caruby-tissue 1.5.6 → 2.1.1

data/bin/crtextract

@@ -1,47 +0,0 @@
-#!/usr/bin/env jruby
-#
-# crtextract: extracts caTissue records which changed during a time interval
-#
-# == Usage
-#
-# catissue-extract.rb [options]
-#
-# --help, -h:
-#    print this help message and exit
-# --target, -t class:
-#    target class to extract (default Specimen)
-# --log file, -l file:
-#    log file (default ./log/migration.log)
-# --since date, -s date:
-#    earliest change date selection condition (optional)
-# --before date, -b date:
-#    latest change date selection condition (optional)
-# --on date, -b date:
-#    change date selection condition (optional)
-# --debug, -d:
-#    print debug messages to log (optional)
-#
-# See the ohsu distribution doc/extract.html file for more information.
-#
-# == License
-#
-# This program is licensed under the terms of the +LEGAL+ file in
-# the source distribution.
-#
-# load the required gems
-require 'rubygems'
-gem 'caruby-tissue'
-
-require 'catissue/cli/command'
-require 'catissue/extract/delta'
-require 'catissue/extract/extractor'
-
-# the command line specification
-spec = [
-  [:version, "--version", "prints the version of caRuby Tissue and the supported caTissue releases"],
-]
-
-# run the command
-CaRuby::Command.new(spec).execute do |opts|
-  if opts[:version] then puts "#{CaTissue::VERSION} for caTissue v#{CaTissue::CATISSUE_VERSIONS}" end
-end

data/examples/galena/conf/extract/simple_fields.yaml

@@ -1,4 +0,0 @@
-MRN: specimen_collection_group.registration.participant_identifier
-SPN: specimen_collection_group.surgical_pathology_number
-Collection Date: specimen_collection_group.collection_event_parameters.timestamp
-Quantity: initial_quantity

data/examples/galena/conf/migration/annotation_defaults.yaml

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

data/examples/galena/conf/migration/filter_defaults.yaml

@@ -1 +0,0 @@
-TissueSpecimen.specimen_type: Fixed Tissue

data/examples/galena/conf/migration/filter_values.yaml

@@ -1,13 +0,0 @@
-# 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 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'. A missing
-# input value is set to 'Fixed Tissue' by the filter_defaults.yaml configuration.
-#
-# A straight-forward value => value mapping would be expressed as:
-#   'TRUE' : 'Frozen Tissue'
-#   'FALSE' : 'Fixed Tissue'
-#
-TissueSpecimen.specimen_type:
-  !ruby/regexp '/TRUE/i' : 'Frozen Tissue'
-  !ruby/regexp '/FALSE/i' : 'Fixed Tissue'

data/examples/galena/conf/migration/participant_fields.yaml

@@ -1,4 +0,0 @@
-SSN: Participant.social_security_number
-First: Participant.first_name
-Middle: Participant.middle_name
-Last: Participant.last_name

data/examples/galena/conf/migration/registration_fields.yaml

@@ -1,5 +0,0 @@
-Protocol: CollectionProtocol.title
-Patient: ParticipantMedicalIdentifier.medical_record_number
-Collection Point: CollectionProtocolEvent.collection_point_label
-Received: ReceivedEventParameters.timestamp
-SCG Name: SpecimenCollectionGroup.name

data/examples/galena/data/participant.csv

@@ -1 +0,0 @@
-SSN,First,Middle,Last

data/examples/galena/lib/galena/tissue/migration/filter_shims.rb

@@ -1,41 +0,0 @@
-require 'uom'
-
-module CaTissue
-  # Declares the classes modified for migration.
-  shims Participant, TissueSpecimen, SpecimenCollectionGroup
-
-  class Participant
-    # Extracts the Participant first name from the +Initials+ input field.
-    def migrate_first_name(value, row)
-      value[0, 1]
-    end
-
-    # Extracts the Participant last name from the +Initials+ input field.
-    def migrate_last_name(value, row)
-      value[-1, 1]
-    end
-  end
-
-  class TissueSpecimen
-    # Transforms the +Frozen?+ flag input field to the caTissue specimen type +Frozen Tissue+ value.
-    def migrate_specimen_type(value, row)
-      value =~ /TRUE/i ? 'Frozen Tissue' : 'Fixed Tissue'
-    end
-    # Parses the source field as a UOM::Measurement if it is a string.
-    # Otherwises, returns the source value.
-    def migrate_initial_quantity(value, row)
-      # if value is not a string, then use it as is
-      return value unless value.is_a?(String)
-      # the value has a unit qualifier; parse the measurement.
-      # the unit is normalized to the Specimen standard unit.
-      value.to_measurement_quantity(standard_unit)
-    end
-  end
-
-  class SpecimenCollectionGroup
-    # Returns whether this SCG has a SPN.
-    def migration_valid?
-      surgical_pathology_number
-    end
-  end
-end

data/examples/galena/lib/galena/tissue/seed/defaults.rb

@@ -1,127 +0,0 @@
-require 'singleton'
-require 'catissue'
-
-module Galena
-  # Creates the {Galena::Seed::Defaults} administrative objects as necessary.
-  def self.seed
-    Seed.defaults.ensure_exists
-  end
-  
-  # Galena example utility module to populate the database with pre-defined administrative objects.
-  module Seed
-    # @return [Defaults] the defaults instance
-    def self.defaults
-      Defaults.instance
-    end
-  
-    # Pre-defined Galena example administrative objects. If the Galena example is already set up
-    # in the caTissue database, then the default object secondary key attributes can be used as a
-    # {CaRuby::Persistable#find} template to retrieve the existing objects. Otherwise, the Defaults
-    # attributes can be created by calling {CaRuby::Persistable#create}.
-    #
-    # In a real-world use case, the administrative objects are typically built in the UI before-hand.
-    # In that case, it is only necessary to define the object secondary key rather than content, e.g.:
-    #   pcl = CaTissue::CollectionProtocol.new(:title => 'Galena CP')
-    # The complete definitions are included in this method for convenience in order to seed the
-    # example in a test database. A real-world migration might find it useful to create a similar
-    # defaults file in order to rapidly seed an empty test or staging database.
-    class Defaults
-      include Singleton
-  
-      attr_reader :protocols, :hospital, :tissue_bank, :freezer_type, :box_type
-  
-      # Creates the Galena example Defaults singleton and populates the attributes.
-      def initialize
-        super
-        @protocols = []
-        populate
-      end
-      
-      # Creates the Galena example administrative objects as necessary.
-      def ensure_exists
-        @protocols.each { |pcl| pcl.find(:create) }
-        @hospital.find(:create)
-        @surgeon.find(:create)
-        unless @box.find then
-          frz = @freezer_type.find_available(@tissue_bank, :create)
-          frz << @box
-          @box.create
-        end
-      end
-      
-      # @return [CaTissue::CollectionProtocol] the primary example protocol
-      def protocol
-        @protocols.first
-      end
-  
-      private
-  
-      # Sets the Galena example Defaults attributes to new objects.
-      def populate
-        galena = CaTissue::Institution.new(:name => 'Galena University')
-  
-        addr = CaTissue::Address.new(
-          :city => 'Galena', :state => 'Illinois', :country => 'United States', :zipCode => '37544',
-          :street => '411 Basin St', :phoneNumber => '311-555-5555')
-  
-        dept = CaTissue::Department.new(:name => 'Pathology')
-  
-        crg = CaTissue::CancerResearchGroup.new(:name => 'Don Thomas Cancer Center')
-  
-        coord = CaTissue::User.new(
-          :email_address => 'corey.nator@galena.edu',
-          :last_name => 'Nator', :first_name => 'Corey', :address => addr.copy,
-          :institution => galena, :department => dept, :cancer_research_group => crg)
-  
-        @hospital = CaTissue::Site.new(
-            :site_type => CaTissue::Site::SiteType::COLLECTION, :name => 'Galena Hospital', 
-            :address => addr.copy, :coordinator => coord)
-  
-        @tissue_bank = CaTissue::Site.new(
-            :site_type => CaTissue::Site::SiteType::REPOSITORY, :name => 'Galena Tissue Bank', 
-            :address => addr.copy, :coordinator => coord)
-  
-        pi = CaTissue::User.new(
-          :email_address => 'vesta.gator@galena.edu',
-          :last_name => 'Gator', :first_name => 'Vesta', :address => addr.copy,
-          :institution => galena, :department => dept, :cancer_research_group => crg)
-  
-        @surgeon = CaTissue::User.new(
-          :email_address => 'serge.on@galena.edu',
-          :first_name => 'Serge', :last_name => 'On', :address => addr.copy,
-          :institution => galena, :department => dept, :cancer_research_group => crg)
-  
-        @protocols << pcl = CaTissue::CollectionProtocol.new(:title => 'Galena Migration', 
-          :principal_investigator => pi, :sites => [@tissue_bank])
-  
-        # CPE has default 1.0 event point and label
-        cpe = CaTissue::CollectionProtocolEvent.new(:collection_protocol => pcl, :event_point => 1.0, :label => 'Galena Migration_1')
-        
-        # The sole specimen requirement. Setting the requirement collection_event attribute to a CPE automatically
-        # sets the CPE requirement inverse attribute in caRuby.
-        CaTissue::TissueSpecimenRequirement.new(:collection_event => cpe, :specimen_type => 'Fixed Tissue')
-  
-        @protocols << pcl2 = CaTissue::CollectionProtocol.new(:title => 'Galena Migration 2', 
-          :principal_investigator => pi, :sites => [@tissue_bank])
-        cpe2 = CaTissue::CollectionProtocolEvent.new(:collection_protocol => pcl2, :event_point => 2.0, :label => 'Galena Migration_2')
-        CaTissue::TissueSpecimenRequirement.new(:collection_event => cpe2, :specimen_type => 'Frozen Tissue')
-  
-        @protocols << pcl3 = CaTissue::CollectionProtocol.new(:title => 'Galena Migration 3', 
-          :principal_investigator => pi, :sites => [@tissue_bank])
-        cpe3 = CaTissue::CollectionProtocolEvent.new(:collection_protocol => pcl3, :event_point => 3.0, :label => 'Galena Migration_3')
-        CaTissue::TissueSpecimenRequirement.new(:collection_event => cpe3, :specimen_type => 'Frozen Tissue')
-  
-        # the storage container type hierarchy
-        @freezer_type = CaTissue::StorageType.new(:name => 'Galena Freezer', :columns => 10, :rows => 1, :column_label => 'Rack')
-        rack_type = CaTissue::StorageType.new(:name => 'Galena Rack', :columns => 10, :rows => 10)
-        @box_type = CaTissue::StorageType.new(:name => 'Galena Box', :columns => 10, :rows => 10)
-        @freezer_type << rack_type
-        rack_type << @box_type
-        @box_type << 'Tissue'
-        
-        # the example tissue box
-        @box = @box_type.new_container(:name => 'Galena Box 1')
-      end
-    end
-  end
-end

data/examples/psbin/README.md

@@ -1,45 +0,0 @@
-PSBIN caRuby Tissue example
-============================
-
-Synopsis
---------
-This directory contains the caRuby Tissue example for the **P**rostate **S**PORE **B**io**I**nformatics **N**etwork
-(PSBIN) initiative.
-The PSBIN initiative shares participant cancer center data in caTissue instances with common
-data elements. The official PSBIN import utility is a Java program which operates on a
-special-purpose input XML file and calls caRuby to create annotations. The example shown
-here is a caRuby Tissue Migrator import which operates on CSV files.
-
-The migration input files are in the `data` directory. The input maps to caTissue entities as follows:
-
-* `patient` => `Participant`
-
-* `biopsy` => prostate biopsy `SpecimenCollectionGroup`
-
-* `surgery` => prostatectomy `SpecimenCollectionGroup`
-
-* `t_stage` => the tumor stage as a lab annotation
-
-* (`neo`)`adjuvant_hormone` => (neo)adjuvant hormone therapy annotation
-
-* (`neo`)`adjuvant_radiation` => (neo)adjuvant radiation therapy annotation
-
-Setup
------
-Configure caRuby and copy the PSBIN example as described in the Galena examples
-[Setup](https://github.com/caruby/tissue/blob/master/examples/galena/README.md).
-
-Create a simple `Prostate SPORE` caTissue collection protocol in a test database.
-
-Migration
----------
-Run the following commands in the copied example location:
-
-    crtmigrate --target Participant --mapping conf/patient_fields.yaml --defaults conf/patient_defaults.yaml data/patient.csv
-    crtmigrate --target SpecimenCollectionGroup --mapping conf/biopsy_fields.yaml --defaults conf/biopsy_defaults.yaml data/biopsy.csv
-    crtmigrate --target SpecimenCollectionGroup --mapping conf/surgery_fields.yaml --defaults conf/surgery_defaults.yaml data/surgery.csv
-    crtmigrate --target Participant::Clinical::LabAnnotation --mapping conf/t_stage_fields.yaml --defaults conf/t_stage_defaults.yaml data/t_stage.csv
-    crtmigrate --target Participant::Clinical::TreatmentAnnotation --mapping conf/therapy_fields.yaml --defaults conf/neoadjuvant_hormone_defaults.yaml data/neoadjuvant_hormone.csv
-    crtmigrate --target Participant::Clinical::RadRXAnnotation --mapping conf/therapy_fields.yaml --defaults conf/neoadjuvant_radiation_defaults.yaml data/neoadjuvant_radiation.csv
-    crtmigrate --target Participant::Clinical::TreatmentAnnotation --mapping conf/therapy_fields.yaml --defaults conf/adjuvant_hormone_defaults.yaml data/adjuvant_hormone.csv
-    crtmigrate --target Participant::Clinical::RadRXAnnotation --mapping conf/therapy_fields.yaml --defaults conf/adjuvant_radiation_defaults.yaml data/adjuvant_radiation.csv

data/examples/psbin/conf/adjuvant_hormone_defaults.yaml

@@ -1,2 +0,0 @@
-Participant::Clinical::TreatmentAnnotation.agent: NOT SPECIFIED
-Participant::Clinical::TreatmentAnnotation.other_agent: adjuvant Hormone Therapy; Not Specified

data/examples/psbin/conf/adjuvant_radiation_defaults.yaml

@@ -1,3 +0,0 @@
-Participant::Clinical::RadRXAnnotation.agent: NOT SPECIFIED
-Participant::Clinical::RadRXAnnotation.other_agent: adjuvant Radiation Therapy
-Participant::Clinical::RadRXAnnotation.dose_units: Gy

data/examples/psbin/conf/biopsy_defaults.yaml

@@ -1,3 +0,0 @@
-Participant::Clinical::NewDiagnosisHealthAnnotation.name_of_procedure: Needle Biopsy of prostate
-SpecimenCollectionGroup.clinical_status: New Diagnosis
-SpecimenCollectionGroup.collection_status: Complete

data/examples/psbin/conf/biopsy_fields.yaml

@@ -1,9 +0,0 @@
-Protocol: CollectionProtocol.title
-Patient: CollectionProtocolRegistration.protocol_participant_identifier
-Specimen Type: TissueSpecimen.specimen_type
-Year of Diagnosis: Participant::Clinical::NewDiagnosisHealthAnnotation.date_of_examination
-# Age requires a custom DE
-#Age at Diagnosis: Participant::Clinical::NewDiagnosisHealthAnnotation.age_at_diagnosis
-Gleason Primary: SpecimenCollectionGroup::Pathology::NeedleBiopsyProstatePathologyAnnotation.gleason_score.primary_pattern_score
-Gleason Secondary: SpecimenCollectionGroup::Pathology::NeedleBiopsyProstatePathologyAnnotation.gleason_score.secondary_pattern_score
-Gleason Tertiary: SpecimenCollectionGroup::Pathology::NeedleBiopsyProstatePathologyAnnotation.gleason_score.tertiary_pattern_score

data/examples/psbin/conf/neoadjuvant_hormone_defaults.yaml

@@ -1,2 +0,0 @@
-Participant::Clinical::TreatmentAnnotation.agent: NOT SPECIFIED
-Participant::Clinical::TreatmentAnnotation.other_agent: Neoadjuvant Hormone Therapy

data/examples/psbin/conf/neoadjuvant_radiation_defaults.yaml

@@ -1,3 +0,0 @@
-Participant::Clinical::RadRXAnnotation.agent: NOT SPECIFIED
-Participant::Clinical::RadRXAnnotation.other_agent: Neoadjuvant Radiation Therapy
-Participant::Clinical::RadRXAnnotation.dose_units: Gy

data/examples/psbin/conf/patient_defaults.yaml

@@ -1,3 +0,0 @@
-Participant::Clinical::LabAnnotation.lab_test_name: 2857-1 ~ Prostate specific Ag - Serum/Plasma - Quantitative - Mass Concentration - Point in time
-Participant::Clinical::LabAnnotation.other_lab_test_name: Pre-Treatment PSA
-Participant::Clinical::LabAnnotation.result_units: ng/ml

data/examples/psbin/conf/patient_fields.yaml

@@ -1,5 +0,0 @@
-Protocol: CollectionProtocol.title
-Patient: CollectionProtocolRegistration.protocol_participant_identifier
-Race: Race.name
-Ethnicity: Participant.ethnicity
-Pre-treatment PSA: Participant::Clinical::LabAnnotation.result

data/examples/psbin/conf/surgery_defaults.yaml

@@ -1,4 +0,0 @@
-Participant::Clinical::TreatmentAnnotation.agent: NOT SPECIFIED
-Participant::Clinical::TreatmentAnnotation.other_agent: Radical Prostatectomy
-SpecimenCollectionGroup.clinical_status: Operative
-SpecimenCollectionGroup.collection_status: Complete

data/examples/psbin/conf/surgery_fields.yaml

@@ -1,15 +0,0 @@
-Protocol: CollectionProtocol.title
-Patient: CollectionProtocolRegistration.protocol_participant_identifier
-Specimen Type: TissueSpecimen.specimen_type
-Year of Surgery: Participant::Clinical::Duration.start_date
-# Age requires a custom DE
-#Age at Surgery: SpecimenCollectionGroup::Pathology::RadicalProstatectomyPathologyAnnotation.age_at_surgery
-Gleason Primary: SpecimenCollectionGroup::Pathology::RadicalProstatectomyPathologyAnnotation.gleason_score.primary_pattern_score
-Gleason Secondary: SpecimenCollectionGroup::Pathology::RadicalProstatectomyPathologyAnnotation.gleason_score.secondary_pattern_score
-Gleason Tertiary: SpecimenCollectionGroup::Pathology::RadicalProstatectomyPathologyAnnotation.gleason_score.tertiary_pattern_score
-Surgical Margin Status: SpecimenCollectionGroup::Pathology::RadicalProstatectomyMargin.margin_status
-Seminal Vesicle Involvement: SpecimenCollectionGroup::Pathology::RadicalProstatectomyPathologyAnnotation.seminal_vesicle_invasion
-Extra-Prostatic Extension Focal?: SpecimenCollectionGroup::Pathology::ExtraprostaticExtension.is_focal
-Extra-Prostatic Extension Status: SpecimenCollectionGroup::Pathology::ExtraprostaticExtension.status
-Lymph Node Metastases: SpecimenCollectionGroup::Pathology::Invasion.lymphatic_invasion
-

data/examples/psbin/conf/t_stage_defaults.yaml

@@ -1 +0,0 @@
-Participant::Clinical::LabAnnotation.other_lab_test_name: TNM

data/examples/psbin/conf/t_stage_fields.yaml

@@ -1,4 +0,0 @@
-Protocol: CollectionProtocol.title
-Patient: CollectionProtocolRegistration.protocol_participant_identifier
-Clinical Staging System: Participant::Clinical::LabAnnotation.other_lab_test_name
-Clinical T Stage: Participant::Clinical::LabAnnotation.result

data/examples/psbin/conf/therapy_fields.yaml

@@ -1,5 +0,0 @@
-Protocol: CollectionProtocol.title
-Patient: CollectionProtocolRegistration.protocol_participant_identifier
-Agent: Participant::Clinical::TreatmentAnnotation.agent
-Dose: Participant::Clinical::TreatmentAnnotation.dose
-Units: Participant::Clinical::TreatmentAnnotation.dose_units

data/examples/psbin/data/adjuvant_hormone.csv

@@ -1 +0,0 @@
-Protocol,Patient,Agent,Dose,Units

data/examples/psbin/data/adjuvant_radiation.csv

@@ -1 +0,0 @@
-Protocol,Patient,Agent,Dose,Units

data/examples/psbin/data/biopsy.csv

@@ -1 +0,0 @@
-Protocol,Patient,Specimen Type,Year of Diagnosis,Age at Diagnosis,Gleason Primary,Gleason Secondary,Gleason Tertiary

data/examples/psbin/data/neoadjuvant_hormone.csv

@@ -1 +0,0 @@
-Protocol,Patient,Agent,Dose,Units

data/examples/psbin/data/neoadjuvant_radiation.csv

@@ -1 +0,0 @@
-Protocol,Patient,Agent,Dose,Units

data/examples/psbin/data/patient.csv

@@ -1 +0,0 @@
-Protocol,Patient,Race,Ethnicity,Pre-treatment PSA

data/examples/psbin/data/surgery.csv

@@ -1 +0,0 @@
-Protocol,Patient,Specimen Type,Year of Surgery,Age at Surgery,Gleason Primary,Gleason Secondary,Gleason Tertiary,Surgical Margin Status,Seminal Vesicle Involvement,Extra-Prostatic Extension Focal?,Extra-Prostatic Extension Status,Lymph Node Metastases

data/examples/psbin/data/t_stage.csv

@@ -1 +0,0 @@
-Protocol,Patient,Clinical Staging System,Clinical T Stage

data/examples/psbin/lib/psbin/biopsy_shims.rb

@@ -1,15 +0,0 @@
-module CaTissue
-  # Declares the classes modified for migration.
-  shims Participant
-
-  class Participant::Clinical::NewDiagnosisHealthAnnotation
-    # Makes a non-PHI date field from the year input value.
-    #
-    # @param [Integer] year the diagnosis year
-    # @param row (see CaRuby::Migratable#migrate)
-    # @return [Date] July 2 of the given year
-    def migrate_date_of_examination(year, row)
-      Date.new(year, 7, 2)
-    end
-  end
-end

data/examples/psbin/lib/psbin/surgery_shims.rb

@@ -1,15 +0,0 @@
-module CaTissue
-  # Declares the classes modified for migration.
-  shims Participant, SpecimenCollectionGroup
-
-  class Participant::Clinical::Duration
-    # Makes a non-PHI date field from the year input value.
-    #
-    # @param [Integer] year the diagnosis year
-    # @param row (see CaRuby::Migratable#migrate)
-    # @return [Date] July 2 of the given year
-    def migrate_start_date(year, row)
-      Date.new(year, 7, 2)
-    end
-  end
-end