caruby-core 1.4.1 → 1.4.2

data/History.txt

@@ -2,3 +2,7 @@
 
 * Initial public release
 
+=== 1.4.2 / 2010-11-30
+
+* Minor Migrator fixes
+

data/LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2010 Oregon Health & Science University Knight Cancer Institute
+Copyright (c) 2010 Oregon Health & Science University
 
 Permission is hereby granted, free of charge, to any person
 obtaining a copy of this software and associated documentation

data/README.md

@@ -1,8 +1,8 @@
 caRuby: Simplifying caBIG(TM)
 =============================
 
-**Home**:          [http://caruby.rubyforge.com](http://caruby.rubyforge.com)
-**Git**:          [http://github.com/caruby/core](http://github.com/caruby/core)   
+**Home**:         [http://caruby.rubyforge.org](http://caruby.rubyforge.org)    
+**Git**:          [http://github.com/caruby/core](http://github.com/caruby/core)       
 **Author**:       OHSU Knight Cancer Institute    
 **Copyright**:    2010    
 **License**:      MIT License    
@@ -35,7 +35,7 @@ is installed.
 Usage
 -----
 
-See the project [http://caruby.rubyforge.com](Home) Page for usage examples. 
+See the project [Home](http://caruby.rubyforge.org) Page for usage examples. 
 
 Changelog
 ---------
@@ -46,6 +46,6 @@ Changelog
 Copyright
 ---------
 
-caRuby © 2010 by [Oregon Health & Science University](mailto:loneyf@ohsu.edu).
+caRuby © 2010 by [Oregon Health & Science University](http://www.ohsu.edu/xd/health/services/cancer/index.cfm).
 caRuby is licensed under the MIT license. Please see the LICENSE and LEGAL
 files for more information.

data/lib/caruby/cli/command.rb

@@ -42,29 +42,43 @@ module CaRuby
       #
       # @param [(<Symbol>, <String, Class>)] specs the arguments and options
       #   described above
-      # @yield [hash] the command executor
-      # @yieldparam [{Symbol => Object}] the argument and option symbol => value hash
+      # @yield (see #run)
+      # @yieldparam (see #run)
       def initialize(specs=[], &executor)
-        unless block_given? then
-          raise ArgumentError.new("Command #{self.class} is missing the required execution block" )
-        end
         @executor = executor
         @opt_specs, @arg_specs = specs.partition { |spec| spec[1][0, 1] == '-' }
         @opt_specs.concat(DEF_OPTS)
         super($0)
       end
   
-      # Runs this command by calling the +execute+ method on the parsed command line
+      # Runs this command by calling the block given to this method, if provided,
+      # otherwise the block given to {#initialize}
       # option or argument symbol => value hash.
+      # @yield [hash] the command execution block
+      # @yieldparam [{Symbol => Object}] hash the argument and option symbol => value hash
       def run
         # the option => value hash
-        hash = get_opts
+        opts = get_opts
         # this base class's options
-        handle_caruby_options(hash)
+        handle_options(opts)
         # add the argument => value hash
-        hash.merge!(get_args)
+        opts.merge!(get_args)
         # call the block
-        @executor.call(hash)
+        block_given? ? yield(opts) : call_executor(opts)
+      end
+  
+      private
+      
+      DEF_OPTS = [
+        [:help, "--help", "Displays this help message"],
+        [:file, "--file FILE", "Configuration file containing other options"],
+        [:log, "--log FILE", "Log file"],
+        [:debug, "--debug", "Displays debug log messages"],
+      ]
+      
+      def call_executor(opts)
+         if @executor.nil? then raise CommandError.new("Command #{self} does not have an execution block") end
+         @executor.call(opts)
       end
       
       # Collects the command line options.
@@ -104,15 +118,6 @@ module CaRuby
         end
         args
       end
-  
-      private
-      
-      DEF_OPTS = [
-        [:help, "--help", "Displays this help message"],
-        [:file, "--file FILE", "Configuration file containing other options"],
-        [:log, "--log FILE", "Log file"],
-        [:debug, "--debug", "Displays debug log messages"],
-      ]
       
       # @param [OptionParser] parser the option parser
       # @return [{Symbol => Object}] the option => value hash
@@ -129,7 +134,7 @@ module CaRuby
       # Processes the built-in options.
       #
       # @param [{Symbol => Object}] the option => value hash
-      def handle_caruby_options(opts)
+      def handle_options(opts)
         # if help, then print usage and exit
         if opts[:help] then halt end
         
@@ -139,7 +144,7 @@ module CaRuby
         if log then
           CaRuby::Log.instance.open(log, :debug => debug)
         elsif debug then
-          CaRuby::logger.level = Logger::DEBUG
+          logger.level = Logger::DEBUG
         end
         
         # if there is a file option, then load additional options from the file

data/lib/caruby/database/persistable.rb

@@ -118,7 +118,8 @@ module CaRuby
     def changed_attributes
       if @snapshot then
         ovh = value_hash(self.class.updatable_attributes)
-        @snapshot.diff(ovh).keys
+        diff = @snapshot.diff(ovh) { |attr, v, ov| Resource.value_equal?(v, ov) }
+        diff.keys
       else
         self.class.updatable_attributes
       end
@@ -284,6 +285,17 @@ module CaRuby
     def snapshot_equal_content?
       vh = @snapshot
       ovh = value_hash(self.class.updatable_attributes)
+      
+      
+      # KLUDGE TODO - fix
+      # In Galena frozen migration example, SpecimenPosition snapshot doesn't include identifier; work around this here
+      if ovh[:identifier] and not @snapshot[:identifier] then
+        @snapshot[:identifier] = ovh[:identifier]
+      end
+      # END OF KLUDGE
+      
+      
+      
       if vh.size < ovh.size then
         attr, oval = ovh.detect { |a, v| not vh.has_key?(a) }
         logger.debug { "#{qp} is missing snapshot #{attr} compared to the current value #{oval.qp}." }

data/lib/caruby/database/reader.rb

@@ -139,7 +139,7 @@ module CaRuby
         elsif obj.collection? then
           obj.all? { |item| exists?(item) }
         else
-          obj.identifier or find(obj)
+          obj.identifier or (obj.searchable? and find(obj))
         end
       end
 

data/lib/caruby/database/writer.rb

@@ -131,7 +131,7 @@ module CaRuby
       # Raises DatabaseError if obj could not be created.
       # The return value is undefined.
       def ensure_exists(obj)
-        raise ArgumentError.new("Database ensure_exists is missing a domain object argument.") if obj.nil_or_empty?
+        raise ArgumentError.new("Database ensure_exists is missing a domain object argument") if obj.nil_or_empty?
         obj.enumerate { |ref| find(ref, :create) unless ref.identifier }
       end
 

data/lib/caruby/domain/attribute_metadata.rb

@@ -77,6 +77,11 @@ module CaRuby
     def inverse
       @inv_md.to_sym if @inv_md
     end
+    
+    # @return [Boolean] whether this attribute does not have an inverse
+    def unidirectional?
+      inverse.nil?
+    end
 
     # Creates a new declarer attribute which restricts this attribute {#type} to the given type.
     #

data/lib/caruby/domain/resource_attributes.rb

@@ -125,6 +125,10 @@ module CaRuby
     def logical_dependent_attributes
       @log_dep_attrs ||= dependent_attributes.compose { |attr_md| attr_md.logical? }
     end
+    
+    def unidirectional_dependent_attributes
+      @uni_dep_attrs ||= dependent_attributes.compose { |attr_md| attr_md.unidirectional? }
+    end
 
     # @return [<Symbol>] the auto-generated attributes
     # @see AttributeMetadata#autogenerated?
@@ -234,17 +238,6 @@ module CaRuby
     def storable_prerequisite_attributes
       @stbl_prereq_dom_attrs ||= attribute_filter { |attr_md| attr_md.storable_prerequisite? }
     end
-    
-    # Returns the domain attributes which are copied to create a storable template.
-    # The default is the {#nondomain_attributes}. An individual Resource class can
-    # override this to provide special reference attributes which must be set in
-    # a save operation.
-    #
-    # @param [Symbol] attribute the refernce attribute of the domain object being copied
-    def storable_copy_attributes(attribute)
-      attrs = @stbl_cp_attrs[attribute] if @stbl_cp_attrs
-      attrs || Array::EMPTY_ARRAY
-    end
 
     # @return [<Symbol>] the attributes which are populated from the database
     # @see AttributeMetadata#fetched?
@@ -430,13 +423,6 @@ module CaRuby
     def add_mandatory_attributes(*attributes)
       attributes.each { |attr| @local_mndty_attrs << standard_attribute(attr) }
     end
-    
-    # @param [Symbol] ref_attr the reference attribute of the domain object being copied
-    # @param [<Symbol>] copy_attrs  the domain attributes to copy
-    def add_storable_copy_attributes(ref_attr, copy_attrs)
-      @stbl_cp_attrs ||= {}
-      @stbl_cp_attrs[ref_attr] = copy_attrs
-    end
 
     # Marks the given attribute with flags supported by {AttributeMetadata#qualify}.
     def qualify_attribute(attribute, *flags)
@@ -483,14 +469,6 @@ module CaRuby
       attribute_metadata_hash.each_value(&block)
     end
 
-    # Makes a new synthetic attribute for each _method_ => _original_ hash entry.
-    #
-    # @param (see Class#offset_attr_accessor)
-    def offset_attribute(hash, offset=nil)
-      offset_attr_accessor(hash, offset)
-      hash.each { |attr, original| add_attribute(attr, attribute_metadata(original).type) }
-    end
-
     # Collects the {AttributeMetadata#fetched_dependent?} and {AttributeMetadata#fetched_independent?}
     # standard domain attributes.
     #

data/lib/caruby/domain/resource_dependency.rb

@@ -106,7 +106,7 @@ module CaRuby
     def add_owner(klass, attribute=nil, inverse=nil)
       logger.debug { "Adding #{qp} owner #{klass.qp}..." }
       if @owner_attr_hash then
-        raise MetadataError.new("Can't add #{qp} owner #{klass.qp} after dependencies have been accessed.")
+        raise MetadataError.new("Can't add #{qp} owner #{klass.qp} after dependencies have been accessed")
       end
       @local_owner_attr_hash ||= {}
       @local_owner_attr_hash[klass] = attribute ||= detect_owner_attribute(klass, inverse)

data/lib/caruby/domain/resource_introspection.rb

@@ -129,6 +129,14 @@ module CaRuby
       add_alias(aliaz, attribute)
     end
 
+    # Makes a new synthetic attribute for each _method_ => _original_ hash entry.
+    #
+    # @param (see Class#offset_attr_accessor)
+    def offset_attribute(hash, offset=nil)
+      offset_attr_accessor(hash, offset)
+      hash.each { |attr, original| add_attribute(attr, attribute_metadata(original).type) }
+    end
+
     # Modifies the given attribute writer method if necessary to update the given inverse_attr value.
     # This method is called on dependent and attributes qualified as inversible.
     #

data/lib/caruby/migration/migratable.rb

@@ -102,7 +102,8 @@ module CaRuby
     # for the _attribute_ to modify.
     #
     # The migratable reference attributes consist of the non-collection
-    # {ResourceAttributes#saved_independent_attributes} which don't already have a value.
+    # {ResourceAttributes#saved_independent_attributes} and 
+    # {ResourceAttributes#unidirectional_dependent_attributes} which don't already have a value.
     # For each such migratable attribute, if there is a single instance of the attribute
     # type in the given migrated domain objects, then the attribute is set to that
     # migrated instance.
@@ -121,6 +122,10 @@ module CaRuby
         ref = migratable__reference_value(attr, migrated) 
         migratable__set_reference(attr, ref, row, mth_hash) if ref
       end
+      self.class.unidirectional_dependent_attributes.each do |attr|
+        ref = migratable__reference_value(attr, migrated) 
+        migratable__set_reference(attr, ref, row, mth_hash) if ref
+      end
     end
     
     private

data/lib/caruby/migration/migrator.rb

@@ -27,11 +27,12 @@ module CaRuby
     # Creates a new Migrator.
     #
     # @param [{Symbol => Object}] opts the migration options
-    # @option opts [String] :database target application {CaRuby::Database}
+    # @option opts [String] :database required application {CaRuby::Database}
     # @option opts [String] :target required target domain class
+    # @option opts [String] :mapping required input field => caTissue attribute mapping file
     # @option opts [String] :input required source file to migrate
     # @option opts [String] :shims optional array of shim files to load
-    # @option opts [String] :bad write each invalid record to the given file and continue migration
+    # @option opts [String] :bad optional invalid record file
     # @option opts [String] :offset zero-based starting source record number to process (default 0)
     def initialize(opts)
       parse_options(opts)
@@ -57,7 +58,7 @@ module CaRuby
     # @yield [target] operation performed on the migration target
     # @yieldparam [Resource] target the migrated target domain object
     def migrate(&block)
-      raise MigrationError.new("No migration block") unless block_given?
+      raise MigrationError.new("The caRuby Migrator migrate block is missing") unless block_given?
       migrate_rows(&block)
     end
 
@@ -307,7 +308,7 @@ module CaRuby
             logger.warn("Migration not performed on record #{rec_no}.")
             @loader.reject(row)
           else
-            raise MigrationError.new("Migration not performed on record #{rec_no}.")
+            raise MigrationError.new("Migration not performed on record #{rec_no}")
           end
         end
         rec_cnt += 1
@@ -437,7 +438,7 @@ module CaRuby
     # @return [Resource, nil] obj if the save is successful, nil otherwise
     def save(obj, database)
       logger.debug { "Migrator saving #{obj}..." }
-      database.create(obj)
+      database.save(obj)
       logger.debug { "Migrator saved #{obj}." }
     end
 

data/lib/caruby/resource.rb

@@ -84,6 +84,11 @@ module CaRuby
       @validated = true
       self
     end
+    
+    # @return [Boolean] whether this domain object has {#searchable_attributes}
+    def searchable?
+      not searchable_attributes.nil?
+    end
 
     # Returns the attributes to use for a search using this domain object as a template, determined
     # as follows:
@@ -338,14 +343,21 @@ module CaRuby
       match_in(others) or others.detect { |other| match_without_owner_attribute(other) }
     end
 
+    # Returns whether the other domain object matches this domain object on a secondary
+    # key without owner attributes. Defaults are added to this object in order to pick up
+    # potential secondary key values.
+    # 
     # @param [<Resource>] other the domain object to match against
-    # @return [Boolean] whether the other domain object matches this domain object on a secondary
-    #   key without owner attributes
+    # @return [Boolean] whether the other domain object matches this domain object on a
+    #   secondary key without owner attributes
     def match_without_owner_attribute(other)
       oattrs = self.class.owner_attributes
       return if oattrs.empty?
+      # add defaults to pick up potential secondary key value
+      add_defaults_local
+      # match on the secondary key
       self.class.secondary_key_attributes.all? do |attr|
-        matches_attribute_value?(other, attr, send(attr))
+        oattrs.include?(attr) or matches_attribute_value?(other, attr, send(attr))
       end
     end
 

data/lib/caruby/util/visitor.rb

@@ -306,7 +306,7 @@ class Visitor
     def visit(*nodes)
       if nodes.size == 1 then
         nodes = nodes.first
-        raise ArgumentError.new("Sync visitor requires a pair of entry nodes.") unless nodes.size == 2
+        raise ArgumentError.new("Sync visitor requires a pair of entry nodes") unless nodes.size == 2
       end
       super(nodes)
     end
@@ -318,7 +318,7 @@ class Visitor
     def to_enum(*nodes)
       if nodes.size == 1 then
         nodes = nodes.first
-        raise ArgumentError.new("Sync visitor requires a pair of entry nodes.") unless nodes.size == 2
+        raise ArgumentError.new("Sync visitor requires a pair of entry nodes") unless nodes.size == 2
       end
       super(nodes)
     end

data/lib/caruby/version.rb

@@ -1,3 +1,3 @@
 module CaRuby
-  VERSION = "1.4.1"
+  VERSION = "1.4.2"
 end

metadata

@@ -6,23 +6,14 @@ executables: []
 
 version: !ruby/object:Gem::Version 
   prerelease: false
-  version: 1.4.1
+  version: 1.4.2
   segments: 
   - 1
   - 4
-  - 1
+  - 2
 post_install_message: 
-date: 2010-10-17 07:00:00 +00:00
+date: 2010-11-30 08:00:00 +00:00
 files: 
-- doc/website/index.html
-- doc/website/install.html
-- doc/website/quick_start.html
-- doc/website/tissue.html
-- doc/website/uom.html
-- doc/website/css/site.css
-- doc/website/images/avatar.png
-- doc/website/images/favicon.ico
-- doc/website/images/logo.png
 - lib/caruby.rb
 - lib/caruby/database.rb
 - lib/caruby/resource.rb
@@ -106,13 +97,13 @@ signing_key:
 cert_chain: []
 
 name: caruby-core
-has_rdoc: true
+has_rdoc: yard
 platform: ruby
 summary: Ruby facade for caBIG applications.
 default_executable: 
 bindir: bin
-licenses: []
-
+licenses: 
+- MIT
 required_rubygems_version: !ruby/object:Gem::Requirement 
   none: false
   requirements: 

data/doc/website/css/site.css

@@ -1 +0,0 @@
-
----------------------------------------------- */
----------------------------------------------- */
----------------------------------------------- */
----------------------------------------------- */
------------------------------------------------ */

data/doc/website/index.html

@@ -1,82 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" >
-<head>
-  <meta http-equiv="content-type" content="text/html; charset=iso-8859-1" />
-  <meta name="author" content="Fred Loney, OHSU" />
-  <meta name="keywords" content="caRuby, caBIG, caSmall, Ruby, JRuby" />
-  <meta name="description" content="caRuby landing page." />
-  <meta name="robots" content="all" />
-  <title>caRuby: caBIG Simplified</title>
-
-  <!-- to correct the unsightly Flash of Unstyled Content. http://www.bluerobot.com/web/css/fouc.asp -->
-  <script type="text/javascript"></script>
-
-  <style type="text/css" title="currentStyle" media="screen">
-    @import "/css/site.css";
-  </style>
-  <link rel='stylesheet' href='css/site.css' type='text/css' media="screen, projection">
-  <link rel="Shortcut Icon" href="images/favicon.ico" />
-</head>
-
-<body id="caruby">
-
-<div id="container">
-  <div id="head">
-    <h1><a href="index.html">caRuby:</a></h1>
-    <h2><a href="http://cabig.nci.nih.gov">caBIG&reg;</a> Simplified</h2>
-    <ul>
-      <li><span class="currentPage">Home</li>
-      <li><a href='quick_start.html'><em>Quick Start</em></a></li>
-      <li><a href='http://caruby.tenderapp.com/'>Help</a></li>
-      <li><a href='http://github.com/caruby'>Source</a></li>
-      <li><a href='/about.html'>About</a></li>
-    </ul>
-    <img src="images/logo.png"/>
-  </div>
-
-  <div id="features">
-    <h3>Features</h3>
-    <ul>
-      <li><a href="/api.html">API</a></li>
-      <li><a href="/tissue.html">Tissue</a></li>
-      <li><a href="/migrator.html">Migrator</a></li>
-      <li><a href="/casmall.html">caSmall</a></li>
-    </ul>
-  </div>
-
-  <div id="supportingText">
-    <h3>Overview</h3>
-    <p>
-      caRuby simplifies interaction with <a href="http://cabig.nci.nih.gov">caBIG&reg;</a> application
-      services. caRuby presents a <a href="http://jruby.org">JRuby</a> caBIG fa&ccedil;ade that
-      supports the following uses:
-      <ul>
-        <li>Migration from legacy systems</li>
-        <li>Incremental update from source applications</li>
-        <li>Extract from a caBIG database</li>
-        <li>Utility administrative tasks</li>
-        <li>Workflow data transformations</li>
-        <li>Lightweight web services</li>
-        <li>Site-specific user interfaces</li>
-      </ul>
-    </p>
-    <h3>Getting Started</h3>
-    <p>
-      <ol>
-        <li>Peruse the <strong>Features</strong> to see what caRuby offers.</li>
-        <li>Follow the <a href='/quick_start.html'>Quick Start</a> instructions to install caRuby.</li>
-        <li>Consult the <a href='/faq.html'>FAQ</a> for usage tips.</li>
-        <li>Visit caRuby <a href='http://caruby.tenderapp.com/'>Support</a> if you run into a problem.</li>
-        <li><a href='/contribute.html'>Contribute</a> a solution if you're feeling ambitious!</li>
-        <li><a href='mailto:caruby.org@gmail.com'>Let us know</a> what you think.</li>
-      </ol>
-    </p>
-
-    <div id="footer">
-    </div>
-  </div>
-</div>
-
-</body>
-</html>

data/doc/website/install.html

@@ -1,87 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" >
-<head>
-  <meta http-equiv="content-type" content="text/html; charset=iso-8859-1" />
-  <meta name="author" content="Fred Loney, OHSU" />
-  <meta name="keywords" content="caRuby" />
-  <meta name="description" content="caRuby Quick Start page." />
-  <meta name="robots" content="all" />
-  <title>caRuby: Installation</title>
-
-  <!-- to correct the unsightly Flash of Unstyled Content. http://www.bluerobot.com/web/css/fouc.asp -->
-  <script type="text/javascript"></script>
-
-  <style type="text/css" title="currentStyle" media="screen">
-    @import "/css/site.css";
-  </style>
-  <link rel='stylesheet' href='css/site.css' type='text/css' media="screen, projection">
-  <link rel="Shortcut Icon" href="images/favicon.ico" />
-</head>
-
-<body id="quick_start">
-
-<div id="container">
-  <div id="head">
-    <h1><a href="index.html">caRuby:</a></h1>
-    <h2><a href="http://cabig.nci.nih.gov">caBIG&reg;</a> Simplified</h2>
-    <ul>
-      <li><a href="/index.html">Home</a></li>
-      <li><span class="currentPage"><em>Quick Start</em></li>
-      <li><a href='http://caruby.tenderapp.com/'>Help</a></li>
-      <li><a href='http://github.com/caruby'>Source</a></li>
-      <li><a href='/about.html'>About</a></li>
-    </ul>
-    <img src="images/logo.png"/>
-  </div>
-
-  <div id="features">
-    <h3>Features</h3>
-    <ul>
-      <li><a href="/api.html">API</a></li>
-      <li><a href="/tissue.html">Tissue</a></li>
-      <li><a href="/migrator.html">Migrator</a></li>
-      <li><a href="/casmall.html">caSmall</a></li>
-    </ul>
-  </div>
-
-  <div id="supportingText">
-    <p>
-      Each caRuby <a href="/components.html">component</a> is packaged as a standard Ruby <a href="http://docs.rubygems.org/shelf/index">gem</a>.
-      Once you've installed <a href="http://jruby.org">JRuby</a> and the target caBIG application API, installing a caRuby gem is done with a one-line
-      command. caRuby runs on any on any workstation or server that supports the target caBIG application Java API.
-      Set up a caRuby environment as follows:
-      <ol>
-        <li>Install the target caBIG application Java API client.
-            Consult the caBIG application Technical Guide for details, available from the caBIG application
-            <a href="https://cabig-kc.nci.nih.gov/MediaWiki/index.php/Knowledge_Center_Index">Knowledge Center</a>.
-        </li>
-        <li>Install <a href="http://jruby.org">JRuby</a>.</li>
-        <li>Open a command console and enter the following:
-          <pre>
-            gem install rubygems
-          </pre>
-        </li>
-      </ol>
-    </p>
-    <p>
-      The preceding steps set up a standard JRuby environment. Now the desired caRuby gem is installed using the <code>gem install</code> command, e.g.:
-      <pre>
-        gem install caruby-tissue
-      </pre>
-    </p>
-    <p>
-      and updated using the <code>gem update</code> command, e.g.:
-      <pre>
-        gem update caruby-tissue
-      </pre>
-    </p>
-    <p>The caRuby gem is now ready for use. Consult the gem <a href="/documentation.html">documentation</a> for usage and examples.
-    </p>
-    <div id="footer">
-    </div>
-  </div>
-</div>
-
-</body>
-</html>

data/doc/website/quick_start.html

@@ -1,87 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" >
-<head>
-  <meta http-equiv="content-type" content="text/html; charset=iso-8859-1" />
-  <meta name="author" content="Fred Loney, OHSU" />
-  <meta name="keywords" content="caRuby" />
-  <meta name="description" content="caRuby Quick Start page." />
-  <meta name="robots" content="all" />
-  <title>caRuby: Quick Start</title>
-
-  <!-- to correct the unsightly Flash of Unstyled Content. http://www.bluerobot.com/web/css/fouc.asp -->
-  <script type="text/javascript"></script>
-
-  <style type="text/css" title="currentStyle" media="screen">
-    @import "/css/site.css";
-  </style>
-  <link rel='stylesheet' href='css/site.css' type='text/css' media="screen, projection">
-  <link rel="Shortcut Icon" href="images/favicon.ico" />
-</head>
-
-<body id="quick_start">
-
-<div id="container">
-  <div id="head">
-    <h1><a href="index.html">caRuby:</a></h1>
-    <h2><a href="http://cabig.nci.nih.gov">caBIG&reg;</a> Simplified</h2>
-    <ul>
-      <li><a href="/index.html">Home</a></li>
-      <li><span class="currentPage"><em>Quick Start</em></li>
-      <li><a href='http://caruby.tenderapp.com/'>Help</a></li>
-      <li><a href='http://github.com/caruby'>Source</a></li>
-      <li><a href='/about.html'>About</a></li>
-    </ul>
-    <img src="images/logo.png"/>
-  </div>
-
-  <div id="features">
-    <h3>Features</h3>
-    <ul>
-      <li><a href="/api.html">API</a></li>
-      <li><a href="/tissue.html">Tissue</a></li>
-      <li><a href="/migrator.html">Migrator</a></li>
-      <li><a href="/casmall.html">caSmall</a></li>
-    </ul>
-  </div>
-  
-  <div id="supportingText">
-    <p>
-      Each caRuby <a href="/components.html">component</a> is packaged as a standard Ruby <a href="http://docs.rubygems.org/shelf/index">gem</a>.
-      Once you've installed <a href="http://jruby.org">JRuby</a> and the target caBIG application API, installing a caRuby gem is done with a one-line
-      command. caRuby runs on any on any workstation or server that supports the target caBIG application Java API.
-      Set up a caRuby environment as follows:
-      <ol>
-        <li>Install the target caBIG application Java API client.
-            Consult the caBIG application Technical Guide for details, available from the caBIG application
-            <a href="https://cabig-kc.nci.nih.gov/MediaWiki/index.php/Knowledge_Center_Index">Knowledge Center</a>.
-        </li>
-        <li>Install <a href="http://jruby.org">JRuby</a>.</li>
-        <li>Open a command console and enter the following:
-          <pre>
-            gem install rubygems
-          </pre>
-        </li>
-      </ol>
-    </p>
-    <p>
-      The preceding steps set up a standard JRuby environment. Now the desired caRuby gem is installed using the <code>gem install</code> command, e.g.:
-      <pre>
-        gem install caruby-tissue
-      </pre>
-    </p>
-    <p>
-      and updated using the <code>gem update</code> command, e.g.:
-      <pre>
-        gem update caruby-tissue
-      </pre>
-    </p>
-    <p>The caRuby gem is now ready for use. Consult the gem <a href="/documentation.html">documentation</a> for usage and examples.
-    </p>
-    <div id="footer">
-    </div>
-  </div>
-</div>
-
-</body>
-</html>

data/doc/website/tissue.html

@@ -1,85 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" >
-<head>
-  <meta http-equiv="content-type" content="text/html; charset=iso-8859-1" />
-  <meta name="author" content="Fred Loney, OHSU" />
-  <meta name="keywords" content="caRuby, caTissue" />
-  <meta name="description" content="caRuby Tissue page." />
-  <meta name="robots" content="all" />
-  <title>caRuby: Quick Start</title>
-
-  <!-- to correct the unsightly Flash of Unstyled Content. http://www.bluerobot.com/web/css/fouc.asp -->
-  <script type="text/javascript"></script>
-
-  <style type="text/css" title="currentStyle" media="screen">
-    @import "/css/site.css";
-  </style>
-  <link rel='stylesheet' href='css/site.css' type='text/css' media="screen, projection">
-  <link rel="Shortcut Icon" href="images/favicon.ico" />
-</head>
-
-<body id="tissue">
-
-<div id="container">
-  <div id="head">
-    <h1><a href="index.html">caRuby:</a></h1>
-    <h2>Tissue</h2>
-    <ul>
-      <li><a href='quick_start.html'><em>Quick Start</em></a></li>
-      <li><a href='faq.html'>FAQ</a></li>
-      <li><a href='http://caruby.tenderapp.com/'>Help</a></li>
-      <li><a href='contribute.html'>Contribute</a></li>
-      <li><a href='about.html'>About</a></li>
-    </ul>
-    <img src="images/logo.png"/>
-  </div>
-
-  <div id="supportingText">
-    <p>
-      The caRuby Tissue component applies the caRuby facade to the
-      <a href="https://cabig-kc.nci.nih.gov/Biospecimen/KC/index.php/CaTissue_Suite">caTissue</a>
-      application. This offers the following features:
-      <ul>
-        <li>flexible server interaction</li>
-        <li>data migration and extraction</li>
-        <li>a foundation for a <a href="casmall.html">caSmall</a> framework</li>
-      </ul>
-    </p>
-    <p>
-      Since the caRuby Tissue component is built on the caTissue API, all of the caTissue business logic applies.
-      In addition, caRuby augments the API as follows:
-      <ul>
-        <li>supplies default attribute values</li>
-        <li>validates mandatory attributes before submission to caTissue</li>
-        <li>validates additional attributes which are permitted by the caTissue API but corrupt the database</li>
-        <li>migrates an input CSV record to a caTissue object based on one simple configuration file</li>
-        <li>validates migration input diagnosis and tissue site permissible values</li>
-        <li>optionally maps diagnosis and tissue site migration input values to caTissue permissible values</li>
-        <li>determines how to save the caTissue object based on the caTissue object model</li>
-        <li>finds referenced objects based on secondary keys and alternative search strategies</li>
-        <li>creates whatever needs to be created in the required order based on the data model associations</li>
-        <li>works around caCORE and caTissue bugs and traps</li>
-        <li>provides helper methods for common tasks, e.g. aliquoting</li>
-      </ul>
-    </p>
-    <p>
-      The sole configuration is the migration mapping file and a small caTissue server access properties file.
-      The defaults and other metadata are defined in Ruby declarations rather than a configuration.
-      These declarations express basic model characteristics, and are expected to be stable and sufficient for most uses.
-      They can, however, be modified in small Ruby shim files.
-      Special-purpose migration code can be added in the shim files as well, as described in the
-      <a href='shims.html'>Shims</a> description.
-    </p>
-    <p>
-      There is almost no class-specific caRuby business logic code similar to that found in caTissue.
-      Rather, there are basic design patterns driven by the model characteristics defined in the Ruby declarations.
-    </p>
-    <div id="footer">
-    </div>
-  </div>
-</div>
-
-</body>
-</html>
-

data/doc/website/uom.html

@@ -1,10 +0,0 @@
-UOM implements Units of Measurement based on the
-<a href=http://physics.nist.gov/Pubs/SP330/sp330.pdf>International System of Units (SI)</a>.
-The base SI units, metric scalar factors and all possible combinations of these units are supported out of the box.
-
-Common alternative non-metric measurement systems, e.g. US Customary units, are supported with conversions between
-these units and the SI units. Additional units can be defined with conversion to an existing unit. UOM infers
-full conversion capability between units of the same dimension from the minimal number of conversion definitions.
-
-Arithmetic operations between UOM Measurement objects converts the measurement units and scalar factors as necessary,
-including unit products, quotients and powers of arbitrary complexity.