From 46736e0e02d239554cf6cf6960a630f02dca0ac7 Mon Sep 17 00:00:00 2001
From: Sarav Shah <saravsshah@gmail.com>
Date: Mon, 27 Aug 2018 15:27:27 -0700
Subject: [PATCH 01/10] Delete all bin files

---
 bin/batch_run          |  42 -----------
 bin/cleanup            |  23 ------
 bin/completion_report  |  41 -----------
 bin/correct_version    | 125 ---------------------------------
 bin/discovery_report   |  30 --------
 bin/get_total_objects  |  26 -------
 bin/mods_report        |  54 --------------
 bin/mods_report2       |  48 -------------
 bin/pre-assemble       |  36 ----------
 bin/project_tag_report |  30 --------
 bin/remediate          | 155 -----------------------------------------
 11 files changed, 610 deletions(-)
 delete mode 100755 bin/batch_run
 delete mode 100755 bin/cleanup
 delete mode 100755 bin/completion_report
 delete mode 100755 bin/correct_version
 delete mode 100755 bin/discovery_report
 delete mode 100755 bin/get_total_objects
 delete mode 100755 bin/mods_report
 delete mode 100755 bin/mods_report2
 delete mode 100755 bin/pre-assemble
 delete mode 100755 bin/project_tag_report
 delete mode 100755 bin/remediate

diff --git a/bin/batch_run b/bin/batch_run
deleted file mode 100755
index f1e50225..00000000
--- a/bin/batch_run
+++ /dev/null
@@ -1,42 +0,0 @@
-#! /bin/bash
-# run with
-#  RAILS_ENV=production bundle exec bin/batch_run YAML_CONFIG [LIMIT_N]
-
-# Load YAML config file for the bundle of materials to be pre-assembled.
-yaml=$1
-if [ $# == 2 ] ; then # if there is a limit specified use it, otherwise use the default of 100
-  limit=$2
-else
-  limit=100
-fi
-
-echo ""
-date
-echo "PROCESSING $yaml"
-echo "LIMIT = $limit"
-
-num_objects="$(bin/get_total_objects $yaml)"
-num_runs=$[num_objects/limit + 1]
-i="1"
-
-echo "$num_objects incomplete objects to process; will require an estimated $num_runs runs with limit of $limit"
-
-echo ""
-
-while [  $num_objects -gt 0 ]; do
-   echo "-------------------------------"
-   echo "  ON RUN NUMBER $i OF $num_runs"
-   cmd="bundle exec bin/pre-assemble $yaml --limit $limit --resume"
-   echo $cmd
-   echo "-------------------------------"
-   bash -c "$cmd"
-   i=$[$i + 1]
-   num_objects="$(bin/get_total_objects $yaml)"
- done
-
- echo ""
- echo "COMPLETED $num_runs RUNS"
- if [ "$num_objects" -ne "0" ] ; then
-    echo "***** WARNING! THERE ARE $num_objects OBJECTS LEFT *****"
- fi
- date
diff --git a/bin/cleanup b/bin/cleanup
deleted file mode 100755
index 5e2cb3d6..00000000
--- a/bin/cleanup
+++ /dev/null
@@ -1,23 +0,0 @@
-#! /usr/bin/env ruby
-
-require File.expand_path(File.dirname(__FILE__) + '/../config/boot')
-
-def help(error_msg)
-  abort "#{error_msg}\n\nUsage:\n    cleanup YAML_CONFIG_FILE stacks,dor,stage,symlinks,workflows [dry_run]\n"
-end
-
-# Load YAML config file for the bundle of materials to be pre-assembled.
-help "Incorrect N of arguments." if ARGV.size < 2
-yaml_config = ARGV.shift
-help "YAML file not found." unless File.file? yaml_config
-params = YAML.load(File.read yaml_config)
-
-steps = ARGV.shift.split(',').collect! { |x| x.to_sym }
-dry_run = ARGV.shift ? true : false
-
-begin
-  b = PreAssembly::Bundle.new(PreAssembly::BundleContext.new(params))
-  b.cleanup!(steps, dry_run)
-rescue PreAssembly::BundleUsageError => e
-  help e.message
-end
diff --git a/bin/completion_report b/bin/completion_report
deleted file mode 100755
index c7b40c90..00000000
--- a/bin/completion_report
+++ /dev/null
@@ -1,41 +0,0 @@
-#! /usr/bin/env ruby
-
-n = 50 # run 50 druids at a time against solr
-
-require File.expand_path(File.dirname(__FILE__) + '/../config/boot')
-
-def help(error_msg)
-  abort "#{error_msg}\n\nUsage:\n    ./bin/completion_report YAML_CONFIG_FILE\n"
-end
-
-help "Incorrect number of arguments." unless ARGV.size == 1
-
-yaml_config = ARGV[0]
-help "YAML file not found." unless File.file? yaml_config
-
-params = YAML.load(File.read yaml_config)
-params['config_filename'] = yaml_config
-progress_filename = params['progress_log_file']
-
-completed_druids = Assembly::Utils.get_druids_from_log(progress_filename, true)
-
-help "no completed druids found in '#{progress_filename}'" if completed_druids.size == 0
-
-puts "Running report with #{completed_druids.size} objects"
-
-batch_druids = completed_druids.each_slice(n).to_a
-
-report_filename = "../log/#{params['project_name']}_completion_report.csv"
-
-CSV.open(File.join(File.expand_path(File.dirname(__FILE__)), report_filename), "wb") do |csv|
-  # header row
-  csv << ["druid", "label", "dc:title", "source_id", "accessioned", "shelved", "purl", "total_files", "files_found"]
-
-  batch_druids.each do |batch|
-    query_tag = "id:\"" + batch.join('" OR id:"') + "\""
-    resp = Dor::SearchService.query query_tag, :rows => n, :fl => 'id, public_dc_title_t, wf_wps_facet, source_id_t, objectLabel_t, content_file_t'
-    resp.docs.each { |doc| csv << Assembly::Utils.solr_doc_parser(doc, true) }
-  end
-
-  puts "Report written to #{report_filename}"
-end
diff --git a/bin/correct_version b/bin/correct_version
deleted file mode 100755
index 1c707160..00000000
--- a/bin/correct_version
+++ /dev/null
@@ -1,125 +0,0 @@
-#! /usr/bin/env ruby
-require File.expand_path(File.dirname(__FILE__) + '/../config/boot')
-
-# Run with
-# RAILS_ENV=test bin/remediate_version apo_1 apo_2
-# Don't include druid:
-# At least one APO druid is needed
-# When testing or debugging, use an APO with few children if possible, large harvests can take quite a significant amount of time
-
-# This script handles cases ther accessionWF lacks an entry for the current workflow in versionMetadata, but accession WF is only behind.  It uses the following remediation procedure
-
-# This will fix errors such as:
-# sdr-ingest-transfer : druid:bj072xp1435 - Item error; caused by #<RuntimeError: Version mismatch in /dor/workspace/bj/072/xp/1435/bj072xp1435/metadata/versionMetadata.xml, expected 2, found 3>
-
-require 'rubygems'
-require 'dor-services'
-require 'dor-workflow-service'
-require 'harvestdor'
-require 'logger'
-
-# Set Up the Various Paths
-current_path = File.dirname(File.expand_path(__FILE__))
-log_path = current_path.split("/bin")[0] + "/log/correct_version/#{Time.now.to_i}/"
-@target_repo = "dor"
-@target_workflow = "accessionWF"
-
-# Make Sure at least APO Druid was provided
-abort("At least one APO druid is required.") if ARGV.size == 0
-
-# Set up the Overall Run Log
-FileUtils.mkdir_p(log_path)
-@run_log = Logger.new(log_path + "run.log")
-@no_action_log = Logger.new(log_path + "versions_match.log")
-@no_ingest_error_log = Logger.new(log_path + "one_version_ahead_no_ingest_error.log")
-@ingest_error_log = Logger.new(log_path + "two_versions_ahead_and_ingest_error.log")
-@too_many_ahead_log = Logger.new(log_path + "too_many_versions_ahead.log")
-
-def correct_versioning_on_druid(druid)
-  begin
-    item = Dor::Item.find(druid)
-  rescue
-    @run_log.error("The object #{druid} was not found via Dor::Item.find(pid).")
-    return
-  end
-
-  dor_version = item.current_version.to_i # gets current version
-
-  begin
-    workflow_xml = Nokogiri.parse(Dor::Config.workflow.client.workflow_resource["dor/objects/#{druid}/workflows"].get) # get all the workflow xml as one chunk
-  rescue
-    run_log.error("Failed to get workflow XML for #{druid}")
-    @run_log.error $!.backtrace
-    return
-  end
-
-  if workflow_xml.xpath("//workflow[@id='#{@target_workflow}']/process[@version='#{dor_version}']").size > 0 # Test to if we have the latest dor workflow
-    # If we have the latest worflow, we're good, at least for the purpose of this script
-    @no_action_log.info(druid)
-
-  elsif workflow_xml.xpath("//workflow[@id='#{@target_workflow}']/process[@version='#{dor_version - 1}']").size > 0
-    begin
-      item.initialize_workflow(@target_workflow)
-      @no_ingest_error_log.info(druid)
-    rescue
-      @run_log.error("Failed to initialize accessioning for #{druid}")
-      @run_log.error $!.backtrace
-    end
-
-  elsif workflow_xml.xpath("//workflow[@id='#{@target_workflow}']/process[@version='#{dor_version - 2}']").size > 0
-    errorNode = workflow_xml.xpath("//workflow[@id='#{@target_workflow}']/process[@status='error']").first
-    unless errorNode.nil?
-      # We need to delete the latest version metadata
-      vmd = item.datastreams['versionMetadata'].ng_xml
-      vmd.xpath("//versionMetadata/version[@versionId=#{dor_version}]").remove
-      item.datastreams['versionMetadata'].content = vmd.to_xml
-      item.datastreams['versionMetadata'].dirty = true
-
-      begin
-        item.datastreams['versionMetadata'].save
-      rescue
-        @run_log.error("Failed to save workflow datastream for #{druid}")
-        @run_log.error $!.backtrace
-      end
-
-      begin
-        Dor::Config.workflow.client.update_workflow_status(@target_repo, druid, @target_workflow, errorNode['name'], 'waiting')
-        @ingest_error_log.info(druid)
-      rescue
-        @run_log.error("DorWorkflowservices error for #{druid}")
-        @run_log.error $!.backtrace
-      end
-
-    end
-
-  else
-    # We're more than ahead, log this as a Case 3 error and handle it elsewhere
-    @too_many_ahead_log.info(druid)
-  end
-end
-
-# TODO: Lots of stuff ripe for parallelization here
-ARGV.each do |apo|
-  @run_log.info("Starting version fixes for #{apo}")
-
-  # oais_returned = true
-  begin
-    client = Harvestdor::Client.new
-    oais = client.oai_headers(:set => "is_governed_by_#{apo}")
-  rescue
-    @run_log.error("#{apo} failed.  Possibly an invalid druid.")
-    @run_log.error $!.backtrace
-    # oais_return = false
-    next # Skip to the next APO
-  end
-
-  @run_log.info("#{oais.size} records returned for APO #{apo}")
-  oais.each do |oai|
-    # Get the Druid Out of the Identifier
-    tuple = oai.identifier.split(':')
-    druid = tuple[tuple.size - 1] # This will not have the druid: prefix
-    druid = ("druid:" + druid).strip # Add druid back on TODO:  Could be regex and avoid these three steps
-    correct_versioning_on_druid(druid)
-  end
-  @run_log.info("Completed version fixes for #{apo}")
-end
diff --git a/bin/discovery_report b/bin/discovery_report
deleted file mode 100755
index a5b0d78b..00000000
--- a/bin/discovery_report
+++ /dev/null
@@ -1,30 +0,0 @@
-#! /usr/bin/env ruby
-
-require File.expand_path(File.dirname(__FILE__) + '/../config/boot')
-
-def help(error_msg)
-  abort "#{error_msg}\n\nUsage:\n    discovery_report YAML_CONFIG_FILE [confirm_checksums check_sourceids no_check_reg show_staged show_other show_smpl_cm]\n"
-end
-
-# Load YAML config file for the bundle of materials to be pre-assembled.
-help "Incorrect N of arguments." if ARGV.size == 0
-yaml_config = ARGV[0]
-
-report_params = {}
-report_params[:confirm_checksums] = ARGV.include? 'confirm_checksums'
-report_params[:check_sourceids] = ARGV.include? 'check_sourceids'
-report_params[:no_check_reg] = ARGV.include? 'no_check_reg'
-report_params[:show_staged] = ARGV.include? 'show_staged'
-report_params[:show_other] = ARGV.include? 'show_other'
-report_params[:show_smpl_cm] = ARGV.include? 'show_smpl_cm'
-
-help "YAML file not found." unless File.file? yaml_config
-params = YAML.load(File.read yaml_config)
-params['config_filename'] = yaml_config
-
-begin
-  b = PreAssembly::Bundle.new(PreAssembly::BundleContext.new(params))
-  b.discovery_report(report_params)
-rescue PreAssembly::BundleUsageError => e
-  help e.message
-end
diff --git a/bin/get_total_objects b/bin/get_total_objects
deleted file mode 100755
index 7d153890..00000000
--- a/bin/get_total_objects
+++ /dev/null
@@ -1,26 +0,0 @@
-#! /usr/bin/env ruby
-
-require File.expand_path(File.dirname(__FILE__) + '/../config/boot')
-
-def help(error_msg)
-  abort "#{error_msg}\n\nUsage:\n    get_total_objects YAML_CONFIG_FILE\n"
-end
-
-# Load YAML config file for the bundle of materials to be pre-assembled.
-help "Incorrect N of arguments." unless ARGV.size == 1
-yaml_config = ARGV.shift
-help "YAML file not found." unless File.file? yaml_config
-params = YAML.load(File.read yaml_config)
-params['config_filename'] = yaml_config
-params['show_progress'] = false
-
-# get total number of objects
-begin
-  b = PreAssembly::Bundle.new(PreAssembly::BundleContext.new(params))
-  b.discover_objects
-  total_objects = b.digital_objects.size
-  objects_remaining = b.objects_to_process.size
-  puts objects_remaining
-rescue PreAssembly::BundleUsageError => e
-  help e.message
-end
diff --git a/bin/mods_report b/bin/mods_report
deleted file mode 100755
index 772ba535..00000000
--- a/bin/mods_report
+++ /dev/null
@@ -1,54 +0,0 @@
-#! /usr/bin/env ruby
-
-# Used to test descriptive Metadata generation given a YAML file referencing a MODs template and a manifest.  This allows you to test how the MODs will be generated during pre-assembly.
-# Iterate through each row in the manifest, use source ID to lookup DRUID, generate new MODs using MODs template.
-
-# Peter Mangiafico
-# January 21, 2014
-#
-# Run with
-# RAILS_ENV=test bin/mods_report YAML_CONFIG_FILE.yml OUTPUT_DIRECTORY
-require File.expand_path(File.dirname(__FILE__) + '/../config/boot')
-
-def help(error_msg)
-  abort "#{error_msg}\n\nUsage:\n ./bin/mods_report YAML_CONFIG_FILE.yml OUTPUT_DIRECTORY\n"
-end
-
-help "Incorrect N of arguments." if ARGV.size != 2
-yaml_config = ARGV.shift
-help "YAML file not found." unless File.file? yaml_config
-params = YAML.load(File.read yaml_config)
-params['config_filename'] = yaml_config
-output_directory = ARGV.shift
-help "Output directory not found or not a directory." unless File.directory? output_directory
-
-mods_template_file = File.join(params['bundle_dir'], params['desc_md_template'])
-manifest_file = File.join(params['bundle_dir'], params['manifest'])
-
-# read in MODs template
-mods_template_xml = IO.read(mods_template_file)
-
-# read input manifest
-@items = PreAssembly::Bundle.import_csv(manifest_file)
-limit = params['limit_n']
-
-puts "Generating #{@items.size} MODs files from #{manifest_file} using MODs template of #{mods_template_file}"
-puts "limiting to #{limit}" unless limit.blank?
-
-@items.each_with_index do |manifest_row, x|
-  break if (!limit.blank? && x > limit)
-  druid = manifest_row[:druid]
-  sourceid = manifest_row[params['manifest_cols']['source_id']]
-  identifier = druid.blank? ? sourceid : druid # what we will call the filename, either by druid or sourceid depending on the project
-  druid = druid.blank? ? "druid:oo000oo0001" : druid # we need a druid to instantiate the object, use the real druid if possible, otherwise just make one up
-  dig_obj = PreAssembly::DigitalObject.new(:pid => druid)
-  dig_obj.manifest_row = manifest_row
-  dig_obj.desc_md_template_xml = mods_template_xml
-  if dig_obj.create_desc_metadata_xml
-    output_mods_file = File.join(output_directory, "#{identifier.gsub('druid:', '')}.xml")
-    File.open(output_mods_file, 'w') { |fh| fh.puts dig_obj.desc_md_xml }
-    puts "Saving MODs for sourceID #{identifier}  [#{x} of #{@items.size}]"
-  else
-    puts "Error: cannot generate desc md xml for #{identifier} [#{x} of #{@items.size}]"
-  end
-end
diff --git a/bin/mods_report2 b/bin/mods_report2
deleted file mode 100755
index 254c6548..00000000
--- a/bin/mods_report2
+++ /dev/null
@@ -1,48 +0,0 @@
-#! /usr/bin/env ruby
-
-# Used to test descriptive Metadata generation given a MODs template and a manifest.  This allows you to test how the MODs will be generated during pre-assembly.
-# Iterate through each row in the manifest, generate MODs files using MODs template in output directory.
-
-# Peter Mangiafico
-# August 21, 2015
-#
-# Run with
-# RAILS_ENV=test bin/mods_report2 manifest.csv mods_template.xml output_directory
-require File.expand_path(File.dirname(__FILE__) + '/../config/boot')
-
-def help(error_msg)
-  abort "#{error_msg}\n\nUsage:\n ./bin/mods_report2 manifest.csv mods_template.xml output_directory\n"
-end
-
-help "Incorrect N of arguments." if ARGV.size != 3
-manifest_file = ARGV.shift
-help "manifest file file not found." unless File.file? manifest_file
-mods_template_file = ARGV.shift
-help "manifest file file not found." unless File.file? mods_template_file
-output_directory = ARGV.shift
-help "Output directory not found or not a directory." unless File.directory? output_directory
-
-# read in MODs template
-mods_template_xml = IO.read(mods_template_file)
-
-# read input manifest
-@items = PreAssembly::Bundle.import_csv(manifest_file)
-
-puts "Generating #{@items.size} MODs files from #{manifest_file} using MODs template of #{mods_template_file}"
-
-@items.each_with_index do |manifest_row, x|
-  druid = manifest_row[:druid]
-  sourceid = manifest_row[:sourceid]
-  identifier = (druid.blank? ? (sourceid.blank? ? x : sourceid) : druid) # what we will call the filename, either by druid or sourceid depending on the project
-  druid = druid.blank? ? "druid:oo000oo0001" : druid # we need a druid to instantiate the object, use the real druid if possible, otherwise just make one up
-  dig_obj = PreAssembly::DigitalObject.new(:pid => druid)
-  dig_obj.manifest_row = manifest_row
-  dig_obj.desc_md_template_xml = mods_template_xml
-  if dig_obj.create_desc_metadata_xml
-    output_mods_file = File.join(output_directory, "#{identifier.gsub('druid:', '')}.xml")
-    File.open(output_mods_file, 'w') { |fh| fh.puts dig_obj.desc_md_xml }
-    puts "Saving MODs for sourceID #{identifier}  [#{x} of #{@items.size}]"
-  else
-    puts "Error: cannot generate desc md xml for #{identifier} [#{x} of #{@items.size}]"
-  end
-end
diff --git a/bin/pre-assemble b/bin/pre-assemble
deleted file mode 100755
index f4024b42..00000000
--- a/bin/pre-assemble
+++ /dev/null
@@ -1,36 +0,0 @@
-#! /usr/bin/env ruby
-
-require File.expand_path(File.dirname(__FILE__) + '/../config/boot')
-
-require 'optparse'
-options = {}
-
-OptionParser.new do |opts|
-  opts.banner = "Usage:\n    pre-assemble YAML_CONFIG_FILE [--resume] [--limit 200]\n"
-  opts.on("-r", "--resume", "Resume") do |_r|
-    options[:resume] = true
-  end
-  opts.on("-l [LIMIT]", "--limit [LIMIT]", "Limit") do |l|
-    options[:limit] = l || 200
-  end
-end.parse!
-
-abort "Incorrect N of arguments - you did not supply a YAML file." unless ARGV.size == 1
-
-# Load YAML config file for the bundle of materials to be pre-assembled.
-
-yaml_config = ARGV.shift
-abort "YAML file not found." unless File.file? yaml_config
-
-params = YAML.load(File.read yaml_config)
-params['resume'] = true if options[:resume]
-params['limit_n'] = options[:limit].to_i if options[:limit]
-params['config_filename'] = yaml_config
-
-# Run pre-assembly.
-begin
-  b = PreAssembly::Bundle.new(PreAssembly::BundleContext.new(params))
-  b.run_pre_assembly
-rescue PreAssembly::BundleUsageError => e
-  abort e.message
-end
diff --git a/bin/project_tag_report b/bin/project_tag_report
deleted file mode 100755
index 892c667c..00000000
--- a/bin/project_tag_report
+++ /dev/null
@@ -1,30 +0,0 @@
-#! /usr/bin/env ruby
-
-require File.expand_path(File.dirname(__FILE__) + '/../config/boot')
-
-def help(error_msg)
-  abort "#{error_msg}\n\nUsage:\n    ./bin/project_tag_report PROJECT_TAG\n"
-end
-
-help "Incorrect number of arguments." unless ARGV.size == 1
-
-project_tag = ARGV.shift
-
-query_tag = "project_tag_facet:\"#{project_tag}\""
-
-resp = Dor::SearchService.query query_tag, :rows => 50000, :fl => 'id, public_dc_title_t, wf_wps_facet, source_id_t, objectLabel_t, content_file_t'
-
-project_file_name = project_tag.gsub(' ', '_').gsub('"', '')
-
-help "no results found for project tag '#{project_tag}'" if resp.docs.size == 0
-
-report_filename = "../log/#{project_file_name}_tag_report.csv"
-
-puts "Running report with #{resp.docs.size} objects"
-
-CSV.open(File.join(File.expand_path(File.dirname(__FILE__)), report_filename), "wb") do |csv|
-  # header row
-  csv << ["druid", "label", "dc:title", "source_id", "accessioned", "shelved", "purl", "total_files", "files_found"]
-  resp.docs.each { |doc|  csv << Assembly::Utils.solr_doc_parser(doc) }
-  puts "Report written to #{report_filename}"
-end
diff --git a/bin/remediate b/bin/remediate
deleted file mode 100755
index 1822e797..00000000
--- a/bin/remediate
+++ /dev/null
@@ -1,155 +0,0 @@
-#! /usr/bin/env ruby
-
-# This action is used to remediate objects in some way that you define.
-# You supply a list of druids to remediate in a CSV file and a Ruby file defining a method that operates on the objects.
-# The code handles all logging and versioning as needed.
-
-# Run with
-# RAILS_ENV=production bin/remediate INPUT_FILE.csv REMEDIATE_LOGIC_FILENAME.rb [PAUSE_TIME_IN_SECONDS]
-
-# eg. RAILS_ENV=production bin/remediate /dor/preassembly/remediation/revs_all_pids.csv /dor/preassembly/remediation/scripts/revs_rights_remediate.rb
-
-# You can specify an optional number of seconds to pause between each object (in seconds) after the remediation logic filename.  If left off, no
-# pause between objects will occur. This can be useful for large remediation jobs that are a low priority, which allows them to run at a slower pace
-# and thus generating less concurrent load on the system while other higher priority jobs are running concurrently.
-# You can also add in optional parameters to override defaults for checking if items are in accessioning or if they require versioning and set to false.
-# Only do this if you are sure you know what you are doing for scripts that for some reason will not work with versioning!  If you want to add these
-# parameters, you must also specify the pause time (which could be 0).
-
-# RAILS_ENV=production bin/remediate INPUT_FILE.csv REMEDIATE_LOGIC_FILENAME.rb [PAUSE_TIME_IN_SECONDS] ignore_versioning ignore_accessioning
-
-# INPUT_FILE can be either a pre-assembly generated YAML log file or a CSV file with one column containing at least a list of druids
-# If a pre-assembly YAML log file is passed in, the successfully accessioned druids will be used.
-# For a CSV file, there should be a header with a column labeled "druid" which indicates which column contains the druid
-# This file should be in a location where the script has read/write access to it.
-
-# e.g.
-# druid,another_column
-# druid:oo000oo0001,other stuff
-# druid:oo000oo0002,ignored
-
-# REMEDIATE_LOGIC_FILENAME is a reference to a Ruby code file that defines what you want the remediation to do.  An example of this
-# file is in lib/remediation/remediate_project_example.rb  Copy that file, and edit it somewhere the script can read it and then pass
-# the filename to the script.
-
-# The result will be some screen output, a detailed .YML file in the same location and with the same name as the input CSV file.
-# The input CSV file will be updated with two additional columns - a status indicating if remediation succeeded and a message.
-# You can re-run remediation with the same CSV file and it will automatically skip already completed objects.
-
-# Note that unless your laptop has access to the Fedora instance you need to remediate (usually Production),
-# you should probably run this from lyberservices-prod to have access to all mounts and configuration.
-
-require File.expand_path(File.dirname(__FILE__) + '/../config/boot')
-require 'rubygems'
-require 'csv'
-require 'csv-mapper'
-
-def help(error_msg)
-  abort "#{error_msg}\n\nUsage:\n  RAILS_ENV=XXXXX remediate INPUT_FILE REMEDIATE_LOGIC_FILENAME [PAUSE_TIME_SECONDS]\n"
-end
-
-help "Incorrect N of arguments." if ARGV.size < 2
-input_file = ARGV[0]
-remediate_logic_file = ARGV[1]
-if ARGV.size > 2
-  pause_time = ARGV[2].to_i
-else
-  pause_time = 0
-end
-
-ignore_accessioning = true if ARGV.include? 'ignore_accessioning' # override config file if supplied
-ignore_versioning = true if ARGV.include? 'ignore_versioning' # override config file if supplied
-
-help "Input file not found." unless File.file?(input_file)
-help "REMEDIATE_LOGIC_FILE file not found." unless File.file?(remediate_logic_file)
-
-require remediate_logic_file
-
-if ignore_accessioning
-  puts "*** OVERRIDING CONFIG: Ignoring accessioning check"
-  Dor::Config.remediation.check_for_in_accessioning = false
-end
-if ignore_versioning
-  puts "*** OVERRIDING CONFIG: Ignoring versioning check"
-  Dor::Config.remediation.check_for_versioning_required = false
-end
-
-source_path = File.dirname(input_file)
-source_ext = File.extname(input_file)
-source_name = File.basename(input_file, source_ext)
-
-help "Input file not a CSV or YAML/YML file." unless ['.csv', '.yml', '.yaml'].include? source_ext.downcase
-
-progress_log_file = File.join(source_path, source_name + '_log.yml')
-csv_out = File.join(source_path, source_name + "_log.csv")
-
-# read in completed druids so we don't reprocess them
-completed_druids = PreAssembly::Remediation::Item.get_druids(progress_log_file)
-
-# read input druids
-if source_ext.downcase == '.csv' # read from CSV file
-  rows = CsvMapper.import(input_file) { read_attributes_from_file }
-  druids = rows.collect { |row| row.druid.include?("druid:") ? row.druid : "druid:#{row.druid}" } # add the druid prefix if missing from input file
-else # this must be a YAML progress log file
-  druids = Assembly::Utils.get_druids_from_log(input_file, true)
-end
-
-total_druids = druids.size
-total_completed = completed_druids.size
-total_to_process = total_druids - total_completed
-
-puts "Input file: #{input_file}"
-puts "Found #{total_to_process} to remediate.  Total in file: #{total_druids}.  Already completed: #{total_completed}"
-puts "Pausing #{pause_time} seconds between objects" if pause_time > 0
-puts "Started at #{Time.now}"
-puts ""
-$stdout.flush
-
-start_time = Time.now
-total_success = 0
-total_failure = 0
-count = 0
-avg_time_per_object = 0
-total_time_remaining = 0
-
-druids.each do |druid|
-  done = completed_druids.include?(druid)
-  unless done
-    count += 1
-    item = PreAssembly::Remediation::Item.new(druid)
-    item.description = File.basename(remediate_logic_file) # added to the version description
-    item.extend(RemediationLogic) # add in our project specific methods
-    success = item.remediate
-    if success
-      total_success += 1
-      result = "success"
-    else
-      result = "FAILURE"
-      total_failure += 1
-    end
-    total_time = Time.now - start_time
-
-    sleep pause_time if pause_time > 0
-
-    remaining_to_process = total_to_process - count
-    avg_time_per_object = total_time / count
-    total_time_remaining = (avg_time_per_object * remaining_to_process).floor
-
-    status = "#{druid} : #{result} : #{count} of #{total_to_process} (#{remaining_to_process} remaining) : #{Time.now} : ~#{PreAssembly::Logging.seconds_to_string(total_time_remaining)} left"
-    item.log_to_progress_file(progress_log_file)
-    item.log_to_csv(csv_out)
-    puts status
-    $stdout.flush
-  end
-end
-
-end_time = Time.now
-total_time = ((end_time - start_time) / 1.hour).round(2)
-
-puts ""
-puts "Input file: #{input_file}"
-puts "Output file: #{csv_out}"
-puts "Ended at #{end_time}.  Total time: #{total_time} hours.  Average time per object: #{(total_time * 3600 / total_to_process).round(2)} seconds (includes any pause time).  Pause time: #{pause_time} seconds"
-puts "Total in file: #{total_druids}. Total processed: #{total_to_process}. Successful: #{total_success}. Completed previously: #{total_completed}.  Failed: #{total_failure}"
-
-$stdout.flush

From 81125dbe7dad310e81915e56a61e213a7a0e2435 Mon Sep 17 00:00:00 2001
From: Sarav Shah <saravsshah@gmail.com>
Date: Mon, 27 Aug 2018 15:31:28 -0700
Subject: [PATCH 02/10] Add gems and update Rakefile

---
 Gemfile      |  3 ++-
 Gemfile.lock | 37 ++++++++++++++++++++++++----
 Rakefile     | 68 +++-------------------------------------------------
 3 files changed, 38 insertions(+), 70 deletions(-)

diff --git a/Gemfile b/Gemfile
index 018b727f..f5604bc9 100644
--- a/Gemfile
+++ b/Gemfile
@@ -30,9 +30,9 @@ gem 'turbolinks'
 gem 'resque', '~> 1.27'
 gem 'resque-lock'
 gem 'resque-pool'
+gem 'config'
 
 group :test do
-  gem 'rspec', '~> 3.0'
   gem 'yard'
   gem 'solr_wrapper'
   gem 'jettywrapper'
@@ -51,6 +51,7 @@ group :development do
 end
 
 group :development, :test do
+  gem 'rspec-rails'
   gem 'byebug'
   gem 'rspec-rails', '~> 3.7'
   gem 'rubocop', '~> 0.58'
diff --git a/Gemfile.lock b/Gemfile.lock
index 38188329..5a69a2c4 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -97,6 +97,10 @@ GEM
     childprocess (0.9.0)
       ffi (~> 1.0, >= 1.0.11)
     concurrent-ruby (1.0.5)
+    config (1.7.0)
+      activesupport (>= 3.0)
+      deep_merge (~> 1.2.1)
+      dry-validation (>= 0.10.4)
     confstruct (0.2.7)
     connection_pool (2.2.2)
     coveralls (0.8.22)
@@ -109,6 +113,7 @@ GEM
     csv-mapper (0.5.1)
       fastercsv
     daemons (1.2.6)
+    deep_merge (1.2.1)
     deprecation (0.99.0)
       activesupport
     diff-lcs (1.3)
@@ -155,6 +160,33 @@ GEM
       nokogiri (~> 1.6)
       retries
     druid-tools (1.0.0)
+    dry-configurable (0.7.0)
+      concurrent-ruby (~> 1.0)
+    dry-container (0.6.0)
+      concurrent-ruby (~> 1.0)
+      dry-configurable (~> 0.1, >= 0.1.3)
+    dry-core (0.4.7)
+      concurrent-ruby (~> 1.0)
+    dry-equalizer (0.2.1)
+    dry-inflector (0.1.2)
+    dry-logic (0.4.2)
+      dry-container (~> 0.2, >= 0.2.6)
+      dry-core (~> 0.2)
+      dry-equalizer (~> 0.2)
+    dry-types (0.13.2)
+      concurrent-ruby (~> 1.0)
+      dry-container (~> 0.3)
+      dry-core (~> 0.4, >= 0.4.4)
+      dry-equalizer (~> 0.2)
+      dry-inflector (~> 0.1, >= 0.1.2)
+      dry-logic (~> 0.4, >= 0.4.2)
+    dry-validation (0.12.1)
+      concurrent-ruby (~> 1.0)
+      dry-configurable (~> 0.1, >= 0.1.3)
+      dry-core (~> 0.2, >= 0.2.1)
+      dry-equalizer (~> 0.2)
+      dry-logic (~> 0.4, >= 0.4.0)
+      dry-types (~> 0.13.1)
     edtf (3.0.4)
       activesupport (>= 3.0, < 6.0)
     equivalent-xml (0.6.0)
@@ -336,10 +368,6 @@ GEM
     rsolr (2.2.1)
       builder (>= 2.1.2)
       faraday (>= 0.9.0)
-    rspec (3.8.0)
-      rspec-core (~> 3.8.0)
-      rspec-expectations (~> 3.8.0)
-      rspec-mocks (~> 3.8.0)
     rspec-core (3.8.0)
       rspec-support (~> 3.8.0)
     rspec-expectations (3.8.1)
@@ -459,6 +487,7 @@ DEPENDENCIES
   capistrano (~> 3)
   capistrano-bundler
   capistrano-rvm
+  config
   coveralls
   csv-mapper
   dlss-capistrano (~> 3.1)
diff --git a/Rakefile b/Rakefile
index f6b70272..e85f9139 100644
--- a/Rakefile
+++ b/Rakefile
@@ -1,68 +1,6 @@
-require_relative 'config/application'
-require 'rspec/core/rake_task'
+# Add your own tasks in files placed in lib/tasks ending in .rake,
+# for example lib/tasks/capistrano.rake, and they will automatically be available to Rake.
 
-begin
-  Bundler.setup(:default, :development)
-rescue Bundler::BundlerError => e
-  $stderr.puts e.message
-  $stderr.puts "Run `bundle install` to install missing gems"
-  exit e.status_code
-end
+require_relative 'config/application'
 
 Rails.application.load_tasks
-
-Dir.glob('lib/tasks/*.rake').each { |r| import r }
-
-desc "Run specs"
-RSpec::Core::RakeTask.new(:spec)
-
-task :default => :spec
-
-if ['test', 'development'].include? ENV['RAILS_ENV']
-  require 'jettywrapper'
-  Jettywrapper.hydra_jetty_version = 'v7.3.0' # this keeps us on fedora 3, hydra-jetty v8.x moves to fedora 4.
-
-  def load_order_files(fedora_files)
-    data_path = File.expand_path('../fedora_conf/data/', __FILE__)
-    fedora_files.delete_if { |f| f.strip.empty? }
-    fedora_files.map { |f| File.join(data_path, f.strip) }
-  end
-
-  namespace :repo do
-    desc "Load XML file(s) into repo (fedora and solr), default: contents of 'load_order' file. With a glob: rake repo:load[fedora_conf/data/*.xml]"
-    task :load, [:glob] do |_task, args|
-      require 'active_fedora'
-      puts "travis_fold:start:repo-load\r" if ENV['TRAVIS'] == 'true'
-
-      file_list = []
-      if args.key?(:glob)
-        file_list = Dir.glob(args[:glob])
-      else
-        puts 'No file glob was specified so file order and inclusion is determined by the load_order file'
-        fedora_files = File.foreach(File.join(File.expand_path('../fedora_conf/data/', __FILE__), 'load_order')).to_a
-
-        file_list = load_order_files(fedora_files)
-      end
-
-      errors = []
-      i = 0
-
-      file_list.each do |file|
-        i += 1
-
-        handler = proc do |e, _attempt_number, _total_delay|
-          puts STDERR.puts "ERROR loading #{file}:\n#{e.message}\n#{e.backtrace.join "\n"}"
-          errors << file
-        end
-        with_retries(:max_tries => 3, :handler => handler, :rescue => [StandardError]) { |attempt|
-          puts "** File #{i}, Try #{attempt} ** repo:load foxml=#{file}"
-          pid = ActiveFedora::FixtureLoader.import_to_fedora(file)
-          ActiveFedora::FixtureLoader.index(pid)
-        }
-      end
-      puts 'Done loading repo files'
-      puts "ERROR in #{errors.size()} of #{i} files" if errors.size() > 0
-      puts "travis_fold:end:repo-load\r" if ENV['TRAVIS'] == 'true'
-    end
-  end # :repo
-end

From 621427029e6c56bbdf150dea527061c315f5ffd7 Mon Sep 17 00:00:00 2001
From: Sarav Shah <saravsshah@gmail.com>
Date: Mon, 27 Aug 2018 15:31:48 -0700
Subject: [PATCH 03/10] Set up config/ in a more rails way

---
 .gitignore                                  |  4 ++
 config/application.rb                       |  5 ++-
 config/boot.rb                              |  7 ++-
 config/environments/development.rb          | 27 ++++++++++-
 config/environments/production.rb           |  2 +-
 config/environments/test.rb                 | 15 ++++++-
 config/initializers/config.rb               | 50 +++++++++++++++++++++
 config/initializers/dor_workflow_service.rb |  5 +++
 config/settings.yml                         |  1 +
 config/settings/development.yml             |  0
 config/settings/production.yml              |  0
 config/settings/test.yml                    |  0
 12 files changed, 109 insertions(+), 7 deletions(-)
 create mode 100644 config/initializers/config.rb
 create mode 100644 config/initializers/dor_workflow_service.rb
 create mode 100644 config/settings.yml
 create mode 100644 config/settings/development.yml
 create mode 100644 config/settings/production.yml
 create mode 100644 config/settings/test.yml

diff --git a/.gitignore b/.gitignore
index 07968053..937de7c7 100644
--- a/.gitignore
+++ b/.gitignore
@@ -23,3 +23,7 @@ coverage
 
 # Ignore master key for decrypting credentials and more.
 /config/master.key
+
+config/settings.local.yml
+config/settings/*.local.yml
+config/environments/*.local.yml
diff --git a/config/application.rb b/config/application.rb
index b8d6643f..0e98a378 100644
--- a/config/application.rb
+++ b/config/application.rb
@@ -1,10 +1,13 @@
 require_relative 'boot'
 
 require 'rails/all'
-
+require 'assembly-utils'
 # Require the gems listed in Gemfile, including any gems
 # you've limited to :test, :development, or :production.
 Bundler.require(*Rails.groups)
+def noko_doc(x)
+  Nokogiri.XML(x) { |conf| conf.default_xml.noblanks }
+end
 
 module PreAssembly
   class Application < Rails::Application
diff --git a/config/boot.rb b/config/boot.rb
index f54a4e85..95ac963d 100644
--- a/config/boot.rb
+++ b/config/boot.rb
@@ -1,3 +1,7 @@
+ENV['BUNDLE_GEMFILE'] ||= File.expand_path('../Gemfile', __dir__)
+
+require 'bundler/setup' # Set up gems listed in the Gemfile.
+
 require 'rubygems'
 require 'bundler/setup'
 require 'logger'
@@ -13,7 +17,6 @@
 # ENV_FILE = PRE_ASSEMBLY_ROOT + "/config/cli_environments/#{environment}.rb"
 require_relative "cli_environments/#{environment}.rb"
 Dor::Config.dor_services.url ||= Dor::Config.dor.service_root
-Dor::Config.workflow.client.configure(Dor::Config.workflow.url, :dor_services_url => Dor::Config.dor_services.url.gsub('/v1', ''))
 
 # Project dir in load path.
 $LOAD_PATH.unshift(PRE_ASSEMBLY_ROOT + '/lib')
@@ -23,4 +26,4 @@
 PreAssembly::Logging.setup PRE_ASSEMBLY_ROOT, environment
 
 # Load the project and its dependencies.
-require 'pre_assembly'
+require 'pre_assembly'
\ No newline at end of file
diff --git a/config/environments/development.rb b/config/environments/development.rb
index 1519dca4..1311e3e4 100644
--- a/config/environments/development.rb
+++ b/config/environments/development.rb
@@ -13,12 +13,13 @@
   config.consider_all_requests_local = true
 
   # Enable/disable caching. By default caching is disabled.
-  if Rails.root.join('tmp/caching-dev.txt').exist?
+  # Run rails dev:cache to toggle caching.
+  if Rails.root.join('tmp', 'caching-dev.txt').exist?
     config.action_controller.perform_caching = true
 
     config.cache_store = :memory_store
     config.public_file_server.headers = {
-      'Cache-Control' => "public, max-age=#{2.days.seconds.to_i}"
+      'Cache-Control' => "public, max-age=#{2.days.to_i}"
     }
   else
     config.action_controller.perform_caching = false
@@ -26,12 +27,34 @@
     config.cache_store = :null_store
   end
 
+  # Store uploaded files on the local file system (see config/storage.yml for options)
+  config.active_storage.service = :local
+
+  # Don't care if the mailer can't send.
+  config.action_mailer.raise_delivery_errors = false
+
+  config.action_mailer.perform_caching = false
+
   # Print deprecation notices to the Rails logger.
   config.active_support.deprecation = :log
 
   # Raise an error on page load if there are pending migrations.
   config.active_record.migration_error = :page_load
 
+  # Highlight code that triggered database queries in logs.
+  config.active_record.verbose_query_logs = true
+
+  # Debug mode disables concatenation and preprocessing of assets.
+  # This option may cause significant delays in view rendering with a large
+  # number of complex assets.
+  config.assets.debug = true
+
+  # Suppress logger output for asset requests.
+  config.assets.quiet = true
+
+  # Raises error for missing translations
+  # config.action_view.raise_on_missing_translations = true
+
   # Use an evented file watcher to asynchronously detect changes in source code,
   # routes, locales, etc. This feature depends on the listen gem.
   config.file_watcher = ActiveSupport::EventedFileUpdateChecker
diff --git a/config/environments/production.rb b/config/environments/production.rb
index 5f7a71c3..40055ee7 100644
--- a/config/environments/production.rb
+++ b/config/environments/production.rb
@@ -54,7 +54,7 @@
   config.log_level = :debug
 
   # Prepend all log lines with the following tags.
-  config.log_tags = [:request_id]
+  config.log_tags = [ :request_id ]
 
   # Use a different cache store in production.
   # config.cache_store = :mem_cache_store
diff --git a/config/environments/test.rb b/config/environments/test.rb
index 841ba3e2..0a38fd3c 100644
--- a/config/environments/test.rb
+++ b/config/environments/test.rb
@@ -15,7 +15,7 @@
   # Configure public file server for tests with Cache-Control for performance.
   config.public_file_server.enabled = true
   config.public_file_server.headers = {
-    'Cache-Control' => "public, max-age=#{1.hour.seconds.to_i}"
+    'Cache-Control' => "public, max-age=#{1.hour.to_i}"
   }
 
   # Show full error reports and disable caching.
@@ -28,6 +28,19 @@
   # Disable request forgery protection in test environment.
   config.action_controller.allow_forgery_protection = false
 
+  # Store uploaded files on the local file system in a temporary directory
+  config.active_storage.service = :test
+
+  config.action_mailer.perform_caching = false
+
+  # Tell Action Mailer not to deliver emails to the real world.
+  # The :test delivery method accumulates sent emails in the
+  # ActionMailer::Base.deliveries array.
+  config.action_mailer.delivery_method = :test
+
   # Print deprecation notices to the stderr.
   config.active_support.deprecation = :stderr
+
+  # Raises error for missing translations
+  # config.action_view.raise_on_missing_translations = true
 end
diff --git a/config/initializers/config.rb b/config/initializers/config.rb
new file mode 100644
index 00000000..776c6b51
--- /dev/null
+++ b/config/initializers/config.rb
@@ -0,0 +1,50 @@
+Config.setup do |config|
+  # Name of the constant exposing loaded settings
+  config.const_name = 'Settings'
+
+  # Ability to remove elements of the array set in earlier loaded settings file. For example value: '--'.
+  #
+  # config.knockout_prefix = nil
+
+  # Overwrite an existing value when merging a `nil` value.
+  # When set to `false`, the existing value is retained after merge.
+  #
+  # config.merge_nil_values = true
+
+  # Overwrite arrays found in previously loaded settings file. When set to `false`, arrays will be merged.
+  #
+  # config.overwrite_arrays = true
+
+  # Load environment variables from the `ENV` object and override any settings defined in files.
+  #
+  # config.use_env = false
+
+  # Define ENV variable prefix deciding which variables to load into config.
+  #
+  # config.env_prefix = 'Settings'
+
+  # What string to use as level separator for settings loaded from ENV variables. Default value of '.' works well
+  # with Heroku, but you might want to change it for example for '__' to easy override settings from command line, where
+  # using dots in variable names might not be allowed (eg. Bash).
+  #
+  # config.env_separator = '.'
+
+  # Ability to process variables names:
+  #   * nil  - no change
+  #   * :downcase - convert to lower case
+  #
+  # config.env_converter = :downcase
+
+  # Parse numeric values as integers instead of strings.
+  #
+  # config.env_parse_values = true
+
+  # Validate presence and type of specific config values. Check https://github.com/dry-rb/dry-validation for details.
+  #
+  # config.schema do
+  #   required(:name).filled
+  #   required(:age).maybe(:int?)
+  #   required(:email).filled(format?: EMAIL_REGEX)
+  # end
+
+end
diff --git a/config/initializers/dor_workflow_service.rb b/config/initializers/dor_workflow_service.rb
new file mode 100644
index 00000000..58c7264a
--- /dev/null
+++ b/config/initializers/dor_workflow_service.rb
@@ -0,0 +1,5 @@
+require 'dor-workflow-service'
+Dor::WorkflowService.configure(
+  Settings.workflow_services_url,
+  :dor_services_url => Dor::Config.dor_services.url.gsub('/v1', '')
+)
diff --git a/config/settings.yml b/config/settings.yml
new file mode 100644
index 00000000..f6e3f046
--- /dev/null
+++ b/config/settings.yml
@@ -0,0 +1 @@
+workflow_services_url: 'https://workflows.example.org/workflow/'
diff --git a/config/settings/development.yml b/config/settings/development.yml
new file mode 100644
index 00000000..e69de29b
diff --git a/config/settings/production.yml b/config/settings/production.yml
new file mode 100644
index 00000000..e69de29b
diff --git a/config/settings/test.yml b/config/settings/test.yml
new file mode 100644
index 00000000..e69de29b

From 8a85f75228189b11238eff7490dd1d8289630c4d Mon Sep 17 00:00:00 2001
From: Sarav Shah <saravsshah@gmail.com>
Date: Mon, 27 Aug 2018 15:32:48 -0700
Subject: [PATCH 04/10] Move specs/ into nested folders and use rails_helper

remove require rails_helper from spec/
---
 .rspec                                        |  2 +-
 spec/{ => lib/pre_assembly}/bundle_spec.rb    | 17 ++--
 .../pre_assembly}/digital_object_spec.rb      |  2 -
 .../pre_assembly}/druid_minter_spec.rb        |  2 -
 .../pre_assembly}/object_file_spec.rb         |  2 -
 .../remediation}/remediate_spec.rb            |  4 +-
 .../smpl_project_specific_spec.rb             |  2 -
 .../test_data/logging/progress_log_file.yml   | 15 ++++
 spec/rails_helper.rb                          |  3 +-
 spec/spec_helper.rb                           | 79 +++++++++++++++----
 10 files changed, 91 insertions(+), 37 deletions(-)
 rename spec/{ => lib/pre_assembly}/bundle_spec.rb (98%)
 rename spec/{ => lib/pre_assembly}/digital_object_spec.rb (99%)
 rename spec/{ => lib/pre_assembly}/druid_minter_spec.rb (93%)
 rename spec/{ => lib/pre_assembly}/object_file_spec.rb (92%)
 rename spec/{ => lib/pre_assembly/remediation}/remediate_spec.rb (91%)
 rename spec/{ => lib/pre_assembly}/smpl_project_specific_spec.rb (99%)
 create mode 100644 spec/lib/test_data/logging/progress_log_file.yml

diff --git a/.rspec b/.rspec
index 83e16f80..0f30adeb 100644
--- a/.rspec
+++ b/.rspec
@@ -1,2 +1,2 @@
 --color
---require spec_helper
+--require rails_helper
diff --git a/spec/bundle_spec.rb b/spec/lib/pre_assembly/bundle_spec.rb
similarity index 98%
rename from spec/bundle_spec.rb
rename to spec/lib/pre_assembly/bundle_spec.rb
index d0f38bc7..cf647077 100644
--- a/spec/bundle_spec.rb
+++ b/spec/lib/pre_assembly/bundle_spec.rb
@@ -1,5 +1,3 @@
-require 'spec_helper'
-
 describe PreAssembly::Bundle do
   let(:md5_regex) { /^[0-9a-f]{32}$/ }
   # TODO: break out tests about BundleContext into separate spec file
@@ -50,10 +48,9 @@ def bundle_setup(bundle_context)
   end
 
   describe '#load_skippables' do
-    it "does nothing if resume returns false" do
-      allow(rumsey).to receive(:resume).and_return(false)
-      expect(rumsey).not_to receive(:read_progress_log)
-      rumsey.load_skippables
+    it "does nothing if @resume is false" do
+      rumsey.resume = false
+      expect(rumsey.load_skippables).to be_nil
     end
 
     it "returns expected hash of skippable items" do
@@ -306,7 +303,7 @@ def bundle_setup(bundle_context)
     end
 
     it "new_object_file() should return an ObjectFile with expected path values" do
-      allow(revs).to receive(:exclude_from_path).and_return(false)
+      allow(revs).to receive(:exclude_from_content).and_return(false)
       tests = [
         # Stageable is a file:
         # - immediately in bundle dir.
@@ -465,8 +462,10 @@ def bundle_setup(bundle_context)
 
   describe '#manifest_rows' do
     it "loads the manifest CSV only once, during the validation phase, and return all three rows even if you access the manifest multiple times" do
-      expect(revs).not_to receive(:load_manifest_rows_from_csv)
-      3.times { revs.manifest_rows.size == 3 }
+      expect(revs.manifest_rows.size).to eq 3
+      expect(revs).not_to receive(:object_discovery)
+      revs.manifest_rows
+
     end
 
     it "returns empty array for bundles that do not use a manifest" do
diff --git a/spec/digital_object_spec.rb b/spec/lib/pre_assembly/digital_object_spec.rb
similarity index 99%
rename from spec/digital_object_spec.rb
rename to spec/lib/pre_assembly/digital_object_spec.rb
index f4ebf05e..071b64a8 100644
--- a/spec/digital_object_spec.rb
+++ b/spec/lib/pre_assembly/digital_object_spec.rb
@@ -1,5 +1,3 @@
-require 'spec_helper'
-
 describe PreAssembly::DigitalObject do
   let(:dru) { 'gn330dv6119' }
   let(:pid) { "druid:#{dru}" }
diff --git a/spec/druid_minter_spec.rb b/spec/lib/pre_assembly/druid_minter_spec.rb
similarity index 93%
rename from spec/druid_minter_spec.rb
rename to spec/lib/pre_assembly/druid_minter_spec.rb
index dfb4824f..7f6c3b05 100644
--- a/spec/druid_minter_spec.rb
+++ b/spec/lib/pre_assembly/druid_minter_spec.rb
@@ -1,5 +1,3 @@
-require 'spec_helper'
-
 describe PreAssembly::DruidMinter do
   it "gets a sequence of druids from calls to next()" do
     exp = described_class.current
diff --git a/spec/object_file_spec.rb b/spec/lib/pre_assembly/object_file_spec.rb
similarity index 92%
rename from spec/object_file_spec.rb
rename to spec/lib/pre_assembly/object_file_spec.rb
index 03daf588..18f990cd 100644
--- a/spec/object_file_spec.rb
+++ b/spec/lib/pre_assembly/object_file_spec.rb
@@ -1,5 +1,3 @@
-require 'spec_helper'
-
 describe PreAssembly::ObjectFile do
   before do
     @f = described_class.new(
diff --git a/spec/remediate_spec.rb b/spec/lib/pre_assembly/remediation/remediate_spec.rb
similarity index 91%
rename from spec/remediate_spec.rb
rename to spec/lib/pre_assembly/remediation/remediate_spec.rb
index 4daeeb6a..b0b132ca 100644
--- a/spec/remediate_spec.rb
+++ b/spec/lib/pre_assembly/remediation/remediate_spec.rb
@@ -1,5 +1,3 @@
-require 'spec_helper'
-
 describe PreAssembly::Remediation::Item do
   let(:pid) { 'druid:cs575bk5522' }
   let(:item) { described_class.new(pid) }
@@ -11,7 +9,7 @@
   end
 
   context 'logging' do
-    let(:log_dir) { File.dirname(__FILE__) + "/test_data/logging" }
+    let(:log_dir) { File.join(File.dirname(__FILE__), "../../test_data/logging") }
     let(:csv_filename) { log_dir + "/csv_log.csv" }
     let(:progress_log_file) { log_dir + "/progress_log_file.yml" }
 
diff --git a/spec/smpl_project_specific_spec.rb b/spec/lib/pre_assembly/smpl_project_specific_spec.rb
similarity index 99%
rename from spec/smpl_project_specific_spec.rb
rename to spec/lib/pre_assembly/smpl_project_specific_spec.rb
index ebbd9c73..8da682b0 100644
--- a/spec/smpl_project_specific_spec.rb
+++ b/spec/lib/pre_assembly/smpl_project_specific_spec.rb
@@ -1,5 +1,3 @@
-require 'spec_helper'
-
 describe PreAssembly::DigitalObject do
   let(:bundle_dir) { File.join(PRE_ASSEMBLY_ROOT, 'spec/test_data/bundle_input_e') }
 
diff --git a/spec/lib/test_data/logging/progress_log_file.yml b/spec/lib/test_data/logging/progress_log_file.yml
new file mode 100644
index 00000000..f1246de0
--- /dev/null
+++ b/spec/lib/test_data/logging/progress_log_file.yml
@@ -0,0 +1,15 @@
+---
+:pid: druid:cs575bk5522
+:remediate_completed: 
+:message: 
+:timestamp: 2018-08-27 15:09:13.779278000 -07:00
+---
+:pid: druid:cs575bk5522
+:remediate_completed: 
+:message: 
+:timestamp: 2018-08-27 15:10:55.044887000 -07:00
+---
+:pid: druid:cs575bk5522
+:remediate_completed: 
+:message: 
+:timestamp: 2018-08-27 16:11:03.600040000 -07:00
diff --git a/spec/rails_helper.rb b/spec/rails_helper.rb
index 4c853b8c..7413a13c 100644
--- a/spec/rails_helper.rb
+++ b/spec/rails_helper.rb
@@ -4,7 +4,6 @@
 require File.expand_path('../config/environment', __dir__)
 # Prevent database truncation if the environment is production
 abort("The Rails environment is running in production mode!") if Rails.env.production?
-
 require 'rspec/rails'
 # Add additional requires below this line. Rails is not loaded until this point!
 
@@ -22,7 +21,7 @@
   # If you're not using ActiveRecord, or you'd prefer not to run each of your
   # examples within a transaction, remove the following line or assign false
   # instead of true.
-  config.use_transactional_fixtures = true
+  # config.use_transactional_fixtures = true
 
   # RSpec Rails can automatically mix in different behaviours to your tests
   # based on their file location, for example enabling you to call `get` and
diff --git a/spec/spec_helper.rb b/spec/spec_helper.rb
index 86e4782a..45bd3f30 100644
--- a/spec/spec_helper.rb
+++ b/spec/spec_helper.rb
@@ -1,21 +1,72 @@
 require 'tmpdir'
 require 'equivalent-xml/rspec_matchers'
 require 'byebug'
-require 'simplecov'
-require 'coveralls'
 
-SimpleCov.formatter = Coveralls::SimpleCov::Formatter
-SimpleCov.start do
-  track_files "bin/**/*"
-end
-ENV['RAILS_ENV'] ||= "test"
-puts "running in #{ENV['RAILS_ENV']} mode"
-bootfile = File.expand_path(File.dirname(__FILE__) + '/../config/boot')
-require bootfile
 
-tmp_output_dir = File.join(PRE_ASSEMBLY_ROOT, 'tmp')
-FileUtils.mkdir_p tmp_output_dir
+RSpec.configure do |config|
+
+  # rspec-expectations config goes here. You can use an alternate
+  # assertion/expectation library such as wrong or the stdlib/minitest
+  # assertions if you prefer.
+  config.expect_with :rspec do |expectations|
+    # This option will default to `true` in RSpec 4. It makes the `description`
+    # and `failure_message` of custom matchers include text for helper methods
+    # defined using `chain`, e.g.:
+    #     be_bigger_than(2).and_smaller_than(4).description
+    #     # => "be bigger than 2 and smaller than 4"
+    # ...rather than:
+    #     # => "be bigger than 2"
+    expectations.include_chain_clauses_in_custom_matcher_descriptions = true
+  end
+
+  config.mock_with :rspec do |mocks|
+    # Prevents you from mocking or stubbing a method that does not exist on a real object.
+    # This is generally recommended, and will default to `true` in RSpec 4.
+    mocks.verify_partial_doubles = true
+  end
+
+  # This option will default to `:apply_to_host_groups` in RSpec 4 (and will
+  # have no way to turn it off -- the option exists only for backwards
+  # compatibility in RSpec 3). It causes shared context metadata to be
+  # inherited by the metadata hash of host groups and examples, rather than
+  # triggering implicit auto-inclusion in groups with matching metadata.
+  config.shared_context_metadata_behavior = :apply_to_host_groups
+
+# The settings below are suggested to provide a good initial experience
+# with RSpec, but feel free to customize to your heart's content.
+=begin
+  # This allows you to limit a spec run to individual examples or groups
+  # you care about by tagging them with `:focus` metadata. When nothing
+  # is tagged with `:focus`, all examples get run. RSpec also provides
+  # aliases for `it`, `describe`, and `context` that include `:focus`
+  # metadata: `fit`, `fdescribe` and `fcontext`, respectively.
+  config.filter_run_when_matching :focus
+
+  # Allows RSpec to persist some state between runs in order to support
+  # the `--only-failures` and `--next-failure` CLI options. We recommend
+  # you configure your source control system to ignore this file.
+  config.example_status_persistence_file_path = "spec/examples.txt"
+
+  # Limits the available syntax to the non-monkey patched syntax that is
+  # recommended. For more details, see:
+  #   - http://rspec.info/blog/2012/06/rspecs-new-expectation-syntax/
+  #   - http://www.teaisaweso.me/blog/2013/05/27/rspecs-new-message-expectation-syntax/
+  #   - http://rspec.info/blog/2014/05/notable-changes-in-rspec-3/#zero-monkey-patching-mode
+  config.disable_monkey_patching!
+
+  # Many RSpec users commonly either run the entire suite or an individual
+  # file, and it's useful to allow more verbose output when running an
+  # individual spec file.
+  if config.files_to_run.one?
+    # Use the documentation formatter for detailed output,
+    # unless a formatter has already been configured
+    # (e.g. via a command-line flag).
+    config.default_formatter = "doc"
+  end
 
-def noko_doc(x)
-  Nokogiri.XML(x) { |conf| conf.default_xml.noblanks }
+  # Print the 10 slowest examples and example groups at the
+  # end of the spec run, to help surface which specs are running
+  # particularly slow.
+  config.profile_examples = 10
+=end
 end

From 2a1c5f84ade8f013e6356e0d21c982e25da4c7d0 Mon Sep 17 00:00:00 2001
From: Sarav Shah <saravsshah@gmail.com>
Date: Mon, 27 Aug 2018 15:33:00 -0700
Subject: [PATCH 05/10] Add a schema for rails

---
 db/schema.rb | 15 +++++++++++++++
 1 file changed, 15 insertions(+)
 create mode 100644 db/schema.rb

diff --git a/db/schema.rb b/db/schema.rb
new file mode 100644
index 00000000..52ab025e
--- /dev/null
+++ b/db/schema.rb
@@ -0,0 +1,15 @@
+# This file is auto-generated from the current state of the database. Instead
+# of editing this file, please use the migrations feature of Active Record to
+# incrementally modify your database, and then regenerate this schema definition.
+#
+# Note that this schema.rb definition is the authoritative source for your
+# database schema. If you need to create the application database on another
+# system, you should be using db:schema:load, not running all the migrations
+# from scratch. The latter is a flawed and unsustainable approach (the more migrations
+# you'll amass, the slower it'll run and the greater likelihood for issues).
+#
+# It's strongly recommended that you check this file into your version control system.
+
+ActiveRecord::Schema.define(version: 0) do
+
+end

From b2c989e106b76d43d7ef2e635109aaa0a4258ab3 Mon Sep 17 00:00:00 2001
From: Sarav Shah <saravsshah@gmail.com>
Date: Mon, 27 Aug 2018 16:46:36 -0700
Subject: [PATCH 06/10]  move lib to app/lib

---
 {lib => app/lib}/pre_assembly.rb                                  | 0
 {lib => app/lib}/pre_assembly/bundle.rb                           | 0
 {lib => app/lib}/pre_assembly/digital_object.rb                   | 0
 {lib => app/lib}/pre_assembly/druid_minter.rb                     | 0
 {lib => app/lib}/pre_assembly/logging.rb                          | 0
 {lib => app/lib}/pre_assembly/object_file.rb                      | 0
 {lib => app/lib}/pre_assembly/project/README.txt                  | 0
 {lib => app/lib}/pre_assembly/project/salt.rb                     | 0
 {lib => app/lib}/pre_assembly/project/smpl.rb                     | 0
 .../remediate.rb => app/lib/pre_assembly/remediation/item.rb      | 0
 .../lib}/pre_assembly/remediation/remediate_project_example.rb    | 0
 {lib => app/lib}/pre_assembly/reporting.rb                        | 0
 {lib => app/lib}/pre_assembly/smpl_precontent_metadata.rb         | 0
 lib/assets/.keep                                                  | 0
 lib/tasks/.keep                                                   | 0
 .../pre_assembly/remediation/{remediate_spec.rb => item_spec.rb}  | 0
 16 files changed, 0 insertions(+), 0 deletions(-)
 rename {lib => app/lib}/pre_assembly.rb (100%)
 rename {lib => app/lib}/pre_assembly/bundle.rb (100%)
 rename {lib => app/lib}/pre_assembly/digital_object.rb (100%)
 rename {lib => app/lib}/pre_assembly/druid_minter.rb (100%)
 rename {lib => app/lib}/pre_assembly/logging.rb (100%)
 rename {lib => app/lib}/pre_assembly/object_file.rb (100%)
 rename {lib => app/lib}/pre_assembly/project/README.txt (100%)
 rename {lib => app/lib}/pre_assembly/project/salt.rb (100%)
 rename {lib => app/lib}/pre_assembly/project/smpl.rb (100%)
 rename lib/pre_assembly/remediation/remediate.rb => app/lib/pre_assembly/remediation/item.rb (100%)
 rename {lib => app/lib}/pre_assembly/remediation/remediate_project_example.rb (100%)
 rename {lib => app/lib}/pre_assembly/reporting.rb (100%)
 rename {lib => app/lib}/pre_assembly/smpl_precontent_metadata.rb (100%)
 delete mode 100644 lib/assets/.keep
 delete mode 100644 lib/tasks/.keep
 rename spec/lib/pre_assembly/remediation/{remediate_spec.rb => item_spec.rb} (100%)

diff --git a/lib/pre_assembly.rb b/app/lib/pre_assembly.rb
similarity index 100%
rename from lib/pre_assembly.rb
rename to app/lib/pre_assembly.rb
diff --git a/lib/pre_assembly/bundle.rb b/app/lib/pre_assembly/bundle.rb
similarity index 100%
rename from lib/pre_assembly/bundle.rb
rename to app/lib/pre_assembly/bundle.rb
diff --git a/lib/pre_assembly/digital_object.rb b/app/lib/pre_assembly/digital_object.rb
similarity index 100%
rename from lib/pre_assembly/digital_object.rb
rename to app/lib/pre_assembly/digital_object.rb
diff --git a/lib/pre_assembly/druid_minter.rb b/app/lib/pre_assembly/druid_minter.rb
similarity index 100%
rename from lib/pre_assembly/druid_minter.rb
rename to app/lib/pre_assembly/druid_minter.rb
diff --git a/lib/pre_assembly/logging.rb b/app/lib/pre_assembly/logging.rb
similarity index 100%
rename from lib/pre_assembly/logging.rb
rename to app/lib/pre_assembly/logging.rb
diff --git a/lib/pre_assembly/object_file.rb b/app/lib/pre_assembly/object_file.rb
similarity index 100%
rename from lib/pre_assembly/object_file.rb
rename to app/lib/pre_assembly/object_file.rb
diff --git a/lib/pre_assembly/project/README.txt b/app/lib/pre_assembly/project/README.txt
similarity index 100%
rename from lib/pre_assembly/project/README.txt
rename to app/lib/pre_assembly/project/README.txt
diff --git a/lib/pre_assembly/project/salt.rb b/app/lib/pre_assembly/project/salt.rb
similarity index 100%
rename from lib/pre_assembly/project/salt.rb
rename to app/lib/pre_assembly/project/salt.rb
diff --git a/lib/pre_assembly/project/smpl.rb b/app/lib/pre_assembly/project/smpl.rb
similarity index 100%
rename from lib/pre_assembly/project/smpl.rb
rename to app/lib/pre_assembly/project/smpl.rb
diff --git a/lib/pre_assembly/remediation/remediate.rb b/app/lib/pre_assembly/remediation/item.rb
similarity index 100%
rename from lib/pre_assembly/remediation/remediate.rb
rename to app/lib/pre_assembly/remediation/item.rb
diff --git a/lib/pre_assembly/remediation/remediate_project_example.rb b/app/lib/pre_assembly/remediation/remediate_project_example.rb
similarity index 100%
rename from lib/pre_assembly/remediation/remediate_project_example.rb
rename to app/lib/pre_assembly/remediation/remediate_project_example.rb
diff --git a/lib/pre_assembly/reporting.rb b/app/lib/pre_assembly/reporting.rb
similarity index 100%
rename from lib/pre_assembly/reporting.rb
rename to app/lib/pre_assembly/reporting.rb
diff --git a/lib/pre_assembly/smpl_precontent_metadata.rb b/app/lib/pre_assembly/smpl_precontent_metadata.rb
similarity index 100%
rename from lib/pre_assembly/smpl_precontent_metadata.rb
rename to app/lib/pre_assembly/smpl_precontent_metadata.rb
diff --git a/lib/assets/.keep b/lib/assets/.keep
deleted file mode 100644
index e69de29b..00000000
diff --git a/lib/tasks/.keep b/lib/tasks/.keep
deleted file mode 100644
index e69de29b..00000000
diff --git a/spec/lib/pre_assembly/remediation/remediate_spec.rb b/spec/lib/pre_assembly/remediation/item_spec.rb
similarity index 100%
rename from spec/lib/pre_assembly/remediation/remediate_spec.rb
rename to spec/lib/pre_assembly/remediation/item_spec.rb

From f2d362f38b2a3d6b58581051bd0414498f140517 Mon Sep 17 00:00:00 2001
From: Sarav Shah <saravsshah@gmail.com>
Date: Mon, 27 Aug 2018 16:47:49 -0700
Subject: [PATCH 07/10] Further application config stuff

---
 app/lib/pre_assembly.rb                     | 19 +------------------
 app/lib/pre_assembly/logging.rb             | 14 ++++++--------
 config/application.rb                       |  6 +++++-
 config/boot.rb                              | 15 ---------------
 config/cli_environments/test.rb             |  2 ++
 config/initializers/dor_workflow_service.rb |  4 ++++
 6 files changed, 18 insertions(+), 42 deletions(-)

diff --git a/app/lib/pre_assembly.rb b/app/lib/pre_assembly.rb
index ad8f174e..880fa91d 100644
--- a/app/lib/pre_assembly.rb
+++ b/app/lib/pre_assembly.rb
@@ -7,14 +7,6 @@
 # auto require any project specific files
 Dir[File.dirname(__FILE__) + '/pre_assembly/project/*.rb'].each { |file| require "pre_assembly/project/#{File.basename(file)}" }
 
-require 'pre_assembly/reporting'
-require 'pre_assembly/druid_minter'
-require 'pre_assembly/bundle'
-require 'pre_assembly/digital_object'
-require 'pre_assembly/object_file'
-require 'pre_assembly/remediation/remediate'
-require 'pre_assembly/smpl_precontent_metadata'
-
 require 'assembly-utils'
 require 'assembly-image'
 require 'rest_client'
@@ -31,13 +23,4 @@
   'Manuscript (image-only)' => :book_as_image,
   'Map' => :map
 }
-
-module PreAssembly
-  def self.retry_handler(method_name, logger, params = {})
-    Proc.new do |_exception, attempt_number, _total_delay|
-      logger.send "      ** #{method_name} FAILED **; with params of #{params.inspect}; and trying attempt #{attempt_number} of #{Dor::Config.dor.num_attempts}; delayed #{Dor::Config.dor.total_delay} seconds"
-    end
-  end
-
-  UnknownError = Class.new(StandardError)
-end
+ 
\ No newline at end of file
diff --git a/app/lib/pre_assembly/logging.rb b/app/lib/pre_assembly/logging.rb
index d365d636..04e45d10 100644
--- a/app/lib/pre_assembly/logging.rb
+++ b/app/lib/pre_assembly/logging.rb
@@ -11,14 +11,12 @@ module Logging
     LOG_FORMAT    = "%-6s -- %s -- %s\n"
     TIME_FORMAT   = "%Y-%m-%d %H:%M:%S"
 
-    def self.setup(project_root, environment)
-      log_file = File.join(project_root, 'log', "#{environment}.log")
-      @@log       ||= Logger.new(log_file)
-      @@log.level   = LEVELS[:info]
-
-      @@log.formatter = proc do |severity, datetime, _progname, msg|
-        LOG_FORMAT % [severity, datetime.strftime(TIME_FORMAT), msg]
-      end
+
+    @@log       ||= Logger.new(File.join(Rails.root, 'log', "#{Rails.env}.log"))
+    @@log.level   = LEVELS[:info]
+
+    @@log.formatter = proc do |severity, datetime, _progname, msg|
+      LOG_FORMAT % [severity, datetime.strftime(TIME_FORMAT), msg]
     end
 
     def log(msg, severity = :info)
diff --git a/config/application.rb b/config/application.rb
index 0e98a378..4b987005 100644
--- a/config/application.rb
+++ b/config/application.rb
@@ -1,10 +1,12 @@
 require_relative 'boot'
-
 require 'rails/all'
 require 'assembly-utils'
+
 # Require the gems listed in Gemfile, including any gems
 # you've limited to :test, :development, or :production.
 Bundler.require(*Rails.groups)
+
+
 def noko_doc(x)
   Nokogiri.XML(x) { |conf| conf.default_xml.noblanks }
 end
@@ -18,5 +20,7 @@ class Application < Rails::Application
     # Application configuration can go into files in config/initializers
     # -- all .rb files in that directory are automatically loaded after loading
     # the framework and any gems in your application.
+
   end
+  UnknownError = Class.new(StandardError)
 end
diff --git a/config/boot.rb b/config/boot.rb
index 95ac963d..719172d5 100644
--- a/config/boot.rb
+++ b/config/boot.rb
@@ -4,26 +4,11 @@
 
 require 'rubygems'
 require 'bundler/setup'
-require 'logger'
 
 environment = ENV['RAILS_ENV'] || 'development'
 PRE_ASSEMBLY_ROOT = File.expand_path(File.dirname(__FILE__) + '/..')
 CERT_DIR = File.join(File.dirname(__FILE__), ".", "certs")
 
-# General DLSS infrastructure.
-require 'dor-services'
-
 # Environment.
 # ENV_FILE = PRE_ASSEMBLY_ROOT + "/config/cli_environments/#{environment}.rb"
 require_relative "cli_environments/#{environment}.rb"
-Dor::Config.dor_services.url ||= Dor::Config.dor.service_root
-
-# Project dir in load path.
-$LOAD_PATH.unshift(PRE_ASSEMBLY_ROOT + '/lib')
-
-# Set up project logger.
-require 'pre_assembly/logging'
-PreAssembly::Logging.setup PRE_ASSEMBLY_ROOT, environment
-
-# Load the project and its dependencies.
-require 'pre_assembly'
\ No newline at end of file
diff --git a/config/cli_environments/test.rb b/config/cli_environments/test.rb
index ff7d397b..c0ff41a2 100644
--- a/config/cli_environments/test.rb
+++ b/config/cli_environments/test.rb
@@ -1,3 +1,5 @@
+require 'dor-services'
+
 Dor::Config.configure do
   dor do
     service_root 'https://example.com/dor/v1'
diff --git a/config/initializers/dor_workflow_service.rb b/config/initializers/dor_workflow_service.rb
index 58c7264a..201dd85e 100644
--- a/config/initializers/dor_workflow_service.rb
+++ b/config/initializers/dor_workflow_service.rb
@@ -1,5 +1,9 @@
+require 'dor-services'
 require 'dor-workflow-service'
+
+Dor::Config.dor_services.url ||= Dor::Config.dor.service_root
 Dor::WorkflowService.configure(
   Settings.workflow_services_url,
   :dor_services_url => Dor::Config.dor_services.url.gsub('/v1', '')
 )
+

From 29de6e42f9ad96991374efd7488e4db35ca69a71 Mon Sep 17 00:00:00 2001
From: Sarav Shah <saravsshah@gmail.com>
Date: Tue, 28 Aug 2018 14:08:03 -0700
Subject: [PATCH 08/10] constant refactoring, smpl_spec refactor and some
 namespacing issues

---
 Gemfile                                       |  1 -
 app/lib/pre_assembly.rb                       | 16 +----
 app/lib/pre_assembly/digital_object.rb        | 17 +++++-
 .../{smpl_precontent_metadata.rb => smpl.rb}  |  0
 ..._project_specific_spec.rb => smpl_spec.rb} | 10 ++--
 .../test_data/logging/progress_log_file.yml   | 60 +++++++++++++++++++
 6 files changed, 81 insertions(+), 23 deletions(-)
 rename app/lib/pre_assembly/{smpl_precontent_metadata.rb => smpl.rb} (100%)
 rename spec/lib/pre_assembly/{smpl_project_specific_spec.rb => smpl_spec.rb} (94%)

diff --git a/Gemfile b/Gemfile
index f5604bc9..d2ba9ba4 100644
--- a/Gemfile
+++ b/Gemfile
@@ -51,7 +51,6 @@ group :development do
 end
 
 group :development, :test do
-  gem 'rspec-rails'
   gem 'byebug'
   gem 'rspec-rails', '~> 3.7'
   gem 'rubocop', '~> 0.58'
diff --git a/app/lib/pre_assembly.rb b/app/lib/pre_assembly.rb
index 880fa91d..3e06403a 100644
--- a/app/lib/pre_assembly.rb
+++ b/app/lib/pre_assembly.rb
@@ -1,8 +1,7 @@
 require 'fileutils'
 require 'erb'
 
-# these are the names of special datastream files that will be staged in the 'metadata' folder instead of the 'content' folder
-METADATA_FILES = ['descMetadata.xml', 'contentMetadata.xml'].map(&:downcase)
+
 
 # auto require any project specific files
 Dir[File.dirname(__FILE__) + '/pre_assembly/project/*.rb'].each { |file| require "pre_assembly/project/#{File.basename(file)}" }
@@ -11,16 +10,3 @@
 require 'assembly-image'
 require 'rest_client'
 require 'honeybadger'
-
-# map the content type tags set inside an object to content metadata creation styles supported by the assembly-objectfile gem
-# format is 'tag_value' => 'gem style name'
-CONTENT_TYPE_TAG_MAPPING = {
-  'Image' => :simple_image,
-  'File' => :file,
-  'Book (flipbook, ltr)' => :simple_book,
-  'Book (image-only)' => :book_as_image,
-  'Manuscript (flipbook, ltr)' => :simple_book,
-  'Manuscript (image-only)' => :book_as_image,
-  'Map' => :map
-}
- 
\ No newline at end of file
diff --git a/app/lib/pre_assembly/digital_object.rb b/app/lib/pre_assembly/digital_object.rb
index 9902852f..0f5f2a66 100644
--- a/app/lib/pre_assembly/digital_object.rb
+++ b/app/lib/pre_assembly/digital_object.rb
@@ -76,11 +76,22 @@ def stager(source, destination)
 
     # set this object's content_md_creation_style
     def content_md_creation_style
+      # map the content type tags set inside an object to content metadata creation styles supported by the assembly-objectfile gem
+      # format is 'tag_value' => 'gem style name'
+      content_type_tag_mapping = {
+        'Image' => :simple_image,
+        'File' => :file,
+        'Book (flipbook, ltr)' => :simple_book,
+        'Book (image-only)' => :book_as_image,
+        'Manuscript (flipbook, ltr)' => :simple_book,
+        'Manuscript (image-only)' => :book_as_image,
+        'Map' => :map
+      }
       # if this object needs to be registered or has no content type tag for a registered object, use the default set in the YAML file
       if !project_style[:content_tag_override] || content_type_tag.blank?
         default_content_md_creation_style
       else # if the object is already registered and there is a content type tag and we allow overrides, use it if we know what it means (else use the default)
-        CONTENT_TYPE_TAG_MAPPING[content_type_tag] || default_content_md_creation_style
+        content_type_tag_mapping[content_type_tag] || default_content_md_creation_style
       end
     end
 
@@ -196,12 +207,14 @@ def prepare_for_reaccession
     # Create the druid tree within the staging directory,
     # and then copy-recursive all stageable items to that area.
     def stage_files
+      # these are the names of special datastream files that will be staged in the 'metadata' folder instead of the 'content' folder
+      metadata_files = ['descMetadata.xml', 'contentMetadata.xml'].map(&:downcase)
       log "    - staging(druid_tree_dir = #{druid_tree_dir.inspect})"
       create_object_directories
       stageable_items.each do |si_path|
         log "      - staging(#{si_path}, #{content_dir})", :debug
         # determine destination of staged file by looking to see if it is a known datastream XML file or not
-        destination = METADATA_FILES.include?(File.basename(si_path).downcase) ? metadata_dir : content_dir
+        destination = metadata_files.include?(File.basename(si_path).downcase) ? metadata_dir : content_dir
         stager si_path, destination
       end
     end
diff --git a/app/lib/pre_assembly/smpl_precontent_metadata.rb b/app/lib/pre_assembly/smpl.rb
similarity index 100%
rename from app/lib/pre_assembly/smpl_precontent_metadata.rb
rename to app/lib/pre_assembly/smpl.rb
diff --git a/spec/lib/pre_assembly/smpl_project_specific_spec.rb b/spec/lib/pre_assembly/smpl_spec.rb
similarity index 94%
rename from spec/lib/pre_assembly/smpl_project_specific_spec.rb
rename to spec/lib/pre_assembly/smpl_spec.rb
index 8da682b0..29d037b1 100644
--- a/spec/lib/pre_assembly/smpl_project_specific_spec.rb
+++ b/spec/lib/pre_assembly/smpl_spec.rb
@@ -1,11 +1,11 @@
-describe PreAssembly::DigitalObject do
+describe PreAssembly::Smpl do
   let(:bundle_dir) { File.join(PRE_ASSEMBLY_ROOT, 'spec/test_data/bundle_input_e') }
 
   describe 'SMPL content metadata generation and techMetadata generation - no thumb declaration' do
     let(:dobj1) { setup_dobj('aa111aa1111', smpl_manifest) }
     let(:dobj2) { setup_dobj('bb222bb2222', smpl_manifest) }
     let(:smpl_manifest) do
-      PreAssembly::Smpl.new(:csv_filename => 'smpl_manifest.csv', :bundle_dir => bundle_dir, :verbose => false)
+      described_class.new(:csv_filename => 'smpl_manifest.csv', :bundle_dir => bundle_dir, :verbose => false)
     end
 
     it "generates technicalMetadata for SMPL by combining all existing _techmd.xml files" do
@@ -29,7 +29,7 @@
 
   describe 'SMPL content metadata generation with thumb declaration' do
     it "generates content metadata from a SMPL manifest with a thumb column set to yes" do
-      smpl_manifest = PreAssembly::Smpl.new(:csv_filename => 'smpl_manifest_with_thumb.csv', :bundle_dir => bundle_dir, :verbose => false)
+      smpl_manifest = described_class.new(:csv_filename => 'smpl_manifest_with_thumb.csv', :bundle_dir => bundle_dir, :verbose => false)
       dobj1 = setup_dobj('aa111aa1111', smpl_manifest)
       dobj2 = setup_dobj('bb222bb2222', smpl_manifest)
       dobj1.create_content_metadata
@@ -39,7 +39,7 @@
     end
 
     it "generates content metadata from a SMPL manifest with a thumb column set to true" do
-      smpl_manifest = PreAssembly::Smpl.new(:csv_filename => 'smpl_manifest_with_thumb_true.csv', :bundle_dir => bundle_dir, :verbose => false)
+      smpl_manifest = described_class.new(:csv_filename => 'smpl_manifest_with_thumb_true.csv', :bundle_dir => bundle_dir, :verbose => false)
       dobj1 = setup_dobj('aa111aa1111', smpl_manifest)
       dobj2 = setup_dobj('bb222bb2222', smpl_manifest)
       dobj1.create_content_metadata
@@ -49,7 +49,7 @@
     end
 
     it "generates content metadata from a SMPL manifest with no thumbs when the thumb column is set to no" do
-      smpl_manifest = PreAssembly::Smpl.new(:csv_filename => 'smpl_manifest_thumb_no.csv', :bundle_dir => bundle_dir, :verbose => false)
+      smpl_manifest = described_class.new(:csv_filename => 'smpl_manifest_thumb_no.csv', :bundle_dir => bundle_dir, :verbose => false)
       dobj1 = setup_dobj('aa111aa1111', smpl_manifest)
       dobj2 = setup_dobj('bb222bb2222', smpl_manifest)
       dobj1.create_content_metadata
diff --git a/spec/lib/test_data/logging/progress_log_file.yml b/spec/lib/test_data/logging/progress_log_file.yml
index f1246de0..6bc13cde 100644
--- a/spec/lib/test_data/logging/progress_log_file.yml
+++ b/spec/lib/test_data/logging/progress_log_file.yml
@@ -13,3 +13,63 @@
 :remediate_completed: 
 :message: 
 :timestamp: 2018-08-27 16:11:03.600040000 -07:00
+---
+:pid: druid:cs575bk5522
+:remediate_completed: 
+:message: 
+:timestamp: 2018-08-27 17:03:36.797315000 -07:00
+---
+:pid: druid:cs575bk5522
+:remediate_completed: 
+:message: 
+:timestamp: 2018-08-27 17:05:55.928477000 -07:00
+---
+:pid: druid:cs575bk5522
+:remediate_completed: 
+:message: 
+:timestamp: 2018-08-27 17:07:21.346747000 -07:00
+---
+:pid: druid:cs575bk5522
+:remediate_completed: 
+:message: 
+:timestamp: 2018-08-27 17:26:25.149300000 -07:00
+---
+:pid: druid:cs575bk5522
+:remediate_completed: 
+:message: 
+:timestamp: 2018-08-27 17:27:31.306870000 -07:00
+---
+:pid: druid:cs575bk5522
+:remediate_completed: 
+:message: 
+:timestamp: 2018-08-27 17:32:39.690777000 -07:00
+---
+:pid: druid:cs575bk5522
+:remediate_completed: 
+:message: 
+:timestamp: 2018-08-28 13:00:37.348480000 -07:00
+---
+:pid: druid:cs575bk5522
+:remediate_completed: 
+:message: 
+:timestamp: 2018-08-28 13:30:52.842153000 -07:00
+---
+:pid: druid:cs575bk5522
+:remediate_completed: 
+:message: 
+:timestamp: 2018-08-28 13:56:51.193539000 -07:00
+---
+:pid: druid:cs575bk5522
+:remediate_completed: 
+:message: 
+:timestamp: 2018-08-28 14:01:18.897071000 -07:00
+---
+:pid: druid:cs575bk5522
+:remediate_completed: 
+:message: 
+:timestamp: 2018-08-28 14:02:33.204399000 -07:00
+---
+:pid: druid:cs575bk5522
+:remediate_completed: 
+:message: 
+:timestamp: 2018-08-28 14:03:13.650553000 -07:00

From 9482e33e2c50b6c5fba9fcaa406fefedc4e85b7b Mon Sep 17 00:00:00 2001
From: Sarav Shah <saravsshah@gmail.com>
Date: Tue, 28 Aug 2018 14:28:16 -0700
Subject: [PATCH 09/10] update gemfile lock

---
 Gemfile.lock | 1 -
 1 file changed, 1 deletion(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index 5a69a2c4..4c78368f 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -509,7 +509,6 @@ DEPENDENCIES
   rest-client
   retries
   roo
-  rspec (~> 3.0)
   rspec-rails (~> 3.7)
   rubocop (~> 0.58)
   rubocop-rspec

From 2ac2239b266c79d68f0e9b98f17d39c076959f71 Mon Sep 17 00:00:00 2001
From: Sarav Shah <saravsshah@gmail.com>
Date: Tue, 28 Aug 2018 17:04:34 -0700
Subject: [PATCH 10/10] Add coveralls back, remove unwanted autoloading in
 pre_assembly.rb and add file to gitignore

---
 .gitignore                                    |  1 +
 app/lib/pre_assembly.rb                       |  7 --
 config/boot.rb                                |  3 -
 config/cli_environments/test.rb               |  1 -
 spec/lib/pre_assembly/bundle_spec.rb          |  2 +-
 .../lib/pre_assembly/remediation/item_spec.rb | 12 ++-
 .../test_data/logging/progress_log_file.yml   | 75 -------------------
 spec/rails_helper.rb                          |  2 +
 spec/spec_helper.rb                           |  1 -
 9 files changed, 13 insertions(+), 91 deletions(-)
 delete mode 100644 spec/lib/test_data/logging/progress_log_file.yml

diff --git a/.gitignore b/.gitignore
index 937de7c7..5cfbd00b 100644
--- a/.gitignore
+++ b/.gitignore
@@ -20,6 +20,7 @@ tags
 tmp
 /workflow_service.log*
 coverage
+spec/lib/test_data/logging/progress_log_file.yml
 
 # Ignore master key for decrypting credentials and more.
 /config/master.key
diff --git a/app/lib/pre_assembly.rb b/app/lib/pre_assembly.rb
index 3e06403a..050e00fe 100644
--- a/app/lib/pre_assembly.rb
+++ b/app/lib/pre_assembly.rb
@@ -1,12 +1,5 @@
 require 'fileutils'
 require 'erb'
-
-
-
-# auto require any project specific files
-Dir[File.dirname(__FILE__) + '/pre_assembly/project/*.rb'].each { |file| require "pre_assembly/project/#{File.basename(file)}" }
-
-require 'assembly-utils'
 require 'assembly-image'
 require 'rest_client'
 require 'honeybadger'
diff --git a/config/boot.rb b/config/boot.rb
index 719172d5..9493f53c 100644
--- a/config/boot.rb
+++ b/config/boot.rb
@@ -1,14 +1,11 @@
 ENV['BUNDLE_GEMFILE'] ||= File.expand_path('../Gemfile', __dir__)
 
 require 'bundler/setup' # Set up gems listed in the Gemfile.
-
 require 'rubygems'
-require 'bundler/setup'
 
 environment = ENV['RAILS_ENV'] || 'development'
 PRE_ASSEMBLY_ROOT = File.expand_path(File.dirname(__FILE__) + '/..')
 CERT_DIR = File.join(File.dirname(__FILE__), ".", "certs")
 
 # Environment.
-# ENV_FILE = PRE_ASSEMBLY_ROOT + "/config/cli_environments/#{environment}.rb"
 require_relative "cli_environments/#{environment}.rb"
diff --git a/config/cli_environments/test.rb b/config/cli_environments/test.rb
index c0ff41a2..bbaba74c 100644
--- a/config/cli_environments/test.rb
+++ b/config/cli_environments/test.rb
@@ -1,5 +1,4 @@
 require 'dor-services'
-
 Dor::Config.configure do
   dor do
     service_root 'https://example.com/dor/v1'
diff --git a/spec/lib/pre_assembly/bundle_spec.rb b/spec/lib/pre_assembly/bundle_spec.rb
index cf647077..7b290df7 100644
--- a/spec/lib/pre_assembly/bundle_spec.rb
+++ b/spec/lib/pre_assembly/bundle_spec.rb
@@ -49,7 +49,7 @@ def bundle_setup(bundle_context)
 
   describe '#load_skippables' do
     it "does nothing if @resume is false" do
-      rumsey.resume = false
+      allow(rumsey).to receive(:resume).and_return(false)
       expect(rumsey.load_skippables).to be_nil
     end
 
diff --git a/spec/lib/pre_assembly/remediation/item_spec.rb b/spec/lib/pre_assembly/remediation/item_spec.rb
index b0b132ca..64b45a05 100644
--- a/spec/lib/pre_assembly/remediation/item_spec.rb
+++ b/spec/lib/pre_assembly/remediation/item_spec.rb
@@ -9,13 +9,19 @@
   end
 
   context 'logging' do
-    let(:log_dir) { File.join(File.dirname(__FILE__), "../../test_data/logging") }
+    let(:log_dir) { File.join(Rails.root, "spec/lib/test_data/logging") }
     let(:csv_filename) { log_dir + "/csv_log.csv" }
     let(:progress_log_file) { log_dir + "/progress_log_file.yml" }
 
-    before { Dir.mkdir(log_dir) unless Dir.exist?(log_dir) }
+    before do
+      FileUtils.mkdir_p(log_dir) unless Dir.exist?(log_dir)
+      FileUtils.touch progress_log_file
+    end
 
-    after { File.delete(csv_filename) if File.exist?(csv_filename) }
+    after do
+      File.delete(csv_filename) if File.exist?(csv_filename)
+      FileUtils.rm_f(progress_log_file) # cleanup
+    end
 
     it "ensures a log file exists" do
       File.delete(csv_filename) if File.exist?(csv_filename)
diff --git a/spec/lib/test_data/logging/progress_log_file.yml b/spec/lib/test_data/logging/progress_log_file.yml
deleted file mode 100644
index 6bc13cde..00000000
--- a/spec/lib/test_data/logging/progress_log_file.yml
+++ /dev/null
@@ -1,75 +0,0 @@
----
-:pid: druid:cs575bk5522
-:remediate_completed: 
-:message: 
-:timestamp: 2018-08-27 15:09:13.779278000 -07:00
----
-:pid: druid:cs575bk5522
-:remediate_completed: 
-:message: 
-:timestamp: 2018-08-27 15:10:55.044887000 -07:00
----
-:pid: druid:cs575bk5522
-:remediate_completed: 
-:message: 
-:timestamp: 2018-08-27 16:11:03.600040000 -07:00
----
-:pid: druid:cs575bk5522
-:remediate_completed: 
-:message: 
-:timestamp: 2018-08-27 17:03:36.797315000 -07:00
----
-:pid: druid:cs575bk5522
-:remediate_completed: 
-:message: 
-:timestamp: 2018-08-27 17:05:55.928477000 -07:00
----
-:pid: druid:cs575bk5522
-:remediate_completed: 
-:message: 
-:timestamp: 2018-08-27 17:07:21.346747000 -07:00
----
-:pid: druid:cs575bk5522
-:remediate_completed: 
-:message: 
-:timestamp: 2018-08-27 17:26:25.149300000 -07:00
----
-:pid: druid:cs575bk5522
-:remediate_completed: 
-:message: 
-:timestamp: 2018-08-27 17:27:31.306870000 -07:00
----
-:pid: druid:cs575bk5522
-:remediate_completed: 
-:message: 
-:timestamp: 2018-08-27 17:32:39.690777000 -07:00
----
-:pid: druid:cs575bk5522
-:remediate_completed: 
-:message: 
-:timestamp: 2018-08-28 13:00:37.348480000 -07:00
----
-:pid: druid:cs575bk5522
-:remediate_completed: 
-:message: 
-:timestamp: 2018-08-28 13:30:52.842153000 -07:00
----
-:pid: druid:cs575bk5522
-:remediate_completed: 
-:message: 
-:timestamp: 2018-08-28 13:56:51.193539000 -07:00
----
-:pid: druid:cs575bk5522
-:remediate_completed: 
-:message: 
-:timestamp: 2018-08-28 14:01:18.897071000 -07:00
----
-:pid: druid:cs575bk5522
-:remediate_completed: 
-:message: 
-:timestamp: 2018-08-28 14:02:33.204399000 -07:00
----
-:pid: druid:cs575bk5522
-:remediate_completed: 
-:message: 
-:timestamp: 2018-08-28 14:03:13.650553000 -07:00
diff --git a/spec/rails_helper.rb b/spec/rails_helper.rb
index 7413a13c..24fe06d3 100644
--- a/spec/rails_helper.rb
+++ b/spec/rails_helper.rb
@@ -7,6 +7,8 @@
 require 'rspec/rails'
 # Add additional requires below this line. Rails is not loaded until this point!
 
+require 'coveralls'
+Coveralls.wear!('rails')
 # auto-require all ruby files in the support directory
 Dir[Rails.root.join('spec', 'support', '*.rb')].each { |f| require f }
 
diff --git a/spec/spec_helper.rb b/spec/spec_helper.rb
index 45bd3f30..4ca49fb0 100644
--- a/spec/spec_helper.rb
+++ b/spec/spec_helper.rb
@@ -2,7 +2,6 @@
 require 'equivalent-xml/rspec_matchers'
 require 'byebug'
 
-
 RSpec.configure do |config|
 
   # rspec-expectations config goes here. You can use an alternate