def get_predictions(db, result_uuid, sort_max_value, limit, offset):
"""
Get predictions of a result with specified properties.
:param db: Database Connection
:param result_uuid: str: uuid of the custom_result to search.
:param sort_max_value: boolean: true if we should sort by max prediction else sort by seq idx.
:param limit: int: how many predictions to return
:param offset: int: offset into results to allow paging
:return: [dict]: list of prediction properties
"""
result = []
query, params = CustomResultData.get_prediction_query_and_params(result_uuid, sort_max_value,
limit, offset)
for row in read_database(db, query, params):
name, max_value, pred, sequence = row
if not sequence:
sequence = SEQUENCE_NOT_FOUND
if CustomResultData.is_none_prediction_values(pred):
pred = []
result.append({
'name': name,
'max': str(max_value),
'values': pred,
'sequence': sequence
})
return result
def get_predictions(db, result_uuid, sort_max_value, limit, offset):
"""
Get predictions of a result with specified properties.
:param db: Database Connection
:param result_uuid: str: uuid of the custom_result to search.
:param sort_max_value: boolean: true if we should sort by max prediction else sort by seq idx.
:param limit: int: how many predictions to return
:param offset: int: offset into results to allow paging
:return: [dict]: list of prediction properties
"""
result = []
query, params = CustomResultData.get_prediction_query_and_params(result_uuid, sort_max_value,
limit, offset)
for row in read_database(db, query, params):
name, max_value, pred, sequence = row
if not sequence:
sequence = SEQUENCE_NOT_FOUND
if CustomResultData.is_none_prediction_values(pred):
pred = []
result.append({
'name': name,
'max': str(max_value),
'values': pred,
'sequence': sequence
})
return result
def find(db, sequence_id, model_name):
"""
Find custom results with the sequence_id and optionally model_name.
:param db: Database Connection
:param sequence_id: str: uuid of the custom sequence to search for
:param model_name: str: name of the model to search for, None if for all model names
:return: [dict]: array of custom result info
"""
try:
val = uuid.UUID(sequence_id, version=4)
except ValueError:
raise ClientException(message="Sequence id is not a valid uuid", error_type=ErrorType.INVALID_SEQUENCE_ID)
select_sql = "select custom_result.id, custom_result.model_name from custom_result " \
" inner join job on job.id = job_id " \
" where seq_id = %s"
params = [sequence_id]
if model_name:
select_sql += " and custom_result.model_name = %s"
params.append(model_name)
result = []
for row in read_database(db, select_sql, params):
values = {
'resultId': row[0],
'modelName': row[1],
'sequenceId': sequence_id,
}
result.append(values)
return result
def bed_file_contents(db, result_id):
select_sql = "select name, start, stop, value from custom_result_row " \
" where result_id = %s"
result = ""
for row in read_database(db, select_sql, [result_id]):
name, start, stop, value = row
line = '\t'.join([name, str(start), str(stop), str(value)])
result += line + '\n'
return result
def bed_file_contents(db, result_id):
select_sql = "select name, start, stop, value from custom_result_row " \
" where result_id = %s"
result = ""
for row in read_database(db, select_sql, [result_id]):
name, start, stop, value = row
line = '\t'.join([name, str(start), str(stop), str(value)])
result += line + '\n'
return result
def load(self, db):
"""
Load self.contents from the database based on self.seq_uuid.
:param db: database connection
"""
rows = read_database(db, "select data, created, title from sequence_list where id = %s", [self.seq_uuid])
if not rows:
raise KeyError("Unable to find sequence for {}".format(self.seq_uuid))
first_row = rows[0]
self.content = first_row[0]
self.created = first_row[1]
self.title = first_row[2]
def load(self, db):
"""
Load self.contents from the database based on self.seq_uuid.
:param db: database connection
"""
rows = read_database(db, "select data, created, title from sequence_list where id = %s", [self.seq_uuid])
if not rows:
raise KeyError("Unable to find sequence for {}".format(self.seq_uuid))
first_row = rows[0]
self.content = first_row[0]
self.created = first_row[1]
self.title = first_row[2]
def determine_last_page(db, result_uuid, per_page):
"""
Determine what the last page in for the specified result_uuid given per_page
:param db: database connection
:param result_uuid: str: uuid of the custom result to query
:param per_page: int: how many items are there per page
:return: int: which page is the last
"""
query, params = CustomResultData.last_page_query_and_params(result_uuid)
rows = read_database(db, query, params)
first_row = rows[0]
items = float(first_row[0])
return int(math.ceil(items / per_page))
def find_one(db, sequence_id, model_name):
"""
Find a single custom result for the specified sequence
:param db: Database Connection
:param sequence_id: str: uuid of the custom sequence to search for
:param model_name: str: name of the model to search for
:return: int value of custom_result or None if not found
"""
select_sql = "select custom_result.id from custom_result " \
" inner join job on job.id = job_id " \
" where seq_id = %s and custom_result.model_name = %s"
for row in read_database(db, select_sql, [sequence_id, model_name]):
return row[0]
return None
def find_one(db, sequence_id, model_name):
"""
Find a single custom result for the specified sequence and model
:param db: Database Connection
:param sequence_id: str: uuid of the custom sequence to search for
:param model_name: str: name of the model to search for
:return: int value of custom_result or None if not found
"""
select_sql = "select custom_result.id from custom_result " \
" inner join job on job.id = job_id " \
" where seq_id = %s and custom_result.model_name = %s"
for row in read_database(db, select_sql, [sequence_id, model_name]):
return row[0]
return None
def find_existing_job(db, job_type, sequence_list, model_name):
"""
Find a single job for the specified properties.
:param db: DatabaseConnection: database to read
:param job_type: str: type of job we are looking for
:param sequence_list: str: uuid of sequence
:param model_name: str: name of the model
:return: CustomJob or None if not found
"""
select_sql = "select id, {} from job " \
" WHERE seq_id = %s and type = %s and model_name = %s".format(CustomJob.NON_KEY_FIELDS)
params = [sequence_list, job_type, model_name]
for row in read_database(db, select_sql, params):
job = CustomJob(row[0])
job._load_non_key(row[1:])
return job
return None
def find_existing_job(db, job_type, sequence_list, model_name):
"""
Find a single job for the specified properties.
:param db: DatabaseConnection: database to read
:param job_type: str: type of job we are looking for
:param sequence_list: str: uuid of sequence
:param model_name: str: name of the model
:return: CustomJob or None if not found
"""
select_sql = "select id, {} from job " \
" WHERE seq_id = %s and type = %s and model_name = %s".format(CustomJob.NON_KEY_FIELDS)
params = [sequence_list, job_type, model_name]
for row in read_database(db, select_sql, params):
job = CustomJob(row[0])
job._load_non_key(row[1:])
return job
return None
def custom_result_sequence_lookup(db, result_id):
"""
Returns name to DNA Sequence dictionary based on the sequence used in a custom result
:param db: Database Connection
:param result_id: uuid of the result we want to lookup
:return: dict: name -> DNA sequence(str)
"""
select_sql = "select sequence_list_item.name, sequence_list_item.sequence " \
"from custom_result " \
"inner join job on job.id = job_id " \
"inner join sequence_list_item on sequence_list_item.seq_id = job.seq_id " \
"where custom_result.id = %s;"
name_to_dna_seq = {}
for row in read_database(db, select_sql, [result_id]):
name, sequence = row
name_to_dna_seq[name] = sequence
return name_to_dna_seq
def bed_file_contents(db, result_id):
"""
Returns bed file contents given a custom result id.
Bed file is just tsv with columns name, start, stop, value, dna sequence
:param db: Database Connection
:param result_id: uuid of the result we want to lookup
:return: str: bed file contents
"""
sequence_lookup = CustomResultData.custom_result_sequence_lookup(db, result_id)
select_sql = "select name, start, stop, value from custom_result_row " \
" where result_id = %s"
result = ""
for row in read_database(db, select_sql, [result_id]):
name, start, stop, value = row
full_dna_sequence = sequence_lookup.get(name)
dna_sequence = full_dna_sequence[start:stop]
line = '\t'.join([name, str(start), str(stop), str(value), dna_sequence])
result += line + '\n'
return result
def find_jobs(db, job_status):
"""
Find jobs with optional job_status filter.
:param db: DatabaseConnection: database to read
:param job_status: str: JobStatus property to filter by
:return: [CustomJob] jobs found
"""
result = []
select_sql = "select id, {} from job".format(CustomJob.NON_KEY_FIELDS)
params = []
if job_status:
select_sql += " WHERE status = %s"
params.append(job_status)
select_sql += " order by created "
for row in read_database(db, select_sql, params):
job = CustomJob(row[0])
job._load_non_key(row[1:])
result.append(job)
return result
def find_jobs(db, job_status):
"""
Find jobs with optional job_status filter.
:param db: DatabaseConnection: database to read
:param job_status: str: JobStatus property to filter by
:return: [CustomJob] jobs found
"""
result = []
select_sql = "select id, {} from job".format(CustomJob.NON_KEY_FIELDS)
params = []
if job_status:
select_sql += " WHERE status = %s"
params.append(job_status)
select_sql += " order by created "
for row in read_database(db, select_sql, params):
job = CustomJob(row[0])
job._load_non_key(row[1:])
result.append(job)
return result
def load(self, db):
select_sql = "select {} from job where id = %s".format(
self.NON_KEY_FIELDS)
rows = read_database(db, select_sql, [self.uuid])
self._load_non_key(rows[0])
def load(self, db):
select_sql = "select {} from job where id = %s".format(self.NON_KEY_FIELDS)
rows = read_database(db, select_sql, [self.uuid])
self._load_non_key(rows[0])