def get_timestamps(src, sql, tol_hrs):
with src.session_ctx() as sess:
result = sess.execute(sql)
ts = array([make_timef(ri[0]) for ri in result.fetchall()])
idxs = bin_timestamps(ts, tol_hrs=tol_hrs)
return ts, idxs
def get_timestamps(src, sql, tol_hrs):
with src.session_ctx() as sess:
result = sess.execute(sql)
ts = array([make_timef(ri[0]) for ri in result.fetchall()])
idxs = bin_timestamps(ts, tol_hrs=tol_hrs)
return ts, idxs
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 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 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 timestampf(self):
return make_timef(self.timestamp)
def timestampf(self):
return make_timef(self.timestamp)
