def test_save_persister():
paths.build('_dev')
dvc = DVC(bind=False)
dvc.db.connect()
per = DVCPersister(dvc=dvc)
run_spec = AutomatedRunSpec()
run_spec.labnumber = '10001'
run_spec.project = 'Test'
arar = ArArAge()
arar.isotopes['Ar40'] = Isotope(xs=[1, 2, 3], ys=[1, 2, 3],
name='Ar40', detector='H1')
sd = {}
dd = {'H1': 100}
gd = {'H1': 1.021}
per_spec = PersistenceSpec(run_spec=run_spec,
arar_age=arar,
spec_dict=sd,
defl_dict=dd,
gains=gd,
positions=[1, ],
experiment_queue_name='testexp.txt',
measurement_name='jan_unknown.py',
extraction_name='foo.py')
per.per_spec_save(per_spec)
def setUpClass(cls):
aspec = AutomatedRunSpec()
aspec.mass_spectrometer = 'jan'
aspec.labnumber = '17005'
aspec.aliquot = 95
a = AutomatedRun()
a.script_info.measurement_script_name = 'unknown_peak_hop'
s = ArgusSpectrometerManager()
ion = IonOpticsManager(spectrometer=s.spectrometer)
s.load(db_mol_weights=False)
a.spectrometer_manager = s
a.ion_optics_manager = ion
a.isotope_group = ArArAge()
a.isotope_group.j = ufloat(0.001, 1e-6)
a._alive = True
a.uuid = '12345-ABCDE'
a.spec = aspec
a._measured = True
a._save_enabled = True
cls.arun = a
def setUpClass(cls):
aspec = AutomatedRunSpec()
aspec.mass_spectrometer = 'jan'
aspec.labnumber = '17005'
aspec.aliquot = 82
aspec.syn_extraction='test'
a = AutomatedRun()
a.script_info.measurement_script_name = 'unknown'
a.script_info.extraction_script_name = 'pause'
s = ArgusSpectrometerManager()
ion = IonOpticsManager(spectrometer=s.spectrometer)
s.load()
a.spectrometer_manager = s
a.ion_optics_manager = ion
a.isotope_group = ArArAge()
a._alive = True
a.uuid = '12345-ABCDE'
a.spec = aspec
a._measured = True
a.persister.save_enabled = True
a.persister.datahub=dh=Datahub(bind_mainstore=False)
dh.mainstore.db.kind='mysql'
dh.mainstore.db.username='******'
dh.mainstore.db.name='pychrondata_dev'
dh.mainstore.db.password='******'
dh.mainstore.db.connect()
cls.arun = a
def get_ic_factor(self, det):
if det in self.ic_factors:
r = self.ic_factors[det]
else:
#get the ic_factor from preferences if available otherwise 1.0
# storing ic_factor in preferences causing issues
# ic_factor stored in detectors.cfg
r = ArArAge.get_ic_factor(self, det)
return r
def get_ic_factor(self, det):
if det in self.ic_factors:
r = self.ic_factors[det]
else:
#get the ic_factor from preferences if available otherwise 1.0
# storing ic_factor in preferences causing issues
# ic_factor stored in detectors.cfg
r = ArArAge.get_ic_factor(self, det)
return r
def setUpClass(cls):
aspec = AutomatedRunSpec()
aspec.mass_spectrometer = 'jan'
aspec.labnumber = '17005'
aspec.aliquot = 82
a = AutomatedRun()
a.script_info.measurement_script_name = 'unknown'
s = SpectrometerManager()
ion = IonOpticsManager(spectrometer=s.spectrometer)
s.load(db_mol_weights=False)
a.spectrometer_manager = s
a.ion_optics_manager = ion
a.arar_age = ArArAge()
a._alive = True
a.uuid = '12345-ABCDE'
a.spec = aspec
a._measured = True
a._save_enabled = True
cls.arun = a
def _make_per_spec(self, lt):
run_spec = AutomatedRunSpec()
per_spec = PersistenceSpec()
arar_age = ArArAge()
# populate per_spec
per_spec.run_spec = run_spec
per_spec.arar_age = arar_age
# popluate run_spec
run_spec.identifier = lt.labnumber
run_spec.aliquot = lt.aliquot
run_spec.step = lt.step
run_spec.username = '******'
run_spec.uuid = lt.uuid
cp = lt.collection_path
man = H5DataManager()
man.open_file(cp)
# add signal/isotopes
group = man.get_group('signal')
for grp in man.get_groups(group):
isok = grp._v_name
iso = Isotope(name=isok,
fit='linear')
# only handle one detector per isotope
tbl = man.get_tables(grp)[0]
iso.detector = tbl._v_name
xs = array([x['time'] for x in tbl.iterrows()])
ys = array([x['value'] for x in tbl.iterrows()])
iso.xs = xs
iso.ys = ys
arar_age.isotopes[isok] = iso
# add sniffs
group = man.get_group('sniff')
for k, iso in arar_age.isotopes.iteritems():
grp = man.get_group(k, group)
tbl = man.get_tables(grp)[0]
iso.sniff.detector = tbl._v_name
xs = array([x['time'] for x in tbl.iterrows()])
ys = array([x['value'] for x in tbl.iterrows()])
iso.sniff.xs = xs
iso.sniff.ys = ys
# add baselines
group = man.get_group('baseline')
for dettbl in man.get_tables(group):
detname = dettbl._v_name
xs = array([x['time'] for x in dettbl.iterrows()])
ys = array([x['value'] for x in dettbl.iterrows()])
for iso in arar_age.isotopes.itervalues():
if iso.detector == detname:
iso.baseline.xs = xs
iso.baseline.ys = ys
iso.baseline.fit = 'average'
return per_spec
def __init__(self):
self.isotope_group = ArArAge()
self.spec = MSpec()
def _make_per_spec(self, lt):
run_spec = AutomatedRunSpec()
per_spec = PersistenceSpec()
arar_age = ArArAge()
# populate per_spec
per_spec.run_spec = run_spec
per_spec.arar_age = arar_age
# popluate run_spec
run_spec.identifier = lt.labnumber
run_spec.aliquot = lt.aliquot
run_spec.step = lt.step
run_spec.username = '******'
run_spec.uuid = lt.uuid
cp = lt.collection_path
man = H5DataManager()
man.open_file(cp)
# add signal/isotopes
group = man.get_group('signal')
for grp in man.get_groups(group):
isok = grp._v_name
iso = Isotope(name=isok, fit='linear')
# only handle one detector per isotope
tbl = man.get_tables(grp)[0]
iso.detector = tbl._v_name
xs = array([x['time'] for x in tbl.iterrows()])
ys = array([x['value'] for x in tbl.iterrows()])
iso.xs = xs
iso.ys = ys
arar_age.isotopes[isok] = iso
# add sniffs
group = man.get_group('sniff')
for k, iso in arar_age.isotopes.iteritems():
grp = man.get_group(k, group)
tbl = man.get_tables(grp)[0]
iso.sniff.detector = tbl._v_name
xs = array([x['time'] for x in tbl.iterrows()])
ys = array([x['value'] for x in tbl.iterrows()])
iso.sniff.xs = xs
iso.sniff.ys = ys
# add baselines
group = man.get_group('baseline')
for dettbl in man.get_tables(group):
detname = dettbl._v_name
xs = array([x['time'] for x in dettbl.iterrows()])
ys = array([x['value'] for x in dettbl.iterrows()])
for iso in arar_age.isotopes.itervalues():
if iso.detector == detname:
iso.baseline.xs = xs
iso.baseline.ys = ys
iso.baseline.fit = 'average'
return per_spec
