Catch sqlite DatabaseErrors in more places when reading the history database.

Closes gh-2097

IPython/core/history.py

@@ -1,770 +1,786 b''
 """ History related magics and functionality """
 #-----------------------------------------------------------------------------
 #  Copyright (C) 2010-2011 The IPython Development Team.
 #
 #  Distributed under the terms of the BSD License.
 #
 #  The full license is in the file COPYING.txt, distributed with this software.
 #-----------------------------------------------------------------------------
 
 #-----------------------------------------------------------------------------
 # Imports
 #-----------------------------------------------------------------------------
 from __future__ import print_function
 
 # Stdlib imports
 import atexit
 import datetime
 import os
 import re
 try:
     import sqlite3
 except ImportError:
     sqlite3 = None
 import threading
 
 # Our own packages
 from IPython.config.configurable import Configurable
 from IPython.external.decorator import decorator
 from IPython.utils.path import locate_profile
 from IPython.utils.traitlets import (
     Any, Bool, Dict, Instance, Integer, List, Unicode, TraitError,
 )
 from IPython.utils.warn import warn
 
 #-----------------------------------------------------------------------------
 # Classes and functions
 #-----------------------------------------------------------------------------
 
 class DummyDB(object):
     """Dummy DB that will act as a black hole for history.
     
     Only used in the absence of sqlite"""
     def execute(*args, **kwargs):
         return []
     
     def commit(self, *args, **kwargs):
         pass
     
     def __enter__(self, *args, **kwargs):
         pass
     
     def __exit__(self, *args, **kwargs):
         pass
 
 
 @decorator
 def needs_sqlite(f, self, *a, **kw):
     """return an empty list in the absence of sqlite"""
     if sqlite3 is None or not self.enabled:
         return []
     else:
         return f(self, *a, **kw)
 
 
+if sqlite3 is not None:
+    DatabaseError = sqlite3.DatabaseError
+else:
+    class DatabaseError(Exception):
+        "Dummy exception when sqlite could not be imported. Should never occur."
+
+@decorator
+def catch_corrupt_db(f, self, *a, **kw):
+    """A decorator which wraps HistoryAccessor method calls to catch errors from
+    a corrupt SQLite database, move the old database out of the way, create a
+    new one, and optionally retry the function.
+    """
+    try:
+        return f(self, *a, **kw)
+    except DatabaseError:
+        if os.path.isfile(self.hist_file):
+            # Try to move the file out of the way
+            base,ext = os.path.splitext(self.hist_file)
+            newpath = base + '-corrupt' + ext
+            os.rename(self.hist_file, newpath)
+            self.init_db()
+            print("ERROR! History file wasn't a valid SQLite database.",
+            "It was moved to %s" % newpath, "and a new file created.")
+            return []
+        
+        else:
+            # The hist_file is probably :memory: or something else.
+            raise
+        
+
+
 class HistoryAccessor(Configurable):
     """Access the history database without adding to it.
     
     This is intended for use by standalone history tools. IPython shells use
     HistoryManager, below, which is a subclass of this."""
 
     # String holding the path to the history file
     hist_file = Unicode(config=True,
         help="""Path to file to use for SQLite history database.
         
         By default, IPython will put the history database in the IPython
         profile directory.  If you would rather share one history among
         profiles, you can set this value in each, so that they are consistent.
         
         Due to an issue with fcntl, SQLite is known to misbehave on some NFS
         mounts.  If you see IPython hanging, try setting this to something on a
         local disk, e.g::
         
             ipython --HistoryManager.hist_file=/tmp/ipython_hist.sqlite
         
         """)
     
     enabled = Bool(True, config=True,
         help="""enable the SQLite history
         
         set enabled=False to disable the SQLite history,
         in which case there will be no stored history, no SQLite connection,
         and no background saving thread.  This may be necessary in some
         threaded environments where IPython is embedded.
         """
     )
     
     connection_options = Dict(config=True,
         help="""Options for configuring the SQLite connection
         
         These options are passed as keyword args to sqlite3.connect
         when establishing database conenctions.
         """
     )
 
     # The SQLite database
     db = Any()
     def _db_changed(self, name, old, new):
         """validate the db, since it can be an Instance of two different types"""
         connection_types = (DummyDB,)
         if sqlite3 is not None:
             connection_types = (DummyDB, sqlite3.Connection)
         if not isinstance(new, connection_types):
             msg = "%s.db must be sqlite3 Connection or DummyDB, not %r" % \
                     (self.__class__.__name__, new)
             raise TraitError(msg)
     
     def __init__(self, profile='default', hist_file=u'', config=None, **traits):
         """Create a new history accessor.
         
         Parameters
         ----------
         profile : str
           The name of the profile from which to open history.
         hist_file : str
           Path to an SQLite history database stored by IPython. If specified,
           hist_file overrides profile.
         config :
           Config object. hist_file can also be set through this.
         """
         # We need a pointer back to the shell for various tasks.
         super(HistoryAccessor, self).__init__(config=config, **traits)
         # defer setting hist_file from kwarg until after init,
         # otherwise the default kwarg value would clobber any value
         # set by config
         if hist_file:
             self.hist_file = hist_file
         
         if self.hist_file == u'':
             # No one has set the hist_file, yet.
             self.hist_file = self._get_hist_file_name(profile)
 
         if sqlite3 is None and self.enabled:
             warn("IPython History requires SQLite, your history will not be saved\n")
             self.enabled = False
         
-        if sqlite3 is not None:
-            DatabaseError = sqlite3.DatabaseError
-        else:
-            DatabaseError = Exception
-        
-        try:
             self.init_db()
-        except DatabaseError:
-            if os.path.isfile(self.hist_file):
-                # Try to move the file out of the way
-                base,ext = os.path.splitext(self.hist_file)
-                newpath = base + '-corrupt' + ext
-                os.rename(self.hist_file, newpath)
-                print("ERROR! History file wasn't a valid SQLite database.",
-                "It was moved to %s" % newpath, "and a new file created.")
-                self.init_db()
-            else:
-                # The hist_file is probably :memory: or something else.
-                raise
     
     def _get_hist_file_name(self, profile='default'):
         """Find the history file for the given profile name.
         
         This is overridden by the HistoryManager subclass, to use the shell's
         active profile.
         
         Parameters
         ----------
         profile : str
           The name of a profile which has a history file.
         """
         return os.path.join(locate_profile(profile), 'history.sqlite')
     
+    @catch_corrupt_db
     def init_db(self):
         """Connect to the database, and create tables if necessary."""
         if not self.enabled:
             self.db = DummyDB()
             return
         
         # use detect_types so that timestamps return datetime objects
         kwargs = dict(detect_types=sqlite3.PARSE_DECLTYPES|sqlite3.PARSE_COLNAMES)
         kwargs.update(self.connection_options)
         self.db = sqlite3.connect(self.hist_file, **kwargs)
         self.db.execute("""CREATE TABLE IF NOT EXISTS sessions (session integer
                         primary key autoincrement, start timestamp,
                         end timestamp, num_cmds integer, remark text)""")
         self.db.execute("""CREATE TABLE IF NOT EXISTS history
                 (session integer, line integer, source text, source_raw text,
                 PRIMARY KEY (session, line))""")
         # Output history is optional, but ensure the table's there so it can be
         # enabled later.
         self.db.execute("""CREATE TABLE IF NOT EXISTS output_history
                         (session integer, line integer, output text,
                         PRIMARY KEY (session, line))""")
         self.db.commit()
 
     def writeout_cache(self):
         """Overridden by HistoryManager to dump the cache before certain
         database lookups."""
         pass
 
     ## -------------------------------
     ## Methods for retrieving history:
     ## -------------------------------
+    @catch_corrupt_db
     def _run_sql(self, sql, params, raw=True, output=False):
         """Prepares and runs an SQL query for the history database.
 
         Parameters
         ----------
         sql : str
           Any filtering expressions to go after SELECT ... FROM ...
         params : tuple
           Parameters passed to the SQL query (to replace "?")
         raw, output : bool
           See :meth:`get_range`
 
         Returns
         -------
         Tuples as :meth:`get_range`
         """
         toget = 'source_raw' if raw else 'source'
         sqlfrom = "history"
         if output:
             sqlfrom = "history LEFT JOIN output_history USING (session, line)"
             toget = "history.%s, output_history.output" % toget
         cur = self.db.execute("SELECT session, line, %s FROM %s " %\
                                 (toget, sqlfrom) + sql, params)
         if output:    # Regroup into 3-tuples, and parse JSON
             return ((ses, lin, (inp, out)) for ses, lin, inp, out in cur)
         return cur
 
     @needs_sqlite
+    @catch_corrupt_db
     def get_session_info(self, session=0):
         """get info about a session
 
         Parameters
         ----------
 
         session : int
             Session number to retrieve. The current session is 0, and negative
             numbers count back from current session, so -1 is previous session.
 
         Returns
         -------
 
         (session_id [int], start [datetime], end [datetime], num_cmds [int],
         remark [unicode])
 
         Sessions that are running or did not exit cleanly will have `end=None`
         and `num_cmds=None`.
 
         """
 
         if session <= 0:
             session += self.session_number
 
         query = "SELECT * from sessions where session == ?"
         return self.db.execute(query, (session,)).fetchone()
 
     def get_tail(self, n=10, raw=True, output=False, include_latest=False):
         """Get the last n lines from the history database.
 
         Parameters
         ----------
         n : int
           The number of lines to get
         raw, output : bool
           See :meth:`get_range`
         include_latest : bool
           If False (default), n+1 lines are fetched, and the latest one
           is discarded. This is intended to be used where the function
           is called by a user command, which it should not return.
 
         Returns
         -------
         Tuples as :meth:`get_range`
         """
         self.writeout_cache()
         if not include_latest:
             n += 1
         cur = self._run_sql("ORDER BY session DESC, line DESC LIMIT ?",
                                 (n,), raw=raw, output=output)
         if not include_latest:
             return reversed(list(cur)[1:])
         return reversed(list(cur))
 
     def search(self, pattern="*", raw=True, search_raw=True,
                output=False, n=None):
         """Search the database using unix glob-style matching (wildcards
         * and ?).
 
         Parameters
         ----------
         pattern : str
           The wildcarded pattern to match when searching
         search_raw : bool
           If True, search the raw input, otherwise, the parsed input
         raw, output : bool
           See :meth:`get_range`
         n : None or int
           If an integer is given, it defines the limit of
           returned entries.
 
         Returns
         -------
         Tuples as :meth:`get_range`
         """
         tosearch = "source_raw" if search_raw else "source"
         if output:
             tosearch = "history." + tosearch
         self.writeout_cache()
         sqlform = "WHERE %s GLOB ?" % tosearch
         params = (pattern,)
         if n is not None:
             sqlform += " ORDER BY session DESC, line DESC LIMIT ?"
             params += (n,)
         cur = self._run_sql(sqlform, params, raw=raw, output=output)
         if n is not None:
             return reversed(list(cur))
         return cur
 
     def get_range(self, session, start=1, stop=None, raw=True,output=False):
         """Retrieve input by session.
 
         Parameters
         ----------
         session : int
             Session number to retrieve.
         start : int
             First line to retrieve.
         stop : int
             End of line range (excluded from output itself). If None, retrieve
             to the end of the session.
         raw : bool
             If True, return untranslated input
         output : bool
             If True, attempt to include output. This will be 'real' Python
             objects for the current session, or text reprs from previous
             sessions if db_log_output was enabled at the time. Where no output
             is found, None is used.
 
         Returns
         -------
         An iterator over the desired lines. Each line is a 3-tuple, either
         (session, line, input) if output is False, or
         (session, line, (input, output)) if output is True.
         """
         if stop:
             lineclause = "line >= ? AND line < ?"
             params = (session, start, stop)
         else:
             lineclause = "line>=?"
             params = (session, start)
 
         return self._run_sql("WHERE session==? AND %s" % lineclause,
                                     params, raw=raw, output=output)
 
     def get_range_by_str(self, rangestr, raw=True, output=False):
         """Get lines of history from a string of ranges, as used by magic
         commands %hist, %save, %macro, etc.
 
         Parameters
         ----------
         rangestr : str
           A string specifying ranges, e.g. "5 ~2/1-4". See
           :func:`magic_history` for full details.
         raw, output : bool
           As :meth:`get_range`
 
         Returns
         -------
         Tuples as :meth:`get_range`
         """
         for sess, s, e in extract_hist_ranges(rangestr):
             for line in self.get_range(sess, s, e, raw=raw, output=output):
                 yield line
 
 
 class HistoryManager(HistoryAccessor):
     """A class to organize all history-related functionality in one place.
     """
     # Public interface
 
     # An instance of the IPython shell we are attached to
     shell = Instance('IPython.core.interactiveshell.InteractiveShellABC')
     # Lists to hold processed and raw history. These start with a blank entry
     # so that we can index them starting from 1
     input_hist_parsed = List([""])
     input_hist_raw = List([""])
     # A list of directories visited during session
     dir_hist = List()
     def _dir_hist_default(self):
         try:
             return [os.getcwdu()]
         except OSError:
             return []
 
     # A dict of output history, keyed with ints from the shell's
     # execution count.
     output_hist = Dict()
     # The text/plain repr of outputs.
     output_hist_reprs = Dict()
 
     # The number of the current session in the history database
     session_number = Integer()
     # Should we log output to the database? (default no)
     db_log_output = Bool(False, config=True)
     # Write to database every x commands (higher values save disk access & power)
     #  Values of 1 or less effectively disable caching. 
     db_cache_size = Integer(0, config=True)
     # The input and output caches
     db_input_cache = List()
     db_output_cache = List()
     
     # History saving in separate thread
     save_thread = Instance('IPython.core.history.HistorySavingThread')
     try:               # Event is a function returning an instance of _Event...
         save_flag = Instance(threading._Event)
     except AttributeError:         # ...until Python 3.3, when it's a class.
         save_flag = Instance(threading.Event)
     
     # Private interface
     # Variables used to store the three last inputs from the user.  On each new
     # history update, we populate the user's namespace with these, shifted as
     # necessary.
     _i00 = Unicode(u'')
     _i = Unicode(u'')
     _ii = Unicode(u'')
     _iii = Unicode(u'')
 
     # A regex matching all forms of the exit command, so that we don't store
     # them in the history (it's annoying to rewind the first entry and land on
     # an exit call).
     _exit_re = re.compile(r"(exit|quit)(\s*\(.*\))?$")
 
     def __init__(self, shell=None, config=None, **traits):
         """Create a new history manager associated with a shell instance.
         """
         # We need a pointer back to the shell for various tasks.
         super(HistoryManager, self).__init__(shell=shell, config=config,
             **traits)
         self.save_flag = threading.Event()
         self.db_input_cache_lock = threading.Lock()
         self.db_output_cache_lock = threading.Lock()
         if self.enabled and self.hist_file != ':memory:':
             self.save_thread = HistorySavingThread(self)
             self.save_thread.start()
 
         self.new_session()
 
     def _get_hist_file_name(self, profile=None):
         """Get default history file name based on the Shell's profile.
         
         The profile parameter is ignored, but must exist for compatibility with
         the parent class."""
         profile_dir = self.shell.profile_dir.location
         return os.path.join(profile_dir, 'history.sqlite')
     
     @needs_sqlite
     def new_session(self, conn=None):
         """Get a new session number."""
         if conn is None:
             conn = self.db
         
         with conn:
             cur = conn.execute("""INSERT INTO sessions VALUES (NULL, ?, NULL,
                             NULL, "") """, (datetime.datetime.now(),))
             self.session_number = cur.lastrowid
             
     def end_session(self):
         """Close the database session, filling in the end time and line count."""
         self.writeout_cache()
         with self.db:
             self.db.execute("""UPDATE sessions SET end=?, num_cmds=? WHERE
                             session==?""", (datetime.datetime.now(),
                             len(self.input_hist_parsed)-1, self.session_number))
         self.session_number = 0
                             
     def name_session(self, name):
         """Give the current session a name in the history database."""
         with self.db:
             self.db.execute("UPDATE sessions SET remark=? WHERE session==?",
                             (name, self.session_number))
                             
     def reset(self, new_session=True):
         """Clear the session history, releasing all object references, and
         optionally open a new session."""
         self.output_hist.clear()
         # The directory history can't be completely empty
         self.dir_hist[:] = [os.getcwdu()]
         
         if new_session:
             if self.session_number:
                 self.end_session()
             self.input_hist_parsed[:] = [""]
             self.input_hist_raw[:] = [""]
             self.new_session()
     
     # ------------------------------
     # Methods for retrieving history
     # ------------------------------
     def _get_range_session(self, start=1, stop=None, raw=True, output=False):
         """Get input and output history from the current session. Called by
         get_range, and takes similar parameters."""
         input_hist = self.input_hist_raw if raw else self.input_hist_parsed
             
         n = len(input_hist)
         if start < 0:
             start += n
         if not stop or (stop > n):
             stop = n
         elif stop < 0:
             stop += n
         
         for i in range(start, stop):
             if output:
                 line = (input_hist[i], self.output_hist_reprs.get(i))
             else:
                 line = input_hist[i]
             yield (0, i, line)
     
     def get_range(self, session=0, start=1, stop=None, raw=True,output=False):
         """Retrieve input by session.
         
         Parameters
         ----------
         session : int
             Session number to retrieve. The current session is 0, and negative
             numbers count back from current session, so -1 is previous session.
         start : int
             First line to retrieve.
         stop : int
             End of line range (excluded from output itself). If None, retrieve
             to the end of the session.
         raw : bool
             If True, return untranslated input
         output : bool
             If True, attempt to include output. This will be 'real' Python
             objects for the current session, or text reprs from previous
             sessions if db_log_output was enabled at the time. Where no output
             is found, None is used.
             
         Returns
         -------
         An iterator over the desired lines. Each line is a 3-tuple, either
         (session, line, input) if output is False, or
         (session, line, (input, output)) if output is True.
         """
         if session <= 0:
             session += self.session_number
         if session==self.session_number:          # Current session
             return self._get_range_session(start, stop, raw, output)
         return super(HistoryManager, self).get_range(session, start, stop, raw,
                                                      output)
 
     ## ----------------------------
     ## Methods for storing history:
     ## ----------------------------
     def store_inputs(self, line_num, source, source_raw=None):
         """Store source and raw input in history and create input cache
         variables _i*.
 
         Parameters
         ----------
         line_num : int
           The prompt number of this input.
 
         source : str
           Python input.
 
         source_raw : str, optional
           If given, this is the raw input without any IPython transformations
           applied to it.  If not given, ``source`` is used.
         """
         if source_raw is None:
             source_raw = source
         source = source.rstrip('\n')
         source_raw = source_raw.rstrip('\n')
 
         # do not store exit/quit commands
         if self._exit_re.match(source_raw.strip()):
             return
 
         self.input_hist_parsed.append(source)
         self.input_hist_raw.append(source_raw)
 
         with self.db_input_cache_lock:
             self.db_input_cache.append((line_num, source, source_raw))
             # Trigger to flush cache and write to DB.
             if len(self.db_input_cache) >= self.db_cache_size:
                 self.save_flag.set()
 
         # update the auto _i variables
         self._iii = self._ii
         self._ii = self._i
         self._i = self._i00
         self._i00 = source_raw
 
         # hackish access to user namespace to create _i1,_i2... dynamically
         new_i = '_i%s' % line_num
         to_main = {'_i': self._i,
                    '_ii': self._ii,
                    '_iii': self._iii,
                    new_i : self._i00 }
 
         self.shell.push(to_main, interactive=False)
 
     def store_output(self, line_num):
         """If database output logging is enabled, this saves all the
         outputs from the indicated prompt number to the database. It's
         called by run_cell after code has been executed.
 
         Parameters
         ----------
         line_num : int
           The line number from which to save outputs
         """
         if (not self.db_log_output) or (line_num not in self.output_hist_reprs):
             return
         output = self.output_hist_reprs[line_num]
 
         with self.db_output_cache_lock:
             self.db_output_cache.append((line_num, output))
         if self.db_cache_size <= 1:
             self.save_flag.set()
 
     def _writeout_input_cache(self, conn):
         with conn:
             for line in self.db_input_cache:
                 conn.execute("INSERT INTO history VALUES (?, ?, ?, ?)",
                                 (self.session_number,)+line)
 
     def _writeout_output_cache(self, conn):
         with conn:
             for line in self.db_output_cache:
                 conn.execute("INSERT INTO output_history VALUES (?, ?, ?)",
                                 (self.session_number,)+line)
 
     @needs_sqlite
     def writeout_cache(self, conn=None):
         """Write any entries in the cache to the database."""
         if conn is None:
             conn = self.db
 
         with self.db_input_cache_lock:
             try:
                 self._writeout_input_cache(conn)
             except sqlite3.IntegrityError:
                 self.new_session(conn)
                 print("ERROR! Session/line number was not unique in",
                       "database. History logging moved to new session",
                                                 self.session_number)
                 try:
                     # Try writing to the new session. If this fails, don't
                     # recurse
                     self._writeout_input_cache(conn)
                 except sqlite3.IntegrityError:
                     pass
             finally:
                 self.db_input_cache = []
 
         with self.db_output_cache_lock:
             try:
                 self._writeout_output_cache(conn)
             except sqlite3.IntegrityError:
                 print("!! Session/line number for output was not unique",
                       "in database. Output will not be stored.")
             finally:
                 self.db_output_cache = []
 
 
 class HistorySavingThread(threading.Thread):
     """This thread takes care of writing history to the database, so that
     the UI isn't held up while that happens.
 
     It waits for the HistoryManager's save_flag to be set, then writes out
     the history cache. The main thread is responsible for setting the flag when
     the cache size reaches a defined threshold."""
     daemon = True
     stop_now = False
     enabled = True
     def __init__(self, history_manager):
         super(HistorySavingThread, self).__init__()
         self.history_manager = history_manager
         self.enabled = history_manager.enabled
         atexit.register(self.stop)
 
     @needs_sqlite
     def run(self):
         # We need a separate db connection per thread:
         try:
             self.db = sqlite3.connect(self.history_manager.hist_file,
                             **self.history_manager.connection_options
             )
             while True:
                 self.history_manager.save_flag.wait()
                 if self.stop_now:
                     return
                 self.history_manager.save_flag.clear()
                 self.history_manager.writeout_cache(self.db)
         except Exception as e:
             print(("The history saving thread hit an unexpected error (%s)."
                    "History will not be written to the database.") % repr(e))
 
     def stop(self):
         """This can be called from the main thread to safely stop this thread.
 
         Note that it does not attempt to write out remaining history before
         exiting. That should be done by calling the HistoryManager's
         end_session method."""
         self.stop_now = True
         self.history_manager.save_flag.set()
         self.join()
 
 
 # To match, e.g. ~5/8-~2/3
 range_re = re.compile(r"""
 ((?P<startsess>~?\d+)/)?
 (?P<start>\d+)                    # Only the start line num is compulsory
 ((?P<sep>[\-:])
  ((?P<endsess>~?\d+)/)?
  (?P<end>\d+))?
 $""", re.VERBOSE)
 
 
 def extract_hist_ranges(ranges_str):
     """Turn a string of history ranges into 3-tuples of (session, start, stop).
 
     Examples
     --------
     list(extract_input_ranges("~8/5-~7/4 2"))
     [(-8, 5, None), (-7, 1, 4), (0, 2, 3)]
     """
     for range_str in ranges_str.split():
         rmatch = range_re.match(range_str)
         if not rmatch:
             continue
         start = int(rmatch.group("start"))
         end = rmatch.group("end")
         end = int(end) if end else start+1   # If no end specified, get (a, a+1)
         if rmatch.group("sep") == "-":       # 1-3 == 1:4 --> [1, 2, 3]
             end += 1
         startsess = rmatch.group("startsess") or "0"
         endsess = rmatch.group("endsess") or startsess
         startsess = int(startsess.replace("~","-"))
         endsess = int(endsess.replace("~","-"))
         assert endsess >= startsess
 
         if endsess == startsess:
             yield (startsess, start, end)
             continue
         # Multiple sessions in one range:
         yield (startsess, start, None)
         for sess in range(startsess+1, endsess):
             yield (sess, 1, None)
         yield (endsess, 1, end)
 
 
 def _format_lineno(session, line):
     """Helper function to format line numbers properly."""
     if session == 0:
         return str(line)
     return "%s#%s" % (session, line)