def setUp(self):
# self.t = LoadingTask()
db = isotope_manager_factory().db
lm = LoadingManager(db=db)
# lm.irradiation = 'NM-251'
# lm.level = 'H'
self.t = LoadingTask(manager=lm)
def setUp(self):
# self.t = LoadingTask()
db = isotope_manager_factory().db
lm = LoadingManager(db=db)
# lm.irradiation = 'NM-251'
# lm.level = 'H'
self.t = LoadingTask(manager=lm)
def run():
hp = hpy()
globalv.experiment_debug = True
# t = ExperimentEditorTask()
# p = os.path.join(paths.experiment_dir, 'demo.txt')
# t._open_experiment(p)
q = ExperimentQueue(delay_before_analyses=0, delay_between_analyses=0)
q.automated_runs = [
AutomatedRunSpec(labnumber='61312',
duration=2.0,
extraction_script='pause',
measurement_script='air',
mass_spectrometer='jan'),
AutomatedRunSpec(labnumber='61312',
duration=2.0,
extraction_script='pause',
measurement_script='air',
mass_spectrometer='jan'),
AutomatedRunSpec(labnumber='61312',
duration=2.0,
extraction_script='pause',
measurement_script='air',
mass_spectrometer='jan'),
AutomatedRunSpec(labnumber='61312',
duration=2.0,
extraction_script='pause',
measurement_script='air',
mass_spectrometer='jan'),
AutomatedRunSpec(labnumber='61312',
duration=2.0,
extraction_script='pause',
measurement_script='air',
mass_spectrometer='jan')
]
dbman = isotope_manager_factory()
specman = SpectrometerManager()
specman.load()
ex = ExperimentExecutor(
db=dbman.db,
spectrometer_manager=specman,
extraction_line_manager='',
executable=True,
)
ex.monitor = None
ex.experiment_queues = [
q,
]
ex.experiment_queue = q
hp.setrelheap()
t = ex.execute()
t.join()
# count_instances(group='sqlalchemy')
return hp
def setUpClass(cls):
cls.isotope_man = isotope_manager_factory(name='pychrondata_minnabluff')
cls.isotope_man.db.connect()
expected_filtered_56954_01A = dict(Ar40bs_c=2.20831,
Ar39bs_c=4.96090e-3,
Ar38bs_c=0.0014621,
Ar37bs_c=1.34848e-3,
Ar36bs_c=7.40844e-3,
Ar40bs=7.50865e-5,
bs_fil=[44],
Ar40_fil=[1, 9, 43],
Ar39_fil=[11, 16],
Ar40bl=0.0328504,
#Ar39_Ar40=0.002255
Ar39_Ar40=1 / 443.1534341,
Ar39_Ar40e=0.000023
)
expected_nonfiltered = dict(Ar40bs_c=2.20908914,
Ar39bs_c=4.96081e-3,
Ar38bs_c=0.0014706,
Ar37bs_c=0.001349,
Ar36bs_c=0.0074384,
Ar40bs=7.50865e-5,
bs_fil=[],
Ar40_fil=[])
expected_filtered = dict(
Ar40bs_c=0.159394,
Ar40bs_ce=2.67938e-4,
Ar39bs_c=1.58288e-2,
Ar39bs_ce=7.9423e-5,
Ar40bl_c=0.129651,
Ar40bl_ce=0.003811,
Ar40bl=0.031794,
Ar40ble=0.0038013,
Ar39_Ar40=0.1226,
Ar39_Ar40e=0.0037,
ar37df=3.348
)
cls.expected = expected_nonfiltered
cls.expected = expected_filtered
man = cls.isotope_man
db = man.db
with db.session_ctx():
ans, tc = db.get_sample_analyses(['AF-72', ], ['Minna Bluff'])
an = man.make_analysis(ans[4])
cls.analysis = an
def setUp(self):
self.experimentor = Experimentor(connect=False,
unique_executor_db=False)
self.experimentor.db = db = isotope_manager_factory().db
self._experiment_file = './data/experiment2.txt'
self.exp_task = ExperimentEditorTask()
self._load_queues()
def setUpClass(cls):
cls.isotope_man = isotope_manager_factory(name='pychrondata_minnabluff')
cls.isotope_man.db.connect()
expected_filtered_56954_01A = dict(Ar40bs_c=2.20831,
Ar39bs_c=4.96090e-3,
Ar38bs_c=0.0014621,
Ar37bs_c=1.34848e-3,
Ar36bs_c=7.40844e-3,
Ar40bs=7.50865e-5,
bs_fil=[44],
Ar40_fil=[1, 9, 43],
Ar39_fil=[11, 16],
Ar40bl=0.0328504,
#Ar39_Ar40=0.002255
Ar39_Ar40=1 / 443.1534341,
Ar39_Ar40e=0.000023
)
expected_nonfiltered = dict(Ar40bs_c=2.20908914,
Ar39bs_c=4.96081e-3,
Ar38bs_c=0.0014706,
Ar37bs_c=0.001349,
Ar36bs_c=0.0074384,
Ar40bs=7.50865e-5,
bs_fil=[],
Ar40_fil=[])
expected_filtered = dict(
Ar40bs_c=0.159394,
Ar40bs_ce=2.67938e-4,
Ar39bs_c=1.58288e-2,
Ar39bs_ce=7.9423e-5,
Ar40bl_c=0.129651,
Ar40bl_ce=0.003811,
Ar40bl=0.031794,
Ar40ble=0.0038013,
Ar39_Ar40=0.1226,
Ar39_Ar40e=0.0037,
ar37df=3.348
)
cls.expected = expected_nonfiltered
cls.expected = expected_filtered
man = cls.isotope_man
db = man.db
with db.session_ctx():
ans, tc = db.get_sample_analyses(['AF-72', ], ['Minna Bluff'])
an = man.make_analysis(ans[4])
cls.analysis = an
def setUp(self):
self.experimentor = Experimentor(connect=False,
unique_executor_db=False
)
self.experimentor.db = db = isotope_manager_factory().db
self._experiment_file = './data/experiment2.txt'
self.exp_task = ExperimentEditorTask()
self._load_queues()
def setUpClass(cls):
cls.isotope_man = isotope_manager_factory(name='pychrondata_dev')
cls.isotope_man.db.connect()
man = cls.isotope_man
db = man.db
with db.session_ctx():
ans, tc = db.get_sample_analyses(['MB06-674', ], ['Minna Bluff'])
an = man.make_analysis(ans[4])
cls._id=ans[4].id
cls.analysis_no_pc = an
def setUpClass(cls):
cls.isotope_man = isotope_manager_factory(name='pychrondata_minnabluff')
cls.isotope_man.db.connect()
man = cls.isotope_man
db = man.db
with db.session_ctx():
ans, tc = db.get_sample_analyses(['AF-72', ], ['Minna Bluff'])
cls.analyses=man.make_analyses(ans)
cls.analysis = ans[0]
cls.pkg=Packager()
def setUpClass(cls):
cls.isotope_man = isotope_manager_factory(name='pychrondata_dev')
cls.isotope_man.db.connect()
man = cls.isotope_man
db = man.db
with db.session_ctx():
ans, tc = db.get_sample_analyses(['MB06-674', ], ['Minna Bluff'])
an = man.make_analysis(ans[4])
cls._id=ans[4].id
cls.analysis_no_pc = an
def setUpClass(cls):
cls.isotope_man = isotope_manager_factory(name='pychrondata_minnabluff')
cls.isotope_man.db.connect()
man = cls.isotope_man
db = man.db
cls.sample_id = sid = 'AF-72'
#cls.analysis_id = aid = string.ascii_uppercase.index('A')
with db.session_ctx():
ans, tc = db.get_sample_analyses([sid, ], ['Minna Bluff'])
cls.analyses = man.make_analyses(ans)
def setUpClass(cls):
cls.isotope_man = isotope_manager_factory(
name='pychrondata_minnabluff')
cls.isotope_man.db.connect()
man = cls.isotope_man
db = man.db
with db.session_ctx():
ans, tc = db.get_sample_analyses([
'AF-72',
], ['Minna Bluff'])
cls.analyses = man.make_analyses(ans)
cls.analysis = ans[0]
cls.pkg = Packager()
def setUpClass(cls):
cls.isotope_man = isotope_manager_factory(
name='pychrondata_minnabluff')
cls.isotope_man.db.connect()
man = cls.isotope_man
db = man.db
cls.sample_id = sid = 'AF-72'
#cls.analysis_id = aid = string.ascii_uppercase.index('A')
with db.session_ctx():
ans, tc = db.get_sample_analyses([
sid,
], ['Minna Bluff'])
cls.analyses = man.make_analyses(ans)
def setUpClass(cls):
cls.isotope_man = isotope_manager_factory(name='pychrondata_minnabluff')
cls.isotope_man.db.connect()
man = cls.isotope_man
db = man.db
cls.sample_id = sid = 'AF-72'
cls.analysis_id = aid = string.ascii_uppercase.index('A')
with db.session_ctx():
ans, tc = db.get_sample_analyses([sid, ], ['Minna Bluff'])
an = man.make_analysis(ans[aid])
cls.analysis = an
p = '../data/autoupdate_AF_72_1'
cls.parser = AutoupdateParser()
cls.parser.parse(p)
def setUpClass(cls):
cls.isotope_man = isotope_manager_factory(
name='pychrondata_minnabluff')
cls.isotope_man.db.connect()
man = cls.isotope_man
db = man.db
cls.sample_id = sid = 'AF-72'
cls.analysis_id = aid = string.ascii_uppercase.index('A')
with db.session_ctx():
ans, tc = db.get_sample_analyses([
sid,
], ['Minna Bluff'])
an = man.make_analysis(ans[aid])
cls.analysis = an
p = '../data/autoupdate_AF_72_1'
cls.parser = AutoupdateParser()
cls.parser.parse(p)
def setUp(self):
db = isotope_manager_factory().db
self.le = LabnumberEntry(db=db)
from pychron.core.helpers.logger_setup import logging_setup
__author__ = 'ross'
import unittest
from pychron.core.ui import set_toolkit
set_toolkit('qt4')
from pychron.processing.autoupdate_parser import AutoupdateParser
from test.database import isotope_manager_factory
ISOTOPE_MANAGER = isotope_manager_factory(name='pychrondata_minnabluff')
ISOTOPE_MANAGER.connect()
SKIP_BLANKS = False, 'skip blanks'
SKIP_SIGNALS = False, 'skip signals'
SKIP_FITS = False, 'skip fits'
logging_setup('arar_diff')
class MassSpecPychronIsotopeTestCase(object):
def setUp(self):
pass
def get_expected_value(self, k):
p = self.parser
def run():
hp = hpy()
globalv.experiment_debug = True
# t = ExperimentEditorTask()
# p = os.path.join(paths.experiment_dir, 'demo.txt')
# t._open_experiment(p)
q = ExperimentQueue(delay_before_analyses=0,
delay_between_analyses=0)
q.automated_runs = [
AutomatedRunSpec(
labnumber='61312',
duration=2.0,
extraction_script='pause',
measurement_script='air',
mass_spectrometer='jan'
),
AutomatedRunSpec(
labnumber='61312',
duration=2.0,
extraction_script='pause',
measurement_script='air',
mass_spectrometer='jan'
),
AutomatedRunSpec(
labnumber='61312',
duration=2.0,
extraction_script='pause',
measurement_script='air',
mass_spectrometer='jan'
),
AutomatedRunSpec(
labnumber='61312',
duration=2.0,
extraction_script='pause',
measurement_script='air',
mass_spectrometer='jan'
),
AutomatedRunSpec(
labnumber='61312',
duration=2.0,
extraction_script='pause',
measurement_script='air',
mass_spectrometer='jan'
)
]
dbman = isotope_manager_factory()
specman = ArgusSpectrometerManager()
specman.load()
ex = ExperimentExecutor(db=dbman.db,
spectrometer_manager=specman,
extraction_line_manager='',
executable=True,
)
ex.monitor = None
ex.experiment_queues = [q, ]
ex.experiment_queue = q
hp.setrelheap()
t = ex.execute()
t.join()
# count_instances(group='sqlalchemy')
return hp
import math
import os
from pychron.core.ui import set_toolkit
set_toolkit('qt4')
from pychron.processing.autoupdate_parser import AutoupdateParser
from test.database import isotope_manager_factory
isotope_man=isotope_manager_factory(name='pychron_dataset')
isotope_man.db.connect(test=True)
pp = os.path.join(os.path.dirname(os.path.dirname(__file__)), 'data', 'massspec_dataset_nofilter')
# pp = '../data/massspec_dataset_nofilter'
parser = AutoupdateParser()
parser.parse(pp)
msid='Unknown'
sid='MB06-507'
pid='Minna Bluff'
class IntensityMixin(object):
@classmethod
def setUpClass(cls):
aid=cls.analysis_id
cls.sample_id = msid
cls.analysis_id = aid
db=isotope_man.db
with db.session_ctx():
ans, tc = db.get_sample_analyses([sid, ], [pid])
def setUp(self):
man = isotope_manager_factory()
self.processor = Processor(bind=False, db=man.db)
#============= standard library imports ========================
#============= local library imports ==========================
@profile
def main(db):
labn = db.get_labnumber('61311',
# options='analyses'
)
print '------------------------- got labnunmber'
an = labn.analyses[0]
print '------------------------- got analysis'
a = IsotopeRecord(_dbrecord=an)
load(a)
print '------------------------- loaded'
# @profile
def load(a):
a.load_isotopes()
print '------------------------- isotopes loaded'
a.calculate_age()
if __name__ == '__main__':
man = isotope_manager_factory()
db = man.db
db.connect()
# db.sess.bind.echo = True
main(db)
#============= EOF =============================================
def setUp(self):
man = isotope_manager_factory()
self.processor = Processor(bind=False,
db=man.db
)
@profile
def main(db):
labn = db.get_labnumber('61311',
# options='analyses'
)
print '------------------------- got labnunmber'
an = labn.analyses[0]
print '------------------------- got analysis'
a = IsotopeRecord(_dbrecord=an)
load(a)
print '------------------------- loaded'
# @profile
def load(a):
a.load_isotopes()
print '------------------------- isotopes loaded'
a.calculate_age()
if __name__ == '__main__':
man = isotope_manager_factory()
db = man.db
db.connect()
# db.sess.bind.echo = True
main(db)
#============= EOF =============================================
import math
import os
from pychron.core.ui import set_toolkit
set_toolkit('qt4')
from pychron.processing.autoupdate_parser import AutoupdateParser
from test.database import isotope_manager_factory
isotope_man = isotope_manager_factory(name='pychron_dataset')
isotope_man.db.connect(test=True)
pp = os.path.join(os.path.dirname(os.path.dirname(__file__)), 'data',
'massspec_dataset_nofilter')
# pp = '../data/massspec_dataset_nofilter'
parser = AutoupdateParser()
parser.parse(pp)
msid = 'Unknown'
sid = 'MB06-507'
pid = 'Minna Bluff'
class IntensityMixin(object):
@classmethod
def setUpClass(cls):
aid = cls.analysis_id
cls.sample_id = msid
cls.analysis_id = aid
db = isotope_man.db
def setUp(self):
self.manager = isotope_manager_factory()
self.manager.db.connect()
def setUp(self):
db = isotope_manager_factory().db
self.le = LabnumberEntry(db=db)
