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 ExperimentNoteChunk(db.Model, MGIModel):
__tablename__ = "mld_expt_notes"
_expt_key = db.Column(db.Integer,
mgi_fk("mld_expts._expt_key"),
primary_key=True)
sequencenum = db.Column(db.Integer, primary_key=True)
note = db.Column(db.String())
class GxdLabel(db.Model, MGIModel):
"""
Label for ProbePrep + AntibodyPrep
"""
__tablename__ = "gxd_label"
_label_key = db.Column(db.Integer, primary_key=True)
label = db.Column(db.String())
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 User(db.Model):
__tablename__ = "cv_user"
key = db.Column(db.Integer, primary_key=True)
login = db.Column(db.String())
active = db.Column(db.Boolean)
class ProbeAlias(db.Model, MGIModel):
__tablename__ = "prb_alias"
_alias_key = db.Column(db.Integer, primary_key=True)
_reference_key = db.Column(db.Integer,
mgi_fk("prb_reference._reference_key"),
primary_key=True)
alias = db.Column(db.String())
class ProbeSource(db.Model, MGIModel):
__tablename__ = "prb_source"
_source_key = db.Column(db.Integer, primary_key=True)
_organism_key = db.Column(db.Integer)
_cellline_key = db.Column(db.Integer)
_gender_key = db.Column(db.Integer)
_refs_key = db.Column(db.Integer, mgi_fk("bib_refs._refs_key"))
_strain_key = db.Column(db.Integer, mgi_fk("prb_strain._strain_key"))
_tissue_key = db.Column(db.Integer)
name = db.Column(db.String())
description = db.Column(db.String())
age = db.Column(db.String())
# column properties
cellline = db.column_property(
db.select([VocTerm.term]).where(VocTerm._term_key == _cellline_key))
gender = db.column_property(
db.select([VocTerm.term]).where(VocTerm._term_key == _gender_key))
organism = db.column_property(
db.select([Organism.commonname
]).where(Organism._organism_key == _organism_key))
tissue = db.column_property(
db.select([ProbeTissue.tissue
]).where(ProbeTissue._tissue_key == _tissue_key))
# relationships
reference = db.relationship("Reference", uselist=False)
strain = db.relationship("Strain", uselist=False)
class MGIUser(db.Model, MGIModel):
__tablename__ = "mgi_user"
_user_key = db.Column(db.Integer, primary_key=True)
_usertype_key = db.Column(db.Integer, mgi_fk("voc_term._term_key"))
_userstatus_key = db.Column(db.Integer, mgi_fk("voc_term._term_key"))
login = db.Column(db.String())
name = db.Column(db.String())
usertype_object = db.relationship(
"VocTerm",
primaryjoin="VocTerm._term_key==MGIUser._usertype_key",
uselist=False)
userstatus_object = db.relationship(
"VocTerm",
primaryjoin="VocTerm._term_key==MGIUser._userstatus_key",
uselist=False)
# Properties for Flask-Login functionality
def is_authenticated(self):
return True
def is_active(self):
return True
def is_anonymous(self):
return False
def get_id(self):
return self.login
class ProbeReferenceNotes(db.Model, MGIModel):
__tablename__ = "prb_ref_notes"
_reference_key = db.Column(db.Integer,
mgi_fk("prb_reference._reference_key"),
primary_key=True)
sequencenum = db.Column(db.Integer, primary_key=True)
note = db.Column(db.String())
class MLDReferenceNoteChunk(db.Model, MGIModel):
__tablename__ = "mld_notes"
_refs_key = db.Column(db.Integer,
mgi_fk("bib_refs._refs_key"),
primary_key=True)
sequencenum = db.Column(db.Integer, primary_key=True)
note = db.Column(db.String())
class AntibodyPrep(db.Model, MGIModel):
__tablename__ = "gxd_antibodyprep"
_antibodyprep_key = db.Column(db.Integer, primary_key=True)
_antibody_key = db.Column(db.Integer, mgi_fk("gxd_antibody._antibody_key"))
_secondary_key = db.Column(db.Integer)
_label_key = db.Column(db.Integer)
label = db.column_property(
db.select([GxdLabel.label]).where(GxdLabel._label_key == _label_key))
secondary = db.column_property(
db.select([GxdSecondary.secondary
]).where(GxdSecondary._secondary_key == _secondary_key))
# Relationships
antibody = db.relationship("Antibody",
backref=db.backref(
"antibodypreps",
order_by="AntibodyPrep._antibodyprep_key"),
uselist=False)
# assay
# backref defined in Assay class
marker = db.relationship("Marker",
secondary=Assay.__table__,
backref="antibodypreps",
uselist=False)
reference = db.relationship("Reference",
secondary=Assay.__table__,
backref="antibodypreps",
uselist=False)
class FixationMethod(db.Model, MGIModel):
"""
Fixation Method for Specimen
"""
__tablename__ = "gxd_fixationmethod"
_fixation_key = db.Column(db.Integer, primary_key=True)
fixation = db.Column(db.String())
class EmbeddingMethod(db.Model, MGIModel):
"""
Embedding Method for Specimen
"""
__tablename__ = "gxd_embeddingmethod"
_embedding_key = db.Column(db.Integer, primary_key=True)
embeddingmethod = db.Column(db.String())
class VisualizationMethod(db.Model, MGIModel):
"""
Visualization Method for ProbePrep
"""
__tablename__ = "gxd_visualizationmethod"
_visualization_key = db.Column(db.Integer, primary_key=True)
visualization = db.Column(db.String())
class ProbeSense(db.Model, MGIModel):
"""
Sense for ProbePrep
"""
__tablename__ = "gxd_probesense"
_sense_key = db.Column(db.Integer, primary_key=True)
sense = db.Column(db.String())
class ImagePaneAssoc(db.Model, MGIModel):
__tablename__ = "img_imagepane_assoc"
_assoc_key = db.Column(db.Integer, primary_key=True)
_object_key = db.Column(db.Integer)
_imagepane_key = db.Column(db.Integer,
mgi_fk("img_imagepane._imagepane_key"))
_mgitype_key = db.Column(db.Integer)
isprimary = db.Column(db.Integer)
class MarkerReferenceCache(db.Model, MGIModel):
__tablename__ = "mrk_reference"
_marker_key = db.Column(db.Integer,
mgi_fk("mrk_marker._marker_key"),
primary_key=True)
_refs_key = db.Column(db.Integer,
mgi_fk("bib_refs._refs_key"),
primary_key=True)
class InSituResultStructure(db.Model, MGIModel):
__tablename__ = "gxd_isresultstructure"
_result_key = db.Column(db.Integer,
mgi_fk("gxd_insituresult._result_key"),
primary_key=True)
_structure_key = db.Column(db.Integer,
mgi_fk("gxd_structure._structure_key"),
primary_key=True)
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 GelLaneStructure(db.Model, MGIModel):
__tablename__ = "gxd_gellanestructure"
_gellane_key = db.Column(db.Integer,
mgi_fk("gxd_gellane._gellane_key"),
primary_key=True)
_structure_key = db.Column(db.Integer,
mgi_fk("gxd_structure._structure_key"),
primary_key=True)
class InSituResultImagePane(db.Model, MGIModel):
__tablename__ = "gxd_insituresultimage"
_result_key = db.Column(db.Integer,
mgi_fk("gxd_insituresult._result_key"),
primary_key=True)
_imagepane_key = db.Column(db.Integer,
mgi_fk("img_imagepane._imagepane_key"),
primary_key=True)
class AntibodyMarkerAssoc(db.Model, MGIModel):
__tablename__ = "gxd_antibodymarker"
_antibody_key = db.Column(db.Integer,
mgi_fk("gxd_antibody._antibody_key"),
primary_key=True)
_marker_key = db.Column(db.Integer,
mgi_fk("mrk_marker._marker_key"),
primary_key=True)
class AlleleMutation(db.Model, MGIModel):
__tablename__ = "all_allele_mutation"
_allele_key = db.Column(db.Integer,
mgi_fk("all_allele._allele_key"),
primary_key=True)
_mutation_key = db.Column(db.Integer(),
mgi_fk("voc_term._term_key"),
primary_key=True)
class CVMixin(object):
"""
Mixin for all controlled vocab tables
with shared columns
"""
key = db.Column(db.Integer, primary_key=True)
name = db.Column(db.String())
description = db.Column(db.String())
active = db.Column(db.Boolean)
class ReferenceAssoc(db.Model, MGIModel):
__tablename__ = "mgi_reference_assoc"
_assoc_key = db.Column(db.Integer, primary_key=True)
_refs_key = db.Column(db.Integer, mgi_fk("bib_refs._refs_key"))
_object_key = db.Column(db.Integer)
_mgitype_key = db.Column(db.Integer)
_refassoctype_key = db.Column(db.Integer)
reference = db.relationship("Reference", uselist=False)
class AccessionReference(db.Model,MGIModel):
__tablename__ = "acc_accessionreference"
_accession_key = db.Column(db.Integer,
mgi_fk("acc_accession._accession_key"),
primary_key=True)
_refs_key = db.Column(db.Integer,
mgi_fk("bib_refs._refs_key"),
primary_key=True)
accession = db.relationship("Accession",
uselist=False)
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 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 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 ProbeAlleleStrain(db.Model, MGIModel):
__tablename__ = "prb_allele_strain"
_allele_key = db.Column(db.Integer,
mgi_fk("prb_allele._allele_key"),
primary_key=True)
_strain_key = db.Column(db.Integer(),
mgi_fk("prb_strain._strain_key"),
primary_key=True)
strain = db.relationship("Strain", uselist=False)
