def __init__(self,
debug=False,
verbose=False,
slackbot_injected=None,
slacker_injected=None):
self.debug = debug
self.verbose = verbose
self.config = config.Config()
slackbot_token = os.getenv(self.config.slackbot_api_token_env_varname)
api_token = os.getenv(self.config.api_token_env_varname)
self.slackbot = slackbot_injected or slackbot.Slackbot(
config.SLACK_NAME, token=slackbot_token)
self.logger = logging.getLogger(__name__)
utils.set_up_logger(self.logger,
log_level_env_var='DESTALINATOR_LOG_LEVEL',
log_to_slack_env_var='DESTALINATOR_LOG_TO_CHANNEL',
log_channel=self.config.log_channel,
slackbot=self.slackbot)
self.destalinator_activated = False
if os.getenv(self.config.destalinator_activated_env_varname):
self.destalinator_activated = True
self.logger.debug("destalinator_activated is %s",
self.destalinator_activated)
self.slacker = slacker_injected or slacker.Slacker(
config.SLACK_NAME, token=api_token, logger=self.logger)
self.ds = destalinator.Destalinator(
slacker=self.slacker,
slackbot=self.slackbot,
activated=self.destalinator_activated,
logger=self.logger)
def __init__(self, debug=False, verbose=False, slackbot_injected=None, slacker_injected=None):
self.debug = debug
self.verbose = verbose
self.config = config.Config()
slackbot_token = os.getenv(self.config.slackbot_api_token_env_varname)
api_token = os.getenv(self.config.api_token_env_varname)
self.slackbot = slackbot_injected or slackbot.Slackbot(config.SLACK_NAME, token=slackbot_token)
self.logger = logging.getLogger(__name__)
utils.set_up_logger(self.logger,
log_level_env_var='DESTALINATOR_LOG_LEVEL',
log_to_slack_env_var='DESTALINATOR_LOG_TO_CHANNEL',
log_channel=self.config.log_channel,
slackbot=self.slackbot)
self.destalinator_activated = False
if os.getenv(self.config.destalinator_activated_env_varname):
self.destalinator_activated = True
self.logger.debug("destalinator_activated is %s", self.destalinator_activated)
self.slacker = slacker_injected or slacker.Slacker(config.SLACK_NAME, token=api_token, logger=self.logger)
self.ds = destalinator.Destalinator(slacker=self.slacker,
slackbot=self.slackbot,
activated=self.destalinator_activated,
logger=self.logger)
def __init__(self, logging_flag=''):
app_name = __file__.split('.')[0]
utils.set_up_logger(app_name, logging_flag)
# Misc. class attributes
self.cursor = None
# Counters
self.count_discarded_urls = 0
self.count_crawled_pages = 0
self.count_downloaded_pages = 0
self.count_no_links_found_pages = 0
self.total_links_added = 0
# Timers
self.crawl_time = 0
self.now = ''
def __init__(self,
prefix="entity",
window_size=2,
entities_only=True,
port=5436,
log_file=os.path.join(os.path.dirname(__file__), "logs/SchemaCreator.log"),
log_level=logging.INFO,
log_verbose=True
):
"""
Set up.
:param prefix: (str) Prefix to the table names.
:param port: (int) Used to connect to the Postgres tables.
:param log_file: (os.path) Path to the file containing the logs.
:param log_level: (logging.LEVEL) Specifies the level to be logged.
:param log_verbose: (boolean) Specifies whether or not to look to stdout as well.
"""
self.logger = set_up_logger(__name__, log_file, log_level, log_verbose)
self.window_size = window_size
self.prefix = prefix + "_" + str(self.window_size)
self.entities_only = entities_only
self.names = self.get_names(self.prefix)
self.port = port
self.pc = PostgresConnector(port=port)
self.logger.info("Successfully registered SchemaGenerator.")
def __init__(self,
secrets=os.path.join(os.path.dirname(__file__),
"secrets.json"),
log_file=os.path.join(os.path.dirname(__file__),
"logs/MongoConnector.log"),
log_level=logging.INFO,
log_verbose=True):
"""
:param secrets: (os.path) Path to the file containing the relevant parameters for the login via a SSHTunnel
into the MongoDB. Will be treated as a JSON object (i.e. dictionary in Python), and must contain
the following parameters:
SSH_HOST, specifies the tunnel address
LDAP_USER, user name for ssh login
LDAP_PASSWORD, corresponding password
MONGODB_PORT, usually 27016 (careful, this has to be an integer)
MONGODB_HOST, host address of the mongodb, usually localhost
MONGODB_AUTH_DB, database which is owned by user
MONGODB_AUTH_USER, username for mongodb
MONGODB_AUTH_PW, corresponding password
MONGODB_NEWS_DB, database which contains the relevant news articles.
Default location is assumed to be in the same directory as the class definition.
:param log_file: (os.path) Path to the file containing the logs
:param log_level: (logging.LEVEL) Specifies the level to be logged
:param log_verbose: (boolean) Specifies whether or not to look to stdout as well.
"""
# read secrets
with open(secrets, "r") as secret_file:
self.secrets = json.load(secret_file)
# set up log file. Specify name and level, and also print message time to it.
self.logger = set_up_logger(__name__, log_file, log_level, log_verbose)
self.logger.info("Successfully registered logger to MongoConnector.")
# name abstraction, since it is frequently used
self.news = self.secrets['MONGODB_NEWS_DB']
def test_set_up_logger(self):
from utils import set_up_logger
from logging import Logger
logger = set_up_logger("test", "test.log")
self.assertIsInstance(logger, Logger)
os.remove("test.log")
def __init__(self, logging_flag):
app_name = __file__.split('.')[0]
utils.set_up_logger(app_name, logging_flag)
# Misc. class attributes
self.soup = None
self.hashed_soup = None
self.compressed_soup = None
self.cursor = None
# Counters
self.urlerrors = 0
self.count_prospective_pages = 0
self.count_saved = 0
self.count_discarded_pages = 0
# Timers
self.start_time = time.time()
self.request_time = 0
self.disk_save_time = 0
def __init__(self,
num_distinct_documents=5000,
replace_entities=True,
max_term_length=127,
remove_stopwords=True,
custom_stopwords=[
',', '.', '-', '\xa0', '“', '”', '"', '\n', '—', ':', '?',
'I', '(', ')'
],
analyze=False,
document_tabe_name="documents",
sentence_table_name="sentences",
sentence_fields=OrderedDict({
"doc_id": "document_id",
"sen_id": "sentence_id",
"content": "sentence_text"
}),
term_table_name="terms",
term_sql_format=("term_id", "term_text", "is_entity"),
term_occurrence_table_name="term_occurrence",
term_occurrence_sql_format=("document_id", "sentence_id",
"term_id"),
entity_table_name="entities",
entity_sql_format=("entity_id", "entity_type"),
database="postgres",
user="******",
password="******",
host="127.0.0.1",
port=5435,
log_file=os.path.join(os.path.dirname(__file__),
"logs/TermGenerator.log"),
log_level=logging.INFO,
log_verbose=True):
"""
Initializes various parameters, registers logger and MongoConnector, and sets up the limit.
:param num_distinct_documents: (int) The number of distinct documents retrieved from the queries.
For performance reasons, this should be limited during debugging/development.
0 (Zero) represents no limit, in accordance with the MongoDB standard for .limit().
:param replace_entities: (boolean) Whether or not the entities in the text should be replaced/recognised.
The reason for this is that single terms might be merged together to one term, i.e. first and last name:
"Dennis" "Aumiller" would be two separate terms in the traditional splitting (replace_entities=False),
whereas - if set to true - "Dennis Aumiller" would represent only one entity.
:param max_term_length: (int) Indicator of how long the terms are supposed to be (varchar property in table).
:param remove_stopwords: (boolean) Determines whether or not stop words are removed. Currently, we are still
deciding on the final set, but likely either one (or both) of NLTK and SpaCy's stop word lists.
:param custom_stopwords: (list of strings) Additional words that will not be considered at adding-time.
:param analyze: (boolean) Whether or not to include analytically relevant metrics.
:param document_tabe_name: (str) Name of the table where the document information is stored.
:param sentence_table_name: (str) Name of the table where the sentence information will be stored.
:param sentence_fields: (OrderedDict) Structure of input to output values from MongoDB to postgres for the
sentence table and its fields.
:param term_table_name: (str) Name of the Postgres tables for the terms.
:param term_sql_format: (tuple) Since those are generated locally, only a tuple of the PostgresColumns suffices.
:param term_occurrence_table_name: (str) Name of the Postgres table for the term occurrences
:param term_occurrence_sql_format: (tuple) Same as term_sql_format, but for the term occurrences.
:param entity_table_name: (str) (Not implemented yet) Name of the table for the entity meta information.
:param entity_sql_format: (str) Same as term_sql_format, but for entities.
:param database: (str) database name.
:param user: (str) User name to get access to the Postgres database.
:param password: (str) Corresponding user password.
:param host: (IP) IP address (in string format) for the host of the postgres database.
:param port: (integer) Port at which to access the database.
"""
# set up logger
self.logger = set_up_logger(__name__, log_file, log_level, log_verbose)
self.logger.info("Successfully registered logger to TermGenerator.")
# register a MongoConnector
self.mc = MongoConnector()
self.logger.info(
"Successfully registered MongoConnector to TermGenerator.")
# PostgresConnector
self.pc = PostgresConnector(database, user, password, host, port)
self.logger.info(
"Successfully registered PostgresConnector to DocumentGenerator.")
self.num_distinct_documents = num_distinct_documents
# do this earlier since we need it already for the distinct documents.
self.document_table_name = document_tabe_name
# get the distinct IDs for the documents so we can match against them later
# since we have removed parts of the document collection, we have to make sure to get this from Postgres.
self.logger.info("Parsing relevant documents from Postgres...")
with self.pc as open_pc:
open_pc.cursor.execute("SELECT document_id FROM {}".format(
self.document_table_name))
self.first_distinct_documents = list(open_pc.cursor.fetchall())
# extract from the tuple structure
self.first_distinct_documents = [
el[0] for el in self.first_distinct_documents
]
self.logger.info("Retrieved all relevant documents from Postgres.")
# additionally restrict if we want only a number of documents.
if self.num_distinct_documents != 0:
self.logger.info(
"Non-zero limit detected. Limiting to the first N entries.")
self.first_distinct_documents = self.first_distinct_documents[:self
.
num_distinct_documents]
self.replace_entities = replace_entities
self.analyze = analyze
self.max_term_length = max_term_length
self.nlp = spacy.load("en")
# construct dictionary with the entries per document/sentence id pair. Thus, we can later check whether
# there are any entities in the current sentence with higher efficiency.
self.occurrence_dict = {}
self.occurring_entities = []
# start building the term dictionary/set, as well as an occurence map. Since terms will be "post-processed",
# it is first created as a list and later cast to Counter and set.
self.terms = [] # cast into a set later on.
self.term_in_sentence = set()
self.term_id = {}
self.term_is_entity = {}
if self.analyze:
self.term_count = Counter()
self.entity_count = Counter()
self.entities = []
self.sentences = []
self.processed_sentences = []
# Postgres tables
if not sentence_fields:
self.logger.error("No sentence fields specified!")
self.sentence_table_name = sentence_table_name
self.sentence_fields = sentence_fields
if not term_sql_format:
self.logger.error("No term fields specified!")
self.term_table_name = term_table_name
self.term_sql_format = ", ".join(term_sql_format)
if not term_occurrence_sql_format:
self.logger.error("No term occurrence fields specified!")
self.term_occurrence_table_name = term_occurrence_table_name
self.term_occurrence_sql_format = ", ".join(term_occurrence_sql_format)
if not entity_sql_format:
self.logger.error("No entity fields specified!")
self.entity_table_name = entity_table_name
self.entity_sql_format = ", ".join(entity_sql_format)
# value retrieving parse:
self.sentence_values_to_retrieve = {
key: 1
for key in self.sentence_fields.keys()
}
# suppress _id if not present:
if "_id" not in self.sentence_values_to_retrieve.keys():
self.sentence_values_to_retrieve["_id"] = 0
self.sentence_sql_format = ", ".join(
[value for value in self.sentence_fields.values()])
# create union of stop words, and add potentially custom stop words
self.remove_stopwords = remove_stopwords
self.removed_counter = 0
self.stopwords = STOP_WORDS.union(set(stopwords.words("english")))
# add custom stopwords.
for word in custom_stopwords:
self.stopwords.add(word)
self.logger.info("Successfully initialized TermGenerator.")
def __init__(self,
window_size=2,
limit_edges=False,
entities_only=False,
document_table_name="documents",
sentence_table_name="sentences",
entity_table_name="entities",
term_table_name="terms",
term_occurrence_table_name="term_occurrence",
hyperedge_table_name="hyperedges",
hyperedge_format=("edge_id", "term_id", "pos"),
hyperedge_document_table_name="hyperedge_document",
hyperedge_document_format=("edge_id", "document_id"),
hyperedge_sentence_table_name="hyperedge_sentences",
hyperedge_sentence_format=("edge_id", "document_id",
"sentence_id", "pos"),
database="postgres",
user="******",
password="******",
host="127.0.0.1",
port=5435,
log_file=os.path.join(os.path.dirname(__file__),
"logs/HyperedgeGenerator.log"),
log_level=logging.INFO,
log_verbose=True):
"""
Initializes hyper edge generator class.
:param window_size: (int) Number of sentences in each direction that will determine the context window size
of the algorithm.
:param limit_edges: (boolean) Experimental: Should limit the maximum number of terms per hyperedge. This would
only be useful in context with other theoretical results.
:param entities_only: (boolean) Indicating whether or not we should only take into account entity terms,
and not the entirety of all term occurrences for the edges.
:param document_table_name: (str) Name of the table where documents are stored.
:param sentence_table_name: (str) Name of the table containing the sentences and their content.
:param entity_table_name: (str) Name of the table containing the entity information and their properties.
:param term_table_name: (str) Name of the table containing the terms and meta data.
:param term_occurrence_table_name: (str) Name of the table containing term occurrence data.
:param hyperedge_table_name: (str) Name of the table containing the general hyper edge information.
:param hyperedge_format: (str) Table structure of hyper edge table.
:param hyperedge_document_table_name: (str) Name of the table containing the document classification.
:param hyperedge_document_format: (str) Table structure of hyper edge document table.
:param hyperedge_sentence_table_name: (str) Name of the tale containing the hyper edge sentence data.
:param hyperedge_sentence_format: (str) Table structure of the hyper edge sentence table.
:param database: (str) database name.
:param user: (str) User name to get access to the Postgres database.
:param password: (str) Corresponding user password.
:param host: (IP) IP address (in string format) for the host of the postgres database.
:param port: (integer) Port at which to access the database.
:param log_file: (os.path) Path to the file containing the logs.
:param log_level: (logging.LEVEL) Specifies the level to be logged.
:param log_verbose: (boolean) Specifies whether or not to look to stdout as well.
"""
self.logger = set_up_logger(__name__, log_file, log_level, log_verbose)
self.logger.info(
"Successfully registered logger to HyperedgeGenerator.")
# important for hyperedges
self.window_size = window_size
self.limit_edges = limit_edges
self.entities_only = entities_only
# table names
self.document_table_name = document_table_name
self.sentence_table_name = sentence_table_name
self.entity_table_name = entity_table_name
self.term_table_name = term_table_name
self.term_occurrence_table_name = term_occurrence_table_name
self.hyperedge_table_name = hyperedge_table_name
self.hyperedge_document_table_name = hyperedge_document_table_name
self.hyperedge_sentence_table_name = hyperedge_sentence_table_name
self.hyperedge_format = ", ".join([el for el in hyperedge_format])
self.hyperedge_document_format = ", ".join(
[el for el in hyperedge_document_format])
self.hyperedge_sentence_format = ",".join(
[el for el in hyperedge_sentence_format])
self.pc = PostgresConnector(database, user, password, host, port)
self.logger.info(
"Successfully registered PostgresConnector to HyperedgeGenerator.")
self.hyperedge = []
self.hyperedge_sentence = []
self.hyperedge_document = []
self.all_hyperedges = []
self.all_hyperedge_sentences = []
# set up the "hyper edge ID counter", which is simply consecutive from 1.
with self.pc as open_pc:
if not check_table_existence(self.logger, open_pc,
self.hyperedge_table_name):
return 0
self.logger.info("Retrieving current hyper edge ID key...")
open_pc.cursor.execute(
"SELECT COUNT(DISTINCT h.edge_id) FROM {} as h".format(
self.hyperedge_table_name))
# either start with 1 or get the current maximum
self.hyperedge_ID = max(1, open_pc.cursor.fetchone()[0])
parser.add_argument('username', help='db user')
parser.add_argument('host', help='db host')
parser.add_argument('db_name', help='db name')
parser.add_argument('password', help='username db password')
parser.add_argument('--version',
'-v',
action='version',
version='%(prog)s 1.0')
parser.add_argument('--debug', action='store_true')
parser.add_argument('--updateVersion')
args = parser.parse_args()
# we can assume the arguments are correct at this point
logger = utils.set_up_logger()
def main():
DB_URL = 'mysql://{user}:{passwd}@{host}/{db}'.format(host=args.host, user=args.username,\
passwd=args.password,db=args.db_name)
logger.debug('DB_URL: {url}'.format(url=DB_URL))
# Error handling for possible sql path location errors.
try:
os.path.exists(args.path_to_sql) or os.path.isdir(args.path_to_sql)
except IOError as e:
logger.error(e)
sys.exit(1)
def __init__(self,
fields=OrderedDict({
"_id": "document_id",
"title": "title",
"feedName": "feedName",
"category": "category",
"feedURL": "feedURL",
"published": "published"
}),
num_distinct_documents=0,
document_table_name="documents",
database="postgres",
user="******",
password="******",
host="127.0.0.1",
port=5435,
log_file=os.path.join(os.path.dirname(__file__),
"logs/DocumentGenerator.log"),
log_level=logging.INFO,
log_verbose=True):
"""
Initializes context, and sets up documents that will be parsed.
Also establishes the PostgresConnector that will later be used to push the retrieved documents.
:param fields: (OrderedDict) Key-value pairs that indicate a mapping of fields that should be retrieved (key),
and the respective field it should be called in the SQL table. Ordered because SQL tables are.
:param num_distinct_documents: (int) As the name indicates, the number of distinct articles that should be used.
Mainly for debugging purposes. 0 means all documents will be used, in accordance with MongoDB standards.
:param document_table_name: (str) Name of the Postgres table that should contain the documents
:param database: (str) database name.
:param user: (str) User name to get access to the Postgres database.
:param password: (str) Corresponding user password.
:param host: (IP) IP address (in string format) for the host of the postgres database.
:param port: (integer) Port at which to access the database.
:param log_file: (os.path) Path to the file containing the logs.
:param log_level: (logging.LEVEL) Specifies the level to be logged.
:param log_verbose: (boolean) Specifies whether or not to look to stdout as well.
"""
# set up logger
self.logger = set_up_logger(__name__, log_file, log_level, log_verbose)
self.logger.info(
"Successfully registered logger to DocumentGenerator.")
# register a MongoConnector
self.mc = MongoConnector()
self.logger.info(
"Successfully registered MongoConnector to DocumentGenerator.")
self.num_distinct_documents = num_distinct_documents
# get the distinct IDs for the documents so we can match against them later
if self.num_distinct_documents != 0:
self.logger.info(
"Non-zero limit detected. Fetching first N distinct document IDs now..."
)
with self.mc as open_mc:
documents = open_mc.client[open_mc.news].articles
self.first_documents = list(documents.find().limit(
self.num_distinct_documents))
# for small enough number, and large enough document collection, this is more efficient:
self.first_documents = [
el["_id"] for el in self.first_documents
]
self.logger.info(
"Successfully registered relevant document IDs.")
else:
# needed to avoid later conflicts
self.first_documents = []
# set up PostgresConnector. Since we only use these once, I don't see any reason to store the connection
# details locally again.
self.pc = PostgresConnector(database, user, password, host, port)
self.logger.info(
"Successfully registered PostgresConnector to DocumentGenerator.")
# format them into a reasonable format
self.fields = fields
if not self.fields:
self.logger.error("No fields for MongoDB table specified!")
self.values_to_retrieve = {key: 1 for key in self.fields.keys()}
# suppress _id if not wanted, as it is returned by default.
if "_id" not in self.values_to_retrieve.keys():
self.values_to_retrieve["_id"] = 0
# TODO
self.sql_format = ", ".join([value for value in self.fields.values()])
self.document_table_name = document_table_name
# preparation for later. According to PEP8
self.data = []
self.logger.info("Successfully set up DocumentGenerator.")
./find_reactions_by_stoichiometry -h
MIT License
Zachary King 2015
"""
from utils import io_args, load_model_any_type, save_model_with_type, set_up_logger
import requests
import logging
from collections import defaultdict
# get command line args and logger
args = io_args()
set_up_logger(**args)
# load the cobra model
model = load_model_any_type(usage=usage, **args)
def has_reaction_id(reaction_id):
url = (
args['host'].rstrip('/') +
'/universal/reactions/' + reaction_id
)
res = requests.get(url)
return res.status_code != 404
# update the model
logging.debug('Running queries')
categories = defaultdict(list)
