def get_project_read_count(project_igf_id,
session_class,
run_attribute_name='R1_READ_COUNT',
active_status='ACTIVE'):
'''
A utility method for fetching sample read counts for an input project_igf_id
:param project_igf_id: A project_igf_id string
:param session_class: A db session class object
:param run_attribute_name: Attribute name from Run_attribute table for read count lookup
:param active_status: text label for active runs, default ACTIVE
:returns: A pandas dataframe containing following columns
project_igf_id
sample_igf_id
flowcell_id
attribute_value
'''
try:
read_count = pd.DataFrame()
pr = ProjectAdaptor(**{'session_class': session_class})
pr.start_session()
query=pr.session.query(Project.project_igf_id,
Sample.sample_igf_id,
Seqrun.flowcell_id,
Run_attribute.attribute_value).\
join(Sample,Project.project_id==Sample.project_id).\
join(Experiment,Sample.sample_id==Experiment.sample_id).\
join(Run,Experiment.experiment_id==Run.experiment_id).\
join(Seqrun,Seqrun.seqrun_id==Run.seqrun_id).\
join(Run_attribute,Run.run_id==Run_attribute.run_id).\
filter(Project.project_igf_id==project_igf_id).\
filter(Sample.project_id==Project.project_id).\
filter(Experiment.sample_id==Sample.sample_id).\
filter(Run.experiment_id==Experiment.experiment_id).\
filter(Seqrun.seqrun_id==Run.seqrun_id).\
filter(Run_attribute.run_id==Run.run_id).\
filter(Run_attribute.attribute_name==run_attribute_name).\
filter(Run.status==active_status).\
filter(Experiment.status==active_status).\
filter(Sample.status==active_status)
results = pr.fetch_records(query=query)
pr.close_session()
if len(results.index) > 0:
read_count = results
return read_count
except:
raise
def get_seqrun_info_for_project(project_igf_id, session_class):
'''
A utility method for fetching seqrun_igf_id and flowcell_id which are linked
to a specific project_igf_id
required params:
project_igf_id: A project_igf_id string
session_class: A db session class object
returns a pandas dataframe containing following columns
seqrun_igf_id
flowcell_id
'''
try:
seqrun_info = pd.DataFrame()
pr = ProjectAdaptor(**{'session_class': session_class})
pr.start_session()
query=pr.session.query(distinct(Seqrun.seqrun_igf_id).\
label('seqrun_igf_id'),
Seqrun.flowcell_id).\
join(Run,Seqrun.seqrun_id==Run.seqrun_id).\
join(Experiment,Experiment.experiment_id==Run.experiment_id).\
join(Sample,Sample.sample_id==Experiment.sample_id).\
join(Project,Project.project_id==Sample.project_id).\
filter(Project.project_id==Sample.project_id).\
filter(Sample.sample_id==Experiment.sample_id).\
filter(Experiment.experiment_id==Run.experiment_id).\
filter(Run.seqrun_id==Seqrun.seqrun_id).\
filter(Project.project_igf_id==project_igf_id)
results = pr.fetch_records(query=query)
pr.close_session()
if len(results.index) > 0:
seqrun_info = results
return seqrun_info
except:
raise