Remove duplicated container scanning findings

This migration will only run in Gitlab.com

changelogs/unreleased/remove-duplicated-cs-findings.yml

+---
+title: Remove duplicated container scanning findings
+merge_request: 42041
+author:
+type: other

db/post_migrate/20200910131217_tmp_index_for_fixing_inconsistent_vulnerability_occurrences.rb

+# frozen_string_literal: true
+
+class TmpIndexForFixingInconsistentVulnerabilityOccurrences < ActiveRecord::Migration[6.0]
+  include Gitlab::Database::MigrationHelpers
+
+  DOWNTIME = false
+  INDEX_NAME = 'tmp_index_for_fixing_inconsistent_vulnerability_occurrences'
+  disable_ddl_transaction!
+
+  def up
+    # report_type: 2 container scanning
+    add_concurrent_index(:vulnerability_occurrences, :id,
+      where: "LENGTH(location_fingerprint) = 40 AND report_type = 2",
+      name: INDEX_NAME)
+  end
+
+  def down
+    remove_concurrent_index_by_name(:vulnerability_occurrences, INDEX_NAME)
+  end
+end

db/post_migrate/20200910131218_remove_duplicated_cs_findings.rb

+# frozen_string_literal: true
+
+class RemoveDuplicatedCsFindings < ActiveRecord::Migration[6.0]
+  include Gitlab::Database::MigrationHelpers
+
+  DOWNTIME = false
+
+  disable_ddl_transaction!
+
+  BATCH_SIZE = 1_000
+  INTERVAL = 2.minutes
+
+  # 23_893 records will be updated
+  # 23_893 records will be deleted
+  def up
+    return unless Gitlab.com?
+
+    migration = Gitlab::BackgroundMigration::RemoveDuplicateCsFindings
+    migration_name = migration.to_s.demodulize
+    relation = migration::Finding.container_scanning.where("LENGTH(location_fingerprint) = 40")
+    queue_background_migration_jobs_by_range_at_intervals(relation,
+                                                            migration_name,
+                                                            INTERVAL,
+                                                            batch_size: BATCH_SIZE)
+  end
+
+  def down
+    # no-op
+    # intentionally blank
+  end
+end

db/schema_migrations/20200910131217

+205580c1ba38fd03ce025dfd1d9be67756ade4fd28ba957bb71cd9e5e89ef190
\ No newline at end of file

db/schema_migrations/20200910131218

+ba431f19818b93da91c4ed2c3f25dc8e2f62c6d9ac07b15f6d01f21f085c1730
\ No newline at end of file

db/structure.sql

@@ -21400,6 +21400,8 @@ CREATE INDEX tmp_build_stage_position_index ON public.ci_builds USING btree (sta
 
 CREATE INDEX tmp_index_for_email_unconfirmation_migration ON public.emails USING btree (id) WHERE (confirmed_at IS NOT NULL);
 
+CREATE INDEX tmp_index_for_fixing_inconsistent_vulnerability_occurrences ON public.vulnerability_occurrences USING btree (id) WHERE ((length(location_fingerprint) = 40) AND (report_type = 2));
+
 CREATE UNIQUE INDEX unique_merge_request_metrics_by_merge_request_id ON public.merge_request_metrics USING btree (merge_request_id);
 
 CREATE UNIQUE INDEX users_security_dashboard_projects_unique_index ON public.users_security_dashboard_projects USING btree (project_id, user_id);

ee/lib/ee/gitlab/background_migration/remove_duplicate_cs_findings.rb

+# frozen_string_literal: true
+
+module EE
+  module Gitlab
+    module BackgroundMigration
+      module RemoveDuplicateCsFindings
+        extend ::Gitlab::Utils::Override
+
+        class Finding < ActiveRecord::Base
+          include ::ShaAttribute
+          include ::EachBatch
+
+          BROKEN_FINGERPRINT_LENGTH = 40
+
+          belongs_to :vulnerability, class_name: 'Vulnerability'
+
+          self.table_name = 'vulnerability_occurrences'
+
+          REPORT_TYPES = {
+            container_scanning: 2
+          }.with_indifferent_access.freeze
+
+          enum report_type: REPORT_TYPES
+
+          sha_attribute :location_fingerprint
+        end
+
+        class Note < ActiveRecord::Base; end
+
+        class Vulnerability < ActiveRecord::Base
+          has_many :findings, class_name: 'Finding', inverse_of: :vulnerability
+          has_many :notes, class_name: 'Note', foreign_key: 'noteable_id'
+
+          def delete_notes
+            Note.where(project_id: project_id, noteable_type: 'Vulnerability', noteable_id: id).delete_all
+          end
+        end
+
+        override :perform
+        def perform(start_id, stop_id)
+          Finding.select(:id, :project_id, :primary_identifier_id, :location_fingerprint, :scanner_id)
+            .container_scanning
+            .where(id: start_id..stop_id)
+            .where("length(location_fingerprint) = ?", Finding::BROKEN_FINGERPRINT_LENGTH)
+            .each do |finding|
+              colliding_fingerprint = ::Gitlab::Database::ShaAttribute.new.serialize(finding.location_fingerprint).to_s
+              duplicated_finding = Finding.container_scanning.where(project_id: finding.project_id,
+                                                primary_identifier_id: finding.primary_identifier_id,
+                                                scanner_id: finding.scanner_id,
+                                                location_fingerprint: colliding_fingerprint).first
+
+              next if duplicated_finding.blank?
+
+              ActiveRecord::Base.transaction do
+                duplicated_finding.vulnerability.delete_notes
+                duplicated_finding.vulnerability.delete
+                duplicated_finding.delete
+
+                # update can be done without violating unique constraint
+                # index_vulnerability_occurrences_on_unique_keys
+                # since we included sha_attribute :location_fingerprint it will be updated in correct format
+                finding.update(location_fingerprint: colliding_fingerprint)
+              end
+            end
+        end
+      end
+    end
+  end
+end

ee/spec/lib/ee/gitlab/background_migration/remove_duplicate_cs_findings_spec.rb

+# frozen_string_literal: true
+
+require 'spec_helper'
+
+RSpec.describe Gitlab::BackgroundMigration::RemoveDuplicateCsFindings, :migration, schema: 20200910131218 do
+  let(:namespaces) { table(:namespaces) }
+  let(:notes) { table(:notes) }
+  let(:group) { namespaces.create!(name: 'foo', path: 'foo') }
+  let(:projects) { table(:projects) }
+  let(:findings) { table(:vulnerability_occurrences) }
+  let(:scanners) { table(:vulnerability_scanners) }
+  let(:issues) { table(:issues) }
+  let(:epics) { table(:epics) }
+
+  let(:identifiers) { table(:vulnerability_identifiers) }
+  let(:vulnerabilities) { table(:vulnerabilities) }
+  let(:issue_links) { table(:vulnerability_issue_links) }
+  let(:finding_identifiers) { table(:vulnerability_occurrence_identifiers) }
+  let(:users) { table(:users) }
+
+  let!(:epic_1) { epics.create!(iid: 14532, title: 'from issue 1', group_id: group.id, author_id: user.id, title_html: 'any') }
+  let!(:project) { projects.create!(id: 12058473, namespace_id: group.id, name: 'gitlab', path: 'gitlab') }
+  let!(:user) { users.create!(id: 13, email: 'author@example.com', username: 'author', projects_limit: 10) }
+  let!(:scanner) do
+    scanners.create!(id: 6, project_id: project.id, external_id: 'clair', name: 'Security Scanner')
+  end
+
+  it 'removes duplicate findings and vulnerabilities' do
+    ids = [231411, 231412, 231413, 231500, 231600, 231700, 231800]
+
+    fingerprints = %w(
+      6c871440eb9f7618b9aef25e5246acddff6ed7a1
+      9d1a47927875f1aee1e2b9f16c25a8ff7586f1a6
+      d7da2cc109c18d890ab239e833524d451cc45246
+      6c871440eb9f7618b9aef25e5246acddff6ed7a1
+      9d1a47927875f1aee1e2b9f16c25a8ff7586f1a6
+      d7da2cc109c18d890ab239e833524d451cc45246
+      d7da2cc109c18d890ab239e833524d453cd45246
+    )
+
+    expected_fingerprints = %w(
+      6c871440eb9f7618b9aef25e5246acddff6ed7a1
+      9d1a47927875f1aee1e2b9f16c25a8ff7586f1a6
+      d7da2cc109c18d890ab239e833524d451cc45246
+      d7da2cc109c18d890ab239e833524d453cd45246
+    )
+
+    7.times.each { |x| identifiers.create!(vulnerability_identifer_params(x, project.id)) }
+    7.times.each { vulnerabilities.create!(vulnerability_params(project.id, user.id)) }
+
+    vulnerability_ids = vulnerabilities.all.ids
+
+    3.times.each { |x| findings.create!(finding_params(x, project.id).merge({ id: ids[x], location_fingerprint: fingerprints[x], vulnerability_id: vulnerability_ids[x] })) }
+    findings.create!(finding_params(0, project.id).merge({ id: ids[3], location_fingerprint: Gitlab::Database::ShaAttribute.new.serialize(fingerprints[3]).to_s, vulnerability_id: vulnerability_ids[3] }))
+    findings.create!(finding_params(1, project.id).merge({ id: ids[4], location_fingerprint: Gitlab::Database::ShaAttribute.new.serialize(fingerprints[4]).to_s, vulnerability_id: vulnerability_ids[4] }))
+    findings.create!(finding_params(2, project.id).merge({ id: ids[5], location_fingerprint: Gitlab::Database::ShaAttribute.new.serialize(fingerprints[5]).to_s, vulnerability_id: vulnerability_ids[5] }))
+    findings.create!(finding_params(3, project.id).merge({ id: ids[6], location_fingerprint: Gitlab::Database::ShaAttribute.new.serialize(fingerprints[6]).to_s, vulnerability_id: vulnerability_ids[6] }))
+
+    7.times.each { |x| finding_identifiers.create!(occurrence_id: ids[x], identifier_id: x ) }
+    1.upto(5).each { |x| issues.create!(description: '1234', state_id: 1, project_id: project.id, id: x) }
+
+    notes.create!(project_id: project.id, noteable_id: vulnerability_ids[4], noteable_type: "Vulnerability", note: "test note", system: true)
+    1.upto(5).each { |x| issue_links.create!(vulnerability_id: vulnerability_ids[x], issue_id: x ) }
+
+    expect(finding_identifiers.all.count). to eq(7)
+    expect(issue_links.all.count). to eq(5)
+
+    described_class.new.perform(231411, 231413)
+
+    expect(findings.ids).to match_array([231800, 231412, 231413, 231411])
+    expect(findings.where(report_type: 2).count). to eq(4)
+    expect(vulnerabilities.all.count). to eq(4)
+    expect(notes.all.count). to eq(0)
+    expect(finding_identifiers.all.count). to eq(4)
+    expect(issue_links.all.count). to eq(2)
+
+    location_fingerprints = findings.pluck(:location_fingerprint).flat_map { |x| Gitlab::Database::ShaAttribute.new.deserialize(x) }
+
+    expect(location_fingerprints).to match_array(expected_fingerprints)
+  end
+
+  def vulnerability_identifer_params(id, project_id)
+    {
+      id: id,
+      project_id: project_id,
+      fingerprint: 'd432c2ad2953e8bd587a3a43b3ce309b5b0154c' + id.to_s,
+      external_type: 'SECURITY_ID',
+      external_id: 'SECURITY_0',
+      name: 'SECURITY_IDENTIFIER 0'
+    }
+  end
+
+  def vulnerability_params(project_id, user_id)
+    {
+      title: 'title',
+      state: 1,
+      confidence: 5,
+      severity: 6,
+      report_type: 2,
+      project_id: project.id,
+      author_id: user.id
+    }
+  end
+
+  def finding_params(primary_identifier_id, project_id)
+    attrs = attributes_for(:vulnerabilities_finding)
+    {
+      severity: 0,
+      confidence: 5,
+      report_type: 2,
+      project_id: project_id,
+      scanner_id: 6,
+      primary_identifier_id: primary_identifier_id,
+      project_fingerprint: attrs[:project_fingerprint],
+      location_fingerprint: Digest::SHA1.hexdigest(SecureRandom.hex(10)),
+      uuid: attrs[:uuid],
+      name: attrs[:name],
+      metadata_version: '1.3',
+      raw_metadata: attrs[:raw_metadata]
+    }
+  end
+end

ee/spec/migrations/remove_duplicated_cs_findings_spec.rb

+# frozen_string_literal: true
+
+require 'spec_helper'
+
+require Rails.root.join('db', 'post_migrate', '20200910131218_remove_duplicated_cs_findings.rb')
+
+RSpec.describe RemoveDuplicatedCsFindings, :migration do
+  let(:migration) { 'RemoveDuplicateCsFindings'}
+  let(:namespaces) { table(:namespaces) }
+  let(:notes) { table(:notes) }
+  let(:group) { namespaces.create!(name: 'foo', path: 'foo') }
+  let(:projects) { table(:projects) }
+  let(:findings) { table(:vulnerability_occurrences) }
+  let(:scanners) { table(:vulnerability_scanners) }
+
+  let(:identifiers) { table(:vulnerability_identifiers) }
+  let!(:project) { projects.create!(id: 12058473, namespace_id: group.id, name: 'gitlab', path: 'gitlab') }
+  let!(:scanner) do
+    scanners.create!(id: 6, project_id: project.id, external_id: 'clair', name: 'Security Scanner')
+  end
+
+  before do
+    stub_const("#{described_class}::BATCH_SIZE", 2)
+  end
+
+  around do |example|
+    Timecop.freeze { Sidekiq::Testing.fake! { example.run } }
+  end
+
+  it 'updates location fingerprint for containter scanning findings', :sidekiq_might_not_need_inline do
+    allow(::Gitlab).to receive(:com?).and_return(true)
+
+    ids = [231411, 231412, 231413, 231500, 231600, 231700]
+
+    fingerprints = %w(
+      6c871440eb9f7618b9aef25e5246acddff6ed7a1
+      9d1a47927875f1aee1e2b9f16c25a8ff7586f1a6
+      d7da2cc109c18d890ab239e833524d451cc45246
+      6c871440eb9f7618b9aef25e5246acddff6ed7a1
+      9d1a47927875f1aee1e2b9f16c25a8ff7586f1a6
+      d7da2cc109c18d890ab239e833524d451cc45246
+    )
+
+    7.times.each { |x| identifiers.create!(vulnerability_identifer_params(x, project.id)) }
+    3.times.each { |x| findings.create!(finding_params(x, project.id).merge({ id: ids[x], location_fingerprint: fingerprints[x] })) }
+    findings.create!(finding_params(0, project.id).merge({ id: ids[3], location_fingerprint: Gitlab::Database::ShaAttribute.new.serialize(fingerprints[3]).to_s }))
+    findings.create!(finding_params(1, project.id).merge({ id: ids[4], location_fingerprint: Gitlab::Database::ShaAttribute.new.serialize(fingerprints[4]).to_s }))
+    findings.create!(finding_params(2, project.id).merge({ id: ids[5], location_fingerprint: Gitlab::Database::ShaAttribute.new.serialize(fingerprints[5]).to_s }))
+
+    migrate!
+
+    expect(migration)
+      .to be_scheduled_delayed_migration(2.minutes, 231411, 231412)
+
+    expect(migration)
+      .to be_scheduled_delayed_migration(4.minutes, 231413, 231413)
+
+    expect(BackgroundMigrationWorker.jobs.size).to eq(2)
+  end
+
+  it 'skips migration for on premise' do
+    allow(::Gitlab).to receive(:com?).and_return(true)
+
+    migrate!
+
+    expect(BackgroundMigrationWorker.jobs.size).to eq(0)
+  end
+
+  def vulnerability_identifer_params(id, project_id)
+    {
+      id: id,
+      project_id: project_id,
+      fingerprint: 'd432c2ad2953e8bd587a3a43b3ce309b5b0154c' + id.to_s,
+      external_type: 'SECURITY_ID',
+      external_id: 'SECURITY_0',
+      name: 'SECURITY_IDENTIFIER 0'
+    }
+  end
+
+  def vulnerability_params(project_id, user_id)
+    {
+      title: 'title',
+      state: 1,
+      confidence: 5,
+      severity: 6,
+      report_type: 2,
+      project_id: project.id,
+      author_id: user.id
+    }
+  end
+
+  def finding_params(primary_identifier_id, project_id)
+    attrs = attributes_for(:vulnerabilities_finding)
+    {
+      severity: 0,
+      confidence: 5,
+      report_type: 2,
+      project_id: project_id,
+      scanner_id: 6,
+      primary_identifier_id: primary_identifier_id,
+      project_fingerprint: attrs[:project_fingerprint],
+      location_fingerprint: Digest::SHA1.hexdigest(SecureRandom.hex(10)),
+      uuid: attrs[:uuid],
+      name: attrs[:name],
+      metadata_version: '1.3',
+      raw_metadata: attrs[:raw_metadata]
+    }
+  end
+
+  def create_identifier(number_of)
+    (1..number_of).each do |identifier_id|
+      identifiers.create!(id: identifier_id,
+                          project_id: 123,
+                          fingerprint: 'd432c2ad2953e8bd587a3a43b3ce309b5b0154c' + identifier_id.to_s,
+                          external_type: 'SECURITY_ID',
+                          external_id: 'SECURITY_0',
+                          name: 'SECURITY_IDENTIFIER 0')
+    end
+  end
+end

lib/gitlab/background_migration/remove_duplicate_cs_findings.rb

+# frozen_string_literal: true
+# rubocop:disable Style/Documentation
+
+module Gitlab
+  module BackgroundMigration
+    class RemoveDuplicateCsFindings
+      def perform(start_id, stop_id)
+      end
+    end
+  end
+end
+
+Gitlab::BackgroundMigration::RemoveDuplicateCsFindings.prepend_if_ee('EE::Gitlab::BackgroundMigration::RemoveDuplicateCsFindings')