def _record_view_factory(self, ai, progress=None, **kw):
iso = IsotopeRecordView(**kw)
iso.create(ai)
if progress:
progress.change_message('Loading {}'.format(iso.record_id))
return iso
def _get_find_parameters(self):
f = FindAssociatedParametersDialog()
ais = self.active_editor.analyses
if ais:
unks = ais
elif self.analysis_table.selected:
ans = self.analysis_table.selected
unks = ans[:]
elif self.selected_samples:
ans = self.analysis_table.analyses
unks = ans[:]
elif self.selected_projects:
with self.manager.db.session_ctx():
ans = self._get_projects_analyzed_analyses(
self.selected_projects)
unks = [IsotopeRecordView(ai) for ai in ans]
else:
self.information_dialog(
'Select a list of projects, samples or analyses')
return
ts = [get_datetime(ai.timestamp) for ai in unks]
lpost, hpost = min(ts), max(ts)
f.model.nominal_lpost_date = lpost.date()
f.model.nominal_hpost_date = hpost.date()
f.model.nominal_lpost_time = lpost.time()
f.model.nominal_hpost_time = hpost.time()
ms = list(set([ai.mass_spectrometer for ai in unks]))
f.model.available_mass_spectrometers = ms
f.model.mass_spectrometers = ms
info = f.edit_traits(kind='livemodal')
if info.result:
return f.model
def func(xi, prog, i, n):
if prog:
prog.change_message('Loading {}'.format(xi.record_id))
return IsotopeRecordView(xi)
def func(a):
# print a, a.plateau_step
ir = IsotopeRecordView(is_plateau_step=a.plateau_step)
ir.create(a.analysis)
return ir
def record_view(self):
iv = self._record_view
if not iv:
iv = IsotopeRecordView()
iv.extract_script_name = self.extractionName
iv.meas_script_name = self.measurementName
irradpos = self.irradiation_position
iv.identifier = irradpos.identifier
iv.irradiation = irradpos.level.irradiation.name
iv.irradiation_level = irradpos.level.name
iv.irradiation_position_position = irradpos.position
iv.labnumber = iv.identifier
iv.experiment_ids = es = [e.experimentName for e in self.experiment_associations]
if len(es) == 1:
iv.experiment_identifier = es[0]
for tag in ('aliquot', 'increment', 'uuid',
'extract_value', 'cleanup', 'duration',
'mass_spectrometer',
'extract_device',
'rundate',
'analysis_type'):
setattr(iv, tag, getattr(self, tag))
if irradpos.sample:
iv.sample = irradpos.sample.name
if irradpos.sample.project:
iv.project = irradpos.sample.project.name
iv.timestampf = make_timef(self.timestamp)
tag = self.change.tag_item
iv.tag = tag.name
iv.tag_dict = {k: getattr(tag, k) for k in ('name',) + OMIT_KEYS}
self._record_view = iv
return iv
def _transfer_analysis(self,
rec,
exp,
overwrite=True,
monitor_mapping=None):
dest = self.dvc.db
proc = self.processor
src = proc.db
# args = rec.split('-')
# idn = '-'.join(args[:-1])
# t = args[-1]
# try:
# aliquot = int(t)
# step = None
# except ValueError:
# aliquot = int(t[:-1])
# step = t[-1]
m = IDENTIFIER_REGEX.match(rec)
if not m:
m = SPECIAL_IDENTIFIER_REGEX.match(rec)
if not m:
self.warning('invalid runid {}'.format(rec))
return
else:
idn = m.group('identifier')
aliquot = m.group('aliquot')
try:
step = m.group('step') or None
except IndexError:
step = None
if idn == '4359':
idn = 'c-01-j'
elif idn == '4358':
idn = 'c-01-o'
# check if analysis already exists. skip if it does
if dest.get_analysis_runid(idn, aliquot, step):
self.warning('{} already exists'.format(
make_runid(idn, aliquot, step)))
return
dban = src.get_analysis_runid(idn, aliquot, step)
iv = IsotopeRecordView()
iv.uuid = dban.uuid
self.debug('make analysis idn:{}, aliquot:{} step:{}'.format(
idn, aliquot, step))
# try:
an = proc.make_analysis(iv,
unpack=True,
use_cache=False,
use_progress=False)
# except BaseException as e:
# self.warning('Failed to make {}'.format(make_runid(idn, aliquot, step)))
# self.warning('exception: {}'.format(e))
# return
self._transfer_meta(dest, dban, monitor_mapping)
# return
dblab = dban.labnumber
if dblab.irradiation_position:
irrad = dblab.irradiation_position.level.irradiation.name
level = dblab.irradiation_position.level.name
irradpos = dblab.irradiation_position.position
else:
irrad = 'NoIrradiation'
level = 'A'
irradpos = self._get_irradpos(dest, irrad, level, dblab.identifier)
# irrad, level, irradpos = '', '', 0
extraction = dban.extraction
ms = dban.measurement.mass_spectrometer.name
if not dest.get_mass_spectrometer(ms):
self.debug('adding mass spectrometer {}'.format(ms))
dest.add_mass_spectrometer(ms)
dest.commit()
ed = extraction.extraction_device.name if extraction.extraction_device else None
if not ed:
ed = 'No Extract Device'
if not dest.get_extraction_device(ed):
self.debug('adding extract device {}'.format(ed))
dest.add_extraction_device(ed)
dest.commit()
if step is None:
inc = -1
else:
inc = alpha_to_int(step)
username = ''
if dban.user:
username = dban.user.name
if not dest.get_user(username):
self.debug('adding user. username:{}'.format(username))
dest.add_user(username)
dest.commit()
if monitor_mapping:
sample_name, material_name, project_name = monitor_mapping
else:
dbsam = dblab.sample
sample_name = dbsam.name
material_name = dbsam.material.name
project_name = format_repository_identifier(dbsam.project.name)
rs = AutomatedRunSpec(labnumber=idn,
username=username,
material=material_name,
project=project_name,
sample=sample_name,
irradiation=irrad,
irradiation_level=level,
irradiation_position=irradpos,
repository_identifier=exp,
mass_spectrometer=ms,
uuid=dban.uuid,
_step=inc,
comment=dban.comment.decode('utf-8') or '',
aliquot=int(aliquot),
extract_device=ed,
duration=extraction.extract_duration,
cleanup=extraction.cleanup_duration,
beam_diameter=extraction.beam_diameter,
extract_units=extraction.extract_units or '',
extract_value=extraction.extract_value,
pattern=extraction.pattern or '',
weight=extraction.weight,
ramp_duration=extraction.ramp_duration or 0,
ramp_rate=extraction.ramp_rate or 0,
collection_version='0.1:0.1',
queue_conditionals_name='',
tray='')
meas = dban.measurement
# get spectrometer parameters
# gains
gains = {}
gain_history = dban.gain_history
if gain_history:
gains = {d.detector.name: d.value for d in gain_history.gains}
# deflections
deflections = {d.detector.name: d.deflection for d in meas.deflections}
# source
src = {
k: getattr(meas.spectrometer_parameters, k)
for k in QTEGRA_SOURCE_KEYS
}
ps = PersistenceSpec(
run_spec=rs,
tag=an.tag.name,
isotope_group=an,
timestamp=dban.analysis_timestamp,
defl_dict=deflections,
gains=gains,
spec_dict=src,
use_repository_association=True,
positions=[p.position for p in extraction.positions])
self.debug('transfer analysis with persister')
self.persister.per_spec_save(ps,
commit=False,
commit_tag='Database Transfer')
return True
db = man.db
db.trait_set(name='pychrondata',
kind='mysql',
host='129.138.12.160',
username='******',
password='******',
echo=False)
db.connect()
with db.session_ctx():
# for si in sams:
_ans, n = db.get_labnumber_analyses([
# '57493',
'62118'
])
ts = [xi.analysis_timestamp for xi in _ans]
lpost, hpost = min(ts), max(ts)
_ans = db.get_analyses_date_range(lpost, hpost, order='asc')
# _ans = db.get_date_range_analyses(lpost, hpost, ordering='asc')
_ans = [IsotopeRecordView(xi) for xi in _ans]
# _ans = sorted(_ans, key=lambda x: x.timestamp)
d = Demo(analyses=_ans)
d.configure_traits()
# print info.result
# if info.result:
# s = g.get_selection()
# for si in s:
# print si, si.analysis_type
# ============= EOF =============================================
def _transfer_analysis(self, rec, exp, overwrite=True, monitor_mapping=None):
dest = self.dvc.db
proc = self.processor
src = proc.db
# args = rec.split('-')
# idn = '-'.join(args[:-1])
# t = args[-1]
# try:
# aliquot = int(t)
# step = None
# except ValueError:
# aliquot = int(t[:-1])
# step = t[-1]
m = IDENTIFIER_REGEX.match(rec)
if not m:
m = SPECIAL_IDENTIFIER_REGEX.match(rec)
if not m:
self.warning('invalid runid {}'.format(rec))
return
else:
idn = m.group('identifier')
aliquot = m.group('aliquot')
try:
step = m.group('step') or None
except IndexError:
step = None
if idn == '4359':
idn = 'c-01-j'
elif idn == '4358':
idn = 'c-01-o'
# check if analysis already exists. skip if it does
if dest.get_analysis_runid(idn, aliquot, step):
self.warning('{} already exists'.format(make_runid(idn, aliquot, step)))
return
dban = src.get_analysis_runid(idn, aliquot, step)
iv = IsotopeRecordView()
iv.uuid = dban.uuid
self.debug('make analysis idn:{}, aliquot:{} step:{}'.format(idn, aliquot, step))
try:
an = proc.make_analysis(iv, unpack=True, use_cache=False, use_progress=False)
except:
self.warning('Failed to make {}'.format(make_runid(idn, aliquot, step)))
return
self._transfer_meta(dest, dban, monitor_mapping)
# return
dblab = dban.labnumber
if dblab.irradiation_position:
irrad = dblab.irradiation_position.level.irradiation.name
level = dblab.irradiation_position.level.name
irradpos = dblab.irradiation_position.position
else:
irrad = 'NoIrradiation'
level = 'A'
irradpos = self._get_irradpos(dest, irrad, level, dblab.identifier)
# irrad, level, irradpos = '', '', 0
extraction = dban.extraction
ms = dban.measurement.mass_spectrometer.name
if not dest.get_mass_spectrometer(ms):
self.debug('adding mass spectrometer {}'.format(ms))
dest.add_mass_spectrometer(ms)
dest.commit()
ed = extraction.extraction_device.name if extraction.extraction_device else None
if not ed:
ed = 'No Extract Device'
if not dest.get_extraction_device(ed):
self.debug('adding extract device {}'.format(ed))
dest.add_extraction_device(ed)
dest.commit()
if step is None:
inc = -1
else:
inc = ALPHAS.index(step)
username = ''
if dban.user:
username = dban.user.name
if not dest.get_user(username):
self.debug('adding user. username:{}'.format(username))
dest.add_user(username)
dest.commit()
if monitor_mapping:
sample_name, material_name, project_name = monitor_mapping
else:
dbsam = dblab.sample
sample_name = dbsam.name
material_name = dbsam.material.name
project_name = format_repository_identifier(dbsam.project.name)
rs = AutomatedRunSpec(labnumber=idn,
username=username,
material=material_name,
project=project_name,
sample=sample_name,
irradiation=irrad,
irradiation_level=level,
irradiation_position=irradpos,
repository_identifier=exp,
mass_spectrometer=ms,
uuid=dban.uuid,
_step=inc,
comment=dban.comment or '',
aliquot=int(aliquot),
extract_device=ed,
duration=extraction.extract_duration,
cleanup=extraction.cleanup_duration,
beam_diameter=extraction.beam_diameter,
extract_units=extraction.extract_units or '',
extract_value=extraction.extract_value,
pattern=extraction.pattern or '',
weight=extraction.weight,
ramp_duration=extraction.ramp_duration or 0,
ramp_rate=extraction.ramp_rate or 0,
collection_version='0.1:0.1',
queue_conditionals_name='',
tray='')
meas = dban.measurement
# get spectrometer parameters
# gains
gains = {}
gain_history = dban.gain_history
if gain_history:
gains = {d.detector.name: d.value for d in gain_history.gains}
# deflections
deflections = {d.detector.name: d.deflection for d in meas.deflections}
# source
src = {k: getattr(meas.spectrometer_parameters, k) for k in QTEGRA_SOURCE_KEYS}
ps = PersistenceSpec(run_spec=rs,
tag=an.tag.name,
arar_age=an,
timestamp=dban.analysis_timestamp,
defl_dict=deflections,
gains=gains,
spec_dict=src,
use_repository_association=True,
positions=[p.position for p in extraction.positions])
self.debug('transfer analysis with persister')
self.persister.per_spec_save(ps, commit=False, msg_prefix='Database Transfer')
return True