def test_seed_new_experiments(self):
pl = PipelineAdaptor(**{'session_class': self.session_class})
pl.start_session()
new_exps,_=\
pl.seed_new_experiments(\
pipeline_name='PrimaryAnalysis',
species_name_list=['HG38'],
fastq_type='demultiplexed_fastq',
)
self.assertEqual(len(new_exps), 1)
self.assertEqual(new_exps[0], 'IGFQ000123_avik_10-4-2018_Miseq')
def find_new_analysis_seeds(dbconfig_path, pipeline_name, project_name_file,
species_name_list, fastq_type,
library_source_list):
'''
A utils method for finding and seeding new experiments for analysis
:param dbconfig_path: A database configuration file
:param slack_config: A slack configuration file
:param pipeline_name:Pipeline name
:param fastq_type: Fastq collection type
:param project_name_file: A file containing the list of projects for seeding pipeline
:param species_name_list: A list of species to consider for seeding analysis
:param library_source_list: A list of library source info to consider for seeding analysis
:returns: List of available experiments or None and a list of seeded experiments or None
'''
try:
available_exps = None
seeded_exps = None
if not os.path.exists(project_name_file):
raise IOError('File {0} not found'.format(project_name_file))
with open(project_name_file, 'r') as fp:
project_list = fp.readlines() # read list of projects from file,
project_list = [i.strip() for i in project_list]
if len(project_list) == 0:
project_list = None
dbparam = read_dbconf_json(dbconfig_path)
pl = PipelineAdaptor(**dbparam)
pl.start_session()
available_exps,seeded_exps=\
pl.seed_new_experiments(\
pipeline_name=pipeline_name,
species_name_list=species_name_list,
fastq_type=fastq_type,
project_list=project_list,
library_source_list=library_source_list
)
pl.close_session()
return available_exps, seeded_exps
except:
raise
def test_seed_new_experiments1(self):
pl = PipelineAdaptor(**{'session_class': self.session_class})
pl.start_session()
new_exps,_=\
pl.seed_new_experiments(\
pipeline_name='PrimaryAnalysis',
species_name_list=['HG38'],
fastq_type='demultiplexed_fastq',
project_list=['IGFQ000123_avik_10-4-2018_Miseq'],
library_source_list=['TRANSCRIPTOMIC_SINGLE_CELL']
)
self.assertFalse(new_exps)
pl.close_session()
pl = PipelineAdaptor(**{'session_class': self.session_class})
pl.start_session()
(_,exp_data)=pl.fetch_pipeline_seed_with_table_data(\
pipeline_name='PrimaryAnalysis',
table_name='experiment',
status='SEEDED')
self.assertEqual(len(list(exp_data['experiment_igf_id'].values)), 1)
self.assertEqual(exp_data['experiment_igf_id'].values[0],
'IGF103923_MISEQ')