class TrackRecChildAssoc(db.Model):
__tablename__ = "wts_trackrec_child"
tr_key = db.Column(db.Integer,
db.ForeignKey("wts_trackrec.key"),
primary_key=True)
child_tr_key = db.Column(db.Integer,
db.ForeignKey("wts_trackrec.key"),
primary_key=True)
class TRAreaAssoc(db.Model):
__tablename__ = "wts_tr_area"
tr_key = db.Column(db.Integer,
db.ForeignKey("wts_trackrec.key"),
index=True,
primary_key=True)
area_key = db.Column(db.Integer,
db.ForeignKey("cv_wts_area.key"),
index=True,
primary_key=True)
class TRRequestedUserAssoc(db.Model):
__tablename__ = "wts_tr_request_user"
tr_key = db.Column(db.Integer,
db.ForeignKey("wts_trackrec.key"),
index=True,
primary_key=True)
user_key = db.Column(db.Integer,
db.ForeignKey("cv_user.key"),
index=True,
primary_key=True)
class TRTypeAssoc(db.Model):
__tablename__ = "wts_tr_type"
tr_key = db.Column(db.Integer,
db.ForeignKey("wts_trackrec.key"),
index=True,
primary_key=True)
type_key = db.Column(db.Integer,
db.ForeignKey("cv_wts_type.key"),
index=True,
primary_key=True)
class StatusHistory(db.Model):
__tablename__ = "wts_status_history"
key = db.Column(db.Integer, primary_key=True)
tr_key = db.Column(db.Integer,
db.ForeignKey("wts_trackrec.key"),
index=True)
status_key = db.Column(db.Integer,
db.ForeignKey("cv_wts_status.key"),
index=True)
user_key = db.Column(db.Integer, db.ForeignKey("cv_user.key"), index=True)
set_date = db.Column(db.DateTime())
class TrackRec(db.Model):
__tablename__ = "wts_trackrec"
key = db.Column(db.Integer, primary_key=True)
priority_key = db.Column(db.Integer, db.ForeignKey("cv_wts_priority.key"))
size_key = db.Column(db.Integer,
db.ForeignKey("cv_wts_size.key"),
index=True)
status_key = db.Column(db.Integer,
db.ForeignKey("cv_wts_status.key"),
index=True)
status_user_key = db.Column(db.Integer,
db.ForeignKey("cv_user.key"),
index=True)
status_set_date = db.Column(db.DateTime())
locked_user_key = db.Column(db.Integer,
db.ForeignKey("cv_user.key"),
index=True)
locked_date = db.Column(db.DateTime())
title = db.Column(db.String())
has_directory = db.Column(db.Boolean)
attention_by = db.Column(db.DateTime())
creation_date = db.Column(db.DateTime(), default=db.func.now())
modification_date = db.Column(db.DateTime(), default=db.func.now())
description = db.Column(db.String())
progress_notes = db.Column(db.String())
priority = db.relationship("Priority", uselist=False, backref="trs")
size = db.relationship("Size", uselist=False, backref="trs")
status = db.relationship("Status", uselist=False, backref="trs")
areas = db.relationship("Area",
secondary=TRAreaAssoc.__table__,
backref="trs")
types = db.relationship("Type",
secondary=TRTypeAssoc.__table__,
backref="trs")
assigned_users = db.relationship("User",
secondary=TRAssignedUserAssoc.__table__)
requested_by = db.relationship("User",
secondary=TRRequestedUserAssoc.__table__)
statusChanges = db.relationship("StatusHistory")
child_trs = db.relationship(
"TrackRec",
secondary=TrackRecChildAssoc.__table__,
primaryjoin="TrackRec.key==TrackRecChildAssoc.tr_key",
secondaryjoin="TrackRec.key==TrackRecChildAssoc.child_tr_key",
backref=db.backref("parent", uselist=False))
class ProbeNoteChunk(db.Model, MGIModel):
__tablename__ = "prb_notes"
_probe_key = db.Column(db.Integer,
db.ForeignKey("prb_probe._probe_key"),
primary_key=True)
note = db.Column(db.String())
sequencenum = db.Column(db.Integer, primary_key=True)
class MarkerDetailClipNoteChunk(db.Model, MGIModel):
__tablename__ = "mrk_notes"
_marker_key = db.Column(db.Integer,
db.ForeignKey("mrk_marker._marker_key"),
primary_key=True)
note = db.Column(db.String())
sequencenum = db.Column(db.Integer, primary_key=True)
class MarkerLocationCache(db.Model, MGIModel):
__tablename__ = "mrk_location_cache"
_cache_key = db.Column(db.Integer, primary_key=True)
_marker_key = db.Column(db.Integer,
db.ForeignKey("mrk_marker._marker_key"))
_organism_key = db.Column(db.Integer())
chromosome = db.Column(db.String())
cytogeneticoffset = db.Column(db.String())
cmoffset = db.Column(db.Float())
genomicchromosome = db.Column(db.String())
startcoordinate = db.Column(db.Float())
endcoordinate = db.Column(db.Float())
strand = db.Column(db.String())
mapunits = db.Column(db.String())
provider = db.Column(db.String())
version = db.Column(db.String())
@property
def providerString(self):
if not self.provider:
return ""
return "From %s annotation of %s" % (self.provider, self.version)
def __repr__(self):
if not self.startcoordinate or not self.endcoordinate:
return "Chr%s" % (self.chromosome)
return "Chr%s:%d-%d bp, %s strand" % (self.chromosome,
self.startcoordinate,
self.endcoordinate, self.strand)
class ReportLabel(db.Model):
__tablename__ = "pwi_report_label"
__bind_key__ = "mgd"
id = db.Column(db.Integer, primary_key=True)
report_id = db.Column(db.Integer,
db.ForeignKey("pwi_report.id"),
index=True)
label = db.Column(db.String(), index=True)
def __repr__(self):
return self.label
def mgi_fk(fkString):
fkString = "mgd." + fkString
fk = db.ForeignKey(fkString)
return fk
class ADStructure(db.Model, MGIModel):
__tablename__ = "gxd_structure"
_structure_key = db.Column(db.Integer, primary_key=True)
_structurename_key = db.Column(
db.Integer, mgi_fk("gxd_structurename._structurename_key"))
_parent_key = db.Column(db.Integer, db.ForeignKey(_structure_key))
_stage_key = db.Column(db.Integer)
printname = db.Column(db.String())
structurenote = db.Column(db.Integer)
# constants
_mgitype_key = 38
# column properties
mgiid = db.column_property(
db.select([Accession.accid]).where(
db.and_(Accession._mgitype_key == _mgitype_key,
Accession.prefixpart == 'MGI:', Accession.preferred == 1,
Accession._logicaldb_key == 1,
Accession._object_key == _structure_key)))
# relationships
mgiid_object = db.relationship(
"Accession",
primaryjoin="and_(Accession._object_key==ADStructure._structure_key,"
"Accession.prefixpart=='MGI:',"
"Accession.preferred==1,"
"Accession._logicaldb_key==1,"
"Accession._mgitype_key==%d)" % _mgitype_key,
foreign_keys="Accession._object_key",
uselist=False)
secondaryids = db.relationship(
"Accession",
primaryjoin="and_(Accession._object_key==ADStructure._structure_key,"
"Accession._logicaldb_key!=1,"
"Accession._mgitype_key==%d)" % _mgitype_key,
foreign_keys="Accession._object_key",
order_by="Accession.accid")
# all names, including synonyms
names = db.relationship(
"ADStructureName",
primaryjoin=
"ADStructureName._structure_key==ADStructure._structure_key",
foreign_keys="[ADStructureName._structure_key]")
# results
# backref in Result class
# only synonyms
synonyms = db.relationship(
"ADStructureName",
primaryjoin=
"and_(ADStructureName._structure_key==ADStructure._structure_key,"
"ADStructureName._structurename_key!=ADStructure._structurename_key)",
foreign_keys=
"[ADStructureName._structure_key,ADStructureName._structurename_key]",
order_by="ADStructureName.structure")
children = db.relationship("ADStructure",
backref=db.backref("parent",
remote_side=_structure_key))
# parent
# backref defined above
@property
def stage(self):
return self._stage_key
@property
def emapsterm(self):
term_object = None
if self.mgiid_object and self.mgiid_object.emapsids:
term_object = self.mgiid_object.emapsids[0].vocterm
return term_object
# for vocterm compatibility
@property
def primaryid(self):
return self.mgiid
@property
def term(self):
return self.printname
@property
def display(self):
return "TS%s: %s" % (self.stage, self.printname)
def __repr__(self):
return self.display
class Category(CVMixin, db.Model):
__tablename__ = "cv_wts_category"
email = db.Column(db.String())
area_key = db.Column(db.Integer, db.ForeignKey("cv_wts_area.key"))
type_key = db.Column(db.Integer, db.ForeignKey("cv_wts_type.key"))
status_key = db.Column(db.Integer, db.ForeignKey("cv_wts_status.key"))