Guard the database update against duplicates and damaged indexes

(cherry picked from commit ea2b73ad78)

CHANGELOG.md

@@ -14,6 +14,7 @@ The format is a modified version of [Keep a Changelog](https://keepachangelog.co
 
 ### Fixed
 - Fix long floating point numbers showing up in Comick progress ([@MajorTanya](https://github.com/MajorTanya)) ([#4090](https://github.com/mihonapp/mihon/pull/4090))
+- Fixed updating from v0.20.x failing when the database had duplicate history or tracking entries, or damaged indexes ([@AntsyLich](https://github.com/AntsyLich))
 
 ## [v0.21.1] - 2026-10-12
 ### Fixed

data/src/main/sqldelight/tachiyomi/migrations/17.sqm

@@ -4,6 +4,64 @@ import kotlin.String;
 import kotlin.collections.List;
 import kotlinx.serialization.json.JsonObject;
 
+-- Every view reads `mangas`, so they are dropped here and recreated against the new tables at the end
+DROP VIEW historyView;
+DROP VIEW libraryView;
+DROP VIEW updatesView;
+
+-- ---------------------------------------------------------------------------------------------------------
+-- damaged indexes
+-- ---------------------------------------------------------------------------------------------------------
+
+-- Some databases hold rows their unique constraints should have rejected, which a damaged index explains. A
+-- write to a table also writes its indexes and fails on a damaged one, and a read through one can miss rows,
+-- so each table changed in place below is first copied from its rows alone, leaving its indexes behind.
+CREATE TABLE mangas_copy AS
+SELECT
+    _id, source, url, artist, author, description, genre, title, status, thumbnail_url, last_update, next_update,
+    initialized, viewer, chapter_flags, cover_last_modified, update_strategy, calculate_interval, notes, memo,
+    favorite_at
+FROM mangas NOT INDEXED;
+DROP TABLE mangas;
+ALTER TABLE mangas_copy RENAME TO mangas;
+
+CREATE TABLE chapters_copy AS
+SELECT
+    _id, manga_id, url, name, scanlator, read, bookmark, last_page_read, chapter_number, source_order, date_fetch,
+    date_upload, memo
+FROM chapters NOT INDEXED;
+DROP TABLE chapters;
+ALTER TABLE chapters_copy RENAME TO chapters;
+
+CREATE TABLE history_copy AS
+SELECT _id, chapter_id, last_read, time_read
+FROM history NOT INDEXED;
+DROP TABLE history;
+ALTER TABLE history_copy RENAME TO history;
+
+CREATE TABLE mangas_categories_copy AS
+SELECT _id, manga_id, category_id
+FROM mangas_categories NOT INDEXED;
+DROP TABLE mangas_categories;
+ALTER TABLE mangas_categories_copy RENAME TO mangas_categories;
+
+CREATE TABLE manga_sync_copy AS
+SELECT
+    _id, manga_id, sync_id, remote_id, library_id, title, last_chapter_read, total_chapters, status, score,
+    remote_url, start_date, finish_date, private
+FROM manga_sync NOT INDEXED;
+DROP TABLE manga_sync;
+ALTER TABLE manga_sync_copy RENAME TO manga_sync;
+
+CREATE TABLE excluded_scanlators_copy AS
+SELECT manga_id, scanlator
+FROM excluded_scanlators NOT INDEXED;
+DROP TABLE excluded_scanlators;
+ALTER TABLE excluded_scanlators_copy RENAME TO excluded_scanlators;
+
+-- Merging duplicate chapters looks their history up by chapter
+CREATE INDEX history_chapter_id_index ON history(chapter_id);
+
 -- ---------------------------------------------------------------------------------------------------------
 -- orphans
 -- ---------------------------------------------------------------------------------------------------------
@@ -21,11 +79,6 @@ DELETE FROM excluded_scanlators WHERE manga_id NOT IN (SELECT _id FROM mangas);
 -- table - manga
 -- ---------------------------------------------------------------------------------------------------------
 
--- Every view reads `mangas`, so they are dropped here and recreated against the new table below
-DROP VIEW historyView;
-DROP VIEW libraryView;
-DROP VIEW updatesView;
-
 -- Entries sharing a source and url are merged into one, since the new table won't hold both. The copies are
 -- ranked with the ones in the library first, since that is the entry the user has, then by age. The first
 -- one stays, takes each detail it is missing from the first copy that has it, and takes over everything
@@ -326,8 +379,7 @@ CREATE INDEX manga_category_category_id_index ON manga_category(category_id);
 -- ---------------------------------------------------------------------------------------------------------
 
 -- `last_read` is when the chapter was last read and `time_read` is how long it has been read for, so
--- both are renamed to say so. The chapter it belongs to is already unique, which leaves
--- `history_history_chapter_id_index` a prefix of that constraint.
+-- both are renamed to say so. The chapter it belongs to is already unique, so the constraint indexes it.
 -- The table keeps its name, so the original is renamed aside and the new one built under
 -- the real name; renaming a table into place makes SQLite rewrite its stored definition,
 -- leaving it spelled differently from the same table on a fresh install. The views were
@@ -349,11 +401,14 @@ CREATE TABLE history(
 -- Reaching the entry a row belongs to meant going through its chapter; it names the entry
 -- itself now, taken from that same chapter. A row whose chapter is already gone cannot name
 -- one and is dropped, which is what the foreign key would do to it once it is enforced again.
+-- Some databases hold more than one row for a chapter despite the old unique constraint, and the new one
+-- rejects them, so they merge the way the history of duplicate chapters does above.
 INSERT INTO history(id, manga_id, chapter_id, read_at, read_duration)
-SELECT H._id, C.manga_id, H.chapter_id, H.last_read, H.time_read
+SELECT min(H._id), C.manga_id, H.chapter_id, max(H.last_read), sum(H.time_read)
 FROM history_temp H
 JOIN chapter C
-ON C.id = H.chapter_id;
+ON C.id = H.chapter_id
+GROUP BY H.chapter_id;
 
 DROP TABLE history_temp;
 
@@ -388,19 +443,20 @@ DROP TABLE excluded_scanlators;
 -- ---------------------------------------------------------------------------------------------------------
 
 -- `manga_sync` is what tracking was called when it was still called syncing; `sync_id` is the tracker.
--- An entry that merged can leave two rows for the same tracker on the survivor, which the unique constraint
--- rejects, so the one to keep is chosen first: one on a copy in the library, then the one furthest read, then
--- the one on the copy ranked first, then the oldest. A track is taken whole rather than merged field by field,
--- because two rows on the same tracker can point at different remote entries.
+-- An entry that merged can leave two rows for the same tracker on the survivor, and an entry that didn't can
+-- still hold two despite the old unique constraint. The new one rejects both, so the one to keep is chosen
+-- first: one on a copy in the library, then the one furthest read, then the one on the copy ranked first, then
+-- the oldest. A track is taken whole rather than merged field by field, because two rows on the same tracker
+-- can point at different remote entries.
 CREATE TEMP TABLE duplicate_tracks AS
 SELECT
     T._id,
     first_value(T._id) OVER (
-        PARTITION BY D.keep_id, T.sync_id
+        PARTITION BY coalesce(D.keep_id, T.manga_id), T.sync_id
         ORDER BY D.favorite DESC, T.last_chapter_read DESC, D.precedence ASC, T._id ASC
     ) AS keep_track_id
 FROM manga_sync T
-JOIN duplicate_mangas D
+LEFT JOIN duplicate_mangas D
 ON D._id = T.manga_id;
 
 DELETE FROM manga_sync