def output(self):
return {
'out1': S3Target(self.bucket + self.outputfile1),
'out2': S3Target(self.bucket + self.outputfile2)
}
def output(self):
#task_uuid = self.get_task_uuid()
#return luigi.LocalTarget('%s/consonance-jobs/RNASeq_3_1_x_Coordinator/fastq_gz/%s/finished.txt' % (self.tmp_dir, task_uuid))
#return S3Target('s3://cgl-core-analysis-run-touch-files/consonance-jobs/RNASeq_3_1_x_Coordinator/%s/finished.txt' % ( task_uuid))
return S3Target('s3://%s/%s_finished.json' % (self.touch_file_path, self.submitter_sample_id ))
def output(self):
return S3Target(self.bucket + self.outfile)
def output_target(self):
return S3Target(self.s3_path, client=self._get_s3_client())
def save_dockstore_json(self):
#task_uuid = self.get_task_uuid()
#luigi.LocalTarget('%s/consonance-jobs/RNASeq_3_1_x_Coordinator/fastq_gz/%s/dockstore_tool.json' % (self.tmp_dir, task_uuid))
#return S3Target('s3://cgl-core-analysis-run-touch-files/consonance-jobs/RNASeq_3_1_x_Coordinator/%s/dockstore_tool.json' % ( task_uuid))
return S3Target('s3://%s/%s_dockstore_tool.json' % (self.touch_file_path, self.submitter_sample_id ))
def input(self):
return S3Target("s3n://bucket.example.org/wordcount.input")
def output(self):
return S3Target('s3n://bucket.example.org/wordcount.output')
def test_read_no_file(self):
client = S3Client(AWS_ACCESS_KEY, AWS_SECRET_KEY)
client.s3.create_bucket('mybucket')
t = S3Target('s3://mybucket/tempfile', client=client)
with self.assertRaises(FileNotFoundException):
t.open()
def output(self):
"""
We want this Task to write its tokens to a unique location,
defined by the name of the class.
"""
return [S3Target('%s/%s' % (self.output_path, self.__class__.__name__))]
def create(self):
S3Target(self.path, self.s3_client).open('w').close()
def output(self):
#task_uuid = self.get_task_uuid()
#return luigi.LocalTarget('%s/consonance-jobs/RNASeq_3_1_x_Coordinator/fastq_gz/%s/finished.txt' % (self.tmp_dir, task_uuid))
return S3Target('s3://%s/%s_finished.json' %
(self.touch_file_path,
self.sample_name + "_" + self.specimen_type))
def save_dockstore_json(self):
#task_uuid = self.get_task_uuid()
#luigi.LocalTarget('%s/consonance-jobs/RNASeq_3_1_x_Coordinator/fastq_gz/%s/dockstore_tool.json' % (self.tmp_dir, task_uuid))
return S3Target('s3://%s/%s_dockstore_tool.json' %
(self.touch_file_path,
self.sample_name + "_" + self.specimen_type))
