Source code for pyrocko.squirrel.io.base

# http://pyrocko.org - GPLv3
#
# The Pyrocko Developers, 21st Century
# ---|P------/S----------~Lg----------

import time
import logging

from pyrocko import util
from pyrocko.io.io_common import FileLoadError
from pyrocko.progress import progress

from .backends import \
    mseed, sac, datacube, stationxml, textfiles, virtual, yaml, tdms_idas

from ..model import to_kind_ids

backend_modules = [
    mseed, sac, datacube, stationxml, textfiles, virtual, yaml, tdms_idas]


logger = logging.getLogger('psq.io')


def make_task(*args):
    return progress.task(*args, logger=logger)


def update_format_providers():
    '''Update global mapping from file format to io backend module.'''

    global g_format_providers
    g_format_providers = {}
    for mod in backend_modules:
        for format in mod.provided_formats():
            if format not in g_format_providers:
                g_format_providers[format] = []

            g_format_providers[format].append(mod)


g_format_providers = {}
update_format_providers()


[docs]class FormatDetectionFailed(FileLoadError): ''' Exception raised when file format detection fails. ''' def __init__(self, path): FileLoadError.__init__( self, 'format detection failed for file: %s' % path)
[docs]class UnknownFormat(Exception): ''' Exception raised when user requests an unknown file format. ''' def __init__(self, format): Exception.__init__( self, 'unknown format: %s' % format)
[docs]def get_backend(fmt): ''' Get squirrel io backend module for a given file format. :param fmt: Format identifier. :type fmt: str ''' try: return g_format_providers[fmt][0] except KeyError: raise UnknownFormat(fmt)
[docs]def detect_format(path): ''' Determine file type from first 512 bytes. :param path: Path to file. :type path: str ''' if path.startswith('virtual:'): return 'virtual' try: with open(path, 'rb') as f: data = f.read(512) except (OSError, IOError): raise FormatDetectionFailed(path) fmt = None for mod in backend_modules: fmt = mod.detect(data) if fmt is not None: return fmt raise FormatDetectionFailed(path)
[docs]def supported_formats(): ''' Get list of file formats supported by Squirrel. ''' return sorted(g_format_providers.keys())
g_content_kinds = ['waveform', 'station', 'channel', 'response', 'event']
[docs]def supported_content_kinds(): ''' Get list of supported content kinds offered through Squirrel. ''' return g_content_kinds + ['waveform_promise']
[docs]def iload( paths, segment=None, format='detect', database=None, check=True, skip_unchanged=False, content=g_content_kinds, show_progress=True, update_selection=None): ''' Iteratively load content or index/reindex meta-information from files. :param paths: Iterator yielding file names to load from or a Squirrel selection object providing the file names. :type paths: iterator yielding :py:class:`str` or :py:class:`~pyrocko.squirrel.selection.Selection` :param segment: File-specific segment identifier (can only be used when loading from a single file). :type segment: int :param format: File format identifier or ``'detect'`` for autodetection. When loading from a selection, per-file format assignation is taken from the hint in the selection and this flag is ignored. :type format: str :param database: Database to use for meta-information caching. When loading from a selection, this should be ``None`` and the database from the selection is used. :type database: :py:class:`~pyrocko.squirrel.database.Database` :param check: If ``True``, investigate modification time and file sizes of known files to debunk modified files (pessimistic mode), or ``False`` to deactivate checks (optimistic mode). :type check: bool :param skip_unchanged: If ``True``, only yield index nuts for new / modified files. :type skip_unchanged: bool :param content: Selection of content types to load. :type content: :py:class:`list` of :py:class:`str` This generator yields :py:class:`~pyrocko.squirrel.model.Nut` objects for individual pieces of information found when reading the given files. Such a nut may represent a waveform, a station, a channel, an event or other data type. The nut itself only contains the meta-information. The actual content information is attached to the nut if requested. All nut meta-information is stored in the squirrel meta-information database. If possible, this function avoids accessing the actual disk files and provides the requested information straight from the database. Modified files are recognized and reindexed as needed. ''' from ..selection import Selection n_db = 0 n_load = 0 selection = None kind_ids = to_kind_ids(content) if isinstance(paths, str): paths = [paths] else: if segment is not None: raise TypeError( 'iload: segment argument can only be used when loading from ' 'a single file') if isinstance(paths, Selection): selection = paths if database is not None: raise TypeError( 'iload: database argument must be None when called with a ' 'selection') database = selection.get_database() if skip_unchanged and not isinstance(paths, Selection): raise TypeError( 'iload: need selection when called with "skip_unchanged=True"') temp_selection = None transaction = None if database: if not selection: # Avoid creating temporary selection for small batches. # this is helpful because then, we can avoid locking the database, # e.g. during loading of content, when the content has not been # modified. paths = util.short_to_list(100, paths) if not (isinstance(paths, list) and len(paths) < 100 and not skip_unchanged): temp_selection = database.new_selection( paths, show_progress=show_progress, format=format) selection = temp_selection if skip_unchanged: selection.flag_modified(check) if selection: # undig_grouped starts a long select which causes deadlocks # when transaction is started after starting the select, therefore # the transaction has to be started before in these cases. # The db will be locked for a long time in this case. This could be # solved either by breaking the indexing into smaller blocks in # the caller or by modifying undig_grouped to allow limit and # offset and add an outer loop below. transaction = database.transaction( 'update content index') transaction.begin() it = selection.undig_grouped(skip_unchanged=skip_unchanged) else: # The list() causes the query to finish, so we don't have to lock, # and can start a transaction only when encountering a modified/new # file. it = list(database.undig_few(paths, format=format)) else: it = (((format, path), []) for path in paths) try: n_files_total = len(it) except TypeError: n_files_total = None task = None if show_progress: if not kind_ids: task = make_task('Indexing files', n_files_total) else: task = make_task('Loading files', n_files_total) n_files = 0 tcommit = time.time() clean = False try: for (format, path), old_nuts in it: if task is not None: condition = '(nuts: %i from file, %i from cache)\n %s' % ( n_load, n_db, path) task.update(n_files, condition) n_files += 1 if database and transaction: tnow = time.time() if tnow - tcommit > 20. or n_files % 1000 == 0: transaction.commit() tcommit = tnow transaction.begin() try: if check and old_nuts and old_nuts[0].file_modified(): old_nuts = [] modified = True else: modified = False if segment is not None: old_nuts = [ nut for nut in old_nuts if nut.file_segment == segment] if old_nuts: db_only_operation = not kind_ids or all( nut.kind_id in kind_ids and nut.content_in_db for nut in old_nuts) if db_only_operation: # logger.debug('using cached information for file %s, ' # % path) for nut in old_nuts: if nut.kind_id in kind_ids: database.undig_content(nut) n_db += 1 yield nut continue if format == 'detect': if old_nuts and not old_nuts[0].file_modified(): format_this = old_nuts[0].file_format else: format_this = detect_format(path) else: format_this = format mod = get_backend(format_this) mtime, size = mod.get_stats(path) if segment is not None: logger.debug( 'Reading file "%s", segment "%s".' % (path, segment)) else: logger.debug( 'Reading file "%s".' % path) nuts = [] for nut in mod.iload(format_this, path, segment, content): nut.file_path = path nut.file_format = format_this nut.file_mtime = mtime nut.file_size = size if nut.content is not None: nut.content._squirrel_key = nut.key nuts.append(nut) n_load += 1 yield nut if database and nuts != old_nuts: if old_nuts or modified: logger.debug( 'File has been modified since last access: %s' % path) if segment is not None: nuts = list(mod.iload(format_this, path, None, [])) for nut in nuts: nut.file_path = path nut.file_format = format_this nut.file_mtime = mtime nut.file_size = size if not transaction: transaction = database.transaction( 'update content index') transaction.begin() database.dig(nuts, transaction=transaction) if update_selection is not None: update_selection._set_file_states_force_check( [path], transaction=transaction) update_selection._update_nuts(transaction=transaction) except FileLoadError: logger.error('Cannot read file: %s' % path) if database: if not transaction: transaction = database.transaction( 'update content index') transaction.begin() database.reset(path, transaction=transaction) clean = True finally: if task is not None: condition = '(nuts: %i from file, %i from cache)' % (n_load, n_db) task.update(n_files, condition) if clean: task.done(condition) else: task.fail(condition + ' terminated') if database and transaction: transaction.commit() transaction.close() if temp_selection: del temp_selection
__all__ = [ 'iload', 'detect_format', 'supported_formats', 'supported_content_kinds', 'get_backend', 'FormatDetectionFailed', 'UnknownFormat', ]