Merge branch 'flask'

5 files changed, 429 insertions, 0 deletions

diff --git a/wqflask/other_config/nginx.conf b/wqflask/other_config/nginx-old.conf
index 65ee768c..65ee768c 100644
--- a/wqflask/other_config/nginx.conf
+++ b/wqflask/other_config/nginx-old.conf
diff --git a/wqflask/other_config/nginx_conf/gn2python.conf b/wqflask/other_config/nginx_conf/gn2python.conf
new file mode 100644
index 00000000..f23e325f
--- /dev/null
+++ b/wqflask/other_config/nginx_conf/gn2python.conf
@@ -0,0 +1,41 @@
+server {
+    # Modeled after http://flask.pocoo.org/docs/deploying/wsgi-standalone/
+    listen 80;
+
+    server_name gn2python.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/gn2python_lei.conf b/wqflask/other_config/nginx_conf/gn2python_lei.conf
new file mode 100644
index 00000000..981bda28
--- /dev/null
+++ b/wqflask/other_config/nginx_conf/gn2python_lei.conf
@@ -0,0 +1,41 @@
+server {
+    # Modeled after http://flask.pocoo.org/docs/deploying/wsgi-standalone/
+    listen 80;
+
+    server_name gn2python_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;
+    }
+}
\ No newline at end of file
diff --git a/wqflask/other_config/pylintrc b/wqflask/other_config/pylintrc
new file mode 100644
index 00000000..b23af7a4
--- /dev/null
+++ b/wqflask/other_config/pylintrc
@@ -0,0 +1,264 @@
+[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/other_config/wqflask-nginx.conf b/wqflask/other_config/wqflask-nginx.conf
new file mode 100644
index 00000000..4e6fd0d9
--- /dev/null
+++ b/wqflask/other_config/wqflask-nginx.conf
@@ -0,0 +1,83 @@
+server {
+    # Modeled after http://flask.pocoo.org/docs/deploying/wsgi-standalone/
+    listen 80;
+
+    server_name gn2python.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;
+    }
+}
+
+server {
+    # Modeled after http://flask.pocoo.org/docs/deploying/wsgi-standalone/
+    listen 80;
+
+    server_name gn2python_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;
+    }
+}