caruby-core 1.4.1 → 1.4.2
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- data/History.txt +4 -0
- data/LICENSE +1 -1
- data/README.md +4 -4
- data/lib/caruby/cli/command.rb +26 -21
- data/lib/caruby/database/persistable.rb +13 -1
- data/lib/caruby/database/reader.rb +1 -1
- data/lib/caruby/database/writer.rb +1 -1
- data/lib/caruby/domain/attribute_metadata.rb +5 -0
- data/lib/caruby/domain/resource_attributes.rb +4 -26
- data/lib/caruby/domain/resource_dependency.rb +1 -1
- data/lib/caruby/domain/resource_introspection.rb +8 -0
- data/lib/caruby/migration/migratable.rb +6 -1
- data/lib/caruby/migration/migrator.rb +6 -5
- data/lib/caruby/resource.rb +15 -3
- data/lib/caruby/util/visitor.rb +2 -2
- data/lib/caruby/version.rb +1 -1
- metadata +6 -15
- data/doc/website/css/site.css +0 -6
- data/doc/website/images/avatar.png +0 -0
- data/doc/website/images/favicon.ico +0 -0
- data/doc/website/images/logo.png +0 -0
- data/doc/website/index.html +0 -82
- data/doc/website/install.html +0 -87
- data/doc/website/quick_start.html +0 -87
- data/doc/website/tissue.html +0 -85
- data/doc/website/uom.html +0 -10
data/History.txt
CHANGED
data/LICENSE
CHANGED
data/README.md
CHANGED
@@ -1,8 +1,8 @@
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1
1
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caRuby: Simplifying caBIG(TM)
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=============================
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3
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-
**Home**:
|
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-
**Git**: [http://github.com/caruby/core](http://github.com/caruby/core)
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+
**Home**: [http://caruby.rubyforge.org](http://caruby.rubyforge.org)
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5
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+
**Git**: [http://github.com/caruby/core](http://github.com/caruby/core)
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6
6
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**Author**: OHSU Knight Cancer Institute
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7
7
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**Copyright**: 2010
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8
8
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**License**: MIT License
|
@@ -35,7 +35,7 @@ is installed.
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35
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Usage
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36
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-----
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-
See the project [http://caruby.rubyforge.
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+
See the project [Home](http://caruby.rubyforge.org) Page for usage examples.
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40
40
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Changelog
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---------
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@@ -46,6 +46,6 @@ Changelog
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Copyright
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---------
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48
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49
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-
caRuby © 2010 by [Oregon Health & Science University](
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+
caRuby © 2010 by [Oregon Health & Science University](http://www.ohsu.edu/xd/health/services/cancer/index.cfm).
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50
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caRuby is licensed under the MIT license. Please see the LICENSE and LEGAL
|
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files for more information.
|
data/lib/caruby/cli/command.rb
CHANGED
@@ -42,29 +42,43 @@ module CaRuby
|
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#
|
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# @param [(<Symbol>, <String, Class>)] specs the arguments and options
|
44
44
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# described above
|
45
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-
# @yield
|
46
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-
# @yieldparam
|
45
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+
# @yield (see #run)
|
46
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+
# @yieldparam (see #run)
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47
47
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def initialize(specs=[], &executor)
|
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-
unless block_given? then
|
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-
raise ArgumentError.new("Command #{self.class} is missing the required execution block" )
|
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-
end
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@executor = executor
|
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49
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@opt_specs, @arg_specs = specs.partition { |spec| spec[1][0, 1] == '-' }
|
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50
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@opt_specs.concat(DEF_OPTS)
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super($0)
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end
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-
# Runs this command by calling the
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+
# Runs this command by calling the block given to this method, if provided,
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# otherwise the block given to {#initialize}
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# option or argument symbol => value hash.
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# @yield [hash] the command execution block
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# @yieldparam [{Symbol => Object}] hash the argument and option symbol => value hash
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def run
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# the option => value hash
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-
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opts = get_opts
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# this base class's options
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-
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handle_options(opts)
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# add the argument => value hash
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-
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opts.merge!(get_args)
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# call the block
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-
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block_given? ? yield(opts) : call_executor(opts)
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+
end
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+
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private
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DEF_OPTS = [
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[:help, "--help", "Displays this help message"],
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[:file, "--file FILE", "Configuration file containing other options"],
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[:log, "--log FILE", "Log file"],
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[:debug, "--debug", "Displays debug log messages"],
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+
]
|
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+
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def call_executor(opts)
|
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if @executor.nil? then raise CommandError.new("Command #{self} does not have an execution block") end
|
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@executor.call(opts)
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end
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# Collects the command line options.
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@@ -104,15 +118,6 @@ module CaRuby
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end
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args
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end
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-
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private
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-
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-
DEF_OPTS = [
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-
[:help, "--help", "Displays this help message"],
|
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-
[:file, "--file FILE", "Configuration file containing other options"],
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[:log, "--log FILE", "Log file"],
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[:debug, "--debug", "Displays debug log messages"],
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-
]
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# @param [OptionParser] parser the option parser
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# @return [{Symbol => Object}] the option => value hash
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@@ -129,7 +134,7 @@ module CaRuby
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# Processes the built-in options.
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#
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# @param [{Symbol => Object}] the option => value hash
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-
def
|
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+
def handle_options(opts)
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# if help, then print usage and exit
|
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if opts[:help] then halt end
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@@ -139,7 +144,7 @@ module CaRuby
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if log then
|
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CaRuby::Log.instance.open(log, :debug => debug)
|
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elsif debug then
|
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-
|
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+
logger.level = Logger::DEBUG
|
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end
|
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|
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# if there is a file option, then load additional options from the file
|
@@ -118,7 +118,8 @@ module CaRuby
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118
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def changed_attributes
|
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119
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if @snapshot then
|
120
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ovh = value_hash(self.class.updatable_attributes)
|
121
|
-
@snapshot.diff(ovh).
|
121
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+
diff = @snapshot.diff(ovh) { |attr, v, ov| Resource.value_equal?(v, ov) }
|
122
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+
diff.keys
|
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123
|
else
|
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self.class.updatable_attributes
|
124
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|
end
|
@@ -284,6 +285,17 @@ module CaRuby
|
|
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|
def snapshot_equal_content?
|
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vh = @snapshot
|
286
287
|
ovh = value_hash(self.class.updatable_attributes)
|
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|
+
|
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|
+
|
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+
# KLUDGE TODO - fix
|
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+
# In Galena frozen migration example, SpecimenPosition snapshot doesn't include identifier; work around this here
|
292
|
+
if ovh[:identifier] and not @snapshot[:identifier] then
|
293
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+
@snapshot[:identifier] = ovh[:identifier]
|
294
|
+
end
|
295
|
+
# END OF KLUDGE
|
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|
+
|
297
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+
|
298
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+
|
287
299
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if vh.size < ovh.size then
|
288
300
|
attr, oval = ovh.detect { |a, v| not vh.has_key?(a) }
|
289
301
|
logger.debug { "#{qp} is missing snapshot #{attr} compared to the current value #{oval.qp}." }
|
@@ -131,7 +131,7 @@ module CaRuby
|
|
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# Raises DatabaseError if obj could not be created.
|
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# The return value is undefined.
|
133
133
|
def ensure_exists(obj)
|
134
|
-
raise ArgumentError.new("Database ensure_exists is missing a domain object argument
|
134
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+
raise ArgumentError.new("Database ensure_exists is missing a domain object argument") if obj.nil_or_empty?
|
135
135
|
obj.enumerate { |ref| find(ref, :create) unless ref.identifier }
|
136
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|
end
|
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137
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|
@@ -77,6 +77,11 @@ module CaRuby
|
|
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77
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def inverse
|
78
78
|
@inv_md.to_sym if @inv_md
|
79
79
|
end
|
80
|
+
|
81
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+
# @return [Boolean] whether this attribute does not have an inverse
|
82
|
+
def unidirectional?
|
83
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+
inverse.nil?
|
84
|
+
end
|
80
85
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|
81
86
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# Creates a new declarer attribute which restricts this attribute {#type} to the given type.
|
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87
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#
|
@@ -125,6 +125,10 @@ module CaRuby
|
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125
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def logical_dependent_attributes
|
126
126
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@log_dep_attrs ||= dependent_attributes.compose { |attr_md| attr_md.logical? }
|
127
127
|
end
|
128
|
+
|
129
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+
def unidirectional_dependent_attributes
|
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+
@uni_dep_attrs ||= dependent_attributes.compose { |attr_md| attr_md.unidirectional? }
|
131
|
+
end
|
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|
129
133
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# @return [<Symbol>] the auto-generated attributes
|
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# @see AttributeMetadata#autogenerated?
|
@@ -234,17 +238,6 @@ module CaRuby
|
|
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|
def storable_prerequisite_attributes
|
235
239
|
@stbl_prereq_dom_attrs ||= attribute_filter { |attr_md| attr_md.storable_prerequisite? }
|
236
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|
end
|
237
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-
|
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-
# Returns the domain attributes which are copied to create a storable template.
|
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-
# The default is the {#nondomain_attributes}. An individual Resource class can
|
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|
-
# override this to provide special reference attributes which must be set in
|
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-
# a save operation.
|
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|
-
#
|
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-
# @param [Symbol] attribute the refernce attribute of the domain object being copied
|
244
|
-
def storable_copy_attributes(attribute)
|
245
|
-
attrs = @stbl_cp_attrs[attribute] if @stbl_cp_attrs
|
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|
-
attrs || Array::EMPTY_ARRAY
|
247
|
-
end
|
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|
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# @return [<Symbol>] the attributes which are populated from the database
|
250
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# @see AttributeMetadata#fetched?
|
@@ -430,13 +423,6 @@ module CaRuby
|
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430
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def add_mandatory_attributes(*attributes)
|
431
424
|
attributes.each { |attr| @local_mndty_attrs << standard_attribute(attr) }
|
432
425
|
end
|
433
|
-
|
434
|
-
# @param [Symbol] ref_attr the reference attribute of the domain object being copied
|
435
|
-
# @param [<Symbol>] copy_attrs the domain attributes to copy
|
436
|
-
def add_storable_copy_attributes(ref_attr, copy_attrs)
|
437
|
-
@stbl_cp_attrs ||= {}
|
438
|
-
@stbl_cp_attrs[ref_attr] = copy_attrs
|
439
|
-
end
|
440
426
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|
441
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# Marks the given attribute with flags supported by {AttributeMetadata#qualify}.
|
442
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|
def qualify_attribute(attribute, *flags)
|
@@ -483,14 +469,6 @@ module CaRuby
|
|
483
469
|
attribute_metadata_hash.each_value(&block)
|
484
470
|
end
|
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|
486
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-
# Makes a new synthetic attribute for each _method_ => _original_ hash entry.
|
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-
#
|
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-
# @param (see Class#offset_attr_accessor)
|
489
|
-
def offset_attribute(hash, offset=nil)
|
490
|
-
offset_attr_accessor(hash, offset)
|
491
|
-
hash.each { |attr, original| add_attribute(attr, attribute_metadata(original).type) }
|
492
|
-
end
|
493
|
-
|
494
472
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# Collects the {AttributeMetadata#fetched_dependent?} and {AttributeMetadata#fetched_independent?}
|
495
473
|
# standard domain attributes.
|
496
474
|
#
|
@@ -106,7 +106,7 @@ module CaRuby
|
|
106
106
|
def add_owner(klass, attribute=nil, inverse=nil)
|
107
107
|
logger.debug { "Adding #{qp} owner #{klass.qp}..." }
|
108
108
|
if @owner_attr_hash then
|
109
|
-
raise MetadataError.new("Can't add #{qp} owner #{klass.qp} after dependencies have been accessed
|
109
|
+
raise MetadataError.new("Can't add #{qp} owner #{klass.qp} after dependencies have been accessed")
|
110
110
|
end
|
111
111
|
@local_owner_attr_hash ||= {}
|
112
112
|
@local_owner_attr_hash[klass] = attribute ||= detect_owner_attribute(klass, inverse)
|
@@ -129,6 +129,14 @@ module CaRuby
|
|
129
129
|
add_alias(aliaz, attribute)
|
130
130
|
end
|
131
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|
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+
# Makes a new synthetic attribute for each _method_ => _original_ hash entry.
|
133
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+
#
|
134
|
+
# @param (see Class#offset_attr_accessor)
|
135
|
+
def offset_attribute(hash, offset=nil)
|
136
|
+
offset_attr_accessor(hash, offset)
|
137
|
+
hash.each { |attr, original| add_attribute(attr, attribute_metadata(original).type) }
|
138
|
+
end
|
139
|
+
|
132
140
|
# Modifies the given attribute writer method if necessary to update the given inverse_attr value.
|
133
141
|
# This method is called on dependent and attributes qualified as inversible.
|
134
142
|
#
|
@@ -102,7 +102,8 @@ module CaRuby
|
|
102
102
|
# for the _attribute_ to modify.
|
103
103
|
#
|
104
104
|
# The migratable reference attributes consist of the non-collection
|
105
|
-
# {ResourceAttributes#saved_independent_attributes}
|
105
|
+
# {ResourceAttributes#saved_independent_attributes} and
|
106
|
+
# {ResourceAttributes#unidirectional_dependent_attributes} which don't already have a value.
|
106
107
|
# For each such migratable attribute, if there is a single instance of the attribute
|
107
108
|
# type in the given migrated domain objects, then the attribute is set to that
|
108
109
|
# migrated instance.
|
@@ -121,6 +122,10 @@ module CaRuby
|
|
121
122
|
ref = migratable__reference_value(attr, migrated)
|
122
123
|
migratable__set_reference(attr, ref, row, mth_hash) if ref
|
123
124
|
end
|
125
|
+
self.class.unidirectional_dependent_attributes.each do |attr|
|
126
|
+
ref = migratable__reference_value(attr, migrated)
|
127
|
+
migratable__set_reference(attr, ref, row, mth_hash) if ref
|
128
|
+
end
|
124
129
|
end
|
125
130
|
|
126
131
|
private
|
@@ -27,11 +27,12 @@ module CaRuby
|
|
27
27
|
# Creates a new Migrator.
|
28
28
|
#
|
29
29
|
# @param [{Symbol => Object}] opts the migration options
|
30
|
-
# @option opts [String] :database
|
30
|
+
# @option opts [String] :database required application {CaRuby::Database}
|
31
31
|
# @option opts [String] :target required target domain class
|
32
|
+
# @option opts [String] :mapping required input field => caTissue attribute mapping file
|
32
33
|
# @option opts [String] :input required source file to migrate
|
33
34
|
# @option opts [String] :shims optional array of shim files to load
|
34
|
-
# @option opts [String] :bad
|
35
|
+
# @option opts [String] :bad optional invalid record file
|
35
36
|
# @option opts [String] :offset zero-based starting source record number to process (default 0)
|
36
37
|
def initialize(opts)
|
37
38
|
parse_options(opts)
|
@@ -57,7 +58,7 @@ module CaRuby
|
|
57
58
|
# @yield [target] operation performed on the migration target
|
58
59
|
# @yieldparam [Resource] target the migrated target domain object
|
59
60
|
def migrate(&block)
|
60
|
-
raise MigrationError.new("
|
61
|
+
raise MigrationError.new("The caRuby Migrator migrate block is missing") unless block_given?
|
61
62
|
migrate_rows(&block)
|
62
63
|
end
|
63
64
|
|
@@ -307,7 +308,7 @@ module CaRuby
|
|
307
308
|
logger.warn("Migration not performed on record #{rec_no}.")
|
308
309
|
@loader.reject(row)
|
309
310
|
else
|
310
|
-
raise MigrationError.new("Migration not performed on record #{rec_no}
|
311
|
+
raise MigrationError.new("Migration not performed on record #{rec_no}")
|
311
312
|
end
|
312
313
|
end
|
313
314
|
rec_cnt += 1
|
@@ -437,7 +438,7 @@ module CaRuby
|
|
437
438
|
# @return [Resource, nil] obj if the save is successful, nil otherwise
|
438
439
|
def save(obj, database)
|
439
440
|
logger.debug { "Migrator saving #{obj}..." }
|
440
|
-
database.
|
441
|
+
database.save(obj)
|
441
442
|
logger.debug { "Migrator saved #{obj}." }
|
442
443
|
end
|
443
444
|
|
data/lib/caruby/resource.rb
CHANGED
@@ -84,6 +84,11 @@ module CaRuby
|
|
84
84
|
@validated = true
|
85
85
|
self
|
86
86
|
end
|
87
|
+
|
88
|
+
# @return [Boolean] whether this domain object has {#searchable_attributes}
|
89
|
+
def searchable?
|
90
|
+
not searchable_attributes.nil?
|
91
|
+
end
|
87
92
|
|
88
93
|
# Returns the attributes to use for a search using this domain object as a template, determined
|
89
94
|
# as follows:
|
@@ -338,14 +343,21 @@ module CaRuby
|
|
338
343
|
match_in(others) or others.detect { |other| match_without_owner_attribute(other) }
|
339
344
|
end
|
340
345
|
|
346
|
+
# Returns whether the other domain object matches this domain object on a secondary
|
347
|
+
# key without owner attributes. Defaults are added to this object in order to pick up
|
348
|
+
# potential secondary key values.
|
349
|
+
#
|
341
350
|
# @param [<Resource>] other the domain object to match against
|
342
|
-
# @return [Boolean] whether the other domain object matches this domain object on a
|
343
|
-
# key without owner attributes
|
351
|
+
# @return [Boolean] whether the other domain object matches this domain object on a
|
352
|
+
# secondary key without owner attributes
|
344
353
|
def match_without_owner_attribute(other)
|
345
354
|
oattrs = self.class.owner_attributes
|
346
355
|
return if oattrs.empty?
|
356
|
+
# add defaults to pick up potential secondary key value
|
357
|
+
add_defaults_local
|
358
|
+
# match on the secondary key
|
347
359
|
self.class.secondary_key_attributes.all? do |attr|
|
348
|
-
matches_attribute_value?(other, attr, send(attr))
|
360
|
+
oattrs.include?(attr) or matches_attribute_value?(other, attr, send(attr))
|
349
361
|
end
|
350
362
|
end
|
351
363
|
|
data/lib/caruby/util/visitor.rb
CHANGED
@@ -306,7 +306,7 @@ class Visitor
|
|
306
306
|
def visit(*nodes)
|
307
307
|
if nodes.size == 1 then
|
308
308
|
nodes = nodes.first
|
309
|
-
raise ArgumentError.new("Sync visitor requires a pair of entry nodes
|
309
|
+
raise ArgumentError.new("Sync visitor requires a pair of entry nodes") unless nodes.size == 2
|
310
310
|
end
|
311
311
|
super(nodes)
|
312
312
|
end
|
@@ -318,7 +318,7 @@ class Visitor
|
|
318
318
|
def to_enum(*nodes)
|
319
319
|
if nodes.size == 1 then
|
320
320
|
nodes = nodes.first
|
321
|
-
raise ArgumentError.new("Sync visitor requires a pair of entry nodes
|
321
|
+
raise ArgumentError.new("Sync visitor requires a pair of entry nodes") unless nodes.size == 2
|
322
322
|
end
|
323
323
|
super(nodes)
|
324
324
|
end
|
data/lib/caruby/version.rb
CHANGED
metadata
CHANGED
@@ -6,23 +6,14 @@ executables: []
|
|
6
6
|
|
7
7
|
version: !ruby/object:Gem::Version
|
8
8
|
prerelease: false
|
9
|
-
version: 1.4.
|
9
|
+
version: 1.4.2
|
10
10
|
segments:
|
11
11
|
- 1
|
12
12
|
- 4
|
13
|
-
-
|
13
|
+
- 2
|
14
14
|
post_install_message:
|
15
|
-
date: 2010-
|
15
|
+
date: 2010-11-30 08:00:00 +00:00
|
16
16
|
files:
|
17
|
-
- doc/website/index.html
|
18
|
-
- doc/website/install.html
|
19
|
-
- doc/website/quick_start.html
|
20
|
-
- doc/website/tissue.html
|
21
|
-
- doc/website/uom.html
|
22
|
-
- doc/website/css/site.css
|
23
|
-
- doc/website/images/avatar.png
|
24
|
-
- doc/website/images/favicon.ico
|
25
|
-
- doc/website/images/logo.png
|
26
17
|
- lib/caruby.rb
|
27
18
|
- lib/caruby/database.rb
|
28
19
|
- lib/caruby/resource.rb
|
@@ -106,13 +97,13 @@ signing_key:
|
|
106
97
|
cert_chain: []
|
107
98
|
|
108
99
|
name: caruby-core
|
109
|
-
has_rdoc:
|
100
|
+
has_rdoc: yard
|
110
101
|
platform: ruby
|
111
102
|
summary: Ruby facade for caBIG applications.
|
112
103
|
default_executable:
|
113
104
|
bindir: bin
|
114
|
-
licenses:
|
115
|
-
|
105
|
+
licenses:
|
106
|
+
- MIT
|
116
107
|
required_rubygems_version: !ruby/object:Gem::Requirement
|
117
108
|
none: false
|
118
109
|
requirements:
|
data/doc/website/css/site.css
DELETED
Binary file
|
Binary file
|
data/doc/website/images/logo.png
DELETED
Binary file
|
data/doc/website/index.html
DELETED
@@ -1,82 +0,0 @@
|
|
1
|
-
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
|
2
|
-
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
|
3
|
-
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" >
|
4
|
-
<head>
|
5
|
-
<meta http-equiv="content-type" content="text/html; charset=iso-8859-1" />
|
6
|
-
<meta name="author" content="Fred Loney, OHSU" />
|
7
|
-
<meta name="keywords" content="caRuby, caBIG, caSmall, Ruby, JRuby" />
|
8
|
-
<meta name="description" content="caRuby landing page." />
|
9
|
-
<meta name="robots" content="all" />
|
10
|
-
<title>caRuby: caBIG Simplified</title>
|
11
|
-
|
12
|
-
<!-- to correct the unsightly Flash of Unstyled Content. http://www.bluerobot.com/web/css/fouc.asp -->
|
13
|
-
<script type="text/javascript"></script>
|
14
|
-
|
15
|
-
<style type="text/css" title="currentStyle" media="screen">
|
16
|
-
@import "/css/site.css";
|
17
|
-
</style>
|
18
|
-
<link rel='stylesheet' href='css/site.css' type='text/css' media="screen, projection">
|
19
|
-
<link rel="Shortcut Icon" href="images/favicon.ico" />
|
20
|
-
</head>
|
21
|
-
|
22
|
-
<body id="caruby">
|
23
|
-
|
24
|
-
<div id="container">
|
25
|
-
<div id="head">
|
26
|
-
<h1><a href="index.html">caRuby:</a></h1>
|
27
|
-
<h2><a href="http://cabig.nci.nih.gov">caBIG®</a> Simplified</h2>
|
28
|
-
<ul>
|
29
|
-
<li><span class="currentPage">Home</li>
|
30
|
-
<li><a href='quick_start.html'><em>Quick Start</em></a></li>
|
31
|
-
<li><a href='http://caruby.tenderapp.com/'>Help</a></li>
|
32
|
-
<li><a href='http://github.com/caruby'>Source</a></li>
|
33
|
-
<li><a href='/about.html'>About</a></li>
|
34
|
-
</ul>
|
35
|
-
<img src="images/logo.png"/>
|
36
|
-
</div>
|
37
|
-
|
38
|
-
<div id="features">
|
39
|
-
<h3>Features</h3>
|
40
|
-
<ul>
|
41
|
-
<li><a href="/api.html">API</a></li>
|
42
|
-
<li><a href="/tissue.html">Tissue</a></li>
|
43
|
-
<li><a href="/migrator.html">Migrator</a></li>
|
44
|
-
<li><a href="/casmall.html">caSmall</a></li>
|
45
|
-
</ul>
|
46
|
-
</div>
|
47
|
-
|
48
|
-
<div id="supportingText">
|
49
|
-
<h3>Overview</h3>
|
50
|
-
<p>
|
51
|
-
caRuby simplifies interaction with <a href="http://cabig.nci.nih.gov">caBIG®</a> application
|
52
|
-
services. caRuby presents a <a href="http://jruby.org">JRuby</a> caBIG façade that
|
53
|
-
supports the following uses:
|
54
|
-
<ul>
|
55
|
-
<li>Migration from legacy systems</li>
|
56
|
-
<li>Incremental update from source applications</li>
|
57
|
-
<li>Extract from a caBIG database</li>
|
58
|
-
<li>Utility administrative tasks</li>
|
59
|
-
<li>Workflow data transformations</li>
|
60
|
-
<li>Lightweight web services</li>
|
61
|
-
<li>Site-specific user interfaces</li>
|
62
|
-
</ul>
|
63
|
-
</p>
|
64
|
-
<h3>Getting Started</h3>
|
65
|
-
<p>
|
66
|
-
<ol>
|
67
|
-
<li>Peruse the <strong>Features</strong> to see what caRuby offers.</li>
|
68
|
-
<li>Follow the <a href='/quick_start.html'>Quick Start</a> instructions to install caRuby.</li>
|
69
|
-
<li>Consult the <a href='/faq.html'>FAQ</a> for usage tips.</li>
|
70
|
-
<li>Visit caRuby <a href='http://caruby.tenderapp.com/'>Support</a> if you run into a problem.</li>
|
71
|
-
<li><a href='/contribute.html'>Contribute</a> a solution if you're feeling ambitious!</li>
|
72
|
-
<li><a href='mailto:caruby.org@gmail.com'>Let us know</a> what you think.</li>
|
73
|
-
</ol>
|
74
|
-
</p>
|
75
|
-
|
76
|
-
<div id="footer">
|
77
|
-
</div>
|
78
|
-
</div>
|
79
|
-
</div>
|
80
|
-
|
81
|
-
</body>
|
82
|
-
</html>
|
data/doc/website/install.html
DELETED
@@ -1,87 +0,0 @@
|
|
1
|
-
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
|
2
|
-
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
|
3
|
-
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" >
|
4
|
-
<head>
|
5
|
-
<meta http-equiv="content-type" content="text/html; charset=iso-8859-1" />
|
6
|
-
<meta name="author" content="Fred Loney, OHSU" />
|
7
|
-
<meta name="keywords" content="caRuby" />
|
8
|
-
<meta name="description" content="caRuby Quick Start page." />
|
9
|
-
<meta name="robots" content="all" />
|
10
|
-
<title>caRuby: Installation</title>
|
11
|
-
|
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|
-
<!-- to correct the unsightly Flash of Unstyled Content. http://www.bluerobot.com/web/css/fouc.asp -->
|
13
|
-
<script type="text/javascript"></script>
|
14
|
-
|
15
|
-
<style type="text/css" title="currentStyle" media="screen">
|
16
|
-
@import "/css/site.css";
|
17
|
-
</style>
|
18
|
-
<link rel='stylesheet' href='css/site.css' type='text/css' media="screen, projection">
|
19
|
-
<link rel="Shortcut Icon" href="images/favicon.ico" />
|
20
|
-
</head>
|
21
|
-
|
22
|
-
<body id="quick_start">
|
23
|
-
|
24
|
-
<div id="container">
|
25
|
-
<div id="head">
|
26
|
-
<h1><a href="index.html">caRuby:</a></h1>
|
27
|
-
<h2><a href="http://cabig.nci.nih.gov">caBIG®</a> Simplified</h2>
|
28
|
-
<ul>
|
29
|
-
<li><a href="/index.html">Home</a></li>
|
30
|
-
<li><span class="currentPage"><em>Quick Start</em></li>
|
31
|
-
<li><a href='http://caruby.tenderapp.com/'>Help</a></li>
|
32
|
-
<li><a href='http://github.com/caruby'>Source</a></li>
|
33
|
-
<li><a href='/about.html'>About</a></li>
|
34
|
-
</ul>
|
35
|
-
<img src="images/logo.png"/>
|
36
|
-
</div>
|
37
|
-
|
38
|
-
<div id="features">
|
39
|
-
<h3>Features</h3>
|
40
|
-
<ul>
|
41
|
-
<li><a href="/api.html">API</a></li>
|
42
|
-
<li><a href="/tissue.html">Tissue</a></li>
|
43
|
-
<li><a href="/migrator.html">Migrator</a></li>
|
44
|
-
<li><a href="/casmall.html">caSmall</a></li>
|
45
|
-
</ul>
|
46
|
-
</div>
|
47
|
-
|
48
|
-
<div id="supportingText">
|
49
|
-
<p>
|
50
|
-
Each caRuby <a href="/components.html">component</a> is packaged as a standard Ruby <a href="http://docs.rubygems.org/shelf/index">gem</a>.
|
51
|
-
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
|
52
|
-
command. caRuby runs on any on any workstation or server that supports the target caBIG application Java API.
|
53
|
-
Set up a caRuby environment as follows:
|
54
|
-
<ol>
|
55
|
-
<li>Install the target caBIG application Java API client.
|
56
|
-
Consult the caBIG application Technical Guide for details, available from the caBIG application
|
57
|
-
<a href="https://cabig-kc.nci.nih.gov/MediaWiki/index.php/Knowledge_Center_Index">Knowledge Center</a>.
|
58
|
-
</li>
|
59
|
-
<li>Install <a href="http://jruby.org">JRuby</a>.</li>
|
60
|
-
<li>Open a command console and enter the following:
|
61
|
-
<pre>
|
62
|
-
gem install rubygems
|
63
|
-
</pre>
|
64
|
-
</li>
|
65
|
-
</ol>
|
66
|
-
</p>
|
67
|
-
<p>
|
68
|
-
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.:
|
69
|
-
<pre>
|
70
|
-
gem install caruby-tissue
|
71
|
-
</pre>
|
72
|
-
</p>
|
73
|
-
<p>
|
74
|
-
and updated using the <code>gem update</code> command, e.g.:
|
75
|
-
<pre>
|
76
|
-
gem update caruby-tissue
|
77
|
-
</pre>
|
78
|
-
</p>
|
79
|
-
<p>The caRuby gem is now ready for use. Consult the gem <a href="/documentation.html">documentation</a> for usage and examples.
|
80
|
-
</p>
|
81
|
-
<div id="footer">
|
82
|
-
</div>
|
83
|
-
</div>
|
84
|
-
</div>
|
85
|
-
|
86
|
-
</body>
|
87
|
-
</html>
|
@@ -1,87 +0,0 @@
|
|
1
|
-
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
|
2
|
-
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
|
3
|
-
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" >
|
4
|
-
<head>
|
5
|
-
<meta http-equiv="content-type" content="text/html; charset=iso-8859-1" />
|
6
|
-
<meta name="author" content="Fred Loney, OHSU" />
|
7
|
-
<meta name="keywords" content="caRuby" />
|
8
|
-
<meta name="description" content="caRuby Quick Start page." />
|
9
|
-
<meta name="robots" content="all" />
|
10
|
-
<title>caRuby: Quick Start</title>
|
11
|
-
|
12
|
-
<!-- to correct the unsightly Flash of Unstyled Content. http://www.bluerobot.com/web/css/fouc.asp -->
|
13
|
-
<script type="text/javascript"></script>
|
14
|
-
|
15
|
-
<style type="text/css" title="currentStyle" media="screen">
|
16
|
-
@import "/css/site.css";
|
17
|
-
</style>
|
18
|
-
<link rel='stylesheet' href='css/site.css' type='text/css' media="screen, projection">
|
19
|
-
<link rel="Shortcut Icon" href="images/favicon.ico" />
|
20
|
-
</head>
|
21
|
-
|
22
|
-
<body id="quick_start">
|
23
|
-
|
24
|
-
<div id="container">
|
25
|
-
<div id="head">
|
26
|
-
<h1><a href="index.html">caRuby:</a></h1>
|
27
|
-
<h2><a href="http://cabig.nci.nih.gov">caBIG®</a> Simplified</h2>
|
28
|
-
<ul>
|
29
|
-
<li><a href="/index.html">Home</a></li>
|
30
|
-
<li><span class="currentPage"><em>Quick Start</em></li>
|
31
|
-
<li><a href='http://caruby.tenderapp.com/'>Help</a></li>
|
32
|
-
<li><a href='http://github.com/caruby'>Source</a></li>
|
33
|
-
<li><a href='/about.html'>About</a></li>
|
34
|
-
</ul>
|
35
|
-
<img src="images/logo.png"/>
|
36
|
-
</div>
|
37
|
-
|
38
|
-
<div id="features">
|
39
|
-
<h3>Features</h3>
|
40
|
-
<ul>
|
41
|
-
<li><a href="/api.html">API</a></li>
|
42
|
-
<li><a href="/tissue.html">Tissue</a></li>
|
43
|
-
<li><a href="/migrator.html">Migrator</a></li>
|
44
|
-
<li><a href="/casmall.html">caSmall</a></li>
|
45
|
-
</ul>
|
46
|
-
</div>
|
47
|
-
|
48
|
-
<div id="supportingText">
|
49
|
-
<p>
|
50
|
-
Each caRuby <a href="/components.html">component</a> is packaged as a standard Ruby <a href="http://docs.rubygems.org/shelf/index">gem</a>.
|
51
|
-
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
|
52
|
-
command. caRuby runs on any on any workstation or server that supports the target caBIG application Java API.
|
53
|
-
Set up a caRuby environment as follows:
|
54
|
-
<ol>
|
55
|
-
<li>Install the target caBIG application Java API client.
|
56
|
-
Consult the caBIG application Technical Guide for details, available from the caBIG application
|
57
|
-
<a href="https://cabig-kc.nci.nih.gov/MediaWiki/index.php/Knowledge_Center_Index">Knowledge Center</a>.
|
58
|
-
</li>
|
59
|
-
<li>Install <a href="http://jruby.org">JRuby</a>.</li>
|
60
|
-
<li>Open a command console and enter the following:
|
61
|
-
<pre>
|
62
|
-
gem install rubygems
|
63
|
-
</pre>
|
64
|
-
</li>
|
65
|
-
</ol>
|
66
|
-
</p>
|
67
|
-
<p>
|
68
|
-
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.:
|
69
|
-
<pre>
|
70
|
-
gem install caruby-tissue
|
71
|
-
</pre>
|
72
|
-
</p>
|
73
|
-
<p>
|
74
|
-
and updated using the <code>gem update</code> command, e.g.:
|
75
|
-
<pre>
|
76
|
-
gem update caruby-tissue
|
77
|
-
</pre>
|
78
|
-
</p>
|
79
|
-
<p>The caRuby gem is now ready for use. Consult the gem <a href="/documentation.html">documentation</a> for usage and examples.
|
80
|
-
</p>
|
81
|
-
<div id="footer">
|
82
|
-
</div>
|
83
|
-
</div>
|
84
|
-
</div>
|
85
|
-
|
86
|
-
</body>
|
87
|
-
</html>
|
data/doc/website/tissue.html
DELETED
@@ -1,85 +0,0 @@
|
|
1
|
-
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
|
2
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<head>
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<meta http-equiv="content-type" content="text/html; charset=iso-8859-1" />
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<meta name="author" content="Fred Loney, OHSU" />
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<meta name="keywords" content="caRuby, caTissue" />
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<meta name="description" content="caRuby Tissue page." />
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<title>caRuby: Quick Start</title>
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@import "/css/site.css";
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</head>
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<body id="tissue">
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<div id="container">
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<div id="head">
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<h1><a href="index.html">caRuby:</a></h1>
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<h2>Tissue</h2>
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<ul>
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<li><a href='quick_start.html'><em>Quick Start</em></a></li>
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<li><a href='faq.html'>FAQ</a></li>
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<li><a href='http://caruby.tenderapp.com/'>Help</a></li>
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<li><a href='contribute.html'>Contribute</a></li>
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<li><a href='about.html'>About</a></li>
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</ul>
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<img src="images/logo.png"/>
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</div>
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<p>
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The caRuby Tissue component applies the caRuby facade to the
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<a href="https://cabig-kc.nci.nih.gov/Biospecimen/KC/index.php/CaTissue_Suite">caTissue</a>
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application. This offers the following features:
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<ul>
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<li>flexible server interaction</li>
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<li>data migration and extraction</li>
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<li>a foundation for a <a href="casmall.html">caSmall</a> framework</li>
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</ul>
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</p>
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<p>
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Since the caRuby Tissue component is built on the caTissue API, all of the caTissue business logic applies.
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In addition, caRuby augments the API as follows:
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<ul>
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<li>supplies default attribute values</li>
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<li>validates mandatory attributes before submission to caTissue</li>
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<li>validates additional attributes which are permitted by the caTissue API but corrupt the database</li>
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<li>migrates an input CSV record to a caTissue object based on one simple configuration file</li>
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<li>validates migration input diagnosis and tissue site permissible values</li>
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<li>optionally maps diagnosis and tissue site migration input values to caTissue permissible values</li>
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<li>determines how to save the caTissue object based on the caTissue object model</li>
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<li>finds referenced objects based on secondary keys and alternative search strategies</li>
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<li>creates whatever needs to be created in the required order based on the data model associations</li>
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<li>works around caCORE and caTissue bugs and traps</li>
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<li>provides helper methods for common tasks, e.g. aliquoting</li>
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</ul>
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</p>
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<p>
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The sole configuration is the migration mapping file and a small caTissue server access properties file.
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The defaults and other metadata are defined in Ruby declarations rather than a configuration.
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These declarations express basic model characteristics, and are expected to be stable and sufficient for most uses.
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They can, however, be modified in small Ruby shim files.
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Special-purpose migration code can be added in the shim files as well, as described in the
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<a href='shims.html'>Shims</a> description.
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</p>
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<p>
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There is almost no class-specific caRuby business logic code similar to that found in caTissue.
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Rather, there are basic design patterns driven by the model characteristics defined in the Ruby declarations.
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</p>
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<div id="footer">
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UOM implements Units of Measurement based on the
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<a href=http://physics.nist.gov/Pubs/SP330/sp330.pdf>International System of Units (SI)</a>.
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The base SI units, metric scalar factors and all possible combinations of these units are supported out of the box.
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Common alternative non-metric measurement systems, e.g. US Customary units, are supported with conversions between
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these units and the SI units. Additional units can be defined with conversion to an existing unit. UOM infers
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full conversion capability between units of the same dimension from the minimal number of conversion definitions.
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Arithmetic operations between UOM Measurement objects converts the measurement units and scalar factors as necessary,
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including unit products, quotients and powers of arbitrary complexity.
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