Add a common logger module for logging in different modules.

candis/app/server/api/data.py

@@ -27,6 +27,9 @@
 from candis.app.server.models.pipeline import Pipeline, Cdata
 from candis.app.server.models.user import User
 from candis.app.server.helpers.fileData import modify_data_path
+from logger import get_logger
+
+log = get_logger()
 
 FFORMATS         = JSON.read(os.path.join(R.Path.DATA, 'file-formats.json'))
 ABSPATH_STARTDIR = os.path.abspath(CONFIG.App.STARTDIR)
@@ -101,7 +104,7 @@ def discover_resource(path, level = None, filter_ = None):
     return tree
 
 def log_times(i):
-    print("No. of times tried to connect to NCBI: {}".format(i))
+    log.info("No. of times tried to connect to NCBI: {}".format(i))
 
 @app.route(CONFIG.App.Routes.API.Data.RESOURCE, methods = ['GET', 'POST'])
 @login_required

candis/app/server/app.py

@@ -1,7 +1,7 @@
 # imports - standard imports
 import os
 import sys
-import logging
+# import logging
 
 # imports - third-party imports
 from flask          import Flask
@@ -17,8 +17,9 @@
 from candis.config   import CONFIG
 from candis.resource import R
 from candis.manager.redis.redis import Redis
+from logger import get_logger
 
-log = logging.getLogger(__name__)
+log = get_logger()
 
 app      = Flask(__name__,
     template_folder = R.Path.TEMPLATES,

candis/app/server/models/pipeline.py

@@ -3,7 +3,9 @@
 
 # imports - module imports
 from candis.app.server.app import db
+from logger import get_logger()
 
+log = get_logger()
 
 class Pipeline(db.Model):
     __tablename__ = 'pipeline'
@@ -24,7 +26,7 @@ def add_pipeline(self):
         except Exception as e:
             db.session.rollback()
             db.session.flush()
-            print(e)  # use logging
+            log.error(e)
 
     def delete_pipeline(self):
         try:
@@ -33,7 +35,7 @@ def delete_pipeline(self):
         except Exception as e:
             db.session.rollback()
             db.session.flush()
-            print(e)  # use logging
+            log.error(e)
 
 
     def update_pipeline(self, **kwargs):
@@ -68,7 +70,7 @@ def add_pipeline_run(self):
         except Exception as e:
             db.session.rollback()
             db.session.flush()
-            print(e)  # use logging
+            log.error(e)
 
 class Cdata(db.Model):
     __tablename__ = 'cdata'
@@ -85,7 +87,7 @@ def add_cdata(self):
         except Exception as e:
             db.session.rollback()
             db.session.flush()
-            print(e)  # TODO: use logging
+            log.error(e)
 
     @classmethod
     def get_cdata(cls, id_=None, name=None):

candis/app/server/models/response.py

@@ -7,6 +7,9 @@
 
 # imports - module imports
 from candis.app.server.app import db
+from logger import get_logger()
+
+log = get_logger()
 
 class Response(db.Model):
     __tablename__ = 'response'
@@ -25,7 +28,7 @@ def add_response(self):
         except Exception as e:
             db.session.rollback()
             db.session.flush()
-            print(e)  # use logging
+            log.error(e)
 
     @classmethod
     def get_response(cls, id=None, version=None, status=None):

candis/app/server/models/user.py

@@ -3,6 +3,9 @@
 
 # imports - module imports
 from candis.app.server.app import db
+from logger import get_logger()
+
+log = get_logger()
 
 class User(db.Model):
     __tablename__ = 'users'
@@ -26,7 +29,7 @@ def add_user(self):
         except Exception as e:
             db.session.rollback()
             db.session.flush()
-            print(e)  # use logging
+            log.error(e)
 
     @classmethod
     def get_user(cls, id_=None, username=None, email=None):
@@ -46,7 +49,7 @@ def delete_user(cls, id_=None, username=None, email=None):
         except Exception as e:
             db.session.rollback()
             db.session.flush()
-            print(e)  # use logging
+            log.error(e)
 
     def _encrypt(self, pswd):
         return generate_password_hash(pswd)

candis/data/GEO/api.py

@@ -7,6 +7,9 @@
 
 # imports - module imports
 from candis.util import assign_if_none
+from logger import get_logger()
+
+log = get_logger()
 
 class API():
     def __init__(self, path='', ftype='suppl'):
@@ -24,7 +27,7 @@ def _ftp_connect(self, host, usr=None, pswd=None):
     def _ftp_close(self):
         if isinstance(self.ftp, FTP):
             self.ftp.quit()
-            print("Closed successfully!")
+            log.info("Closed successfully!")
         self.ftp = None
 
     def raw_data(self, ftp_link, series_accession, path=None):
@@ -50,12 +53,12 @@ def raw_data(self, ftp_link, series_accession, path=None):
         file_path = os.path.join(self.path, tar_file)
 
         with open(file_path, 'wb') as f:
-            print("\n Downloading {} at {} \n".format(tar_file, os.path.abspath(self.path)))
+            log.info("\n Downloading {} at {} \n".format(tar_file, os.path.abspath(self.path)))
             try:
                 self.ftp.retrbinary('RETR '+ file_name, f.write)
-                print("Downloaded!")
+                log.info("Downloaded!")
             except EOFError:
-                print("Connection closed, couldn't download")
+                log.error("Connection closed, couldn't download")
             except Exception as e:
-                print("Error {}".format(e))
+                log.error("Error {}".format(e))
             self._ftp_close()

candis/data/entrez/api.py

@@ -13,6 +13,9 @@
 from candis.util import validate_email
 from candis.config import CONFIG
 from candis.manager import Redis
+from logger import get_logger()
+
+log = get_logger()
 
 def sanitize_response(response, type_ = 'json'):
     if type_ == 'json':
@@ -71,7 +74,7 @@ def __init__(self, email, name = None, api_key = None):
             except ResponseError:
                 # exception caught is custom ResponseError of redis.
                 # TODO: instead of raising exception, give a warning or use logging.captureWarning or log INFO
-                print('redis key "databases" must be a list, refreshing cache.')
+                log.info('redis key "databases" must be a list, refreshing cache.')
             else:
                 return None
 
@@ -168,7 +171,7 @@ def summary(self, db = 'pubmed', id = [], **optional):
         if(optional.get('query_key') and optional.get('WebEnv')):
             if db not in self.databases:
                 raise ValueError('database should be from : {}'.format(self.databases))            
-            # print("Using WebEnv and query_key") - TODO: Use logging instead
+            log.info("Using WebEnv and query_key")
             optional.update({'db': db})
             data = self.request('get', URL.SUMMARY, optional)
             return data

candis/ios/cdata/cdata.py

@@ -26,6 +26,9 @@
 from candis.resource import R
 from candis.util     import assign_if_none
 from candis.ios      import json as JSON
+from logger import get_logger()
+
+log = get_logger()
 
 ATTRIBUTE_TYPES = JSON.read(os.path.join(R.Path.DATA, 'attribute-types.json'))
 
@@ -262,7 +265,7 @@ def to_json(self, buffer_):
                 cnames.append(cname)
             buffer_.update({"cnames": cnames})
         except Exception as e:
-            print(str(e))
+            log.error(str(e))
 
     def to_dict(self):
         data       = self.data.copy()

logger.py

@@ -0,0 +1,23 @@
+# imports - standard imports
+import logging
+
+def get_logger(name=None, logfile=None):
+    logging.basicConfig()
+    logger = logging.getLogger(name or __name__)
+    logger.setLevel(logging.DEBUG)
+    logger.propagate = False
+
+    if not logger.handlers:
+        formatter = logging.Formatter("%(asctime)s | {%(pathname)s:%(lineno)d - %(funcName)s} %(levelname)s %(message)s", "%H:%M:%S")
+
+        fileHandler   = logging.FileHandler(logfile or 'candis.log', mode='a')
+        fileHandler.setFormatter(formatter)
+        logger.addHandler(fileHandler)
+
+        formatter = logging.Formatter("%(asctime)s | %(message)s", "%H:%M:%S")
+
+        handler   = logging.StreamHandler()
+        handler.setFormatter(formatter)
+        logger.addHandler(handler)
+
+    return logger