async def setUpAsync(self):
await super().setUpAsync()
self.job_id_01 = str(uuid.uuid4())
self.job_id_02 = str(uuid.uuid4())
self.job_id_03 = str(uuid.uuid4())
self.date_01 = datetime.datetime.now()
self.date_02 = datetime.datetime.now() - datetime.timedelta(days=2)
self.date_03 = datetime.datetime.now() - datetime.timedelta(days=8)
async with self.app['engine'].acquire() as connection:
await connection.execute(Job.insert().values(
id=self.job_id_01,
query='',
submitted=self.date_01,
status=JOB_STATUS_CHOICES.started))
await connection.execute(Job.insert().values(
id=self.job_id_02,
query='',
submitted=self.date_02,
status=JOB_STATUS_CHOICES.started))
await connection.execute(Job.insert().values(
id=self.job_id_03,
query='',
submitted=self.date_03,
status=JOB_STATUS_CHOICES.started))
async def setUpAsync(self):
await super().setUpAsync()
async with self.app['engine'].acquire() as connection:
self.consumer_ip = get_ip(self.app)
self.consumer_port = '8000'
await connection.execute(Consumer.insert().values(
ip=self.consumer_ip,
status='avaiable',
port=self.consumer_port))
self.job_id = str(uuid.uuid4())
await connection.execute(Job.insert().values(
id=self.job_id,
query='AACAGCATGAGTGCGCTGGATGCTG',
submitted=datetime.datetime.now(),
status=JOB_STATUS_CHOICES.started))
self.job_chunk_id = await connection.scalar(
JobChunk.insert().values(
job_id=self.job_id,
database='mirbase',
submitted=datetime.datetime.now(),
status=JOB_CHUNK_STATUS_CHOICES.started,
consumer=self.consumer_ip))
async def setUpAsync(self):
await super().setUpAsync()
self.job_id = str(uuid.uuid4())
async with self.app['engine'].acquire() as connection:
await connection.execute(
Job.insert().values(
id=self.job_id,
query='AACAGCATGAGTGCGCTGGATGCTG',
submitted=datetime.datetime.now(),
status=JOB_STATUS_CHOICES.started
)
)
await connection.execute(
Consumer.insert().values(ip='192.168.0.2', status=CONSUMER_STATUS_CHOICES.busy)
)
self.job_chunk_id = await connection.scalar(
JobChunk.insert().values(
job_id=self.job_id,
database='mirbase',
submitted=datetime.datetime.now(),
status=JOB_CHUNK_STATUS_CHOICES.pending,
consumer='192.168.0.2'
)
)
async def test_job_priority(self):
job_id3 = str(uuid.uuid4())
async with self.app['engine'].acquire() as connection:
await connection.execute(
Job.insert().values(
id=job_id3,
query='GGACGGAGGCGCGCCCGAGAUGAGUAG',
submitted=datetime.datetime.now(),
priority='high',
status=JOB_STATUS_CHOICES.started
)
)
await connection.scalar(
JobChunk.insert().values(
job_id=job_id3,
database='rfam',
submitted=datetime.datetime.now(),
status=JOB_CHUNK_STATUS_CHOICES.pending
)
)
chunks = await find_highest_priority_jobs(self.app['engine'])
assert len(chunks) == 3
job_id, priority, submitted, database = chunks[0]
assert job_id == job_id3
assert database == 'rfam'
async def setUpAsync(self):
await super().setUpAsync()
self.job_id = str(uuid.uuid4())
self.job_id2 = str(uuid.uuid4())
async with self.app['engine'].acquire() as connection:
await connection.execute(
Job.insert().values(
id=self.job_id,
query='AACAGCATGAGTGCGCTGGATGCTG',
submitted=datetime.datetime.now(),
priority='low',
status=JOB_STATUS_CHOICES.started
)
)
await connection.execute(
Job.insert().values(
id=self.job_id2,
query='CGTGCTGAATAGCTGGAGAGGCTCAT',
submitted=datetime.datetime.now(),
priority='low',
status=JOB_STATUS_CHOICES.started
)
)
self.job_chunk_id1 = await connection.scalar(
JobChunk.insert().values(
job_id=self.job_id,
database='mirbase',
submitted=datetime.datetime.now(),
status=JOB_CHUNK_STATUS_CHOICES.pending
)
)
self.job_chunk_id2 = await connection.scalar(
JobChunk.insert().values(
job_id=self.job_id2,
database='pombase',
submitted=datetime.datetime.now(),
status=JOB_CHUNK_STATUS_CHOICES.pending
)
)
async def setUpAsync(self):
await super().setUpAsync()
async with self.app['engine'].acquire() as connection:
await connection.execute(Job.insert().values(
id=self.job_id,
query='AACAGCATGAGTGCGCTGGATGCTG',
description='',
submitted=datetime.datetime.now(),
status=JOB_STATUS_CHOICES.started))
async def setUpAsync(self):
await super().setUpAsync()
self.job_id = str(uuid.uuid4())
async with self.app['engine'].acquire() as connection:
await connection.execute(Job.insert().values(
id=self.job_id,
query='',
submitted=datetime.datetime.now(),
status=JOB_STATUS_CHOICES.started))
async def setUpAsync(self):
await super().setUpAsync()
consumer_ip = get_ip(self.app)
async with self.app['engine'].acquire() as connection:
await connection.execute(Job.insert().values(
id=self.job_id,
query='AACAGCATGAGTGCGCTGGATGCTG',
description='CATE_ECOLI',
submitted=datetime.datetime.now(),
status=JOB_STATUS_CHOICES.started))
async with self.app['engine'].acquire() as connection:
await connection.execute(Consumer.insert().values(
ip=consumer_ip, status='avaiable', port='8000'))
async def setUpAsync(self):
await super().setUpAsync()
self.consumer_ip = get_ip(self.app)
async with self.app['engine'].acquire() as connection:
await connection.execute(Job.insert().values(
id=self.job_id,
query=
'AGUUACGGCCAUACCUCAGAGAAUAUACCGUAUCCCGUUCGAUCUGCGAAGUUAAGCUCUGAAGGGCGUCGUCAGUACUAUAGUGGGUGACCAUAUGGGAAUACGACGUGCUGUAGCUU',
submitted=datetime.datetime.now(),
status=JOB_STATUS_CHOICES.started))
async with self.app['engine'].acquire() as connection:
await connection.execute(InfernalJob.insert().values(
job_id=self.job_id, ))
async def setUpAsync(self):
await super().setUpAsync()
async with self.app['engine'].acquire() as connection:
await connection.execute(Job.insert().values(
id=self.job_id,
query=
'CACGGUGGGGGCGCGCCGGUCUCCCGGAGCGGGACCGGGUCGGAGGAUGGACGAGAAUCAC',
description='testing',
submitted=datetime.datetime.now(),
status=JOB_STATUS_CHOICES.started))
self.infernal_job_id = await connection.scalar(
InfernalJob.insert().values(
job_id=self.job_id,
submitted=datetime.datetime.now(),
status=JOB_CHUNK_STATUS_CHOICES.pending))
async def setUpAsync(self):
await super().setUpAsync()
self.job_id = str(uuid.uuid4())
async with self.app['engine'].acquire() as connection:
await connection.execute(Job.insert().values(
id=self.job_id,
query='',
submitted=datetime.datetime.now(),
status=JOB_STATUS_CHOICES.started))
self.job_chunk_id1 = await connection.scalar(
JobChunk.insert().values(
job_id=self.job_id,
database='mirbase',
submitted=datetime.datetime.now(),
status=JOB_CHUNK_STATUS_CHOICES.started))
await connection.scalar(JobChunk.insert().values(
job_id=self.job_id,
database='pombase',
submitted=datetime.datetime.now(),
status=JOB_CHUNK_STATUS_CHOICES.started))
await connection.scalar(JobChunkResult.insert().values(
job_chunk_id=self.job_chunk_id1,
rnacentral_id='URS000075D2D2_10090',
description='Mus musculus miR - 1195 stem - loop',
score=6.5,
bias=0.7,
e_value=32,
target_length=98,
alignment=
"Query 8 GAGUUUGAGACCAGCCUGGCCA 29\n| | | | | | | | | | | | | | | | | |\nSbjct_10090\n22\nGAGUUCGAGGCCAGCCUGCUCA\n43",
alignment_length=22,
gap_count=0,
match_count=18,
nts_count1=22,
nts_count2=0,
identity=81.81818181818183,
query_coverage=73.33333333333333,
target_coverage=0,
gaps=0,
query_length=30,
result_id=1))
async def setUpAsync(self):
await super().setUpAsync()
async with self.app['engine'].acquire() as connection:
await connection.execute(Job.insert().values(
id=self.job_id,
query=
'CACGGUGGGGGCGCGCCGGUCUCCCGGAGCGGGACCGGGUCGGAGGAUGGACGAGAAUCAC',
description='testing',
submitted=datetime.datetime.now(),
status=JOB_STATUS_CHOICES.started))
self.infernal_job_id = await connection.scalar(
InfernalJob.insert().values(
job_id=self.job_id,
submitted=datetime.datetime.now(),
status=JOB_CHUNK_STATUS_CHOICES.pending))
self.results = [{
'target_name': 'SSU_rRNA_eukarya',
'accession_rfam': 'RF01960',
'query_name': 'query',
'accession_seq': '-',
'mdl': 'cm',
'mdl_from': 1,
'mdl_to': 609,
'seq_from': 1764,
'seq_to': 2417,
'strand': '+',
'trunc': "3'",
'pipeline_pass': 3,
'gc': 0.56,
'bias': 0.0,
'score': 559.2,
'e_value': 4.6e-167,
'inc': '!',
'description': 'Eukaryotic small subunit ribosomal RNA',
'alignment': ''
}]