def test_database_function(self):
# SETUP ALL DATABASE CONNECTIONS
# SETUP ALL DATABASE CONNECTIONS
from sherlock import database
db = database(
log=log,
settings=settings
)
dbConns, dbVersions = db.connect()
self.transientsDbConn = dbConns["transients"]
self.cataloguesDbConn = dbConns["catalogues"]
from fundamentals.mysql import readquery
sqlQuery = u"""
SELECT VERSION();
""" % locals()
rows = readquery(
log=log,
sqlQuery=sqlQuery,
dbConn=self.transientsDbConn,
quiet=False
)
print(rows)
rows = readquery(
log=log,
sqlQuery=sqlQuery,
dbConn=self.cataloguesDbConn,
quiet=False
)
print(rows)
def __init__(
self,
log,
settings=False,
):
self.log = log
log.debug("instansiating a new 'update_wiki_pages' object")
self.settings = settings
# INITIAL ACTIONS
# SETUP ALL DATABASE CONNECTIONS
from sherlock import database
db = database(log=self.log, settings=self.settings)
dbConns, dbVersions = db.connect()
self.transientsDbConn = dbConns["transients"]
self.cataloguesDbConn = dbConns["catalogues"]
self.basicColumns = [
"view_name",
"master table",
"description",
"version_number",
"object_types",
"object_type",
"number_of_rows",
"url",
"object_type_accuracy",
"last_updated",
]
return None
def __init__(
self,
log,
settings=False,
update=False,
transientIdList=[]
):
self.log = log
log.debug("instansiating a new 'classifier' object")
self.settings = settings
self.update = update
self.transientIdList = transientIdList
# xt-self-arg-tmpx
# VARIABLE DATA ATRRIBUTES
self.transientsMetadataList = []
# INITIAL ACTIONS
# SETUP DATABASE CONNECTIONS
from sherlock import database
db = database(
log=self.log,
settings=self.settings
)
self.transientsDbConn, self.cataloguesDbConn, self.pmDbConn = db.get()
return None
def __init__(
self,
log,
settings=False,
):
self.log = log
log.debug("instansiating a new 'cleanup_database_tables' object")
self.settings = settings
# xt-self-arg-tmpx
# 2. @flagged: what are the default attrributes each object could have? Add them to variable attribute set here
# Variable Data Atrributes
# 3. @flagged: what variable attrributes need overriden in any baseclass(es) used
# Override Variable Data Atrributes
# Initial Actions
from sherlock import database
db = database(
log=self.log,
settings=self.settings
)
self.transientsDbConn, self.cataloguesDbConn, self.pmDbConn = db.get()
return None
def test_crossmatching(self):
# SETUP ALL DATABASE CONNECTIONS
from sherlock import database
db = database(log=log, settings=settings)
dbConns, dbVersions = db.connect()
transientsDbConn = dbConns["transients"]
cataloguesDbConn = dbConns["catalogues"]
pmDbConn = dbConns["marshall"]
from sherlock.commonutils import get_crossmatch_catalogues_column_map
colMaps = get_crossmatch_catalogues_column_map(log=log,
dbConn=cataloguesDbConn)
from sherlock import transient_classifier
classifier = transient_classifier(log=log, settings=settings)
transientsMetadataList = classifier._get_transient_metadata_from_database_list(
)
crossmatches = classifier._crossmatch_transients_against_catalogues(
colMaps=colMaps, transientsMetadataList=transientsMetadataList)
classifications, crossmatches = classifier._rank_classifications(
colMaps=colMaps, crossmatches=crossmatches)
classifier._update_transient_database(
classifications=classifications,
transientsMetadataList=transientsMetadataList,
colMaps=colMaps,
crossmatches=crossmatches)
def test_tunnel(self):
from sherlock import database
db = database(log=log, settings=settings)
sshPort = db._setup_tunnel(
tunnelParameters=settings["database settings"]["static catalogues"]
["tunnel"])
return
def test_database_function_exception(self):
from sherlock import database
try:
this = database(log=log,
settings=settings,
fakeKey="break the code")
this.get()
assert False
except Exception, e:
assert True
print str(e)
def test_classification_annotations(self):
from sherlock import database
db = database(log=log, settings=settings)
dbConns, dbVersions = db.connect()
transientsDbConn = dbConns["transients"]
cataloguesDbConn = dbConns["catalogues"]
from sherlock.commonutils import get_crossmatch_catalogues_column_map
colMaps = get_crossmatch_catalogues_column_map(log=log,
dbConn=cataloguesDbConn)
from sherlock import transient_classifier
classifier = transient_classifier(log=log, settings=settings)
classifier.classification_annotations()
def __init__(self,
log,
settings=False,
pathToDataFile=False,
version=False,
catalogueName="",
coordinateList=[],
radiusArcsec=False):
self.log = log
log.debug("instansiating a new '_base_importer' object")
self.settings = settings
self.pathToDataFile = pathToDataFile
self.version = version
self.catalogueName = catalogueName
self.coordinateList = coordinateList
self.radiusArcsec = radiusArcsec
self.myPid = str(os.getpid())
# xt-self-arg-tmpx
# INITIAL ACTIONS
# SETUP DATABASE CONNECTIONS
# SETUP ALL DATABASE CONNECTIONS
from sherlock import database
db = database(log=self.log, settings=self.settings)
dbConns, dbVersions = db.connect()
self.transientsDbConn = dbConns["transients"]
self.cataloguesDbConn = dbConns["catalogues"]
self.pmDbConn = dbConns["marshall"]
# OPEN THE FILE TO IMPORT THE DATA FROM
if pathToDataFile:
pathToReadFile = pathToDataFile
try:
self.log.debug("attempting to open the file %s" %
(pathToReadFile, ))
readFile = codecs.open(pathToReadFile, mode='r')
self.catData = readFile.read()
readFile.close()
except IOError, e:
message = 'could not open the file %s' % (pathToReadFile, )
self.log.critical(message)
raise IOError(message)
readFile.close()
def __init__(
self,
log,
settings=False,
):
self.log = log
log.debug("instansiating a new 'database_cleaner' object")
self.settings = settings
# xt-self-arg-tmpx
# INITIAL ACTIONS# Initial Actions
# SETUP ALL DATABASE CONNECTIONS
from sherlock import database
db = database(log=self.log, settings=self.settings)
dbConns, dbVersions = db.connect()
self.transientsDbConn = dbConns["transients"]
self.cataloguesDbConn = dbConns["catalogues"]
self.pmDbConn = dbConns["marshall"]
return None
def __init__(
self,
log,
settings=False,
pathToDataFile=False,
version=False,
catalogueName="",
coordinateList=[]
):
self.log = log
log.debug("instansiating a new '_base_importer' object")
self.settings = settings
self.pathToDataFile = pathToDataFile
self.version = version
self.catalogueName = catalogueName
self.coordinateList = coordinateList
# xt-self-arg-tmpx
# INITIAL ACTIONS
# SETUP DATABASE CONNECTIONS
from sherlock import database
db = database(
log=self.log,
settings=self.settings
)
self.transientsDbConn, self.cataloguesDbConn, self.pmDbConn = db.get()
if pathToDataFile:
pathToReadFile = pathToDataFile
try:
self.log.debug("attempting to open the file %s" %
(pathToReadFile,))
readFile = codecs.open(pathToReadFile, mode='r')
self.catData = readFile.read()
readFile.close()
except IOError, e:
message = 'could not open the file %s' % (pathToReadFile,)
self.log.critical(message)
raise IOError(message)
readFile.close()
try:
shutil.rmtree(pathToOutputDir)
except:
pass
# COPY INPUT TO OUTPUT DIR
shutil.copytree(pathToInputDir, pathToOutputDir)
# Recursively create missing directories
if not os.path.exists(pathToOutputDir):
os.makedirs(pathToOutputDir)
# SETUP ALL DATABASE CONNECTIONS
from sherlock import database
db = database(
log=log,
settings=settings
)
dbConns, dbVersions = db.connect()
transientsDbConn = dbConns["transients"]
cataloguesDbConn = dbConns["catalogues"]
class test_get_crossmatch_catalogues_column_map(unittest.TestCase):
def test_get_crossmatch_catalogues_column_map_function(self):
from sherlock.commonutils import get_crossmatch_catalogues_column_map
colMaps = get_crossmatch_catalogues_column_map(
log=log,
dbConn=cataloguesDbConn
)
