class Project(db.Model):
'''
Represents BMS Genomics Project, where id is BMS ProjectID
'''
id = db.Column(db.VARCHAR(50), primary_key=True)
rnaseq_qc_report = db.Column(db.VARCHAR(255), default=None)
wes_qc_report = db.Column(db.VARCHAR(255), default=None)
xpress_project_id = db.Column(db.INT, default=None)
def to_dict(self):
data = {
'id': self.id,
'rnaseq_qc_report_url': self.rnaseq_qc_report,
'wes_qc_report_url': self.wes_qc_report,
'xpress_project_id': self.xpress_project_id
}
return data
def from_dict(self, data):
for field in ['rnaseq_qc_report', 'wes_qc_report', 'xpress_project_id']:
if field in data:
setattr(self, field, data[field])
def __repr__(self):
return '<Project {}>'.format(self.id)
class Notification(db.Model):
'''
This class/table represents a notification to a user
'''
id = db.Column(db.Integer, primary_key=True)
user = db.Column(db.VARCHAR(12))
batchjob_id = db.Column(db.VARCHAR(45))
seen = db.Column(db.Integer, default=0, nullable=False)
occurred_on = db.Column(db.DATETIME(), default=datetime.utcnow)
def to_dict(self):
data = {
'id': self.id,
'user': self.user,
'batchjob_id': self.batchjob_id,
'seen': self.seen,
'occurred_on': self.occurred_on.isoformat() + 'Z'
}
return data
def from_dict(self, data):
for field in ['user', 'batchjob_id', 'seen', 'occurred_on']:
if field in data:
setattr(self, field, data[field])
def __repr__(self):
return '<Notification {}>'.format(self.id)
class RunToSamples(db.Model):
"""
Model for database table that maps SequencingRuns to Sample IDs
and Project IDs. For now, the Project IDs and Sample IDs are stored
as strings (VARCHAR), in case the Project associated with the Run
does not exist in the database yet.
"""
id = db.Column(db.Integer, primary_key=True)
sequencing_run_id = db.Column(db.Integer, db.ForeignKey('sequencing_run.id'))
sample_id = db.Column(db.VARCHAR(512), default=None)
project_id = db.Column(db.VARCHAR(50), default=None)
def to_dict(self):
return {
'id': self.id,
'sequencing_run_id': self.sequencing_run_id,
'sample_id': self.sample_id,
'project_id': self.project_id
}
def from_dict(self, data):
for field in data:
setattr(self, field, data[field])
def __repr__(self):
return ('<RunToSamples mapping with SequencingRun {}, Sample ID {},'
' and Project ID {}>'.format(self.sequencing_run_id, self.sample_id,
self.project_id))
class ProjectSample(db.Model):
"""
Model to store Sample to Project association. Attributes, such as the read files
(R1, and possibly R2 as well) associated with the Sample, will be in a seperate table.
"""
id = db.Column(db.Integer, primary_key=True)
sample_id = db.Column(db.VARCHAR(100), nullable=False)
project_id = db.Column(db.VARCHAR(50), default=None)
def to_dict(self):
data = {
'id': self.id,
'sample_id': self.sample_id,
'project_id': self.project_id,
'_href': '/api/v0/samples/%s' % self.id
}
return data
def __repr__(self):
return 'ProjectSample object with Sample ID {} and Project ID {}'.format(
self.sample_id, self.project_id)
class BatchJob(db.Model):
'''
Represeents an AWS Batch Job, where id is the AWS Batch Job ID.
If this gets updated, make sure to update in batchEventTrigger-lambda function
'''
id = db.Column(db.VARCHAR(45), primary_key=True)
name = db.Column(db.VARCHAR(255))
command = db.Column(db.VARCHAR(1024))
user = db.Column(db.VARCHAR(12))
submitted_on = db.Column(db.DATETIME(), default=datetime.utcnow)
log_stream_name = db.Column(db.VARCHAR(255))
status = db.Column(db.VARCHAR(15))
viewed = db.Column(db.Integer, default=1, nullable=False)
def to_dict(self):
data = {
'id': self.id,
'name': self.name,
'command': self.command,
'user': self.user,
'submitted_on': self.submitted_on.isoformat() + 'Z',
'log_stream_name': self.log_stream_name,
'status': self.status,
'viewed': self.viewed
}
return data
def from_dict(self, data):
for field in ['log_stream_name']:
if field in data:
setattr(self, field, data[field])
def __repr__(self):
return '<BatchJob {}>'.format(self.id)
class SequencingRun(db.Model):
'''
This class/table represents an Illumina sequencing run
'''
id = db.Column(db.Integer, primary_key=True)
run_date = db.Column(db.DATE)
machine_id = db.Column(db.VARCHAR(25))
run_number = db.Column(db.VARCHAR(5))
flowcell_id = db.Column(db.VARCHAR(25))
experiment_name = db.Column(db.VARCHAR(255))
s3_run_folder_path = db.Column(db.VARCHAR(255))
@staticmethod
def is_data_valid(data):
for field in ['experiment_name', 's3_run_folder_path']:
if field not in data:
return False
return True
def to_dict(self):
data = {
'id': self.id,
'run_date': self.run_date.strftime("%Y-%m-%d"),
'machine_id': self.machine_id,
'run_number': self.run_number,
'flowcell_id': self.flowcell_id,
'experiment_name': self.experiment_name,
's3_run_folder_path': self.s3_run_folder_path
}
return data
def from_dict(self, data):
for field in data:
setattr(self, field, data[field])
def __repr__(self):
return '<SequencingRun {}>'.format(self.id)