[chore] migration to update statuses.thread_id to be notnull (#4160)

# Description

This is quite a complex database migration that updates the `statuses.thread_id` column to be notnull, in order that statuses always be threaded, which will be useful in various pieces of upcoming work. This is unfortunately a migration that acts over the entire statuses table, and is quite complex in order to ensure that all existing statuses get correctly threaded together, and where possible fix any issues of statuses in the same thread having incorrect thread_ids.

TODO:
- ~~update testrig models to all be threaded~~
- ~~update code to ensure thread_id is always set~~
- ~~run on **a copy** of an sqlite production database~~
- ~~run on **a copy** of a postgres production database~~

## Checklist

- [x] I/we have read the [GoToSocial contribution guidelines](https://codeberg.org/superseriousbusiness/gotosocial/src/branch/main/CONTRIBUTING.md).
- [x] I/we have discussed the proposed changes already, either in an issue on the repository, or in the Matrix chat.
- [x] I/we have not leveraged AI to create the proposed changes.
- [x] I/we have performed a self-review of added code.
- [x] I/we have written code that is legible and maintainable by others.
- [x] I/we have commented the added code, particularly in hard-to-understand areas.
- [ ] I/we have made any necessary changes to documentation.
- [x] I/we have added tests that cover new code.
- [x] I/we have run tests and they pass locally with the changes.
- [x] I/we have run `go fmt ./...` and `golangci-lint run`.

Reviewed-on: https://codeberg.org/superseriousbusiness/gotosocial/pulls/4160
Co-authored-by: kim <grufwub@gmail.com>
Co-committed-by: kim <grufwub@gmail.com>

internal/db/bundb/migrations/util.go

@@ -26,6 +26,7 @@ import (
 	"strconv"
 	"strings"
 
+	"code.superseriousbusiness.org/gotosocial/internal/config"
 	"code.superseriousbusiness.org/gotosocial/internal/gtserror"
 	"code.superseriousbusiness.org/gotosocial/internal/id"
 	"code.superseriousbusiness.org/gotosocial/internal/log"
@@ -37,6 +38,112 @@ import (
 	"github.com/uptrace/bun/schema"
 )
 
+// doWALCheckpoint attempt to force a WAL file merge on SQLite3,
+// which can be useful given how much can build-up in the WAL.
+//
+// see: https://www.sqlite.org/pragma.html#pragma_wal_checkpoint
+func doWALCheckpoint(ctx context.Context, db *bun.DB) error {
+	if db.Dialect().Name() == dialect.SQLite && strings.EqualFold(config.GetDbSqliteJournalMode(), "WAL") {
+		_, err := db.ExecContext(ctx, "PRAGMA wal_checkpoint(RESTART);")
+		if err != nil {
+			return gtserror.Newf("error performing wal_checkpoint: %w", err)
+		}
+	}
+	return nil
+}
+
+// batchUpdateByID performs the given updateQuery with updateArgs
+// over the entire given table, batching by the ID of batchByCol.
+func batchUpdateByID(
+	ctx context.Context,
+	tx bun.Tx,
+	table string,
+	batchByCol string,
+	updateQuery string,
+	updateArgs []any,
+) error {
+	// Get a count of all in table.
+	total, err := tx.NewSelect().
+		Table(table).
+		Count(ctx)
+	if err != nil {
+		return gtserror.Newf("error selecting total count: %w", err)
+	}
+
+	// Query batch size
+	// in number of rows.
+	const batchsz = 5000
+
+	// Stores highest batch value
+	// used in iterate queries,
+	// starting at highest possible.
+	highest := id.Highest
+
+	// Total updated rows.
+	var updated int
+
+	for {
+		// Limit to batchsz
+		// items at once.
+		batchQ := tx.
+			NewSelect().
+			Table(table).
+			Column(batchByCol).
+			Where("? < ?", bun.Ident(batchByCol), highest).
+			OrderExpr("? DESC", bun.Ident(batchByCol)).
+			Limit(batchsz)
+
+		// Finalize UPDATE to act only on batch.
+		qStr := updateQuery + " WHERE ? IN (?)"
+		args := append(slices.Clone(updateArgs),
+			bun.Ident(batchByCol),
+			batchQ,
+		)
+
+		// Execute the prepared raw query with arguments.
+		res, err := tx.NewRaw(qStr, args...).Exec(ctx)
+		if err != nil {
+			return gtserror.Newf("error updating old column values: %w", err)
+		}
+
+		// Check how many items we updated.
+		thisUpdated, err := res.RowsAffected()
+		if err != nil {
+			return gtserror.Newf("error counting affected rows: %w", err)
+		}
+
+		if thisUpdated == 0 {
+			// Nothing updated
+			// means we're done.
+			break
+		}
+
+		// Update the overall count.
+		updated += int(thisUpdated)
+
+		// Log helpful message to admin.
+		log.Infof(ctx, "migrated %d of %d %s (up to %s)",
+			updated, total, table, highest)
+
+		// Get next highest
+		// id for next batch.
+		if err := tx.
+			NewSelect().
+			With("batch_query", batchQ).
+			ColumnExpr("min(?) FROM ?", bun.Ident(batchByCol), bun.Ident("batch_query")).
+			Scan(ctx, &highest); err != nil {
+			return gtserror.Newf("error selecting next highest: %w", err)
+		}
+	}
+
+	if total != int(updated) {
+		// Return error here in order to rollback the whole transaction.
+		return fmt.Errorf("total=%d does not match updated=%d", total, updated)
+	}
+
+	return nil
+}
+
 // convertEnums performs a transaction that converts
 // a table's column of our old-style enums (strings) to
 // more performant and space-saving integer types.