extindex: implement --dedupe to fix old extindices

This is intended to fix older indices that had deduplication
bugs for matching content.  It'll also make dealing with
future changes to ContentHash easier since that's never
guaranteed stable.

It also supports --dry-run to print changes only without
making them.

4 files changed, 137 insertions, 3 deletions

diff --git a/lib/PublicInbox/ExtSearchIdx.pm b/lib/PublicInbox/ExtSearchIdx.pm
index 29414e4a..495579a2 100644
--- a/lib/PublicInbox/ExtSearchIdx.pm
+++ b/lib/PublicInbox/ExtSearchIdx.pm
@@ -844,6 +844,98 @@ sub sync_inbox {
         warn $err, "\n" if defined($err);
 }
 
+sub dd_smsg { # git->cat_async callback
+        my ($bref, $oid, $type, $size, $dd) = @_;
+        my $smsg = $dd->{smsg} // die 'BUG: dd->{smsg} missing';
+        my $self = $dd->{self} // die 'BUG: {self} missing';
+        my $per_mid = $dd->{per_mid} // die 'BUG: {per_mid} missing';
+        if ($type eq 'missing') {
+                _blob_missing($dd, $smsg);
+        } elsif (!is_bad_blob($oid, $type, $size, $smsg->{blob})) {
+                local $self->{current_info} = "$self->{current_info} $oid";
+                my $chash = content_hash(PublicInbox::Eml->new($bref));
+                push(@{$per_mid->{dd_chash}->{$chash}}, $smsg);
+        }
+        return if $per_mid->{last_smsg} != $smsg;
+        while (my ($chash, $ary) = each %{$per_mid->{dd_chash}}) {
+                my $keep = shift @$ary;
+                next if !scalar(@$ary);
+                $per_mid->{sync}->{dedupe_cull} += scalar(@$ary);
+                print STDERR
+                        "# <$keep->{mid}> keeping #$keep->{num}, dropping ",
+                        join(', ', map { "#$_->{num}" } @$ary),"\n";
+                next if $per_mid->{sync}->{-opt}->{'dry-run'};
+                my $oidx = $self->{oidx};
+                for my $smsg (@$ary) {
+                        my $gone = $smsg->{num};
+                        $oidx->merge_xref3($keep->{num}, $gone, $smsg->{blob});
+                        $self->idx_shard($gone)->ipc_do('xdb_remove', $gone);
+                        $oidx->delete_by_num($gone);
+                }
+        }
+}
+
+sub eidx_dedupe ($$) {
+        my ($self, $sync) = @_;
+        $sync->{dedupe_cull} = 0;
+        my $candidates = 0;
+        my $nr_mid = 0;
+        return unless eidxq_lock_acquire($self);
+        my $iter;
+        my $min_id = 0;
+        local $sync->{-regen_fmt} = "dedupe %u/".$self->{oidx}->max."\n";
+dedupe_restart:
+        $iter = $self->{oidx}->dbh->prepare(<<EOS);
+SELECT DISTINCT(mid),id FROM msgid WHERE id IN
+(SELECT id FROM id2num WHERE id > ? GROUP BY num HAVING COUNT(num) > 1)
+ORDER BY id
+EOS
+        $iter->execute($min_id);
+        local $SIG{__WARN__} = sub {
+                return if PublicInbox::Eml::warn_ignore(@_);
+                warn @_;
+        };
+        while (my ($mid, $id) = $iter->fetchrow_array) {
+                last if $sync->{quit};
+                $self->{current_info} = "dedupe $mid";
+                ${$sync->{nr}} = $min_id = $id;
+                my ($n, $prv, @smsg);
+                while (my $x = $self->{oidx}->next_by_mid($mid, \$n, \$prv)) {
+                        push @smsg, $x;
+                }
+                next if scalar(@smsg) < 2;
+                my $per_mid = {
+                        dd_chash => {}, # chash => [ary of smsgs]
+                        last_smsg => $smsg[-1],
+                        sync => $sync
+                };
+                $nr_mid++;
+                $candidates += scalar(@smsg) - 1;
+                for my $smsg (@smsg) {
+                        my $dd = {
+                                per_mid => $per_mid,
+                                smsg => $smsg,
+                                self => $self,
+                        };
+                        $self->git->cat_async($smsg->{blob}, \&dd_smsg, $dd);
+                }
+                # need to wait on every single one
+                $self->git->async_wait_all;
+
+                # is checkpoint needed? $iter is a very expensive query to restart
+                if (0 && checkpoint_due($sync)) {
+                        undef $iter;
+                        reindex_checkpoint($self, $sync);
+                        goto dedupe_restart;
+                }
+        }
+        my $n = delete $sync->{dedupe_cull};
+        if (my $pr = $sync->{-opt}->{-progress}) {
+                $pr->("culled $n/$candidates candidates ($nr_mid msgids)\n");
+        }
+        ${$sync->{nr}} = 0;
+}
+
 sub eidx_sync { # main entry point
         my ($self, $opt) = @_;
 
@@ -873,6 +965,10 @@ sub eidx_sync { # main entry point
         for my $ibx (@{$self->{ibx_list}}) {
                 $ibx->{-ibx_id} //= $self->{oidx}->ibx_id($ibx->eidx_key);
         }
+        if (delete($opt->{dedupe})) {
+                local $sync->{checkpoint_unlocks} = 1;
+                eidx_dedupe($self, $sync);
+        }
         if (delete($opt->{reindex})) {
                 local $sync->{checkpoint_unlocks} = 1;
                 eidx_reindex($self, $sync);
diff --git a/lib/PublicInbox/OverIdx.pm b/lib/PublicInbox/OverIdx.pm
index 5f96a5b0..8f7cf2bb 100644
--- a/lib/PublicInbox/OverIdx.pm
+++ b/lib/PublicInbox/OverIdx.pm
@@ -656,6 +656,26 @@ UPDATE over SET ddd = ? WHERE num = ?
         $sth->execute;
 }
 
+sub merge_xref3 { # used for "-extindex --dedupe"
+        my ($self, $keep_docid, $drop_docid, $oidhex) = @_;
+        my $oidbin = pack('H*', $oidhex);
+        my $sth = $self->{dbh}->prepare_cached(<<'');
+UPDATE OR IGNORE xref3 SET docid = ? WHERE docid = ? AND oidbin = ?
+
+        $sth->bind_param(1, $keep_docid);
+        $sth->bind_param(2, $drop_docid);
+        $sth->bind_param(3, $oidbin, SQL_BLOB);
+        $sth->execute;
+
+        # drop anything that conflicted
+        $sth = $self->{dbh}->prepare_cached(<<'');
+DELETE FROM xref3 WHERE docid = ? AND oidbin = ?
+
+        $sth->bind_param(1, $drop_docid);
+        $sth->bind_param(2, $oidbin, SQL_BLOB);
+        $sth->execute;
+}
+
 sub eidxq_add {
         my ($self, $docid) = @_;
         $self->dbh->prepare_cached(<<'')->execute($docid);
diff --git a/script/public-inbox-extindex b/script/public-inbox-extindex
index 771486c4..dcb12e5a 100755
--- a/script/public-inbox-extindex
+++ b/script/public-inbox-extindex
@@ -17,7 +17,9 @@ usage: public-inbox-extindex [options] [EXTINDEX_DIR] [INBOX_DIR...]
   --batch-size=BYTES  flush changes to OS after a given number of bytes
   --max-size=BYTES    do not index messages larger than the given size
   --gc                perform garbage collection instead of indexing
+  --dedupe            fix prior deduplication errors
   --verbose | -v      increase verbosity (may be repeated)
+  --dry-run | -n      dry-run on --dedupe
 
 BYTES may use `k', `m', and `g' suffixes (e.g. `10m' for 10 megabytes)
 See public-inbox-extindex(1) man page for full documentation.
@@ -27,7 +29,7 @@ GetOptions($opt, qw(verbose|v+ reindex rethread compact|c+ jobs|j=i
                 fsync|sync!
                 indexlevel|index-level|L=s max_size|max-size=s
                 batch_size|batch-size=s
-                gc commit-interval=i watch scan!
+                dedupe gc commit-interval=i watch scan! dry-run|n
                 all help|h))
         or die $help;
 if ($opt->{help}) { print $help; exit 0 };
@@ -50,11 +52,16 @@ unless (defined $eidx_dir) {
 my @ibxs;
 if ($opt->{gc}) {
         die "E: inbox paths must not be specified with --gc\n" if @ARGV;
-        die "E: --all not compatible with --gc\n" if $opt->{all};
-        die "E: --watch is not compatible with --gc\n" if $opt->{watch};
+        for my $sw (qw(all watch dry-run dedupe)) {
+                die "E: --$sw is not compatible with --gc\n" if $opt->{$sw};
+        }
 } else {
         @ibxs = PublicInbox::Admin::resolve_inboxes(\@ARGV, $opt, $cfg);
 }
+if ($opt->{'dry-run'} && !$opt->{dedupe}) {
+        die "E: --dry-run only affects --dedupe\n";
+}
+
 PublicInbox::Admin::require_or_die(qw(-search));
 PublicInbox::Config::json() or die "Cpanel::JSON::XS or similar missing\n";
 PublicInbox::Admin::progress_prepare($opt);
diff --git a/t/extsearch.t b/t/extsearch.t
index ae889ac6..5f0cd866 100644
--- a/t/extsearch.t
+++ b/t/extsearch.t
@@ -368,4 +368,15 @@ if ('remove v1test and test gc') {
         is(scalar(@it), 1, 'only one inbox left');
 }
 
+if ('dedupe + dry-run') {
+        my @cmd = ('-extindex', "$home/extindex");
+        my $opt = { 2 => \(my $err = '') };
+        ok(run_script([@cmd, '--dedupe'], undef, $opt), '--dedupe');
+        ok(run_script([@cmd, qw(--dedupe --dry-run)], undef, $opt),
+                '--dry-run --dedupe');
+        is $err, '', 'no errors';
+        ok(!run_script([@cmd, qw(--dry-run)], undef, $opt),
+                '--dry-run alone fails');
+}
+
 done_testing;