From 540926af239735854084ec1cfe06a3bd4fed8977 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sat, 18 Jun 2016 06:24:01 +0000
Subject: Logger: introducing logging

---
 wqflask/utility/logger.py                              |  8 ++++++++
 wqflask/utility/tools.py                               | 15 +++++++++------
 wqflask/wqflask/correlation_matrix/show_corr_matrix.py |  2 +-
 3 files changed, 18 insertions(+), 7 deletions(-)
 create mode 100644 wqflask/utility/logger.py

diff --git a/wqflask/utility/logger.py b/wqflask/utility/logger.py
new file mode 100644
index 00000000..85a64438
--- /dev/null
+++ b/wqflask/utility/logger.py
@@ -0,0 +1,8 @@
+# GeneNetwork logger
+#
+# The standard python logging module is very good. This logger adds a
+# few facilities on top of that. Main one being that it picks up
+# settings for log levels (global and by module) and (potentially)
+# offers some fine grained log levels for the standard levels.
+#
+# Global settings (defined in default_settings.py).
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 6e9f6d4a..d43e2132 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -3,8 +3,12 @@
 
 import os
 import sys
+import logging
 from wqflask import app
 
+logger = logging.getLogger(__name__ )
+logging.basicConfig(level=logging.INFO)
+
 def get_setting(command_id,guess=None):
     """Resolve a setting from the environment or the global settings in
     app.config, with valid_path is a function checking whether the
@@ -37,7 +41,7 @@ def get_setting(command_id,guess=None):
             return None
 
     # ---- Check whether environment exists
-    # sys.stderr.write("Looking for "+command_id+"\n")
+    logger.debug("Looking for "+command_id+"\n")
     command = value(os.environ.get(command_id))
     if not command:
         # ---- Check whether setting exists in app
@@ -46,7 +50,7 @@ def get_setting(command_id,guess=None):
             command = value(guess)
             if not command:
                 raise Exception(command_id+' setting unknown or faulty (update settings.py?).')
-    sys.stderr.write("Set "+command_id+"="+str(command)+"\n")
+    logger.info("Set "+command_id+"="+str(command))
     return command
 
 def valid_bin(bin):
@@ -101,7 +105,7 @@ def locate(name, subdir=None):
     if valid_path(base):
         lookfor = base + "/" + name
         if valid_file(lookfor):
-            print("Found: file "+lookfor+"\n")
+            logger.info("Found: file "+lookfor+"\n")
             return lookfor
         else:
             raise Exception("Can not locate "+lookfor)
@@ -121,9 +125,9 @@ def locate_ignore_error(name, subdir=None):
     if valid_path(base):
         lookfor = base + "/" + name
         if valid_file(lookfor):
-            print("Found: file "+name+"\n")
+            logger.debug("Found: file "+name+"\n")
             return lookfor
-    sys.stderr.write("WARNING: file "+name+" not found\n")
+    logger.info("WARNING: file "+name+" not found\n")
     return None
 
 def tempdir():
@@ -141,4 +145,3 @@ GEMMA_COMMAND      = gemma_command()
 PLINK_COMMAND      = plink_command()
 FLAT_FILES         = flat_files()
 TEMPDIR            = tempdir()
-
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index 5c3354f1..7b67e626 100755
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -21,7 +21,7 @@
 from __future__ import absolute_import, print_function, division
 
 import sys
-sys.path.append(".")
+# sys.path.append(".")   Never do this in a webserver!
 
 import gc
 import string
-- 
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