def load_database(connection_string):
# Create and load the database
create_database(connection_string)
# Now that the database is created, connect to it and load up the JSON data
db = Database(connection_string, reference_tables=REFERENCE_TABLES)
db.load_database(DB_PATH, verbose=False)
print('New database generated.')
# Close all connections
db.session.close()
db.engine.dispose()
def db():
# Create a fresh temporary database and assert it exists
# Because we've imported simple.schema, we will be using that schema for the database
if os.path.exists(DB_NAME):
os.remove(DB_NAME)
connection_string = 'sqlite:///' + DB_NAME
create_database(connection_string)
assert os.path.exists(DB_NAME)
# Connect to the new database and confirm it has the Sources table
db = Database(connection_string)
assert db
assert 'source' in [c.name for c in db.Sources.columns]
return db
def load_db():
# Utility function to load the database
db_file = 'SIMPLE.db'
db_file_path = Path(db_file)
db_connection_string = 'sqlite:///SIMPLE.db' # SQLite browser
if RECREATE_DB and db_file_path.exists():
os.remove(db_file) # removes the current .db file if one already exists
if not db_file_path.exists():
create_database(db_connection_string) # creates empty database based on the simple schema
db = Database(db_connection_string) # connects to the empty database
db.load_database('data/') # loads the data from the data files into the database
else:
db = Database(db_connection_string) # if database already exists, connects to .db file
return db
def db():
# Create a fresh temporary database and assert it exists
# Because we've imported simple.schema, we will be using that schema for the database
if os.path.exists(DB_NAME):
os.remove(DB_NAME)
connection_string = 'sqlite:///' + DB_NAME
create_database(connection_string)
assert os.path.exists(DB_NAME)
# Connect to the new database and confirm it has the Sources table
db = Database(connection_string)
assert db
assert 'source' in [c.name for c in db.Sources.columns]
# Load the database contents
# This should take care of finding serious issues (key/column violations)
db.load_database(DB_PATH, verbose=False)
return db
def load_simpledb(db_file, recreatedb=True):
# Utility function to load the database
db_file_path = Path(db_file)
db_connection_string = 'sqlite:///' + db_file
if recreatedb and db_file_path.exists():
os.remove(
db_file) # removes the current .db file if one already exists
if not db_file_path.exists():
try: # Use fancy in-memory database, if supported by astrodbkit2
db = Database(
'sqlite://'
) # creates and connects to a temporary in-memory database
db.load_database(
'data/'
) # loads the data from the data files into the database
db.dump_sqlite(db_file) # dump in-memory database to file
db = Database(db_connection_string
) # replace database object with new file version
except RuntimeError:
# use in-file database
create_database(
db_connection_string
) # creates empty database based on the simple schema
db = Database(
db_connection_string) # connects to the empty database
db.load_database(
'data/'
) # loads the data from the data files into the database
else:
db = Database(db_connection_string
) # if database already exists, connects to .db file
return db
# Script to add Y dwarfs spectral types
from astrodbkit2.astrodb import create_database
from astrodbkit2.astrodb import Database
#from simple.schema import *
from astropy.table import Table
import numpy as np
import re
from utils import convert_spt_string_to_code
connection_string = 'sqlite:///../../SIMPLE.db' # SQLite
create_database(connection_string)
db = Database(connection_string)
db.load_database('../../data')
# load table
ingest_table = Table.read('Y-dwarf_table.csv', data_start=2)
names = ingest_table['source']
n_sources = len(names)
regime = ['infrared'
] * n_sources # all source have IR spectral classifications
spectral_types = ingest_table['SpT']
spt_refs = ingest_table['spt_ref']
# sources names in database Names table
db_names = []
for name in names:
db_name = db.search_object(name, output_table='Sources')[0].source
db_names.append(db_name)
# Convert SpT string to code
DRY_RUN = False #modifies .db file but not the data files
RECREATE_DB = True #recreates the .db file from the data files
VERBOSE = False
verboseprint = print if VERBOSE else lambda *a, **k: None
db_file = 'SIMPLE.db'
db_file_path = Path(db_file)
db_connection_string = 'sqlite:///SIMPLE.db' # SQLite browser
if RECREATE_DB and db_file_path.exists():
os.remove(db_file) #removes the current .db file if one already exists
if not db_file_path.exists():
create_database(db_connection_string
) #creates empty database based on the simple schema
db = Database(db_connection_string) #connects to the empty database
db.load_database(
'data/') #loads the data from the data files into the database
else:
db = Database(db_connection_string
) #if database already exists, connects to .db file
#Adding missing publications to publication table
add_publication(db, name='Sahl16', bibcode='J/MNRAS/455/357', dryrun=False)
add_publication(db, name='Liu16', bibcode='J/ApJ/833/96', dryrun=False)
add_publication(db, name='Wang18', bibcode='2018PASP..130f4402W', dryrun=False)
add_publication(db, name='Bedi17', bibcode='2017MNRAS.470.1140B', dryrun=False)
add_publication(db, name='Delo17', bibcode='2017A&A...608A..79D', dryrun=False)
add_publication(db, name='Luhm16', bibcode='2016AJ....152...78L', dryrun=False)