caruby-scat 1.2.1

data/public/stylesheets/layout.css

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+/*
+* Skeleton V1.1
+* Copyright 2011, Dave Gamache
+* www.getskeleton.com
+* Free to use under the MIT license.
+* http://www.opensource.org/licenses/mit-license.php
+* 8/17/2011
+*/
+
+/* Table of Content
+==================================================
+	#Site Styles
+	#Page Styles
+	#Media Queries
+	#Font-Face */
+
+/* #Site Styles
+================================================== */
+
+/* #Page Styles
+================================================== */
+
+/* #Media Queries
+================================================== */
+
+	/* Smaller than standard 960 (devices and browsers) */
+	@media only screen and (max-width: 959px) {}
+
+	/* Tablet Portrait size to standard 960 (devices and browsers) */
+	@media only screen and (min-width: 768px) and (max-width: 959px) {}
+
+	/* All Mobile Sizes (devices and browser) */
+	@media only screen and (max-width: 767px) {}
+
+	/* Mobile Landscape Size to Tablet Portrait (devices and browsers) */
+	@media only screen and (min-width: 480px) and (max-width: 767px) {}
+
+	/* Mobile Portrait Size to Mobile Landscape Size (devices and browsers) */
+	@media only screen and (max-width: 479px) {}
+
+
+/* #Font-Face
+================================================== */
+/* 	This is the proper syntax for an @font-face file
+		Just create a "fonts" folder at the root,
+		copy your FontName into code below and remove
+		comment brackets */
+
+/*	@font-face {
+	    font-family: 'FontName';
+	    src: url('../fonts/FontName.eot');
+	    src: url('../fonts/FontName.eot?iefix') format('eot'),
+	         url('../fonts/FontName.woff') format('woff'),
+	         url('../fonts/FontName.ttf') format('truetype'),
+	         url('../fonts/FontName.svg#webfontZam02nTh') format('svg');
+	    font-weight: normal;
+	    font-style: normal; }
+*/

data/public/stylesheets/scat.css

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+body {
+  background: #FAFFF6
+}
+
+h1.application {
+  font-family: "Handwriting - Dakota", Pristina, "Rage Italic", "Comic Sans MS", Georgia, serif;
+  font-weight: bold;
+  color: DarkBlue;
+}
+
+a.help {
+  display: block;
+  float: left;
+  left: -20px;
+  top: 4px;
+  text-decoration: none;
+  position: relative;
+}
+
+a.help img {
+  width: 15px;
+  height: 15px;
+}
+
+a.help span {
+  display: none;
+}
+
+a.help:hover span {
+  display: block;
+  position: absolute;
+  width: 180px;
+  padding: 5px 5px;
+  margin: 0 0 1px;
+  border: 1px solid black;
+  z-index: 100;
+  background-color: #eeeeee;
+  font: 10px sans-serif;
+}
+
+label {
+  left: -15px;
+  position: relative;
+}
+
+.ui-menu .ui-menu-item a {
+  font-size: smaller;
+  line-height: 1;
+}
+
+input[type='checkbox'] {
+  position: relative;
+  left: -1em;
+  margin-bottom: 20px;
+}
+
+#malignant label {
+  float: left;
+}
+
+#quantity input {
+  max-width: 8em;
+}
+

data/public/stylesheets/skeleton.css

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+/*
+* Skeleton V1.1
+* Copyright 2011, Dave Gamache
+* www.getskeleton.com
+* Free to use under the MIT license.
+* http://www.opensource.org/licenses/mit-license.php
+* 8/17/2011
+*/
+
+
+/* Table of Contents
+==================================================
+    #Base 960 Grid
+    #Tablet (Portrait)
+    #Mobile (Portrait)
+    #Mobile (Landscape)
+    #Clearing */
+
+
+
+/* #Base 960 Grid
+================================================== */
+
+    .container                                  { position: relative; width: 960px; margin: 0 auto; padding: 0; }
+    .container .column,
+    .container .columns                         { float: left; display: inline; margin-left: 10px; margin-right: 10px; }
+    .row                                        { margin-bottom: 20px; }
+
+    /* Nested Column Classes */
+    .column.alpha, .columns.alpha               { margin-left: 0; }
+    .column.omega, .columns.omega               { margin-right: 0; }
+
+    /* Base Grid */
+    .container .one.column,
+    .container .one.columns                     { width: 40px;  }
+    .container .two.columns                     { width: 100px; }
+    .container .three.columns                   { width: 160px; }
+    .container .four.columns                    { width: 220px; }
+    .container .five.columns                    { width: 280px; }
+    .container .six.columns                     { width: 340px; }
+    .container .seven.columns                   { width: 400px; }
+    .container .eight.columns                   { width: 460px; }
+    .container .nine.columns                    { width: 520px; }
+    .container .ten.columns                     { width: 580px; }
+    .container .eleven.columns                  { width: 640px; }
+    .container .twelve.columns                  { width: 700px; }
+    .container .thirteen.columns                { width: 760px; }
+    .container .fourteen.columns                { width: 820px; }
+    .container .fifteen.columns                 { width: 880px; }
+    .container .sixteen.columns                 { width: 940px; }
+
+    .container .one-third.column                { width: 300px; }
+    .container .two-thirds.column               { width: 620px; }
+
+    /* Offsets */
+    .container .offset-by-one                   { padding-left: 60px;  }
+    .container .offset-by-two                   { padding-left: 120px; }
+    .container .offset-by-three                 { padding-left: 180px; }
+    .container .offset-by-four                  { padding-left: 240px; }
+    .container .offset-by-five                  { padding-left: 300px; }
+    .container .offset-by-six                   { padding-left: 360px; }
+    .container .offset-by-seven                 { padding-left: 420px; }
+    .container .offset-by-eight                 { padding-left: 480px; }
+    .container .offset-by-nine                  { padding-left: 540px; }
+    .container .offset-by-ten                   { padding-left: 600px; }
+    .container .offset-by-eleven                { padding-left: 660px; }
+    .container .offset-by-twelve                { padding-left: 720px; }
+    .container .offset-by-thirteen              { padding-left: 780px; }
+    .container .offset-by-fourteen              { padding-left: 840px; }
+    .container .offset-by-fifteen               { padding-left: 900px; }
+
+
+
+/* #Tablet (Portrait)
+================================================== */
+
+    /* Note: Design for a width of 768px */
+
+    @media only screen and (min-width: 768px) and (max-width: 959px) {
+        .container                                  { width: 768px; }
+        .container .column,
+        .container .columns                         { margin-left: 10px; margin-right: 10px;  }
+        .column.alpha, .columns.alpha               { margin-left: 0; margin-right: 10px; }
+        .column.omega, .columns.omega               { margin-right: 0; margin-left: 10px; }
+        .alpha.omega                                { margin-left: 0; margin-right: 0; }
+
+        .container .one.column,
+        .container .one.columns                     { width: 28px; }
+        .container .two.columns                     { width: 76px; }
+        .container .three.columns                   { width: 124px; }
+        .container .four.columns                    { width: 172px; }
+        .container .five.columns                    { width: 220px; }
+        .container .six.columns                     { width: 268px; }
+        .container .seven.columns                   { width: 316px; }
+        .container .eight.columns                   { width: 364px; }
+        .container .nine.columns                    { width: 412px; }
+        .container .ten.columns                     { width: 460px; }
+        .container .eleven.columns                  { width: 508px; }
+        .container .twelve.columns                  { width: 556px; }
+        .container .thirteen.columns                { width: 604px; }
+        .container .fourteen.columns                { width: 652px; }
+        .container .fifteen.columns                 { width: 700px; }
+        .container .sixteen.columns                 { width: 748px; }
+
+        .container .one-third.column                { width: 236px; }
+        .container .two-thirds.column               { width: 492px; }
+
+        /* Offsets */
+        .container .offset-by-one                   { padding-left: 48px; }
+        .container .offset-by-two                   { padding-left: 96px; }
+        .container .offset-by-three                 { padding-left: 144px; }
+        .container .offset-by-four                  { padding-left: 192px; }
+        .container .offset-by-five                  { padding-left: 240px; }
+        .container .offset-by-six                   { padding-left: 288px; }
+        .container .offset-by-seven                 { padding-left: 336px; }
+        .container .offset-by-eight                 { padding-left: 384px; }
+        .container .offset-by-nine                  { padding-left: 432px; }
+        .container .offset-by-ten                   { padding-left: 480px; }
+        .container .offset-by-eleven                { padding-left: 528px; }
+        .container .offset-by-twelve                { padding-left: 576px; }
+        .container .offset-by-thirteen              { padding-left: 624px; }
+        .container .offset-by-fourteen              { padding-left: 672px; }
+        .container .offset-by-fifteen               { padding-left: 720px; }
+    }
+
+
+/*  #Mobile (Portrait)
+================================================== */
+
+    /* Note: Design for a width of 320px */
+
+    @media only screen and (max-width: 767px) {
+        .container { width: 300px; }
+        .container .columns,
+        .container .column { margin: 0; }
+
+        .container .one.column,
+        .container .one.columns,
+        .container .two.columns,
+        .container .three.columns,
+        .container .four.columns,
+        .container .five.columns,
+        .container .six.columns,
+        .container .seven.columns,
+        .container .eight.columns,
+        .container .nine.columns,
+        .container .ten.columns,
+        .container .eleven.columns,
+        .container .twelve.columns,
+        .container .thirteen.columns,
+        .container .fourteen.columns,
+        .container .fifteen.columns,
+        .container .sixteen.columns,
+        .container .one-third.column,
+        .container .two-thirds.column  { width: 300px; }
+
+        /* Offsets */
+        .container .offset-by-one,
+        .container .offset-by-two,
+        .container .offset-by-three,
+        .container .offset-by-four,
+        .container .offset-by-five,
+        .container .offset-by-six,
+        .container .offset-by-seven,
+        .container .offset-by-eight,
+        .container .offset-by-nine,
+        .container .offset-by-ten,
+        .container .offset-by-eleven,
+        .container .offset-by-twelve,
+        .container .offset-by-thirteen,
+        .container .offset-by-fourteen,
+        .container .offset-by-fifteen { padding-left: 0; }
+
+    }
+
+
+/* #Mobile (Landscape)
+================================================== */
+
+    /* Note: Design for a width of 480px */
+
+    @media only screen and (min-width: 480px) and (max-width: 767px) {
+        .container { width: 420px; }
+        .container .columns,
+        .container .column { margin: 0; }
+
+        .container .one.column,
+        .container .one.columns,
+        .container .two.columns,
+        .container .three.columns,
+        .container .four.columns,
+        .container .five.columns,
+        .container .six.columns,
+        .container .seven.columns,
+        .container .eight.columns,
+        .container .nine.columns,
+        .container .ten.columns,
+        .container .eleven.columns,
+        .container .twelve.columns,
+        .container .thirteen.columns,
+        .container .fourteen.columns,
+        .container .fifteen.columns,
+        .container .sixteen.columns,
+        .container .one-third.column,
+        .container .two-thirds.column { width: 420px; }
+    }
+
+
+/* #Clearing
+================================================== */
+
+    /* Self Clearing Goodness */
+    .container:after { content: "\0020"; display: block; height: 0; clear: both; visibility: hidden; }
+
+    /* Use clearfix class on parent to clear nested columns,
+    or wrap each row of columns in a <div class="row"> */
+    .clearfix:before,
+    .clearfix:after,
+    .row:before,
+    .row:after {
+      content: '\0020';
+      display: block;
+      overflow: hidden;
+      visibility: hidden;
+      width: 0;
+      height: 0; }
+    .row:after,
+    .clearfix:after {
+      clear: both; }
+    .row,
+    .clearfix {
+      zoom: 1; }
+
+    /* You can also use a <br class="clear" /> to clear columns */
+    .clear {
+      clear: both;
+      display: block;
+      overflow: hidden;
+      visibility: hidden;
+      width: 0;
+      height: 0;
+    }

data/spec/autocomplete_spec.rb

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+require 'spec/spec_helper'
+
+describe Scat do
+  describe 'Auto-complete' do
+    include Scat::Autocomplete
+    
+    AC_TARGET ||= 'Malignant lymphoma'
+    
+    it "should find matching diagnoses" do
+      matches = autocomplete(:clinical_diagnosis, AC_TARGET) 
+      matches.should_not be_empty
+      matches.each do |cv|
+        cv.downcase.should match AC_TARGET.downcase
+      end
+    end
+  end
+end

data/spec/edit_spec.rb

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+require 'spec/spec_helper'
+require 'jinx/helpers/string_uniquifier'
+require 'scat/edit'
+require File.dirname(__FILE__) + '/../test/fixtures/seed'
+
+describe Scat do
+  describe 'Edit' do
+    before(:all) do
+      title = Jinx::StringUniquifier.uniquify('Scat')
+      pcl = Scat::Seed.protocol_for(title).find(:create)
+      @params = {
+        :user => pcl.coordinators.first,
+        :protocol => title,
+        :mrn => Jinx::StringUniquifier.uniquify('Test'),
+        :spn => Jinx::StringUniquifier.uniquify('Test'),
+        :diagnosis => '[M]Adrenal cortical adenoma NOS',
+        :tissue_site => 'Adrenal gland, NOS',
+        :malignant => 'Malignant',
+        :quantity => '4'
+      }
+      @spc = Scat::Edit.instance.save(@params)
+    end
+    
+    subject { @spc }
+    
+    it "should save the specimen" do
+      subject.identifier.should_not be nil
+    end
+    
+    it "should set the properties" do
+      subject.pathological_status.should == 'Malignant' 
+      scg = subject.specimen_collection_group
+      scg.clinical_diagnosis.should == '[M]Adrenal cortical adenoma NOS' 
+      subject.characteristics.tissue_site.should == 'Adrenal gland, NOS' 
+      subject.initial_quantity.should == 4.0 
+    end
+    
+    context "add a normal specimen to an existing SCG" do
+      before(:all) do
+        oparams = @params.delete_if { |k, v| k == :malignant }
+        oparams[:quantity] = '5'
+        @other = Scat::Edit.instance.save(oparams)
+      end  
+      
+      it "should save the additional specimen" do 
+        @other.identifier.should_not be nil
+        @other.identifier.should_not == subject.identifier
+        @other.initial_quantity.should == 5.0 
+      end
+      
+      it "should be non-malignant" do 
+        @other.pathological_status.should == 'Non-Malignant'
+      end
+      
+      it "should use the same SCG" do
+        @other.specimen_collection_group.identifier.should be subject.specimen_collection_group.identifier
+      end
+    end
+  end
+end

data/spec/spec_helper.rb

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+require 'rubygems'
+require 'bundler/setup'
+Bundler.require(:test, :development)
+require 'scat'
+
+module Scat::Test
+  RESULTS = File.dirname(__FILE__) + '/../test/results'
+end
+
+# Open the logger.
+logger(Scat::Test::RESULTS + '/log/scat.log', :debug => true)
+
+Dir[File.dirname(__FILE__) + '/support/**/*.rb'].each { |f| require f }