def write_analyses_to_csv(p, ms):
man = IsotopeDatabaseManager(bind=False, connect=False)
man.db.trait_set(name='pychrondata',
kind='mysql',
host='129.138.12.160',
username='******',
password='******')
man.connect()
db = man.db
with db.session_ctx():
h = datetime.now()
l = h - timedelta(days=60)
ans = db.get_analyses_date_range(l, h, mass_spectrometers=ms)
with open(p, 'w') as wfile:
writer = csv.writer(wfile)
n = len(ans)
for i, ai in enumerate(ans):
if not (i + 1) % 10:
print '{}/{}'.format(i + 1, n)
try:
t = ai.timestamp
pc = ai.peak_center.center
# print ai.analysis_timestamp, t, pc
writer.writerow([t, pc])
except AttributeError:
pass
def write_analyses_to_csv(p, ms):
man = IsotopeDatabaseManager(bind=False, connect=False)
man.db.trait_set(
name="pychrondata",
kind="mysql",
host=os.environ.get("HOST"),
username="******",
password=os.environ.get("DB_PWD"),
)
man.connect()
db = man.db
with db.session_ctx():
h = datetime.now()
l = h - timedelta(days=60)
ans = db.get_analyses_date_range(l, h, mass_spectrometers=ms)
with open(p, "w") as wfile:
writer = csv.writer(wfile)
n = len(ans)
for i, ai in enumerate(ans):
# if not (i + 1) % 10:
# print '{}/{}'.format(i + 1, n)
try:
t = ai.timestamp
# print ai.id
pc = ai.peak_center.center
print ai.analysis_timestamp, ai.record_id, t, pc
writer.writerow([t, pc])
except AttributeError, e:
print e
def write_analyses_to_csv(p, ms):
man = IsotopeDatabaseManager(bind=False, connect=False)
man.db.trait_set(name='pychrondata',
kind='mysql',
host='129.138.12.160',
username='******',
password='******')
man.connect()
db = man.db
with db.session_ctx():
h = datetime.now()
l = h - timedelta(days=60)
ans = db.get_analyses_date_range(l, h, mass_spectrometers=ms)
with open(p, 'w') as wfile:
writer = csv.writer(wfile)
n = len(ans)
for i, ai in enumerate(ans):
if not (i + 1) % 10:
print '{}/{}'.format(i + 1, n)
try:
t = ai.timestamp
pc = ai.peak_center.center
# print ai.analysis_timestamp, t, pc
writer.writerow([t, pc])
except AttributeError:
pass
def isotope_manager_factory(name='pychrondata_dev'):
man = IsotopeDatabaseManager(connect=False, bind=False)
man.db.kind = 'mysql'
man.db.name = name
man.db.password = '******'
man.db.username = '******'
man.db.host = 'localhost'
man.connect()
return man
def isotope_manager_factory(name='pychrondata_dev'):
man = IsotopeDatabaseManager(connect=False, bind=False)
man.db.kind = 'mysql'
man.db.name = name
man.db.password = '******'
man.db.username = '******'
man.db.host = 'localhost'
man.connect()
return man
def load(self, db_mol_weights=True):
self.debug('******************************* LOAD Spec')
if db_mol_weights:
# get the molecular weights from the database
dbm = IsotopeDatabaseManager(application=self.application,
warn=False)
self.db = dbm
if dbm.isConnected():
self.info('loading molecular_weights from database')
mws = dbm.db.get_molecular_weights()
# convert to a dictionary
m = dict([(mi.name, mi.mass) for mi in mws])
self.spectrometer.molecular_weights = m
if not self.spectrometer.molecular_weights:
import csv
# load the molecular weights dictionary
p = os.path.join(paths.spectrometer_dir, 'molecular_weights.csv')
if os.path.isfile(p):
self.info('loading "molecular_weights.csv" file')
with open(p, 'U') as f:
reader = csv.reader(f, delimiter='\t')
args = [[l[0], float(l[1])] for l in reader]
self.spectrometer.molecular_weights = dict(args)
else:
self.info('writing a default "molecular_weights.csv" file')
# make a default molecular_weights.csv file
from pychron.spectrometer.molecular_weights import MOLECULAR_WEIGHTS as mw
with open(p, 'U') as f:
writer = csv.writer(f, delimiter='\t')
data = [a for a in mw.itervalues()]
data = sorted(data, key=lambda x: x[1])
for row in data:
writer.writerow(row)
self.spectrometer.molecular_weights = mw
#config = self.get_configuration(path=os.path.join(paths.spectrometer_dir, 'detectors.cfg'))
#for name in config.sections():
# relative_position = self.config_get(config, name, 'relative_position', cast='float')
# color = self.config_get(config, name, 'color', default='black')
# default_state = self.config_get(config, name, 'default_state', default=True, cast='boolean')
# isotope = self.config_get(config, name, 'isotope')
# kind = self.config_get(config, name, 'kind', default='Faraday', optional=True)
# self.spectrometer.add_detector(name=name,
# relative_position=relative_position,
# color=color,
# active=default_state,
# isotope=isotope,
# kind=kind)
self.spectrometer.load()
return True
def load(self, db_mol_weights=True):
self.debug('******************************* LOAD Spec')
if db_mol_weights:
# get the molecular weights from the database
dbm = IsotopeDatabaseManager(application=self.application,
warn=False)
self.db = dbm
if dbm.isConnected():
self.info('loading molecular_weights from database')
mws = dbm.db.get_molecular_weights()
# convert to a dictionary
m = dict([(mi.name, mi.mass) for mi in mws])
self.spectrometer.molecular_weights = m
if not self.spectrometer.molecular_weights:
import csv
# load the molecular weights dictionary
p = os.path.join(paths.spectrometer_dir, 'molecular_weights.csv')
if os.path.isfile(p):
self.info('loading "molecular_weights.csv" file')
with open(p, 'U') as f:
reader = csv.reader(f, delimiter='\t')
args = [[l[0], float(l[1])] for l in reader]
self.spectrometer.molecular_weights = dict(args)
else:
self.info('writing a default "molecular_weights.csv" file')
# make a default molecular_weights.csv file
from pychron.spectrometer.molecular_weights import MOLECULAR_WEIGHTS as mw
with open(p, 'U') as f:
writer = csv.writer(f, delimiter='\t')
data = [a for a in mw.itervalues()]
data = sorted(data, key=lambda x: x[1])
for row in data:
writer.writerow(row)
self.spectrometer.molecular_weights = mw
#config = self.get_configuration(path=os.path.join(paths.spectrometer_dir, 'detectors.cfg'))
#for name in config.sections():
# relative_position = self.config_get(config, name, 'relative_position', cast='float')
# color = self.config_get(config, name, 'color', default='black')
# default_state = self.config_get(config, name, 'default_state', default=True, cast='boolean')
# isotope = self.config_get(config, name, 'isotope')
# kind = self.config_get(config, name, 'kind', default='Faraday', optional=True)
# self.spectrometer.add_detector(name=name,
# relative_position=relative_position,
# color=color,
# active=default_state,
# isotope=isotope,
# kind=kind)
self.spectrometer.load()
return True
def setup_source(self):
src = IsotopeDatabaseManager(connect=False, bind=False)
db = src.db
db.trait_set(name='pychrondata',
kind='mysql',
host='129.138.12.160',
username='******',
password='******')
self.source = src
def setup_source(self):
src = IsotopeDatabaseManager(connect=False, bind=False)
db = src.db
db.trait_set(name='pychrondata',
kind='mysql',
host=os.environ.get('HOST'),
username='******',
password=os.environ.get('DB_PWD'))
self.source = src
def _scanner_default(self):
spec = self.spectrometer_manager.spectrometer
s = MassCalibratorSweep(spectrometer=spec, db=IsotopeDatabaseManager())
if spec.simulation:
s.integration_time = 0.065536
s.verbose = True
return s
def _source_default(self):
r = IsotopeDatabaseManager(connect=False, bind=False)
r.db.trait_set(kind='mysql',
host='localhost',
username='******',
password='******',
name='pychrondata_dev')
r.db.connect()
return r
def perform(self, event):
from pychron.entry.loaders.irradiation_holder_loader import IrradiationHolderLoader
from pychron.database.isotope_database_manager import IsotopeDatabaseManager
man = IsotopeDatabaseManager()
db = man.db
if db.connect():
a = IrradiationHolderLoader()
a.do_import(db)
def load(self, db_mol_weights=True):
spec = self.spectrometer
mftable = spec.magnet.mftable
self.debug('******************************* LOAD Spec')
if db_mol_weights:
# get the molecular weights from the database
dbm = IsotopeDatabaseManager(application=self.application,
warn=False)
if dbm.is_connected():
self.info('loading molecular_weights from database')
mws = dbm.db.get_molecular_weights()
# convert to a dictionary
m = dict([(mi.name, mi.mass) for mi in mws])
spec.molecular_weights = m
mftable.db = dbm.db
if not spec.molecular_weights:
import csv
# load the molecular weights dictionary
p = os.path.join(paths.spectrometer_dir, 'molecular_weights.csv')
if os.path.isfile(p):
self.info('loading "molecular_weights.csv" file')
with open(p, 'U') as f:
reader = csv.reader(f, delimiter='\t')
args = [[l[0], float(l[1])] for l in reader]
spec.molecular_weights = dict(args)
else:
self.info('writing a default "molecular_weights.csv" file')
# make a default molecular_weights.csv file
from pychron.spectrometer.molecular_weights import MOLECULAR_WEIGHTS as mw
with open(p, 'U') as f:
writer = csv.writer(f, delimiter='\t')
data = [a for a in mw.itervalues()]
data = sorted(data, key=lambda x: x[1])
for row in data:
writer.writerow(row)
spec.molecular_weights = mw
self.spectrometer.load()
mftable.spectrometer_name = self.spectrometer.name
return True
def _get_database_manager(self, connect=True):
if not self._db:
iso = IsotopeDatabaseManager(application=self.application,
warn=False,
version_warn=False,
attribute_warn=False,
connect=connect)
self._db = iso
return self._db
def init(self):
conn = dict(
host=os.environ.get('ARGONSERVER_HOST'),
username='******', # os.environ.get('ARGONSERVER_DB_USER'),
password=os.environ.get('ARGONSERVER_DB_PWD'),
kind='mysql')
use_local = False
if use_local:
meta_name = 'MetaDataDev'
dest_conn = dict(
host='localhost',
username=os.environ.get('LOCALHOST_DB_USER'),
password=os.environ.get('LOCALHOST_DB_PWD'),
kind='mysql',
# echo=True,
name='pychrondvc_dev')
else:
meta_name = 'NMGRLMetaData'
dest_conn = conn.copy()
dest_conn['name'] = 'pychrondvc'
self.dvc = DVC(bind=False,
organization='NMGRLData',
meta_repo_name=meta_name)
paths.meta_root = os.path.join(paths.dvc_dir, self.dvc.meta_repo_name)
self.dvc.db.trait_set(**dest_conn)
if not self.dvc.initialize():
self.warning_dialog('Failed to initialize DVC')
return
self.dvc.meta_repo.smart_pull(quiet=self.quiet)
self.persister = DVCPersister(dvc=self.dvc,
stage_files=False,
bind=False)
proc = IsotopeDatabaseManager(bind=False, connect=False)
use_local_src = False
if use_local_src:
conn = dict(
host='localhost',
username=os.environ.get('LOCALHOST_DB_USER'),
password=os.environ.get('LOCALHOST_DB_PWD'),
kind='mysql',
# echo=True,
name='pychrondata')
else:
conn['name'] = 'pychrondata'
proc.db.trait_set(**conn)
src = proc.db
src.connect()
self.processor = proc
def get_project_bins(project):
# src = self.processor.db
src = IsotopeDatabaseManager(
dict(
host='localhost',
username=os.environ.get('LOCALHOST_DB_USER'),
password=os.environ.get('LOCALHOST_DB_PWD'),
kind='mysql',
# echo=True,
name='pychrondata'))
tol_hrs = 6
# self.debug('bulk import project={}, pi={}'.format(project, principal_investigator))
ts, idxs = get_project_timestamps(src.db, project, tol_hrs=tol_hrs)
# repository_identifier = project
# def filterfunc(x):
# a = x.labnumber.irradiation_position is None
# b = False
# if not a:
# b = x.labnumber.irradiation_position.level.irradiation.name == irradname
#
# d = False
# if x.extraction:
# ed = x.extraction.extraction_device
# if not ed:
# d = True
# else:
# d = ed.name == 'Fusions CO2'
#
# return (a or b) and d
#
for ms in ('jan', 'obama'):
for i, ais in enumerate(array_split(ts, idxs + 1)):
if not ais.shape[0]:
continue
low = get_datetime(ais[0]) - timedelta(hours=tol_hrs / 2.)
high = get_datetime(ais[-1]) + timedelta(hours=tol_hrs / 2.)
print ms, low, high
def bind_preferences(self):
# massspec
prefid = 'pychron.massspec.database'
bind_preference(self, 'massspec_enabled', '{}.enabled'.format(prefid))
if self.massspec_enabled:
from pychron.experiment.utilities.mass_spec_database_importer import MassSpecDatabaseImporter
store = MassSpecDatabaseImporter()
bind_preference(store.db, 'name', '{}.name'.format(prefid))
bind_preference(store.db, 'host', '{}.host'.format(prefid))
bind_preference(store.db, 'username', '{}.username'.format(prefid))
bind_preference(store.db, 'password', '{}.password'.format(prefid))
prefid = 'pychron.massspec.config'
bind_preference(store, 'reference_detector_name',
'{}.reference_detector_name'.format(prefid))
bind_preference(store, 'reference_isotope_name',
'{}.reference_isotope_name'.format(prefid))
bind_preference(
store, 'use_reference_detector_by_isotope',
'{}.use_reference_detector_by_isotope'.format(prefid))
self.stores['massspec'] = store
# isotopedb
prefid = 'pychron.pychron.database'
bind_preference(self, 'isotopedb_enabled', '{}.enabled'.format(prefid))
if self.isotopedb_enabled:
from pychron.database.isotope_database_manager import IsotopeDatabaseManager
store = IsotopeDatabaseManager()
bind_preference(store.db, 'name', '{}.name'.format(prefid))
bind_preference(store.db, 'host', '{}.host'.format(prefid))
bind_preference(store.db, 'username', '{}.username'.format(prefid))
bind_preference(store.db, 'password', '{}.password'.format(prefid))
self.stores['isotopedb'] = store
self.stores['dvc'] = self.mainstore
def start(self):
iso = IsotopeDatabaseManager()
iso.populate_default_tables()
def _manager_default(self):
return IsotopeDatabaseManager(connect=False, bind=False)
v = View('test')
return v
p = Permutator()
p.path = './tests/data/config.yaml'
logging_setup('perm')
from pychron.database.isotope_database_manager import IsotopeDatabaseManager
class Record(object):
analysis_type = 'unknown'
def __init__(self, u):
self.uuid = u
man = IsotopeDatabaseManager(bind=False, connect=False)
db = man.db
db.trait_set(kind='mysql',
host='localhost',
name='pychrondata_dev',
username='******',
password='******')
db.connect()
ans = man.make_analyses(
[
Record('65c1c4a9-e317-452b-9654-3f06efcbe664'),
# Record('39b6e623-e178-4dc4-bf5c-14c81485bd54')
],
use_cache=False,
unpack=True)
def start(self):
iso = IsotopeDatabaseManager()
iso.populate_default_tables()
def __init__(self, connect=True, *args, **kw):
super(MFTableHistory, self).__init__(*args, **kw)
self.dbm = IsotopeDatabaseManager(bind=connect, connect=connect)
self._add_meta(d)
def _add_meta(self, d):
print d['project'], d['sample']
if __name__ == '__main__':
from pychron.core.helpers.logger_setup import logging_setup
logging_setup('analysis_loader')
# al = YAMLAnalysisLoader()
# p = '/Users/ross/Sandbox/analysis_import_template.yml'
# al.load_analyses(p)
from pychron.database.isotope_database_manager import IsotopeDatabaseManager
man = IsotopeDatabaseManager(bind=False, connect=False)
db = man.db
db.trait_set(kind='mysql',
username='******',
password='******',
host='localhost',
name='pychrondata_dev')
db.connect()
al = XLSAnalysisLoader()
al.db = db
al.load_analyses(
'/Users/ross/Programming/git/pychron_dev/pychron/entry/tests/data/analysis_import.xls'
)
al.import_analyses()
# al.delete_analyses()
v = View("test")
return v
p = Permutator()
p.path = "./tests/data/config.yaml"
logging_setup("perm")
from pychron.database.isotope_database_manager import IsotopeDatabaseManager
class Record(object):
analysis_type = "unknown"
def __init__(self, u):
self.uuid = u
man = IsotopeDatabaseManager(bind=False, connect=False)
db = man.db
db.trait_set(kind="mysql", host="localhost", name="pychrondata_dev", username="******", password="******")
db.connect()
ans = man.make_analyses(
[
Record("65c1c4a9-e317-452b-9654-3f06efcbe664"),
# Record('39b6e623-e178-4dc4-bf5c-14c81485bd54')
],
use_cache=False,
unpack=True,
)
# a.j = ufloat(1e-4, 1e-7)
p.oanalyses = ans
def _mainstore_default(self):
mainstore = IsotopeDatabaseManager(precedence=1,
connect=self.bind_mainstore,
bind=self.bind_mainstore)
return mainstore
