class ReferenceSequence(db.Model): __bind_key__ = 'symportal_database' __tablename__ = 'dbApp_referencesequence' id = db.Column(db.Integer, primary_key=True) data_set_sample_sequences = db.relationship('DataSetSampleSequence', backref='referencesequence', lazy='select') data_set_sample_sequences_pm = db.relationship('DataSetSampleSequencePM', backref='referencesequence', lazy='select') name = db.Column(db.String(30), default='noName') has_name = db.Column(db.Boolean, default=False) clade = db.Column(db.String(30)) accession = db.Column(db.String(50), nullable=True) sequence = db.Column(db.String(500), nullable=False) def __str__(self): if self.has_name: return self.name else: return f'{self.id}_{self.clade}' def __repr__(self): if self.has_name: return self.name else: return f'{self.id}_{self.clade}'
class DataSetSample(db.Model): __bind_key__ = 'symportal_database' __tablename__ = 'dbApp_datasetsample' id = db.Column(db.Integer, primary_key=True) data_submission_from_id = db.Column(db.Integer, db.ForeignKey('dbApp_dataset.id'), nullable=False) clade_collections = db.relationship('CladeCollection', backref='dataset_sample') data_set_sample_sequences = db.relationship('DataSetSampleSequence', backref='datasetsample') data_set_sample_sequences_pm = db.relationship('DataSetSampleSequencePM', backref='datasetsample') name = db.Column(db.String(200), nullable=False) # This is the absolute number of sequences after make.contigs num_contigs = db.Column(db.Integer, default=0) # store the aboslute number of sequences after inital mothur QC i.e. before tax and size screening post_qc_absolute_num_seqs = db.Column(db.Integer, default=0) # This is the unique number of sequences after inital mothur QC i.e. before tax and size screening post_qc_unique_num_seqs = db.Column(db.Integer, default=0) # Absolute number of sequences after sequencing QC and screening for Symbiodinium (i.e. Symbiodinium only) absolute_num_sym_seqs = db.Column(db.Integer, default=0) # Same as above but the number of unique seqs unique_num_sym_seqs = db.Column(db.Integer, default=0) # store the abosolute number of sequenes that were not considered Symbiodinium non_sym_absolute_num_seqs = db.Column(db.Integer, default=0) # This is the number of unique sequences that were not considered Symbiodinium non_sym_unique_num_seqs = db.Column(db.Integer, default=0) # store the abosulte number of sequences that were lost during the size selection size_violation_absolute = db.Column(db.Integer, default=0) # store the unique number of sequences that were lost during the size screening size_violation_unique = db.Column(db.Integer, default=0) # store the number of absolute sequences remaining after MED post_med_absolute = db.Column(db.Integer, default=0) # store the number of unique sequences remaining after MED (nodes) post_med_unique = db.Column(db.Integer, default=0) error_in_processing = db.Column(db.Boolean, default=False) error_reason = db.Column(db.String(100), nullable=False) cladal_seq_totals = db.Column(db.String(5000), nullable=False) # Meta data for the sample sample_type = db.Column(db.String(50), nullable=False) host_phylum = db.Column(db.String(50), nullable=False) host_class = db.Column(db.String(50), nullable=False) host_order = db.Column(db.String(50), nullable=False) host_family = db.Column(db.String(50), nullable=False) host_genus = db.Column(db.String(50), nullable=False) host_species = db.Column(db.String(50), nullable=False) collection_latitude = db.Column(db.Numeric(11, 8), nullable=False) collection_longitude = db.Column(db.Numeric(11, 8), nullable=False) # do not use the django date field as this causes problems when trying to dump and load the database collection_date = db.Column(db.String(40), nullable=False) # store a string rather than a number as this may be given as a range e.g. 6 - 12 collection_date = db.Column(db.String(40), nullable=False) def __str__(self): return self.name def __repr__(self): return f'<DataSetSample {self.name}>'
class Study(db.Model): __bind_key__ = 'symportal_database' __tablename__ = 'dbApp_study' id = db.Column(db.Integer, primary_key=True) name = db.Column(db.String(100), index=True, unique=True, nullable=False) title = db.Column(db.String(250), nullable=True) is_published = db.Column(db.Boolean, default=False) location = db.Column(db.String(50), nullable=True) run_type = db.Column(db.String(50), default='remote') article_url = db.Column(db.String(250), nullable=True) display_online = db.Column(db.Boolean, default=False) data_url = db.Column(db.String(250), nullable=True) data_explorer = db.Column(db.Boolean, default=False) analysis = db.Column(db.Boolean, default=True) author_list_string = db.Column(db.String(500)) additional_markers = db.Column(db.String(200)) creation_time_stamp = db.Column(db.String(100), default=set_creation_time_stamp_default) data_set_samples = db.relationship('DataSetSample', secondary=Study__DataSetSample, lazy='dynamic', backref=db.backref('studies', lazy='dynamic')) # num_samples = self.get_num_samples() def __str__(self): return self.name def __repr__(self): return f'<Study {self.name}>' def get_num_samples(self): return len(list(self.data_set_samples))
class CladeCollection(db.Model): __bind_key__ = 'symportal_database' __tablename__ = 'dbApp_cladecollection' id = db.Column(db.Integer, primary_key=True) data_set_sample_from_id = db.Column( db.Integer, db.ForeignKey('dbApp_datasetsample.id'), nullable=False) analysis_types = db.relationship('AnalysisType', secondary=cladeCollectionType, backref=db.backref('clade_collections')) data_set_sample_sequences = db.relationship('DataSetSampleSequence', backref='cladecollection') # data_set_sample_from = models.ForeignKey(DataSetSample, on_delete=models.CASCADE, null=True) clade = db.Column(db.String(1), nullable=False) # the method below to get the footprint of the clade_collection_object is incredibly slow. # Hopefully a much faster way will be to store the ID's of the refseqs that make up the footprint # I will therefore store the reference uids in the field below footprint = db.Column(db.String(100000), nullable=False) def __str__(self): return self.datasetsample.name
class DataAnalysis(db.Model): __bind_key__ = 'symportal_database' __tablename__ = 'dbApp_dataanalysis' id = db.Column(db.Integer, primary_key=True) analysis_types = db.relationship('AnalysisType', backref='data_analysis') # This will be a jsoned list of uids of the dataSubmissions that are included in this analysis list_of_data_set_uids = db.Column(db.String(500), nullable=True) # within_clade_cutoff = models.FloatField(default=0.04) within_clade_cutoff = db.Column(db.Float(), nullable=False) name = db.Column(db.String(500), nullable=True) # name = models.CharField(max_length=100, null=True) # description = models.CharField(max_length=5000, null=True) description = db.Column(db.String(5000), nullable=True) time_stamp = db.Column(db.String(100), nullable=False) submitting_user = db.Column(db.String(100), nullable=False) submitting_user_email = db.Column(db.String(100), nullable=False) analysis_complete_time_stamp = db.Column(db.String(100), nullable=False)
class SPDataSet(db.Model): __bind_key__ = 'symportal_database' __tablename__ = 'dbApp_dataset' id = db.Column(db.Integer, primary_key=True) name = db.Column(db.String(30), nullable=False) reference_fasta_database_used = db.Column(db.String(60), nullable=False) submitting_user = db.Column(db.String(100), nullable=False) submitting_user_email = db.Column(db.String(100), nullable=False) working_directory = db.Column(db.String(300), nullable=False) time_stamp = db.Column(db.String(100), nullable=False) loading_complete_time_stamp = db.Column(db.String(100), nullable=False) data_set_samples = db.relationship('DataSetSample', backref='dataset') def __str__(self): return self.name def __repr__(self): return f'<SPDataSet {self.name}>'
class SPUser(db.Model): __bind_key__ = 'symportal_database' __tablename__ = 'dbApp_user' id = db.Column(db.Integer, primary_key=True) name = db.Column(db.String(100), index=True, unique=True, nullable=False) studies = db.relationship('Study', secondary=SPUser__Study, lazy='dynamic', backref=db.backref('users', lazy='dynamic')) # This is set to False when User is created. Upon upload to symportal.org # a user that matches this name will be searched for in the app.db database. # If no matching user if found, an error will be thrown. If a user is found, # This value will be set to true, and the ID of the User in the app.db database # will be stored in app_db_key below. # The id of this object will also be stored in the app.db User object that matches app_db_key_is_set = db.Column(db.Boolean, default=False) app_db_key_id = db.Column(db.Integer, nullable=True) def __repr__(self): return f'<SPUser {self.name}>'