# -*- coding: utf-8 -*-
# vim: tabstop=4 shiftwidth=4 softtabstop=4
#
# Copyright (C) 2015-2023 GEM Foundation
#
# OpenQuake is free software: you can redistribute it and/or modify it
# under the terms of the GNU Affero General Public License as published
# by the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# OpenQuake is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with OpenQuake. If not, see <http://www.gnu.org/licenses/>.
import io
import os
import re
import gzip
import collections
import numpy
import h5py
from openquake.baselib import hdf5, performance, general
from openquake.commonlib.logs import (
get_datadir, get_last_calc_id, CALC_REGEX, dbcmd, init)
# FIXME: you should never use this
[docs]def hdf5new(datadir=None):
"""
Return a new `hdf5.File by` instance with name determined by the last
calculation in the datadir (plus one). Set the .path attribute to the
generated filename.
"""
datadir = datadir or get_datadir()
if not os.path.exists(datadir):
os.makedirs(datadir)
calc_id = get_last_calc_id(datadir) + 1
fname = os.path.join(datadir, 'calc_%d.hdf5' % calc_id)
new = hdf5.File(fname, 'w')
new.path = fname
performance.init_performance(new)
return new
def _read(calc_id: int, datadir, mode, haz_id=None):
# low level function to read a datastore file
ddir = datadir or get_datadir()
ppath = None
# look in the db
job = dbcmd('get_job', calc_id)
if job:
jid = job.id
path = job.ds_calc_dir + '.hdf5'
hc_id = job.hazard_calculation_id
if not hc_id and haz_id:
dbcmd('update_job', jid, {'hazard_calculation_id': haz_id})
hc_id = haz_id
if hc_id and hc_id != jid:
hc = dbcmd('get_job', hc_id)
if hc:
ppath = hc.ds_calc_dir + '.hdf5'
else:
ppath = os.path.join(ddir, 'calc_%d.hdf5' % hc_id)
else: # when using oq run there is no job in the db
path = os.path.join(ddir, 'calc_%s.hdf5' % calc_id)
return DataStore(path, ppath, mode)
[docs]def read(calc_id, mode='r', datadir=None, parentdir=None, read_parent=True):
"""
:param calc_id: calculation ID or filename
:param mode: 'r' or 'w'
:param datadir: the directory where to look
:param parentdir: the datadir of the parent calculation
:param read_parent: read the parent calculation if it is there
:returns: the corresponding DataStore instance
Read the datastore, if it exists and it is accessible.
"""
if isinstance(calc_id, str): # pathname
dstore = DataStore(calc_id, mode=mode)
else:
dstore = _read(calc_id, datadir, mode)
try:
hc_id = dstore['oqparam'].hazard_calculation_id
except KeyError: # no oqparam
hc_id = None
if read_parent and hc_id:
dstore.parent = _read(hc_id, datadir, mode='r')
dstore.ppath = dstore.parent.filename
return dstore.open(mode)
[docs]def new(calc_id, oqparam, datadir=None, mode=None):
"""
:param calc_id:
if integer > 0 look in the database and then on the filesystem
if integer < 0 look at the old calculations in the filesystem
:param oqparam:
OqParam instance with the validated parameters of the calculation
:returns:
a DataStore instance associated to the given calc_id
"""
dstore = _read(calc_id, mode, datadir)
dstore['oqparam'] = oqparam
if oqparam.hazard_calculation_id:
dstore.ppath = read(calc_id, 'r', datadir).ppath
return dstore
[docs]def build_dstore_log(description='custom calculation', parent=(), ini=None):
"""
:returns: DataStore instance associated to the .calc_id
"""
if ini is not None:
dic = ini
else:
dic = dict(description=description, calculation_mode='custom')
log = init('job', dic)
dstore = new(log.calc_id, log.get_oqparam(validate=False))
dstore.parent = parent
return dstore, log
[docs]def read_hc_id(hdf5):
"""
Getting the hazard_calculation_id, if any
"""
try:
oq = hdf5['oqparam']
except KeyError: # oqparam not saved yet
return
except OSError: # file open by another process with oqparam not flushed
return
return oq.hazard_calculation_id
[docs]class DataStore(collections.abc.MutableMapping):
"""
DataStore class to store the inputs/outputs of a calculation on the
filesystem.
Here is a minimal example of usage:
>>> dstore, log = build_dstore_log()
>>> with dstore, log:
... dstore['example'] = 42
... print(dstore['example'][()])
42
When reading the items, the DataStore will return a generator. The
items will be ordered lexicographically according to their name.
There is a serialization protocol to store objects in the datastore.
An object is serializable if it has a method `__toh5__` returning
an array and a dictionary, and a method `__fromh5__` taking an array
and a dictionary and populating the object.
For an example of use see :class:`openquake.hazardlib.site.SiteCollection`.
"""
calc_id = None # set at instantiation time
job = None # set at instantiation time
opened = 0
closed = 0
def __init__(self, path, ppath=None, mode=None):
self.filename = path
self.ppath = ppath
self.calc_id, datadir = extract_calc_id_datadir(path)
self.tempname = self.filename[:-5] + '_tmp.hdf5'
if not os.path.exists(datadir) and mode != 'r':
os.makedirs(datadir)
self.parent = () # can be set later
self.datadir = datadir
self.mode = mode or ('r+' if os.path.exists(self.filename) else 'w')
if self.mode == 'r' and not os.path.exists(self.filename):
raise IOError('File not found: %s' % self.filename)
self.hdf5 = () # so that `key in self.hdf5` is valid
self.open(self.mode)
if mode != 'r': # w, a or r+
performance.init_performance(self.hdf5)
[docs] def open(self, mode):
"""
Open the underlying .hdf5 file
"""
if self.hdf5 == (): # not already open
try:
self.hdf5 = hdf5.File(self.filename, mode)
except OSError as exc:
raise OSError('%s in %s' % (exc, self.filename))
hc_id = read_hc_id(self.hdf5)
if hc_id:
self.parent = read(hc_id)
return self
@property
def export_dir(self):
"""
Return the underlying export directory
"""
edir = getattr(self, '_export_dir', None) or self['oqparam'].export_dir
return edir
@export_dir.setter
def export_dir(self, value):
"""
Set the export directory
"""
self._export_dir = value
[docs] def getitem(self, name):
"""
Return a dataset by using h5py.File.__getitem__
"""
try:
return h5py.File.__getitem__(self.hdf5, name)
except KeyError:
if self.parent != ():
if not self.parent.hdf5:
self.parent.open('r')
return self.parent.getitem(name)
else:
raise
[docs] def swmr_on(self):
"""
Enable the SWMR mode on the underlying HDF5 file
"""
self.close() # flush everything
self.open('a')
if self.parent != ():
self.parent.open('r')
try:
self.hdf5.swmr_mode = True
except (ValueError, RuntimeError): # already set
pass
[docs] def set_attrs(self, key, **kw):
"""
Set the HDF5 attributes of the given key
"""
self.hdf5.save_attrs(key, kw)
[docs] def set_shape_descr(self, key, **kw):
"""
Set shape attributes
"""
hdf5.set_shape_descr(self.hdf5, key, kw)
[docs] def get_attr(self, key, name, default=None):
"""
:param key: dataset path
:param name: name of the attribute
:param default: value to return if the attribute is missing
"""
try:
obj = h5py.File.__getitem__(self.hdf5, key)
except KeyError:
if self.parent != ():
return self.parent.get_attr(key, name, default)
else:
raise
try:
return obj.attrs[name]
except KeyError:
if default is None:
raise
return default
[docs] def get_attrs(self, key):
"""
:param key: dataset path
:returns: dictionary of attributes for that path
"""
try:
dset = h5py.File.__getitem__(self.hdf5, key)
except KeyError:
if self.parent != ():
dset = h5py.File.__getitem__(self.parent.hdf5, key)
else:
raise
return dict(dset.attrs)
[docs] def create_dset(self, key, dtype, shape=(None,), compression=None,
fillvalue=0, attrs=None):
"""
Create a one-dimensional HDF5 dataset.
:param key: name of the dataset
:param dtype: dtype of the dataset (usually composite)
:param shape: shape of the dataset, possibly extendable
:param compression: the kind of HDF5 compression to use
:param attrs: dictionary of attributes of the dataset
:returns: a HDF5 dataset
"""
if isinstance(dtype, numpy.ndarray):
dset = hdf5.create(
self.hdf5, key, dtype.dtype, dtype.shape,
compression, fillvalue, attrs)
dset[:] = dtype
return dset
return hdf5.create(
self.hdf5, key, dtype, shape, compression, fillvalue, attrs)
[docs] def create_df(self, key, nametypes, compression=None, **kw):
"""
Create a HDF5 datagroup readable as a pandas DataFrame
:param key:
name of the dataset
:param nametypes:
list of pairs (name, dtype) or (name, array) or DataFrame
:param compression:
the kind of HDF5 compression to use
:param kw:
extra attributes to store
"""
return self.hdf5.create_df(key, nametypes, compression, **kw)
[docs] def export_path(self, relname, export_dir=None):
"""
Return the path of the exported file by adding the export_dir in
front, the calculation ID at the end.
:param relname: relative file name
:param export_dir: export directory (if None use .export_dir)
"""
# removing inner slashed to avoid creating intermediate directories
name, ext = relname.replace('/', '-').rsplit('.', 1)
newname = '%s_%s.%s' % (name, self.calc_id, ext)
if export_dir is None:
export_dir = self.export_dir
return os.path.join(export_dir, newname)
[docs] def build_fname(self, prefix, postfix, fmt, export_dir=None):
"""
Build a file name from a realization, by using prefix and extension.
:param prefix: the prefix to use
:param postfix: the postfix to use (can be a realization object)
:param fmt: the extension ('csv', 'xml', etc)
:param export_dir: export directory (if None use .export_dir)
:returns: relative pathname including the extension
"""
if hasattr(postfix, 'sm_lt_path'): # is a realization
fname = '%s-rlz-%03d.%s' % (prefix, postfix.ordinal, fmt)
else:
fname = prefix + ('-%s' % postfix if postfix else '') + '.' + fmt
return self.export_path(fname, export_dir)
[docs] def flush(self):
"""Flush the underlying hdf5 file"""
if self.parent != ():
self.parent.flush()
if self.hdf5: # is open
self.hdf5.flush()
[docs] def close(self):
"""Close the underlying hdf5 file"""
if self.parent != ():
self.parent.flush()
self.parent.close()
if self.hdf5: # is open
self.hdf5.flush()
self.hdf5.close()
self.hdf5 = ()
[docs] def clear(self):
"""Remove the datastore from the file system"""
self.close()
os.remove(self.filename)
[docs] def getsize(self, key='/'):
"""
Return the size in byte of the output associated to the given key.
If no key is given, returns the total size of all files.
"""
if key == '/':
return os.path.getsize(self.filename)
try:
dset = self.getitem(key)
except KeyError:
if self.parent != ():
dset = self.parent.getitem(key)
else:
raise
return hdf5.ByteCounter.get_nbytes(dset)
[docs] def get(self, key, default):
"""
:returns: the value associated to the datastore key, or the default
"""
try:
return self[key]
except KeyError:
return default
[docs] def store_files(self, fnames, where='input/'):
"""
:param fnames: a set of full pathnames
"""
prefix = len(os.path.commonprefix(fnames))
for fname in fnames:
with open(fname, 'rb') as f:
data = gzip.compress(f.read())
self[where + fname[prefix:]] = numpy.void(data)
[docs] def retrieve_files(self, prefix='input'):
"""
:yields: pairs (relative path, data)
"""
for k, v in self[prefix].items():
if hasattr(v, 'items'):
yield from self.retrieve_files(prefix + '/' + k)
else:
yield prefix + '/' + k, gzip.decompress(
bytes(numpy.asarray(v[()])))
[docs] def get_file(self, key):
"""
:returns: a BytesIO object
"""
data = bytes(numpy.asarray(self[key][()]))
return io.BytesIO(gzip.decompress(data))
[docs] def read_df(self, key, index=None, sel=(), slc=slice(None)):
"""
:param key: name of the structured dataset
:param index: pandas index (or multi-index), possibly None
:param sel: dictionary used to select subsets of the dataset
:param slc: slice object to extract a slice of the dataset
:returns: pandas DataFrame associated to the dataset
"""
if key in self.hdf5:
return self.hdf5.read_df(key, index, sel, slc)
if self.parent:
return self.parent.read_df(key, index, sel, slc)
raise KeyError(key)
[docs] def read_unique(self, key, field):
"""
:param key: key to a dataset containing a structured array
:param field: a field in the structured array
:returns: sorted, unique values
Works with chunks of 1M records
"""
unique = set()
dset = self.getitem(key)
for slc in general.gen_slices(0, len(dset), 10_000_000):
arr = numpy.unique(dset[slc][field])
unique.update(arr)
return sorted(unique)
[docs] def sel(self, key, **kw):
"""
Select a dataset with shape_descr. For instance
dstore.sel('hcurves', imt='PGA', sid=2)
"""
return hdf5.sel(self.getitem(key), kw)
@property
def metadata(self):
"""
:returns: datastore metadata version, date, checksum as a dictionary
"""
a = self.hdf5.attrs
return dict(generated_by='OpenQuake engine %s' % a['engine_version'],
start_date=a['date'], checksum=a['checksum32'])
def __getitem__(self, key):
if self.hdf5 == (): # the datastore is closed
raise ValueError('Cannot find %s in %s' % (key, self))
try:
val = self.hdf5[key]
except KeyError:
if self.parent != ():
self.parent.open('r')
try:
val = self.parent[key]
except KeyError:
raise KeyError(
'No %r found in %s and ancestors' % (key, self))
else:
raise KeyError('No %r found in %s' % (key, self))
return val
def __setitem__(self, key, val):
if key in self.hdf5:
# there is a bug in the current version of HDF5 for composite
# arrays: is impossible to save twice the same key; so we remove
# the key first, then it is possible to save it again
del self[key]
try:
self.hdf5[key] = val
except RuntimeError as exc:
raise RuntimeError('Could not save %s: %s in %s' %
(key, exc, self.filename))
def __delitem__(self, key):
del self.hdf5[key]
def __enter__(self):
self.was_close = self.hdf5 == ()
if self.was_close:
self.open(self.mode)
return self
def __exit__(self, etype, exc, tb):
if self.was_close: # and has been opened in __enter__, close it
self.close()
del self.was_close
def __getstate__(self):
# make the datastore pickleable
return dict(mode='r',
parent=self.parent,
calc_id=self.calc_id,
hdf5=(),
filename=self.filename,
ppath=self.ppath)
def __iter__(self):
if not self.hdf5:
raise RuntimeError('%s is closed' % self)
for path in sorted(self.hdf5):
yield path
def __contains__(self, key):
return key in self.hdf5 or self.parent and key in self.parent.hdf5
def __len__(self):
if self.hdf5 == (): # closed
return 1
return sum(1 for f in self.hdf5)
def __hash__(self):
return self.calc_id
def __repr__(self):
status = 'open' if self.hdf5 else 'closed'
return '<%s %s %s>' % (self.__class__.__name__, self.filename, status)
