# http://pyrocko.org - GPLv3
#
# The Pyrocko Developers, 21st Century
# ---|P------/S----------~Lg----------
from __future__ import absolute_import, print_function
import sys
import os
import logging
import sqlite3
import re
import time
from pyrocko.io.io_common import FileLoadError
from pyrocko import util
from pyrocko.guts import Object, Int, List, Dict, Tuple, String
from . import error, io
from .model import Nut, to_kind_id, to_kind, separator
from .error import SquirrelError
logger = logging.getLogger('psq.database')
guts_prefix = 'squirrel'
def abspath(path):
if not path.startswith('virtual:') and not path.startswith('client:'):
return os.path.abspath(path)
else:
return path
class ExecuteGet1Error(SquirrelError):
pass
def execute_get1(connection, sql, args):
rows = list(connection.execute(sql, args))
if len(rows) == 1:
return rows[0]
else:
raise ExecuteGet1Error('Expected database entry not found.')
g_databases = {}
def get_database(path):
path = os.path.abspath(path)
if path not in g_databases:
g_databases[path] = Database(path)
return g_databases[path]
def close_database(database):
path = os.path.abspath(database._database_path)
database._conn.close()
if path in g_databases:
del g_databases[path]
class Transaction(object):
def __init__(self, conn, mode='immediate', retry_interval=0.1):
self.cursor = conn.cursor()
assert mode in ('deferred', 'immediate', 'exclusive')
self.mode = mode
self.depth = 0
self.rollback_wanted = False
self.retry_interval = retry_interval
def begin(self):
if self.depth == 0:
tries = 0
while True:
try:
tries += 1
self.cursor.execute('BEGIN %s' % self.mode.upper())
break
except sqlite3.OperationalError as e:
if not str(e) == 'database is locked':
raise
logger.info(
'Database is locked retrying in %s s. Tries: %i'
% (self.retry_interval, tries))
time.sleep(self.retry_interval)
self.depth += 1
def commit(self):
self.depth -= 1
if self.depth == 0:
if not self.rollback_wanted:
self.cursor.execute('COMMIT')
else:
self.cursor.execute('ROLLBACK')
logger.warning('Deferred rollback executed.')
self.rollback_wanted = False
def rollback(self):
self.depth -= 1
if self.depth == 0:
self.cursor.execute('ROLLBACK')
self.rollback_wanted = False
else:
logger.warning('Deferred rollback scheduled.')
self.rollback_wanted = True
def close(self):
self.cursor.close()
def __enter__(self):
self.begin()
return self.cursor
def __exit__(self, exc_type, exc_value, traceback):
if exc_type is None:
self.commit()
else:
self.rollback()
if self.depth == 0:
self.close()
[docs]class Database(object):
'''
Shared meta-information database used by Squirrel.
'''
def __init__(self, database_path=':memory:', log_statements=False):
self._database_path = database_path
if database_path != ':memory:':
util.ensuredirs(database_path)
try:
logger.debug('Opening connection to database: %s' % database_path)
self._conn = sqlite3.connect(database_path, isolation_level=None)
except sqlite3.OperationalError:
raise error.SquirrelError(
'Cannot connect to database: %s' % database_path)
self._conn.text_factory = str
self._tables = {}
if log_statements:
self._conn.set_trace_callback(self._log_statement)
self._initialize_db()
self._basepath = None
def set_basepath(self, basepath):
if basepath is not None:
self._basepath = os.path.abspath(basepath)
else:
self._basepath = None
def relpath(self, path):
if self._basepath is not None and path.startswith(
self._basepath + os.path.sep):
return path[len(self._basepath) + 1:]
else:
return path
def abspath(self, path):
if self._basepath is not None and not path.startswith('virtual:') \
and not path.startswith('client:') \
and not os.path.isabs(path):
return os.path.join(self._basepath, path)
else:
return path
def _log_statement(self, statement):
logger.debug(statement)
def get_connection(self):
return self._conn
def transaction(self, mode='immediate'):
return Transaction(self._conn, mode)
def _register_table(self, s):
m = re.search(r'(\S+)\s*\(([^)]+)\)', s)
table_name = m.group(1)
dtypes = m.group(2)
table_header = []
for dele in dtypes.split(','):
table_header.append(dele.split()[:2])
self._tables[table_name] = table_header
return s
def _initialize_db(self):
with self.transaction() as cursor:
cursor.execute(
'''PRAGMA recursive_triggers = true''')
cursor.execute(
'''PRAGMA busy_timeout = 30000''')
if 2 == len(list(
cursor.execute(
'''
SELECT name FROM sqlite_master
WHERE type = 'table' AND name IN (
'files',
'persistent')
'''))):
return
cursor.execute(self._register_table(
'''
CREATE TABLE IF NOT EXISTS files (
file_id integer PRIMARY KEY,
path text,
format text,
mtime float,
size integer)
'''))
cursor.execute(
'''
CREATE UNIQUE INDEX IF NOT EXISTS index_files_path
ON files (path)
''')
cursor.execute(self._register_table(
'''
CREATE TABLE IF NOT EXISTS nuts (
nut_id integer PRIMARY KEY AUTOINCREMENT,
file_id integer,
file_segment integer,
file_element integer,
kind_id integer,
kind_codes_id integer,
tmin_seconds integer,
tmin_offset integer,
tmax_seconds integer,
tmax_offset integer,
kscale integer)
'''))
cursor.execute(
'''
CREATE UNIQUE INDEX IF NOT EXISTS index_nuts_file_element
ON nuts (file_id, file_segment, file_element)
''')
cursor.execute(self._register_table(
'''
CREATE TABLE IF NOT EXISTS kind_codes (
kind_codes_id integer PRIMARY KEY,
kind_id integer,
codes text,
deltat float)
'''))
cursor.execute(
'''
CREATE UNIQUE INDEX IF NOT EXISTS index_kind_codes
ON kind_codes (kind_id, codes, deltat)
''')
cursor.execute(self._register_table(
'''
CREATE TABLE IF NOT EXISTS kind_codes_count (
kind_codes_id integer PRIMARY KEY,
count integer)
'''))
cursor.execute(
'''
CREATE INDEX IF NOT EXISTS index_nuts_file_id
ON nuts (file_id)
''')
cursor.execute(
'''
CREATE TRIGGER IF NOT EXISTS delete_nuts_on_delete_file
BEFORE DELETE ON files FOR EACH ROW
BEGIN
DELETE FROM nuts where file_id == old.file_id;
END
''')
# trigger only on size to make silent update of mtime possible
cursor.execute(
'''
CREATE TRIGGER IF NOT EXISTS delete_nuts_on_update_file
BEFORE UPDATE OF size ON files FOR EACH ROW
BEGIN
DELETE FROM nuts where file_id == old.file_id;
END
''')
cursor.execute(
'''
CREATE TRIGGER IF NOT EXISTS increment_kind_codes
BEFORE INSERT ON nuts FOR EACH ROW
BEGIN
INSERT OR IGNORE INTO kind_codes_count
VALUES (new.kind_codes_id, 0);
UPDATE kind_codes_count
SET count = count + 1
WHERE new.kind_codes_id == kind_codes_id;
END
''')
cursor.execute(
'''
CREATE TRIGGER IF NOT EXISTS decrement_kind_codes
BEFORE DELETE ON nuts FOR EACH ROW
BEGIN
UPDATE kind_codes_count
SET count = count - 1
WHERE old.kind_codes_id == kind_codes_id;
END
''')
cursor.execute(self._register_table(
'''
CREATE TABLE IF NOT EXISTS persistent (
name text UNIQUE)
'''))
[docs] def dig(self, nuts, transaction=None):
'''
Store or update content meta-information.
Given ``nuts`` are assumed to represent an up-to-date and complete
inventory of a set of files. Any old information about these files is
first pruned from the database (via database triggers). If such content
is part of a live selection, it is also removed there. Then the new
content meta-information is inserted into the main database. The
content is not automatically inserted into the live selections again.
It is in the responsibility of the selection object to perform this
step.
'''
nuts = list(nuts)
if not nuts:
return
files = set()
kind_codes = set()
for nut in nuts:
files.add((
self.relpath(nut.file_path),
nut.file_format,
nut.file_mtime,
nut.file_size))
kind_codes.add((nut.kind_id, nut.codes, nut.deltat or 0.0))
with (transaction or self.transaction()) as c:
c.executemany(
'INSERT OR IGNORE INTO files VALUES (NULL,?,?,?,?)', files)
c.executemany(
'''UPDATE files SET
format = ?, mtime = ?, size = ?
WHERE path == ?
''',
((x[1], x[2], x[3], x[0]) for x in files))
c.executemany(
'INSERT OR IGNORE INTO kind_codes VALUES (NULL,?,?,?)',
kind_codes)
c.executemany(
'''
INSERT INTO nuts VALUES
(NULL, (
SELECT file_id FROM files
WHERE path == ?
),?,?,?,
(
SELECT kind_codes_id FROM kind_codes
WHERE kind_id == ? AND codes == ? AND deltat == ?
), ?,?,?,?,?)
''',
((self.relpath(nut.file_path),
nut.file_segment, nut.file_element,
nut.kind_id,
nut.kind_id, nut.codes, nut.deltat or 0.0,
nut.tmin_seconds, nut.tmin_offset,
nut.tmax_seconds, nut.tmax_offset,
nut.kscale) for nut in nuts))
def undig(self, path):
path = self.relpath(abspath(path))
sql = '''
SELECT
files.path,
files.format,
files.mtime,
files.size,
nuts.file_segment,
nuts.file_element,
kind_codes.kind_id,
kind_codes.codes,
nuts.tmin_seconds,
nuts.tmin_offset,
nuts.tmax_seconds,
nuts.tmax_offset,
kind_codes.deltat
FROM files
INNER JOIN nuts ON files.file_id = nuts.file_id
INNER JOIN kind_codes
ON nuts.kind_codes_id == kind_codes.kind_codes_id
WHERE path == ?
'''
return [Nut(values_nocheck=(self.abspath(row[0]),) + row[1:])
for row in self._conn.execute(sql, (path,))]
def undig_all(self):
sql = '''
SELECT
files.path,
files.format,
files.mtime,
files.size,
nuts.file_segment,
nuts.file_element,
kind_codes.kind_id,
kind_codes.codes,
nuts.tmin_seconds,
nuts.tmin_offset,
nuts.tmax_seconds,
nuts.tmax_offset,
kind_codes.deltat
FROM files
INNER JOIN nuts ON files.file_id == nuts.file_id
INNER JOIN kind_codes
ON nuts.kind_codes_id == kind_codes.kind_codes_id
'''
nuts = []
path = None
for values in self._conn.execute(sql):
if path is not None and values[0] != path:
yield path, nuts
nuts = []
path = self.abspath(values[0])
if values[1] is not None:
nuts.append(Nut(values_nocheck=(path,) + values[1:]))
if path is not None:
yield path, nuts
def undig_many(self, paths, show_progress=True):
selection = self.new_selection(paths, show_progress=show_progress)
for (_, path), nuts in selection.undig_grouped():
yield path, nuts
del selection
def new_selection(self, paths=None, show_progress=True):
from .selection import Selection
selection = Selection(self)
if paths:
selection.add(paths, show_progress=show_progress)
return selection
def undig_content(self, nut):
return None
[docs] def remove(self, path):
'''
Prune content meta-information about a given file.
All content pieces belonging to file ``path`` are removed from the
main database and any attached live selections (via database triggers).
'''
path = self.relpath(abspath(path))
with self.transaction() as cursor:
cursor.execute(
'DELETE FROM files WHERE path = ?', (path,))
[docs] def remove_glob(self, pattern):
'''
Prune content meta-information about files matching given pattern.
All content pieces belonging to files who's pathes match the given
``pattern`` are removed from the main database and any attached live
selections (via database triggers).
'''
with self.transaction() as cursor:
return cursor.execute(
'DELETE FROM files WHERE path GLOB ?', (pattern,)).rowcount
def _remove_volatile(self):
'''
Prune leftover volatile content from database.
If the cleanup handler of an attached selection is not called, e.g. due
to a crash or terminated process, volatile content will not be removed
properly. This method will delete such leftover entries.
This is a mainenance operatation which should only be called when no
apps are using the database because it would remove volatile content
currently used by the apps.
'''
with self.transaction() as cursor:
return cursor.execute(
'''
DELETE FROM files
WHERE path LIKE "virtual:volatile:%"').rowcount
''').rowcount
[docs] def reset(self, path, transaction=None):
'''
Prune information associated with a given file, but keep the file path.
This method is called when reading a file failed. File attributes,
format, size and modification time are set to NULL. File content
meta-information is removed from the database and any attached live
selections (via database triggers).
'''
path = self.relpath(abspath(path))
with (transaction or self.transaction()) as cursor:
cursor.execute(
'''
UPDATE files SET
format = NULL,
mtime = NULL,
size = NULL
WHERE path = ?
''', (path,))
[docs] def silent_touch(self, path):
'''
Update modification time of file without initiating reindexing.
Useful to prolong validity period of data with expiration date.
'''
apath = abspath(path)
path = self.relpath(apath)
with self.transaction() as cursor:
sql = 'SELECT format, size FROM files WHERE path = ?'
fmt, size = execute_get1(cursor, sql, (path,))
mod = io.get_backend(fmt)
mod.touch(apath)
file_stats = mod.get_stats(apath)
if file_stats[1] != size:
raise FileLoadError(
'Silent update for file "%s" failed: size has changed.'
% apath)
sql = '''
UPDATE files
SET mtime = ?
WHERE path = ?
'''
cursor.execute(sql, (file_stats[0], path))
def _iter_counts(self, kind=None, kind_codes_count='kind_codes_count'):
args = []
sel = ''
if kind is not None:
sel = 'AND kind_codes.kind_id == ?'
args.append(to_kind_id(kind))
sql = ('''
SELECT
kind_codes.kind_id,
kind_codes.codes,
kind_codes.deltat,
%(kind_codes_count)s.count
FROM %(kind_codes_count)s
INNER JOIN kind_codes
ON %(kind_codes_count)s.kind_codes_id
== kind_codes.kind_codes_id
WHERE %(kind_codes_count)s.count > 0
''' + sel + '''
''') % {'kind_codes_count': kind_codes_count}
for kind_id, codes, deltat, count in self._conn.execute(sql, args):
yield (
to_kind(kind_id),
tuple(codes.split(separator)),
deltat), count
def _iter_deltats(self, kind=None, kind_codes_count='kind_codes_count'):
args = []
sel = ''
if kind is not None:
assert isinstance(kind, str)
sel = 'AND kind_codes.kind_id == ?'
args.append(to_kind_id(kind))
sql = ('''
SELECT DISTINCT kind_codes.deltat FROM %(kind_codes_count)s
INNER JOIN kind_codes
ON %(kind_codes_count)s.kind_codes_id
== kind_codes.kind_codes_id
WHERE %(kind_codes_count)s.count > 0
''' + sel + '''
ORDER BY kind_codes.deltat
''') % {'kind_codes_count': kind_codes_count}
for row in self._conn.execute(sql, args):
yield row[0]
def _iter_codes(self, kind=None, kind_codes_count='kind_codes_count'):
args = []
sel = ''
if kind is not None:
assert isinstance(kind, str)
sel = 'AND kind_codes.kind_id == ?'
args.append(to_kind_id(kind))
sql = ('''
SELECT DISTINCT kind_codes.codes FROM %(kind_codes_count)s
INNER JOIN kind_codes
ON %(kind_codes_count)s.kind_codes_id
== kind_codes.kind_codes_id
WHERE %(kind_codes_count)s.count > 0
''' + sel + '''
ORDER BY kind_codes.codes
''') % {'kind_codes_count': kind_codes_count}
for row in self._conn.execute(sql, args):
yield tuple(row[0].split(separator))
def _iter_kinds(self, codes=None, kind_codes_count='kind_codes_count'):
args = []
sel = ''
if codes is not None:
assert isinstance(codes, tuple)
sel = 'AND kind_codes.codes == ?'
args.append(separator.join(codes))
sql = ('''
SELECT DISTINCT kind_codes.kind_id FROM %(kind_codes_count)s
INNER JOIN kind_codes
ON %(kind_codes_count)s.kind_codes_id
== kind_codes.kind_codes_id
WHERE %(kind_codes_count)s.count > 0
''' + sel + '''
ORDER BY kind_codes.kind_id
''') % {'kind_codes_count': kind_codes_count}
for row in self._conn.execute(sql, args):
yield to_kind(row[0])
def iter_paths(self):
for row in self._conn.execute('''SELECT path FROM files'''):
yield self.abspath(row[0])
def iter_nnuts_by_file(self):
sql = '''
SELECT
path,
(SELECT COUNT(*) FROM nuts WHERE nuts.file_id = files.file_id)
FROM files
'''
for row in self._conn.execute(sql):
yield (self.abspath(row[0]),) + row[1:]
def iter_kinds(self, codes=None):
return self._iter_kinds(codes=codes)
def iter_codes(self, kind=None):
return self._iter_codes(kind=kind)
def iter_counts(self, kind=None):
return self._iter_counts(kind=kind)
def get_paths(self):
return list(self.iter_paths())
def get_kinds(self, codes=None):
return list(self.iter_kinds(codes=codes))
def get_codes(self, kind=None):
return list(self.iter_codes(kind=kind))
def get_counts(self, kind=None):
d = {}
for (k, codes, deltat), count in self.iter_counts():
if k not in d:
v = d[k] = {}
else:
v = d[k]
if codes not in v:
v[codes] = 0
v[codes] += count
if kind is not None:
return d[kind]
else:
return d
def get_nfiles(self):
sql = '''SELECT COUNT(*) FROM files'''
for row in self._conn.execute(sql):
return row[0]
def get_nnuts(self):
sql = '''SELECT COUNT(*) FROM nuts'''
for row in self._conn.execute(sql):
return row[0]
def get_nnuts_by_file(self):
return list(self.iter_nnuts_by_file())
def get_total_size(self):
sql = '''
SELECT SUM(files.size) FROM files
'''
for row in self._conn.execute(sql):
return row[0] or 0
def get_persistent_names(self):
sql = '''
SELECT name FROM persistent
'''
return [row[0] for row in self._conn.execute(sql)]
def get_stats(self):
return DatabaseStats(
nfiles=self.get_nfiles(),
nnuts=self.get_nnuts(),
kinds=self.get_kinds(),
codes=self.get_codes(),
counts=self.get_counts(),
total_size=self.get_total_size(),
persistent=self.get_persistent_names())
def __str__(self):
return str(self.get_stats())
def print_tables(self, stream=None):
for table in [
'persistent',
'files',
'nuts',
'kind_codes',
'kind_codes_count']:
self.print_table(table, stream=stream)
def print_table(self, name, stream=None):
if stream is None:
stream = sys.stdout
class hstr(str):
def __repr__(self):
return self
w = stream.write
w('\n')
w('\n')
w(name)
w('\n')
sql = 'SELECT * FROM %s' % name
tab = []
if name in self._tables:
headers = self._tables[name]
tab.append([None for _ in headers])
tab.append([hstr(x[0]) for x in headers])
tab.append([hstr(x[1]) for x in headers])
tab.append([None for _ in headers])
for row in self._conn.execute(sql):
tab.append([x for x in row])
widths = [
max((len(repr(x)) if x is not None else 0) for x in col)
for col in zip(*tab)]
for row in tab:
w(' '.join(
(repr(x).ljust(wid) if x is not None else ''.ljust(wid, '-'))
for (x, wid) in zip(row, widths)))
w('\n')
w('\n')
[docs]class DatabaseStats(Object):
'''
Container to hold statistics about contents cached in meta-information db.
'''
nfiles = Int.T(
help='Number of files in database.')
nnuts = Int.T(
help='Number of index nuts in database.')
codes = List.T(
Tuple.T(content_t=String.T()),
help='Available code sequences in database, e.g. '
'(agency, network, station, location) for stations nuts.')
kinds = List.T(
String.T(),
help='Available content types in database.')
total_size = Int.T(
help='Aggregated file size of files referenced in database.')
counts = Dict.T(
String.T(), Dict.T(Tuple.T(content_t=String.T()), Int.T()),
help='Breakdown of how many nuts of any content type and code '
'sequence are available in database, ``counts[kind][codes]``.')
persistent = List.T(
String.T(),
help='Names of persistent selections stored in database.')
def __str__(self):
kind_counts = dict(
(kind, sum(self.counts[kind].values())) for kind in self.kinds)
codes = ['.'.join(x) for x in self.codes]
if len(codes) > 20:
scodes = '\n' + util.ewrap(codes[:10], indent=' ') \
+ '\n [%i more]\n' % (len(codes) - 20) \
+ util.ewrap(codes[-10:], indent=' ')
else:
scodes = '\n' + util.ewrap(codes, indent=' ') \
if codes else '<none>'
s = '''
Available codes: %s
Number of files: %i
Total size of known files: %s
Number of index nuts: %i
Available content kinds: %s
Persistent selections: %s''' % (
scodes,
self.nfiles,
util.human_bytesize(self.total_size),
self.nnuts,
', '.join('%s: %i' % (
kind, kind_counts[kind]) for kind in sorted(self.kinds)),
', '.join(self.persistent))
return s
__all__ = [
'Database',
'DatabaseStats',
]
