def is_conflict(self, spec):
"""
return str listing the differences if databases are in conflict
"""
self._new_step = -1
self._new_aliquot = 1
self.debug('check for conflicts')
if check_massspec_database_save(spec.identifier):
self.store_connect('massspec')
# self.secondary_connect()
self.debug('connected to massspec')
self.store_connect('isotopedb')
if spec.is_step_heat():
k = 'Stepheat'
self.debug('get greatest steps')
ps, ns, vs = self._get_greatest_steps(spec.identifier,
spec.aliquot)
mv = max(vs) + 1
step = make_step(mv)
# print ps, ns, vs, spec.identifier
self._new_runid = make_aliquot_step(spec.aliquot, step)
self._new_step = mv
self._new_aliquot = spec.aliquot
else:
k = 'Fusion'
self.debug('get greatest aliquots for {}'.format(spec.identifier))
try:
ps, ns, vs = self._get_greatest_aliquots(spec.identifier)
self.debug(
'greatest aliquots. Sources: {}, Precedences: {}, Aliquots: {}'
.format(ns, ps, vs))
mv = max(vs)
self._new_runid = make_aliquot_step(mv + 1, '')
self._new_aliquot = mv + 1
except MissingAliquotPychronException:
self.warning('secondary db analyses missing aliquot_pychron')
return 'secondary db analyses missing aliquot_pychron'
self.debug(
'{} conflict args. precedence={}, names={}, values={}'.format(
k, ps, ns, vs))
if not check_list(list(vs)):
hn, hv = ns[0], vs[0]
txt = []
for ln, lv in zip(ns[1:], vs[1:]):
if lv != hv:
txt.append('{}!={} {}!={}'.format(hn, ln, hv, lv))
err = ', '.join(txt)
self.warning('Datastore conflicts. {}'.format(err))
return err
def is_conflict(self, spec):
"""
return str listing the differences if databases are in conflict
"""
self._new_step = -1
self._new_aliquot = 1
self.debug('check for conflicts')
if check_massspec_database_save(spec.identifier):
self.store_connect('massspec')
# self.secondary_connect()
self.debug('connected to massspec')
self.store_connect('isotopedb')
if spec.is_step_heat():
k = 'Stepheat'
self.debug('get greatest steps')
ps, ns, vs = self._get_greatest_steps(spec.identifier, spec.aliquot)
mv = max(vs) + 1
step = make_step(mv)
# print ps, ns, vs, spec.identifier
self._new_runid = make_aliquot_step(spec.aliquot, step)
self._new_step = mv
self._new_aliquot = spec.aliquot
else:
k = 'Fusion'
self.debug('get greatest aliquots for {}'.format(spec.identifier))
try:
ps, ns, vs = self._get_greatest_aliquots(spec.identifier)
self.debug('greatest aliquots. Sources: {}, Precedences: {}, Aliquots: {}'.format(ns, ps, vs))
mv = max(vs)
self._new_runid = make_aliquot_step(mv + 1, '')
self._new_aliquot = mv + 1
except MissingAliquotPychronException:
self.warning('secondary db analyses missing aliquot_pychron')
return 'secondary db analyses missing aliquot_pychron'
self.debug('{} conflict args. precedence={}, names={}, values={}'.format(k, ps, ns, vs))
if not check_list(list(vs)):
hn, hv = ns[0], vs[0]
txt = []
for ln, lv in zip(ns[1:], vs[1:]):
if lv != hv:
txt.append('{}!={} {}!={}'.format(hn, ln, hv, lv))
err = ', '.join(txt)
self.warning('Datastore conflicts. {}'.format(err))
return err
def _get_aliquot_text(self):
al = ''
it = self.item
if it.aliquot != 0:
al = make_aliquot_step(it.aliquot, it.step)
return al
def load_meta(self, jd):
self.measurement_script_name = jd.get('measurement', NULL_STR)
self.extraction_script_name = jd.get('extraction', NULL_STR)
src = jd.get('source')
if src:
self.filament_parameters = src
for attr in META_ATTRS:
v = jd.get(attr)
# print 'attr={},{}'.format(attr, v)
if v is not None:
setattr(self, attr, v)
if self.increment is not None:
self.step = make_step(self.increment)
ts = jd['timestamp']
for fmt in ('%Y-%m-%dT%H:%M:%S', '%Y-%m-%dT%H:%M:%S.%f', '%Y-%m-%d %H:%M:%S'):
try:
self.rundate = datetime.datetime.strptime(ts, fmt)
break
except ValueError:
continue
self.timestamp = self.timestampf = make_timef(self.rundate)
self.aliquot_step_str = make_aliquot_step(self.aliquot, self.step)
# self.collection_version = jd['collection_version']
self._set_isotopes(jd)
if self.analysis_type.lower() == 'sample':
self.analysis_type = 'unknown'
self.arar_mapping = jd.get('arar_mapping', ARAR_MAPPING)
def _get_aliquot_text(self):
al = ''
it = self.item
if it.aliquot != 0:
al = make_aliquot_step(it.aliquot, it.step)
return al
def load_meta(self, jd):
self.measurement_script_name = jd.get('measurement', NULL_STR)
self.extraction_script_name = jd.get('extraction', NULL_STR)
src = jd.get('source')
if src:
self.filament_parameters = src
for attr in META_ATTRS:
v = jd.get(attr)
# print 'attr={},{}'.format(attr, v)
if v is not None:
setattr(self, attr, v)
if self.increment is not None:
self.step = make_step(self.increment)
ts = jd['timestamp']
for fmt in ('%Y-%m-%dT%H:%M:%S', '%Y-%m-%dT%H:%M:%S.%f', '%Y-%m-%d %H:%M:%S'):
try:
self.rundate = datetime.datetime.strptime(ts, fmt)
break
except ValueError:
continue
self.timestamp = self.timestampf = make_timef(self.rundate)
self.aliquot_step_str = make_aliquot_step(self.aliquot, self.step)
# self.collection_version = jd['collection_version']
self._set_isotopes(jd)
if self.analysis_type.lower() == 'sample' or not self.analysis_type:
self.analysis_type = 'unknown'
self.arar_mapping = jd.get('arar_mapping', ARAR_MAPPING)
def __init__(self, record_id, repository_identifier, *args, **kw):
super(DVCAnalysis, self).__init__(*args, **kw)
self.record_id = record_id
path = analysis_path(record_id, repository_identifier)
self.repository_identifier = repository_identifier
self.rundate = datetime.datetime.now()
root = os.path.dirname(path)
bname = os.path.basename(path)
head, ext = os.path.splitext(bname)
jd = dvc_load(os.path.join(root, 'extraction', '{}.extr{}'.format(head, ext)))
for attr in EXTRACTION_ATTRS:
tag = attr
if attr == 'cleanup_duration':
if attr not in jd:
tag = 'cleanup'
elif attr == 'extract_duration':
if attr not in jd:
tag = 'duration'
v = jd.get(tag)
if v is not None:
setattr(self, attr, v)
pd = jd.get('positions')
if pd:
ps = sorted(pd, key=lambda x: x['position'])
self.position = ','.join([str(pp['position']) for pp in ps])
self.xyz_position = ';'.join([','.join(map(str, (pp['x'], pp['y'], pp['z']))) for pp in ps if pp['x'] is
not None])
if not self.extract_units:
self.extract_units = 'W'
jd = dvc_load(path)
for attr in META_ATTRS:
v = jd.get(attr)
self.debug('{}={}'.format(attr, v))
if v is not None:
setattr(self, attr, v)
if self.increment is not None:
self.step = make_step(self.increment)
ts = jd['timestamp']
try:
self.rundate = datetime.datetime.strptime(ts, '%Y-%m-%dT%H:%M:%S')
except ValueError:
self.rundate = datetime.datetime.strptime(ts, '%Y-%m-%dT%H:%M:%S.%f')
self.collection_version = jd['collection_version']
self._set_isotopes(jd)
self.timestamp = make_timef(self.rundate)
self.aliquot_step_str = make_aliquot_step(self.aliquot, self.step)
self.load_paths()
self.load_spectrometer_parameters(jd['spec_sha'])
def __init__(self, record_id, experiment_id, *args, **kw):
super(DVCAnalysis, self).__init__(*args, **kw)
self.record_id = record_id
path = analysis_path(record_id, experiment_id)
self.experiment_identifier = experiment_id
self.rundate = datetime.datetime.now()
root = os.path.dirname(path)
bname = os.path.basename(path)
head, ext = os.path.splitext(bname)
with open(os.path.join(root, 'extraction', '{}.extr{}'.format(head, ext))) as rfile:
jd = json.load(rfile)
for attr in EXTRACTION_ATTRS:
tag = attr
if attr == 'cleanup_duration':
if attr not in jd:
tag = 'cleanup'
elif attr == 'extract_duration':
if attr not in jd:
tag = 'duration'
v = jd.get(tag)
if v is not None:
setattr(self, attr, v)
with open(path, 'r') as rfile:
jd = json.load(rfile)
for attr in META_ATTRS:
v = jd.get(attr)
if v is not None:
setattr(self, attr, v)
try:
self.rundate = datetime.datetime.strptime(jd['timestamp'], '%Y-%m-%dT%H:%M:%S')
except ValueError:
self.rundate = datetime.datetime.strptime(jd['timestamp'], '%Y-%m-%dT%H:%M:%S.%f')
self.collection_version = jd['collection_version']
self._set_isotopes(jd)
self.timestamp = make_timef(self.rundate)
for tag in ('intercepts', 'baselines', 'blanks', 'icfactors'):
# print tag
with open(self._analysis_path(modifier=tag), 'r') as rfile:
jd = json.load(rfile)
func = getattr(self, '_load_{}'.format(tag))
func(jd)
self.aliquot_step_str = make_aliquot_step(self.aliquot, self.step)
def _get_aliquot_text(self):
return make_aliquot_step(self.item.aliquot, self.item.step)
def sync(self, obj, **kw):
self._sync(obj, **kw)
self.aliquot_step_str = make_aliquot_step(self.aliquot, self.step)
def _get_aliquot_text(self):
return make_aliquot_step(self.item.aliquot, self.item.step)
def sync(self, obj, **kw):
self._sync(obj, **kw)
self.aliquot_step_str = make_aliquot_step(self.aliquot, self.step)
