Remove cleaned up OIDs from database and cache

14 files changed, 302 insertions, 123 deletions

diff --git a/GITALY_SERVER_VERSION b/GITALY_SERVER_VERSION
index 32b7211cb61..7d47e599800 100644
--- a/GITALY_SERVER_VERSION
+++ b/GITALY_SERVER_VERSION
@@ -1 +1 @@
-1.40.0
+1.41.0
diff --git a/app/models/merge_request_diff.rb b/app/models/merge_request_diff.rb
index 5f5d92bc2f0..f45bd0e03de 100644
--- a/app/models/merge_request_diff.rb
+++ b/app/models/merge_request_diff.rb
@@ -51,6 +51,10 @@ class MergeRequestDiff < ApplicationRecord
     joins(:merge_request_diff_commits).where(merge_request_diff_commits: { sha: sha }).reorder(nil)
   end
 
+  scope :by_project_id, -> (project_id) do
+    joins(:merge_request).where(merge_requests: { target_project_id: project_id })
+  end
+
   scope :recent, -> { order(id: :desc).limit(100) }
   scope :files_in_database, -> { where(stored_externally: [false, nil]) }
 
diff --git a/app/models/note_diff_file.rb b/app/models/note_diff_file.rb
index 9afb94c869a..fcc9e2b3fd8 100644
--- a/app/models/note_diff_file.rb
+++ b/app/models/note_diff_file.rb
@@ -7,6 +7,10 @@ class NoteDiffFile < ApplicationRecord
     joins(:diff_note).where("resolved_at IS NULL OR noteable_type = 'Commit'")
   end
 
+  scope :referencing_sha, -> (oids, project_id:) do
+    joins(:diff_note).where(notes: { project_id: project_id, commit_id: oids })
+  end
+
   delegate :original_position, :project, to: :diff_note
 
   belongs_to :diff_note, inverse_of: :note_diff_file
diff --git a/app/services/projects/cleanup_service.rb b/app/services/projects/cleanup_service.rb
index 12103ea34b5..5972bfd4071 100644
--- a/app/services/projects/cleanup_service.rb
+++ b/app/services/projects/cleanup_service.rb
@@ -18,9 +18,6 @@ module Projects
     # per rewritten object, with the old and new SHAs space-separated. It can be
     # used to update or remove content that references the objects that BFG has
     # altered
-    #
-    # Currently, only the project repository is modified by this service, but we
-    # may wish to modify other data sources in the future.
     def execute
       apply_bfg_object_map!
 
@@ -41,10 +38,52 @@ module Projects
       raise NoUploadError unless project.bfg_object_map.exists?
 
       project.bfg_object_map.open do |io|
-        repository_cleaner.apply_bfg_object_map(io)
+        repository_cleaner.apply_bfg_object_map_stream(io) do |response|
+          cleanup_diffs(response)
+        end
+      end
+    end
+
+    def cleanup_diffs(response)
+      old_commit_shas = extract_old_commit_shas(response.entries)
+
+      ActiveRecord::Base.transaction do
+        cleanup_merge_request_diffs(old_commit_shas)
+        cleanup_note_diff_files(old_commit_shas)
       end
     end
 
+    def extract_old_commit_shas(batch)
+      batch.lazy.select { |entry| entry.type == :COMMIT }.map(&:old_oid).force
+    end
+
+    def cleanup_merge_request_diffs(old_commit_shas)
+      merge_request_diffs = MergeRequestDiff
+        .by_project_id(project.id)
+        .by_commit_sha(old_commit_shas)
+
+      # It's important to run the ActiveRecord callbacks here
+      merge_request_diffs.destroy_all # rubocop:disable Cop/DestroyAll
+
+      # TODO: ensure the highlight cache is removed immediately. It's too hard
+      # to calculate the Redis keys at present.
+      #
+      # https://gitlab.com/gitlab-org/gitlab-ce/issues/61115
+    end
+
+    def cleanup_note_diff_files(old_commit_shas)
+      # Pluck the IDs instead of running the query twice to ensure we clear the
+      # cache for exactly the note diffs we remove
+      ids = NoteDiffFile
+        .referencing_sha(old_commit_shas, project_id: project.id)
+        .pluck_primary_key
+
+      NoteDiffFile.id_in(ids).delete_all
+
+      # A highlighted version of the diff is stored in redis. Remove it now.
+      Gitlab::DiscussionsDiff::HighlightCache.clear_multiple(ids)
+    end
+
     def repository_cleaner
       @repository_cleaner ||= Gitlab::Git::RepositoryCleaner.new(repository.raw)
     end
diff --git a/changelogs/unreleased/30093-apply-bfg-object-map-to-database.yml b/changelogs/unreleased/30093-apply-bfg-object-map-to-database.yml
new file mode 100644
index 00000000000..ec851dfcacc
--- /dev/null
+++ b/changelogs/unreleased/30093-apply-bfg-object-map-to-database.yml
@@ -0,0 +1,5 @@
+---
+title: Remove cleaned up OIDs from database and cache
+merge_request: 26555
+author:
+type: added
diff --git a/doc/user/project/repository/reducing_the_repo_size_using_git.md b/doc/user/project/repository/reducing_the_repo_size_using_git.md
index 672567a8d7d..2339759ecc8 100644
--- a/doc/user/project/repository/reducing_the_repo_size_using_git.md
+++ b/doc/user/project/repository/reducing_the_repo_size_using_git.md
@@ -98,6 +98,12 @@ up its own internal state, maximizing the space saved.
     `git gc` against the repository. You will receive an email once it has
     completed.
 
+This process will remove some copies of the rewritten commits from GitLab's
+cache and database, but there are still numerous gaps in coverage - at present,
+some of the copies may persist indefinitely. [Clearing the instance cache]
+(../../../administration/raketasks/maintenance.md#clear-redis-cache) may help to
+remove some of them, but it should not be depended on for security purposes!
+
 ## Using `git filter-branch`
 
 1. Navigate to your repository:
diff --git a/lib/gitlab/discussions_diff/highlight_cache.rb b/lib/gitlab/discussions_diff/highlight_cache.rb
index 270cfb89488..369c6b87fb4 100644
--- a/lib/gitlab/discussions_diff/highlight_cache.rb
+++ b/lib/gitlab/discussions_diff/highlight_cache.rb
@@ -52,6 +52,19 @@ module Gitlab
           end
         end
 
+        # Clears multiple cache keys at once.
+        #
+        # raw_keys - An Array of unique cache keys, without namespaces.
+        #
+        # It returns the number of cache keys cleared. Ex.: 42
+        def clear_multiple(raw_keys)
+          return [] if raw_keys.empty?
+
+          keys = raw_keys.map { |id| cache_key_for(id) }
+
+          Redis::Cache.with { |redis| redis.del(keys) }
+        end
+
         def cache_key_for(raw_key)
           "#{cache_key_prefix}:#{raw_key}"
         end
diff --git a/lib/gitlab/git/repository_cleaner.rb b/lib/gitlab/git/repository_cleaner.rb
index 2d1d8435cf3..9dd0ddfb44b 100644
--- a/lib/gitlab/git/repository_cleaner.rb
+++ b/lib/gitlab/git/repository_cleaner.rb
@@ -12,9 +12,9 @@ module Gitlab
         @repository = repository
       end
 
-      def apply_bfg_object_map(io)
+      def apply_bfg_object_map_stream(io, &blk)
         wrapped_gitaly_errors do
-          gitaly_cleanup_client.apply_bfg_object_map(io)
+          gitaly_cleanup_client.apply_bfg_object_map_stream(io, &blk)
         end
       end
 
diff --git a/lib/gitlab/gitaly_client/cleanup_service.rb b/lib/gitlab/gitaly_client/cleanup_service.rb
index 3e8d6a773ca..a56bc35f6d7 100644
--- a/lib/gitlab/gitaly_client/cleanup_service.rb
+++ b/lib/gitlab/gitaly_client/cleanup_service.rb
@@ -12,25 +12,32 @@ module Gitlab
         @storage = repository.storage
       end
 
-      def apply_bfg_object_map(io)
-        first_request = Gitaly::ApplyBfgObjectMapRequest.new(repository: gitaly_repo)
+      def apply_bfg_object_map_stream(io, &blk)
+        responses = GitalyClient.call(
+          storage,
+          :cleanup_service,
+          :apply_bfg_object_map_stream,
+          build_object_map_enum(io),
+          timeout: GitalyClient.no_timeout
+        )
+
+        responses.each(&blk)
+      end
+
+      private
 
-        enum = Enumerator.new do |y|
-          y.yield first_request
+      def build_object_map_enum(io)
+        Enumerator.new do |y|
+          # First request. For simplicity, doesn't include any object map data
+          y << Gitaly::ApplyBfgObjectMapStreamRequest.new(repository: gitaly_repo)
 
+          # Now stream the BFG object map file to gitaly in chunks
           while data = io.read(RepositoryService::MAX_MSG_SIZE)
-            y.yield Gitaly::ApplyBfgObjectMapRequest.new(object_map: data)
+            y << Gitaly::ApplyBfgObjectMapStreamRequest.new(object_map: data)
+
             break if io&.eof?
           end
         end
-
-        GitalyClient.call(
-          storage,
-          :cleanup_service,
-          :apply_bfg_object_map,
-          enum,
-          timeout: GitalyClient.no_timeout
-        )
       end
     end
   end
diff --git a/spec/lib/gitlab/discussions_diff/highlight_cache_spec.rb b/spec/lib/gitlab/discussions_diff/highlight_cache_spec.rb
index fe26ebb8796..15ee8c40b55 100644
--- a/spec/lib/gitlab/discussions_diff/highlight_cache_spec.rb
+++ b/spec/lib/gitlab/discussions_diff/highlight_cache_spec.rb
@@ -3,31 +3,32 @@
 require 'spec_helper'
 
 describe Gitlab::DiscussionsDiff::HighlightCache, :clean_gitlab_redis_cache do
+  def fake_file(offset)
+    {
+      text: 'foo',
+      type: 'new',
+      index: 2 + offset,
+      old_pos: 10 + offset,
+      new_pos: 11 + offset,
+      line_code: 'xpto',
+      rich_text: '<blips>blops</blips>'
+    }
+  end
+
+  let(:mapping) do
+    {
+      3 => [
+        fake_file(0),
+        fake_file(1)
+      ],
+      4 => [
+        fake_file(2)
+      ]
+    }
+  end
+
   describe '#write_multiple' do
     it 'sets multiple keys serializing content as JSON' do
-      mapping = {
-        3 => [
-          {
-            text: 'foo',
-            type: 'new',
-            index: 2,
-            old_pos: 10,
-            new_pos: 11,
-            line_code: 'xpto',
-            rich_text: '<blips>blops</blips>'
-          },
-          {
-            text: 'foo',
-            type: 'new',
-            index: 3,
-            old_pos: 11,
-            new_pos: 12,
-            line_code: 'xpto',
-            rich_text: '<blops>blips</blops>'
-          }
-        ]
-      }
-
       described_class.write_multiple(mapping)
 
       mapping.each do |key, value|
@@ -41,53 +42,16 @@ describe Gitlab::DiscussionsDiff::HighlightCache, :clean_gitlab_redis_cache do
 
   describe '#read_multiple' do
     it 'reads multiple keys and serializes content into Gitlab::Diff::Line objects' do
-      mapping = {
-        3 => [
-          {
-            text: 'foo',
-            type: 'new',
-            index: 2,
-            old_pos: 11,
-            new_pos: 12,
-            line_code: 'xpto',
-            rich_text: '<blips>blops</blips>'
-          },
-          {
-            text: 'foo',
-            type: 'new',
-            index: 3,
-            old_pos: 10,
-            new_pos: 11,
-            line_code: 'xpto',
-            rich_text: '<blips>blops</blips>'
-          }
-        ]
-      }
-
       described_class.write_multiple(mapping)
 
       found = described_class.read_multiple(mapping.keys)
 
-      expect(found.size).to eq(1)
+      expect(found.size).to eq(2)
       expect(found.first.size).to eq(2)
       expect(found.first).to all(be_a(Gitlab::Diff::Line))
     end
 
     it 'returns nil when cached key is not found' do
-      mapping = {
-        3 => [
-          {
-            text: 'foo',
-            type: 'new',
-            index: 2,
-            old_pos: 11,
-            new_pos: 12,
-            line_code: 'xpto',
-            rich_text: '<blips>blops</blips>'
-          }
-        ]
-      }
-
       described_class.write_multiple(mapping)
 
       found = described_class.read_multiple([2, 3])
@@ -95,8 +59,30 @@ describe Gitlab::DiscussionsDiff::HighlightCache, :clean_gitlab_redis_cache do
       expect(found.size).to eq(2)
 
       expect(found.first).to eq(nil)
-      expect(found.second.size).to eq(1)
+      expect(found.second.size).to eq(2)
       expect(found.second).to all(be_a(Gitlab::Diff::Line))
     end
   end
+
+  describe '#clear_multiple' do
+    it 'removes all named keys' do
+      described_class.write_multiple(mapping)
+
+      described_class.clear_multiple(mapping.keys)
+
+      expect(described_class.read_multiple(mapping.keys)).to all(be_nil)
+    end
+
+    it 'only removed named keys' do
+      to_clear, to_leave = mapping.keys
+
+      described_class.write_multiple(mapping)
+      described_class.clear_multiple([to_clear])
+
+      cleared, left = described_class.read_multiple([to_clear, to_leave])
+
+      expect(cleared).to be_nil
+      expect(left).to all(be_a(Gitlab::Diff::Line))
+    end
+  end
 end
diff --git a/spec/lib/gitlab/git/repository_cleaner_spec.rb b/spec/lib/gitlab/git/repository_cleaner_spec.rb
index 6602f22843f..7bba0107e58 100644
--- a/spec/lib/gitlab/git/repository_cleaner_spec.rb
+++ b/spec/lib/gitlab/git/repository_cleaner_spec.rb
@@ -6,55 +6,62 @@ describe Gitlab::Git::RepositoryCleaner do
   let(:project) { create(:project, :repository) }
   let(:repository) { project.repository }
   let(:head_sha) { repository.head_commit.id }
-  let(:object_map_data) { "#{head_sha} #{'0' * 40}" }
+  let(:object_map_data) { "#{head_sha} #{Gitlab::Git::BLANK_SHA}" }
 
-  subject(:cleaner) { described_class.new(repository.raw) }
+  let(:clean_refs) { %W[refs/environments/1 refs/merge-requests/1 refs/keep-around/#{head_sha}] }
+  let(:keep_refs) { %w[refs/heads/_keep refs/tags/_keep] }
 
-  describe '#apply_bfg_object_map' do
-    let(:clean_refs) { %W[refs/environments/1 refs/merge-requests/1 refs/keep-around/#{head_sha}] }
-    let(:keep_refs) { %w[refs/heads/_keep refs/tags/_keep] }
+  subject(:cleaner) { described_class.new(repository.raw) }
 
+  shared_examples_for '#apply_bfg_object_map_stream' do
     before do
       (clean_refs + keep_refs).each { |ref| repository.create_ref(head_sha, ref) }
     end
 
-    context 'from StringIO' do
-      let(:object_map) { StringIO.new(object_map_data) }
+    it 'removes internal references' do
+      entries = []
 
-      it 'removes internal references' do
-        cleaner.apply_bfg_object_map(object_map)
+      cleaner.apply_bfg_object_map_stream(object_map) do |rsp|
+        entries.concat(rsp.entries)
+      end
 
-        aggregate_failures do
-          clean_refs.each { |ref| expect(repository.ref_exists?(ref)).to be_falsy }
-          keep_refs.each { |ref| expect(repository.ref_exists?(ref)).to be_truthy }
-        end
+      aggregate_failures do
+        clean_refs.each { |ref| expect(repository.ref_exists?(ref)).to be(false) }
+        keep_refs.each { |ref| expect(repository.ref_exists?(ref)).to be(true) }
+
+        expect(entries).to contain_exactly(
+          Gitaly::ApplyBfgObjectMapStreamResponse::Entry.new(
+            type: :COMMIT,
+            old_oid: head_sha,
+            new_oid: Gitlab::Git::BLANK_SHA
+          )
+        )
       end
     end
+  end
 
-    context 'from Gitlab::HttpIO' do
-      let(:url) { 'http://example.com/bfg_object_map.txt' }
-      let(:tempfile) { Tempfile.new }
-      let(:object_map) { Gitlab::HttpIO.new(url, object_map_data.size) }
+  describe '#apply_bfg_object_map_stream (from StringIO)' do
+    let(:object_map) { StringIO.new(object_map_data) }
 
-      around do |example|
-        tempfile.write(object_map_data)
-        tempfile.close
+    include_examples '#apply_bfg_object_map_stream'
+  end
 
-        example.run
-      ensure
-        tempfile.unlink
-      end
+  describe '#apply_bfg_object_map_stream (from Gitlab::HttpIO)' do
+    let(:url) { 'http://example.com/bfg_object_map.txt' }
+    let(:tempfile) { Tempfile.new }
+    let(:object_map) { Gitlab::HttpIO.new(url, object_map_data.size) }
 
-      it 'removes internal references' do
-        stub_remote_url_200(url, tempfile.path)
+    around do |example|
+      tempfile.write(object_map_data)
+      tempfile.close
 
-        cleaner.apply_bfg_object_map(object_map)
+      stub_remote_url_200(url, tempfile.path)
 
-        aggregate_failures do
-          clean_refs.each { |ref| expect(repository.ref_exists?(ref)).to be_falsy }
-          keep_refs.each { |ref| expect(repository.ref_exists?(ref)).to be_truthy }
-        end
-      end
+      example.run
+    ensure
+      tempfile.unlink
     end
+
+    include_examples '#apply_bfg_object_map_stream'
   end
 end
diff --git a/spec/lib/gitlab/gitaly_client/cleanup_service_spec.rb b/spec/lib/gitlab/gitaly_client/cleanup_service_spec.rb
index 369deff732a..c42332dc27b 100644
--- a/spec/lib/gitlab/gitaly_client/cleanup_service_spec.rb
+++ b/spec/lib/gitlab/gitaly_client/cleanup_service_spec.rb
@@ -6,14 +6,14 @@ describe Gitlab::GitalyClient::CleanupService do
   let(:relative_path) { project.disk_path + '.git' }
   let(:client) { described_class.new(project.repository) }
 
-  describe '#apply_bfg_object_map' do
-    it 'sends an apply_bfg_object_map message' do
+  describe '#apply_bfg_object_map_stream' do
+    it 'sends an apply_bfg_object_map_stream message' do
       expect_any_instance_of(Gitaly::CleanupService::Stub)
-        .to receive(:apply_bfg_object_map)
+        .to receive(:apply_bfg_object_map_stream)
         .with(kind_of(Enumerator), kind_of(Hash))
-        .and_return(double)
+        .and_return([])
 
-      client.apply_bfg_object_map(StringIO.new)
+      client.apply_bfg_object_map_stream(StringIO.new)
     end
   end
 end
diff --git a/spec/models/note_diff_file_spec.rb b/spec/models/note_diff_file_spec.rb
index 99eeac8d778..b15bedd257e 100644
--- a/spec/models/note_diff_file_spec.rb
+++ b/spec/models/note_diff_file_spec.rb
@@ -10,4 +10,31 @@ describe NoteDiffFile do
   describe 'validations' do
     it { is_expected.to validate_presence_of(:diff_note) }
   end
+
+  describe '.referencing_sha' do
+    let!(:diff_note) { create(:diff_note_on_commit) }
+
+    let(:note_diff_file) { diff_note.note_diff_file }
+    let(:project) { diff_note.project }
+
+    it 'finds note diff files by project and sha' do
+      found = described_class.referencing_sha(diff_note.commit_id, project_id: project.id)
+
+      expect(found).to contain_exactly(note_diff_file)
+    end
+
+    it 'excludes note diff files with the wrong project' do
+      other_project = create(:project)
+
+      found = described_class.referencing_sha(diff_note.commit_id, project_id: other_project.id)
+
+      expect(found).to be_empty
+    end
+
+    it 'excludes note diff files with the wrong sha' do
+      found = described_class.referencing_sha(Gitlab::Git::BLANK_SHA, project_id: project.id)
+
+      expect(found).to be_empty
+    end
+  end
 end
diff --git a/spec/services/projects/cleanup_service_spec.rb b/spec/services/projects/cleanup_service_spec.rb
index 29eabc86327..5c246854eb7 100644
--- a/spec/services/projects/cleanup_service_spec.rb
+++ b/spec/services/projects/cleanup_service_spec.rb
@@ -6,13 +6,13 @@ describe Projects::CleanupService do
   let(:project) { create(:project, :repository, bfg_object_map: fixture_file_upload('spec/fixtures/bfg_object_map.txt')) }
   let(:object_map) { project.bfg_object_map }
 
+  let(:cleaner) { service.__send__(:repository_cleaner) }
+
   subject(:service) { described_class.new(project) }
 
   describe '#execute' do
-    it 'runs the apply_bfg_object_map gitaly RPC' do
-      expect_next_instance_of(Gitlab::Git::RepositoryCleaner) do |cleaner|
-        expect(cleaner).to receive(:apply_bfg_object_map).with(kind_of(IO))
-      end
+    it 'runs the apply_bfg_object_map_stream gitaly RPC' do
+      expect(cleaner).to receive(:apply_bfg_object_map_stream).with(kind_of(IO))
 
       service.execute
     end
@@ -37,10 +37,91 @@ describe Projects::CleanupService do
       expect(object_map.exists?).to be_falsy
     end
 
+    context 'with a tainted merge request diff' do
+      let(:merge_request) { create(:merge_request, source_project: project, target_project: project) }
+      let(:diff) { merge_request.merge_request_diff }
+      let(:entry) { build_entry(diff.commits.first.id) }
+
+      before do
+        allow(cleaner)
+          .to receive(:apply_bfg_object_map_stream)
+          .and_yield(Gitaly::ApplyBfgObjectMapStreamResponse.new(entries: [entry]))
+      end
+
+      it 'removes the tainted commit from the database' do
+        service.execute
+
+        expect(MergeRequestDiff.exists?(diff.id)).to be_falsy
+      end
+
+      it 'ignores non-commit responses from Gitaly' do
+        entry.type = :UNKNOWN
+
+        service.execute
+
+        expect(MergeRequestDiff.exists?(diff.id)).to be_truthy
+      end
+    end
+
+    context 'with a tainted diff note' do
+      let(:diff_note) { create(:diff_note_on_commit, project: project) }
+      let(:note_diff_file) { diff_note.note_diff_file }
+      let(:entry) { build_entry(diff_note.commit_id) }
+
+      let(:highlight_cache) { Gitlab::DiscussionsDiff::HighlightCache }
+      let(:cache_id) { note_diff_file.id }
+
+      before do
+        allow(cleaner)
+          .to receive(:apply_bfg_object_map_stream)
+          .and_yield(Gitaly::ApplyBfgObjectMapStreamResponse.new(entries: [entry]))
+      end
+
+      it 'removes the tainted commit from the database' do
+        service.execute
+
+        expect(NoteDiffFile.exists?(note_diff_file.id)).to be_falsy
+      end
+
+      it 'removes the highlight cache from redis' do
+        write_cache(highlight_cache, cache_id, [{}])
+
+        expect(read_cache(highlight_cache, cache_id)).not_to be_nil
+
+        service.execute
+
+        expect(read_cache(highlight_cache, cache_id)).to be_nil
+      end
+
+      it 'ignores non-commit responses from Gitaly' do
+        entry.type = :UNKNOWN
+
+        service.execute
+
+        expect(NoteDiffFile.exists?(note_diff_file.id)).to be_truthy
+      end
+    end
+
     it 'raises an error if no object map can be found' do
       object_map.remove!
 
       expect { service.execute }.to raise_error(described_class::NoUploadError)
     end
   end
+
+  def build_entry(old_oid)
+    Gitaly::ApplyBfgObjectMapStreamResponse::Entry.new(
+      type: :COMMIT,
+      old_oid: old_oid,
+      new_oid: Gitlab::Git::BLANK_SHA
+    )
+  end
+
+  def read_cache(cache, key)
+    cache.read_multiple([key]).first
+  end
+
+  def write_cache(cache, key, value)
+    cache.write_multiple(key => value)
+  end
 end