def __init__(self, verbose=False, quiet=True):
ETL.__init__(self, verbose=verbose)
self.read_configfiles()
self.config["plugins"] = []
def run_etl_groups(cls, logger, data_manager, neo_transactor):
"""This function runs each of the ETL in parallel"""
etl_time_tracker_list = []
for etl_group in cls.etl_groups:
etl_group_start_time = time.time()
logger.info("Starting ETL group: %s" % etl_group)
thread_pool = []
for etl_name in etl_group:
logger.info("ETL Name: %s" % etl_name)
config = data_manager.get_config(etl_name)
if config is not None:
etl = cls.etl_dispatch[etl_name](config)
process = multiprocessing.Process(target=etl.run_etl)
process.start()
thread_pool.append(process)
else:
logger.info("No Config found for: %s" % etl_name)
ETL.wait_for_threads(thread_pool)
logger.info("Waiting for Queues to sync up")
neo_transactor.check_for_thread_errors()
neo_transactor.wait_for_queues()
etl_elapsed_time = time.time() - etl_group_start_time
etl_time_message = (
"Finished ETL group: %s, Elapsed time: %s" %
(etl_group,
time.strftime("%H:%M:%S", time.gmtime(etl_elapsed_time))))
logger.info(etl_time_message)
etl_time_tracker_list.append(etl_time_message)
return etl_time_tracker_list
def export_row_data_to_index(self, data, rownumber):
parameters = self.config.copy()
# todo: all content plugins configurated, not only this one
parameters['plugins'] = [
'enhance_path',
'enhance_entity_linking',
'enhance_multilingual',
]
etl = ETL()
try:
etl.process( parameters=parameters, data=data)
# if exception because user interrupted by keyboard, respect this and abbort
except KeyboardInterrupt:
raise KeyboardInterrupt
except BaseException as e:
sys.stderr.write( "Exception adding CSV row {} : {}".format(rownumber, e) )
if 'raise_pluginexception' in self.config:
if self.config['raise_pluginexception']:
raise e
def __init__(self, verbose=False):
ETL.__init__(self, verbose=verbose)
self.verbose = verbose
self.read_configfiles()
# Watched events
#
# We need IN_MOVE_SELF to track moved folder paths
# pyinotify-internally. If omitted, the os instructions
# mv /docs/src /docs/dest; touch /docs/dest/doc.pdf
# will produce a IN_MOVED_TO pathname=/docs/dest/ followed by
# IN_CLOSE_WRITE pathname=/docs/src/doc.pdf
# where we would like a IN_CLOSE_WRITE pathname=/docs/dest/doc.pdf
self.mask = (pyinotify.IN_DELETE
| pyinotify.IN_CLOSE_WRITE
| pyinotify.IN_MOVED_TO
| pyinotify.IN_MOVED_FROM
| pyinotify.IN_MOVE_SELF)
self.watchmanager = pyinotify.WatchManager() # Watch Manager
self.handler = EventHandler()
self.notifier = pyinotify.Notifier(self.watchmanager, self.handler)
def set_configdefaults(self):
#
# Standard config
#
# Do not edit config here! Overwrite options in /etc/etl/ or /etc/opensemanticsearch/connector-files
#
ETL.set_configdefaults(self)
self.config['force'] = False
# filename to URI mapping
self.config['mappings'] = {"/": "file:///"}
self.config['facet_path_strip_prefix'] = [
"file://", "http://www.", "https://www.", "http://", "https://"
]
self.config['plugins'] = [
'enhance_mapping_id',
'filter_blacklist',
'filter_file_not_modified',
'enhance_extract_text_tika_server',
'enhance_detect_language_tika_server',
'enhance_contenttype_group',
'enhance_pst',
'enhance_csv',
'enhance_file_mtime',
'enhance_path',
'enhance_extract_hashtags',
'enhance_warc',
'enhance_zip',
'clean_title',
'enhance_multilingual',
]
self.config['blacklist'] = [
"/etc/opensemanticsearch/blacklist/blacklist-url"
]
self.config['blacklist_prefix'] = [
"/etc/opensemanticsearch/blacklist/blacklist-url-prefix"
]
self.config['blacklist_suffix'] = [
"/etc/opensemanticsearch/blacklist/blacklist-url-suffix"
]
self.config['blacklist_regex'] = [
"/etc/opensemanticsearch/blacklist/blacklist-url-regex"
]
self.config['whitelist'] = [
"/etc/opensemanticsearch/blacklist/whitelist-url"
]
self.config['whitelist_prefix'] = [
"/etc/opensemanticsearch/blacklist/whitelist-url-prefix"
]
self.config['whitelist_suffix'] = [
"/etc/opensemanticsearch/blacklist/whitelist-url-suffix"
]
self.config['whitelist_regex'] = [
"/etc/opensemanticsearch/blacklist/whitelist-url-regex"
]
def export_row_data_to_index(self, data, rownumber):
parameters = self.config.copy()
# todo: all content plugins configurated, not only this one
parameters['plugins'] = [
'enhance_path',
]
etl = ETL()
try:
etl.process(parameters=parameters, data=data)
# if exception because user interrupted by keyboard, respect this and abbort
except KeyboardInterrupt:
raise KeyboardInterrupt
except BaseException as e:
sys.stderr.write("Exception adding CSV row {} : {}".format(
rownumber, e.message))
if 'raise_pluginexception' in self.config:
if self.config['raise_pluginexception']:
raise e
def getTargetDdl(self, tableformat, external=True, _ddl=""):
ddl = _ddl
databasename = self.metaresultlist[0].target_database
tablename = self.metaresultlist[0].target_table
tablelocation = self.metaresultlist[0].target_file_path
if external is True and ETL.isNullOrEmpty(databasename) is None:
ddl = f"CREATE EXTERNAL TABLE {tablename}(\n"
elif external is True and ETL.isNullOrEmpty(databasename) is not None:
ddl = f"CREATE EXTERNAL TABLE {databasename}.{tablename}(\n"
elif external is False and ETL.isNullOrEmpty(databasename) is None:
ddl = f"CREATE TABLE {tablename}(\n"
elif external is False and ETL.isNullOrEmpty(databasename) is not None:
ddl = f"CREATE TABLE {databasename}.{tablename}(\n"
else:
ddl = f"CREATE EXTERNAL TABLE {databasename}.{tablename}(\n"
for metares in self.metaresultlist:
if int(str(metares.src_table_order).strip()).__eq__(0):
ddl = f"{ddl}`{metares.target_col}` {metares.target_col_datatype},\n"
ddl = f"{ddl}--End"
ddl = ddl.strip(',\n--End')
ddl = f"{ddl}\n)" \
f"STORED AS {tableformat}"
if ETL.isNullOrEmpty(tablelocation) is not None and external is True:
ddl = f"{ddl}\nLOCATION {tablelocation}"
return ddl
def __init__(self, verbose=False, quiet=True): ETL.__init__(self, verbose=verbose) self.read_configfiles() self.config["plugins"] = []
def count_word(self):
"""
Count stop words and output statistics.
"""
word_list = []
result = ETL().extract_word()
count, total = 0, len(result)
for row in result:
count += 1
test_id = row[0]
print(f"{test_id}, {count}/{total}")
try:
dump = ETL().extract_cdb(test_id)
processed = Process(dump).internal_process()
except (IndexError, UnicodeDecodeError):
continue
if "\n\n" in dump:
exceptions = dump[dump.index("\n\n") + len("\n\n"):]
try:
header = "exception throw location:\n"
stack = exceptions[exceptions.index(header) + len(header):]
except ValueError:
continue
# extract root cause from exceptions
if dump.count(header) > 1:
stack = stack[:stack.index("\n\n")]
roots = re.findall(r"^\d+:[ ](.+)[ ]at[ ].+", stack, re.M)
words = self.obtain_word(roots, processed)
word_list += words
Log().chart_print(Counter(word_list).most_common(10))
class Task:
def __init__(self, name, question, db_table, row_handler, answer_cql):
self._name = name
self._question = question
self._db_table = db_table
self._answer_cql = answer_cql
self._etl = ETL(
f"{name} ETL",
[helper.join_path(TEMP_DIR, 'staging.csv')],
{
"target": 'Cassandra',
"table": db_table["table_name"],
"is_file": False
},
[i[0] for i in db_table["cols"]],
row_handler,
)
logger.info(f"{self._name} - Question: {self._question}")
def _create_table(self):
table_name, cols, key = self._db_table.values()
cql_col_types = ', '.join([f"{col[0]} {col[1]}" for col in cols])
db.execute(
f"CREATE TABLE IF NOT EXISTS {table_name} ({cql_col_types}, PRIMARY KEY({key}))"
)
logger.info(f"{self._name} - Create '{table_name}' table")
def _get_result(self):
result = db.fetch(self._answer_cql)
result_col_name = helper.get_str_between(self._answer_cql, 'SELECT',
'FROM')[0].strip().split(', ')
try:
with open(helper.join_path(RESULT_DIR, f'{self._name}.csv'),
'a') as target_file:
writer = csv.writer(target_file, dialect='Dialect')
writer.writerow(result_col_name)
for row in result:
writer.writerow(row)
except IOError as e:
logger.error(e)
except:
logger.error(f"Unexpected error: {sys.exc_info()[0]}")
logger.info(
f"{self._name} - Complete generate '{self._name}.csv' file")
def run(self):
self._create_table()
self._etl.run()
logger.info(f"{self._name} - Complete ETL process")
self._get_result()
def transform(self):
# Get Unique source table names for Transformation
srctables = set()
for metares in self.model.metaresultlist:
srctables.add(metares.src_table)
# For each source table create SourceTable object and assign transform columns
for srctable in srctables:
tablemetaresult = self.model.filterMetaResultBySourceTable(
srctbl=srctable)
tblinfo: MetaResult = tablemetaresult[0]
fklist = []
for item in self.model.datamodel.keys():
if self.model.datamodel[item][
'fk'] is not None or self.model.datamodel[item][
'fk'] is {}:
if srctable in self.model.datamodel[item]['fk'].keys():
fklist.extend(self.model.datamodel[item]['fk']
[srctable]['fk_pk'])
sourcetable: SourceTable = SourceTable(
sourcesystem=tblinfo.src_system,
tablename=tblinfo.src_table,
pk=self.model.datamodel[tblinfo.src_table]['pk'],
fk=fklist,
database=tblinfo.src_database,
filepath=tblinfo.src_file_path,
filetype=tblinfo.src_filetype,
modeltableorder=tblinfo.src_table_order)
self.sourcetables.append(sourcetable)
for tbl in tablemetaresult:
sourcetable.addColumn(
name=tbl.src_col,
type=tbl.src_col_datatype,
pk=(True, False)[tbl.src_key_constraints.__eq__('pk')],
udf=tbl.udf,
udfargs=tbl.udfarguments,
casttype=tbl.target_col_datatype,
aliasname=tbl.target_col,
filterclause=tbl.src_col_filter,
fk={})
# Read file as dataframe
sourcetable.readFileFromSource(spark=self.spark)
ETL.registerAllUDF(sc=self.spark)
for sourcetable in self.sourcetables:
sourcetable.applyTransform()
self.applyJoin()
self.applyFilters()
self.applyGroupAggregation()
self.targetdf.show()
def __init__(self, verbose=False, quiet=True): ETL.__init__(self, verbose=verbose) self.quiet = quiet self.set_configdefaults() self.read_configfiles()
def applyColTransform(self, query, src_table, src_col, target_col, target_col_datatype, udf, udfarguments):
if ETL.isNullOrEmpty(udf) is not None and len(udfarguments) is not 0:
query = f"{query} CAST({udf}({src_table}.`{src_col}`, {','.join(udfarguments)}) AS {target_col_datatype}) AS {target_col},"
elif ETL.isNullOrEmpty(udf) is not None and len(udfarguments) is 0:
query = f"{query} CAST({udf}({src_table}.`{src_col}`) AS {target_col_datatype}) AS {target_col},"
else:
query = f"{query} CAST({src_table}.`{src_col}` AS {target_col_datatype}) AS {target_col},"
return query
def _load_and_process_data(self):
thread_pool = []
for sub_type in self.data_type_config.get_sub_type_objects():
process = multiprocessing.Process(target=self._process_sub_type, args=(sub_type,))
process.start()
thread_pool.append(process)
ETL.wait_for_threads(thread_pool)
def __init__(self, verbose=False, quiet=True):
ETL.__init__(self, verbose=verbose)
self.quiet = quiet
self.set_configdefaults()
self.read_configfiles()
def set_configdefaults(self):
#
# Standard config
#
# Do not edit config here! Overwrite options in /etc/etl/ or /etc/opensemanticsearch/connector-files
#
ETL.set_configdefaults(self)
self.config['force'] = False
def set_configdefaults(self):
#
# Standard config
#
# Do not edit config here! Overwrite options in /etc/etl/ or /etc/opensemanticsearch/connector-files
#
ETL.set_configdefaults(self)
self.config['force'] = False
def setUp(self):
self.etl = ETL()
data = {
'customer_id': [1, 1],
'order_id': [1, 2],
'order_item_id': [5, 6],
'num_items': [2, 3],
'revenue': [90, 50],
'created_at_date': [datetime(2017, 10, 5),
datetime(2017, 10, 12)]
}
self.test_df = pd.DataFrame.from_dict(data)
def _load_and_process_data(self):
thread_pool = []
ensg_to_gene_primary_id_map = self._get_primary_gene_ids_to_ensembl_ids(
)
for sub_type in self.data_type_config.get_sub_type_objects():
process = multiprocessing.Process(
target=self._process_sub_type,
args=(sub_type, ensg_to_gene_primary_id_map))
process.start()
thread_pool.append(process)
ETL.wait_for_threads(thread_pool)
def ETI_TEST():
print("Staring ETL Test Job !!!!")
var = Variable()
var.INPUT_DATA = "/input/employee.csv"
csvParser = csv_parser(var.INPUT_DATA)
if csvParser.file_exist(var.INPUT_DATA):
TABLE_NAME = csvParser.get_table_name(
var.INPUT_DATA) # Takes Table name from Filename
if var.CREATE_TABLE and not var.RELATION:
ob = ETL(TABLE_NAME, var.INPUT_DATA)
ob.etl_process(csvParser.check_header(), 20)
def main():
print("Staring ETL Job !!!!")
var = Variable()
csvParser = csv_parser(var.INPUT_DATA)
if csvParser.file_exist(var.INPUT_DATA):
TABLE_NAME = csvParser.get_table_name(
var.INPUT_DATA) # Takes Table name from Filename
if var.CREATE_TABLE and not var.RELATION:
ob = ETL(TABLE_NAME, var.INPUT_DATA)
ob.etl_process(csvParser.check_header())
def enrich(plugins, uri, wait=0):
if wait:
time.sleep(wait)
etl = ETL()
etl.read_configfile('/etc/opensemanticsearch/etl')
etl.read_configfile('/etc/opensemanticsearch/enhancer-rdf')
etl.config['plugins'] = plugins.split(',')
filename = uri
# if exist delete protocoll prefix file://
if filename.startswith("file://"):
filename = filename.replace("file://", '', 1)
parameters = etl.config.copy()
parameters['id'] = uri
parameters['filename'] = filename
parameters, data = etl.process(parameters=parameters, data={})
return data
def main():
"""The `main` function, to be called from commandline, like `python src/main.py -c etl.cfg`.
Args:
-c --config <config_file> the Stetl config file.
-s --section <section_name> the section in the Stetl config (ini) file to execute (default is [etl]).
-a --args <arglist> substitutable args for symbolic, {arg}, values in Stetl config file, in format "arg1=foo arg2=bar" etc.
"""
args = parse_args()
# Do the ETL
etl = ETL(vars(args), args.config_args)
etl.run()
def main():
parser = argparse.ArgumentParser(
description='CLI for the pldb application.')
parser.add_argument(
'--update',
action='store_true',
help='Download season data and update the JSON file and the database.')
parser.add_argument(
'--table',
action='store_true',
help=
'Display the current standings table (calculated from data in the database).'
)
parser.add_argument(
'--club',
type=str,
default=None,
help=
'Display info for all the matches for the given club in the season.')
args = parser.parse_args()
if args.update:
print("Updating season data...")
etl = ETL()
etl.run()
print("done.")
elif args.table:
query = Query()
table_data = query.table()
print("#\tClub\tPlayed\tWon\tDrawn\tLost\tGD\tPoints")
for rank in range(len(table_data)):
row = table_data[rank]
print(
f"{rank + 1}\t{row['club']}\t{row['matches_played']}\t"
f"{row['wins']}\t{row['draws']}\t{row['losses']}\t{row['goal_diff']}\t"
f"{row['points']}")
elif args.club:
query = Query()
for match in query.club(args.club):
kick_time = match['kickoff'] / 1000
kick_time = datetime.datetime.fromtimestamp(kick_time).strftime(
"%a %d %b %H:%M")
if match['status'] == 'C':
score = f"{match['away_goals']} {match['home_goals']}"
else:
score = ' @ '
print(
f"{kick_time} {match['away_club']['abbr']} "
f"{score} {match['home_club']['abbr']} {match['ground']['name']}"
)
def main():
"""The `main` function, to be called from commandline, like `python src/main.py -c etl.cfg`.
Args:
-c --config <config_file> the Stetl config file.
-s --section <section_name> the section in the Stetl config (ini) file to execute (default is [etl]).
-a --args <arglist> substitutable args for symbolic, {arg}, values in Stetl config file, in format "arg1=foo arg2=bar" etc.
"""
args = parse_args()
# Do the ETL
etl = ETL(vars(args), args.config_args)
etl.run()
def __init__(self, verbose=False):
ETL.__init__(self, verbose=verbose)
self.verbose = verbose
self.read_configfiles()
self.mask = pyinotify.IN_DELETE | pyinotify.IN_CLOSE_WRITE | pyinotify.IN_MOVED_TO | pyinotify.IN_MOVED_FROM # watched events
self.watchmanager = pyinotify.WatchManager() # Watch Manager
self.handler = EventHandler()
self.notifier = pyinotify.Notifier(self.watchmanager, self.handler)
def __init__(self, verbose = False ): ETL.__init__(self, verbose=verbose) self.verbose=verbose self.read_configfiles() self.mask = pyinotify.IN_DELETE | pyinotify.IN_CLOSE_WRITE | pyinotify.IN_MOVED_TO | pyinotify.IN_MOVED_FROM # watched events self.watchmanager = pyinotify.WatchManager() # Watch Manager self.handler = EventHandler() self.notifier = pyinotify.Notifier(self.watchmanager, self.handler)
def __init__(self, plugins=[], verbose=False ):
ETL.__init__(self, plugins=plugins, verbose=verbose)
self.read_configfile ('/etc/etl/config')
self.read_configfile ('/etc/opensemanticsearch/etl')
self.read_configfile ('/etc/opensemanticsearch/enhancer-rdf')
self.fields = self.getfieldnames_from_plugins()
# init exporter (todo: exporter as extended PySolr)
self.export_solr = export_solr.export_solr()
# init PySolr
solr_uri = self.config['solr']
if not solr_uri.endswith('/'):
solr_uri += '/'
solr_uri += self.config['index']
self.solr = pysolr.Solr( solr_uri )
self.threads_max = None
# if not set explicit, autodetection of count of CPUs for amount of threads
if not self.threads_max:
import multiprocessing
self.threads_max = multiprocessing.cpu_count()
if self.verbose:
print ( "Setting threads to count of CPUs: " + str(self.threads_max) )
self.rows_per_step = 100
if self.rows_per_step < self.threads_max * 2:
self.rows_per_step = self.threads_max * 2
self.work_in_progress = []
self.delete_from_work_in_progress_lock = threading.Lock()
self.delete_from_work_in_progress_after_commit = []
self.work_in_progress_lock = threading.Lock()
self.e_job_done = threading.Event()
def run_etl():
#initialize auth_controller
auth_controller = AuthController('http://restservice:8001/ETL/api/v1.0/', 'auths')
#initialize data_controller
data_controller = DataController('http://restservice:8001/ETL/api/v1.0/')
#initialize sftp_controller
sftp_controller = SftpController('sftpserver.pyc.test', 'etluser', 'sftpserver_keys/sftpserver_rsa', 'IntuitPYC')
#initialize vertica_controller
vertica_controller = VerticaController('config/vsql.config')
etl = ETL(auth_controller, data_controller, sftp_controller, vertica_controller)
etl.run()
def getWhereClauses(self):
def matchEqualityOperator(expression):
expr = str(expression).strip()
if expr.__contains__('eq'):
expr = expr.replace('eq(', '=').replace(')', '', 1)
if expr.__contains__('gt'):
expr = expr.replace('gt(', '>').replace(')', '', 1)
elif expr.__contains__('lt'):
expr = expr.replace('lt(', '<').replace(')', '', 1)
elif expr.__contains__('lte'):
expr = expr.replace('lte(', '<=').replace(')', '', 1)
elif expr.__contains__('gte'):
expr = expr.replace('gte(', '>=').replace(')', '', 1)
elif expr.__contains__('notin'):
expr = expr.replace('notin(', 'NOT IN').replace(')', '', 1)
elif expr.__contains__('in'):
expr = expr.replace('in(', 'IN').replace(')', '', 1)
elif expr.__contains__('ne'):
expr = expr.replace('ne(', '<>').replace(')', '', 1)
else:
expr = str(expression).strip()
return expr
query, joindict = self.joinSQL(self.datamodel, 'purchase', 'product', 'store')
wherequery = ""
for metares in self.metaresultlist:
if str(metares.src_col_filter).strip() is not None and not str(metares.src_col_filter).strip().__eq__(""):
wherequery = f"{metares.src_table}.`{metares.src_col}` {self.matchEqualityOperator(metares.src_col_filter)}"
if ETL.isNullOrEmpty(wherequery) is not None:
query = f"{query} WHERE {wherequery}"
return query
def __init__(self, src_system, src_database, src_table, src_filetype, src_file_path, src_col, src_col_datatype,
src_key_constraints,
src_col_filter,
src_col_aggregator,
src_col_aggregator_filter,
src_table_order,
target_database,
target_table,
target_filetype,
target_file_path, target_col, target_col_datatype, udf="", udfarguments=""):
self.metacolumnslist = {}
self.src_system = src_system
self.src_database = src_database
self.src_table = src_table
self.src_filetype = src_filetype
self.src_file_path = src_file_path
self.src_col = src_col
self.src_col_datatype = str(src_col_datatype).lower()
self.src_key_constraints = str(src_key_constraints).lower()
self.src_col_filter = src_col_filter
self.src_col_aggregator = src_col_aggregator
self.src_col_aggregator_filter = src_col_aggregator_filter
self.src_table_order = int(str(src_table_order).strip())
self.target_database = target_database
self.target_table = target_table
self.target_filetype = target_filetype
self.target_file_path = target_file_path
self.target_col = target_col
self.target_col_datatype = target_col_datatype
self.target_col_aggregator = ""
self.target_col_aggregator_filter = ""
self.udf = udf
if ETL.isNullOrEmpty(udfarguments) is not None:
self.udfarguments = udfarguments.split('|')
else:
self.udfarguments = []
self.metacolumnslist.update({'src_filetype': self.src_filetype})
self.metacolumnslist.update({'src_system': self.src_system})
self.metacolumnslist.update({'src_database': self.src_database})
self.metacolumnslist.update({'src_table': self.src_table})
self.metacolumnslist.update({'src_file_path': self.src_table})
self.metacolumnslist.update({'src_col': self.src_table})
self.metacolumnslist.update({'src_col_datatype': self.src_col_datatype})
self.metacolumnslist.update({'src_key_constraints': self.src_key_constraints})
self.metacolumnslist.update({'src_col_filter': self.src_col_filter})
self.metacolumnslist.update({'src_col_aggregator': self.src_col_aggregator})
self.metacolumnslist.update({'src_col_aggregator_filter': self.src_col_aggregator_filter})
self.metacolumnslist.update({'src_table_order': self.src_table_order})
self.metacolumnslist.update({'target_database': self.target_database})
self.metacolumnslist.update({'target_table': self.target_table})
self.metacolumnslist.update({'target_filetype': self.target_filetype})
self.metacolumnslist.update({'target_file_path': self.target_file_path})
self.metacolumnslist.update({'target_col': self.target_col})
self.metacolumnslist.update({'target_col_datatype': self.target_col_datatype})
self.metacolumnslist.update({'target_col_aggregator': self.target_col_aggregator})
self.metacolumnslist.update({'target_col_aggregator_filter': self.target_col_aggregator_filter})
self.metacolumnslist.update({'udf': self.udf})
self.metacolumnslist.update({'udfarguments': self.udfarguments})
def __init__(self, verbose=False, quiet=True):
ETL.__init__(self, verbose=verbose)
self.quiet = quiet
self.set_configdefaults()
self.read_configfiles()
# read on what DB or search server software our index is
export = self.config['export']
# call delete function of the configured exporter
module = importlib.import_module(export)
objectreference = getattr(module, export)
self.connector = objectreference()
def __init__(self, verbose=False, quiet=True):
ETL.__init__(self, verbose=verbose)
self.quiet = quiet
self.set_configdefaults()
self.read_configfiles()
# read on what DB or search server software our index is
export = self.config['export']
# call delete function of the configured exporter
module = importlib.import_module(export)
objectreference = getattr(module, export)
self.connector = objectreference()
def enrich(plugins, uri, wait=0):
if wait:
time.sleep(wait)
etl = ETL()
etl.read_configfile('/etc/opensemanticsearch/etl')
etl.read_configfile('/etc/opensemanticsearch/enhancer-rdf')
etl.config['plugins'] = plugins.split(',')
filename = uri
# if exist delete protocoll prefix file://
if filename.startswith("file://"):
filename = filename.replace("file://", '', 1)
parameters = etl.config.copy()
parameters['id'] = uri
parameters['filename'] = filename
parameters, data = etl.process (parameters=parameters, data={})
return data
def __init__(self, name, question, db_table, row_handler, answer_cql):
self._name = name
self._question = question
self._db_table = db_table
self._answer_cql = answer_cql
self._etl = ETL(
f"{name} ETL",
[helper.join_path(TEMP_DIR, 'staging.csv')],
{
"target": 'Cassandra',
"table": db_table["table_name"],
"is_file": False
},
[i[0] for i in db_table["cols"]],
row_handler,
)
logger.info(f"{self._name} - Question: {self._question}")
def _load_and_process_data(self):
thread_pool = []
query_tracking_list = multiprocessing.Manager().list()
for sub_type in self.data_type_config.get_sub_type_objects():
process = multiprocessing.Process(target=self._process_sub_type,
args=(sub_type,
query_tracking_list))
process.start()
thread_pool.append(process)
ETL.wait_for_threads(thread_pool)
queries = []
for item in query_tracking_list:
queries.append(item)
Neo4jTransactor.execute_query_batch(queries)
def update_mapping_new_product_id(self):
logging.info("Create new product id after pruning dataset")
_r_map = self.dataset[['PRODUCT_ID', 'NEW_PRODUCT_ID']]
mm = [_r_map['PRODUCT_ID'].unique(), _r_map['NEW_PRODUCT_ID'].unique()]
mapping = pd.DataFrame(data=np.array(mm).T,
columns=["product_id", "new_product_id"])
logging.info("Save new product id into db")
ETL(DATA_PATH, CONFIG_PATH,
SCHEMA_PATH).insert_new_product_id_table(mapping)
def __init__(self, verbose=False, quiet=True):
ETL.__init__(self, verbose=verbose)
self.quiet = quiet
self.set_configdefaults()
self.read_configfiles()
# if not set explicit, autodetection of count of CPUs for amount of threads
if not self.threads_max:
import multiprocessing
self.threads_max = multiprocessing.cpu_count()
if self.verbose:
print("Setting threads to count of CPUs: " +
str(self.threads_max))
self.e_job_done = threading.Event()
def _load_and_process_data(self):
sub_types = []
for sub_type in self.data_type_config.get_sub_type_objects():
sub_types.append(sub_type.get_data_provider())
thread_pool = []
query_tracking_list = multiprocessing.Manager().list()
for sub_type in self.data_type_config.get_sub_type_objects():
process = multiprocessing.Process(target=self._process_sub_type,
args=(sub_type, sub_types,
query_tracking_list))
process.start()
thread_pool.append(process)
ETL.wait_for_threads(thread_pool)
queries = []
for item in query_tracking_list:
queries.append(item)
algo_queries = []
for item in queries:
if "algorithm" in item[1]:
algo_queries.append(item)
main_list = self.get_randomized_list(sub_types)
for file_set in main_list:
for pair in file_set:
for item in queries:
if pair[0] + "_" + pair[1] in item[1]:
self.logger.debug("Pair: %s Item: %s", pair, item[1])
Neo4jTransactor.execute_query_batch([item])
Neo4jTransactor().wait_for_queues()
Neo4jTransactor.execute_query_batch(algo_queries)
self.error_messages()
def set_configdefaults(self):
#
# Standard config
#
# Do not edit config here! Overwrite options in /etc/etl/ or /etc/opensemanticsearch/connector-files
#
ETL.set_configdefaults(self)
self.config['force'] = False
# filename to URI mapping
self.config['mappings'] = { "/": "file:///" }
self.config['facet_path_strip_prefix'] = [ "file://", "http://www.", "https://www.", "http://", "https://" ]
self.config['plugins'] = [
'enhance_mapping_id',
'filter_blacklist',
'filter_file_not_modified',
'enhance_extract_text_tika_server',
'enhance_detect_language_tika_server',
'enhance_contenttype_group',
'enhance_pst',
'enhance_csv',
'enhance_file_mtime',
'enhance_path',
'enhance_extract_hashtags',
'enhance_warc',
'enhance_zip',
'clean_title',
'enhance_multilingual',
]
self.config['blacklist'] = ["/etc/opensemanticsearch/blacklist/blacklist-url"]
self.config['blacklist_prefix'] = ["/etc/opensemanticsearch/blacklist/blacklist-url-prefix"]
self.config['blacklist_suffix'] = ["/etc/opensemanticsearch/blacklist/blacklist-url-suffix"]
self.config['blacklist_regex'] = ["/etc/opensemanticsearch/blacklist/blacklist-url-regex"]
self.config['whitelist'] = ["/etc/opensemanticsearch/blacklist/whitelist-url"]
self.config['whitelist_prefix'] = ["/etc/opensemanticsearch/blacklist/whitelist-url-prefix"]
self.config['whitelist_suffix'] = ["/etc/opensemanticsearch/blacklist/whitelist-url-suffix"]
self.config['whitelist_regex'] = ["/etc/opensemanticsearch/blacklist/whitelist-url-regex"]
def main():
"""The `main` function, to be called from commandline, like `python src/main.py -c etl.cfg`.
Args:
-c --config <config_file> the Stetl config file.
-s --section <section_name> the section in the Stetl config (ini) file to execute (default is [etl]).
-a --args <arglist> substitutable args for symbolic, {arg}, values in Stetl config file, in format "arg1=foo arg2=bar" etc.
-d --doc <class> Get component documentation like its configuration parameters, e.g. stetl --doc stetl.inputs.fileinput.FileInput
-h --help get help info
"""
args = parse_args()
if args.config_file:
# Do the ETL
etl = ETL(vars(args), args.config_args)
etl.run()
elif args.doc_args:
print_doc(args.doc_args)
else:
print('Unknown option, try stetl -h for help')
def etl_graph(self, parameters):
if self.verbose:
print("Graph has {} triples.".format(len(self.graph)) )
count_triple = 0
count_subjects = 0
part_parameters = {}
part_parameters['plugins'] = []
part_parameters['export'] = parameters['export']
property2facet = {}
if 'property2facet' in parameters:
property2facet = parameters['property2facet']
etl_processor = ETL()
etl_processor.verbose = self.verbose
class_properties = []
class_properties.append(rdflib.term.URIRef(u'http://www.w3.org/1999/02/22-rdf-syntax-ns#type'))
class_properties.append(rdflib.term.URIRef(u'http://www.wikidata.org/prop/direct/P31'))
# since there can be multiple triples/values for same property in/from different graphs or graph describes existing other file/document,
# do not overwrite document but add value to existent document & values of the facet/field/property
part_parameters['add'] = True
# use SPARQL query with distinct to get subjects only once
res = self.graph.query(
"""SELECT DISTINCT ?subject
WHERE {
?subject ?predicate ?object .
}""")
for row in res:
count_subjects += 1
if self.verbose:
print( "Importing entity / subject {}".format(count_subjects) )
# get subject of the concept from first column
subj = row[0]
if self.verbose:
print ( "Processing RDF subject {}".format(subj) )
part_data = {}
part_data['content_type_group_ss'] = 'Knowledge graph'
# subject as URI/ID
part_parameters['id'] = subj
preferred_label = self.get_preferred_label(subject=subj)
part_data['title_txt'] = preferred_label
count_subject_triple = 0
# get all triples for this subject
for pred, obj in self.graph.predicate_objects(subject=subj):
count_triple += 1
count_subject_triple += 1
if self.verbose:
print( "Importing subjects triple {}".format(count_subject_triple) )
print( "Predicate / property: {}".format(pred) )
print( "Object / value: {}".format(obj) )
try:
# if class add preferredlabel of this entity to facet of its class (RDF rdf:type or Wikidata "instance of" (Property:P31)),
# so its name (label) will be available in entities view and as filter for faceted search
if pred in class_properties:
class_facet = str(obj)
# map class to facet, if mapping for class exist
if class_facet in property2facet:
class_facet = property2facet[class_facet]
if class_facet in parameters['facets']:
part_data['content_type_ss'] = 'Knowledge graph class {}'.format(parameters['facets'][class_facet]['label'])
etl.append(data=part_data, facet=class_facet, values=preferred_label)
#
# Predicate/property to facet/field
#
# set Solr datatype strings so facets not available yet in Solr schema can be inserted automatically (dynamic fields) with right datatype
facet = pred + '_ss'
facet_uri = facet + '_uri_ss'
facet_preferred_label_and_uri = facet + '_preflabel_and_uri_ss'
if self.verbose:
print ( "Facet: {}".format(facet) )
#
# get values or labels of this object
#
values = self.get_values(obj=obj)
if self.verbose:
print ( "Values: {}".format(values) )
# insert or append value (object of triple) to data
etl.append(data=part_data, facet=facet, values=values)
# if object is reference/URI append URI
if type(obj) == rdflib.URIRef:
uri = obj
etl.append( data=part_data, facet=facet_uri, values=uri )
# append mixed field with preferred label and URI of the object for disambiguation of different Entities/IDs/URIs with same names/labels in faceted search
preferredlabel_and_uri = "{} <{}>".format ( self.get_preferred_label(subject=obj), obj)
else:
preferredlabel_and_uri = self.get_preferred_label(subject=obj)
etl.append(data=part_data, facet=facet_preferred_label_and_uri, values=preferredlabel_and_uri)
except KeyboardInterrupt:
raise KeyboardInterrupt
except BaseException as e:
sys.stderr.write( "Exception while triple {} of subject {}: {}\n".format(count_subject_triple, subj, e) )
# index triple
etl_processor.process( part_parameters, part_data)
def run(self):
print("running")
etl = ETL()
etl.run()
def process (self, parameters={}, data={} ):
verbose = False
if 'verbose' in parameters:
if parameters['verbose']:
verbose = True
if 'id' in data:
docid = data['id']
else:
docid = parameters['id']
# default classifier
classifier = 'en_core_web_sm'
if 'spacy_ner_classifier_default' in parameters:
classifier = parameters['spacy_ner_classifier_default']
# set language specific classifier, if configured and document language detected
if 'spacy_ner_classifiers' in parameters and 'language_s' in data:
# is a language speciic cassifier there for the detected language?
if data['language_s'] in parameters['spacy_ner_classifiers']:
classifier = parameters['spacy_ner_classifiers'][data['language_s']]
analyse_fields = ['content_txt','ocr_t','ocr_descew_t']
text = ''
for field in analyse_fields:
if field in data:
text = "{}{}\n".format(text, data[field])
# extract sentences from text
url = "http://localhost:8080/sents"
headers = {'content-type': 'application/json'}
d = {'text': text, 'model': classifier}
response = requests.post(url, data=json.dumps(d), headers=headers)
sentences = response.json()
etl = ETL()
sentencenumber = 0
for sentence in sentences:
sentencenumber +=1
partdocid = docid + '#sentence' + str(sentencenumber)
partparameters = parameters.copy()
partparameters['plugins'] = ['enhance_path', 'enhance_detect_language_tika_server', 'enhance_entity_linking', 'enhance_multilingual']
if 'enhance_ner_spacy' in parameters['plugins']:
partparameters['plugins'].append('enhance_ner_spacy')
if 'enhance_ner_stanford' in parameters['plugins']:
partparameters['plugins'].append('enhance_ner_stanford')
sentencedata = {}
sentencedata['id'] = partdocid
sentencedata['container_s'] = docid
if 'author_ss' in data:
sentencedata['author_ss'] = data['author_ss']
sentencedata['content_type_group_ss'] = "Sentence"
sentencedata['content_type_ss'] = "Sentence"
sentencedata['content_txt'] = sentence
# index sentence
try:
partparameters, sentencedata = etl.process( partparameters, sentencedata )
except BaseException as e:
sys.stderr.write( "Exception adding sentence {} : {}".format(sentencenumber, e) )
data['sentences_i'] = sentencenumber
return parameters, data
def segment_pdf_to_pages ( self, parameters={}, data={} ):
verbose = False
if 'verbose' in parameters:
if parameters['verbose']:
verbose = True
if 'id' in data:
docid = data['id']
else:
docid = parameters['id']
filename = parameters['filename']
#defaults, if pdfinfo will not detect them
pages = 1
title = 'No title'
author = None
# get pagecount with pdfinfo command line tool
pdfinfo = subprocess.check_output(['pdfinfo', '-enc', 'UTF-8', filename])
# decode
pdfinfo = pdfinfo.decode(encoding='UTF-8')
# get the count of pages from pdfinfo result
# its a text with a line per parameter
for line in pdfinfo.splitlines():
line=line.strip()
# we want only the line with the pagecount
if line.startswith('Pages:'):
pages = int( line.split()[1] )
if line.startswith('Title:'):
title = line.replace("Title:", '', 1)
title = title.strip()
if line.startswith('Author:'):
author = line.replace("Author:", '', 1)
author = author.strip()
etl = ETL()
# export and index each page
for pagenumber in range(1, pages + 1):
if verbose:
print ("Extracting PDF page {} of {}".format(pagenumber, pages))
# generate temporary filename
md5hash = hashlib.md5(filename.encode('utf-8')).hexdigest()
temp_filename = tempfile.gettempdir() + os.path.sep + "opensemanticetl_pdftotext_" + md5hash + "_" + str(pagenumber)
# call pdftotext to write the text of page into tempfile
try:
result = subprocess.check_call(['pdftotext', '-enc', 'UTF-8','-f', str(pagenumber), '-l', str(pagenumber), filename, temp_filename])
except BaseException as e:
sys.stderr.write( "Exception extracting text from PDF page {}: {}\n".format(pagenumber, e) )
# read text from tempfile
f = open(temp_filename, "r", encoding="utf-8")
text = f.read()
os.remove(temp_filename)
partdocid = docid + '#page=' + str(pagenumber)
partparameters = parameters.copy()
partparameters['plugins'] = ['enhance_path', 'enhance_detect_language_tika_server', 'enhance_entity_linking', 'enhance_multilingual']
if 'enhance_ner_spacy' in parameters['plugins']:
partparameters['plugins'].append('enhance_ner_spacy')
if 'enhance_ner_stanford' in parameters['plugins']:
partparameters['plugins'].append('enhance_ner_stanford')
pagedata = {}
pagedata['id'] = partdocid
pagedata['page_i'] = pagenumber
pagedata['pages_i'] = pages
pagedata['container_s'] = docid
pagedata['title_txt'] = title
if author:
pagedata['author_ss'] = author
pagedata['content_type_group_ss'] = "Page"
pagedata['content_type_ss'] = "PDF page"
pagedata['content_txt'] = text
if verbose:
print ( "Indexing extracted page {}".format(pagenumber) )
# index page
try:
partparameters, pagedata = etl.process( partparameters, pagedata)
except BaseException as e:
sys.stderr.write( "Exception adding PDF page {} : {}".format(pagenumber, e) )
data['pages_i'] = pages
return parameters, data