From 54bf5d7035ffd00ebbd2d219e5db644855b388fb Mon Sep 17 00:00:00 2001
From: Kirk Wang <kirk.wang@scientist.com>
Date: Tue, 17 Sep 2024 11:04:06 -0700
Subject: [PATCH 1/5] =?UTF-8?q?=F0=9F=8E=81=20Implement=20all=5Ftext=20sea?=
 =?UTF-8?q?rching=20in=20Valkyrie=20for=20PDF?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

This commit will introduce the Hyku::Indexers::FileSetIndexer to add
indexing logic for born digital PDFs when using PDF.js.  We also change
the works' indexing field to match the file sets' indexing field
(all_text_tsimv).  We also "valyrized" the logic in the HykuIndexing
module to accomplish this.

Ref:
- https://github.com/scientist-softserv/adventist_knapsack/issues/769
---
 app/controllers/catalog_controller.rb         |  8 +++-
 app/indexers/concerns/hyku_indexing.rb        |  2 +-
 .../hyku/indexers/file_set_indexer.rb         | 42 +++++++++++++++++++
 config/initializers/hyrax.rb                  |  2 +
 4 files changed, 51 insertions(+), 3 deletions(-)
 create mode 100644 app/indexers/hyku/indexers/file_set_indexer.rb

diff --git a/app/controllers/catalog_controller.rb b/app/controllers/catalog_controller.rb
index 01940996a..fcf381063 100644
--- a/app/controllers/catalog_controller.rb
+++ b/app/controllers/catalog_controller.rb
@@ -41,7 +41,7 @@ def self.uploaded_field
 
     # IiifPrint index fields
     config.add_index_field 'all_text_timv'
-    config.add_index_field 'file_set_text_tsimv', label: "Item contents", highlight: true, helper_method: :render_ocr_snippets
+    config.add_index_field 'all_text_tsimv', label: "Item contents", highlight: true, helper_method: :render_ocr_snippets, if: :query_present?
 
     # configuration for Blacklight IIIF Content Search
     config.iiif_search = {
@@ -83,7 +83,7 @@ def self.uploaded_field
       rows: 10,
       qf: (
         IiifPrint.config.metadata_fields.keys.map { |attribute| "#{attribute}_tesim" } +
-        ["title_tesim", "description_tesim", "all_text_timv", "file_set_text_tsimv"]
+        ["title_tesim", "description_tesim", "all_text_timv", "all_text_tsimv"]
       ).uniq.join(' '),
       "hl": true,
       "hl.simple.pre": "<span class='highlight'>",
@@ -638,5 +638,9 @@ def show
   def render_bookmarks_control?
     false
   end
+
+  def query_present?
+    params[:q].present?
+  end
 end
 # rubocop:enable Metrics/ClassLength, Metrics/BlockLength
diff --git a/app/indexers/concerns/hyku_indexing.rb b/app/indexers/concerns/hyku_indexing.rb
index 41a834a90..5747a01cb 100644
--- a/app/indexers/concerns/hyku_indexing.rb
+++ b/app/indexers/concerns/hyku_indexing.rb
@@ -22,7 +22,7 @@ module HykuIndexing
         solr_doc['valkyrie_bsi'] = object.kind_of?(Valkyrie::Resource)
         solr_doc['member_ids_ssim'] = object.member_ids.map(&:id) if object.kind_of?(Valkyrie::Resource)
         # TODO: Reinstate once valkyrie fileset work is complete - https://github.com/scientist-softserv/hykuup_knapsack/issues/34
-        solr_doc['all_text_tsimv'] = full_text(object.file_sets.first&.id) if object.kind_of?(ActiveFedora::Base)
+        solr_doc['all_text_tsimv'] = full_text(Hyrax.custom_queries.find_child_file_sets(resource: resource).first.id.to_s)
         # rubocop:enable Style/ClassCheck
         solr_doc['title_ssim'] = SortTitle.new(object.title.first).alphabetical
         solr_doc['depositor_ssi'] = object.depositor
diff --git a/app/indexers/hyku/indexers/file_set_indexer.rb b/app/indexers/hyku/indexers/file_set_indexer.rb
new file mode 100644
index 000000000..a7cd8f319
--- /dev/null
+++ b/app/indexers/hyku/indexers/file_set_indexer.rb
@@ -0,0 +1,42 @@
+# frozen_string_literal: true
+
+module Hyku
+  module Indexers
+    class FileSetIndexer < Hyrax::Indexers::FileSetIndexer
+      include Hyrax::Indexer(:bulkrax_metadata)
+      include Hyrax::Indexer(:hyku_file_set_metadata)
+
+      def to_solr
+        return super unless Flipflop.default_pdf_viewer?
+
+        super.tap do |solr_doc|
+          solr_doc['all_text_timv'] = solr_doc['all_text_tsimv'] = pdf_text
+        end
+      end
+
+      private
+
+      # rubocop:disable Metrics/MethodLength
+      def pdf_text
+        return unless resource.original_file.pdf?
+        return unless resource.original_file&.content.is_a? String
+
+        begin
+          text = IO.popen(['pdftotext', '-', '-'], 'r+b') do |pdftotext|
+            pdftotext.write(resource.original_file.content)
+            pdftotext.close_write
+            pdftotext.read
+          end
+
+          text.tr("\n", ' ')
+              .squeeze(' ')
+              .encode('UTF-8', 'binary', invalid: :replace, undef: :replace, replace: '') # remove non-UTF-8 characters
+        rescue Errno::ENOENT => e
+          raise e unless e.message.include?("No such file or directory - pdftotext")
+          Rails.logger.warn("`pdfinfo' is not installed; unable to extract text from the PDF's content")
+        end
+      end
+      # rubocop:enable Metrics/MethodLength
+    end
+  end
+end
diff --git a/config/initializers/hyrax.rb b/config/initializers/hyrax.rb
index 01d5fe380..f45a40cb1 100644
--- a/config/initializers/hyrax.rb
+++ b/config/initializers/hyrax.rb
@@ -242,6 +242,8 @@
   # essence a "super" method.
   original_translator = config.translate_id_to_uri
   config.translate_id_to_uri = ->(id) { original_translator.call(id.to_s) }
+
+  config.file_set_indexer = Hyku::Indexers::FileSetIndexer
 end
 # rubocop:enable Metrics/BlockLength
 

From b666d84b9b33d1fa5f7a41ac11be3c7ba565fc22 Mon Sep 17 00:00:00 2001
From: Kirk Wang <kirk.wang@scientist.com>
Date: Tue, 17 Sep 2024 11:48:58 -0700
Subject: [PATCH 2/5] =?UTF-8?q?=F0=9F=8E=81=20Add=20logic=20for=20snippets?=
 =?UTF-8?q?=20when=20splitting=20PDFs?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

This commit will add logic to add the ability to see search snippets
with PDFs that were split through IIIF Print.
---
 app/indexers/concerns/hyku_indexing.rb | 33 +++++++++++++++++++++++---
 1 file changed, 30 insertions(+), 3 deletions(-)

diff --git a/app/indexers/concerns/hyku_indexing.rb b/app/indexers/concerns/hyku_indexing.rb
index 5747a01cb..51a7f2f64 100644
--- a/app/indexers/concerns/hyku_indexing.rb
+++ b/app/indexers/concerns/hyku_indexing.rb
@@ -22,7 +22,7 @@ module HykuIndexing
         solr_doc['valkyrie_bsi'] = object.kind_of?(Valkyrie::Resource)
         solr_doc['member_ids_ssim'] = object.member_ids.map(&:id) if object.kind_of?(Valkyrie::Resource)
         # TODO: Reinstate once valkyrie fileset work is complete - https://github.com/scientist-softserv/hykuup_knapsack/issues/34
-        solr_doc['all_text_tsimv'] = full_text(Hyrax.custom_queries.find_child_file_sets(resource: resource).first.id.to_s)
+        solr_doc['all_text_tsimv'] = full_text(object)
         # rubocop:enable Style/ClassCheck
         solr_doc['title_ssim'] = SortTitle.new(object.title.first).alphabetical
         solr_doc['depositor_ssi'] = object.depositor
@@ -38,12 +38,39 @@ module HykuIndexing
 
   private
 
-  def full_text(file_set_id)
-    return if !Flipflop.default_pdf_viewer? || file_set_id.blank?
+  def full_text(object)
+    child_works = Hyrax.custom_queries.find_child_works(resource: object)
+
+    if child_works.empty?
+      extract_text_from_pdf_directly(object)
+    else
+      file_set_texts = child_works_file_sets(child_works).map { |fs| all_text(fs) }.select(&:present?)
+      if file_set_texts.join.blank?
+        extract_text_from_pdf_directly(object)
+      else
+        file_set_texts.join("\n---------------------------\n")
+      end
+    end
+  end
+
+  def extract_text_from_pdf_directly(object)
+    file_set_id = Hyrax.custom_queries.find_child_file_sets(resource: object).first&.id&.to_s
+    return if file_set_id.blank?
 
     SolrDocument.find(file_set_id)['all_text_tsimv']
   end
 
+  def child_works_file_sets(child_works)
+    child_works.map { |child_work| Hyrax.custom_queries.find_child_file_sets(resource: child_work) }.flatten
+  end
+
+  def all_text(fs)
+    text = IiifPrint::Data::WorkDerivatives.data(from: fs, of_type: 'txt') || ''
+    return text if text.empty?
+
+    text.tr("\n", ' ').squeeze(' ')
+  end
+
   def add_date(solr_doc)
     date_string = solr_doc['date_created_tesim']&.first
     return unless date_string

From 9aa21fc2726107ed0cbf73b793baaeaf4a2f4232 Mon Sep 17 00:00:00 2001
From: Kirk Wang <kirk.wang@scientist.com>
Date: Wed, 18 Sep 2024 08:53:35 -0700
Subject: [PATCH 3/5] =?UTF-8?q?=E2=9C=85=20Add=20test=20for=20file=20set?=
 =?UTF-8?q?=20indexer=20logic?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

This commit will add a simple test for the FileSetIndexer logic to check
that the text extraction from a born digital pdf works as expected.
---
 spec/fixtures/pdf/pdf_sample.pdf              | Bin 0 -> 13264 bytes
 .../hyku/indexers/file_set_indexer_spec.rb    |  23 ++++++++++++++++++
 2 files changed, 23 insertions(+)
 create mode 100644 spec/fixtures/pdf/pdf_sample.pdf
 create mode 100644 spec/indexers/hyku/indexers/file_set_indexer_spec.rb

diff --git a/spec/fixtures/pdf/pdf_sample.pdf b/spec/fixtures/pdf/pdf_sample.pdf
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literal 0
HcmV?d00001

diff --git a/spec/indexers/hyku/indexers/file_set_indexer_spec.rb b/spec/indexers/hyku/indexers/file_set_indexer_spec.rb
new file mode 100644
index 000000000..5d0fef968
--- /dev/null
+++ b/spec/indexers/hyku/indexers/file_set_indexer_spec.rb
@@ -0,0 +1,23 @@
+# frozen_string_literal: true
+
+RSpec.describe Hyku::Indexers::FileSetIndexer do
+  let(:indexer_class) { described_class }
+  let(:resource)      { Hyrax.config.file_set_model.constantize.new }
+  let(:original_file) { Hyrax::FileMetadata.new }
+
+  it 'is the configured file set indexer' do
+    expect(Hyrax.config.file_set_indexer).to eq described_class
+  end
+
+  describe '#to_solr' do
+    let(:stream) { File.open('spec/fixtures/pdf/pdf_sample.pdf').read }
+    it 'indexes the text of a pdf that has text already' do
+      allow(Flipflop).to receive(:default_pdf_viewer?).and_return(true)
+      allow(resource).to receive(:original_file).and_return(original_file)
+      allow(original_file).to receive(:pdf?).and_return(true)
+      allow(original_file).to receive(:content).and_return(stream)
+
+      expect(resource.to_solr['all_text_tsimv']).to include('Dummy PDF file')
+    end
+  end
+end

From 685266d84bf3548e436a9503629d4eca72b1cb4c Mon Sep 17 00:00:00 2001
From: Shana Moore <shana@scientist.com>
Date: Wed, 18 Sep 2024 15:30:08 -0700
Subject: [PATCH 4/5] Update app/indexers/concerns/hyku_indexing.rb

---
 app/indexers/concerns/hyku_indexing.rb | 1 -
 1 file changed, 1 deletion(-)

diff --git a/app/indexers/concerns/hyku_indexing.rb b/app/indexers/concerns/hyku_indexing.rb
index 51a7f2f64..7fe0d2b8e 100644
--- a/app/indexers/concerns/hyku_indexing.rb
+++ b/app/indexers/concerns/hyku_indexing.rb
@@ -21,7 +21,6 @@ module HykuIndexing
         solr_doc['account_institution_name_ssim'] = Site.instance.institution_label
         solr_doc['valkyrie_bsi'] = object.kind_of?(Valkyrie::Resource)
         solr_doc['member_ids_ssim'] = object.member_ids.map(&:id) if object.kind_of?(Valkyrie::Resource)
-        # TODO: Reinstate once valkyrie fileset work is complete - https://github.com/scientist-softserv/hykuup_knapsack/issues/34
         solr_doc['all_text_tsimv'] = full_text(object)
         # rubocop:enable Style/ClassCheck
         solr_doc['title_ssim'] = SortTitle.new(object.title.first).alphabetical

From 617bc248e0c66e638cba5ab625b39cdcb891cf9b Mon Sep 17 00:00:00 2001
From: Kirk Wang <kirk.wang@scientist.com>
Date: Wed, 18 Sep 2024 18:23:46 -0700
Subject: [PATCH 5/5] =?UTF-8?q?=E2=9C=85=20Fix=20indexer=20specs?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

This commit will rename the #full_text method to #extract_full_text
because it was causing weird issues with super.
---
 app/indexers/concerns/hyku_indexing.rb         | 4 ++--
 app/indexers/hyku/indexers/file_set_indexer.rb | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/app/indexers/concerns/hyku_indexing.rb b/app/indexers/concerns/hyku_indexing.rb
index 7fe0d2b8e..17073eb6e 100644
--- a/app/indexers/concerns/hyku_indexing.rb
+++ b/app/indexers/concerns/hyku_indexing.rb
@@ -21,7 +21,7 @@ module HykuIndexing
         solr_doc['account_institution_name_ssim'] = Site.instance.institution_label
         solr_doc['valkyrie_bsi'] = object.kind_of?(Valkyrie::Resource)
         solr_doc['member_ids_ssim'] = object.member_ids.map(&:id) if object.kind_of?(Valkyrie::Resource)
-        solr_doc['all_text_tsimv'] = full_text(object)
+        solr_doc['all_text_tsimv'] = extract_full_text(object)
         # rubocop:enable Style/ClassCheck
         solr_doc['title_ssim'] = SortTitle.new(object.title.first).alphabetical
         solr_doc['depositor_ssi'] = object.depositor
@@ -37,7 +37,7 @@ module HykuIndexing
 
   private
 
-  def full_text(object)
+  def extract_full_text(object)
     child_works = Hyrax.custom_queries.find_child_works(resource: object)
 
     if child_works.empty?
diff --git a/app/indexers/hyku/indexers/file_set_indexer.rb b/app/indexers/hyku/indexers/file_set_indexer.rb
index a7cd8f319..febbb2dd7 100644
--- a/app/indexers/hyku/indexers/file_set_indexer.rb
+++ b/app/indexers/hyku/indexers/file_set_indexer.rb
@@ -18,7 +18,7 @@ def to_solr
 
       # rubocop:disable Metrics/MethodLength
       def pdf_text
-        return unless resource.original_file.pdf?
+        return unless resource.original_file&.pdf?
         return unless resource.original_file&.content.is_a? String
 
         begin