tests: fix test databases

The following sequence could lead to this corruption:
  (1) Append new data to bulkdata
  (2) Update interval file positions in SQL
  (3) Flush (2)
  (4) Crash before flushing (1)
  (5) Reload database without running fsck
  (6) Start writing new data to end of bulkdata and introduce new interval

nilmdb/fsck/fsck.py

@@ -39,6 +39,10 @@ class RetryFsck(FsckError):
     pass
 
 
+class FsckFormatError(FsckError):
+    pass
+
+
 def log(format, *args):
     printf(format, *args)
 
@@ -48,7 +52,7 @@ def err(format, *args):
 
 
 # Decorator that retries a function if it returns a specific value
-def retry_if_raised(exc, message=None, max_retries=100):
+def retry_if_raised(exc, message=None, max_retries=1000):
     def f1(func):
         def f2(*args, **kwargs):
             for n in range(max_retries):
@@ -56,7 +60,7 @@ def retry_if_raised(exc, message=None, max_retries=100):
                     return func(*args, **kwargs)
                 except exc:
                     if message:
-                        log("%s\n\n", message)
+                        log(f"{message} ({n+1})\n\n")
             raise Exception("Max number of retries (%d) exceeded; giving up" %
                             max_retries)
         return f2
@@ -234,42 +238,97 @@ class Fsck(object):
                         try:
                             posiset += new
                         except IntervalError:
-                            raise FsckError("%s: overlap in file offsets:\n"
+                            self.fix_row_overlap(sid, path, posiset, new)
-                                            "set: %s\nnew: %s",
-                                            path, str(posiset), str(new))
 
-                # check bulkdata
+                try:
+                    # Check bulkdata
                     self.check_bulkdata(sid, path, bulk)
 
                     # Check that we can open bulkdata
-                try:
                     tab = nilmdb.server.bulkdata.Table(bulk)
-                except Exception as e:  # pragma: no cover --
+                except FsckFormatError:
-                    # No coverage here because, in the current code,
+                    # If there are no files except _format, try deleting
-                    # everything that would cause the bulkdata to fail
+                    # the entire stream; this may remove metadata, but
-                    # has been already checked.
+                    # it's probably unimportant.
+                    files = list(os.listdir(bulk))
+                    if len(files) > 1:
+                        raise FsckFormatError(f"{path}: can't load _format, "
+                                              f"but data is also present")
+
+                    # Since the stream was empty, just remove it
+                    self.fix_remove_stream(sid, path, bulk,
+                                           "empty, with corrupted format file")
+                except FsckError as e:
+                    raise e
+                except Exception as e:  # pragma: no cover
+                    # No coverage because this is an unknown/unexpected error
                     raise FsckError("%s: can't open bulkdata: %s",
                                     path, str(e))
                 tab.close()
 
+    def fix_row_overlap(self, sid, path, existing, new):
+        # If the file rows (spos, epos) overlap in the interval table,
+        # and the overlapping ranges look like this:
+        #    A --------- C
+        #           B -------- D
+        # Then we can try changing the first interval to go from
+        # A to B instead.
+        msg = (f"{path}: overlap in file offsets:\n"
+               f"existing ranges: {existing}\n"
+               f"overlapping interval: {new}")
+        if not self.fix:
+            raise FixableFsckError(msg)
+        err(f"\n{msg}\nSeeing if we can truncate one of them...\n")
+
+        # See if there'e exactly one interval that overlaps the
+        # conflicting one in the right way
+        match = None
+        for intv in self.stream_interval[sid]:
+            (stime, etime, spos, epos) = intv
+            if spos < new.start and epos > new.start:
+                if match:
+                    err(f"no, more than one interval matched:\n"
+                        f"{intv}\n{match}\n")
+                    raise FsckError(f"{path}: unfixable overlap")
+                match = intv
+        if match is None:
+            err("no intervals overlapped in the right way\n")
+            raise FsckError(f"{path}: unfixable overlap")
+
+        # Truncate the file position
+        err(f"truncating {match}\n")
+        with self.sql:
+            cur = self.sql.cursor()
+            cur.execute("UPDATE ranges SET end_pos=? "
+                        "WHERE stream_id=? AND start_time=? AND "
+                        "end_time=? AND start_pos=? AND end_pos=?",
+                        (new.start, sid, *match))
+            if cur.rowcount != 1:  # pragma: no cover (shouldn't fail)
+                raise FsckError("failed to fix SQL database")
+        raise RetryFsck
+
     ### Check that bulkdata is good enough to be opened
 
     @retry_if_raised(RetryFsck)
     def check_bulkdata(self, sid, path, bulk):
+        try:
             with open(os.path.join(bulk, b"_format"), "rb") as f:
                 fmt = pickle.load(f)
+        except Exception as e:
+            raise FsckFormatError(f"{path}: can't load _format file ({e})")
+
         if fmt["version"] != 3:
-            raise FsckError("%s: bad or unsupported bulkdata version %d",
+            raise FsckFormatError("%s: bad or unsupported bulkdata version %d",
                                   path, fmt["version"])
         rows_per_file = int(fmt["rows_per_file"])
         if rows_per_file < 1:
-            raise FsckError(f"{path}: bad rows_per_file {rows_per_file}")
+            raise FsckFormatError(f"{path}: bad rows_per_file {rows_per_file}")
         files_per_dir = int(fmt["files_per_dir"])
         if files_per_dir < 1:
-            raise FsckError(f"{path}: bad files_per_dir {files_per_dir}")
+            raise FsckFormatError(f"{path}: bad files_per_dir {files_per_dir}")
         layout = fmt["layout"]
         if layout != self.stream_layout[sid]:
-            raise FsckError("%s: layout mismatch %s != %s", path,
+            raise FsckFormatError("%s: layout mismatch %s != %s", path,
                                   layout, self.stream_layout[sid])
 
         # Every file should have a size that's the multiple of the row size
@@ -287,7 +346,7 @@ class Fsck(object):
             files = list(filter(regex.search, os.listdir(subpath)))
             if not files:
                 self.fix_empty_subdir(subpath)
-                raise RetryFsck  # pragma: no cover; raised by fix_empty_subdir
+
             # Verify that their size is a multiple of the row size
             for filename in files:
                 filepath = os.path.join(subpath, filename)
@@ -328,6 +387,24 @@ class Fsck(object):
             f.truncate(newsize)
             raise RetryFsck
 
+    def fix_remove_stream(self, sid, path, bulk, reason):
+        msg = f"stream {path} is corrupted: {reason}"
+        if not self.fix:
+            raise FixableFsckError(msg)
+        # Remove the stream from disk and the database
+        err(f"\n{msg}\n")
+        err(f"Removing stream {path} from disk and database\n")
+        shutil.rmtree(bulk)
+        with self.sql:
+            cur = self.sql.cursor()
+            cur.execute("DELETE FROM streams WHERE id=?",
+                        (sid,))
+            if cur.rowcount != 1:  # pragma: no cover (shouldn't fail)
+                raise FsckError("failed to remove stream")
+            cur.execute("DELETE FROM ranges WHERE stream_id=?", (sid,))
+            cur.execute("DELETE FROM metadata WHERE stream_id=?", (sid,))
+        raise RetryFsck
+
     ### Check interval endpoints
 
     def check_intervals(self):
@@ -364,7 +441,7 @@ class Fsck(object):
                 erow = tab[epos-1]  # noqa: F841 unused
             except Exception as e:
                 self.fix_bad_interval(sid, intv, tab, str(e))
-                raise RetryFsck  # pragma: no cover; raised by fix_bad_interval
+
         return len(ints)
 
     def fix_bad_interval(self, sid, intv, tab, msg):
@@ -400,9 +477,9 @@ class Fsck(object):
 
         # Otherwise, the only hope is to delete the interval entirely.
         err("*** Deleting the entire interval from SQL.\n")
-        err("This may leave stale data on disk.  To fix that, copy all\n")
+        err("This may leave stale data on disk.  To fix that, copy all "
-        err("data from this stream to a new stream, then remove all data\n")
+            "data from this stream to a new stream using nilm-copy, then\n")
-        err("from and destroy %s.\n", path)
+        err("remove all data from and destroy %s.\n", path)
         with self.sql:
             cur = self.sql.cursor()
             cur.execute("DELETE FROM ranges WHERE "
@@ -473,18 +550,35 @@ class Fsck(object):
                 # Verify that all timestamps are in range.
                 match = (ts < stime) | (ts >= etime)
                 if match.any():
-                    row = start + numpy.argmax(match)
+                    row = numpy.argmax(match)
+                    if ts[row] != 0:
                         raise FsckError("%s: data timestamp %d at row %d "
                                         "outside interval range [%d,%d)",
-                                    path, data['timestamp'][row], row,
+                                        path, ts[row], row + start,
                                         stime, etime)
 
+                    # Timestamp is zero and out of the expected range;
+                    # assume file ends with zeroed data and just truncate it.
+                    self.fix_table_by_truncating(
+                        path, tab, row + start,
+                        "data timestamp is out of range, and zero")
+
                 # Verify that timestamps are monotonic
                 match = numpy.diff(ts) <= 0
                 if match.any():
-                    row = start + numpy.argmax(match)
+                    row = numpy.argmax(match)
-                    raise FsckError("%s: non-monotonic timestamp (%d -> %d) "
+                    if ts[row+1] != 0:
-                                    "at row %d", path, ts[row], ts[row+1], row)
+                        raise FsckError(
+                            "%s: non-monotonic timestamp (%d -> %d) "
+                            "at row %d", path, ts[row], ts[row+1],
+                            row + start)
+
+                    # Timestamp is zero and non-monotonic;
+                    # assume file ends with zeroed data and just truncate it.
+                    self.fix_table_by_truncating(
+                        path, tab, row + start + 1,
+                        "data timestamp is non-monotonic, and zero")
+
                 first_ts = ts[0]
                 if last_ts is not None and first_ts <= last_ts:
                     raise FsckError("%s: first interval timestamp %d is not "
@@ -502,3 +596,15 @@ class Fsck(object):
                 done += count
                 update(done)
         return done
+
+    def fix_table_by_truncating(self, path, tab, row, reason):
+        # Simple fix for bad data: truncate the table at the given row.
+        # On retry, fix_bad_interval will correct the database and timestamps
+        # to account for this truncation.
+        msg = f"{path}: bad data in table, starting at row {row}: {reason}"
+        if not self.fix:
+            raise FixableFsckError(msg)
+        err(f"\n{msg}\nWill try truncating table\n")
+        (subdir, fname, offs, count) = tab._offset_from_row(row)
+        tab._remove_or_truncate_file(subdir, fname, offs)
+        raise RetryFsck

nilmdb/server/bulkdata.py

@@ -293,8 +293,8 @@ class Table():
             "layout": layout,
             "version": 3
         }
-        with open(os.path.join(root, b"_format"), "wb") as f:
+        nilmdb.utils.atomic.replace_file(
-            pickle.dump(fmt, f, 2)
+            os.path.join(root, b"_format"), pickle.dumps(fmt, 2))
 
     # Normal methods
     def __init__(self, root, initial_nrows=0):

tests/test_fsck.py

@@ -123,7 +123,7 @@ class TestFsck(object):
         self.failmsg("test2h", "missing bulkdata dir")
         self.failmsg("test2i", "bad bulkdata table")
         self.failmsg("test2j", "overlap in intervals")
-        self.failmsg("test2k", "overlap in file offsets")
+        self.failmsg("test2k", "overlap in file offsets", fix=False)
         self.ok("test2k1")
         self.failmsg("test2l", "unsupported bulkdata version")
         self.failmsg("test2m", "bad rows_per_file")
@@ -163,3 +163,22 @@ class TestFsck(object):
             raise Exception("hi")
         with assert_raises(Exception):
             foo()
+
+        self.failmsg("test2v", "can't load _format, but data is also present")
+        self.failmsg("test2v1", "bad bulkdata table")
+        self.failmsg("test2v2", "empty, with corrupted format file", fix=False)
+        self.okmsg("test2v2", "empty, with corrupted format file")
+
+        self.failmsg("test2w1", "out of range, and zero", fix=False)
+        self.okmsg("test2w1", "Will try truncating table")
+        self.contain("Deleting the entire interval")
+
+        self.failmsg("test2w2", "non-monotonic, and zero", fix=False)
+        self.okmsg("test2w2", "Will try truncating table")
+        self.contain("new end: time 237000001, pos 238")
+
+        self.failmsg("test2x1", "overlap in file offsets", fix=False)
+        self.okmsg("test2x1", "truncating")
+
+        self.failmsg("test2x2", "unfixable overlap")
+        self.failmsg("test2x3", "unfixable overlap")