diff options
| -rwxr-xr-x | bin/mechnical-rob | 111 | ||||
| -rw-r--r-- | etc/VERSION | 2 | ||||
| -rw-r--r-- | etc/nginx-genenetwork.conf | 54 | ||||
| -rw-r--r-- | test/lib/gntest.rb | 6 | ||||
| -rw-r--r-- | test/lib/link_checker.rb | 50 | ||||
| -rw-r--r-- | test/lib/main_web_functionality.rb | 62 | ||||
| -rw-r--r-- | test/lib/mapping.rb | 58 | ||||
| -rw-r--r-- | test/lib/navigation.rb | 43 | ||||
| -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/collect.py | 1 | ||||
| -rw-r--r-- | wqflask/wqflask/static/dbdoc/TODO.md | 1 | ||||
| -rw-r--r-- | wqflask/wqflask/user_manager.py | 18 |
19 files changed, 3 insertions, 1244 deletions
diff --git a/bin/mechnical-rob b/bin/mechnical-rob deleted file mode 100755 index be223d94..00000000 --- a/bin/mechnical-rob +++ /dev/null @@ -1,111 +0,0 @@ -#!/usr/bin/env ruby - - -USAGE = <<EOT -This is Mechanical-Rob - an automated web server tester for - Genenetwork.org that uses the brilliant - mechanize gem with minitest. - -To use this software you need to install mechanize. Run it from -the root of the genenetwork2 source tree as, for example, - - ./bin/test-website http://localhost:5003/ (default) - -If you are using the small deployment database you can use - - ./bin/test-website --skip -n - -To run all tests - - ./bin/test-website --all - -To run individual tests on localhost you can do - - ruby -Itest -Itest/lib test/lib/mapping.rb --name="/Mapping/" - -For more information see http://genenetwork.org/ - -EOT -$stderr.print USAGE - -require 'optparse' - -options = { database: :small, link_checker: false} -opts = OptionParser.new do |o| - o.banner = "Usage: #{File.basename($0)} [options] URL" - - o.on('-d','--database', String, 'Use database (default db_webqtl_s)') do |s| - options[:database] = - case s - when 'xx' - :unknown - else - :small - end - end - - o.on('--all', 'Run all tests') do - options[:all] = true - end - - o.on('-l','--link-checker', 'Check for dead links') do - options[:link_checker] = true - end - - o.on('--navigation', 'Check for navigation') do - options[:navigation] = true - end - - o.on('--mapping', 'Check for mapping') do - options[:mapping] = true - end - - o.on('--skip-broken', 'Skip tests that are known to be broken') do - options[:skip_broken] = true - end - - o.separator "" - o.on_tail('-h', '--help', 'display this help and exit') do - options[:show_help] = true - end -end - -opts.parse!(ARGV) - -if options[:show_help] - print opts - exit 1 -end - -$options = options # we are using a global here -$host = - if ARGV.size>0 - ARGV.shift - else - "http://localhost:5003" - end - -$stderr.print "Testing <",$host,">\n" - -require 'mechanize' -require 'minitest/spec' -require 'minitest/autorun' - -# These are the actual testing modules - -libpath = File.dirname(File.dirname(__FILE__)) -$: << File.join(libpath,'test/lib') - -require 'main_web_functionality' - -if options[:all] or options[:mapping] - require 'mapping' -end - -if options[:all] or options[:link_checker] - require 'link_checker' -end - -if options[:all] or options[:navigation] - require 'navigation' -end diff --git a/etc/VERSION b/etc/VERSION index ca9e199c..a4320e6f 100644 --- a/etc/VERSION +++ b/etc/VERSION @@ -1 +1 @@ -2.11-rc1 +2.11-rc2 diff --git a/etc/nginx-genenetwork.conf b/etc/nginx-genenetwork.conf deleted file mode 100644 index 06fd3c57..00000000 --- a/etc/nginx-genenetwork.conf +++ /dev/null @@ -1,54 +0,0 @@ -user nobody; -worker_processes 4; -pid /var/run/nginx.pid; - -error_log /var/log/nginx/error.log; - -events { - worker_connections 16; -} - -http { - include mime.types; - # default_type application/octet-stream; - - # sendfile on; - keepalive_timeout 480; - - server { - listen 80; - server_name localhost; - - location / { - root html; - index index.html index.htm; - } - - error_page 500 502 503 504 /50x.html; - location = /50x.html { - root html; - } - } - - server { - listen 80; - server_name test-gn2.genenetwork.org; - access_log logs/test-gn2.access.log; - - proxy_connect_timeout 3000; - proxy_send_timeout 3000; - proxy_read_timeout 3000; - send_timeout 3000; - - location / { - # proxy_set_header Host $host; - proxy_set_header Host $http_host; - # proxy_redirect off; - proxy_set_header Connection keep-alive; - proxy_set_header X-Real-IP $remote_addr; - proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; - proxy_set_header X-Forwarded-Host $server_name; - proxy_pass http://127.0.0.1:5003; - } - } -} diff --git a/test/lib/gntest.rb b/test/lib/gntest.rb deleted file mode 100644 index 5b21b3d5..00000000 --- a/test/lib/gntest.rb +++ /dev/null @@ -1,6 +0,0 @@ -require 'minitest/autorun' -require 'mechanize' -require 'json' - -# ---- Use some default parameters if not set -$host = "http://localhost:5003" if !$host diff --git a/test/lib/link_checker.rb b/test/lib/link_checker.rb deleted file mode 100644 index 36cb36c8..00000000 --- a/test/lib/link_checker.rb +++ /dev/null @@ -1,50 +0,0 @@ - -SKIP = "mailto:" - -class LinkChecker -end - -describe LinkChecker do - before do - @agent = Mechanize.new - @agent.agent.http.ca_file = '/etc/ssl/certs/ca-certificates.crt' - end - - it "Get to front page" do - page = @agent.get($host) - page.links.each do |link| - puts link.href - if link.href !~ /#{SKIP}/ # /static\/dbdoc\/Hippocampus/ and link.href !~ /mailto:|glossary.html|sample_r|grits.eecs.utk.edu|correlationAnnotation.html/ - # Fetch link, program will crash with exception if link is broken - linkpage = @agent.get(link.href) - puts "Link to #{link.href} is valid, response code #{linkpage.code}" - end - end - - end - - describe LinkChecker do - it "Get to trait page" do - page = @agent.get($host+'/show_trait?trait_id=1435395_s_at&dataset=HC_M2_0606_P') - # p page - - # Get to trait page for 1435395_s_at - # form2 = show_trait_page.forms_with("trait_page")[0] - # form2.fields[30].name.must_equal "variance:C57BL/6J" - # form2.fields[30].value.must_equal "15.287" - - # Test every link on the page to check if it's broken or not - page.links.each do |link| - puts link.href - if link.href !~ /#{SKIP}/ # /static\/dbdoc\/Hippocampus/ and link.href !~ /mailto:|glossary.html|sample_r|grits.eecs.utk.edu|correlationAnnotation.html/ - # Fetch link, program will crash with exception if link is broken - linkpage = @agent.get(link.href) - puts "Link to #{link.href} is valid, response code #{linkpage.code}" - end - end - - end - - end - -end diff --git a/test/lib/main_web_functionality.rb b/test/lib/main_web_functionality.rb deleted file mode 100644 index 9ae49995..00000000 --- a/test/lib/main_web_functionality.rb +++ /dev/null @@ -1,62 +0,0 @@ -# In these tests we navigate from the main page to search - -class MainWebFunctionality -end - -describe MainWebFunctionality do - before do - @agent = Mechanize.new - @agent.agent.http.ca_file = '/etc/ssl/certs/ca-certificates.crt' - end - - describe MainWebFunctionality do - - it "Get to trait page" do - page = @agent.get($host) - p page - form = page.forms[1] - form.buttons[0].value.must_equal "Search" # main menu is loaded - - # http://localhost:5003/search?species=mouse&group=BXD&type=Hippocampus+mRNA&dataset=HC_M2_0606_P&search_terms_or=&search_terms_and=MEAN%3D%2815+16%29+LRS%3D%2823+46%29&FormID=searchResult - form.fields[0].value.must_equal "searchResult" - form.fields[2].value = "MEAN=(15 16) LRS=(23 46)" - form.fields[3].value = "mouse" - form.fields[4].value = "BXD" - form.fields[5].value = "Hippocampus mRNA" - form.fields[6].value = "HC_M2_0606_P" - search_page = @agent.submit(form, form.buttons.first) - p "==================" - p search_page - probe_link = search_page.links.find { |l| l.text =~ /1435395_s_at/ } - probe_link.uri.to_s.must_equal "/show_trait?trait_id=1435395_s_at&dataset=HC_M2_0606_P" - show_trait_page = probe_link.click - # p show_trait_page - - # Get to trait page for 1435395_s_at - - form2 = show_trait_page.forms_with("trait_page")[0] - # [name: corr_dataset value: HC_M2_0606_P] - form2.fields.select { |fld| fld.name == 'corr_dataset' }.first.value.must_equal 'HC_M2_0606_P' - if $options[:database] == :small - form2.fields[30].name.must_equal "value:DBA/2J" - else - form2.fields[30].name.must_equal "variance:C57BL/6J" - end - # form2.fields[30].value.must_equal "15.287" - - # Test every link on the page to check if it's broken or not - break if not $options[:link_checker] - show_trait_page.links.each do |link| - puts link.href - if link.href !~ /static\/dbdoc\/Hippocampus/ and link.href !~ /glossary.html|sample_r|grits.eecs.utk.edu|correlationAnnotation.html/ - # Fetch link, program will crash with exception if link is broken - linkpage = @agent.get(link.href) - puts "Link to #{link.href} is valid, response code #{linkpage.code}" - end - end - - end - - end - -end diff --git a/test/lib/mapping.rb b/test/lib/mapping.rb deleted file mode 100644 index 20e5bd40..00000000 --- a/test/lib/mapping.rb +++ /dev/null @@ -1,58 +0,0 @@ -# In these tests we navigate from the main page to a specific trait then hit the different mapping tool buttons (In this case pylMM and r/qtl) followed by computing the results (marker regressions). - -require 'gntest' - -class MappingTest -end - -describe MappingTest do - before do - @agent = Mechanize.new - @agent.agent.http.ca_file = '/etc/ssl/certs/ca-certificates.crt' - end - - describe MappingTest do - it "pylmm mapping tool selection" do - url = $host+'/marker_regression' - - json = JSON::load(File.read('test/data/input/mapping/1435395_s_at_HC_M2_0606_P.json')) - json["method"] = "pylmm" - # p json - page = @agent.post(URI.encode(url), json) - # Unpacking the page is slow - somehow - but the run is enough as a test - # form = page.forms_with("marker_regression")[0] - # form.fields.select { |fld| fld.name == 'dataset' }.first.value.must_equal 'HC_M2_0606_P' - # form.fields.select { |fld| fld.name == 'value:BXD1' }.first.value.must_equal '6.749' - end - end - - describe MappingTest do - it "R/qtl mapping tool selection" do - url = $host+'/marker_regression' # ?trait_id=1435395_s_at&dataset=HC_M2_0606_P' - - json = JSON::load(File.read('test/data/input/mapping/1435395_s_at_HC_M2_0606_P.json')) - # p json - page = @agent.post(URI.encode(url), - json, - ({'Content-Type' => 'application/x-www-form-urlencoded'})) - form = page.forms_with("marker_regression")[0] - p form - form.fields.select { |fld| fld.name == 'dataset' }.first.value.must_equal 'HC_M2_0606_P' - form.fields.select { |fld| fld.name == 'value:BXD1' }.first.value.must_equal "15.034" - end - end - - describe MappingTest do - it "CIM mapping tool selection (using reaper)" do - url = $host+'/marker_regression' - - json = JSON::load(File.read('test/data/input/mapping/1435395_s_at_HC_M2_0606_P.json')) - json["method"] = "reaper" - page = @agent.post(URI.encode(url), json) - form = page.forms_with("marker_regression")[0] - form.fields.select { |fld| fld.name == 'dataset' }.first.value.must_equal 'HC_M2_0606_P' - form.fields.select { |fld| fld.name == 'value:BXD1' }.first.value.must_equal "15.034" - end - end - -end diff --git a/test/lib/navigation.rb b/test/lib/navigation.rb deleted file mode 100644 index ee9f41d2..00000000 --- a/test/lib/navigation.rb +++ /dev/null @@ -1,43 +0,0 @@ -# In these tests we navigate from the main page to a specific trait then hit the different mapping tool buttons (In this case pylMM and r/qtl) followed by computing the results (marker regressions). - - -class MappingTest -end - -describe MappingTest do - before do - @agent = Mechanize.new - @agent.agent.http.ca_file = '/etc/ssl/certs/ca-certificates.crt' - end - - describe MappingTest do - it "pyLMM mapping tool selection" do - break if $options[:skip_broken] - page = @agent.get($host+'/show_trait?trait_id=1435395_s_at&dataset=HC_M2_0606_P') -#Navigates to http://localhost:5003/show_trait?trait_id=1435395_s_at&dataset=HC_M2_0606_P and clicks respective buttons. - link = page.link_with(text: 'pyLMM') - page = link.click - puts page.uri - link = page.link_with(text: 'Compute') - page = link.click - puts page.uri - probe_link.uri.to_s.must_equal "/marker_regression" - end - end - -end - -describe MappingTest do - it "R/qtl mapping tool selection" do - break if $options[:skip_broken] - page = @agent.get($host+'/show_trait?trait_id=1435395_s_at&dataset=HC_M2_0606_P') - link = page.link_with(text: 'R/qtl') - page = link.click - puts page.uri - form.field_with(:name => 'Methods').options[2].select - link = page.link_with(text: 'Compute') - page = link.click - puts page.uri - probe_link.uri.to_s.must_equal "/marker_regression" - end -end 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 629977ac..ffc698de 100644 --- a/wqflask/wqflask/collect.py +++ b/wqflask/wqflask/collect.py @@ -227,6 +227,7 @@ 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 logger.debug("user_collections are:", user_collections) return render_template("collections/add.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 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): |