class GelBand(db.Model, MGIModel):
__tablename__ = "gxd_gelband"
_gelband_key = db.Column(db.Integer, primary_key=True)
_gelrow_key = db.Column(db.Integer, mgi_fk("gxd_gelrow._gelrow_key"))
_gellane_key = db.Column(db.Integer, mgi_fk("gxd_gellane._gellane_key"))
_strength_key = db.Column(db.Integer)
bandnote = db.Column(db.String())
strength = db.column_property(
db.select([GxdStrength.strength
]).where(GxdStrength._strength_key == _strength_key))
gelrow_sequencenum = db.column_property(
db.select([GelRow.sequencenum
]).where(GelRow._gelrow_key == _gelrow_key))
gelrow = db.relationship("GelRow", uselist=False)
class GelRow(db.Model, MGIModel):
__tablename__ = "gxd_gelrow"
_gelrow_key = db.Column(db.Integer, primary_key=True)
_assay_key = db.Column(db.Integer, mgi_fk("gxd_assay._assay_key"))
_gelunits_key = db.Column(db.Integer)
sequencenum = db.Column(db.Integer)
rownote = db.Column(db.String())
size = db.Column(db.Float())
gelunits = db.column_property(
db.select([GelUnits.units
]).where(GelUnits._gelunits_key == _gelunits_key))
@property
def size_and_units(self):
return "%s %s" % (self.size, self.gelunits)
class Sequence(db.Model, MGIModel):
__tablename__ = "seq_sequence"
_sequence_key = db.Column(db.Integer, primary_key=True)
_sequencetype_key = db.Column(db.Integer)
_sequencequality_key = db.Column(db.Integer)
_sequencestatus_key = db.Column(db.Integer)
_sequenceprovider_key = db.Column(db.Integer)
_organism_key = db.Column(db.Integer, mgi_fk("mgi_organism._organism_key"))
length = db.Column(db.String())
description = db.Column(db.String())
version = db.Column(db.String())
division = db.Column(db.String())
# constants
_mgitype_key = 19
# column definitions
type = db.column_property(
db.select([VocTerm.term
]).where(VocTerm._term_key == _sequencetype_key))
#relationships
markers = db.relationship(
"Marker",
secondary=SeqMarkerCache.__table__,
primaryjoin="Sequence._sequence_key==SeqMarkerCache._sequence_key",
secondaryjoin="SeqMarkerCache._marker_key==Marker._marker_key",
foreign_keys="[Sequence._sequence_key,Marker._marker_key]",
backref="sequences",
order_by="Marker.symbol")
# sequence can have multiple IDs
accession_objects = db.relationship(
"Accession",
primaryjoin="and_(Accession._object_key==Sequence._sequence_key,"
"Accession.preferred==1,"
"Accession._mgitype_key==%s)" % (_mgitype_key),
foreign_keys="[Accession._object_key]",
order_by="Accession.accid")
source = db.relationship("ProbeSource",
secondary=SeqSourceAssoc.__table__,
uselist=False)
class Note(db.Model, MGIModel):
__tablename__ = "mgi_note"
_note_key = db.Column(db.Integer, primary_key=True)
_object_key = db.Column(db.Integer)
_mgitype_key = db.Column(db.Integer)
_notetype_key = db.Column(db.Integer)
notetype = db.column_property(
db.select([NoteType.notetype
]).where(NoteType._notetype_key == _notetype_key))
chunks = db.relationship("NoteChunk", order_by="NoteChunk.sequencenum")
@property
def text(self):
return ''.join([c.note for c in self.chunks])
def __repr__(self):
return self.text
class SeqMarkerCache(db.Model, MGIModel):
__tablename__ = "seq_marker_cache"
_cache_key = db.Column(db.Integer, primary_key=True)
_sequence_key = db.Column(db.Integer, mgi_fk("seq_sequence._sequence_key"))
_marker_key = db.Column(db.Integer, mgi_fk("mrk_marker._marker_key"))
_organism_key = db.Column(db.Integer)
_logicaldb_key = db.Column(db.Integer,
mgi_fk("acc_logicaldb._logicaldb_key"))
accid = db.Column(db.String())
rawbiotype = db.Column(db.String())
_sequenceprovider_key = db.Column(db.Integer)
_biotypeconflict_key = db.Column(db.Integer, mgi_fk("voc_term._term_key"))
annotation_date = db.Column(db.DateTime)
# constants
# the biotype conflict term
_biotypeconflict_yes_key = 5420767
# column properties
sequenceprovider = db.column_property(
db.select([VocTerm.term
]).where(VocTerm._term_key == _sequenceprovider_key))
marker = db.relationship("Marker")
logicaldb_obj = db.relationship("LogicalDb")
@property
def sequence_url(self):
"""
This requires loading logicaldb_obj
and logicaldb_obj.actualdb
"""
url = ""
if self.logicaldb_obj and \
self.logicaldb_obj.actualdb:
url = self.logicaldb_obj.actualdb.url.replace("@@@@", self.accid)
return url
