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-rw-r--r--[-rwxr-xr-x]wqflask/utility/AJAX_table.py2
-rw-r--r--wqflask/utility/Plot.py15
-rw-r--r--[-rwxr-xr-x]wqflask/utility/TDCell.py0
-rw-r--r--[-rwxr-xr-x]wqflask/utility/THCell.py0
-rw-r--r--[-rwxr-xr-x]wqflask/utility/__init__.py0
-rw-r--r--[-rwxr-xr-x]wqflask/utility/after.py0
-rw-r--r--[-rwxr-xr-x]wqflask/utility/benchmark.py31
-rw-r--r--[-rwxr-xr-x]wqflask/utility/corr_result_helpers.py0
-rw-r--r--[-rwxr-xr-x]wqflask/utility/db_tools.py0
-rw-r--r--[-rwxr-xr-x]wqflask/utility/formatting.py0
-rw-r--r--[-rwxr-xr-x]wqflask/utility/helper_functions.py0
-rw-r--r--wqflask/utility/logger.py137
-rw-r--r--[-rwxr-xr-x]wqflask/utility/svg.py0
-rw-r--r--[-rwxr-xr-x]wqflask/utility/temp_data.py0
-rw-r--r--wqflask/utility/tools.py86
-rw-r--r--[-rwxr-xr-x]wqflask/utility/webqtlUtil.py0
16 files changed, 234 insertions, 37 deletions
diff --git a/wqflask/utility/AJAX_table.py b/wqflask/utility/AJAX_table.py
index 083d1c0d..d70acfcd 100755..100644
--- a/wqflask/utility/AJAX_table.py
+++ b/wqflask/utility/AJAX_table.py
@@ -68,6 +68,8 @@ class AJAX_table:
workbook = xl.Writer('%s.xls' % (webqtlConfig.TMPDIR+file))
worksheet = workbook.add_worksheet()
+ logger.warning("Creating new MySQLdb cursor (this method is OBSOLETE!)")
+
con = MySQLdb.Connect(db=webqtlConfig.DB_NAME,host=webqtlConfig.MYSQL_SERVER, user=webqtlConfig.DB_USER,passwd=webqtlConfig.DB_PASSWD)
cursor = con.cursor()
diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py
index 063de387..d60e2bb2 100644
--- a/wqflask/utility/Plot.py
+++ b/wqflask/utility/Plot.py
@@ -29,8 +29,6 @@ from __future__ import print_function
import piddle as pid
from pprint import pformat as pf
-print("Lysol")
-
from math import *
import random
import sys, os
@@ -38,14 +36,15 @@ from numarray import linear_algebra as la
from numarray import ones, array, dot, swapaxes
import reaper
-sys.path.append("..")
-print(sys.path)
+# sys.path.append("..") Never in a running webserver
from basicStatistics import corestats
import svg
import webqtlUtil
from base import webqtlConfig
+import utility.logger
+logger = utility.logger.getLogger(__name__ )
def cformat(d, rank=0):
'custom string format'
@@ -297,10 +296,10 @@ def find_outliers(vals):
"""
- print("xerxes vals is:", pf(vals))
+ logger.debug("xerxes vals is:", pf(vals))
if vals:
- #print("vals is:", pf(vals))
+ #logger.debug("vals is:", pf(vals))
stats = corestats.Stats(vals)
low_hinge = stats.percentile(25)
up_hinge = stats.percentile(75)
@@ -313,7 +312,7 @@ def find_outliers(vals):
upper_bound = None
lower_bound = None
- print(pf(locals()))
+ logger.debug(pf(locals()))
return upper_bound, lower_bound
@@ -436,7 +435,7 @@ def plotBoxPlot(canvas, data, offset= (40, 40, 40, 40), XLabel="Category", YLabe
canvas.drawCross(XCoord, plotHeight + yTopOffset - (catMean-Yll)*plotHeight/(Yur - Yll), \
color=pid.blue,size=3)
- #print (catMean, catMedian, cat25per, cat75per)
+ #print(catMean, catMedian, cat25per, cat75per)
pass
XCoord += stepX
diff --git a/wqflask/utility/TDCell.py b/wqflask/utility/TDCell.py
index 8de8e050..8de8e050 100755..100644
--- a/wqflask/utility/TDCell.py
+++ b/wqflask/utility/TDCell.py
diff --git a/wqflask/utility/THCell.py b/wqflask/utility/THCell.py
index dde221b5..dde221b5 100755..100644
--- a/wqflask/utility/THCell.py
+++ b/wqflask/utility/THCell.py
diff --git a/wqflask/utility/__init__.py b/wqflask/utility/__init__.py
index d9856eed..d9856eed 100755..100644
--- a/wqflask/utility/__init__.py
+++ b/wqflask/utility/__init__.py
diff --git a/wqflask/utility/after.py b/wqflask/utility/after.py
index a3bb85e9..a3bb85e9 100755..100644
--- a/wqflask/utility/after.py
+++ b/wqflask/utility/after.py
diff --git a/wqflask/utility/benchmark.py b/wqflask/utility/benchmark.py
index d5b32703..8c97370d 100755..100644
--- a/wqflask/utility/benchmark.py
+++ b/wqflask/utility/benchmark.py
@@ -3,34 +3,39 @@ from __future__ import print_function, division, absolute_import
import collections
import inspect
import time
+from utility.tools import LOG_BENCH
+from utility.logger import getLogger
+logger = getLogger(__name__ )
class Bench(object):
entries = collections.OrderedDict()
- def __init__(self, name=None):
+ def __init__(self, name=None, write_output=True):
self.name = name
+ self.write_output = write_output
def __enter__(self):
- if self.name:
- print("Starting benchmark: %s" % (self.name))
- else:
- print("Starting benchmark at: %s [%i]" % (inspect.stack()[1][3], inspect.stack()[1][2]))
+ if self.write_output:
+ if self.name:
+ logger.debug("Starting benchmark: %s" % (self.name))
+ else:
+ logger.debug("Starting benchmark at: %s [%i]" % (inspect.stack()[1][3], inspect.stack()[1][2]))
self.start_time = time.time()
def __exit__(self, type, value, traceback):
- if self.name:
- name = self.name
- else:
- name = "That"
-
time_taken = time.time() - self.start_time
- print(" %s took: %f seconds" % (name, (time_taken)))
+ if self.write_output:
+ if self.name:
+ name = self.name
+ else:
+ name = "That"
+
+ logger.info(" %s took: %f seconds" % (name, (time_taken)))
if self.name:
Bench.entries[self.name] = Bench.entries.get(self.name, 0) + time_taken
-
@classmethod
def report(cls):
total_time = sum((time_taken for time_taken in cls.entries.itervalues()))
@@ -42,4 +47,4 @@ class Bench(object):
def reset(cls):
"""Reset the entries"""
- cls.entries = collections.OrderedDict() \ No newline at end of file
+ cls.entries = collections.OrderedDict()
diff --git a/wqflask/utility/corr_result_helpers.py b/wqflask/utility/corr_result_helpers.py
index ef644d85..ef644d85 100755..100644
--- a/wqflask/utility/corr_result_helpers.py
+++ b/wqflask/utility/corr_result_helpers.py
diff --git a/wqflask/utility/db_tools.py b/wqflask/utility/db_tools.py
index 4034f39c..4034f39c 100755..100644
--- a/wqflask/utility/db_tools.py
+++ b/wqflask/utility/db_tools.py
diff --git a/wqflask/utility/formatting.py b/wqflask/utility/formatting.py
index e53dda22..e53dda22 100755..100644
--- a/wqflask/utility/formatting.py
+++ b/wqflask/utility/formatting.py
diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py
index 15f60765..15f60765 100755..100644
--- a/wqflask/utility/helper_functions.py
+++ b/wqflask/utility/helper_functions.py
diff --git a/wqflask/utility/logger.py b/wqflask/utility/logger.py
new file mode 100644
index 00000000..86ee1c52
--- /dev/null
+++ b/wqflask/utility/logger.py
@@ -0,0 +1,137 @@
+# 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.
+#
+# All behaviour is defined here. Global settings (defined in
+# default_settings.py).
+#
+# To use logging and settings put this at the top of a module:
+#
+# import utility.logger
+# logger = utility.logger.getLogger(__name__ )
+#
+# To override global behaviour set the LOG_LEVEL in default_settings.py
+# or use an environment variable, e.g.
+#
+# env LOG_LEVEL=INFO ./bin/genenetwork2
+#
+# To override log level for a module replace that with, for example,
+#
+# import logging
+# import utility.logger
+# logger = utility.logger.getLogger(__name__,level=logging.DEBUG)
+#
+# We'll add more overrides soon.
+
+import logging
+import string
+from inspect import isfunction
+from pprint import pformat as pf
+from inspect import stack
+
+from utility.tools import LOG_LEVEL, LOG_LEVEL_DEBUG, LOG_SQL, LOG_FORMAT
+
+class GNLogger:
+ """A logger class with some additional functionality, such as
+ multiple parameter logging, SQL logging, timing, colors, and lazy
+ functions.
+
+ """
+
+ def __init__(self,name):
+ self.logger = logging.getLogger(name)
+
+ def setLevel(self,value):
+ """Set the undelying log level"""
+ self.logger.setLevel(value)
+
+ def debug(self,level=0,*args):
+ """Call logging.debug for multiple args. Use level=num to filter on
+LOG_LEVEL_DEBUG.
+
+ """
+ if level <= LOG_LEVEL_DEBUG:
+ self.collect(self.logger.debug,*args)
+
+ def info(self,*args):
+ """Call logging.info for multiple args"""
+ self.collect(self.logger.info,*args)
+
+ def warning(self,*args):
+ """Call logging.warning for multiple args"""
+ self.collect(self.logger.warning,*args)
+ self.logger.warning(self.collect(*args))
+
+ def error(self,*args):
+ """Call logging.error for multiple args"""
+ self.collect(self.logger.error,*args)
+
+ def infof(self,*args):
+ """Call logging.info for multiple args lazily"""
+ # only evaluate function when logging
+ if self.logger.getEffectiveLevel() < 30:
+ self.collectf(self.logger.debug,*args)
+
+ def debugf(self,level=0,*args):
+ """Call logging.debug for multiple args lazily"""
+ # only evaluate function when logging
+ if level <= LOG_LEVEL_DEBUG:
+ if self.logger.getEffectiveLevel() < 20:
+ self.collectf(self.logger.debug,*args)
+
+ def sql(self, sqlcommand, fun = None):
+ """Log SQL command, optionally invoking a timed fun"""
+ if LOG_SQL:
+ caller = stack()[1][3]
+ if caller in ['fetchone','fetch1','fetchall']:
+ caller = stack()[2][3]
+ self.info(caller,sqlcommand)
+ if fun:
+ result = fun(sqlcommand)
+ if LOG_SQL:
+ self.info(result)
+ return result
+
+ def collect(self,fun,*args):
+ """Collect arguments and use fun to output"""
+ out = "."+stack()[2][3]
+ for a in args:
+ if len(out)>1:
+ out += ": "
+ if isinstance(a, str):
+ out = out + a
+ else:
+ out = out + pf(a,width=160)
+ fun(out)
+
+ def collectf(self,fun,*args):
+ """Collect arguments and use fun to output one by one"""
+ out = "."+stack()[2][3]
+ for a in args:
+ if len(out)>1:
+ out += ": "
+ if isfunction(a):
+ out += a()
+ else:
+ if isinstance(a, str):
+ out = out + a
+ else:
+ out = out + pf(a,width=160)
+ fun(out)
+
+# Get the module logger. You can override log levels at the
+# module level
+def getLogger(name, level = None):
+ gnlogger = GNLogger(name)
+ logger = gnlogger.logger
+
+ if level:
+ logger.setLevel(level)
+ else:
+ logger.setLevel(LOG_LEVEL)
+
+ logger.info("Log level of "+name+" set to "+logging.getLevelName(logger.getEffectiveLevel()))
+ return gnlogger
diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py
index 512bc9e6..512bc9e6 100755..100644
--- a/wqflask/utility/svg.py
+++ b/wqflask/utility/svg.py
diff --git a/wqflask/utility/temp_data.py b/wqflask/utility/temp_data.py
index 5bf700c9..5bf700c9 100755..100644
--- a/wqflask/utility/temp_data.py
+++ b/wqflask/utility/temp_data.py
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 11441d7a..bb8241f5 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -5,14 +5,18 @@ import os
import sys
from wqflask import app
+# Use the standard logger here to avoid a circular dependency
+import logging
+logger = logging.getLogger(__name__ )
+
def get_setting(command_id,guess=None):
"""Resolve a setting from the environment or the global settings in
- app.config, with get_valid_path is a function checking whether the
+ app.config, with valid_path is a function checking whether the
path points to an expected directory and returns the full path to
the binary command
guess = os.environ.get('HOME')+'/pylmm'
- get_setting('PYLMM_PATH',guess)
+ valid_path(get_setting('PYLMM_PATH',guess))
first tries the environment variable in +id+, next gets the Flask
app setting for the same +id+ and finally does an educated
@@ -31,23 +35,39 @@ def get_setting(command_id,guess=None):
"""
def value(command):
if command:
- sys.stderr.write("Found path "+command+"\n")
+ # sys.stderr.write("Found "+command+"\n")
return command
else:
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:
+ if command is None or command == "":
# ---- Check whether setting exists in app
command = value(app.config.get(command_id))
- if not command:
+ if command is None:
command = value(guess)
- if not command:
- raise Exception(command_id+' path unknown or faulty (update settings.py?). '+command_id+' should point to the path')
+ if command is None or command == "":
+ print command
+ raise Exception(command_id+' setting unknown or faulty (update default_settings.py?).')
+ logger.debug("Set "+command_id+"="+str(command))
return command
+def get_setting_bool(id):
+ v = get_setting(id)
+ if v not in [0,False,'False','FALSE',None]:
+ return True
+ return False
+
+def get_setting_int(id):
+ v = get_setting(id)
+ if isinstance(v, str):
+ return int(v)
+ if v is None:
+ return 0
+ return v
+
def valid_bin(bin):
if os.path.islink(bin) or valid_file(bin):
return bin
@@ -100,7 +120,7 @@ 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)
@@ -120,18 +140,52 @@ 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():
return valid_path(get_setting("TEMPDIR","/tmp"))
+BLUE = '\033[94m'
+GREEN = '\033[92m'
+BOLD = '\033[1m'
+ENDC = '\033[0m'
+
+def show_settings():
+ from utility.tools import LOG_LEVEL
+
+ print("Set global log level to "+BLUE+LOG_LEVEL+ENDC)
+ log_level = getattr(logging, LOG_LEVEL.upper())
+ logging.basicConfig(level=log_level)
+
+ logger.info(BLUE+"Mr. Mojo Risin 2"+ENDC)
+ print "runserver.py: ****** The webserver has the following configuration ******"
+ keylist = app.config.keys()
+ keylist.sort()
+ for k in keylist:
+ try:
+ print("%s %s%s%s%s" % (k,BLUE,BOLD,get_setting(k),ENDC))
+ except:
+ print("%s %s%s%s%s" % (k,GREEN,BOLD,app.config[k],ENDC))
+
# Cached values
-PYLMM_COMMAND = pylmm_command()
-GEMMA_COMMAND = gemma_command()
-PLINK_COMMAND = plink_command()
-FLAT_FILES = flat_files()
-TEMPDIR = tempdir()
+WEBSERVER_MODE = get_setting('WEBSERVER_MODE')
+GN_SERVER_URL = get_setting('GN_SERVER_URL')
+SQL_URI = get_setting('SQL_URI')
+LOG_LEVEL = get_setting('LOG_LEVEL')
+LOG_LEVEL_DEBUG = get_setting_int('LOG_LEVEL_DEBUG')
+LOG_SQL = get_setting_bool('LOG_SQL')
+LOG_SQLALCHEMY = get_setting_bool('LOG_SQLALCHEMY')
+LOG_BENCH = get_setting_bool('LOG_BENCH')
+LOG_FORMAT = "%(message)s" # not yet in use
+USE_REDIS = get_setting_bool('USE_REDIS')
+USE_GN_SERVER = get_setting_bool('USE_GN_SERVER')
+
+PYLMM_COMMAND = pylmm_command()
+GEMMA_COMMAND = gemma_command()
+PLINK_COMMAND = plink_command()
+FLAT_FILES = flat_files()
+TEMPDIR = tempdir()
diff --git a/wqflask/utility/webqtlUtil.py b/wqflask/utility/webqtlUtil.py
index 4fc978f5..4fc978f5 100755..100644
--- a/wqflask/utility/webqtlUtil.py
+++ b/wqflask/utility/webqtlUtil.py
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 15:15:50 +0000