class UserTbl(Base, BaseMixin):
name = Column(String(45), primary_key=True)
affiliation = stringcolumn(80)
category = stringcolumn(80)
email = stringcolumn(80)
media = relationship('MediaTbl', backref='user')
class AnalysisChangeTbl(Base, BaseMixin):
idanalysischangeTbl = Column(Integer, primary_key=True)
# tag = Column(String(40), ForeignKey('TagTbl.name'))
tag = stringcolumn(40)
timestamp = Column(TIMESTAMP)
user = stringcolumn(40)
analysisID = Column(Integer, ForeignKey('AnalysisTbl.id'))
class PrincipalInvestigatorTbl(Base, BaseMixin):
name = Column(String(140), primary_key=True)
affiliation = stringcolumn(140)
email = stringcolumn(140)
@property
def record_view(self):
from pychron.envisage.browser.record_views import PrincipalInvestigatorRecordView
r = PrincipalInvestigatorRecordView(self)
return r
class SampleTbl(Base, NameMixin):
materialID = Column(Integer, ForeignKey('MaterialTbl.id'))
projectID = Column(Integer, ForeignKey('ProjectTbl.id'))
note = stringcolumn(140)
igsn = stringcolumn(140)
lat = Column(Float)
lon = Column(Float)
storage_location = deferred(stringcolumn(140))
lithology = deferred(stringcolumn(140))
unit = deferred(stringcolumn(80))
lithology_class = deferred(stringcolumn(140))
lithology_type = deferred(stringcolumn(140))
lithology_group = deferred(stringcolumn(140))
location = deferred(stringcolumn(140))
approximate_age = deferred(Column(Float))
elevation = deferred(Column(Float))
create_date = deferred(Column(DateTime, default=func.now()))
update_date = deferred(
Column(DateTime, onupdate=func.now(), default=func.now()))
positions = relationship('IrradiationPositionTbl',
backref='sample',
lazy='joined')
class ProjectTbl(Base, NameMixin):
principal_investigatorID = Column(Integer, ForeignKey('PrincipalInvestigatorTbl.id'))
samples = relationship('SampleTbl', backref='project')
analysis_groups = relationship('AnalysisGroupTbl', backref='project')
checkin_date = Column(DATE)
comment = Column(TEXT)
lab_contact = stringcolumn(80)
institution = stringcolumn(80)
@property
def pname(self):
return '{} ({})'.format(self.name, self.principal_investigator.name) if self.principal_investigator else \
self.name
class LevelTbl(Base, NameMixin):
irradiationID = Column(Integer, ForeignKey('IrradiationTbl.id'))
# productionID = Column(Integer, ForeignKey('ProductionTbl.id'))
holder = stringcolumn(45)
z = Column(Float)
positions = relationship('IrradiationPositionTbl',
backref='level',
lazy='joined')
note = Column(TEXT)
@property
def projects(self):
ps = []
for p in self.positions:
try:
name = p.sample.project.name
if name != 'Irradiation-{}'.format(self.irradiation.name):
ps.append(p.sample.project.pname)
except AttributeError:
pass
return list(set(ps))
class AnalysisGroupTbl(Base, IDMixin):
name = stringcolumn(140)
create_date = Column(TIMESTAMP, default=func.now())
projectID = Column(Integer, ForeignKey('ProjectTbl.id'))
user = Column(String(140), ForeignKey('UserTbl.name'))
sets = relationship('AnalysisGroupSetTbl', backref='group')
class MaterialTbl(Base, NameMixin):
id = primary_key()
samples = relationship('SampleTbl', backref='material')
grainsize = stringcolumn(80)
@property
def gname(self):
return '{} ({})'.format(self.name, self.grainsize) if self.grainsize else self.name
class SamplePrepStepTbl(Base, IDMixin):
sampleID = Column(Integer, ForeignKey('SampleTbl.id'))
sessionID = Column(Integer, ForeignKey('SamplePrepSessionTbl.id'))
crush = Column(String(140))
wash = Column(String(140))
sieve = Column(String(140))
frantz = Column(String(140))
acid = Column(String(140))
heavy_liquid = Column(String(140))
pick = Column(String(140))
mount = stringcolumn(140)
gold_table = stringcolumn(140)
us_wand = stringcolumn(140)
eds = stringcolumn(140)
cl = stringcolumn(140)
bse = stringcolumn(140)
se = stringcolumn(140)
status = Column(String(32))
comment = Column(String(300))
timestamp = Column(DATETIME, default=func.now())
added = Column(Boolean)
images = relationship('SamplePrepImageTbl', backref='step')
class InterpretedAgeSetTbl(Base, BaseMixin):
idinterpretedagesettbl = Column(Integer, primary_key=True)
interpreted_ageID = Column(Integer, ForeignKey('InterpretedAgeTbl.idinterpretedagetbl'))
analysisID = Column(Integer, ForeignKey('AnalysisTbl.id'))
forced_plateau_step = Column(Boolean)
plateau_step = Column(Boolean)
tag = stringcolumn(80)
analysis = relationship('AnalysisTbl', uselist=False)
class InterpretedAgeTbl(Base, BaseMixin):
idinterpretedagetbl = Column(Integer, primary_key=True)
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)
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)
analyses = relationship('InterpretedAgeSetTbl', backref='interpreted_age')
class PrincipalInvestigatorTbl(Base, IDMixin):
affiliation = stringcolumn(140)
email = stringcolumn(140)
last_name = Column(String(140))
first_initial = Column(String(10))
projects = relationship('ProjectTbl', backref='principal_investigator')
repositories = relationship('RepositoryTbl', backref='principal_investigator')
irs = relationship('IRTbl', backref='principal_investigator')
@property
def name(self):
return '{}, {}'.format(self.last_name, self.first_initial) if self.first_initial else self.last_name
@property
def record_view(self):
from pychron.envisage.browser.record_views import PrincipalInvestigatorRecordView
r = PrincipalInvestigatorRecordView(self)
return r
class LevelTbl(Base, NameMixin):
id = primary_key()
irradiationID = Column(Integer, ForeignKey('IrradiationTbl.id'))
productionID = Column(Integer, ForeignKey('ProductionTbl.id'))
holder = stringcolumn(45)
z = Column(Float)
positions = relationship('IrradiationPositionTbl', backref='level')
note = Column(BLOB)
class MaterialTbl(Base, NameMixin):
samples = relationship('SampleTbl', backref='material')
grainsize = stringcolumn(80)
@property
def gname(self):
return '{} ({})'.format(self.name, self.grainsize) if self.grainsize else self.name
def __repr__(self):
return '{}<{}>'.format(self.__class__.__name__, self.gname)
class CurrentTbl(Base, IDMixin):
value = Column(Float(32))
error = Column(Float(32))
unit = stringcolumn(40)
parameterID = Column(Integer, ForeignKey('ParameterTbl.id'))
analysisID = Column(Integer, ForeignKey('AnalysisTbl.id'))
parameter = relationship('ParameterTbl', uselist=False)
analysis = relationship('AnalysisTbl', uselist=False)
class IrradiationPositionTbl(Base, IDMixin):
identifier = stringcolumn(80)
sampleID = Column(Integer, ForeignKey('SampleTbl.id'))
levelID = Column(Integer, ForeignKey('LevelTbl.id'))
position = Column(Integer)
note = Column(TEXT)
weight = Column(Float)
j = Column(Float)
j_err = Column(Float)
packet = stringcolumn(40)
# analyses = relationship('AnalysisTbl', backref='irradiation_position')
@property
def analysis_count(self):
return object_session(self).query(AnalysisTbl).with_parent(self).count()
@property
def analyzed(self):
return bool(self.analysis_count)
class IrradiationPositionTbl(Base, BaseMixin):
id = primary_key()
identifier = stringcolumn(80)
sampleID = Column(Integer, ForeignKey('SampleTbl.id'))
levelID = Column(Integer, ForeignKey('LevelTbl.id'))
position = Column(Integer)
note = Column(BLOB)
weight = Column(Float)
j = Column(Float)
j_err = Column(Float)
analyses = relationship('AnalysisTbl', backref='irradiation_position')
class UserTbl(Base, BaseMixin):
name = Column(String(45), primary_key=True)
affiliation = stringcolumn(80)
category = stringcolumn(80)
email = stringcolumn(80)
class NameMixin(BaseMixin):
name = stringcolumn(80)
def __repr__(self):
return '{}<{}>'.format(self.__class__.__name__, self.name)
class MassSpectrometerTbl(Base, BaseMixin):
name = Column(String(45), primary_key=True)
kind = stringcolumn(45)
class RestrictedNameTbl(Base, IDMixin):
name = stringcolumn()
category = stringcolumn()
class AnalysisTbl(Base, BaseMixin):
id = primary_key()
timestamp = Column(TIMESTAMP)
# tag = stringcolumn(45)
uuid = stringcolumn(32)
analysis_type = stringcolumn(45)
aliquot = Column(Integer)
increment = Column(Integer)
irradiation_positionID = Column(Integer, ForeignKey('IrradiationPositionTbl.id'))
measurementName = stringcolumn(45)
extractionName = stringcolumn(45)
postEqName = stringcolumn(45)
postMeasName = stringcolumn(45)
mass_spectrometer = Column(String(45), ForeignKey('MassSpectrometerTbl.name'))
extract_device = stringcolumn(45)
extract_value = Column(Float)
extract_units = stringcolumn(45)
cleanup = Column(Float)
duration = Column(Float)
weight = Column(Float)
comment = stringcolumn(80)
repository_associations = relationship('RepositoryAssociationTbl', backref='analysis')
group_sets = relationship('AnalysisGroupSetTbl', backref='analysis')
change = relationship('AnalysisChangeTbl', uselist=False, backref='analysis')
measured_position = relationship('MeasuredPositionTbl', uselist=False, backref='analysis')
_record_view = None
group_id = 0
@property
def is_plateau_step(self):
return
@property
def timestampf(self):
return make_timef(self.timestamp)
@property
def identifier(self):
return self.irradiation_position.identifier
@property
def irradiation(self):
return self.irradiation_position.level.irradiation.name
@property
def irradiation_level(self):
return self.irradiation_position.level.name
@property
def project(self):
return self.irradiation_position.sample.project.name
@property
def sample(self):
return self.irradiation_position.sample.name
@property
def irradiation_position_position(self):
return self.irradiation_position.position
@property
def tag_dict(self):
return {k: getattr(self.change.tag_item, k) for k in ('name',) + OMIT_KEYS}
# @property
# def labnumber(self):
# return self.irradiation_position
@property
def analysis_timestamp(self):
return self.timestamp
@property
def rundate(self):
return self.timestamp
@property
def repository_identifier(self):
if self.repository_associations and len(self.repository_associations) == 1:
return self.repository_associations[0].repository
@property
def record_id(self):
return make_runid(self.irradiation_position.identifier, self.aliquot, self.increment)
@property
def repository_identifier(self):
es = [e.repository for e in self.repository_associations]
if len(es) == 1:
return es[0]
@property
def record_views(self):
# iv = self._record_view
# if not iv:
repos = self.repository_associations
if len(repos) == 1:
return self._make_record_view(repos[0].repository),
else:
return [self._make_record_view(r.repository, use_suffix=True) for r in repos]
def make_record_view(self, repository, use_suffix=False):
for repo in self.repository_associations:
if repo.repository == repository:
return self._make_record_view(repo.repository, use_suffix=use_suffix)
else:
return self._make_record_view(self.repository_associations[0].repository)
def _make_record_view(self, repo, use_suffix=False):
iv = DVCIsotopeRecordView(self)
# iv.repository_ids = es = [e.repository for e in self.repository_associations]
# if len(es) == 1:
# iv.repository_identifier = es[0]
iv.repository_identifier = repo
iv.use_repository_suffix = use_suffix
iv.init()
return iv
class UnitsTbl(Base, IDMixin):
name = stringcolumn(40)
class AnalysisTbl(Base, IDMixin):
experiment_type = stringcolumn(32)
timestamp = Column(DATETIME)
# tag = stringcolumn(45)
uuid = stringcolumn(32)
analysis_type = stringcolumn(45)
aliquot = Column(Integer)
increment = Column(Integer)
irradiation_positionID = Column(Integer,
ForeignKey('IrradiationPositionTbl.id'))
# simple_identifier = Column(Integer, ForeignKey('SimpleIdentifier.identifier'))
measurementName = stringcolumn(45)
extractionName = stringcolumn(45)
postEqName = stringcolumn(45)
postMeasName = stringcolumn(45)
mass_spectrometer = Column(String(45),
ForeignKey('MassSpectrometerTbl.name'))
extract_device = stringcolumn(45)
extract_value = Column(Float)
extract_units = stringcolumn(45)
cleanup = Column(Float)
duration = Column(Float)
weight = Column(Float)
comment = stringcolumn(200)
repository_associations = relationship('RepositoryAssociationTbl',
backref='analysis',
lazy='joined')
group_sets = relationship('AnalysisGroupSetTbl', backref='analysis')
change = relationship('AnalysisChangeTbl',
uselist=False,
backref='analysis',
lazy='joined')
measured_positions = relationship('MeasuredPositionTbl',
backref='analysis')
media = relationship('MediaTbl', backref='analysis')
irradiation_position = relationship('IrradiationPositionTbl',
backref='analysis',
lazy='joined')
_record_view = None
group_id = 0
frozen = False
delta_time = 0
review_status = None
repository_identifier = ''
is_plateau_step = None
load_name = ''
load_holder = ''
_temporary_tag = None
@property
def step(self):
print(self.increment, alphas(self.increment))
return alphas(self.increment)
@property
def position(self):
if self.measured_positions:
return ','.join([
'{}'.format(p.position) for p in self.measured_positions
if p.position
])
else:
return ''
@property
def meas_script_name(self):
return self.measurementName
@property
def extract_script_name(self):
return self.extractionName
@property
def timestampf(self):
return make_timef(self.timestamp)
@property
def identifier(self):
return self.irradiation_position.identifier
@property
def irradiation_info(self):
return '{}{} {}'.format(self.irradiation, self.irradiation_level,
self.irradiation_position_position)
@property
def irradiation(self):
return self.irradiation_position.level.irradiation.name
@property
def irradiation_level(self):
return self.irradiation_position.level.name
@property
def packet(self):
return self.irradiation_position.packet or ''
@property
def project(self):
try:
return self.irradiation_position.sample.project.name
except AttributeError:
return ''
@property
def principal_investigator(self):
try:
return self.irradiation_position.sample.project.principal_investigator.name
except AttributeError:
return ''
@property
def sample(self):
try:
return self.irradiation_position.sample.name
except AttributeError:
return ''
@property
def irradiation_position_position(self):
return self.irradiation_position.position
@property
def material(self):
try:
return self.irradiation_position.sample.material.name
except AttributeError:
return ''
@property
def tag(self):
if self._temporary_tag:
tag = self._temporary_tag
else:
tag = self.change.tag
return tag
def set_tag(self, t):
self._temporary_tag = t
@property
def analysis_timestamp(self):
return self.timestamp
@property
def rundate(self):
return self.timestamp
@property
def record_id(self):
return make_runid(self.irradiation_position.identifier, self.aliquot,
self.increment)
@property
def repository_identifier(self):
if self.repository_associations and len(
self.repository_associations) == 1:
return self.repository_associations[0].repository
@property
def display_uuid(self):
u = self.uuid
if not u:
u = ''
return u[:8]
def get_load_name(self):
ln = ''
if self.measured_positions:
ln = self.measured_positions[0].loadName or ''
return ln
def get_load_holder(self):
lh = ''
if self.measured_positions:
load = self.measured_positions[0].load
if load:
lh = load.holderName
return lh
def bind(self):
self.load_name = self.get_load_name()
self.load_holder = self.get_load_holder()
# force binding of irradiation_position
self.irradiation_position
self.irradiation_level
self.irradiation
class SamplePrepImageTbl(Base, IDMixin):
stepID = Column(Integer, ForeignKey('SamplePrepStepTbl.id'))
host = stringcolumn(45)
path = stringcolumn(45)
timestamp = Column(DATETIME, default=func.now())
note = Column(TEXT)
class RestrictedNameTbl(Base, BaseMixin):
id = primary_key()
name = stringcolumn()
category = stringcolumn()
class ParameterTbl(Base, IDMixin):
name = stringcolumn(40)
class SamplePrepChoicesTbl(Base, IDMixin):
tag = stringcolumn(140)
value = stringcolumn(140)
