orchestrator_1 just runs redcap gear

orchestrator_1.py

@@ -4,6 +4,8 @@
 import flywheel
 import sys
 
+log = logging.getLogger(__name__)
+logging.basicConfig(level=logging.INFO)
 
 def run_gear(gear, inputs, config, dest, tags=None):
     """Submits a job with specified gear and inputs.
@@ -27,91 +29,19 @@ def run_gear(gear, inputs, config, dest, tags=None):
     except flywheel.rest.ApiException:
         log.exception('An exception was raised when attempting to submit a job for %s', file_obj.name)
 
-logging.basicConfig(level=logging.INFO)
-log = logging.getLogger('root')
-
-fw = flywheel.Client(os.environ['FW_API_KEY'])
-redcap_api_key = os.environ.get('REDCAP_API_KEY')
-redcap_gear = fw.lookup('gears/wbhi-redcap')
-deid_gear = fw.lookup('gears/deid-export')
-
-ignore_until_n_days_old = 1
-site_list = ['ucsb', 'uci']
-wbhi_project_path = 'wbhi/wbhi'
-wbhi_project = fw.lookup(wbhi_project_path)
-deid_config = {
-    'project_path': wbhi_project_path,
-    'overwrite_files': True,
-}
-
-# Run redcap gear in each site's project
-redcap_job_list = []
-for site in site_list:
-    source_project_path = site + '/Inbound Data'
-    #source_project_path = 'joe_test/ucsb_copy3'
-    source_project = fw.lookup(source_project_path)
-    deid_template = source_project.get_file('deid_profile.yaml')
-    deid_inputs = {'deid_profile': deid_template}
+def main():
+    client = flywheel.Client(os.environ['FW_API_KEY']) 
+    redcap_api_key = os.environ.get('REDCAP_API_KEY')
 
+    redcap_gear = client.lookup('gears/wbhi-redcap')
+    pre_deid_project = client.lookup('wbhi/pre-deid')
     redcap_config = {
         'redcap_api_key': redcap_api_key,
-        'ignore_until_n_days_old': ignore_until_n_days_old
+        'ignore_until_n_days_old': 1
     }
-    redcap_job_id = run_gear(redcap_gear, None, redcap_config, source_project)
-    redcap_job_list.append((site, redcap_job_id))
-
-# Run deid gear after completion of redcap gear for each site
-deid_jobs_all = []
-for site, redcap_job_id in redcap_job_list:
-    start = time.time()
-    while fw.get_job(redcap_job_id).state.name in ('PENDING', 'RUNNING'): 
-        time.sleep(5)
-    end = time.time()
-    print(end - start)
-    if fw.get_job(redcap_job_id).state.name != 'COMPLETE':
-        print(f'wbhi-redcap gear failed for {site}')
-        continue
-
-    to_deid_list =  [s for s in source_project.sessions() if 'wbhi' in s.tags and 'deid-wbhi' not in s.tags]
-    deid_jobs = []
 
-    for session in to_deid_list:
-        deid_job_id = run_gear(deid_gear, deid_inputs, deid_config, session)
-        deid_jobs.append((deid_job_id, session))
-    deid_jobs_all.append((site, deid_jobs))
-
-# Wait for completeion of deid jobs and tag 'deid-wbhi'  
-for site, deid_jobs in deid_jobs_all:
-    for job_id, session in deid_jobs:
-        start = time.time()
-        while fw.get_job(redcap_job_id).state.name in ('PENDING', 'RUNNING'):
-            time.sleep(5)
-        end = time.time()
-        print(end - start)
-        if fw.get_job(redcap_job_id).state.name != 'COMPLETE':
-            print(f'deid gear failed for {job_id}')
-            continue
-        else:
-            session.add_tag('deid-wbhi')
-
-# Wait for completion of all jobs in wbhi project
-start = time.time()
-while True:
-    time.sleep(30)
-    jobs = fw.get_current_user_jobs()['jobs']
-    wbhi_jobs = [j for j in jobs if 'wbhi' in j.related_container_ids]
-    current_wbhi_jobs = [j.state for j in wbhi_jobs if j.state not in ('complete', 'failed')]
-    print(current_wbhi_jobs)
-    if not current_wbhi_jobs:
-        break
-end = time.time()
-print(end - start)
+    run_gear(redcap_gear, None, redcap_config, pre_deid_project)
 
-# Run bids-pre-curate gear
-wbhi_subs = wbhi_project.subjects()
-wbhi_subs_no_precurate = [s for s in wbhi_subs if 'pre-curate' not in s.tags]
 
-
-
-
-
+if __name__ == "__main__":
+    main()