[HYC 2115] - NSF Backlog Ingest Utility

app/helpers/work_utils_helper.rb

@@ -7,14 +7,7 @@ def self.fetch_work_data_by_alternate_identifier(identifier)
     admin_set_name = work_data['admin_set_tesim']&.first
     admin_set_data = admin_set_name ? ActiveFedora::SolrService.get("title_tesim:#{admin_set_name} AND has_model_ssim:(\"AdminSet\")", { :rows => 1, 'df' => 'title_tesim'})['response']['docs'].first : {}
     Rails.logger.warn(self.generate_warning_message(admin_set_name, identifier)) if admin_set_data.blank?
-    result = {
-      work_id: work_data['id'],
-      work_type: work_data.dig('has_model_ssim', 0),
-      title: work_data['title_tesim']&.first,
-      admin_set_id: admin_set_data['id'],
-      admin_set_name: admin_set_name,
-      file_set_ids: work_data['file_set_ids_ssim']
-    }
+    result = self.generate_result_hash(work_data, admin_set_data, admin_set_name)
     result.compact.empty? ? nil : result
   end
   def self.fetch_work_data_by_fileset_id(fileset_id)
@@ -24,14 +17,7 @@ def self.fetch_work_data_by_fileset_id(fileset_id)
     admin_set_name = work_data['admin_set_tesim']&.first
     admin_set_data = admin_set_name ? ActiveFedora::SolrService.get("title_tesim:#{admin_set_name} AND has_model_ssim:(\"AdminSet\")", { :rows => 1, 'df' => 'title_tesim'})['response']['docs'].first : {}
     Rails.logger.warn(self.generate_warning_message(admin_set_name, fileset_id, :fileset)) if admin_set_data.blank?
-    result = {
-      work_id: work_data['id'],
-      work_type: work_data.dig('has_model_ssim', 0),
-      title: work_data['title_tesim']&.first,
-      admin_set_id: admin_set_data['id'],
-      admin_set_name: admin_set_name,
-      file_set_ids: work_data['file_set_ids_ssim']
-    }
+    result = self.generate_result_hash(work_data, admin_set_data, admin_set_name)
     result.compact.empty? ? nil : result
   end
   def self.fetch_work_data_by_id(work_id)
@@ -40,14 +26,7 @@ def self.fetch_work_data_by_id(work_id)
     admin_set_name = work_data['admin_set_tesim']&.first
     admin_set_data = admin_set_name ? ActiveFedora::SolrService.get("title_tesim:#{admin_set_name} AND has_model_ssim:(\"AdminSet\")", { :rows => 1, 'df' => 'title_tesim'})['response']['docs'].first : {}
     Rails.logger.warn(self.generate_warning_message(admin_set_name, work_id)) if admin_set_data.blank?
-    result = {
-      work_id: work_data['id'],
-      work_type: work_data.dig('has_model_ssim', 0),
-      title: work_data['title_tesim']&.first,
-      admin_set_id: admin_set_data['id'],
-      admin_set_name: admin_set_name,
-      file_set_ids: work_data['file_set_ids_ssim']
-    }
+    result = self.generate_result_hash(work_data, admin_set_data, admin_set_name)
     result.compact.empty? ? nil : result
   end
 
@@ -58,7 +37,7 @@ def self.fetch_work_data_by_doi(doi)
 
     # Step 2: If that fails, normalize DOI and search identifier_tesim with wildcard
     if work_data.blank?
-      normalized_doi = normalize_if_doi(doi)
+      normalized_doi = normalize_doi(doi)
       if normalized_doi
         fallback_value = "DOI: https://dx.doi.org/#{normalized_doi}"
         fallback_query = "identifier_tesim:\"#{fallback_value}\" NOT has_model_ssim:(\"FileSet\")"
@@ -82,16 +61,28 @@ def self.fetch_work_data_by_doi(doi)
 
     Rails.logger.warn(self.generate_warning_message(admin_set_name, doi, :doi)) if admin_set_data.blank?
 
-    result = {
+    result = self.generate_result_hash(work_data, admin_set_data, admin_set_name)
+    result.compact.empty? ? nil : result
+  end
+
+  def self.generate_result_hash(work_data, admin_set_data, admin_set_name)
+    identifiers = work_data['identifier_tesim'] || []
+
+    pmid  = identifiers.find { |id| id.match?(/\APMID:\s*\d+/i) }&.split(':')&.last&.strip
+    pmcid = identifiers.find { |id| id.match?(/\APMCID:\s*\S+/i) }&.split(':')&.last&.strip
+    doi   = identifiers.find { |id| id.match?(/\ADOI:\s*\S+/i) }&.split(':', 2)&.last&.strip
+
+    {
       work_id: work_data['id'],
       work_type: work_data.dig('has_model_ssim', 0),
       title: work_data['title_tesim']&.first,
       admin_set_id: admin_set_data['id'],
-      admin_set_name: admin_set_name,
-      file_set_ids: work_data['file_set_ids_ssim']
+      admin_set_name: admin_set_data['title_tesim']&.first,
+      file_set_ids: work_data['file_set_ids_ssim'],
+      pmid: pmid,
+      pmcid: pmcid,
+      doi: doi
     }
-
-    result.compact.empty? ? nil : result
   end
 
   def self.get_permissions_attributes(admin_set_id)
@@ -187,7 +178,7 @@ def self.generate_warning_message(admin_set_name, id, concern = :id)
     end
   end
 
-  def self.normalize_if_doi(identifier)
+  def self.normalize_doi(identifier)
     return identifier unless identifier.is_a?(String)
     # Strip prefix if it's a full DOI URL
     if identifier.match?(%r{\Ahttps?://(dx\.)?doi\.org/}i)
@@ -199,5 +190,27 @@ def self.normalize_if_doi(identifier)
     end
   end
 
+  # Wrapper to find best work match by trying each alternate identifier in order
+  def self.find_best_work_match_by_alternate_id(doi: nil, pmcid: nil, pmid: nil)
+    alt_ids = { doi: doi, pmcid: pmcid, pmid: pmid }.compact
+    return nil if alt_ids.empty?
+
+    alt_ids.each do |key, id|
+      next if id.blank?
+
+      work_data =
+        case key.to_s
+        when 'doi'
+          WorkUtilsHelper.fetch_work_data_by_doi(id)
+        else
+          WorkUtilsHelper.fetch_work_data_by_alternate_identifier(id)
+        end
+
+      return work_data if work_data.present?
+    end
+
+    nil
+  end
+
   private_class_method :build_cdr_url, :log_and_nil, :generate_warning_message
 end

app/mailers/base_ingest_report_mailer.rb

@@ -0,0 +1,26 @@
+# frozen_string_literal: true
+class BaseIngestReportMailer < ApplicationMailer
+  def ingest_report_email(report:, zip_path:, template_name:)
+    if zip_path.blank? || !File.exist?(zip_path)
+      LogUtilsHelper.double_log(
+        'No ZIP provided for attachment; sending email without attachments.',
+        :warn,
+        tag: "#{template_name}_report_email"
+      )
+    else
+      attachments[File.basename(zip_path)] = File.read(zip_path)
+      LogUtilsHelper.double_log(
+        "Attached ZIP file: #{zip_path}",
+        :info,
+        tag: "#{template_name}_report_email"
+      )
+    end
+
+    @report = report
+    mail(
+      to: report[:to] || '[email protected]',
+      subject: report[:subject],
+      template_name: template_name
+    )
+  end
+end

app/mailers/nsf_report_mailer.rb

@@ -0,0 +1,10 @@
+# frozen_string_literal: true
+class NSFReportMailer < BaseIngestReportMailer
+  def nsf_report_email(report:, zip_path: nil)
+    ingest_report_email(
+      report: report,
+      zip_path: zip_path,
+      template_name: 'nsf_report_email'
+    )
+  end
+end

app/mailers/pubmed_report_mailer.rb

@@ -1,19 +1,10 @@
 # frozen_string_literal: true
-class PubmedReportMailer < ApplicationMailer
-  def pubmed_report_email(report)
-    @report = report
-    mail(to: '[email protected]', subject: report[:subject])
-  end
-
-  def truncated_pubmed_report_email(report, zip_path)
-    if zip_path.blank? || !File.exist?(zip_path)
-      LogUtilsHelper.double_log('No ZIP provided for attachment; sending email without attachments.', :warn, tag: 'truncated_pubmed_report_email')
-    else
-      attachments[File.basename(zip_path)] = File.read(zip_path)
-      LogUtilsHelper.double_log("Attached ZIP file: #{zip_path}", :info, tag: 'truncated_pubmed_report_email')
-    end
-
-    @report = report
-    mail(to: '[email protected]', subject: report[:subject], template_name: 'pubmed_report_email')
+class PubmedReportMailer < BaseIngestReportMailer
+  def pubmed_report_email(report:, zip_path: nil)
+    ingest_report_email(
+      report: report,
+      zip_path: zip_path,
+      template_name: 'pubmed_report_email'
+    )
   end
 end

app/services/tasks/dimensions_ingest_service.rb

@@ -1,8 +1,8 @@
 # frozen_string_literal: true
 module Tasks
-  require 'tasks/ingest_helper'
+  require 'tasks/ingest_helper_utils/ingest_helper'
   class DimensionsIngestService
-    include Tasks::IngestHelper
+    include Tasks::IngestHelperUtils::IngestHelper
     attr_reader :admin_set, :depositor
     UNC_GRID_ID = 'grid.410711.2'
 
@@ -43,7 +43,10 @@ def process_publication(publication)
       create_sipity_workflow(work: article)
       pdf_path = extract_pdf(publication)
       if pdf_path
-        pdf_file = attach_pdf_to_work(article, pdf_path, @depositor, article.visibility)
+        pdf_file = attach_pdf_to_work(work: article,
+                                      file_path: pdf_path,
+                                      depositor: @depositor,
+                                      visibility: article.visibility)
         pdf_file.update(permissions_attributes: group_permissions(@admin_set))
       end
       article