caruby-tissue 1.5.6 → 2.1.1

data/Gemfile

@@ -0,0 +1,17 @@
+source :rubygems
+gemspec
+
+group :development do
+  # The Galena example gem
+  gem 'galena', :path => File.dirname(__FILE__) + '/examples/galena'
+
+  # Uncomment the following lines as needed if there are changes to a
+  # dependency gem. Change the path option to your workspace location.
+  # Commit the changed Gemfile and Gemfile.lock to a local git branch
+  # rather than to the master branch. Do not check in the local change.
+  gem 'jinx', :path => File.dirname(__FILE__) + '/../../jinx/core'
+  gem 'jinx-json', :path => File.dirname(__FILE__) + '/../../jinx/json'
+  gem 'jinx-migrate', :path => File.dirname(__FILE__) + '/../../jinx/migrate'
+  gem 'caruby-core', :path => File.dirname(__FILE__) + '/../core', :require => 'caruby'
+  gem 'caruby-tissue', :path => File.dirname(__FILE__), :require => 'catissue'
+end

data/History.md

@@ -1,6 +1,10 @@
-This history lists major release themes. See the GitHub Commits (https://github.com/caruby/tissue)
+This history lists major release themes. See the GitHub commits (https://github.com/caruby/tissue)
 for change details.
 
+2.1.1 / 2012-04-13
+------------------
+* Jinx-based refactoring.
+
 1.5.6 / 2011-09-30
 ------------------
 * Added validate function back into migrate.

data/README.md

@@ -4,7 +4,7 @@ caRuby Tissue: Simplifying caTissue
 **Home**:         [http://caruby.rubyforge.org/catissue.html](http://caruby.rubyforge.org/catissue.html)    
 **Git**:          [http://github.com/caruby/tissue](http://github.com/caruby/tissue)       
 **Author**:       OHSU Knight Cancer Institute    
-**Copyright**:    2010, 2011    
+**Copyright**:    2010, 2011, 2012    
 **License**:      MIT License    
 
 Synopsis
@@ -41,6 +41,6 @@ The caRuby Tissue [FAQ](https://caruby.tenderapp.com/dashboard/sections/tissue)
 Copyright
 ---------
 
-caRuby © 2010, 2011 by [Oregon Health & Science University](http://www.ohsu.edu/xd/health/services/cancer/index.cfm).
+caRuby © 2010, 2011, 2012 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/bin/crtdump

@@ -3,14 +3,7 @@
 # crtdump: Dumps the content of a caTissue object to stdout
 #
 
-# load the caruby-tissue gem
-require 'rubygems'
-gem 'caruby-tissue'
-
-# the default log file
-DEF_LOG_FILE = 'log/catissue.log'
-
-require 'catissue/cli/command'
+require File.dirname(__FILE__) + '/../lib/catissue/cli/command'
       
 SPECS = [
   [:class, "class", "The class of the object"],
@@ -32,3 +25,4 @@ CaTissue::CLI::Command.new(SPECS).start do |opts|
   # print the object graph
   puts obj.database.lazy_loader.suspend { obj.dump }
 end
+exit 0

data/bin/crtexample

@@ -3,11 +3,8 @@
 # crtexample: list and run caRuby Tissue examples
 #
 
-# load the caruby-tissue gem
-require 'rubygems'
-gem 'caruby-tissue'
-
-require 'catissue/cli/example'
+require File.dirname(__FILE__) + '/../lib/catissue/cli/example'
 
 # run the command
 CaTissue::CLI::Example.new.start
+exit 0

data/bin/crtmigrate

@@ -3,10 +3,7 @@
 # crtmigrate: migrates a source file to caTissue
 #
 
-# load the required gems
-require 'rubygems'
-gem 'caruby-tissue'
+require File.dirname(__FILE__) + '/../lib/catissue/cli/migrate'
 
-require 'catissue/cli/migrate'
-
-CaTissue::CLI::Migrate.new.start
+CaTissue::CLI::Migrate.new.start
+exit 0

data/bin/crtsmoke

@@ -8,15 +8,10 @@ quiet = ARGV.include?('--help') || ARGV.include?('--version')
 
 puts "Starting the smoke test..." unless quiet
 
-puts "Loading the caruby-tissue gem..." unless quiet
+puts "Loading the caTissue Tissue client..." unless quiet
 
-# load the caruby-tissue gem
-require 'rubygems'
-gem 'caruby-tissue'
-
-puts "Loading the caTissue client..." unless quiet
-
-require 'catissue/cli/smoke'
+require File.dirname(__FILE__) + '/../lib/catissue/cli/smoke'
 
 # run the command
 CaTissue::CLI::Smoke.new.start
+exit 0

data/conf/wustl/{log4j.properties → linux/log4j.properties}

@@ -1,12 +1,12 @@
-log4j.rootLogger==ERROR, clientLog, catissuecoreclientLog
+log4j.rootLogger=ERROR, clientLog, catissuecoreclientLog
 
 log4j.appender.clientLog=org.apache.log4j.FileAppender
-log4j.appender.clientLog.File=./log/client.log
+log4j.appender.clientLog.File=/dev/null
 log4j.appender.clientLog.layout=org.apache.log4j.PatternLayout
 log4j.appender.clientLog.layout.ConversionPattern=%d{ABSOLUTE} %5p %c{1}:%L - %m%n
 
 log4j.appender.catissuecoreclientLog=org.apache.log4j.FileAppender
-log4j.appender.catissuecoreclientLog.File=./log/catissuecoreclient.log
+log4j.appender.catissuecoreclientLog.File=/dev/null
 log4j.appender.catissuecoreclientLog.layout=org.apache.log4j.PatternLayout
 log4j.appender.catissuecoreclientLog.layout.ConversionPattern=%d{ABSOLUTE} %5p %c{1} - %m%n
 

data/conf/wustl/windows/log4j.properties

@@ -0,0 +1,40 @@
+log4j.rootLogger=ERROR, clientLog, catissuecoreclientLog
+
+log4j.appender.clientLog=org.apache.log4j.FileAppender
+log4j.appender.clientLog.File=NUL
+log4j.appender.clientLog.layout=org.apache.log4j.PatternLayout
+log4j.appender.clientLog.layout.ConversionPattern=%d{ABSOLUTE} %5p %c{1}:%L - %m%n
+
+log4j.appender.catissuecoreclientLog=org.apache.log4j.FileAppender
+log4j.appender.catissuecoreclientLog.File=NUL
+log4j.appender.catissuecoreclientLog.layout=org.apache.log4j.PatternLayout
+log4j.appender.catissuecoreclientLog.layout.ConversionPattern=%d{ABSOLUTE} %5p %c{1} - %m%n
+
+log4j.appender.stdout=org.apache.log4j.ConsoleAppender
+log4j.appender.stdout.layout=org.apache.log4j.PatternLayout
+log4j.appender.stdout.layout.ConversionPattern=%d{ABSOLUTE} %5p %c{1}:%L - %m%n
+
+### set log levels - for more verbose logging change 'info' to 'debug' ###
+
+log4j.rootLogger=warn, clientLog
+
+log4j.logger.org.hibernate=info
+
+## log the SQL
+log4j.logger.org.hibernate.SQL=debug
+
+### log JDBC bind parameters ###
+log4j.logger.org.hibernate.type=info
+
+### log schema export/update ###
+log4j.logger.org.hibernate.tool.hbm2ddl=debug
+
+### log cache activity ###
+#log4j.logger.org.hibernate.cache=debug
+
+### log JDBC resource acquisition
+#log4j.logger.org.hibernate.jdbc=debug
+
+### enable the following line if you want to track down connection ###
+### leakages when using DriverManagerConnectionProvider ###
+#log4j.logger.org.hibernate.connection.DriverManagerConnectionProvider=trace

data/examples/galena/Gemfile

@@ -0,0 +1,16 @@
+source :rubygems
+gemspec
+
+group :development do
+  # The Galena example gem
+  gem 'galena', :path => File.dirname(__FILE__)
+  # Uncomment the following lines as needed if there are changes to a
+  # dependency gem. Change the path option to your workspace location.
+  # Commit the changed Gemfile and Gemfile.lock to a local git branch
+  # rather than to the master branch. Do not check in the local change.
+  gem 'jinx', :path => File.dirname(__FILE__) + '/../../../../jinx/core'
+  gem 'jinx-migrate', :path => File.dirname(__FILE__) + '/../../../../jinx/migrate'
+  gem 'jinx-json', :path => File.dirname(__FILE__) + '/../../../../jinx/json'
+  gem 'caruby-core', :path => File.dirname(__FILE__) + '/../../../core', :require => 'caruby'
+  gem 'caruby-tissue', :path => File.dirname(__FILE__) + '/../../../tissue', :require => 'catissue'
+end

data/examples/galena/Gemfile.lock

@@ -0,0 +1,88 @@
+PATH
+  remote: /Users/loneyf/workspace/caruby/core
+  specs:
+    caruby-core (2.1.1)
+      bundler
+      fastercsv
+      jinx (~> 2.1.1)
+      jinx-json (~> 2.1.1)
+      json_pure
+      rack
+      rdbi
+
+PATH
+  remote: /Users/loneyf/workspace/caruby/tissue
+  specs:
+    caruby-tissue (2.1.1)
+      bundler
+      jinx (>= 2.1.1)
+      jinx-json (>= 2.1.1)
+      jinx-migrate (>= 2.1.1)
+      uom (>= 1.2.2)
+
+PATH
+  remote: .
+  specs:
+    galena (2.1.1-java)
+      caruby-tissue (>= 2.1.1)
+
+PATH
+  remote: /Users/loneyf/workspace/jinx/core
+  specs:
+    jinx (2.1.1)
+      bundler
+
+PATH
+  remote: /Users/loneyf/workspace/jinx/json
+  specs:
+    jinx-json (2.1.1)
+      bundler
+      jinx
+      json_pure
+
+PATH
+  remote: /Users/loneyf/workspace/jinx/migrate
+  specs:
+    jinx-migrate (2.1.1)
+      bundler
+      fastercsv
+      rack
+
+GEM
+  remote: http://rubygems.org/
+  specs:
+    diff-lcs (1.1.3)
+    epoxy (0.3.1)
+    extensional (1.3.1)
+    fastercsv (1.5.4)
+    json_pure (1.6.5)
+    methlab (0.1.0)
+    rack (1.4.1)
+    rdbi (0.9.1)
+      epoxy (>= 0.3.1)
+      methlab (>= 0.0.9)
+      typelib
+    rspec (2.8.0)
+      rspec-core (~> 2.8.0)
+      rspec-expectations (~> 2.8.0)
+      rspec-mocks (~> 2.8.0)
+    rspec-core (2.8.0)
+    rspec-expectations (2.8.0)
+      diff-lcs (~> 1.1.2)
+    rspec-mocks (2.8.0)
+    typelib (0.1.0)
+    uom (1.2.2)
+      extensional
+
+PLATFORMS
+  java
+
+DEPENDENCIES
+  bundler
+  caruby-core!
+  caruby-tissue!
+  galena!
+  jinx!
+  jinx-json!
+  jinx-migrate!
+  rspec (>= 2.6)

data/examples/galena/README.md

@@ -35,9 +35,9 @@ Migration
 The example migration input data resides in the `data` directory.
 Each CSV input file holds one row for each specimen.
 
-Each example has a field mapping configuration in the `conf/migration` directory.
+Each example has a field mapping configuration in the `conf/` directory.
 For example, the `simple.csv` input file is migrated into caTissue using the
-`simple_migration.yaml` configuration file.
+`simple/migration.yaml` configuration file.
 
 Migrate the Galena `simple` example as follows:
 
@@ -52,10 +52,10 @@ Migrate the Galena `simple` example as follows:
 
 3. Run the following:
 
-   `crtmigrate --target TissueSpecimen --mapping conf/migration/simple_fields.yaml data/simple.csv`
+   `crtmigrate --target TissueSpecimen --mapping conf/simple/fields.yaml data/simple.csv`
 
    This command migrates the CSV record in the `simple.csv` input file into a caTissue
-   `TissueSpecimen` based on the `simple_fields.yaml` mapping file.
+   `TissueSpecimen` based on the `simple/fields.yaml` mapping file.
    Peruse the configuration and data files to see which data are migrated and
    where this data ends up in caTissue.
    
@@ -65,29 +65,29 @@ Migrate the Galena `simple` example as follows:
 The other examples are run in a similar manner. Each example demonstrates different
 features of the caRuby Migration utility as follows:
 
-* <tt>simple</tt> - a good starting point with limited input fields
+* <tt>registration</tt> - registers participants in a collection protocol
 
-  `crtmigrate --target TissueSpecimen --mapping conf/migration/simple_fields.yaml data/simple.csv`
+  `crtmigrate --target CollectionProtocolRegistration --mapping conf/registration/fields.yaml --defaults conf/defaults.yaml data/registration.csv`
 
-* <tt>general</tt> - lots of input fields, no custom Ruby code
+* <tt>simple</tt> - migrates one specimen with limited input fields
 
-  `crtmigrate --target TissueSpecimen --mapping conf/migration/general_fields.yaml data/general.csv`
+  `crtmigrate --target TissueSpecimen --mapping conf/simple/fields.yaml --defaults conf/defaults.yaml data/simple.csv`
 
-* <tt>filter</tt> - custom default, value filter, and shim code to convert input values to caTissue values and reject an incomplete migration
+* <tt>general</tt> - migrates specimens with lots of input fields and a minimal configuration
 
-  `crtmigrate --target TissueSpecimen --mapping conf/migration/filter_fields.yaml --defaults conf/migration/filter_defaults.yaml --filters conf/migration/filter_values.yaml --shims lib/galena/tissue/migration/filter_shims.rb --bad bad.csv data/filter.csv`
+  `crtmigrate --target TissueSpecimen --mapping conf/general/fields.yaml data/general.csv`
 
-* <tt>frozen</tt> - storage locations
+* <tt>filter</tt> - applies a value filter and shim code to convert input values to caTissue values and reject an incomplete migration
 
-  `crtmigrate --target TissueSpecimen --mapping conf/migration/frozen_fields.yaml --defaults conf/migration/frozen_defaults.yaml --shims lib/galena/tissue/migration/frozen_shims.rb data/frozen.csv`
+  `crtmigrate --target TissueSpecimen --mapping conf/filter/fields.yaml  --defaults conf/defaults.yaml --filters conf/filter/values.yaml --shims lib/galena/filter.rb --bad bad.csv data/filter.csv`
 
-* <tt>annotation</tt> - Dynamic Extension annotations
+* <tt>frozen</tt> - adds a custom default and places specimens in storage locations
 
-  `crtmigrate --target TissueSpecimen --mapping conf/migration/annotation_fields.yaml --defaults conf/migration/annotation_defaults.yaml data/annotation.csv`
+  `crtmigrate --target TissueSpecimen --mapping conf/frozen/fields.yaml --defaults conf/defaults.yaml,conf/frozen/defaults.yaml --shims lib/galena/frozen.rb data/frozen.csv`
 
-* <tt>registration</tt> - register participants in a Collection Protocol without specimens
+* <tt>annotation</tt> - annotates the specimens with Dynamic Extensions
 
-  `crtmigrate --target SpecimenCollectionGroup --mapping conf/migration/registration_fields.yaml data/registration.csv`
+  `crtmigrate --target SpecimenCollectionGroup::Pathology::RadicalProstatectomyPathologyAnnotation --mapping conf/annotation/fields.yaml --defaults conf/defaults.yaml,conf/annotation/defaults.yaml data/annotation.csv`
 
 Try running an example with the `--debug` flag and look at the `log/migration.log` file to see
 what caRuby is up to behind the scenes (hint: a lot!).

data/examples/galena/Rakefile

@@ -0,0 +1,30 @@
+require 'fileutils'
+require File.expand_path('version', File.dirname(__FILE__) + '/lib/galena')
+
+# the gem name
+GEM = 'galena'
+GEM_VERSION = Galena::VERSION
+
+WINDOWS = (Config::CONFIG['host_os'] =~ /mingw|win32|cygwin/ ? true : false) rescue false
+SUDO = WINDOWS ? '' : 'sudo'
+
+desc "Makes the API documentation"
+task :doc do
+  FileUtils.rm_rf 'doc/api'
+  `yardoc`
+end
+
+desc "Builds the gem"
+task :gem do
+  `jgem build #{GEM}.gemspec`
+end
+
+desc "Installs the gem"
+task :install => :gem do
+  `#{SUDO} jgem install #{GEM}-#{GEM_VERSION}.gem`
+end
+
+desc "Runs all tests"
+task :test do
+  `rspec examples/galena`
+end

data/examples/galena/bin/seed

@@ -3,19 +3,13 @@
 # seed: seeds the Galena example administrative objects in the database
 #
 
-# load the caRuby Tissue gem
-require 'rubygems'
-gem 'caruby-tissue'
-
-# add the Galena lib to the path
+# Add the Galena lib to the path.
 $:.unshift File.join(File.dirname(__FILE__), '..', 'lib')
 
-# the default log file
-DEF_LOG_FILE = 'log/migration.log'
-
+require 'rubygems'
 require 'catissue'
 require 'catissue/cli/command'
+require 'galena/seed'
 
-require 'galena/tissue/seed/defaults'
-
-CaTissue::CLI::Command.new.start { Galena::Seed.defaults.ensure_exists }
+CaTissue::CLI::Command.new.start { Galena.seed }
+exit 0

data/examples/galena/conf/annotation/defaults.yaml

@@ -0,0 +1,2 @@
+RadicalProstatectomyPathologyAnnotation.comment: Imported annotation
+HistologicGrade.grading_system_name: WHO Grade I

data/examples/galena/conf/{migration/annotation_fields.yaml → annotation/fields.yaml}

@@ -1,8 +1,6 @@
 # This is the Galena annotation example migration field mapping file.
 # This example extends the simple migration with annotation fields.
-
-Protocol: CollectionProtocol.title
 MRN: ParticipantMedicalIdentifier.medical_record_number, Participant.last_name
 SPN: SpecimenCollectionGroup.surgical_pathology_number
-Gleason: SpecimenCollectionGroup::Pathology::GleasonScore.primary_pattern_score
-Grade: SpecimenCollectionGroup::Pathology::HistologicGrade.grade
+Gleason: GleasonScore.primary_pattern_score
+Grade: HistologicGrade.grade

data/examples/galena/conf/defaults.yaml

@@ -0,0 +1,9 @@
+# This is the Galena example migration defaults file.
+# Each entry is in the format:
+#   property: value
+
+# The collection protocol title.
+CollectionProtocol.title: Galena Migration
+
+# The collection site.
+Site.name: Galena Hospital

data/examples/galena/conf/{migration/filter_fields.yaml → filter/fields.yaml}

@@ -1,4 +1,3 @@
-Protocol: CollectionProtocol.title
 MRN: ParticipantMedicalIdentifier.medical_record_number
 Initials: Participant.first_name, Participant.last_name
 Frozen?: TissueSpecimen.specimen_type

data/examples/galena/conf/filter/values.yaml

@@ -0,0 +1,8 @@
+# This value filter configuration file demonstrates how to transform an input field value
+# to a caTissue value. The specimen type input field is a string which can be a
+# case-insensitive variation of TRUE, FALSE or missing. If the input value matches the
+# case-insensitive regular expression /TRUE/i, then the input value is transformed to
+# the caTissue value 'Frozen Tissue'. Otherwise, the specimen type is set to 'Fixed Tissue'.
+TissueSpecimen.specimen_type:
+  /TRUE/i : 'Frozen Tissue'
+  /.*/ : 'Fixed Tissue'