mirror of
https://github.com/chenasraf/snpr.git
synced 2026-05-18 01:39:01 +00:00
further work on bootstrap-variant
This commit is contained in:
2
.rvmrc
2
.rvmrc
@@ -4,7 +4,7 @@
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# development environment upon cd'ing into the directory
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# First we specify our desired <ruby>[@<gemset>], the @gemset name is optional.
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environment_id="ruby-1.9.2-p290@rails3"
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environment_id="ruby-1.9.2-p290@opensnp"
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#
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# Uncomment following line if you want options to be set only for given project.
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16
Gemfile.lock
16
Gemfile.lock
@@ -1,8 +1,8 @@
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GIT
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remote: https://github.com/norman/friendly_id.git
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revision: 7ddf7ae5a23795e5d08c643c0ec68ed14bfa9e27
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revision: e39e8e0cbdf3f64350aac14ad7ece85ecf824092
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specs:
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friendly_id (4.0.8)
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friendly_id (4.0.6)
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GIT
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remote: https://github.com/paulasmuth/recommendify.git
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@@ -13,7 +13,7 @@ GIT
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GIT
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remote: https://github.com/ryanb/nested_form.git
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revision: 504985118c2205f36e42417e6d99cecf23385290
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revision: 1cbf61517348c701e08beea41a39f04b35115e6b
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specs:
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nested_form (0.2.1)
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@@ -52,9 +52,11 @@ GEM
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activesupport (3.0.10)
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archive-tar-minitar (0.5.2)
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arel (2.0.10)
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authlogic (3.1.3)
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authlogic (3.1.2)
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activerecord (>= 3.0.0)
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activerecord (>= 3.0.7)
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activesupport (>= 3.0.0)
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activesupport (>= 3.0.7)
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bartt-ssl_requirement (1.4.2)
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bcrypt-ruby (3.0.1)
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builder (2.1.2)
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@@ -63,7 +65,7 @@ GEM
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erubis (2.6.6)
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abstract (>= 1.0.0)
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escape (0.0.4)
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factory_girl (3.4.2)
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factory_girl (3.3.0)
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activesupport (>= 3.0.0)
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i18n (0.5.0)
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jquery-rails (1.0.19)
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@@ -84,7 +86,7 @@ GEM
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mime-types (1.18)
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mocha (0.11.4)
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metaclass (~> 0.0.1)
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nokogiri (1.5.4)
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nokogiri (1.5.3)
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paperclip (2.7.0)
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activerecord (>= 2.3.0)
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activesupport (>= 2.3.2)
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@@ -143,7 +145,7 @@ GEM
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archive-tar-minitar (>= 0.5.2)
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rubyzip (0.9.5)
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shoulda-context (1.0.0)
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shoulda-matchers (1.2.0)
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shoulda-matchers (1.1.0)
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activesupport (>= 3.0.0)
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sinatra (1.2.8)
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rack (~> 1.1)
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@@ -1,5 +1,5 @@
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<div class="row">
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<div class="span8 columns">
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<div class="span6 columns">
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<%= form_for(@genotype,:html => {:class => "form-stacked", :multipart => true}) do |f| %>
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<%= render 'shared/error_messages', :target => @genotype %>
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<div class="well">
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@@ -41,7 +41,7 @@
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</div>
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</div>
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<div class="actions">
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<%= f.submit "Upload", :class => "primary btn" %>
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<%= f.submit "Upload", :class => "btn btn-primary" %>
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</div>
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<% end %>
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</div>
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@@ -10,7 +10,7 @@
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<%end%>
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<h5><a href="https://github.com/superbobry/snpy">Python-library to parse the provided files</a>, courtesy of <a href="https://github.com/superbobry/">Sergei Lebedev</a></h5>
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<table class="zebra-striped" id="all_genotypes">
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<table class="table table-striped" id="all_genotypes">
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<thead>
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<tr>
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<th>#</th>
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@@ -1,7 +1,7 @@
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<div class="leftside">
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<h1>Welcome to <em>openSNP</em></h1>
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<p><%=image_tag "/images/microarray.png",:style => "float:left;margin: 10px"%></p>
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<p><h7><em>openSNP</em> allows customers of direct-to-customer genetic tests to publish their test results, find others with similar genetic variations, learn more about their results, find the latest primary literature on their variations and help scientists to find new associations.</h7></p> <center><a href="/signup" class="btn large primary">Sign Up!</a></center><br/><br/>
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<p><h7><em>openSNP</em> allows customers of direct-to-customer genetic tests to publish their test results, find others with similar genetic variations, learn more about their results, find the latest primary literature on their variations and help scientists to find new associations.</h7></p> <center><a href="/signup" class="btn btn-primary btn-large">Sign Up!</a></center><br/><br/>
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<div id="tab-container">
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<ul class="nav nav-tabs">
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<li><a href="#dtcustomers">For Genotyping Users</a></li>
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@@ -41,21 +41,21 @@
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<div class="row">
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<div class="span5 columns offset">
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<div class="alert-message block-message success" data-alert="alert">
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<h5>Search for phenotypes</h5>
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<h4 class="alert-heading">Search for phenotypes</h4>
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<%=image_tag("/images/phenotypesearch.png")%>
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Many diseases and traits are suspected to have genetical components. Genome Wide Association Studies are a simple tool find genetic markers. Easily find people with the variation you are interested in via openSNP.<br/><br/>The variation you are looking for is not entered yet? Just add it to <em>openSNP</em>
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</div>
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</div>
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<div class="span5 columns">
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<div class="alert-message block-message success" data-alert="alert">
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<h5>Easily download datasets</h5>
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<h4 class="alert-heading">Easily download datasets</h4>
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<%=image_tag("/images/filedownload.png")%>
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The mass download-function of <em>openSNP</em> allows you to easily download the full genotyping raw-data in the file formats that are provided by <em>23andMe</em> and <em>deCODEme</em>.<br/><br/>As the files can be grouped by their variations for specific phenotypes it is easy to get datasets that are already usable for association studies.
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</div>
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</div>
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<div class="span5 columns">
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<div class="alert-message block-message success" data-alert="alert">
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<h5>Get notified about new data</h5>
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<h4 class="alert-heading">Get notified about new data</h4>
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<%=image_tag("/images/rss.png")%>
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<em>openSNP</em> delivers a RSS-feed for each phenotype. So you can easily get all new datasets that get available for the phenotypes of your interest, without the need to check for new entries by hand.<br/><br/>For all data junkies that need more data: There is also a feed that carries all new datasets.
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</div>
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@@ -33,7 +33,7 @@
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<ul class="nav secondary-nav">
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<% if current_user %>
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<li class="dropdown">
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<a href="#" class="dropdown-toggle"><%= image_tag current_user.avatar.url(:head),:style => "vertical-align:middle"%> <%= current_user.name %></a>
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<a href="#" class="dropdown-toggle"><%= image_tag current_user.avatar.url(:head),:style => "vertical-align:middle"%> <%= current_user.name %><b class="caret"></b></a>
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<ul class="dropdown-menu">
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<li><%= link_to("Settings", :controller => "users", :action => "edit",:id => current_user) %></li>
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<li><%= link_to("Edit Your Phenotypes", "/users/"+current_user.id.to_s+"/edit#phenotypes")%>
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@@ -56,35 +56,35 @@
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<div class="container">
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<%if current_user %>
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<%unless (current_user.help_one or current_user.has_sequence) && (current_user.help_two or current_user.user_phenotypes != []) && (current_user.help_three or current_user.phenotype_creation_counter != 0) == true%>
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<div class ="well">
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<div class ="alert alert-block alert-success">
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<div class="row">
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<center><h4>Welcome to openSNP. Here are some first steps you could do:</h4></center>
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<center><h3>Welcome to openSNP. Here are some first steps you could do:</h3></center>
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<%if current_user.has_sequence == false and current_user.help_one == false%>
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<div class="span5 columns offset1">
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<div class="span3 offset1">
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<div class="alert-message block-message success" data-alert="alert">
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<%=link_to(raw("×"),{:controller => "users", :action => "remove_help_one", :id => current_user},:remote => true, id: "remove_help_one", :class => "close")%>
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<h5>Upload Your Genotyping File</h5>
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<%=link_to(image_tag("/images/fileupload.png"), "/genotypes/new")%>
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<h4 class="alert-heading">Upload Your Genotyping File</h4>
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<%=link_to(image_tag("/images/fileupload.png"), "/genotypes/new")%><br/>
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<%=link_to("Upload the genotyping raw-data you got","/genotypes/new")%> from <em>23andMe</em> or <em>deCODEme</em> to the database of <em>openSNP</em> to share it with other personal genomics customers and scientists from all over the world.
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</div>
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</div>
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<%end%>
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<%if current_user.user_phenotypes == [] and current_user.help_two == false%>
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<div class="span5 columns">
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<div class="span3 offset1">
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<div class="alert-message block-message success" data-alert="alert">
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<%=link_to(raw("×"),{:controller => "users", :action => "remove_help_two", :id => current_user},:remote => true, id: "remove_help_two", :class => "close")%>
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<h5>Enter Your Variations</h5>
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<%=link_to(image_tag("/images/phenotypes.png"), "/users/"+current_user.id.to_s+"#unentered_variations")%>
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<h4 class="alert-heading">Enter Your Variations</h4>
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<%=link_to(image_tag("/images/phenotypes.png"), "/users/"+current_user.id.to_s+"#unentered_variations")%><br/>
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Let us, and the other <em>openSNP</em>-users, know some of your characteristics. Like hair or eye color. Or about some diseases? <%=link_to("Whatever you feel like sharing","/users/"+current_user.id.to_s+"#unentered_variations")%>.
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</div>
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</div>
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<%end%>
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<%if current_user.phenotype_creation_counter == 0 and current_user.help_three == false %>
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<div class="span5 columns">
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<div class="span3 offset1">
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<div class="alert-message block-message success" data-alert="alert">
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<%=link_to(raw("×"),{:controller => "users", :action => "remove_help_three", :id => current_user},:remote => true, id: "remove_help_three", :class => "close")%>
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<h5>Enter a New Phenotype</h5>
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<%=link_to(image_tag("/images/addphenotype.png"), "/phenotypes/new")%>
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<h4 class="alert-heading">Enter a New Phenotype</h4>
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<%=link_to(image_tag("/images/addphenotype.png"), "/phenotypes/new")%><br/>
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Got an idea for a phenotype that has not been asked about yet and that could have genetical roots? <%=link_to("Great, you can easily add this","/phenotypes/new")%> to the <em>openSNP</em>-database.
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</div>
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</div>
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@@ -96,28 +96,29 @@
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<%end%>
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<div class="container" id="alert-messages">
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<div id="flash_notice" class="alert-message success" style="display:none"></div>
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<div id="flash_notice" class="alert alert-success" style="display:none"></div>
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<% if flash[:notice] %>
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<div class="alert-message success" data-alert="alert">
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<div class="alert alert-success" data-alert="alert">
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<a class="close" href="#">x</a>
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<p><%= flash[:notice] %></p>
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<strong><%= flash[:notice] %></strong>
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</div>
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<% end %>
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<% if flash[:warning] %>
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<div class="alert-message error" data-alert="alert">
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<div class="alert alert-error" data-alert="alert">
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<a class="close" href="#">x</a>
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<p><%= flash[:warning] %></p>
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<strong><%= flash[:warning] %></strong>
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</div>
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<% end %>
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<% if flash[:achievement] %>
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<div class="alert-message info" data-alert="alert">
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<div class="alert alert-info" data-alert="alert">
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<a class="close" href="#">x</a>
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<p><%= flash[:achievement] %></p>
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<strong><%= flash[:achievement] %></strong>
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</div>
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<% end %>
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<%= yield %>
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</div>
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</div>
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<hr />
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<footer class="footer">
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||||
<div class="container">
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<p>
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@@ -19,6 +19,6 @@
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</div>
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</div>
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<div class="actions">
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<%= f.submit "Send", :class => "primary btn"%>
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<%= f.submit "Send", :class => "btn btn-primary"%>
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</div>
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<% end %>
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@@ -1,6 +1,6 @@
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<h1>News</h1>
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<div id="tab-container">
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<ul class="tabs">
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||||
<ul class="nav nav-tabs">
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<li><a href="#general">On openSNP</a></li>
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<li><a href="#users">New users</a></li>
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<li><a href="#genotypes">New genotypes</a></li>
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@@ -57,7 +57,7 @@ Hello everyone! We've implemented a minor change, you can now access SNPs over t
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<%=auto_discovery_link_tag(:rss,"/rss", {:title => "RSS for all genotypes"})%>
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<h2>Genotypes</h2>
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<%=link_to(image_tag("/images/rss_small.png"),"/rss")%>
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<table class="common-table zebra-striped">
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||||
<table class="table table-striped">
|
||||
<tr>
|
||||
<th>#</th>
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||||
<th>Genotype-ID</th>
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||||
@@ -80,7 +80,7 @@ Hello everyone! We've implemented a minor change, you can now access SNPs over t
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||||
</div>
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||||
<div id="users">
|
||||
<h2>Users</h2>
|
||||
<table class="common-table zebra-striped">
|
||||
<table class="table table-striped">
|
||||
<tr>
|
||||
<td>#</th>
|
||||
<th>ID</th>
|
||||
@@ -101,7 +101,7 @@ Hello everyone! We've implemented a minor change, you can now access SNPs over t
|
||||
</div>
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||||
<div id="phenotypes">
|
||||
<h2>Phenotypes</h2>
|
||||
<table class="common-table zebra-striped">
|
||||
<table class="table table-striped">
|
||||
<tr>
|
||||
<th>Name</th>
|
||||
<th>Variations</th>
|
||||
@@ -119,7 +119,7 @@ Hello everyone! We've implemented a minor change, you can now access SNPs over t
|
||||
|
||||
<div id="phenotypecomments">
|
||||
<h2>Phenotype Comments</h2>
|
||||
<table class="common-table zebra-striped">
|
||||
<table class="table table-striped">
|
||||
<tr>
|
||||
<th>Phenotype</th>
|
||||
<th>Comment By</th>
|
||||
@@ -141,7 +141,7 @@ Hello everyone! We've implemented a minor change, you can now access SNPs over t
|
||||
|
||||
<div id="snpcomments">
|
||||
<h2>SNP Comments</h2>
|
||||
<table class="common-table zebra-striped">
|
||||
<table class="table table-striped">
|
||||
<tr>
|
||||
<th>SNP</th>
|
||||
<th>Comment By</th>
|
||||
@@ -163,7 +163,7 @@ Hello everyone! We've implemented a minor change, you can now access SNPs over t
|
||||
<%=link_to(image_tag("/images/rss_small.png"),"/paper/rss")%>
|
||||
<%=auto_discovery_link_tag(:rss,"/paper/rss", {:title => "RSS for latest publications"})%>
|
||||
<h2>Latest publications</h2>
|
||||
<table class="common-table zebra-striped">
|
||||
<table class="table table-striped">
|
||||
<tr>
|
||||
<th>SNP</th>
|
||||
<th>Author</th>
|
||||
|
||||
@@ -6,5 +6,5 @@ Fill out the form below and instructions to reset your password will be emailed
|
||||
<% form_tag password_resets_path do %>
|
||||
<label>Email:</label>
|
||||
<%= text_field_tag "email" %>
|
||||
<%= submit_tag "Reset my password", :class => "primary btn" %>
|
||||
<%= submit_tag "Reset my password", :class => "btn btn-primary" %>
|
||||
<% end %>
|
||||
|
||||
@@ -12,6 +12,6 @@
|
||||
<%= f.text_area :comment_text, :size => "20x5" %>
|
||||
</div>
|
||||
|
||||
<%= f.submit "Comment", :class => "primary btn" %>
|
||||
<%= f.submit "Comment", :class => "btn btn-primary" %>
|
||||
<% end %>
|
||||
</div>
|
||||
|
||||
@@ -1,5 +1,5 @@
|
||||
<h3>Your Download can start soon...</h3>
|
||||
|
||||
<div class="alert-message block-message success">
|
||||
<div class="alert alert-block alert-success">
|
||||
<%=image_tag("/images/filedownload.png",:style => "float:left")%><h7>Our servers are working hard to deliver you a file that includes all the genotyping files of users with a variation of <em><%=@variation%></em> at the phenotype <em><%=@phenotype.characteristic%></em>.<br/><br/>The genotyping-files currently get zipped to lighten your download. You will receive the download-link via the eMail-address you registered your account with, as soon as the file is ready.</h7></div>
|
||||
<%=link_to "Go Back","/phenotypes/"+@phenotype.id.to_s%>
|
||||
@@ -1,6 +1,6 @@
|
||||
<h1>Listing all Phenotypes</h1>
|
||||
<%if current_user%><div class="row"><div class="span10 columns offset6"><h5><%=link_to(image_tag("/images/addphenotype_small.png",:style => "vertical-align:middle" ),:action =>"new")%> <%=link_to "The phenotype of your interest is missing? Add a new one!",:action => "new"%></h5></div></div><%end%>
|
||||
<table class="zebra-striped" id="no_snp_overview">
|
||||
<table class="table table-striped" id="no_snp_overview">
|
||||
<thead>
|
||||
<tr>
|
||||
<th>#</th>
|
||||
|
||||
@@ -29,5 +29,5 @@
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<%= f.submit :class => "primary btn" %>
|
||||
<%= f.submit :class => "btn btn-primary" %>
|
||||
<% end %>
|
||||
|
||||
@@ -19,7 +19,7 @@ Below you find <%=@similar_phenotypes.size%> <%if @similar_phenotypes.size > 1%>
|
||||
<div class="row">
|
||||
<%@similar_phenotypes.each do |s|%>
|
||||
<div class="span<%=(16/@similar_phenotypes.size).to_i%> columns">
|
||||
<div class="alert-message block-message success" data-alert="alert">
|
||||
<div class="alert alert-block alert-success" data-alert="alert">
|
||||
<h6><%=link_to s.characteristic,s%></h6>
|
||||
Description: <em><%=s.description%></em>
|
||||
</div>
|
||||
|
||||
@@ -25,7 +25,7 @@
|
||||
</ul>
|
||||
|
||||
<div id="tab-container">
|
||||
<ul class="tabs">
|
||||
<ul class="nav nav-tabs">
|
||||
<li><a href="#description">Description</a></li>
|
||||
<li><a href="#similar">Similar phenotypes</a></li>
|
||||
<li><a href="#users">Users sharing this phenotype (<%=@phenotype.user_phenotypes.length%>)</a></li>
|
||||
@@ -38,7 +38,7 @@
|
||||
</div>
|
||||
</div>
|
||||
<div id="users">
|
||||
<table class="zebra-striped">
|
||||
<table class="table table-striped">
|
||||
<tr>
|
||||
<th>User</th>
|
||||
<th>Variation</th>
|
||||
@@ -65,7 +65,7 @@
|
||||
</div>
|
||||
|
||||
<div id="similar">
|
||||
<table class="zebra-striped">
|
||||
<table class="table table-striped">
|
||||
<tr>
|
||||
<th>Phenotype</th>
|
||||
<th>Number of Users</th>
|
||||
|
||||
@@ -1,5 +1,5 @@
|
||||
<% if target.errors.any? %>
|
||||
<div class="alert-message block-message error">
|
||||
<div class="alert alert-block alert-error">
|
||||
<% target.errors.full_messages.each do |msg| %>
|
||||
<%= msg %><br/>
|
||||
<% end %>
|
||||
|
||||
@@ -1,6 +1,6 @@
|
||||
<div class="row">
|
||||
<div class="span14 columns offset1">
|
||||
<div class="alert-message block-message error">
|
||||
<div class="span12">
|
||||
<div class="alert alert-block alert-error">
|
||||
<p><strong>Important:</strong> Please carefully read the disclaimer on the right-hand side.</p>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
@@ -1,4 +1,4 @@
|
||||
<div class="span8 columns">
|
||||
<div class="span6 columns">
|
||||
<div class="well">
|
||||
<p><strong>By signing up for openSNP you declare that you have understood the possible risks and side-effects that can occur by making your genetical and medical information available on this platform. In short:</strong><br/><br/></p>
|
||||
<p><ul>
|
||||
|
||||
@@ -1,6 +1,6 @@
|
||||
<h3>Frequently Asked Questions</h3>
|
||||
<div id="tab-container">
|
||||
<ul class="tabs">
|
||||
<ul class="nav nav-tabs">
|
||||
<li><a href="#dtcustomers"><%=image_tag("/images/fileupload_small.png",:style => "vertical-align:middle" )%> Uploading data</a></li>
|
||||
<li><a href="#scientists"><%=image_tag("/images/filedownload_small.png",:style => "vertical-align:middle" )%> Downloading data</a></li>
|
||||
<li><a href="#enteringphenotypes"><%=image_tag("/images/add_variation_small.png",:style => "vertical-align:middle")%> Entering phenotypes</a></li>
|
||||
|
||||
@@ -3,7 +3,7 @@
|
||||
<%= render 'shared/error_messages', :target => @user %>
|
||||
<div id="post_errors" style="display:none"></div>
|
||||
<div id="tab-container">
|
||||
<ul class="tabs">
|
||||
<ul class="nav nav-tabs">
|
||||
<li><a href="#general">General</a></li>
|
||||
<li><a href="#phenotypes">Phenotypes</a></li>
|
||||
<li><a href="#details">Details</a></li>
|
||||
@@ -118,6 +118,6 @@
|
||||
|
||||
|
||||
<div class="actions">
|
||||
<%= f.submit "Update Information", :class => "primary btn", :id => "update_user" %>
|
||||
<%= f.submit "Update Information", :class => "btn btn-primary", :id => "update_user" %>
|
||||
</div>
|
||||
<% end %>
|
||||
|
||||
@@ -1,5 +1,5 @@
|
||||
<div class="row">
|
||||
<div class="span8 columns">
|
||||
<div class="span6 columns">
|
||||
<% # helper thing so we don't have to put up fields into every page %>
|
||||
<div class="well">
|
||||
<%= form_for @user, :html => {:class => "form-stacked"} do |f| %>
|
||||
|
||||
@@ -40,7 +40,7 @@
|
||||
<% end %>
|
||||
</p>
|
||||
<div id="tab-container">
|
||||
<ul class="tabs">
|
||||
<ul class="nav nav-tabs">
|
||||
<% if 1==2 %><li><a href="#snps"><%=@first_name%>'s SNPs</a></li><% end %>
|
||||
<li><a href="#variations"><%= @first_name %>'s variations</a></li>
|
||||
</ul>
|
||||
|
||||
@@ -24,7 +24,7 @@
|
||||
<% end %>
|
||||
|
||||
<div id="tab-container">
|
||||
<ul class="tabs">
|
||||
<ul class="nav nav-tabs">
|
||||
<%if @unentered_phenotypes != []%>
|
||||
<li><a href="#unentered_variations">Variations you did not enter yet (<%=@unentered_phenotypes.length%>)</a></li>
|
||||
<%end%>
|
||||
@@ -139,7 +139,7 @@
|
||||
<% if @paginated_phenotype_replies != [] %>
|
||||
<h4>Latest replies on your comments on Phenotypes</h4>
|
||||
|
||||
<table class="zebra-striped" id="phenotype_reply_comments">
|
||||
<table class="table table-striped" id="phenotype_reply_comments">
|
||||
<thead>
|
||||
<tr>
|
||||
<th>On Phenotype</th>
|
||||
@@ -166,7 +166,7 @@
|
||||
|
||||
<% if @paginated_snp_replies != [] %>
|
||||
<h4>Latest replies on your comments on SNPs</h4>
|
||||
<table class="zebra-striped" id="snp_reply_comments">
|
||||
<table class="table table-striped" id="snp_reply_comments">
|
||||
<thead>
|
||||
<tr>
|
||||
<th>On SNP</th>
|
||||
|
||||
@@ -1,4 +1,4 @@
|
||||
<table class="common-table zebra-striped">
|
||||
<table class="table table-striped">
|
||||
<tr>
|
||||
<th>Characteristic</th>
|
||||
<th>Variation</th>
|
||||
|
||||
@@ -1,6 +1,6 @@
|
||||
<h3>Change your email-address and password</h3>
|
||||
<div class="row">
|
||||
<div class="span8 columns">
|
||||
<div class="span12 columns">
|
||||
<% # helper thing so we don't have to put up fields into every page %>
|
||||
<div class="well">
|
||||
<%= form_for @user, :html => {:class => "form-stacked"} do |f| %>
|
||||
@@ -22,7 +22,7 @@
|
||||
</div>
|
||||
|
||||
<div class="actions">
|
||||
<%= f.submit "Update Information",:class => "primary btn"%>
|
||||
<%= f.submit "Update Information",:class => "btn btn-primary"%>
|
||||
</div>
|
||||
<% end %>
|
||||
</div>
|
||||
|
||||
@@ -1,6 +1,6 @@
|
||||
<div class="row">
|
||||
<div class="span10"><h1>Edit your details</h1></div>
|
||||
<div class="span6"><%= link_to 'Back Home', current_user %></div>
|
||||
<div class="span8"><h1>Edit your details</h1></div>
|
||||
<div class="span4"><%= link_to 'Back Home', current_user %></div>
|
||||
</div>
|
||||
<%= render 'edit' %>
|
||||
|
||||
|
||||
Reference in New Issue
Block a user