def insert_species_data(self, species, node, update=False):
"""
Inserts new species into the local database
species: species which will be inserted
node: vamdc-node / type: instance(nodes.node)
update: if True then all entries in the local database with the same
species-id will be deleted before the insert is performed.
"""
# create a list of names. New names have not to be in that list
names_black_list = []
cursor = self.conn.cursor()
cursor.execute("SELECT PF_Name FROM Partitionfunctions")
rows = cursor.fetchall()
for row in rows:
names_black_list.append(row[0])
#----------------------------------------------------------
# Create a list of species for which transitions will be
# retrieved and inserted in the database.
# Species have to be in the Partitionfunctions - table
if not functions.isiterable(species):
species = [species]
#--------------------------------------------------------------
for specie in species:
num_transitions = {}
# will contain a list of names which belong to one specie
species_names = {}
# list will contain species whose insert-failed
species_with_error = []
# check if specie is of type Molecule
if isinstance(specie, specmodel.Molecule):
speciesid = specie.SpeciesID
vamdcspeciesid = specie.VAMDCSpeciesID
formula = specie.OrdinaryStructuralFormula
else:
try:
if isinstance(specie, str) and len(specie) == 27:
vamdcspeciesid = specie
speciesid = None
except:
print "Specie is not of wrong type"
print "Type Molecule or string (Inchikey) is allowed"
continue
if speciesid:
print "Processing: {speciesid}".format(speciesid = speciesid)
else:
print "Processing: {vamdcspeciesid}".format(vamdcspeciesid = vamdcspeciesid)
try:
# Create query string
query_string = "SELECT ALL WHERE VAMDCSpeciesID='%s'" % vamdcspeciesid
query = q.Query()
result = results.Result()
# Get data from the database
query.set_query(query_string)
query.set_node(node)
result.set_query(query)
result.do_query()
result.populate_model()
except:
print " -- Error: Could not fetch and process data"
continue
#---------------------------------------
cursor = self.conn.cursor()
cursor.execute('BEGIN TRANSACTION')
#------------------------------------------------------------------------------------------------------
# if update is allowed then all entries in the database for the given species-id will be
# deleted, and thus replaced by the new data
if update:
cursor.execute("SELECT PF_Name FROM Partitionfunctions WHERE PF_SpeciesID = ?", (speciesid, ))
rows = cursor.fetchall()
for row in rows:
names_black_list.remove(row[0])
cursor.execute("DELETE FROM Transitions WHERE T_Name = ?", (row[0], ))
cursor.execute("DELETE FROM Partitionfunctions WHERE PF_Name = ?", (row[0], ))
#------------------------------------------------------------------------------------------------------
#------------------------------------------------------------------------------------------------------
# Insert all transitions
num_transitions_found = len(result.data['RadiativeTransitions'])
counter_transitions = 0
for trans in result.data['RadiativeTransitions']:
counter_transitions+=1
print "\r insert transition %d of %d" % (counter_transitions, num_transitions_found),
# data might contain transitions for other species (if query is based on ichikey/vamdcspeciesid).
# Insert transitions only if they belong to the correct specie
if result.data['RadiativeTransitions'][trans].SpeciesID == speciesid or speciesid is None:
id = str(result.data['RadiativeTransitions'][trans].SpeciesID)
# if an error has occured already then there will be no further insert
if id in species_with_error:
continue
formula = str(result.data['Molecules'][id].OrdinaryStructuralFormula)
# Get upper and lower state from the states table
try:
upper_state = result.data['States']["%s" % result.data['RadiativeTransitions'][trans].UpperStateRef]
lower_state = result.data['States']["%s" % result.data['RadiativeTransitions'][trans].LowerStateRef]
except (KeyError, AttributeError):
print " -- Error: State is missing"
species_with_error.append(id)
continue
# Get string which identifies the vibrational states involved in the transition
t_state = self.getvibstatelabel(upper_state, lower_state)
# Get hyperfinestructure info if hfsInfo is None
# only then the hfsInfo has not been inserted in the species name
# (there can be multiple values in the complete dataset
t_hfs = ''
try:
for pc in result.data['RadiativeTransitions'][trans].ProcessClass:
if str(pc)[:3] == 'hyp':
t_hfs = str(pc)
except Exception, e:
print "Error: %s", e
t_name = "%s; %s; %s" % (formula, t_state, t_hfs)
t_name = t_name.strip()
# check if name is in the list of forbidden names and add counter if so
i = 1
while t_name in names_black_list:
t_name = "%s#%d" % (t_name.split('#')[0], i)
i += 1
# update list of distinct species names.
if id in species_names:
if not t_name in species_names[id]:
species_names[id].append(t_name)
num_transitions[t_name] = 0
else:
species_names[id] = [t_name]
num_transitions[t_name] = 0
frequency = float(result.data['RadiativeTransitions'][trans].FrequencyValue)
try:
uncertainty = "%lf" % float(result.data['RadiativeTransitions'][trans].FrequencyAccuracy)
except TypeError:
print " -- Error uncertainty not available"
species_with_error.append(id)
continue
# Get statistical weight if present
try:
weight = int(upper_state.TotalStatisticalWeight)
except:
print " -- Error statistical weight not available"
species_with_error.append(id)
continue
# Get nuclear spin isomer (ortho/para) if present
#print "%s; %s" % (result.data['RadiativeTransitions'][trans].Id, upper_state.Id)
try:
nsiName = upper_state.NuclearSpinIsomerName
except AttributeError:
nsiName = None
# Insert transition into database
try:
cursor.execute("""INSERT INTO Transitions (
T_Name,
T_Frequency,
T_EinsteinA,
T_Uncertainty,
T_EnergyLower,
T_UpperStateDegeneracy,
T_HFS,
T_UpperStateQuantumNumbers,
T_LowerStateQuantumNumbers) VALUES
(?, ?,?,?,?, ?,?, ?,?)""",
(t_name,
"%lf" % frequency,
"%g" % float(result.data['RadiativeTransitions'][trans].TransitionProbabilityA),
uncertainty, "%lf" % float(lower_state.StateEnergyValue),
weight,
#upper_state.QuantumNumbers.case,
t_hfs,
str(upper_state.QuantumNumbers.qn_string),
str(lower_state.QuantumNumbers.qn_string),
))
num_transitions[t_name] += 1
except Exception, e:
print "Transition has not been inserted:\n Error: %s" % e
def update_database(self, add_nodes = None, insert_only = False, update_only = False):
"""
Checks if there are updates available for all entries. Updates will
be retrieved from the resource specified in the database.
All resources will be searched for new entries, which will be inserted
if available. Additional resources can be specified via add_nodes.
add_nodes: Single or List of node-instances (nodes.Node)
"""
# counter to identify which entry is currently processed
counter = 0
# counter to count available updates
count_updates = 0
# list of database - nodes which are currently in the local database
dbnodes = []
# create an instance with all available vamdc-nodes
nl = nodes.Nodelist()
# attach additional nodes to the list of dbnodes (for insert)
if not functions.isiterable(add_nodes):
add_nodes = [add_nodes]
for node in add_nodes:
if node is None:
pass
elif not isinstance(node, nodes.Node):
print "Could not attach node. Wrong type, it should be type <nodes.Node>"
else:
dbnodes.append(node)
#--------------------------------------------------------------------
# Check if updates are available for entries
# Get list of species in the database
cursor = self.conn.cursor()
cursor.execute("SELECT PF_Name, PF_SpeciesID, PF_VamdcSpeciesID, datetime(PF_Timestamp), PF_ResourceID FROM Partitionfunctions ")
rows = cursor.fetchall()
num_rows = len(rows)
query = q.Query()
result = results.Result()
if not insert_only:
print("----------------------------------------------------------")
print "Looking for updates"
print("----------------------------------------------------------")
for row in rows:
counter += 1
print "%5d/%5d: Check specie %-55s (%-15s): " % (counter, num_rows, row[0], row[1]),
try:
node = nl.getnode(str(row[4]))
except:
node = None
if node is None:
print " -- RESOURCE NOT AVAILABLE"
continue
else:
if node not in dbnodes:
dbnodes.append(node)
vamdcspeciesid = row[2]
query_string = "SELECT ALL WHERE SpeciesID=%s" % row[1][6:]
query.set_query(query_string)
query.set_node(node)
result.set_query(query)
try:
changedate = result.getChangeDate()
except:
changedate = None
tstamp = parser.parse(row[3] + " GMT")
if changedate is None:
print " -- UNKNOWN (Could not retrieve information)"
continue
if tstamp < changedate:
print " -- UPDATE AVAILABLE "
count_updates += 1
print " -- PERFORM UPDATE -- "
query_string = "SELECT SPECIES WHERE SpeciesID=%s" % row[1][6:]
query.set_query(query_string)
query.set_node(node)
result.set_query(query)
result.do_query()
result.populate_model()
insert_species_data(result.data['Molecules'], update = True)
print " -- UPDATE DONE -- "
else:
print " -- up to date"
if count_updates == 0:
print "\r No updates for your entries available"
print "Done"
else:
cursor.execute("SELECT distinct PF_ResourceID FROM Partitionfunctions ")
rows = cursor.fetchall()
for row in rows:
try:
node = nl.getnode(str(row[0]))
except:
node = None
if node is None:
print " -- RESOURCE NOT AVAILABLE"
continue
else:
if node not in dbnodes:
dbnodes.append(node)
if update_only:
return
# Check if there are new entries available
#---------------------------------------------------------
# Check all dbnodes for new species
counter = 0
insert_molecules_list = []
for node in dbnodes:
print("----------------------------------------------------------")
print "Query '{dbname}' for new species ".format(dbname=node.name)
print("----------------------------------------------------------")
node.get_species()
for id in node.Molecules:
try:
cursor.execute("SELECT PF_Name, PF_SpeciesID, PF_VamdcSpeciesID, PF_Timestamp FROM Partitionfunctions WHERE PF_SpeciesID=?", [(id)])
exist = cursor.fetchone()
if exist is None:
print " %s" % node.Molecules[id]
insert_molecules_list.append(node.Molecules[id])
counter += 1
except Exception, e:
print e
print id
print "There are %d new species available" % counter
print("----------------------------------------------------------")
print "Start insert"
print("----------------------------------------------------------")
self.insert_species_data(insert_molecules_list, node)
print("----------------------------------------------------------")
print "Done"
def insert_radiativetransitions(self, species, node):
"""
"""
# will contain a list of names which belong to one specie
species_names = {}
#----------------------------------------------------------
# Create a list of species for which transitions will be
# retrieved and inserted in the database.
# Species have to be in the Partitionfunctions - table
if not functions.isiterable(species):
species = [species]
species_list = []
cursor = self.conn.cursor()
for specie in species:
cursor.execute("SELECT PF_Name, PF_SpeciesID, PF_VamdcSpeciesID, PF_HFS FROM Partitionfunctions WHERE PF_SpeciesID=? or PF_VamdcSpeciesID=?",
(specie, specie))
rows = cursor.fetchall()
for row in rows:
species_list.append([row[0], row[1], row[2], row[3]])
#--------------------------------------------------------------
for specie in species_list:
num_transitions = {}
#------------------------------------
# Retrieve data from the database
id = specie[1]
vamdcspeciesid = specie[2]
hfs = specie[3]
name = specie[0]
# name should be formated like 'formula; state-info; hfs-info'
name_array = name.split(';')
formula = name_array[0].strip()
try:
stateInfo = name_array[1].strip()
except:
stateInfo = ''
# get hfs-flag from the name.
try:
hfsInfo = name_array[2].strip()
except:
hfsInfo = ''
# Create query string
query_string = "SELECT ALL WHERE VAMDCSpeciesID='%s'" % vamdcspeciesid
if hfs is not None and hfs.strip() != '':
query_string += " and RadTransCode='%s'" % hfs
query = q.Query()
result = results.Result()
# Get data from the database
query.set_query(query_string)
query.set_node(node)
result.set_query(query)
result.do_query()
result.populate_model()
#---------------------------------------
cursor = self.conn.cursor()
cursor.execute('BEGIN TRANSACTION')
cursor.execute("DELETE FROM Transitions WHERE T_Name = ?", (name,))
for trans in result.data['RadiativeTransitions']:
# data might contain transitions for other species (if query is based on ichikey/vamdcspeciesid).
# Insert transitions only if they belong to the correct specie
if result.data['RadiativeTransitions'][trans].SpeciesID == id:
# Get upper and lower state from the states table
upper_state = result.data['States']["%s" % result.data['RadiativeTransitions'][trans].UpperStateRef]
lower_state = result.data['States']["%s" % result.data['RadiativeTransitions'][trans].LowerStateRef]
# Get string which identifies the vibrational states involved in the transition
try:
if upper_state.QuantumNumbers.vibstate == lower_state.QuantumNumbers.vibstate:
t_state = str(upper_state.QuantumNumbers.vibstate).strip()
else:
#vup = upper_state.QuantumNumbers.vibstate.split(",")
#vlow = lower_state.QuantumNumbers.vibstate.split(",")
v_dict = {}
for label in list(set(upper_state.QuantumNumbers.qn_dict.keys() + lower_state.QuantumNumbers.qn_dict.keys())):
if isVibrationalStateLabel(label):
try:
value_up = upper_state.QuantumNumbers.qn_dict[label]
except:
value_up = 0
try:
value_low = lower_state.QuantumNumbers.qn_dict[label]
except:
value_low = 0
v_dict[label] = [value_up, value_low]
v_string = ''
valup_string = ''
vallow_string = ''
for v in v_dict:
v_string += "%s," % v
valup_string += "%s," % v_dict[v][0]
vallow_string += "%s," % v_dict[v][1]
if len(v_dict) > 1:
t_state = "(%s)=(%s)-(%s)" % (v_string[:-1], valup_string[:-1], vallow_string[:-1])
else:
t_state = "%s=%s-%s" % (v_string[:-1], valup_string[:-1], vallow_string[:-1])
#t_state = '(%s)-(%s)' % (upper_state.QuantumNumbers.vibstate,lower_state.QuantumNumbers.vibstate)
except:
t_state = ''
# go to the next transition if state does not match
if t_state != stateInfo and stateInfo is not None and stateInfo != '':
continue
# Get hyperfinestructure info if hfsInfo is None
# only then the hfsInfo has not been inserted in the species name
# (there can be multiple values in the complete dataset
if hfsInfo == '':
t_hfs = ''
try:
for pc in result.data['RadiativeTransitions'][trans].ProcessClass:
if str(pc)[:3] == 'hyp':
t_hfs = str(pc)
except Exception, e:
print "Error: %s", e
else:
t_hfs = hfsInfo
# if hfs is not None and empty then only Transitions without hfs-flag
# should be processed
if hfs is not None and hfs != t_hfs:
continue
t_name = "%s; %s; %s" % (formula, t_state, t_hfs)
t_name = t_name.strip()
# update list of distinct species names.
if id in species_names:
if not t_name in species_names[id]:
species_names[id].append(t_name)
num_transitions[t_name] = 0
else:
species_names[id] = [t_name]
num_transitions[t_name] = 0
frequency = float(result.data['RadiativeTransitions'][trans].FrequencyValue)
uncertainty = "%lf" % float(result.data['RadiativeTransitions'][trans].FrequencyAccuracy)
# Get statistical weight if present
if upper_state.TotalStatisticalWeight:
weight = int(upper_state.TotalStatisticalWeight)
else:
weight = None
# Get nuclear spin isomer (ortho/para) if present
try:
nsiName = upper_state.NuclearSpinIsomerName
except AttributeError:
nsiName = None
# Insert transition into database
try:
cursor.execute("""INSERT INTO Transitions (
T_Name,
T_Frequency,
T_EinsteinA,
T_Uncertainty,
T_EnergyLower,
T_UpperStateDegeneracy,
T_HFS,
T_UpperStateQuantumNumbers,
T_LowerStateQuantumNumbers) VALUES
(?, ?,?,?,?, ?,?, ?,?)""",
(t_name,
"%lf" % frequency,
"%g" % float(result.data['RadiativeTransitions'][trans].TransitionProbabilityA),
uncertainty, "%lf" % float(lower_state.StateEnergyValue),
weight,
#upper_state.QuantumNumbers.case,
t_hfs,
str(upper_state.QuantumNumbers.qn_string),
str(lower_state.QuantumNumbers.qn_string),
))
num_transitions[t_name] += 1
except Exception, e:
print "Transition has not been inserted:\n Error: %s" % e
def update_database(self, add_nodes = None, insert_only = False, update_only = False):
"""
Checks if there are updates available for all entries. Updates will
be retrieved from the resource specified in the database.
All resources will be searched for new entries, which will be inserted
if available. Additional resources can be specified via add_nodes.
add_nodes: Single or List of node-instances (nodes.Node)
"""
# counter to identify which entry is currently processed
counter = 0
# counter to count available updates
count_updates = 0
# list of database - nodes which are currently in the local database
dbnodes = []
# create an instance with all available vamdc-nodes
nl = nodes.Nodelist()
# attach additional nodes to the list of dbnodes (for insert)
if not functions.isiterable(add_nodes):
add_nodes = [add_nodes]
for node in add_nodes:
if node is None:
pass
elif not isinstance(node, nodes.Node):
print "Could not attach node. Wrong type, it should be type <nodes.Node>"
else:
dbnodes.append(node)
#--------------------------------------------------------------------
# Check if updates are available for entries
# Get list of species in the database
cursor = self.conn.cursor()
cursor.execute("SELECT PF_Name, PF_SpeciesID, PF_VamdcSpeciesID, datetime(PF_Timestamp), PF_ResourceID FROM Partitionfunctions ")
rows = cursor.fetchall()
num_rows = len(rows)
query = q.Query()
request = r.Request()
if not insert_only:
print("----------------------------------------------------------")
print "Looking for updates"
print("----------------------------------------------------------")
for row in rows:
counter += 1
print "%5d/%5d: Check specie %-55s (%-15s): " % (counter, num_rows, row[0], row[1]),
try:
node = nl.getnode(str(row[4]))
except:
node = None
if node is None:
print " -- RESOURCE NOT AVAILABLE"
continue
else:
if node not in dbnodes:
dbnodes.append(node)
vamdcspeciesid = row[2]
# Currently the database prefix XCDMS- or XJPL- has to be removed
speciesid = row[1].split("-")[1]
query_string = "SELECT ALL WHERE SpeciesID=%s" % speciesid
request.setnode(node)
request.setquery(query_string)
errorcode = None
try:
changedate = request.getlastmodified()
# except r.TimeOutError, e:
# errorcode = e.strerror
# changedate = None
except Exception, e:
errorcode = e.strerror
changedate = None
tstamp = parser.parse(row[3] + " GMT")
if changedate is None:
if errorcode is None:
errorcode = "UNKNOWN"
print " -- %s (Could not retrieve information)" % errorcode
continue
if tstamp < changedate:
print " -- UPDATE AVAILABLE "
count_updates += 1
print " -- PERFORM UPDATE -- "
query_string = "SELECT SPECIES WHERE SpeciesID=%s" % speciesid
request.setquery(query_string)
result = request.dorequest()
try:
result.populate_model()
except:
print " Error: Could not process data "
continue
try:
self.insert_species_data(result.data['Molecules'], node, update = True)
except:
print " Error: Could not update data "
continue
print " -- UPDATE DONE -- "
else:
print " -- up to date"
if count_updates == 0:
print "\r No updates for your entries available"
print "Done"
def update_database(self, add_nodes = None, insert_only = False, update_only = False, delete_archived = False):
"""
Checks if there are updates available for all entries. Updates will
be retrieved from the resource specified in the database.
All resources will be searched for new entries, which will be inserted
if available. Additional resources can be specified via add_nodes.
:ivar nodes.Node add_nodes: Single or List of node-instances.
:ivar boolean insert_only: Just insert new species and skip updates if True
:ivar boolean update_only: Just updates species and skip inserts if True
"""
# counter to identify which entry is currently processed
counter = 0
# counter to count available updates
count_updates = 0
# list of database - nodes which are currently in the local database
dbnodes = []
# create an instance with all available vamdc-nodes
nl = nodes.Nodelist()
# attach additional nodes to the list of dbnodes (for insert)
if not functions.isiterable(add_nodes):
add_nodes = [add_nodes]
for node in add_nodes:
if node is None:
pass
elif not isinstance(node, nodes.Node):
print "Could not attach node. Wrong type, it should be type <nodes.Node>"
else:
dbnodes.append(node)
#--------------------------------------------------------------------
# Check if updates are available for entries
# Get list of species in the database
cursor = self.conn.cursor()
cursor.execute("SELECT PF_Name, PF_SpeciesID, PF_VamdcSpeciesID, datetime(PF_Timestamp), PF_ResourceID FROM Partitionfunctions ")
rows = cursor.fetchall()
num_rows = len(rows)
query = q.Query()
request = r.Request()
if not insert_only:
print("----------------------------------------------------------")
print "Looking for updates"
print("----------------------------------------------------------")
for row in rows:
counter += 1
print "%5d/%5d: Check specie %-55s (%-15s): " % (counter, num_rows, row[0], row[1]),
try:
node = nl.getnode(str(row[4]))
except:
node = None
if node is None:
print " -- RESOURCE NOT AVAILABLE"
continue
else:
if node not in dbnodes:
dbnodes.append(node)
vamdcspeciesid = row[2]
# Currently the database prefix XCDMS- or XJPL- has to be removed
speciesid = row[1].split("-")[1]
query_string = "SELECT ALL WHERE SpeciesID=%s" % speciesid
request.setnode(node)
request.setquery(query_string)
errorcode = None
try:
changedate = request.getlastmodified()
except r.NoContentError, e:
# Delete entries which are not available anymore
if request.status == 204:
if delete_archived:
print " -- ENTRY ARCHIVED AND WILL BE DELETED -- "
del_specie = self.delete_species(row[1])
if len(del_specie) > 0:
print "\r Done"
else:
print " -- ENTRY ARCHIVED -- "
continue
except r.TimeOutError, e:
# errorcode = e.strerror
# changedate = None
print " -- TIMEOUT: Could not check entry -- "
continue
except:
def update_database(self, add_nodes = None, insert_only = False, update_only = False, delete_archived = False):
"""
Checks if there are updates available for all entries. Updates will
be retrieved from the resource specified in the database.
All resources will be searched for new entries, which will be inserted
if available. Additional resources can be specified via add_nodes.
:ivar nodes.Node add_nodes: Single or List of node-instances.
:ivar boolean insert_only: Just insert new species and skip updates if True
:ivar boolean update_only: Just updates species and skip inserts if True
"""
# counter to identify which entry is currently processed
counter = 0
# counter to count available updates
count_updates = 0
# list of database - nodes which are currently in the local database
dbnodes = []
# create an instance with all available vamdc-nodes
nl = nodes.Nodelist()
# attach additional nodes to the list of dbnodes (for insert)
if not functions.isiterable(add_nodes):
add_nodes = [add_nodes]
for node in add_nodes:
if node is None:
pass
elif not isinstance(node, nodes.Node):
print("Could not attach node. Wrong type, it should be type <nodes.Node>")
else:
dbnodes.append(node)
#--------------------------------------------------------------------
# Check if updates are available for entries
# Get list of species in the database
cursor = self.conn.cursor()
cursor.execute("SELECT PF_Name, PF_SpeciesID, PF_VamdcSpeciesID, datetime(PF_Timestamp), PF_ResourceID FROM Partitionfunctions ")
rows = cursor.fetchall()
num_rows = len(rows)
query = q.Query()
request = r.Request()
if not insert_only:
print("----------------------------------------------------------")
print("Looking for updates")
print("----------------------------------------------------------")
for row in rows:
counter += 1
print("%5d/%5d: Check specie %-55s (%-15s): " % (counter, num_rows, row[0], row[1]), end=' ')
try:
node = nl.getnode(str(row[4]))
except:
node = None
if node is None:
print(" -- RESOURCE NOT AVAILABLE")
continue
else:
if node not in dbnodes:
dbnodes.append(node)
vamdcspeciesid = row[2]
# Currently the database prefix XCDMS- or XJPL- has to be removed
speciesid = row[1].split("-")[1]
query_string = "SELECT ALL WHERE SpeciesID=%s" % speciesid
request.setnode(node)
request.setquery(query_string)
errorcode = None
try:
changedate = request.getlastmodified()
except r.NoContentError as e:
# Delete entries which are not available anymore
if request.status == 204:
if delete_archived:
print(" -- ENTRY ARCHIVED AND WILL BE DELETED -- ")
del_specie = self.delete_species(row[1])
if len(del_specie) > 0:
print("\r Done")
else:
print(" -- ENTRY ARCHIVED -- ")
continue
except r.TimeOutError as e:
# errorcode = e.strerror
# changedate = None
print(" -- TIMEOUT: Could not check entry -- ")
continue
except:
changedate = None
print("Could not retrieve information - Unexpected error:", sys.exc_info()[0])
continue
tstamp = parser.parse(row[3] + " GMT")
if changedate is None:
if errorcode is None:
errorcode = "UNKNOWN"
print(" -- %s (Could not retrieve information)" % errorcode)
continue
if tstamp < changedate:
print(" -- UPDATE AVAILABLE ")
count_updates += 1
print(" -- PERFORM UPDATE -- ")
query_string = "SELECT SPECIES WHERE SpeciesID=%s" % speciesid
request.setquery(query_string)
result = request.dorequest()
try:
result.populate_model()
except:
print(" Error: Could not process data ")
continue
try:
self.insert_species_data(result.data['Molecules'], node, update = True)
except:
print(" Error: Could not update data ")
continue
print(" -- UPDATE DONE -- ")
else:
print(" -- up to date")
if count_updates == 0:
print("\r No updates for your entries available")
print("Done")
else:
cursor.execute("SELECT distinct PF_ResourceID FROM Partitionfunctions ")
rows = cursor.fetchall()
for row in rows:
try:
node = nl.getnode(str(row[0]))
except:
node = None
if node is None:
print(" -- RESOURCE NOT AVAILABLE")
continue
else:
if node not in dbnodes:
dbnodes.append(node)
if update_only:
return
# Check if there are new entries available
#---------------------------------------------------------
# Check all dbnodes for new species
for node in dbnodes:
counter = 0
insert_molecules_list = []
print("----------------------------------------------------------")
print("Query '{dbname}' for new species ".format(dbname=node.name))
print("----------------------------------------------------------")
request.setnode(node)
result = request.getspecies()
for id in result.data['Molecules']:
try:
cursor.execute("SELECT PF_Name, PF_SpeciesID, PF_VamdcSpeciesID, PF_Timestamp FROM Partitionfunctions WHERE PF_SpeciesID=?", [(id)])
exist = cursor.fetchone()
if exist is None:
print(" %s" % result.data['Molecules'][id])
insert_molecules_list.append(result.data['Molecules'][id])
counter += 1
except Exception as e:
print(e)
print(id)
print("There are %d new species available" % counter)
print("----------------------------------------------------------")
print("Start insert")
print("----------------------------------------------------------")
self.insert_species_data(insert_molecules_list, node)
print("----------------------------------------------------------")
print("Done")
def insert_species_data(self, species, node, update=False):
"""
Checks the VAMDC database node for new species and inserts them into the local database
:ivar list species: species which will be inserted
:ivar nodes.Node node: vamdc-node / type: instance(nodes.node)
:ivar boolean update: if True then all entries in the local database with the same
species-id will be deleted before the insert is performed.
"""
# create a list of names. New names have not to be in that list
names_black_list = []
cursor = self.conn.cursor()
cursor.execute("SELECT PF_Name FROM Partitionfunctions")
rows = cursor.fetchall()
for row in rows:
names_black_list.append(row[0])
#----------------------------------------------------------
# Create a list of species for which transitions will be
# retrieved and inserted in the database.
# Species have to be in the Partitionfunctions - table
if not functions.isiterable(species):
species = [species]
#--------------------------------------------------------------
for specie in species:
# if species is a dictionary (e.g. specmodel.Molecules)
# then get the species-instance instead of only the key.
if isinstance(species, dict):
specie = species[specie]
num_transitions = {}
# will contain a list of names which belong to one specie
species_names = {}
# list will contain species whose insert-failed
species_with_error = []
# check if specie is of type Molecule
if isinstance(specie, specmodel.Molecule):
speciesid = specie.SpeciesID
vamdcspeciesid = specie.VAMDCSpeciesID
formula = specie.OrdinaryStructuralFormula
if isinstance(specie, specmodel.Atom):
speciesid = specie.SpeciesID
vamdcspeciesid = specie.VAMDCSpeciesID
# formula = specie.OrdinaryStructuralFormula
else:
try:
if isinstance(specie, str) and len(specie) == 27:
vamdcspeciesid = specie
speciesid = None
except:
print("Specie is not of wrong type")
print("Type Molecule or string (Inchikey) is allowed")
continue
if speciesid:
print("Processing: {speciesid}".format(speciesid = speciesid))
else:
print("Processing: {vamdcspeciesid}".format(vamdcspeciesid = vamdcspeciesid))
try:
# Create query string
query_string = "SELECT ALL WHERE VAMDCSpeciesID='%s'" % vamdcspeciesid
request = r.Request()
# Get data from the database
request.setnode(node)
request.setquery(query_string)
result = request.dorequest()
#result.populate_model()
except Exception as e:
print(" -- Error %s: Could not fetch and process data" % e.strerror)
continue
#---------------------------------------
cursor = self.conn.cursor()
cursor.execute('BEGIN TRANSACTION')
#------------------------------------------------------------------------------------------------------
# if update is allowed then all entries in the database for the given species-id will be
# deleted, and thus replaced by the new data
if update:
if speciesid is None:
for sid in list(result.data['Molecules'].keys()) + list(result.data['Atoms'].keys()):
deleted_species = self.delete_species(sid)
for ds in deleted_species:
names_black_list.remove(ds)
else:
deleted_species = self.delete_species(speciesid)
for ds in deleted_species:
names_black_list.remove(ds)
#------------------------------------------------------------------------------------------------------
#------------------------------------------------------------------------------------------------------
# Insert all transitions
num_transitions_found = len(result.data['RadiativeTransitions'])
counter_transitions = 0
for trans in result.data['RadiativeTransitions']:
counter_transitions+=1
print("\r insert transition %d of %d" % (counter_transitions, num_transitions_found), end=' ')
# data might contain transitions for other species (if query is based on ichikey/vamdcspeciesid).
# Insert transitions only if they belong to the correct specie
if result.data['RadiativeTransitions'][trans].SpeciesID == speciesid or speciesid is None:
id = str(result.data['RadiativeTransitions'][trans].SpeciesID)
# if an error has occured already then there will be no further insert
if id in species_with_error:
continue
# Get upper and lower state from the states table
try:
upper_state = result.data['States']["%s" % result.data['RadiativeTransitions'][trans].UpperStateRef]
lower_state = result.data['States']["%s" % result.data['RadiativeTransitions'][trans].LowerStateRef]
except (KeyError, AttributeError):
print(" -- Error: State is missing")
species_with_error.append(id)
continue
if id in result.data['Atoms'].keys():
is_atom = True
is_molecule = False
atomname = self.createatomname(result.data['Atoms'][id])
elif id in result.data['Molecules'].keys():
is_atom = False
is_molecule = True
formula = str(result.data['Molecules'][id].OrdinaryStructuralFormula)
# Get string which identifies the vibrational states involved in the transition
t_state = self.getvibstatelabel(upper_state, lower_state)
else:
continue
# Get hyperfinestructure info if hfsInfo is None
# only then the hfsInfo has not been inserted in the species name
# (there can be multiple values in the complete dataset
t_hfs = ''
try:
for pc in result.data['RadiativeTransitions'][trans].ProcessClass:
if str(pc)[:3] == 'hyp':
t_hfs = str(pc)
except Exception as e:
print("Error: %s", e)
frequency = float(result.data['RadiativeTransitions'][trans].FrequencyValue)
try:
uncertainty = "%lf" % float(result.data['RadiativeTransitions'][trans].FrequencyAccuracy)
except TypeError:
print(" -- Error uncertainty not available")
species_with_error.append(id)
continue
# Get statistical weight if present
try:
weight = int(upper_state.TotalStatisticalWeight)
except:
print(" -- Error statistical weight not available")
species_with_error.append(id)
continue
# Get nuclear spin isomer (ortho/para) if present
try:
nsiName = upper_state.NuclearSpinIsomerName
except AttributeError:
nsiName = None
# if nuclear spin isomer is defined then two entries have to be generated
if nsiName is not None and nsiName != '':
nsinames = [nsiName, None]
nsiStateOrigin = result.data['States']["%s" % upper_state.NuclearSpinIsomerLowestEnergy]
nsiEnergyOffset = float(nsiStateOrigin.StateEnergyValue)
else:
nsinames = [None]
for nsiName in nsinames:
# create name
if is_atom == True:
t_name = atomname
else:
t_affix = ";".join([affix for affix in [t_hfs, nsiName] if affix is not None and affix!=''])
t_name = "%s;%s;%s" % (formula, t_state, t_affix)
t_name = t_name.strip()
# remove all blanks in the name
t_name = t_name.replace(' ','')
# check if name is in the list of forbidden names and add counter if so
i = 1
while t_name in names_black_list:
t_name = "%s#%d" % (t_name.split('#')[0], i)
i += 1
# update list of distinct species names.
if id in species_names:
if not t_name in species_names[id]:
species_names[id].append(t_name)
num_transitions[t_name] = 0
else:
species_names[id] = [t_name]
num_transitions[t_name] = 0
if nsiName is not None:
lowerStateEnergy = float(lower_state.StateEnergyValue) - nsiEnergyOffset
else:
lowerStateEnergy = float(lower_state.StateEnergyValue)
# Insert transition into database
try:
cursor.execute("""INSERT INTO Transitions (
T_Name,
T_Frequency,
T_EinsteinA,
T_Uncertainty,
T_EnergyLower,
T_UpperStateDegeneracy,
T_HFS,
T_UpperStateQuantumNumbers,
T_LowerStateQuantumNumbers) VALUES
(?, ?,?,?,?, ?,?, ?,?)""",
(t_name,
"%lf" % frequency,
"%g" % float(result.data['RadiativeTransitions'][trans].TransitionProbabilityA),
uncertainty, "%lf" % lowerStateEnergy,
weight,
#upper_state.QuantumNumbers.case,
t_hfs,
str(upper_state.QuantumNumbers.qn_string),
str(lower_state.QuantumNumbers.qn_string),
))
num_transitions[t_name] += 1
except Exception as e:
print("Transition has not been inserted:\n Error: %s" % e)
print("\n")
#------------------------------------------------------------------------------------------------------
#------------------------------------------------------------------------------------------------------
# delete transitions for all entries where an error occured during the insert
for id in species_with_error:
print(" -- Species {id} has not been inserted due to an error ".format(id=str(id)))
try:
for name in species_names[id]:
cursor.execute("DELETE FROM Transitions WHERE T_Name=?", (str(name),))
print(" -- {name} ".format(name=str(name)))
except:
pass
#------------------------------------------------------------------------------------------------------
# insert specie in Partitionfunctions (header) table
if node:
resourceID = node.identifier
url = node.url
else:
resourceID = 'NULL'
url = 'NULL'
# Insert molecules
for id in species_names:
if id in species_with_error:
continue
for name in species_names[id]:
# determine hyperfine-structure affix and nuclear spin isomer affix
try:
hfs = ''
nsi = ''
for affix in name.split("#")[0].split(';',2)[2].split(";"):
if affix.strip()[:3] == 'hyp':
hfs = affix.strip()
else:
# if affix does not identify hyperfine structure
# it identifies the nuclear spin isomer
nsi = affix.strip()
except:
hfs = ''
# Insert row in partitionfunctions
try:
if id in result.data['Atoms']:
if 'Comment' not in result.data['Atoms'][id].__dict__:
result.data['Atoms'][id].Comment = ""
cursor.execute("INSERT INTO Partitionfunctions (PF_Name, PF_SpeciesID, PF_VamdcSpeciesID, PF_Comment, PF_ResourceID, PF_URL, PF_Timestamp) VALUES (?,?,?,?,?,?,?)",
("%s" % name,
id,
"%s" % (result.data['Atoms'][id].VAMDCSpeciesID),
"%s" % (result.data['Atoms'][id].Comment),
resourceID,
"%s%s%s" % (url, "sync?LANG=VSS2&REQUEST=doQuery&FORMAT=XSAMS&QUERY=Select+*+where+SpeciesID%3D", id),
datetime.now(), ))
else:
cursor.execute("INSERT INTO Partitionfunctions (PF_Name, PF_SpeciesID, PF_VamdcSpeciesID, PF_HFS, PF_NuclearSpinIsomer, PF_Comment, PF_ResourceID, PF_URL, PF_Timestamp) VALUES (?,?,?,?,?,?,?,?,?)",
("%s" % name,
id,
"%s" % (result.data['Molecules'][id].VAMDCSpeciesID),
hfs,
nsi,
"%s" % (result.data['Molecules'][id].Comment),
resourceID,
"%s%s%s" % (url, "sync?LANG=VSS2&REQUEST=doQuery&FORMAT=XSAMS&QUERY=Select+*+where+SpeciesID%3D", id),
datetime.now(), ))
except sqlite3.Error as e:
print("An error occurred:", e.args[0])
except Exception as e:
print("An error occurred:", e.args[0])
print(list(result.data['Molecules'].keys()))
# Update Partitionfunctions
if id in result.data['Atoms'].keys():
for temperature in Temperatures:
pf_values = specmodel.calculate_partitionfunction(result.data['States'], temperature = temperature)
try:
field = ("PF_%.3lf" % float(temperature)).replace('.', '_')
sql = "UPDATE Partitionfunctions SET %s=? WHERE PF_SpeciesID=? " % field
cursor.execute(sql, (pf_values[id], id))
except Exception as e:
print("SQL-Error: %s " % sql)
print(pf_value, id)
print("Error: %d: %s" % (e.args[0], e.args[1]))
else:
try:
for pfs in result.data['Molecules'][id].PartitionFunction:
if 'NuclearSpinIsomer' not in pfs.__dict__:
nsi = ''
else:
nsi = pfs.NuclearSpinIsomer
for temperature in pfs.values.keys():
try:
field = ("PF_%.3lf" % float(temperature)).replace('.', '_')
sql = "UPDATE Partitionfunctions SET %s=? WHERE PF_SpeciesID=? AND IFNULL(PF_NuclearSpinIsomer,'')=?" % field
cursor.execute(sql, (pfs.values[temperature], id, nsi))
except Exception as e:
print("SQL-Error: %s " % sql)
print(pfs.values[temperature], id)
print("Error: %d: %s" % (e.args[0], e.args[1]))
except:
pass
#------------------------------------------------------------------------------------------------------
for row in num_transitions:
print(" for %s inserted %d transitions" % (row, num_transitions[row]))
self.conn.commit()
cursor.close()
