class proc_FitTable(Base, BaseMixin):
history_id = foreignkey('proc_FitHistoryTable')
isotope_id = foreignkey('meas_IsotopeTable')
fit = stringcolumn()
error_type = stringcolumn(default='SD')
filter_outliers = Column(Boolean)
filter_outlier_iterations = Column(Integer, default=1)
filter_outlier_std_devs = Column(Integer, default=1)
include_baseline_error = Column(Boolean)
time_zero_offset = Column(Float)
use_standard_deviation_filtering = False
truncate = False
@property
def isotope_label(self):
name = self.isotope.molecular_weight.name
if self.isotope.kind == 'baseline':
name = '{}bs'.format(name)
return name
def make_summary(self):
f = self.fit[:1].upper()
name = self.isotope_label
s = '{}{}'.format(name, f)
return s
class meas_ExtractionTable(Base, BaseMixin):
# position = Column(Integer)
extract_value = Column(Float)
extract_duration = Column(Float)
cleanup_duration = Column(Float)
extract_units = stringcolumn(5)
# experiment_blob = Column(BLOB)
weight = Column(Float)
sensitivity_multiplier = Column(Float)
is_degas = Column(Boolean)
beam_diameter = Column(Float)
pattern = stringcolumn(100)
ramp_rate = Column(Float)
ramp_duration = Column(Float)
mask_position = Column(Float)
mask_name = stringcolumn(100)
attenuator = Column(Float)
reprate = Column(Float)
sensitivity_id = foreignkey('gen_SensitivityTable')
extract_device_id = foreignkey('gen_ExtractionDeviceTable')
script_id = foreignkey('meas_ScriptTable')
experiment_blob_id = foreignkey('meas_ScriptTable')
image_id = foreignkey('med_ImageTable')
analyses = relationship('meas_AnalysisTable', backref='extraction')
positions = relationship('meas_PositionTable', backref='extraction')
snapshots = relationship('med_SnapshotTable', backref='extraction')
class proc_DetectorIntercalibrationTable(Base, BaseMixin):
history_id = foreignkey('proc_DetectorIntercalibrationHistoryTable')
detector_id = foreignkey('gen_DetectorTable')
user_value = Column(Float)
user_error = Column(Float)
fit = stringcolumn()
error_type = stringcolumn(default='SD')
set_id = Column(Integer)
class proc_BackgroundsTable(Base, BaseMixin):
history_id = foreignkey('proc_BackgroundsHistoryTable')
user_value = Column(Float)
user_error = Column(Float)
use_set = Column(Boolean)
isotope = stringcolumn()
fit = stringcolumn()
error_type = stringcolumn(default='SD')
set_id = Column(Integer)
class meas_MonitorTable(Base, NameMixin):
data = Column(BLOB)
parameter = stringcolumn()
criterion = stringcolumn()
comparator = stringcolumn()
action = stringcolumn()
tripped = Column(Boolean)
analysis_id = foreignkey('meas_AnalysisTable')
class proc_InterpretedAgeHistoryTable(Base, BaseMixin):
create_date = Column(DateTime, default=func.now())
user = stringcolumn()
interpreted_age = relationship('proc_InterpretedAgeTable', backref='history', uselist=False)
identifier = stringcolumn(80)
selected = relationship('gen_LabTable',
backref='selected_interpreted_age',
uselist=False)
group_sets = relationship('proc_InterpretedAgeGroupSetTable', backref='history')
class meas_AnalysisTable(Base, BaseMixin):
lab_id = foreignkey('gen_LabTable')
extraction_id = foreignkey('meas_ExtractionTable')
measurement_id = foreignkey('meas_MeasurementTable')
experiment_id = foreignkey('meas_ExperimentTable')
import_id = foreignkey('gen_ImportTable')
user_id = foreignkey('gen_UserTable')
uuid = stringcolumn(40, default=lambda: str(uuid.uuid4()))
analysis_timestamp = Column(DateTime, default=func.now())
endtime = Column(Time)
status = Column(Integer, default=0)
aliquot = Column(Integer)
step = stringcolumn(10)
comment = Column(BLOB)
tag = Column(String(40), ForeignKey('proc_TagTable.name'), default='ok')
# meas relationships
isotopes = relationship('meas_IsotopeTable', backref='analysis')
peak_center = relationship('meas_PeakCenterTable',
backref='analysis',
uselist=False)
# proc relationships
blanks_histories = relationship('proc_BlanksHistoryTable',
backref='analysis')
blanks_sets = relationship('proc_BlanksSetTable', backref='analysis')
interpreted_age_sets = relationship('proc_InterpretedAgeSetTable',
backref='analysis')
backgrounds_histories = relationship('proc_BackgroundsHistoryTable',
backref='analysis')
backgrounds_sets = relationship('proc_BackgroundsSetTable',
backref='analysis')
detector_intercalibration_histories = relationship(
'proc_DetectorIntercalibrationHistoryTable', backref='analysis')
detector_intercalibration_sets = relationship(
'proc_DetectorIntercalibrationSetTable', backref='analysis')
detector_param_histories = relationship('proc_DetectorParamHistoryTable',
backref='analysis')
fit_histories = relationship('proc_FitHistoryTable', backref='analysis')
selected_histories = relationship('proc_SelectedHistoriesTable',
backref='analysis',
uselist=False)
arar_histories = relationship('proc_ArArHistoryTable', backref='analysis')
# figure_analyses = relationship('proc_FigureAnalysisTable', backref='analysis')
notes = relationship('proc_NotesTable', backref='analysis')
monitors = relationship('meas_MonitorTable', backref='analysis')
class gen_LabTable(Base, BaseMixin):
identifier = stringcolumn()
# aliquot = Column(Integer)
sample_id = foreignkey('gen_SampleTable')
irradiation_id = foreignkey('irrad_PositionTable')
selected_flux_id = foreignkey('flux_HistoryTable')
selected_interpreted_age_id = foreignkey('proc_InterpretedAgeHistoryTable')
note = stringcolumn(140)
analyses = relationship('meas_AnalysisTable', backref='labnumber')
figures = relationship('proc_FigureLabTable', backref='labnumber')
class gen_UserTable(Base, NameMixin):
analyses = relationship('meas_AnalysisTable', backref='user')
# project_id = foreignkey('gen_ProjectTable')
projects = relationship('gen_ProjectTable', secondary=association_table)
password = stringcolumn(80)
salt = stringcolumn(80)
#===========================================================================
# permissions
#===========================================================================
max_allowable_runs = Column(Integer, default=25)
can_edit_scripts = Column(Boolean, default=False)
class proc_BackgroundsTable(Base, BaseMixin):
history_id = foreignkey('proc_BackgroundsHistoryTable')
user_value = Column(Float)
user_error = Column(Float)
use_set = Column(Boolean)
isotope = stringcolumn()
fit = stringcolumn()
error_type = stringcolumn(default='SD')
set_id = Column(String(40), ForeignKey('proc_BackgroundsSetTable.set_id'))
# set_id = Column(Integer)
analysis_set = relationship('proc_BackgroundsSetTable',
primaryjoin='proc_BackgroundsTable.set_id==proc_BackgroundsSetTable.set_id',
uselist=True)
class proc_FitTable(Base, BaseMixin):
history_id = foreignkey('proc_FitHistoryTable')
isotope_id = foreignkey('meas_IsotopeTable')
fit = stringcolumn()
error_type=stringcolumn(default='SD')
filter_outliers = Column(Boolean)
filter_outlier_iterations = Column(Integer, default=1)
filter_outlier_std_devs = Column(Integer, default=1)
def make_summary(self):
f = self.fit[:1].upper()
s = '{}{}'.format(self.isotope.molecular_weight.name, f)
return s
class gen_SampleTable(Base, NameMixin):
material_id = foreignkey('gen_MaterialTable')
project_id = foreignkey('gen_ProjectTable')
labnumbers = relationship('gen_LabTable', backref='sample')
monitors = relationship('flux_MonitorTable', backref='sample')
igsn = Column(CHAR(9))
location = stringcolumn(80)
lat = Column(Float)
long = Column(Float)
elevation = Column(Float)
note = Column(BLOB)
alt_name = stringcolumn(80)
lithology = stringcolumn(80)
class proc_ActionTable(Base, BaseMixin):
create_date = Column(DateTime, default=func.now())
session = stringcolumn()
user_id = foreignkey('gen_UserTable')
action = Column(BLOB)
blank_histories = relationship('proc_BlanksHistoryTable', backref='action')
fit_histories = relationship('proc_FitHistoryTable', backref='action')
class proc_InterpretedAgeGroupHistoryTable(Base, BaseMixin):
project_id = foreignkey('gen_ProjectTable')
name = stringcolumn(80)
create_date = Column(DateTime, default=func.now())
interpreted_ages = relationship('proc_InterpretedAgeGroupSetTable',
backref='group')
class gen_DetectorTable(Base, NameMixin):
kind = stringcolumn()
isotopes = relationship('meas_IsotopeTable', backref='detector')
deflections = relationship('meas_SpectrometerDeflectionsTable', backref='detector')
intercalibrations = relationship('proc_DetectorIntercalibrationTable', backref='detector')
detector_parameters = relationship('proc_DetectorParamTable', backref='detector')
gains = relationship('meas_GainTable', backref='detector')
class meas_GainHistoryTable(Base, UserMixin):
create_date = Column(DateTime, default=func.now())
applied_date = Column(DateTime, default=func.now())
hash = stringcolumn(32)
gains = relationship('meas_GainTable')
analyses = relationship('meas_AnalysisTable', backref='gain_history')
save_type = Column(String(20), default=1)
class History(object):
@declared_attr
def analysis_id(self):
return foreignkey('meas_AnalysisTable')
create_date = Column(DateTime, default=func.now())
user = stringcolumn()
class gen_SensitivityTable(Base, BaseMixin):
mass_spectrometer_id = foreignkey('gen_MassSpectrometerTable')
sensitivity = Column(Float(32))
create_date = Column(DateTime, default=func.now())
user = stringcolumn()
note = Column(BLOB)
extractions = relationship('meas_ExtractionTable', backref='sensitivity')
class proc_DataReductionTagTable(Base, BaseMixin):
name = stringcolumn(140)
create_date = Column(TIMESTAMP, default=func.now())
comment = Column(BLOB)
user_id = foreignkey('gen_UserTable')
analyses = relationship('proc_DataReductionTagSetTable', backref='tag')
analysis = relationship('meas_AnalysisTable', backref='data_reduction_tag')
class proc_InterpretedAgeTable(Base, BaseMixin):
history_id = foreignkey('proc_InterpretedAgeHistoryTable')
age_kind = stringcolumn(32)
age = Column(Float)
age_err = Column(Float)
wtd_kca = Column(Float)
wtd_kca_err = Column(Float)
mswd = Column(Float)
sets = relationship('proc_InterpretedAgeSetTable', backref='analyses')
class flux_HistoryTable(Base, BaseMixin):
irradiation_position_id = foreignkey('irrad_PositionTable')
note = Column(BLOB)
create_date = Column(DateTime, default=func.now())
source = stringcolumn(140)
selected = relationship('gen_LabTable',
backref='selected_flux_history',
uselist=False)
flux = relationship('flux_FluxTable', backref='history', uselist=False)
class gen_UserTable(Base, NameMixin):
analyses = relationship('meas_AnalysisTable', backref='user')
dr_tags = relationship('proc_DataReductionTagTable', backref='user')
gain_histories = relationship('meas_GainHistoryTable', backref='user')
# project_id = foreignkey('gen_ProjectTable')
password = stringcolumn(80)
salt = stringcolumn(80)
email = stringcolumn(140)
affiliation = stringcolumn(140)
category = Column(Integer, default=0)
# ===========================================================================
# permissions
# ===========================================================================
max_allowable_runs = Column(Integer, default=25)
can_edit_scripts = Column(Boolean, default=False)
class proc_FigureTable(Base, NameMixin):
create_date = Column(DateTime, default=func.now())
user = stringcolumn()
project_id = foreignkey('gen_ProjectTable')
labnumbers = relationship('proc_FigureLabTable', backref='figure')
analyses = relationship('proc_FigureAnalysisTable', backref='figure')
preference = relationship('proc_FigurePrefTable', backref='figure',
uselist=False)
class meas_IsotopeTable(Base, BaseMixin):
molecular_weight_id = foreignkey('gen_MolecularWeightTable')
analysis_id = foreignkey('meas_AnalysisTable')
detector_id = foreignkey('gen_DetectorTable')
kind = stringcolumn()
signal = relationship('meas_SignalTable', backref='isotope', uselist=False)
fits = relationship('proc_FitTable', backref='isotope')
results = relationship('proc_IsotopeResultsTable', backref='isotope')
class proc_TagTable(Base):
__tablename__ = 'proc_TagTable'
name = Column(String(40), primary_key=True)
create_date = Column(DateTime, default=func.now())
user = stringcolumn()
omit_ideo = Column(Boolean)
omit_spec = Column(Boolean)
omit_iso = Column(Boolean)
omit_series = Column(Boolean)
analyses = relationship('meas_AnalysisTable', backref='tag_item')
class proc_BlanksTable(Base, BaseMixin):
history_id = foreignkey('proc_BlanksHistoryTable')
user_value = Column(Float)
user_error = Column(Float)
use_set = Column(Boolean)
isotope = stringcolumn()
fit = stringcolumn()
error_type = stringcolumn(default='SD')
set_id = Column(String(40), ForeignKey('proc_BlanksSetTable.set_id'))
# set_id = Column(Integer, ForeignKey('proc_BlanksSetTable.set_id'))
# set_id = Column(Integer)
# set_id = foreignkey('proc_BlanksSetTable')
preceding_id = foreignkey('meas_AnalysisTable')
analysis_set = relationship(
'proc_BlanksSetTable',
primaryjoin='proc_BlanksTable.set_id==proc_BlanksSetTable.set_id',
backref='blanks',
uselist=True)
# analysis_set = relationship('proc_BlanksSetTable')
value_set = relationship('proc_BlanksSetValueTable', backref='blank')
def make_summary(self):
s = 'Pr'
f = self.fit
if f:
if not f in INTERPOLATE_TYPES:
f = f[:1].upper()
s = '{}{}'.format(self.isotope, f)
if self.preceding_id:
p = self.preceding_analysis
rid = make_runid(p.labnumber.identifier, p.aliquot, p.step)
s = '{} ({})'.format(s, rid)
return s
class meas_ExtractionTable(Base, BaseMixin):
# extract_value = deferred(Column(Float))
# extract_duration = deferred(Column(Float))
# cleanup_duration = deferred(Column(Float))
# extract_units = deferred(stringcolumn(5))
extract_value = Column(Float)
extract_duration = Column(Float)
cleanup_duration = Column(Float)
extract_units = stringcolumn(5)
weight = deferred(Column(Float))
sensitivity_multiplier = deferred(Column(Float))
is_degas = deferred(Column(Boolean))
beam_diameter = Column(Float)
pattern = stringcolumn(100)
ramp_rate = Column(Float)
ramp_duration = Column(Float)
mask_position = deferred(Column(Float))
mask_name = deferred(stringcolumn(100))
attenuator = deferred(Column(Float))
reprate = deferred(Column(Float))
response_blob = deferred(Column(BLOB))
output_blob = deferred(Column(BLOB))
sensitivity_id = foreignkey('gen_SensitivityTable')
extract_device_id = foreignkey('gen_ExtractionDeviceTable')
script_id = foreignkey('meas_ScriptTable')
experiment_blob_id = foreignkey('meas_ScriptTable')
image_id = foreignkey('med_ImageTable')
analysis = relationship('meas_AnalysisTable',
uselist=False,
backref='extraction')
positions = relationship('meas_PositionTable', backref='extraction')
snapshots = relationship('med_SnapshotTable', backref='extraction')
class gen_SampleTable(Base, NameMixin):
material_id = foreignkey('gen_MaterialTable')
project_id = foreignkey('gen_ProjectTable')
labnumbers = relationship('gen_LabTable', backref='sample')
monitors = relationship('flux_MonitorTable', backref='sample')
images = relationship('med_SampleImageTable', backref='sample')
igsn = Column(CHAR(9))
location = stringcolumn(80)
lat = Column(Float)
long = Column(Float)
elevation = Column(Float)
note = Column(BLOB)
alt_name = stringcolumn(80)
lithology = stringcolumn(80)
environment = stringcolumn(140)
rock_type = stringcolumn(80)
sio2 = Column(Float(32))
na2o = Column(Float(32))
k2o = Column(Float(32))
class proc_InterpretedAgeTable(Base, BaseMixin):
history_id = foreignkey('proc_InterpretedAgeHistoryTable')
age_kind = stringcolumn(32)
kca_kind = stringcolumn(32)
age = Column(Float)
age_err = Column(Float)
display_age_units = stringcolumn(2)
kca = Column(Float)
kca_err = Column(Float)
# wtd_kca = Column(Float)
# wtd_kca_err = Column(Float)
# arith_kca = Column(Float)
# arith_kca_err = Column(Float)
mswd = Column(Float)
age_error_kind = stringcolumn(80)
include_j_error_in_mean = Column(Boolean)
include_j_error_in_plateau = Column(Boolean)
include_j_error_in_individual_analyses = Column(Boolean)
sets = relationship('proc_InterpretedAgeSetTable', backref='analyses')
class proc_TagTable(Base):
__tablename__ = 'proc_TagTable'
name = Column(String(40), primary_key=True)
create_date = Column(DateTime, default=func.now())
user = stringcolumn()
omit_ideo = Column(Boolean)
omit_spec = Column(Boolean)
omit_iso = Column(Boolean)
omit_series = Column(Boolean)
analyses = relationship('meas_AnalysisTable', backref='tag_item')
def to_dict(self):
return {k: getattr(self, k) for k in ('name', 'omit_ideo', 'omit_series',
'omit_spec', 'omit_iso')}
