Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing

11 files changed, 53 insertions, 891 deletions

diff --git a/wqflask/other_config/dot.pylintrc b/wqflask/other_config/dot.pylintrc
deleted file mode 100644
index 2774300a..00000000
--- a/wqflask/other_config/dot.pylintrc
+++ /dev/null
@@ -1,249 +0,0 @@
-[MASTER]
-
-# Specify a configuration file.
-#rcfile=
-
-# Python code to execute, usually for sys.path manipulation such as
-# pygtk.require().
-#init-hook=
-
-# Profiled execution.
-profile=no
-
-# Add files or directories to the blacklist. They should be base names, not
-# paths.
-ignore=CVS
-
-# Pickle collected data for later comparisons.
-persistent=yes
-
-# List of plugins (as comma separated values of python modules names) to load,
-# usually to register additional checkers.
-load-plugins=
-
-
-[MESSAGES CONTROL]
-
-# Enable the message, report, category or checker with the given id(s). You can
-# either give multiple identifier separated by comma (,) or put this option
-# multiple time.
-#enable=
-
-# Disable the message, report, category or checker with the given id(s). You
-# can either give multiple identifier separated by comma (,) or put this option
-# multiple time (only on the command line, not in the configuration file where
-# it should appear only once).
-#disable=
-
-
-[REPORTS]
-
-# Set the output format. Available formats are text, parseable, colorized, msvs
-# (visual studio) and html
-output-format=colorized
-
-# Include message's id in output
-include-ids=no
-
-# Put messages in a separate file for each module / package specified on the
-# command line instead of printing them on stdout. Reports (if any) will be
-# written in a file name "pylint_global.[txt|html]".
-files-output=no
-
-# Tells whether to display a full report or only the messages
-reports=yes
-
-# Python expression which should return a note less than 10 (10 is the highest
-# note). You have access to the variables errors warning, statement which
-# respectively contain the number of errors / warnings messages and the total
-# number of statements analyzed. This is used by the global evaluation report
-# (RP0004).
-evaluation=10.0 - ((float(5 * error + warning + refactor + convention) / statement) * 10)
-
-# Add a comment according to your evaluation note. This is used by the global
-# evaluation report (RP0004).
-comment=no
-
-
-[MISCELLANEOUS]
-
-# List of note tags to take in consideration, separated by a comma.
-notes=FIXME,XXX,TODO
-
-
-[TYPECHECK]
-
-# Tells whether missing members accessed in mixin class should be ignored. A
-# mixin class is detected if its name ends with "mixin" (case insensitive).
-ignore-mixin-members=yes
-
-# List of classes names for which member attributes should not be checked
-# (useful for classes with attributes dynamically set).
-ignored-classes=SQLObject
-
-# When zope mode is activated, add a predefined set of Zope acquired attributes
-# to generated-members.
-zope=no
-
-# List of members which are set dynamically and missed by pylint inference
-# system, and so shouldn't trigger E0201 when accessed. Python regular
-# expressions are accepted.
-generated-members=REQUEST,acl_users,aq_parent
-
-
-[SIMILARITIES]
-
-# Minimum lines number of a similarity.
-min-similarity-lines=4
-
-# Ignore comments when computing similarities.
-ignore-comments=yes
-
-# Ignore docstrings when computing similarities.
-ignore-docstrings=yes
-
-
-[BASIC]
-
-# Required attributes for module, separated by a comma
-required-attributes=
-
-# List of builtins function names that should not be used, separated by a comma
-bad-functions=map,filter,apply,input
-
-# Regular expression which should only match correct module names
-module-rgx=(([a-z_][a-z0-9_]*)|([A-Z][a-zA-Z0-9]+))$
-
-# Regular expression which should only match correct module level names
-const-rgx=(([A-Z_][A-Z0-9_]*)|(__.*__))$
-
-# Regular expression which should only match correct class names
-class-rgx=[A-Z_][a-zA-Z0-9]+$
-
-# Regular expression which should only match correct function names
-function-rgx=[a-z_][a-z0-9_]{2,30}$
-
-# Regular expression which should only match correct method names
-method-rgx=[a-z_][a-z0-9_]{2,30}$
-
-# Regular expression which should only match correct instance attribute names
-attr-rgx=[a-z_][a-z0-9_]{2,30}$
-
-# Regular expression which should only match correct argument names
-argument-rgx=[a-z_][a-z0-9_]{2,30}$
-
-# Regular expression which should only match correct variable names
-variable-rgx=[a-z_][a-z0-9_]{2,30}$
-
-# Regular expression which should only match correct list comprehension /
-# generator expression variable names
-inlinevar-rgx=[A-Za-z_][A-Za-z0-9_]*$
-
-# Good variable names which should always be accepted, separated by a comma
-good-names=i,j,k,ex,Run,_
-
-# Bad variable names which should always be refused, separated by a comma
-bad-names=foo,bar,baz,toto,tutu,tata
-
-# Regular expression which should only match functions or classes name which do
-# not require a docstring
-no-docstring-rgx=__.*__
-
-
-[VARIABLES]
-
-# Tells whether we should check for unused import in __init__ files.
-init-import=no
-
-# A regular expression matching the beginning of the name of dummy variables
-# (i.e. not used).
-dummy-variables-rgx=_|dummy
-
-# List of additional names supposed to be defined in builtins. Remember that
-# you should avoid to define new builtins when possible.
-additional-builtins=
-
-
-[FORMAT]
-
-# Maximum number of characters on a single line.
-max-line-length=100
-
-# Maximum number of lines in a module
-max-module-lines=1000
-
-# String used as indentation unit. This is usually " " (4 spaces) or "\t" (1
-# tab).
-indent-string='    '
-
-
-[IMPORTS]
-
-# Deprecated modules which should not be used, separated by a comma
-deprecated-modules=regsub,string,TERMIOS,Bastion,rexec
-
-# Create a graph of every (i.e. internal and external) dependencies in the
-# given file (report RP0402 must not be disabled)
-import-graph=
-
-# Create a graph of external dependencies in the given file (report RP0402 must
-# not be disabled)
-ext-import-graph=
-
-# Create a graph of internal dependencies in the given file (report RP0402 must
-# not be disabled)
-int-import-graph=
-
-
-[DESIGN]
-
-# Maximum number of arguments for function / method
-max-args=5
-
-# Argument names that match this expression will be ignored. Default to name
-# with leading underscore
-ignored-argument-names=_.*
-
-# Maximum number of locals for function / method body
-max-locals=15
-
-# Maximum number of return / yield for function / method body
-max-returns=6
-
-# Maximum number of branch for function / method body
-max-branchs=12
-
-# Maximum number of statements in function / method body
-max-statements=50
-
-# Maximum number of parents for a class (see R0901).
-max-parents=7
-
-# Maximum number of attributes for a class (see R0902).
-max-attributes=7
-
-# Minimum number of public methods for a class (see R0903).
-min-public-methods=2
-
-# Maximum number of public methods for a class (see R0904).
-max-public-methods=20
-
-
-[CLASSES]
-
-# List of interface methods to ignore, separated by a comma. This is used for
-# instance to not check methods defines in Zope's Interface base class.
-ignore-iface-methods=isImplementedBy,deferred,extends,names,namesAndDescriptions,queryDescriptionFor,getBases,getDescriptionFor,getDoc,getName,getTaggedValue,getTaggedValueTags,isEqualOrExtendedBy,setTaggedValue,isImplementedByInstancesOf,adaptWith,is_implemented_by
-
-# List of method names used to declare (i.e. assign) instance attributes.
-defining-attr-methods=__init__,__new__,setUp
-
-# List of valid names for the first argument in a class method.
-valid-classmethod-first-arg=cls
-
-
-[EXCEPTIONS]
-
-# Exceptions that will emit a warning when being caught. Defaults to
-# "Exception"
-overgeneral-exceptions=Exception
diff --git a/wqflask/other_config/nginx-old.conf b/wqflask/other_config/nginx-old.conf
deleted file mode 100644
index 65ee768c..00000000
--- a/wqflask/other_config/nginx-old.conf
+++ /dev/null
@@ -1,108 +0,0 @@
-
-#user  nobody;
-worker_processes  1;
-
-#error_log  logs/error.log;
-#error_log  logs/error.log  notice;
-#error_log  logs/error.log  info;
-
-#pid        logs/nginx.pid;
-
-
-events {
-    worker_connections  1024;
-}
-
-
-http {
-    include       mime.types;
-    default_type  application/octet-stream;
-
-    #log_format  main  '$remote_addr - $remote_user [$time_local] "$request" '
-    #                  '$status $body_bytes_sent "$http_referer" '
-    #                  '"$http_user_agent" "$http_x_forwarded_for"';
-
-    #access_log  logs/access.log  main;
-
-    sendfile        on;
-    #tcp_nopush     on;
-
-    #keepalive_timeout  0;
-    keepalive_timeout  65;
-
-    gzip  on;
-
-    server {
-	# Modeled after http://flask.pocoo.org/docs/deploying/wsgi-standalone/
-	listen 80;
-
-    	server_name _;
-
-    	access_log  /var/log/nginx/access.log;
-    	error_log  /var/log/nginx/error.log;
-
-	location ^~ /css/ {
-		root /home/sam/gene/wqflask/wqflask/static/;
-	}
-
-	location ^~ /javascript/ {
-		root /home/sam/gene/wqflask/wqflask/static/;
-	}
-
-#    location ^~ /image/ {
-#		root /home/sam/gene/wqflask/wqflask/static/;
-#	}
-
-	location ^~ /images/ {
-		root /home/sam/gene/wqflask/wqflask/static/;
-	}
-
-    	location / {
-        	proxy_pass         http://127.0.0.1:5000/;
-        	proxy_redirect     off;
-
-        	proxy_set_header   Host             $host;
-        	proxy_set_header   X-Real-IP        $remote_addr;
-        	proxy_set_header   X-Forwarded-For  $proxy_add_x_forwarded_for;
-   	 }
-
-    }
-
-
-    # another virtual host using mix of IP-, name-, and port-based configuration
-    #
-    #server {
-    #    listen       8000;
-    #    listen       somename:8080;
-    #    server_name  somename  alias  another.alias;
-
-    #    location / {
-    #        root   html;
-    #        index  index.html index.htm;
-    #    }
-    #}
-
-
-    # HTTPS server
-    #
-    #server {
-    #    listen       443;
-    #    server_name  localhost;
-
-    #    ssl                  on;
-    #    ssl_certificate      cert.pem;
-    #    ssl_certificate_key  cert.key;
-
-    #    ssl_session_timeout  5m;
-
-    #    ssl_protocols  SSLv2 SSLv3 TLSv1;
-    #    ssl_ciphers  HIGH:!aNULL:!MD5;
-    #    ssl_prefer_server_ciphers   on;
-
-    #    location / {
-    #        root   html;
-    #        index  index.html index.htm;
-    #    }
-    #}
-
-}
diff --git a/wqflask/other_config/nginx_conf/gn2-lei.conf b/wqflask/other_config/nginx_conf/gn2-lei.conf
deleted file mode 100644
index 893ad435..00000000
--- a/wqflask/other_config/nginx_conf/gn2-lei.conf
+++ /dev/null
@@ -1,41 +0,0 @@
-server {
-    # Modeled after http://flask.pocoo.org/docs/deploying/wsgi-standalone/
-    listen 80;
-
-    server_name gn2-lei.genenetwork.org;
-
-    access_log  /var/log/nginx/lei_access.log;
-    error_log  /var/log/nginx/lei_error.log;
-
-    location ^~ /css/ {
-            root /gene/wqflask/wqflask/static/;
-    }
-
-    location ^~ /javascript/ {
-            root /gene/wqflask/wqflask/static/;
-    }
-
-#    location ^~ /image/ {
-#           root /gene/wqflask/wqflask/static/;
-#       }
-
-    location ^~ /images/ {
-            root /gene/wqflask/wqflask/static/;
-    }
-    
-    ### New - added by Sam
-    #location ^~ /static/ {
-    #       root /gene/wqflask/wqflask/static/;
-    #}
-
-    location / {
-            proxy_pass         http://127.0.0.1:5001/;
-            proxy_redirect     off;
-
-            proxy_set_header   Host             $host;
-            proxy_set_header   X-Real-IP        $remote_addr;
-            proxy_set_header   X-Forwarded-For  $proxy_add_x_forwarded_for;
-            
-            proxy_read_timeout 40m;
-    }
-}
diff --git a/wqflask/other_config/nginx_conf/gn2-zach.conf b/wqflask/other_config/nginx_conf/gn2-zach.conf
deleted file mode 100644
index 38347292..00000000
--- a/wqflask/other_config/nginx_conf/gn2-zach.conf
+++ /dev/null
@@ -1,52 +0,0 @@
-server {
-    # Modeled after http://flask.pocoo.org/docs/deploying/wsgi-standalone/
-    listen 80;
-
-    server_name gn2-zach.genenetwork.org;
-
-    access_log  /var/log/nginx/access.log;
-    error_log  /var/log/nginx/error.log;
-
-    location ^~ /css/ {
-            root /gene/wqflask/wqflask/static/;
-    }
-
-    location ^~ /javascript/ {
-            root /gene/wqflask/wqflask/static/;
-    }
-
-#    location ^~ /image/ {
-#           root /gene/wqflask/wqflask/static/;
-#       }
-
-    location ^~ /images/ {
-            root /gene/wqflask/wqflask/static/;
-    }
-    
-    ### New - added by Sam
-    #location ^~ /static/ {
-    #       root /gene/wqflask/wqflask/static/;
-    #}
-
-	location /plink_gemma/ {
-		root /home/zas1024/gene/wqflask/wqflask/;
-		autoindex on;
-	}
-
-	location /download/ {
-		root /home/zas1024/gene/wqflask/wqflask/;
-		autoindex on;
-	}
-
-    location / {
-            proxy_pass         http://127.0.0.1:5002/;
-            proxy_redirect     off;
-
-            proxy_set_header   Host             $host;
-            proxy_set_header   X-Real-IP        $remote_addr;
-            proxy_set_header   X-Forwarded-For  $proxy_add_x_forwarded_for;
-            
-            proxy_read_timeout 40m;
-    }
-}
-
diff --git a/wqflask/other_config/nginx_conf/gn2.conf b/wqflask/other_config/nginx_conf/gn2.conf
deleted file mode 100644
index a51b4113..00000000
--- a/wqflask/other_config/nginx_conf/gn2.conf
+++ /dev/null
@@ -1,41 +0,0 @@
-server {
-    # Modeled after http://flask.pocoo.org/docs/deploying/wsgi-standalone/
-    listen 80;
-
-    server_name gn2.genenetwork.org;
-
-    access_log  /var/log/nginx/access.log;
-    error_log  /var/log/nginx/error.log;
-
-    location ^~ /css/ {
-            root /gene/wqflask/wqflask/static/;
-    }
-
-    location ^~ /javascript/ {
-            root /gene/wqflask/wqflask/static/;
-    }
-
-#    location ^~ /image/ {
-#           root /gene/wqflask/wqflask/static/;
-#       }
-
-    location ^~ /images/ {
-            root /gene/wqflask/wqflask/static/;
-    }
-    
-    ### New - added by Sam
-    #location ^~ /static/ {
-    #       root /gene/wqflask/wqflask/static/;
-    #}
-
-    location / {
-            proxy_pass         http://127.0.0.1:5000/;
-            proxy_redirect     off;
-
-            proxy_set_header   Host             $host;
-            proxy_set_header   X-Real-IP        $remote_addr;
-            proxy_set_header   X-Forwarded-For  $proxy_add_x_forwarded_for;
-            
-            proxy_read_timeout 40m;
-    }
-}
diff --git a/wqflask/other_config/nginx_conf/gn2_sam.conf b/wqflask/other_config/nginx_conf/gn2_sam.conf
deleted file mode 100644
index f9abbbd2..00000000
--- a/wqflask/other_config/nginx_conf/gn2_sam.conf
+++ /dev/null
@@ -1,42 +0,0 @@
-server {
-    # Modeled after http://flask.pocoo.org/docs/deploying/wsgi-standalone/
-    listen 80;
-
-    server_name gn2_sam.genenetwork.org;
-
-    access_log  /var/log/nginx/access.log;
-    error_log  /var/log/nginx/error.log;
-
-    location ^~ /css/ {
-            root /gene/wqflask/wqflask/static/;
-    }
-
-    location ^~ /javascript/ {
-            root /gene/wqflask/wqflask/static/;
-    }
-
-#    location ^~ /image/ {
-#           root /gene/wqflask/wqflask/static/;
-#       }
-
-    location ^~ /images/ {
-            root /gene/wqflask/wqflask/static/;
-    }
-    
-    ### New - added by Sam
-    #location ^~ /static/ {
-    #       root /gene/wqflask/wqflask/static/;
-    #}
-
-    location / {
-            proxy_pass         http://127.0.0.1:5005/;
-            proxy_redirect     off;
-
-            proxy_set_header   Host             $host;
-            proxy_set_header   X-Real-IP        $remote_addr;
-            proxy_set_header   X-Forwarded-For  $proxy_add_x_forwarded_for;
-            
-            proxy_read_timeout 40m;
-    }
-}
-
diff --git a/wqflask/other_config/nginx_conf/penguin.conf b/wqflask/other_config/nginx_conf/penguin.conf
deleted file mode 100644
index c819951c..00000000
--- a/wqflask/other_config/nginx_conf/penguin.conf
+++ /dev/null
@@ -1,44 +0,0 @@
-server {
-    # Modeled after http://flask.pocoo.org/docs/deploying/wsgi-standalone/
-
-    client_max_body_size 20M;
-    listen 80;
-
-    server_name penguin.uthsc.edu;
-
-    access_log  /var/log/nginx/access.log;
-    error_log  /var/log/nginx/error.log;
-
-    location ^~ /css/ {
-            root /gene/wqflask/wqflask/static/;
-    }
-
-    location ^~ /javascript/ {
-            root /gene/wqflask/wqflask/static/;
-    }
-
-#    location ^~ /image/ {
-#           root /gene/wqflask/wqflask/static/;
-#       }
-
-    location ^~ /images/ {
-            root /gene/wqflask/wqflask/static/;
-    }
-    
-    ### New - added by Sam
-    #location ^~ /static/ {
-    #       root /gene/wqflask/wqflask/static/;
-    #}
-
-    location / {
-            proxy_pass         http://127.0.0.1:5000/;
-            proxy_redirect     off;
-
-            proxy_set_header   Host             $host;
-            proxy_set_header   X-Real-IP        $remote_addr;
-            proxy_set_header   X-Forwarded-For  $proxy_add_x_forwarded_for;
-            
-            proxy_read_timeout 40m;
-    }
-}
-
diff --git a/wqflask/other_config/pylintrc b/wqflask/other_config/pylintrc
deleted file mode 100644
index b23af7a4..00000000
--- a/wqflask/other_config/pylintrc
+++ /dev/null
@@ -1,264 +0,0 @@
-[MASTER]
-
-# Specify a configuration file.
-#rcfile=
-
-# Python code to execute, usually for sys.path manipulation such as
-# pygtk.require().
-#init-hook=
-
-# Profiled execution.
-profile=no
-
-# Add files or directories to the blacklist. They should be base names, not
-# paths.
-ignore=CVS
-
-# Pickle collected data for later comparisons.
-persistent=yes
-
-# List of plugins (as comma separated values of python modules names) to load,
-# usually to register additional checkers.
-load-plugins=
-
-
-[MESSAGES CONTROL]
-
-# Enable the message, report, category or checker with the given id(s). You can
-# either give multiple identifier separated by comma (,) or put this option
-# multiple time. See also the "--disable" option for examples.
-#enable=
-
-# Disable the message, report, category or checker with the given id(s). You
-# can either give multiple identifiers separated by comma (,) or put this
-# option multiple times (only on the command line, not in the configuration
-# file where it should appear only once).You can also use "--disable=all" to
-# disable everything first and then reenable specific checks. For example, if
-# you want to run only the similarities checker, you can use "--disable=all
-# --enable=similarities". If you want to run only the classes checker, but have
-# no Warning level messages displayed, use"--disable=all --enable=classes
-# --disable=W"
-disable=no-init, star-args, no-member, import-error
-
-
-[REPORTS]
-
-# Set the output format. Available formats are text, parseable, colorized, msvs
-# (visual studio) and html. You can also give a reporter class, eg
-# mypackage.mymodule.MyReporterClass.
-output-format=text
-
-# Include message's id in output
-include-ids=no
-
-# Include symbolic ids of messages in output
-symbols=no
-
-# Put messages in a separate file for each module / package specified on the
-# command line instead of printing them on stdout. Reports (if any) will be
-# written in a file name "pylint_global.[txt|html]".
-files-output=no
-
-# Tells whether to display a full report or only the messages
-reports=yes
-
-# Python expression which should return a note less than 10 (10 is the highest
-# note). You have access to the variables errors warning, statement which
-# respectively contain the number of errors / warnings messages and the total
-# number of statements analyzed. This is used by the global evaluation report
-# (RP0004).
-evaluation=10.0 - ((float(5 * error + warning + refactor + convention) / statement) * 10)
-
-# Add a comment according to your evaluation note. This is used by the global
-# evaluation report (RP0004).
-comment=no
-
-
-[SIMILARITIES]
-
-# Minimum lines number of a similarity.
-min-similarity-lines=4
-
-# Ignore comments when computing similarities.
-ignore-comments=yes
-
-# Ignore docstrings when computing similarities.
-ignore-docstrings=yes
-
-# Ignore imports when computing similarities.
-ignore-imports=no
-
-
-[VARIABLES]
-
-# Tells whether we should check for unused import in __init__ files.
-init-import=no
-
-# A regular expression matching the beginning of the name of dummy variables
-# (i.e. not used).
-dummy-variables-rgx=_|dummy
-
-# List of additional names supposed to be defined in builtins. Remember that
-# you should avoid to define new builtins when possible.
-additional-builtins=
-
-
-[BASIC]
-
-# Required attributes for module, separated by a comma
-required-attributes=
-
-# List of builtins function names that should not be used, separated by a comma
-bad-functions=map,filter,apply,input
-
-# Regular expression which should only match correct module names
-module-rgx=(([a-z_][a-z0-9_]*)|([A-Z][a-zA-Z0-9]+))$
-
-# Regular expression which should only match correct module level names
-const-rgx=(([A-Z_][A-Za-z0-9_]*)|(__.*__))$
-
-# Regular expression which should only match correct class names
-class-rgx=[A-Z_][a-zA-Z0-9]+$
-
-# Regular expression which should only match correct function names
-function-rgx=[a-z_][a-z0-9_]{2,30}$
-
-# Regular expression which should only match correct method names
-method-rgx=[a-z_][a-z0-9_]{2,30}$
-
-# Regular expression which should only match correct instance attribute names
-attr-rgx=[a-z_][a-z0-9_]{2,30}$
-
-# Regular expression which should only match correct argument names
-argument-rgx=[a-z_][a-z0-9_]{2,30}$
-
-# Regular expression which should only match correct variable names
-variable-rgx=[a-z_][a-z0-9_]{2,30}$
-
-# Regular expression which should only match correct list comprehension /
-# generator expression variable names
-inlinevar-rgx=[A-Za-z_][A-Za-z0-9_]*$
-
-# Good variable names which should always be accepted, separated by a comma
-good-names=i,j,k,ex,Run,_
-
-# Bad variable names which should always be refused, separated by a comma
-bad-names=foo,bar,baz,toto,tutu,tata
-
-# Regular expression which should only match functions or classes name which do
-# not require a docstring
-no-docstring-rgx=__.*__
-
-
-[FORMAT]
-
-# Maximum number of characters on a single line.
-max-line-length=100
-
-# Maximum number of lines in a module
-max-module-lines=1000
-
-# String used as indentation unit. This is usually " " (4 spaces) or "\t" (1
-# tab).
-indent-string='    '
-
-
-[MISCELLANEOUS]
-
-# List of note tags to take in consideration, separated by a comma.
-notes=FIXME,XXX,TODO
-
-
-[TYPECHECK]
-
-# Tells whether missing members accessed in mixin class should be ignored. A
-# mixin class is detected if its name ends with "mixin" (case insensitive).
-ignore-mixin-members=yes
-
-# List of classes names for which member attributes should not be checked
-# (useful for classes with attributes dynamically set).
-ignored-classes=SQLObject
-
-# When zope mode is activated, add a predefined set of Zope acquired attributes
-# to generated-members.
-zope=no
-
-# List of members which are set dynamically and missed by pylint inference
-# system, and so shouldn't trigger E0201 when accessed. Python regular
-# expressions are accepted.
-generated-members=REQUEST,acl_users,aq_parent
-
-
-[DESIGN]
-
-# Maximum number of arguments for function / method
-max-args=5
-
-# Argument names that match this expression will be ignored. Default to name
-# with leading underscore
-ignored-argument-names=_.*
-
-# Maximum number of locals for function / method body
-max-locals=15
-
-# Maximum number of return / yield for function / method body
-max-returns=6
-
-# Maximum number of branch for function / method body
-max-branchs=12
-
-# Maximum number of statements in function / method body
-max-statements=50
-
-# Maximum number of parents for a class (see R0901).
-max-parents=7
-
-# Maximum number of attributes for a class (see R0902).
-max-attributes=7
-
-# Minimum number of public methods for a class (see R0903).
-min-public-methods=2
-
-# Maximum number of public methods for a class (see R0904).
-max-public-methods=20
-
-
-[IMPORTS]
-
-# Deprecated modules which should not be used, separated by a comma
-deprecated-modules=regsub,string,TERMIOS,Bastion,rexec
-
-# Create a graph of every (i.e. internal and external) dependencies in the
-# given file (report RP0402 must not be disabled)
-import-graph=
-
-# Create a graph of external dependencies in the given file (report RP0402 must
-# not be disabled)
-ext-import-graph=
-
-# Create a graph of internal dependencies in the given file (report RP0402 must
-# not be disabled)
-int-import-graph=
-
-
-[CLASSES]
-
-# List of interface methods to ignore, separated by a comma. This is used for
-# instance to not check methods defines in Zope's Interface base class.
-ignore-iface-methods=isImplementedBy,deferred,extends,names,namesAndDescriptions,queryDescriptionFor,getBases,getDescriptionFor,getDoc,getName,getTaggedValue,getTaggedValueTags,isEqualOrExtendedBy,setTaggedValue,isImplementedByInstancesOf,adaptWith,is_implemented_by
-
-# List of method names used to declare (i.e. assign) instance attributes.
-defining-attr-methods=__init__,__new__,setUp
-
-# List of valid names for the first argument in a class method.
-valid-classmethod-first-arg=cls
-
-# List of valid names for the first argument in a metaclass class method.
-valid-metaclass-classmethod-first-arg=mcs
-
-
-[EXCEPTIONS]
-
-# Exceptions that will emit a warning when being caught. Defaults to
-# "Exception"
-overgeneral-exceptions=Exception
diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index 0f72b29d..ffc698de 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -36,6 +36,10 @@ from utility.formatting import numify
 from base import trait
 from base.data_set import create_dataset
 
+import logging
+from utility.logger import getLogger
+logger = getLogger(__name__)
+
 def get_collection():
     if g.user_session.logged_in:
         return UserCollection()
@@ -93,7 +97,7 @@ class AnonCollection(object):
         self.traits = list(process_traits(params['traits']))
         #len_before = len(Redis.smembers(self.key))
         existing_collections = Redis.get(self.key)
-        print("existing_collections:", existing_collections)
+        logger.debug("existing_collections:", existing_collections)
         if existing_collections != None and existing_collections != "None":
             collections_list = json.loads(existing_collections)
             collection_position = 0 #ZS: Position of collection in collection_list, if it exists
@@ -158,8 +162,8 @@ class UserCollection(object):
     """User is logged in"""
 
     def add_traits(self, params, collection_name):
-        print("---> params are:", params.keys())
-        print("     type(params):", type(params))
+        logger.debug("---> params are:", params.keys())
+        logger.debug("     type(params):", type(params))
         if collection_name=="Default":
             uc = g.user_session.user_ob.get_collection_by_name("Default")
             # Doesn't exist so we'll create it
@@ -187,7 +191,7 @@ class UserCollection(object):
 
         db_session.commit()
 
-        print("added to existing, now set is:" + str(uc.members))
+        logger.debug("added to existing, now set is:" + str(uc.members))
         report_change(len_before, len_now)
 
         # Probably have to change that
@@ -210,12 +214,12 @@ def process_traits(unprocessed_traits):
 def report_change(len_before, len_now):
     new_length = len_now - len_before
     if new_length:
-        print("We've added {} to your collection.".format(
+        logger.debug("We've added {} to your collection.".format(
             numify(new_length, 'new trait', 'new traits')))
         flash("We've added {} to your collection.".format(
             numify(new_length, 'new trait', 'new traits')))
     else:
-        print("No new traits were added.")
+        logger.debug("No new traits were added.")
 
 
 @app.route("/collections/add")
@@ -223,8 +227,9 @@ def collections_add():
     traits=request.args['traits']
 
     if g.user_session.logged_in:
+        logger.debug("user_session",g.user_session)
         user_collections = g.user_session.user_ob.user_collections
-        print("user_collections are:", user_collections)
+        logger.debug("user_collections are:", user_collections)
         return render_template("collections/add.html",
                                traits = traits,
                                collections = user_collections,
@@ -246,11 +251,11 @@ def collections_new():
     if "sign_in" in params:
         return redirect(url_for('login'))
     if "create_new" in params:
-        print("in create_new")
+        logger.debug("in create_new")
         collection_name = params['new_collection']
         return create_new(collection_name)
     elif "add_to_existing" in params:
-        print("in add to existing")
+        logger.debug("in add to existing")
         collection_name = params['existing_collection'].split(":")[1]
         if g.user_session.logged_in:
             return UserCollection().add_traits(params, collection_name)
@@ -270,7 +275,7 @@ def create_new(collection_name):
     if g.user_session.logged_in:
         uc = model.UserCollection()
         uc.name = collection_name
-        print("user_session:", g.user_session.__dict__)
+        logger.debug("user_session:", g.user_session.__dict__)
         uc.user = g.user_session.user_id
         uc.members = json.dumps(list(traits))
         db_session.add(uc)
@@ -286,17 +291,17 @@ def create_new(collection_name):
 @app.route("/collections/list")
 def list_collections():
     params = request.args
-    print("PARAMS:", params)
+    logger.debug("PARAMS:", params)
     if g.user_session.logged_in:
         user_collections = list(g.user_session.user_ob.user_collections)
-        print("user_collections are:", user_collections)
+        logger.debug("user_collections are:", user_collections)
         return render_template("collections/list.html",
                                params = params,
                                collections = user_collections,
                                )
     else:
         anon_collections = user_manager.AnonUser().get_collections()
-        print("anon_collections are:", anon_collections)
+        logger.debug("anon_collections are:", anon_collections)
         return render_template("collections/list.html",
                                params = params,
                                collections = anon_collections)
@@ -305,17 +310,17 @@ def list_collections():
 @app.route("/collections/remove", methods=('POST',))
 def remove_traits():
     params = request.form
-    print("params are:", params)
+    logger.debug("params are:", params)
 
     if "uc_id" in params:
         uc_id = params['uc_id']
         uc = model.UserCollection.query.get(uc_id)
         traits_to_remove = params.getlist('traits[]')
         traits_to_remove = process_traits(traits_to_remove)
-        print("\n\n  after processing, traits_to_remove:", traits_to_remove)
+        logger.debug("\n\n  after processing, traits_to_remove:", traits_to_remove)
         all_traits = uc.members_as_set()
         members_now = all_traits - traits_to_remove
-        print("  members_now:", members_now)
+        logger.debug("  members_now:", members_now)
         uc.members = json.dumps(list(members_now))
         uc.changed_timestamp = datetime.datetime.utcnow()
         db_session.commit()
@@ -332,7 +337,7 @@ def remove_traits():
 @app.route("/collections/delete", methods=('POST',))
 def delete_collection():
     params = request.form
-    print("params:", params)
+    logger.debug("params:", params)
     if g.user_session.logged_in:
         uc_id = params['uc_id']
         if len(uc_id.split(":")) > 1:
@@ -363,7 +368,7 @@ def delete_collection():
 @app.route("/collections/view")
 def view_collection():
     params = request.args
-    print("PARAMS in view collection:", params)
+    logger.debug("PARAMS in view collection:", params)
 
     if "uc_id" in params:
         uc_id = params['uc_id']
@@ -379,7 +384,7 @@ def view_collection():
         #this_collection = user_collections[params['collection_id']]
         traits = this_collection['members']
 
-    print("in view_collection traits are:", traits)
+    logger.debug("in view_collection traits are:", traits)
 
     trait_obs = []
     json_version = []
@@ -405,7 +410,7 @@ def view_collection():
         collection_info = dict(trait_obs=trait_obs,
                                collection_name=this_collection['name'])
     if "json" in params:
-        print("json_version:", json_version)
+        logger.debug("json_version:", json_version)
         return json.dumps(json_version)
     else:
         return render_template("collections/view.html",
diff --git a/wqflask/wqflask/static/dbdoc/TODO.md b/wqflask/wqflask/static/dbdoc/TODO.md
deleted file mode 100644
index c0a8bab7..00000000
--- a/wqflask/wqflask/static/dbdoc/TODO.md
+++ /dev/null
@@ -1 +0,0 @@
-TODO: Add all database documentation into this folder
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index c55649f3..a0605803 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -23,9 +23,6 @@ import urlparse
 
 import simplejson as json
 
-import sqlalchemy
-from sqlalchemy import orm
-
 #from redis import StrictRedis
 import redis
 Redis = redis.StrictRedis()
@@ -46,7 +43,6 @@ from wqflask.database import db_session
 from wqflask import model
 
 from utility import Bunch, Struct, after
-from utility.tools import LOG_SQL, LOG_SQL_ALCHEMY
 
 import logging
 from utility.logger import getLogger
@@ -55,7 +51,10 @@ logger = getLogger(__name__)
 from base.data_set import create_datasets_list
 
 import requests
-from utility.elasticsearch_tools import get_elasticsearch_connection, get_user_by_unique_column, save_user
+from utility.elasticsearch_tools import get_elasticsearch_connection, get_user_by_unique_column, get_item_by_unique_column, save_user, es_save_data
+
+from smtplib import SMTP
+from utility.tools import SMTP_CONNECT, SMTP_USERNAME, SMTP_PASSWORD
 
 THREE_DAYS = 60 * 60 * 24 * 3
 #THREE_DAYS = 45
@@ -220,6 +219,7 @@ class UserSession(object):
     def user_ob(self):
         """Actual sqlalchemy record"""
         # Only look it up once if needed, then store it
+        raise "OBSOLETE: use ElasticSearch instead"
         try:
             if LOG_SQL_ALCHEMY:
                 logging.getLogger('sqlalchemy.pool').setLevel(logging.DEBUG)
@@ -386,6 +386,7 @@ class ForgotPasswordEmail(VerificationEmail):
             "email_address": toaddr,
             "timestamp": timestamp()
         }
+        es = get_elasticsearch_connection()
         es_save_data(es, self.key_prefix, "local", data, verification_code)
 
         subject = self.subject
@@ -437,12 +438,12 @@ def verify_email():
 @app.route("/n/password_reset", methods=['GET'])
 def password_reset():
     logger.debug("in password_reset request.url is:", request.url)
-
     # We do this mainly just to assert that it's in proper form for displaying next page
     # Really not necessary but doesn't hurt
     # user_encode = DecodeUser(ForgotPasswordEmail.key_prefix).reencode_standalone()
     verification_code = request.args.get('code')
     hmac = request.args.get('hm')
+    es = get_elasticsearch_connection()
     if verification_code:
         code_details = get_item_by_unique_column(
             es
@@ -466,7 +467,6 @@ def password_reset():
 
 @app.route("/n/password_reset_step2", methods=('POST',))
 def password_reset_step2():
-    from utility.elasticsearch_tools import es
     logger.debug("in password_reset request.url is:", request.url)
 
     errors = []
@@ -748,6 +748,7 @@ def forgot_password():
 def forgot_password_submit():
     params = request.form
     email_address = params['email_address']
+    es = get_elasticsearch_connection()
     user_details = get_user_by_unique_column(es, "email_address", email_address)
     if user_details:
         ForgotPasswordEmail(user_details["email_address"])
@@ -840,19 +841,6 @@ def register():
     return render_template("new_security/register_user.html", values=params, errors=errors)
 
 
-
-
-#@app.route("/n/login", methods=('GET', 'POST'))
-#def login():
-#    return user_manager.login()
-#
-#@app.route("/manage/verify")
-#def verify():
-#    user_manager.verify_email()
-#    return render_template("new_security/verified.html")
-
-
-
 ################################# Sign and unsign #####################################
 
 def url_for_hmac(endpoint, **values):
@@ -914,15 +902,26 @@ app.jinja_env.globals.update(url_for_hmac=url_for_hmac,
 #     Redis.rpush("mail_queue", msg)
 
 def send_email(toaddr, msg, fromaddr="no-reply@genenetwork.org"):
-    from smtplib import SMTP
-    from utility.tools import SMTP_CONNECT, SMTP_USERNAME, SMTP_PASSWORD
-    server = SMTP(SMTP_CONNECT)
-    server.starttls()
-    server.login(SMTP_USERNAME, SMTP_PASSWORD)
-    server.sendmail(fromaddr, toaddr, msg)
-    server.quit()
-
-
+    """Send an E-mail through SMTP_CONNECT host. If SMTP_USERNAME is not
+    'UNKNOWN' TLS is used
+
+    """
+    if SMTP_USERNAME == 'UNKNOWN':
+        logger.debug("SMTP: connecting with host "+SMTP_CONNECT)
+        server = SMTP(SMTP_CONNECT)
+        server.sendmail(fromaddr, toaddr, msg)
+    else:
+        logger.debug("SMTP: connecting TLS with host "+SMTP_CONNECT)
+        server = SMTP(SMTP_CONNECT)
+        server.starttls()
+        logger.debug("SMTP: login with user "+SMTP_USERNAME)
+        server.login(SMTP_USERNAME, SMTP_PASSWORD)
+        logger.debug("SMTP: "+fromaddr)
+        logger.debug("SMTP: "+toaddr)
+        logger.debug("SMTP: "+msg)
+        server.sendmail(fromaddr, toaddr, msg)
+        server.quit()
+    logger.info("Successfully sent email to "+toaddr)
 
 class GroupsManager(object):
     def __init__(self, kw):