    if len(current_tag_value) > 0:
        for tagupdate in [row for row in dat.VIRTUALAUTHOR_DATA
                          if ((row['virtualauthorid'] == va_id)
                              and (row['tag'] == tag))]:
            tagupdate['tag'] = tag
            tagupdate['value'] = value

        dat.update_log("touched_vas", va_id)
    else:
        add_virtualauthor_record(va_id, tag, value)
def delete_virtual_author(va_id):
    '''
    This will delete a virtual author while cascading the change through the
    different storages and instances: ra_data, ras, va_data and vas

    @param va_id: the virtual author to be deleted
    @type va_id: int

    @return: success or failure of the process
    @rtype: boolean
    '''
    if not isinstance(va_id, int):
        try:
            va_id = int(va_id)
        except (ValueError, TypeError):
            raise ValueError("Expecting the va id to be an int.")

    tags = get_virtualauthor_record_tags()

    for tag in tags:
        delete_virtualauthor_record(va_id, tag)

    for deletion_candidate in list([row for row in dat.VIRTUALAUTHORS
                               if row['virtualauthorid'] == va_id]):
        dat.VIRTUALAUTHORS.remove(deletion_candidate)

    dat.update_log("deleted_vas", va_id)

    return True
예제 #3
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def update_virtualauthor_record(va_id, tag, value):
    '''
    Change the value associated to the given tag for a certain virtual author

    @param va_id: ID of the virtual author
    @type va_id: int
    @param tag: tag to be updated
    @type tag: string
    @param value: value to be written for the tag
    @type value: string
    '''
    current_tag_value = [
        row for row in dat.VIRTUALAUTHOR_DATA
        if ((row['virtualauthorid'] == va_id) and (row['tag'] == tag))
    ]

    if len(current_tag_value) > 0:
        for tagupdate in [
                row for row in dat.VIRTUALAUTHOR_DATA
                if ((row['virtualauthorid'] == va_id) and (row['tag'] == tag))
        ]:
            tagupdate['tag'] = tag
            tagupdate['value'] = value

        dat.update_log("touched_vas", va_id)
    else:
        add_virtualauthor_record(va_id, tag, value)
예제 #4
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def delete_virtual_author(va_id):
    '''
    This will delete a virtual author while cascading the change through the
    different storages and instances: ra_data, ras, va_data and vas

    @param va_id: the virtual author to be deleted
    @type va_id: int

    @return: success or failure of the process
    @rtype: boolean
    '''
    if not isinstance(va_id, int):
        try:
            va_id = int(va_id)
        except (ValueError, TypeError):
            raise ValueError("Expecting the va id to be an int.")

    tags = get_virtualauthor_record_tags()

    for tag in tags:
        delete_virtualauthor_record(va_id, tag)

    for deletion_candidate in list(
        [row for row in dat.VIRTUALAUTHORS
         if row['virtualauthorid'] == va_id]):
        dat.VIRTUALAUTHORS.remove(deletion_candidate)

    dat.update_log("deleted_vas", va_id)

    return True
def delete_virtualauthor_record(va_id, tag):
    '''
    Remove a tag field from the virtualauthor_data table

    @param va_id: ID of the virtual author
    @type va_id: int
    @param tag: tag of the record to be deleted
    @type tag: string
    '''
    for tagupdate in list([row for row in dat.VIRTUALAUTHOR_DATA
                      if ((row['virtualauthorid'] == va_id)
                          and (row['tag'] == tag))]):
        dat.VIRTUALAUTHOR_DATA.remove(tagupdate)

    dat.update_log("touched_vas", va_id)
예제 #6
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def delete_virtualauthor_record(va_id, tag):
    '''
    Remove a tag field from the virtualauthor_data table

    @param va_id: ID of the virtual author
    @type va_id: int
    @param tag: tag of the record to be deleted
    @type tag: string
    '''
    for tagupdate in list([
            row for row in dat.VIRTUALAUTHOR_DATA
            if ((row['virtualauthorid'] == va_id) and (row['tag'] == tag))
    ]):
        dat.VIRTUALAUTHOR_DATA.remove(tagupdate)

    dat.update_log("touched_vas", va_id)
def create_new_realauthor(va_id):
    """
    Create a new real author connected to the given virtual author; the trust
    value for the virtual author is obviously 1 because this virtual author is
    incompatible with every other real author and is the first
    one in this new real author.

    RETURNS: the newly created realauthorid
    """
    current_ra_id = dat.increment_tracker("raid_counter")
    dat.REALAUTHORS.append({"realauthorid": current_ra_id, "virtualauthorid": va_id, "p": 1})
    dat.update_log("new_ras", current_ra_id)
    update_realauthor_data_by_vid(current_ra_id, va_id)
    #    update_realauthor_names(current_ra_id)

    return current_ra_id
def create_new_realauthor(va_id):
    """
    Create a new real author connected to the given virtual author; the trust
    value for the virtual author is obviously 1 because this virtual author is
    incompatible with every other real author and is the first
    one in this new real author.

    RETURNS: the newly created realauthorid
    """
    current_ra_id = dat.increment_tracker("raid_counter")
    dat.REALAUTHORS.append({'realauthorid': current_ra_id,
                         'virtualauthorid': va_id,
                         'p': 1})
    dat.update_log("new_ras", current_ra_id)
    update_realauthor_data_by_vid(current_ra_id, va_id)
#    update_realauthor_names(current_ra_id)

    return current_ra_id
def add_virtualauthor_record(va_id, tag, value):
    '''
    Adds a record to the virtualauthor_data table

    @param va_id: id of the virtual author to attach the attribute to
    @type va_id: int
    @param tag: tag to alter the value of
    @type tag: string
    @param value: the new value of the tag
    @type value: string
    '''
    dat.VIRTUALAUTHOR_DATA.append({'virtualauthorid': va_id,
                                   'tag': tag,
                                   'value': value})

    if not tag == "updated":
        update_virtualauthor_record(va_id, 'updated', 'True')

    dat.update_log("touched_vas", va_id)
예제 #10
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def add_virtualauthor_record(va_id, tag, value):
    '''
    Adds a record to the virtualauthor_data table

    @param va_id: id of the virtual author to attach the attribute to
    @type va_id: int
    @param tag: tag to alter the value of
    @type tag: string
    @param value: the new value of the tag
    @type value: string
    '''
    dat.VIRTUALAUTHOR_DATA.append({
        'virtualauthorid': va_id,
        'tag': tag,
        'value': value
    })

    if not tag == "updated":
        update_virtualauthor_record(va_id, 'updated', 'True')

    dat.update_log("touched_vas", va_id)
def add_minimum_virtualauthor(orig_authornames_id,
                                       orig_name_string,
                                       bibrec_id,
                                       author_index,
                                       authorname_p_list,
                                       refrec=""):
    '''
    Adds a complete virtual author to the virtual authors table.

    @param orig_authornames_id: ID of the name in authornames table
    @type orig_authornames_id: int
    @param orig_name_string: String of the author name
    @type orig_name_string: string
    @param bibrec_id: ID of the record
    @type bibrec_id: int
    @param author_index: number of the author
    @type author_index: int
    @param authorname_p_list: list of authornamesID with confidence index
        associated [[id1,p], [id2,p], .., [idn,p]]
    @type authorname_p_list: list of lists
    @param refrec: The bibref-bibrec pair of this author on a paper in format
        "100:14424,12441"
    @type refrec: string
    '''
    if authorname_p_list:
        pass

    current_va = create_new_virtualauthor(orig_authornames_id,
                                         orig_name_string)

    add_virtualauthor_record(current_va, 'bibrec_id', bibrec_id)
    add_virtualauthor_record(current_va, 'author_index', author_index)

    if refrec:
        pair = "%s,%s" % (refrec, bibrec_id)
        add_virtualauthor_record(current_va, 'bibrefrecpair', pair)

    dat.update_log("new_vas", current_va)
    update_virtualauthor_cluster(current_va)
def add_minimum_virtualauthor(orig_authornames_id,
                              orig_name_string,
                              bibrec_id,
                              author_index,
                              authorname_p_list,
                              refrec=""):
    '''
    Adds a complete virtual author to the virtual authors table.

    @param orig_authornames_id: ID of the name in authornames table
    @type orig_authornames_id: int
    @param orig_name_string: String of the author name
    @type orig_name_string: string
    @param bibrec_id: ID of the record
    @type bibrec_id: int
    @param author_index: number of the author
    @type author_index: int
    @param authorname_p_list: list of authornamesID with confidence index
        associated [[id1,p], [id2,p], .., [idn,p]]
    @type authorname_p_list: list of lists
    @param refrec: The bibref-bibrec pair of this author on a paper in format
        "100:14424,12441"
    @type refrec: string
    '''
    if authorname_p_list:
        pass

    current_va = create_new_virtualauthor(orig_authornames_id,
                                          orig_name_string)

    add_virtualauthor_record(current_va, 'bibrec_id', bibrec_id)
    add_virtualauthor_record(current_va, 'author_index', author_index)

    if refrec:
        pair = "%s,%s" % (refrec, bibrec_id)
        add_virtualauthor_record(current_va, 'bibrefrecpair', pair)

    dat.update_log("new_vas", current_va)
    update_virtualauthor_cluster(current_va)
def _update_authorid_universe():
    '''
    Updates all data related to the authorid algorithm.

    Sequence of operations:
        - Get all recently updated papers and remember time in the log
        - Get all authors on all papers
        - Extract collection of last names
        - For each last name:
            - Populate mem cache with cluster data
            - Delete updated records and their virtual authors from mem cache
            - Create virtual authors for new and updated records
            - Start matching algorithm
        - Update tables with results of the computation
        - Start personid update procedure
    '''

    def create_vas_from_specific_doclist(bibrec_ids):
        '''
        Processes the document list and creates a new minimal virtual author
        for each author in each record specified in the given list.

        @param bibrec_ids: Record IDs to concern in this update
        @type bibrec_ids: list of int
        '''
        num_docs = len([row for row in dat.DOC_LIST
                     if row['bibrecid'] in bibrec_ids])

        bconfig.LOGGER.log(25, "Creating minimal virtual authors for "
                                "all loaded docs (%s)"
                                % (num_docs))

        for docs in [row for row in dat.DOC_LIST
                     if row['bibrecid'] in bibrec_ids]:
            for author_id in docs['authornameids']:
                author_name = [an['name'] for an in dat.AUTHOR_NAMES
                               if an['id'] == author_id]
                refrecs = [ref[1] for ref in docs['authornameid_bibrefrec']
                           if ref[0] == author_id]
                refrec = -1

                if len(refrecs) > 1:
                    print "SCREEEEEEWWWWWWED!!! Several bibrefs on one paper?!"
                    refrec = refrecs[0]
                elif refrecs:
                    refrec = refrecs[0]

                if refrec and author_name:
                    add_minimum_virtualauthor(author_id, author_name[0],
                                              docs['bibrecid'], 0, [], refrec)
                elif author_name:
                    add_minimum_virtualauthor(author_id, author_name[0],
                                              docs['bibrecid'], 0, [])

    dat.reset_mem_cache(True)
    last_log = get_user_log(userinfo='daemon',
                            action='update_aid',
                            only_most_recent=True)
    updated_records = []

    if last_log:
        #select only the most recent papers
        recently_modified, last_update_time = get_papers_recently_modified(
                                                        date=last_log[0][2])
        insert_user_log('daemon', '-1', 'update_aid', 'bibsched', 'status',
                    comment='bibauthorid_daemon, update_authorid_universe',
                    timestamp=last_update_time[0][0])
        bibtask.write_message("Update authorid will operate on %s records."
                              % (len(recently_modified)), stream=sys.stdout,
                              verbose=0)

        if not recently_modified:
            bibtask.write_message("Update authorid: Nothing to do",
                                  stream=sys.stdout, verbose=0)
            return

        for rec in recently_modified:
            updated_records.append(rec[0])
            dat.update_log("rec_updates", rec[0])

    else:
        bibtask.write_message("Update authorid: Nothing to do",
                              stream=sys.stdout, verbose=0)
        return

    authors = []
    author_last_names = set()

    bibtask.task_update_progress('Reading authors from updated records')
    bibtask.write_message("Reading authors from updated records",
                                stream=sys.stdout, verbose=0)
    updated_ras = set()

    # get all authors from all updated records
    for rec in updated_records:
        rec_authors = get_field_values_on_condition(rec, ['100', '700'], "a",
                                                    source="API")

        for rec_author in rec_authors:
            if not rec_author:
                bconfig.LOGGER.error("Invalid empty author string, which "
                                     "will be skipped on record %s"
                                     % (rec))
                continue

            author_in_list = [row for row in authors
                              if row['db_name'] == rec_author]

            if author_in_list:
                for upd in [row for row in authors
                            if row['db_name'] == rec_author]:
                    upd['records'].append(rec)
            else:
                last_name = split_name_parts(rec_author)[0]
                author_last_names.add(last_name)
                authors.append({'db_name': rec_author,
                                'records': [rec],
                                'last_name': last_name})

    for status, author_last_name in enumerate(author_last_names):
        current_authors = [row for row in authors
                           if row['last_name'] == author_last_name]
        total_lnames = len(author_last_names)
        total_authors = len(current_authors)
        bibtask.task_update_progress('Processing %s of %s cluster: "%s" '
                                     '(%s authors)'
                                     % (status + 1, total_lnames,
                                        author_last_name, total_authors))
        bibtask.write_message('Processing %s of %s cluster: "%s" '
                              '(%s authors)'
                              % (status + 1, total_lnames, author_last_name,
                                 total_authors), stream=sys.stdout, verbose=0)
        dat.reset_mem_cache(True)
        init_authornames(author_last_name)
        load_mem_cache_from_tables()
        bconfig.LOGGER.log(25, "-- Relevant data successfully read into memory"
                               " to start processing")

        for current_author in current_authors:
            load_records_to_mem_cache(current_author['records'])
            authornamesid = [row['id'] for row in dat.AUTHOR_NAMES
                             if row['db_name'] == current_author['db_name']]

            if not authornamesid:
                bconfig.LOGGER.error("The author '%s' rec '%s' is not in authornames "
                                     "and will be skipped. You might want "
                                     "to run authornames update before?"
                                     % (current_author['db_name'], rec))
                continue
            else:
                try:
                    authornamesid = int(authornamesid[0])
                except (IndexError, TypeError, ValueError):
                    bconfig.LOGGER.error("Invalid authornames ID!")
                    continue

            if not current_author['records']:
                bconfig.LOGGER.error("The author '%s' is not associated to any"
                                     " document and will be skipped."
                                     % (current_author['db_name']))
                continue

            for rec in current_author['records']:
                # remove VAs already existing for the record
                va_ids = get_va_ids_by_recid_lname(rec,
                                                   current_author["last_name"])

                if va_ids:
                    for va_id in va_ids:
                        ra_list = get_realauthors_by_virtuala_id(va_id)

                        for ra_id in ra_list:
                            remove_va_from_ra(ra_id, va_id)
                            del_ra_data_by_vaid(ra_id, va_id)

                        va_anames_id = get_virtualauthor_records(va_id,
                                                        "orig_authorname_id")

                        for an_list in [row['authornameids'] for row in
                                    dat.DOC_LIST if row['bibrecid'] == rec]:
                            try:
                                an_list.remove(va_anames_id)
                            except (ValueError):
                                # This names id is not in the list...don't care
                                pass

                        delete_virtual_author(va_id)

                # create new VAs for the record.
                update_doclist(rec, authornamesid)
                dat.update_log("rec_updates", rec)

            create_vas_from_specific_doclist(current_author['records'])

        bconfig.LOGGER.log(25, "-- Relevant data pre-processed successfully.")
        start_computation(process_doclist=False,
                          process_orphans=True,
                          print_stats=True)
        bconfig.LOGGER.log(25, "-- Computation finished. Will write back to "
                               "the database now.")
        update_db_result = update_tables_from_mem_cache(return_ra_updates=True)

        if not update_db_result[0]:
            bconfig.LOGGER.log(25, "Writing to persistence layer failed.")
        else:
            if update_db_result[1]:
                for updated_ra in update_db_result[1]:
                    if updated_ra:
                        updated_ras.add(updated_ra[0])

            bconfig.LOGGER.log(25, "Done updating authorid universe.")

    personid_ra_format = []

    for ra_id in updated_ras:
        personid_ra_format.append((ra_id,))

    bconfig.LOGGER.log(25, "Will now run personid update to make the "
                       "changes visible also on the front end and to "
                       "create person IDs for %s newly created and changed "
                       "authors." % len(updated_ras))
    bibtask.task_update_progress('Updating persistent Person IDs')
    update_personID_from_algorithm(personid_ra_format)
    bconfig.LOGGER.log(25, "Done updating everything. Thanks for flying "
                       "with bibauthorid!")
def _update_authorid_universe():
    '''
    Updates all data related to the authorid algorithm.

    Sequence of operations:
        - Get all recently updated papers and remember time in the log
        - Get all authors on all papers
        - Extract collection of last names
        - For each last name:
            - Populate mem cache with cluster data
            - Delete updated records and their virtual authors from mem cache
            - Create virtual authors for new and updated records
            - Start matching algorithm
        - Update tables with results of the computation
        - Start personid update procedure
    '''
    def create_vas_from_specific_doclist(bibrec_ids):
        '''
        Processes the document list and creates a new minimal virtual author
        for each author in each record specified in the given list.

        @param bibrec_ids: Record IDs to concern in this update
        @type bibrec_ids: list of int
        '''
        num_docs = len(
            [row for row in dat.DOC_LIST if row['bibrecid'] in bibrec_ids])

        bconfig.LOGGER.log(
            25, "Creating minimal virtual authors for "
            "all loaded docs (%s)" % (num_docs))

        for docs in [
                row for row in dat.DOC_LIST if row['bibrecid'] in bibrec_ids
        ]:
            for author_id in docs['authornameids']:
                author_name = [
                    an['name'] for an in dat.AUTHOR_NAMES
                    if an['id'] == author_id
                ]
                refrecs = [
                    ref[1] for ref in docs['authornameid_bibrefrec']
                    if ref[0] == author_id
                ]
                refrec = -1

                if len(refrecs) > 1:
                    print "SCREEEEEEWWWWWWED!!! Several bibrefs on one paper?!"
                    refrec = refrecs[0]
                elif refrecs:
                    refrec = refrecs[0]

                if refrec and author_name:
                    add_minimum_virtualauthor(author_id, author_name[0],
                                              docs['bibrecid'], 0, [], refrec)
                elif author_name:
                    add_minimum_virtualauthor(author_id, author_name[0],
                                              docs['bibrecid'], 0, [])

    dat.reset_mem_cache(True)
    last_log = get_user_log(userinfo='daemon',
                            action='update_aid',
                            only_most_recent=True)
    updated_records = []

    if last_log:
        #select only the most recent papers
        recently_modified, last_update_time = get_papers_recently_modified(
            date=last_log[0][2])
        insert_user_log('daemon',
                        '-1',
                        'update_aid',
                        'bibsched',
                        'status',
                        comment='bibauthorid_daemon, update_authorid_universe',
                        timestamp=last_update_time[0][0])
        bibtask.write_message("Update authorid will operate on %s records." %
                              (len(recently_modified)),
                              stream=sys.stdout,
                              verbose=0)

        if not recently_modified:
            bibtask.write_message("Update authorid: Nothing to do",
                                  stream=sys.stdout,
                                  verbose=0)
            return

        for rec in recently_modified:
            updated_records.append(rec[0])
            dat.update_log("rec_updates", rec[0])

    else:
        bibtask.write_message("Update authorid: Nothing to do",
                              stream=sys.stdout,
                              verbose=0)
        return

    authors = []
    author_last_names = set()

    bibtask.task_update_progress('Reading authors from updated records')
    bibtask.write_message("Reading authors from updated records",
                          stream=sys.stdout,
                          verbose=0)
    updated_ras = set()

    # get all authors from all updated records
    for rec in updated_records:
        rec_authors = get_field_values_on_condition(rec, ['100', '700'],
                                                    "a",
                                                    source="API")

        for rec_author in rec_authors:
            if not rec_author:
                bconfig.LOGGER.error("Invalid empty author string, which "
                                     "will be skipped on record %s" % (rec))
                continue

            author_in_list = [
                row for row in authors if row['db_name'] == rec_author
            ]

            if author_in_list:
                for upd in [
                        row for row in authors if row['db_name'] == rec_author
                ]:
                    upd['records'].append(rec)
            else:
                last_name = split_name_parts(rec_author)[0]
                author_last_names.add(last_name)
                authors.append({
                    'db_name': rec_author,
                    'records': [rec],
                    'last_name': last_name
                })

    for status, author_last_name in enumerate(author_last_names):
        current_authors = [
            row for row in authors if row['last_name'] == author_last_name
        ]
        total_lnames = len(author_last_names)
        total_authors = len(current_authors)
        bibtask.task_update_progress(
            'Processing %s of %s cluster: "%s" '
            '(%s authors)' %
            (status + 1, total_lnames, author_last_name, total_authors))
        bibtask.write_message(
            'Processing %s of %s cluster: "%s" '
            '(%s authors)' %
            (status + 1, total_lnames, author_last_name, total_authors),
            stream=sys.stdout,
            verbose=0)
        dat.reset_mem_cache(True)
        init_authornames(author_last_name)
        load_mem_cache_from_tables()
        bconfig.LOGGER.log(
            25, "-- Relevant data successfully read into memory"
            " to start processing")

        for current_author in current_authors:
            load_records_to_mem_cache(current_author['records'])
            authornamesid = [
                row['id'] for row in dat.AUTHOR_NAMES
                if row['db_name'] == current_author['db_name']
            ]

            if not authornamesid:
                bconfig.LOGGER.error(
                    "The author '%s' rec '%s' is not in authornames "
                    "and will be skipped. You might want "
                    "to run authornames update before?" %
                    (current_author['db_name'], rec))
                continue
            else:
                try:
                    authornamesid = int(authornamesid[0])
                except (IndexError, TypeError, ValueError):
                    bconfig.LOGGER.error("Invalid authornames ID!")
                    continue

            if not current_author['records']:
                bconfig.LOGGER.error("The author '%s' is not associated to any"
                                     " document and will be skipped." %
                                     (current_author['db_name']))
                continue

            for rec in current_author['records']:
                # remove VAs already existing for the record
                va_ids = get_va_ids_by_recid_lname(rec,
                                                   current_author["last_name"])

                if va_ids:
                    for va_id in va_ids:
                        ra_list = get_realauthors_by_virtuala_id(va_id)

                        for ra_id in ra_list:
                            remove_va_from_ra(ra_id, va_id)
                            del_ra_data_by_vaid(ra_id, va_id)

                        va_anames_id = get_virtualauthor_records(
                            va_id, "orig_authorname_id")

                        for an_list in [
                                row['authornameids'] for row in dat.DOC_LIST
                                if row['bibrecid'] == rec
                        ]:
                            try:
                                an_list.remove(va_anames_id)
                            except (ValueError):
                                # This names id is not in the list...don't care
                                pass

                        delete_virtual_author(va_id)

                # create new VAs for the record.
                update_doclist(rec, authornamesid)
                dat.update_log("rec_updates", rec)

            create_vas_from_specific_doclist(current_author['records'])

        bconfig.LOGGER.log(25, "-- Relevant data pre-processed successfully.")
        start_computation(process_doclist=False,
                          process_orphans=True,
                          print_stats=True)
        bconfig.LOGGER.log(
            25, "-- Computation finished. Will write back to "
            "the database now.")
        update_db_result = update_tables_from_mem_cache(return_ra_updates=True)

        if not update_db_result[0]:
            bconfig.LOGGER.log(25, "Writing to persistence layer failed.")
        else:
            if update_db_result[1]:
                for updated_ra in update_db_result[1]:
                    if updated_ra:
                        updated_ras.add(updated_ra[0])

            bconfig.LOGGER.log(25, "Done updating authorid universe.")

    personid_ra_format = []

    for ra_id in updated_ras:
        personid_ra_format.append((ra_id, ))

    bconfig.LOGGER.log(
        25, "Will now run personid update to make the "
        "changes visible also on the front end and to "
        "create person IDs for %s newly created and changed "
        "authors." % len(updated_ras))
    bibtask.task_update_progress('Updating persistent Person IDs')
    update_personID_from_algorithm(personid_ra_format)
    bconfig.LOGGER.log(
        25, "Done updating everything. Thanks for flying "
        "with bibauthorid!")