Beta

Docker/app/cbio_client.py

@@ -35,7 +35,7 @@ PORT = conf.PORT
 CON_TIMEOUT = conf.CON_TIMEOUT
 
 # END
-ID = os.environ.get('ID', 754)
+ID = os.environ.get('ID', 52)
 HOST = os.environ.get('DBHOST', 'test')
 
 DB_INTERFACE = None
@@ -115,7 +115,7 @@ def process_by_meta_files(meta_files, study, tmp_id_study, samples):
             if metadata_type == 'SAMPLE_ATTRIBUTES':
                 Sample(metadata, study, samples).process()
             if metadata_type == 'CANCER_TYPE':
-                Cancer_type(metadata, study).process()
+                CancerType(metadata, study).process()
 
     if len(mut) != 0:
         CaseList(study, 'sequenced', 'Mutations all', 'All samples with mutations', mut).process()
@@ -199,6 +199,7 @@ def import_data(studies):
     Import studies
     :return: void
     """
+
     for study in list(studies.values()):
         command = 'cbioportalImporter.py -s ./' + study['name']
         import subprocess
@@ -237,6 +238,9 @@ def main():
     Get all samples for each studies and then remove samples which user did not select.
     Then we can apply parallel processing for each study.
     """
+
+    logging.debug('----- Hello world / Ahoj svete ----- ')
+
     if imported():
         exit(0)
     DB_INTERFACE.start_initialization()
@@ -245,6 +249,7 @@ def main():
     study_dic = {}
 
     tmp_id = str(ID)
+
     all_samples = ApiHandler.call(APPLICATION + TMP + '/' + tmp_id + PDXMODELS, 'pdxmodels for tmplist: ' + tmp_id)
     for study in studies:
         all_samples_for_study = ApiHandler.call(APPLICATION + STUDY + '/' + study['name'] + PDXMODELS,