ndr_workflow 1.2.5

checksums.yaml

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data/CHANGELOG.md

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+## [Unreleased]
+* No unreleased changes
+
+## 1.2.5 / 2026-07-13
+### Fixed
+* Support Ruby 3.4. Drop support for Rails 7.0, Ruby 3.1
+* Support Rails 8.1, Ruby 4.0. Drop support for Ruby 3.2
+
+## 1.2.4 / 2024-11-13
+### Fixed
+* Support Rails 7.1, 7.2, 8.0, Ruby 3.2. Drop support for Rails 6.1
+
+## 1.2.3 / 2022-12-02
+### Fixed
+* Support Ruby 3.1, Rails 7.0
+* Drop support for Ruby 2.6, Rails 5.2
+* Replace Public Health England naming with NHS Digital
+
+## 1.2.2 / 2021-01-25
+### Fixed
+* Ensure app/ subdirectories are autoloadable by `zeitwerk`
+
+## 1.2.1 / 2021-01-11
+### Fixed
+* Remove deprecations in Rails 6
+
+## 1.2.0 / 2020-07-01
+### Added
+* Add `e_batch.e_actions.restart` method
+* Start of CHANGELOG

data/MIT-LICENSE

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+Copyright 2015 YOURNAME
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.rdoc

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+# NdrWorkflow
+
+** THIS ENGINE IS NOT FOR PUBLIC DEPLOYMENT IN ITS CURRENT FORMAT ** 
+
+This is the NHS Digital (NHS-D) National Disease Registers (NDR) Workflow ruby gem, providing:
+
+1. core model definitions derived from ERA to allow for workflows and batch processing
+Core tables included: 
+EWorkflow, EBatch, EAction
+Supporting lookup tables include:
+ZeActiontype, ZeType, Zprovider, Zuser
+
+Currently excluded:
+Conformance data
+Queued_Job
+Back end daemons
+ZPostCode - referenced heavily in Zprovider
+
+## Considerations
+1. Postgres only implementation for creating underlying db tables (will work with oracle but no migrations)
+2. FK constraints managed through DB rather than ActiveRecord
+3. Table names set in Engine models - not standard rails
+4. 
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'ndr_workflow', path: "PATH_TO_YOUR_GIT_SVN/non-era/gems/ndr_workflow"
+```
+
+And then execute:
+
+    $ bundle install
+    
+If the application needs the physical tables creating in Postgres: 
+  
+    $ rails g ndr_workflow:install
+    $ rake db:migrate
+    
+## Usage
+
+# Rails 3
+
+Protected attributes 
+Disabe globally in your app in conf/application.rb, with 
+config.active_record.whitelist_attributes = false
+OR
+for specific models using attr_accessible : create new model definition in your app dir based on template files in enginer in :
+test/dummy/app/model/NAME.rb
+
+# Rails 4 
+
+Will need to use strong parameters 
+
+
+# When extending already present models (ERA)
+copy and uncomment the first line from test/dummy/app/model/NAME.rb to app/model/NAME.rb eg: 
+```require NdrWorkflow::Engine.root.join('app', 'models', 'e_action')```
+
+# When you want to extend the Engine
+create new model definition in your app dir based on file in engines dummy app ie test/dummy/app/model/NAME.rb
+
+
+# Test Data
+
+All test data in this repository is fictitious. Any resemblance to real persons, living or dead, is purely coincidental.
+
+Note: Real codes exist in the tests, postcodes for example, but bear no relation to real patient data. Please ensure that you *always* only ever commit dummy data when contributing to this project.
+
+
+= Using same class names in app and engine tricky .... (hence use of require)
+http://stackoverflow.com/questions/5045068/extending-controllers-of-a-rails-3-engine-in-the-main-app
+
+= TESTING
+BUNDLE_GEMFILE=gemfiles/Gemfile.rails-3.0.x bundle install
+BUNDLE_GEMFILE=gemfiles/Gemfile.rails-3.0.x bundle exec rake test 
+
+NDR_WORKFLOW
+================================================================================================================================
+-- Dummy lookup data
+ZeType.create(:shortdesc => "National Prostate Cancer Audit"){|ze_type| ze_type.ze_typeid = "NPCA"}
+ZeActiontype.create(:shortdesc => "Initialize batch"){|ze_actiontype| ze_actiontype.ze_actiontypeid = "NEW"}
+ZeActiontype.create(:shortdesc => "Initialize batch"){|ze_actiontype| ze_actiontype.ze_actiontypeid = "AIMP"}
+ZeActiontype.create(:shortdesc => "Initialize batch"){|ze_actiontype| ze_actiontype.ze_actiontypeid = "PRECHECK"}
+ZeActiontype.create(:shortdesc => "Initialize batch"){|ze_actiontype| ze_actiontype.ze_actiontypeid = "APOST"}
+ZeActiontype.create(:shortdesc => "Initialize batch"){|ze_actiontype| ze_actiontype.ze_actiontypeid = "MPOST"}
+ZeActiontype.create(:shortdesc => "Initialize batch"){|ze_actiontype| ze_actiontype.ze_actiontypeid = "CREA"}
+ZeActiontype.create(:shortdesc => "Initialize batch"){|ze_actiontype| ze_actiontype.ze_actiontypeid = "RECO"}
+ZeActiontype.create(:shortdesc => "Initialize batch"){|ze_actiontype| ze_actiontype.ze_actiontypeid = "CHECK"}
+ZeActiontype.create(:shortdesc => "Initialize batch"){|ze_actiontype| ze_actiontype.ze_actiontypeid = "AMCH"}
+ZeActiontype.create(:shortdesc => "Initialize batch"){|ze_actiontype| ze_actiontype.ze_actiontypeid = "MMCH"}
+ZeActiontype.create(:shortdesc => "Initialize batch"){|ze_actiontype| ze_actiontype.ze_actiontypeid = "STOP"}
+-- NO POSTCODES 
+Zprovider.create(:shortdesc => "ECRIC CAMBRIDGE", :exportid => "0402", :startdate => "007-06-01", :sort => 1, :role => "H", :linac => 0){|ze_provider| ze_provider.zproviderid = "0402"}
+Zuser.create(:zuserid => "ben", :shortdesc => "bens_test_user", :registryid => "0402") 
+
+-- Workflow model NPCA
+SEQUENCE = %w{NEW AIMP PRECHECK APOST MPOST CREA RECO CHECK AMCH MMCH STOP}
+SEQUENCE.each_with_index do |action, index|
+  EWorkflow.create(:e_type => 'NPCA', :last_e_actiontype => action, :next_e_actiontype => SEQUENCE[index+1]) unless SEQUENCE[index+1].nil?
+end
+
+-- Create batch for workflow
+EBatch.create(:e_type => "NPCA", :provider => "0402", :registryid => "0402", :media => 'Email', :original_filename => 'textfile_batch.txt',
+              :cleaned_filename => '', :numberofrecords => 3, :date_reference1 => '2005.05.05', :date_reference2 => '2007.01.01',
+              :e_batchid_traced => '', :comments => 'Addenbrookes, plain text file', :digest => '1b2bd8aecffcaf099b4d529498615ef2c765d1b5',
+              :lock_version => 0)
+
+-- Create first action for batch 
+EAction.create!(:e_batchid => 1, :e_actiontype => "NEW", :started => Time.now, :finished => nil, :startedby => 'ben', :status => '')
+--
+EBatch.new(:e_type => 'NPCA', :original_filename => 'svn/')
+EBatch.first.e_actions.start_and_finish('NEW','ben')
+
+
+

data/Rakefile

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+#!/usr/bin/env rake
+require 'ndr_dev_support/tasks'
+begin
+  require 'bundler/setup'
+rescue LoadError
+  puts 'You must `gem install bundler` and `bundle install` to run rake tasks'
+end
+begin
+  require 'rdoc/task'
+rescue LoadError
+  require 'rdoc/rdoc'
+  require 'rake/rdoctask'
+  RDoc::Task = Rake::RDocTask
+end
+
+RDoc::Task.new(:rdoc) do |rdoc|
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title    = 'NdrWorkflow'
+  rdoc.options << '--line-numbers'
+  rdoc.rdoc_files.include('README.rdoc')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end
+
+APP_RAKEFILE = File.expand_path("../test/dummy/Rakefile", __FILE__)
+load 'rails/tasks/engine.rake'
+
+
+
+Bundler::GemHelper.install_tasks
+
+require 'rake/testtask'
+
+Rake::TestTask.new(:test) do |t|
+  t.libs << 'lib'
+  t.libs << 'test'
+  t.pattern = 'test/**/*_test.rb'
+  t.verbose = false
+  t.warning = false
+end
+
+
+task :default => :test

data/SECURITY.md

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+# Security
+
+NHS England takes security and the protection of private data extremely seriously. If you believe you have found a vulnerability or other issue which has compromised or could compromise the security of any of our systems and/or private data managed by our systems, please do not hesitate to contact us using the methods outlined below.
+
+## Table of Contents
+
+- [Security](#security)
+  - [Table of Contents](#table-of-contents)
+  - [Reporting a vulnerability](#reporting-a-vulnerability)
+    - [Email](#email)
+    - [NCSC](#ncsc)
+  - [General Security Enquiries](#general-security-enquiries)
+
+## Reporting a vulnerability
+
+Please note, email is our preferred method of receiving reports.
+
+### Email
+
+If you wish to notify us of a vulnerability via email, please include detailed information on the nature of the vulnerability and any steps required to reproduce it.
+
+You can reach us at:
+
+- [Brian.Shand@nhs.net](mailto:Brian.Shand@nhs.net)
+- [cybersecurity@nhs.net](mailto:cybersecurity@nhs.net)
+
+### NCSC
+
+You can send your report to the National Cyber Security Centre, who will assess your report and pass it on to NHS England if necessary.
+
+You can report vulnerabilities here: [https://www.ncsc.gov.uk/information/vulnerability-reporting](https://www.ncsc.gov.uk/information/vulnerability-reporting)
+
+## General Security Enquiries
+
+If you have general enquiries regarding our cybersecurity, please reach out to us at [cybersecurity@nhs.net](mailto:cybersecurity@nhs.net)

data/app/constants/esource_constants.rb

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+# Make this exist, so autoloaders are happy
+module EsourceConstants; end
+
+# Constants that are used in a number of e-source-related programs.
+# The model classes corresponding to 'e_type' strings in e_batch records
+PERMITTED_LISTS_FROM_LOOKUPS = [:laterality] unless defined?(PERMITTED_LISTS_FROM_LOOKUPS)
+
+ERROR_INFO = {
+  :started => ['Action in progress', 'The action has been started by someone else.'],
+  :nobatch => ['Invalid batch', 'Unable to find certain batch in database.'],
+  :nocommit => ['Invalid access', "You didn't specify an valid operation."],
+  :perform => ['Invalid operation', "You didn't specify an valid operation."],
+  :yaml => ['Yaml file', 'Failed to load mapping file.'],
+  :wrongdate => ['Invalid date', 'Incorrect file received date.'],
+  :nofile => ['Invalid file', 'No file selected.'],
+  :nolibrary => ['Missing software', 'Cannot understand this file as no software driver was found.'],
+  :wrongformat => ['Invalid file format', 'File format is not accepted by this source.'],
+  :fileexisted => ['File existed', 'The file is currently being processed.'],
+  :digest => ['File existed', 'File with same digest has been found in repository.'],
+  :extinrep => ['File existed', 'File with same name has been found in repository.'],
+  :batch => ['Create Batch', 'Failed to create a batch record.'],
+  :action_create => ['Create Action', 'Failed to create an action record.'],
+  :action_update => ['Update Action', 'Failed to update an action record.'],
+  :imported => ['Import', 'This table has already been imported.'],
+  :pattern => ['Pattern error', "Data doesn't match the pattern specified in yaml file."],
+  :nomapping => ['Unrecognised batch', 'No columns mapping provided for this source.'],
+  :nodatereference => ['Invalid date', 'Unspecified date reference.'],
+  :baddatereference => ['Invalid date', 'Bad date(s) specified in Date Reference field. '],
+  :password => ['Invalid password', "Password doesn't match selected xls file."],
+  :blankfile => ['Blank file', 'No data found in specified file.'],
+  :header => ['Header line error', 'No header line found or header line conflicts with specified source'],
+  :difference => ['Uneven records', 'Some records have at least 3 columns less than others in that batch']
+} unless defined?(ERROR_INFO)
+
+DATA_MEDIA = ['Email', 'Floppy Disk', 'CD/DVD', 'Others'] unless defined?(DATA_MEDIA)
+
+MATCH_STATUS = {
+	:perfect => 'Definite Match', 		# AMCH_STATUS
+	:possible => 'Possible Matches',  # AMCH_STATUS
+  :none => 'No Match',							# AMCH_STATUS
+  :alias => 'Alias',								# MMCH_STATUS
+  :new => 'New',										# MMCH_STATUS & DEDU_STATUS
+  :manual => 'Manual',							# MMCH_STATUS & DEDU_STATUS
+  :match => 'Match',								# MMCH_STATUS & DEDU_STATUS
+  :reset => nil			  							# MMCH_STATUS & DEDU_STATUS, used for "change this decision"
+} unless defined?(MATCH_STATUS)
+
+# Batch stats default timeline base
+# If the typical_batch_interval is 1.month,
+# Then the default timeline is 3 * 1.month = 3 months
+BATCH_STATS_TIMELINE_BASE = 3 unless defined?(BATCH_STATS_TIMELINE_BASE)

data/app/models/e_action.rb

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+# EAction table.
+class EAction < NdrWorkflow.abstract_model_class
+  include NdrWorkflow::EActionProgress
+
+  self.table_name    = 'e_action'
+  self.sequence_name = 'e_action_seq'
+  self.primary_key   = 'e_actionid'
+
+  belongs_to :e_batch,
+             foreign_key: 'e_batchid'
+
+  # using 'completed' instead of 'finished' because 'finished'
+  # should be named 'finished_at'
+  scope :completed, -> { where('finished is not null') }
+
+  before_save :ensure_timestamp_consistency
+  validate :ensure_actiontype_not_nil
+  validate :ensure_valid_actiontype
+  validate :ensure_startedby_not_nil
+  validate :ensure_valid_startedby
+  validate :ensure_batchid_not_nil
+  validate :ensure_batch_not_nil
+  validate :ensure_started_not_nil
+  validate :ensure_action_not_in_future
+  validate :ensure_started_not_after_finished
+
+  def ensure_timestamp_consistency
+    if started_changed? && (e_batch.e_actions.collect(&:finished).compact.max || started) > started then
+      raise RuntimeError, "EBatch already has an action with a timestamp greater than #{started} - Possible clock drift or other inconsitency"
+    end
+  end
+
+  # rdoc validation
+  # e_actiontype cannot be nil.
+  def ensure_actiontype_not_nil
+    errors.add(:e_action, 'e_actiontype can not be nil.') if e_actiontype.blank?
+  end
+
+  # rdoc validation
+  # e_actiontype must exist in our lookup table.
+  def ensure_valid_actiontype
+    return if ZeActiontype.valid_value?(e_actiontype)
+    errors.add(:e_action, 'e_actiontype does not exist.')
+  end
+
+  # rdoc validation
+  # startedby user cannot be nil.
+  def ensure_startedby_not_nil
+    errors.add(:e_action, 'user can not be nil.') if startedby.blank?
+  end
+
+  # rdoc validation
+  # startedby user must exist in our lookup table.
+  def ensure_valid_startedby
+    return if Zuser.valid_value?(startedby)
+    errors.add(:e_action, 'user does not exist.')
+  end
+
+  # rdoc validation
+  # e_batchid cannot be nil.
+  def ensure_batchid_not_nil
+    errors.add(:e_action, 'e_batchid cannot be nil.') if e_batchid.blank?
+  end
+
+  # rdoc validation
+  # batch cannot be nil.
+  def ensure_batch_not_nil
+    errors.add(:e_action, 'does not belong to any batch.') if e_batch.nil?
+  end
+
+  # rdoc validation
+  # started cannot be nil.
+  def ensure_started_not_nil
+    if started.blank?
+      errors.add(:e_action, 'does not have a start time.')
+      return
+    end
+  end
+
+  # rdoc validation
+  # started or finished cannot be in the future
+  def ensure_action_not_in_future
+    unless finished.blank? || started.blank?
+      if started > Time.now || finished > Time.now
+        errors.add(:e_action, 'action can not be in the future.')
+      end
+    end
+  end
+
+  # rdoc validation
+  # started must not be after finished
+  def ensure_started_not_after_finished
+    unless finished.blank? || started.blank?
+      if started > finished
+        errors.add(:e_action, 'action can not be finished before it started.')
+      end
+    end
+  end
+
+  # A quick and simple way to create a single EAction.
+  def self.make_and_save!(e_batchid, actiontype, started, finished, userid, status = nil)
+    a = create(
+      e_batchid: e_batchid,
+      e_actiontype: actiontype,
+      started: started,
+      finished: finished,
+      startedby: userid,
+      status: status
+    )
+    if a.errors.to_a.blank?
+      a
+    else
+      raise and return a.errors
+    end
+  end
+end

data/app/models/e_batch.rb

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+require 'ndr_support/daterange'
+require 'ndr_support/string/conversions'
+
+# The EBatch table
+class EBatch < NdrWorkflow.abstract_model_class
+  self.table_name = 'e_batch'
+  self.primary_key = 'e_batchid'
+  self.sequence_name = 'e_batch_seq'
+
+  before_save :clean_filename_for_import!
+
+  # Rails 4 implementation of has_many with scope (order)
+  has_many :e_actions, -> { order('e_actionid') }, class_name: 'EAction',
+                                                   foreign_key: 'e_batchid',
+                                                   dependent: :destroy do
+    # starts an action
+    def start(actiontype, userid)
+      proxy_association.owner.assign_to(userid)
+
+      attributes = { started: Time.now, startedby: userid, comments: nil }
+
+      if actiontype == 'CREA'
+        create! attributes.merge(e_actiontype: actiontype)
+      else
+        find_or_create_by!(e_actiontype: actiontype) do |record|
+          record.assign_attributes(attributes)
+        end
+      end
+    end
+
+    # restart an action
+    def restart(actiontype, userid)
+      action = where(e_actiontype: actiontype).order('e_actionid desc').first!
+      proxy_association.owner.assign_to(userid)
+      comments = "#{action.comments} Action was started by #{action.startedby} on #{action.started};"
+      action.update!(started: Time.now, startedby: userid, comments: comments)
+      action
+    end
+
+    # updating the progress of an action could go here?
+    # finishes an action
+    def finish(actiontype, comments = nil, status = nil)
+      action = where(e_actiontype: actiontype).order('e_actionid desc').first!
+      action.update!(finished: Time.now, comments: comments, status: status)
+
+      begin
+        e_batch = proxy_association.owner
+        e_batch.unlock
+      rescue ActiveRecord::StaleObjectError
+        Rails.logger.warn("NdrWorkflow: failed to unlock stale batch #{e_batch.id}!")
+      end
+    end
+
+    # manual tasks are frequently completed by symultaneously
+    # starting and finishing an action
+    def start_and_finish(actiontype, userid, comments = nil, status = nil)
+      start(actiontype, userid)
+      finish(actiontype, comments, status)
+    end
+  end
+
+  validate :ensure_provider_not_blank
+  validate :ensure_registryid_not_blank
+  validate :ensure_valid_type
+  validate :ensure_valid_provider
+  validate :ensure_valid_registryid
+  # validate :ensure_datereference_present_once_required
+  # --
+  # TODO: Replace the code below with x_daterange :date_reference or x_daterange :datereference
+  # Either updating calls to datereference with calls to date_reference or rename table columns
+  # ++
+  composed_of :datereference,
+              class_name: 'Daterange',
+              mapping:
+                [
+                  [:date_reference1, :date1],
+                  [:date_reference2, :date2]
+                ]
+
+  # rdoc validation
+  # provider cannot be nil.
+  def ensure_provider_not_blank
+    errors.add(:provider, 'cannot be blank.') if provider.blank?
+  end
+
+  # rdoc validation
+  # registryid cannot be nil.
+  def ensure_registryid_not_blank
+    errors.add(:registry, 'cannot be blank.') if registryid.blank?
+  end
+
+  # rdoc validation
+  # e_type must exist in our lookup table.
+  def ensure_valid_type
+    return if ZeType.valid_value?(e_type)
+    errors.add(:e_type, 'does not exist.')
+  end
+
+  # rdoc validation
+  # provider must exist in our lookup table.
+  def ensure_valid_provider
+    return if Zprovider.valid_value?(provider)
+    errors.add(:provider, 'does not exist.')
+  end
+
+  # rdoc validation
+  # registryid must exist in our lookup table.
+  def ensure_valid_registryid
+    return if Zprovider.valid_value?(registryid)
+    errors.add(:registry, 'does not exist.')
+  end
+
+  def provider_desc
+    lookup = Zprovider.find_by_zproviderid(provider)
+    if lookup
+      description = lookup.shortdesc
+      return (description.upcase == description ? description.titlecase : description)
+    else
+      return provider
+    end
+  end
+
+  def assign_to(user)
+    update_attribute(:inprogress, user)
+  end
+
+  def unlock
+    assign_to(nil)
+  end
+
+  def last_finished_action
+    e_actions.completed.except(:order).order('finished desc, e_actionid desc').first
+  end
+
+
+
+
+  # Returns the actiontype that is available for this batch (if known)
+  # Method is updated on 2 Mar, 2009: each action will only have one proceeded action
+  # in Unified Esources. (Removed old PAS's RECE and MANU actions)
+  def next_available_action
+    begin
+      # TODO: Output of this sometimes disagrees with ROVBATCHACTION, resulting
+      #       in inconsistent orderings, and batch automator failures. At very
+      #       least, the batch automator should object more vigorously if the
+      #       next_available_action disagrees with the ROVBATCHACTION output.
+      if la = last_finished_action
+        EWorkflow.next_action(e_type, la.e_actiontype)
+      end
+    end
+  end
+
+  # Is the batch past `target_action' in the workflow?
+  def done_action?(target_action)
+    return false if last_finished_action.nil? # Haven't start any e_actions
+
+    at_new  = false                 # Reached the start of the workflow?
+    done_it = false                 # Have we done `target_action'?
+    # Where are we in the workflow?
+    action  = next_available_action || last_finished_action.e_actiontype
+
+    # Traverse the workflow in reverse from the current action to see
+    # if there is a prior `target_action` step for this batch type:
+    begin
+      step = EWorkflow.find_by_e_type_and_next_e_actiontype(e_type, action)
+
+      at_new  = step.nil?
+      action  = step.try(:last_e_actiontype)
+      done_it = (target_action == action)
+    end until (done_it || at_new)
+
+    done_it
+  end
+
+
+
+  def in_progress?
+    !inprogress.nil?
+  end
+
+  def belongs_to?(user)
+    inprogress == user.to_s
+  end
+  def free?(user)
+    !in_progress? || belongs_to?(user)
+  end
+
+
+
+
+
+  # Check if a batch is in progress.
+  # Return true if the batch is free or was launched by the current user
+  def self.free?(batchid, user)
+    find(batchid).free?(user)
+  end
+
+  def clean_filename_for_import!
+    unless original_filename.blank?
+      # The file path may be pasted in from the Windows command prompt,
+      # so swap back slashes for forward slashes
+      original_filename.gsub!('\\', '/')
+      original_filename.sub!(/\Asvn[\/]/i, 'svn/') # TODO: required?
+      original_filename.strip!
+    end
+  end
+end

data/app/models/e_workflow.rb

@@ -0,0 +1,23 @@
+# EWorkflow describes transitions between E_ACTIONS for the different E_BATCH.E_TYPES.
+class EWorkflow < NdrWorkflow.abstract_model_class
+  self.table_name    = 'e_workflow'
+  self.sequence_name = 'e_workflow_seq'
+  self.primary_key   = 'e_workflowid'
+
+  class << self
+    # Returns the name of the next step on the waterfall. Caches all results.
+    # EWorkflow.next_action('COSD_XML', 'AIMP')
+    # #=> "PRECHECK"
+    # EWorkflow.next_action('COSD_XML', 'GENA')
+    # #=> nil
+
+    def next_action(e_type, last_e_actiontype)
+      @next_actions ||= Hash.new do |hash, (type, last_action)|
+        scope = { e_type: type, last_e_actiontype: last_action }
+        hash[[type, last_action]] = where(scope).pluck(:next_e_actiontype).first
+      end
+
+      @next_actions[[e_type, last_e_actiontype]]
+    end
+  end
+end

data/app/models/ze_actiontype.rb

@@ -0,0 +1,13 @@
+class ZeActiontype < ZlookupCached
+  self.table_name    = 'ze_actiontype'
+  self.primary_key = 'ze_actiontypeid'
+  # This method caches the ZeActiontype ids and their descriptions.
+  # With the new class loader of Rails 2.2 and later, we cannot prepopulate a
+  # constant with this data (as we did in Rails 1.2 and 2.1). Instead, we cache
+  # the result in the model.
+  def self.type_descriptions
+    @@type_descriptions ||= all.inject({}) do |hash, l| 
+      hash.merge!(l.id.to_sym => l.shortdesc)
+    end
+  end
+end

data/app/models/ze_type.rb

@@ -0,0 +1,6 @@
+# ZeType
+class ZeType < ZlookupCached
+  self.table_name    = 'ze_type'
+  self.primary_key = 'ze_typeid'
+
+end

data/app/models/zlookup.rb

@@ -0,0 +1,9 @@
+# Zlookup pattern copied from ERA to allow easy integration of Engine with ERA
+class Zlookup < NdrWorkflow.abstract_model_class
+  self.abstract_class = true
+  def self.valid_value?(key, strict = false)
+    return true if key.blank?
+    scope = strict ? current : self
+    scope.where(primary_key => key).count == 1
+  end
+end

data/app/models/zlookup_cached.rb

@@ -0,0 +1,5 @@
+# Zlookup pattern copied from ERA to allow easy integration of Engine with ERA
+class ZlookupCached < Zlookup
+  # This class doesn't have a table, subclasses will have their own
+  self.abstract_class = true
+end

data/app/models/zprovider.rb

@@ -0,0 +1,9 @@
+# Zprovider represents providers of health services, e.g. hospitals, GP
+# see modell definition in ERA for standard Zprovider infomration / methods,
+# it was thought this was too far from workflow to be extracted - can always
+# be added back later
+class Zprovider < Zlookup
+  self.table_name    = 'zprovider'
+  self.primary_key = 'zproviderid'
+
+end

data/app/models/zuser.rb

@@ -0,0 +1,5 @@
+# Standard Zuser class def, originally from ERA
+class Zuser < ZlookupCached
+  self.table_name    = 'zuser'
+  self.primary_key = 'zuserid'
+end

data/config/routes.rb

@@ -0,0 +1,2 @@
+Rails.application.routes.draw do
+end

data/db/migrate/20160707141753_create_e_batch.rb

@@ -0,0 +1,25 @@
+# EBatch
+class CreateEBatch < NdrWorkflow.migration_class
+  def change
+    create_table :e_batch, id: false do |t|
+      t.primary_key   :e_batchid, limit: 8
+      t.string    :e_type, limit: 255
+      t.string    :provider, limit: 255
+      t.string    :media, limit: 255
+      t.string    :original_filename, limit: 255
+      t.string    :cleaned_filename, limit: 255
+      t.integer   :numberofrecords, limit: 8    # bigint
+      t.datetime  :date_reference1
+      t.datetime  :date_reference2
+      t.integer   :e_batchid_traced, limit: 8
+      t.string    :comments, limit: 255
+      t.string    :digest, limit: 40
+      t.integer   :lock_version, limit: 8, default: 0, null: false
+      t.string    :inprogress, limit: 50
+      t.string    :registryid, limit: 255
+      t.integer   :on_hold, limit: 2    # smallint
+    end
+
+    add_index :e_batch, [:registryid, :e_type, :provider]
+  end
+end

data/db/migrate/20160707141754_create_e_action.rb

@@ -0,0 +1,16 @@
+# EAction migration
+class CreateEAction < NdrWorkflow.migration_class
+  def change
+    create_table :e_action, id: false do |t|
+      t.primary_key   :e_actionid, limit: 8
+      t.integer   :e_batchid, limit: 8, index: true
+      t.string    :e_actiontype, limit: 255
+      t.datetime  :started
+      t.string    :startedby, limit: 255
+      t.datetime  :finished
+      t.string    :comments, limit: 4000
+      t.string    :status, limit: 255, index: true
+      t.integer   :lock_version, limit: 8, default: 0, null: false
+    end
+  end
+end

data/db/migrate/20160707141755_create_e_workflow.rb

@@ -0,0 +1,17 @@
+# EWorflow
+class CreateEWorkflow < NdrWorkflow.migration_class
+  def change
+    create_table :e_workflow, id: false do |t|
+      t.primary_key   :e_workflowid, limit: 8
+      t.string    :e_type, limit: 255
+      t.string    :provider, limit: 255
+      t.string    :last_e_actiontype, limit: 255
+      t.string    :next_e_actiontype, limit: 255
+      t.string    :comments, limit: 255
+      t.integer   :sort, limit: 2   # smallint
+    end
+
+    add_index :e_workflow, [:e_type, :last_e_actiontype, :next_e_actiontype],
+                :name => 'e_workflow_etype_leat_neat_ix'
+  end
+end

data/db/migrate/20160707141756_create_zuser.rb

@@ -0,0 +1,16 @@
+# ZUser
+class CreateZuser < NdrWorkflow.migration_class
+  def change
+    create_table :zuser, id: false do |t|
+      t.string    :zuserid, limit: 255, primary_key: true, default: 1, null: false
+      t.string    :shortdesc, limit: 64
+      t.string    :description, limit: 2000
+      t.string    :exportid, limit: 64
+      t.datetime  :startdate
+      t.datetime  :enddate
+      t.integer   :sort, limit: 8 # bigint
+      t.string    :registryid, limit: 5
+      t.string    :qa_supervisorid, limit: 255
+    end
+  end
+end

data/db/migrate/20160707141757_create_ze_actiontype.rb

@@ -0,0 +1,14 @@
+# ZEActionType
+class CreateZeActiontype < NdrWorkflow.migration_class
+ def change
+    create_table :ze_actiontype, id: false do |t|
+      t.string    :ze_actiontypeid, limit: 255, primary_key: true, default: 1, null: false
+      t.string    :shortdesc, limit: 64
+      t.string    :description, limit: 255
+      t.datetime  :startdate
+      t.datetime  :enddate
+      t.integer   :sort, limit: 8 # bigint
+      t.string    :comments, limit: 255
+    end
+  end
+end

data/db/migrate/20160707141758_create_ze_type.rb

@@ -0,0 +1,14 @@
+# ZEType
+class CreateZeType < NdrWorkflow.migration_class
+  def change
+    create_table :ze_type, id: false do |t|
+      t.string    :ze_typeid, limit: 255, primary_key: true, default: 1, null: false
+      t.string    :shortdesc, limit: 64
+      t.string    :description, limit: 255
+      t.datetime  :startdate
+      t.datetime  :enddate
+      t.integer   :sort, limit: 8 # bigint
+      t.string    :comments, limit: 255
+    end
+  end
+end

data/db/migrate/20160707141759_create_z_provider.rb

@@ -0,0 +1,28 @@
+# ZProvider
+class CreateZProvider < NdrWorkflow.migration_class
+  def change
+    create_table :zprovider, id: false do |t|
+      t.string    :zproviderid, limit: 255, primary_key: true, default: 1, null: false
+      t.string    :shortdesc, limit: 128
+      t.string    :description, limit: 2000
+      t.string    :exportid, limit: 64
+      t.datetime  :startdate
+      t.datetime  :enddate
+      t.integer   :sort, limit: 8 # bigint
+      t.string    :role, limit: 1
+      t.integer   :local_hospital, limit: 2, default: 0, null: false    # smallint
+      t.integer   :breast_screening_unit, limit: 2, default: 0, null: false
+      t.integer   :historical, limit: 2, default: 0, null: false
+      t.string    :lpi_providercode, limit: 255
+      t.string    :zpostcodeid, limit: 255
+      # Provider has a linear particle accelerator
+      t.integer   :linac, limit: 2, default: 0, null: false
+      t.string    :analysisid, limit: 255
+      t.integer   :nacscode, limit: 2
+      t.string    :nacs5id, limit: 5
+      t.string    :successorid, limit: 255
+      t.string    :local_registryid, limit: 5
+      t.string    :source, limit: 255
+    end
+  end
+end

data/db/migrate/20160707141800_create_constraint.rb

@@ -0,0 +1,23 @@
+# Add FK constraints to tables
+class CreateConstraint < NdrWorkflow.migration_class
+  def change
+    unless respond_to?(:add_foreign_key)
+      warn "CreateConstraint: `add_foreign_key` is not supported on #{Rails.version}, skipping."
+      return
+    end
+
+    add_foreign_key :e_action, :e_batch, column: :e_batchid, primary_key: 'e_batchid'
+    add_foreign_key :e_action, :ze_actiontype, column: :e_actiontype, primary_key: 'ze_actiontypeid'
+
+    add_foreign_key :e_batch, :ze_type, column: :e_type, primary_key: 'ze_typeid'
+    add_foreign_key :e_batch, :zprovider, column: :provider, primary_key: 'zproviderid'
+    add_foreign_key :e_batch, :zprovider, column: :registryid, primary_key: 'zproviderid'
+
+    add_foreign_key :e_workflow, :ze_actiontype, column: :last_e_actiontype, primary_key: 'ze_actiontypeid'
+    add_foreign_key :e_workflow, :ze_actiontype, column: :next_e_actiontype, primary_key: 'ze_actiontypeid'
+    add_foreign_key :e_workflow, :ze_type, column: :e_type, primary_key: 'ze_typeid'
+    add_foreign_key :e_workflow, :zprovider, column: :provider, primary_key: 'zproviderid'
+
+    add_foreign_key :zuser, :zuser, column: :qa_supervisorid, primary_key: 'zuserid'
+  end
+end

data/lib/ndr_workflow/e_action_progress.rb

@@ -0,0 +1,121 @@
+require 'ndr_support/ourdate'
+require 'ndr_support/ourtime'
+
+module NdrWorkflow
+  # Logic to be shared by EAction and QueuedJob:
+  module EActionProgress
+    # Classes allowed inside YAML-serialized comments
+    COMMENT_CLASSES = [Ourdate, DateTime, Time, Date, ActiveSupport::TimeWithZone,
+                       ActiveSupport::TimeZone, ActiveSupport::HashWithIndifferentAccess,
+                       Symbol].freeze
+
+    # Set the progress percentage of an activity. Progress will range from
+    # min_percent to max_percent as i varies from 0 to total.
+    # Sample usage:
+    #   total = items.length
+    #   items.each_with_index do |item, i|
+    #     do_something
+    #     action.update_percentage(i+1, total)
+    #   end
+    def update_percentage(i, total, min_percent = 0, max_percent = 100)
+      @last_updated_at ||= progress['updated_at']
+      @last_percentage ||= progress['percentage']
+
+      current_percentage = total == 0 ? 0 : (min_percent + i * (max_percent - min_percent) / total).to_i
+      if @last_updated_at.nil? || @last_percentage.nil? ||
+         (current_percentage < @last_percentage) || # Always show negative changes
+         (current_percentage > @last_percentage && @last_updated_at < 5.minutes.ago) || # Rate limit positive changes to once every 5 minutes...
+         (current_percentage.divmod(5).first > @last_percentage.divmod(5).first && @last_updated_at < 1.minute.ago) # ...but allow >5% changes every 1 minute
+        @last_updated_at = Time.now
+        @last_percentage = current_percentage
+        # yaml = YAML.dump( progress.merge({'percentage' => @last_percentage, 'updated_at' => @last_updated_at}))
+        yaml = YAML.dump({'percentage' => @last_percentage, 'updated_at' => @last_updated_at})
+        begin
+          raise(ActiveRecord::StatementInvalid, <<-DESC) if Rails.env.test?
+            libutils is not reliably available in the test schema, so we
+            test the fallback behaviour. This ensures it is the fallback
+            behaviour that we get, even if libutils is present.
+          DESC
+
+          # Try to update the progress in an anonymous transaction, providing feedback when we
+          # wouldn't otherwise get any (i.e. when the update is in a transaction)
+          # TODO: Test for the corner case where the e_action is updateed within a transaction and
+          # where this is blocked, causing it to fail over to a standard (transaction based) update.
+          # The SQL statement is sanitized for security.
+          # SECURE: BNS 2012-10-09
+          sanitized_sql = self.class.send(:sanitize_sql_array,[
+            "BEGIN libutils.set_e_action_comments(?, ?); END;", self.e_actionid, yaml
+          ])
+          ActiveRecord::Base.connection.execute(sanitized_sql)
+        rescue ActiveRecord::StatementInvalid => e
+          # Update the old way, using standard update
+          Rails.logger.warn("EAction#update_percentage failed to use libutils.set_e_action_comments (#{e.message})")
+          puts "EAction#update_percentage failed to use libutils.set_e_action_comments (#{e.message})" unless Rails.env.test?
+
+          # The EAction could be stale as a result of PREP. Eg ChildhoodPreallocator
+          reload unless changed?
+          update(comments: yaml)
+        end
+      end
+    end
+
+    def progress
+      if comments
+        deserialised_comments = YAML.safe_load(comments, permitted_classes: COMMENT_CLASSES.freeze,
+                                                         aliases: true)
+        case deserialised_comments
+        when Integer
+          # Legacy number
+          return {'percentage' => comments.to_i}
+        when String
+          return {'message' => deserialised_comments}
+        when Hash
+          return deserialised_comments
+        end
+      end
+      return {}
+    end
+
+    # This method takes an exception and updates the e_action so that it can be
+    # seen easily through the UI.
+    def log_error(error, extramessage = nil)
+      self.reload unless new_record?
+
+      error_info = {
+        'error_message' => [error.message, extramessage].compact.join(': '),
+        'updated_at'    => Time.now
+      }
+
+      begin
+        if defined?(NdrError)
+          fingerprint, log = NdrError.log(error, { :user_id => self.startedby, :user_roles => '(BATCH)' }, nil)
+          error_info['error_fingerprint'] = fingerprint.id if fingerprint
+        else
+          logger.warn("Failed to log EAction exception in the DB! (#{$!.to_s})")
+        end
+      rescue
+        logger.warn("Failed to log EAction exception in the DB! (#{$!.to_s})")
+      end
+
+      data = progress.merge(error_info)
+      max_len = (EAction.columns_hash['comments'].sql_type.match(/([0-9]*)\)/).nil? ? 0 : EAction.columns_hash['comments'].sql_type.match(/([0-9]*)\)/)[1]).to_i 
+  #    if Era.db_oracle?
+  #      max_len = EAction.columns_hash['comments'].sql_type.match(/VARCHAR2\(([0-9]*)\)/)[1].to_i
+  #    elsif Era.db_postgres?
+  #      max_len = EAction.columns_hash['comments'].sql_type.match(/character varying\(([0-9]*)\)/)[1].to_i
+  #    end
+      if YAML.dump(data).length > max_len
+        # Horribly inefficient; preserve as much information as possible.
+        len2 = max_len - YAML.dump(data.merge('error_message' => nil)).size
+        while YAML.dump(data).length > max_len do
+          len2 -= 1
+          data['error_message'] = [error.message, extramessage].compact.collect{|s|
+            "#{s.to_s[0..len2]}#{'...' if len2 < s.to_s.length}"
+          }.join(': ')
+        end
+        logger.warn("EAction#log_error: Warning: Truncated error message: #{[error.message, extramessage].inspect} for EAction(#{id})")
+      end
+      update(comments: YAML.dump(data))
+    end
+  end
+end

data/lib/ndr_workflow/engine.rb

@@ -0,0 +1,5 @@
+module NdrWorkflow
+  # NdrWorkflow is an engine; add config here
+  class Engine < ::Rails::Engine
+  end
+end

data/lib/ndr_workflow/version.rb

@@ -0,0 +1,5 @@
+# frozen_string_literal: true
+
+module NdrWorkflow
+  VERSION = '1.2.5'
+end

data/lib/ndr_workflow.rb

@@ -0,0 +1,19 @@
+require 'ndr_workflow/e_action_progress'
+require 'ndr_workflow/engine'
+require 'ndr_workflow/version'
+
+# NdrWorkflow
+module NdrWorkflow
+  # Allows the host to define a parent for all models.
+  # Defaults to ActiveRecord::Base.
+  mattr_accessor :abstract_model_class
+  self.abstract_model_class = ActiveRecord::Base
+
+  # Rails 5 uses versioned migrations (required as of 5.1). This helper method returns an
+  # appropriate migration superclass for the Rails version of the host application. Note that the
+  # 4.2 compatability layer is targetted since all the bundled migrations were written prior to
+  # Rails 5.
+  def self.migration_class
+    Rails::VERSION::MAJOR < 5 ? ActiveRecord::Migration : ActiveRecord::Migration[4.2]
+  end
+end

data/lib/tasks/ndr_workflow_tasks.rake

@@ -0,0 +1,4 @@
+# desc "Explaining what the task does"
+# task :ndr_workflow_e do
+#   # Task goes here
+# end

metadata

@@ -0,0 +1,157 @@
+--- !ruby/object:Gem::Specification
+name: ndr_workflow
+version: !ruby/object:Gem::Version
+  version: 1.2.5
+platform: ruby
+authors:
+- NCRS Development team
+bindir: bin
+cert_chain: []
+date: 1980-01-02 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: rails
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '7.1'
+    - - "<"
+      - !ruby/object:Gem::Version
+        version: '8.2'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '7.1'
+    - - "<"
+      - !ruby/object:Gem::Version
+        version: '8.2'
+- !ruby/object:Gem::Dependency
+  name: ndr_support
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '5.0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '5.0'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: ndr_dev_support
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '6.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '6.0'
+- !ruby/object:Gem::Dependency
+  name: test-unit
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: pg
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+description: Core EWorkflow, Ebatch and EAction models mapped from ERA to postgres
+  implem.
+email: []
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- CHANGELOG.md
+- MIT-LICENSE
+- README.rdoc
+- Rakefile
+- SECURITY.md
+- app/constants/esource_constants.rb
+- app/models/e_action.rb
+- app/models/e_batch.rb
+- app/models/e_workflow.rb
+- app/models/ze_actiontype.rb
+- app/models/ze_type.rb
+- app/models/zlookup.rb
+- app/models/zlookup_cached.rb
+- app/models/zprovider.rb
+- app/models/zuser.rb
+- config/routes.rb
+- db/migrate/20160707141753_create_e_batch.rb
+- db/migrate/20160707141754_create_e_action.rb
+- db/migrate/20160707141755_create_e_workflow.rb
+- db/migrate/20160707141756_create_zuser.rb
+- db/migrate/20160707141757_create_ze_actiontype.rb
+- db/migrate/20160707141758_create_ze_type.rb
+- db/migrate/20160707141759_create_z_provider.rb
+- db/migrate/20160707141800_create_constraint.rb
+- lib/ndr_workflow.rb
+- lib/ndr_workflow/e_action_progress.rb
+- lib/ndr_workflow/engine.rb
+- lib/ndr_workflow/version.rb
+- lib/tasks/ndr_workflow_tasks.rake
+licenses: []
+metadata: {}
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '3.3'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubygems_version: 3.6.9
+specification_version: 4
+summary: Base workflow schema
+test_files: []