diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/other_config/dot.pylintrc | 249 | ||||
| -rw-r--r-- | wqflask/other_config/nginx-old.conf | 108 | ||||
| -rw-r--r-- | wqflask/other_config/nginx_conf/gn2-lei.conf | 41 | ||||
| -rw-r--r-- | wqflask/other_config/nginx_conf/gn2-zach.conf | 52 | ||||
| -rw-r--r-- | wqflask/other_config/nginx_conf/gn2.conf | 41 | ||||
| -rw-r--r-- | wqflask/other_config/nginx_conf/gn2_sam.conf | 42 | ||||
| -rw-r--r-- | wqflask/other_config/nginx_conf/penguin.conf | 44 | ||||
| -rw-r--r-- | wqflask/other_config/pylintrc | 264 | ||||
| -rw-r--r-- | wqflask/wqflask/correlation/show_corr_results.py | 43 | ||||
| -rw-r--r-- | wqflask/wqflask/do_search.py | 1 | ||||
| -rw-r--r-- | wqflask/wqflask/static/dbdoc/TODO.md | 1 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/show_trait.js | 176 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/base.html | 3 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/marker_regression_gn1.html | 9 | ||||
| -rw-r--r-- | wqflask/wqflask/user_manager.py | 18 |
15 files changed, 159 insertions, 933 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/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 2c6c3a14..73072423 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -196,28 +196,29 @@ class CorrelationResults(object): self.get_sample_r_and_p_values(trait, self.target_dataset.trait_data[trait]) elif self.corr_type == "sample": - if self.dataset.type == "ProbeSet" and cache_available: - dataset_file = open(webqtlConfig.GENERATED_TEXT_DIR+db_filename,'r') - - #XZ, 01/08/2009: read the first line - line = dataset_file.readline() - dataset_strains = webqtlUtil.readLineCSV(line)[1:] - - self.this_trait_vals = [] - for item in dataset_strains: - if item in self.sample_data: - self.this_trait_vals.append(self.sample_data[item]) - else: - self.this_trait_vals.append("None") - num_overlap = len(self.this_trait_vals) - logger.debug("DOING PARALLEL") - self.do_parallel_correlation(db_filename, num_overlap) - else: - for trait, values in self.target_dataset.trait_data.iteritems(): - self.get_sample_r_and_p_values(trait, values) + #ZS: Commented out since parallel correlation has issues with gunicorn + # if self.dataset.type == "ProbeSet" and cache_available: + # dataset_file = open(webqtlConfig.GENERATED_TEXT_DIR+db_filename,'r') + + ##XZ, 01/08/2009: read the first line + # line = dataset_file.readline() + # dataset_strains = webqtlUtil.readLineCSV(line)[1:] + + # self.this_trait_vals = [] + # for item in dataset_strains: + # if item in self.sample_data: + # self.this_trait_vals.append(self.sample_data[item]) + # else: + # self.this_trait_vals.append("None") + # num_overlap = len(self.this_trait_vals) + # logger.debug("DOING PARALLEL") + # self.do_parallel_correlation(db_filename, num_overlap) + # else: + for trait, values in self.target_dataset.trait_data.iteritems(): + self.get_sample_r_and_p_values(trait, values) - self.correlation_data = collections.OrderedDict(sorted(self.correlation_data.items(), - key=lambda t: -abs(t[1][0]))) + self.correlation_data = collections.OrderedDict(sorted(self.correlation_data.items(), + key=lambda t: -abs(t[1][0]))) if self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Geno": diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index e1df1e63..17625474 100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -989,3 +989,4 @@ if __name__ == "__main__": #results = GoSearch("0045202", dataset, cursor, db_conn).run() logger.debug("results are:", pf(results)) + db_conn.close() 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/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js index df10c060..117d8f12 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait.js +++ b/wqflask/wqflask/static/new/javascript/show_trait.js @@ -250,15 +250,29 @@ }; redraw_box_plot = function() { - var x; - var _i, _len, _ref, data; - _ref = _.values(root.selected_samples[root.stats_group]); - trait_vals = []; - for (_i = 0, _len = _ref.length; _i < _len; _i++) { - x = _ref[_i]; - trait_vals.push(x.value); + var y_value_list = [] + for (var sample_group in root.selected_samples){ + var trait_sample_data = _.values(root.selected_samples[sample_group]) + var trait_vals = []; + for (i = 0, len = trait_sample_data.length; i < len; i++) { + this_sample_data = trait_sample_data[i]; + trait_vals.push(this_sample_data.value); + } + y_value_list.push(trait_vals) + } + + if (Object.keys(js_data.sample_group_types).length > 1) { + var update = { + y: y_value_list + } + console.log("REDRAW UPDATE:", update) + Plotly.restyle('box_plot', update, [0, 1, 2]) + } else { + var update = { + y: y_value_list + } + Plotly.restyle('box_plot', update) } - Plotly.restyle('box_plot', 'y', [trait_vals]) } redraw_prob_plot = function() { @@ -640,6 +654,108 @@ }; root.stats_group = 'samples_primary'; + + if (Object.keys(js_data.sample_group_types).length > 1) { + full_sample_lists = [sample_lists[0], sample_lists[1], sample_lists[0].concat(sample_lists[1])] + sample_group_list = [js_data.sample_group_types['samples_primary'], js_data.sample_group_types['samples_other'], js_data.sample_group_types['samples_all']] + } else { + full_sample_lists = [sample_lists[0]] + sample_group_list = [js_data.sample_group_types['samples_primary']] + } + + if (full_sample_lists.length > 1) { + var box_layout = { + width: 1200, + height: 500, + margin: { + l: 50, + r: 30, + t: 30, + b: 80 + } + }; + var trace1 = { + y: get_sample_vals(full_sample_lists[0]), + type: 'box', + name: sample_group_list[0], + boxpoints: 'all', + jitter: 0.5, + whiskerwidth: 0.2, + fillcolor: 'cls', + marker: { + size: 2 + }, + line: { + width: 1 + } + } + var trace2 = { + y: get_sample_vals(full_sample_lists[1]), + type: 'box', + name: sample_group_list[1], + boxpoints: 'all', + jitter: 0.5, + whiskerwidth: 0.2, + fillcolor: 'cls', + marker: { + size: 2 + }, + line: { + width: 1 + } + } + var trace3 = { + y: get_sample_vals(full_sample_lists[2]), + type: 'box', + name: sample_group_list[2], + boxpoints: 'all', + jitter: 0.5, + whiskerwidth: 0.2, + fillcolor: 'cls', + marker: { + size: 2 + }, + line: { + width: 1 + } + } + box_data = [trace1, trace2, trace3] + } else { + var box_layout = { + width: 500, + height: 500, + margin: { + l: 50, + r: 30, + t: 30, + b: 80 + } + }; + box_data = [ + { + type: 'box', + y: get_sample_vals(full_sample_lists[0]), + name: sample_group_list[0], + boxpoints: 'all', + jitter: 0.5, + whiskerwidth: 0.2, + fillcolor: 'cls', + marker: { + size: 2 + }, + line: { + width: 1 + } + } + ] + } + + obj = { + data: box_data, + layout: box_layout + } + Plotly.newPlot('box_plot', obj); + // Histogram var hist_trace = { x: get_sample_vals(sample_lists[0]), @@ -686,50 +802,6 @@ root.bar_layout = layout Plotly.newPlot('bar_chart', root.bar_data, layout) - if (Object.keys(js_data.sample_group_types).length > 1) { - full_sample_lists = [sample_lists[0], sample_lists[1], sample_lists[0].concat(sample_lists[1])] - sample_group_list = [js_data.sample_group_types['samples_primary'], js_data.sample_group_types['samples_other'], js_data.sample_group_types['samples_all']] - } else { - full_sample_lists = [sample_lists[0]] - sample_group_list = [js_data.sample_group_types['samples_primary']] - } - - data = [] - for ( var i = 0; i < full_sample_lists.length; i ++ ) { - var box_trace = { - type: 'box', - y: get_sample_vals(full_sample_lists[i]), - name: sample_group_list[i], - boxpoints: 'all', - jitter: 0.5, - whiskerwidth: 0.2, - fillcolor: 'cls', - marker: { - size: 2 - }, - line: { - width: 1 - } - }; - data.push(box_trace) - }; - layout = { - title: 'Box Plot', - yaxis: { - autorange: true, - showgrid: true, - zeroline: true - }, - margin: { - l: 50, - r: 30, - t: 80, - b: 80 - } - }; - - Plotly.newPlot('box_plot', data, layout); - $('.histogram_samples_group').val(root.stats_group); $('.histogram_samples_group').change(function() { root.stats_group = $(this).val(); diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html index 237a65f3..41bdaddc 100644 --- a/wqflask/wqflask/templates/base.html +++ b/wqflask/wqflask/templates/base.html @@ -77,6 +77,9 @@ {% endif %} </li> <li style="margin-left: 20px;"> + <a href="http://gn2-guix.genenetwork.org" style="font-weight: bold;" >Use Staging Branch</a> + </li> + <li style="margin-left: 20px;"> <a href="http://www.genenetwork.org" style="font-weight: bold;" >Use GeneNetwork 1</a> </li> </ul> diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html index 08a934a6..fd083983 100644 --- a/wqflask/wqflask/templates/marker_regression_gn1.html +++ b/wqflask/wqflask/templates/marker_regression_gn1.html @@ -183,6 +183,13 @@ {% if selectedChr == -1 %} <div class="container" style="padding-left: 30px; width:{% if 'additive' in trimmed_markers[0] %}45%{% else %}35%{% endif %};"> <h2>Mapping Statistics</h2> + <br /> + <button class="btn btn-default" id="select_all"><span class="glyphicon glyphicon-ok"></span> Select All</button> + <button class="btn btn-default" id="deselect_all"><span class="glyphicon glyphicon-remove"></span> Deselect All</button> + <button class="btn btn-default" id="invert"><span class="glyphicon glyphicon-resize-vertical"></span> Invert</button> + <button class="btn btn-default" id="add" disabled><span class="glyphicon glyphicon-plus-sign"></span> Add</button> + <br /> + <br /> <div id="table_container" style="border-style: solid; border-width: 1px; border-color: black;"> <table id="trait_table" class="table table-hover table-striped nowrap"> <thead> @@ -211,7 +218,7 @@ <td align="center" style="padding-right: 0px;"> <input type="checkbox" name="selectCheck" class="checkbox trait_checkbox" - value="{{ marker.name }}"> + value="{{ data_hmac('{}:{}Geno'.format(marker.name, dataset.group.name)) }}"> </td> <td align="right">{{ loop.index }}</td> <td>{% if geno_db_exists == "True" %}<a href="/show_trait?trait_id={{ marker.name }}&dataset={{ dataset.group.name }}Geno">{{ marker.name }}</a>{% else %}{{ marker.name }}{% endif %}</td> diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py index ebca4807..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 @@ -223,6 +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) @@ -844,19 +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): |