Issue #1332: Update pypies to create/use condensed group structure
Change-Id: I2e7311b063df1a217a2fe37c0e470272e4e85e92 Former-commit-id:756a5311a3[formerly768ed3b2ed] [formerlyc72c0b9f98] [formerly756a5311a3[formerly768ed3b2ed] [formerlyc72c0b9f98] [formerlydbe4290f45[formerlyc72c0b9f98[formerly 90f3cac62473c66dcdef73a6a605becf08868316]]]] Former-commit-id:dbe4290f45Former-commit-id:78088888b6[formerly9e51ff1b8a] [formerly f6a83e648173e5af75f219096c477aeab116e566 [formerly2b3f0a2938]] Former-commit-id: 7f3757e8dc095f9ffdc6417bfe1e82fcbd2a49f1 [formerlya0827f476e] Former-commit-id:9fbabfde61
This commit is contained in:
Richard Peter
parent
070ea47301
commit
3d92a176c6
1 changed files with 265 additions and 196 deletions
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@ -1,19 +1,19 @@
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##
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# This software was developed and / or modified by Raytheon Company,
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# pursuant to Contract DG133W-05-CQ-1067 with the US Government.
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#
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#
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# U.S. EXPORT CONTROLLED TECHNICAL DATA
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# This software product contains export-restricted data whose
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# export/transfer/disclosure is restricted by U.S. law. Dissemination
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# to non-U.S. persons whether in the United States or abroad requires
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# an export license or other authorization.
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#
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#
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# Contractor Name: Raytheon Company
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# Contractor Address: 6825 Pine Street, Suite 340
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# Mail Stop B8
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# Omaha, NE 68106
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# 402.291.0100
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#
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#
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# See the AWIPS II Master Rights File ("Master Rights File.pdf") for
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# further licensing information.
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##
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@ -21,17 +21,17 @@
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#
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# h5py implementation of IDataStore
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#
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#
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#
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#
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# SOFTWARE HISTORY
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#
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#
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# Date Ticket# Engineer Description
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# ------------ ---------- ----------- --------------------------
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# 06/16/10 njensen Initial Creation.
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# 05/03/11 9134 njensen Optimized for pointdata
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# 10/09/12 rjpeter Optimized __getGroup for retrievals
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#
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#
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# 10/09/12 rjpeter Optimized __getGroup for retrievals
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#
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#
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#
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import h5py, os, numpy, pypies, re, logging, shutil, time, types
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@ -48,7 +48,7 @@ from dynamicserialize.dstypes.com.raytheon.uf.common.pypies.response import *
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logger = pypies.logger
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timeMap = pypies.timeMap
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vlen_str_type = h5py.new_vlen(str)
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dataRecordMap = {
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@ -70,12 +70,12 @@ REQUEST_ALL.setType('ALL')
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PURGE_REGEX = re.compile('(/[a-zA-Z]{1,25})/([0-9]{4}-[0-9]{2}-[0-9]{2})_([0-9]{2}):[0-9]{2}:[0-9]{2}')
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class H5pyDataStore(IDataStore.IDataStore):
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def __init__(self):
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pass
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def store(self, request):
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fn = request.getFilename()
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pass
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def store(self, request):
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fn = request.getFilename()
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f, lock = self.__openFile(fn, 'w')
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try:
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recs = request.getRecords()
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@ -94,18 +94,18 @@ class H5pyDataStore(IDataStore.IDataStore):
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except:
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logger.warn("Exception occurred on file " + fn + ":" + IDataStore._exc())
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exc.append(IDataStore._exc())
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failRecs.append(r)
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if ss:
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failRecs.append(r)
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if ss:
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status.setOperationPerformed(ss['op'])
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if ss.has_key('index'):
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if ss.has_key('index'):
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status.setIndexOfAppend(ss['index'])
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t1=time.time()
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timeMap['store']=t1-t0
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resp = StoreResponse()
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resp.setStatus(status)
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resp.setExceptions(exc)
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resp.setFailedRecords(failRecs)
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resp.setFailedRecords(failRecs)
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return resp
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finally:
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t0=time.time()
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@ -113,33 +113,34 @@ class H5pyDataStore(IDataStore.IDataStore):
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t1=time.time()
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timeMap['closeFile']=t1-t0
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LockManager.releaseLock(lock)
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def __writeHDF(self, f, record, storeOp):
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props = record.getProps()
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if props and not props.getChunked() and props.getCompression() and \
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props.getCompression() != 'NONE':
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props.getCompression() != 'NONE':
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raise StorageException('Data must be chunked to be compressed')
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data = record.retrieveDataObject()
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group = self.__getGroup(f, record.getGroup(), create=True)
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rootNode=f['/']
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group = self.__getNode(rootNode, record.getGroup(), None, create=True)
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if record.getMinIndex() is not None and len(record.getMinIndex()):
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ss = self.__writePartialHDFDataset(f, data, record.getDimension(), record.getSizes(), record.getName(),
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group, props, record.getMinIndex())
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ss = self.__writePartialHDFDataset(f, data, record.getDimension(), record.getSizes(),
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group[record.getName()], props, record.getMinIndex())
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else:
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ss = self.__writeHDFDataset(f, data, record.getDimension(), record.getSizes(), record.getName(),
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group, props, self.__getHdf5Datatype(record), storeOp, record)
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if props and props.getDownscaled():
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if props and props.getDownscaled():
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intName = record.getGroup() + '/' + record.getName() + '-interpolated'
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self.__getGroup(f, intName, True)
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self.__link(group, intName + '/0', group[record.getName()])
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intGroup = self.__getNode(rootNode, intName, None, create=True)
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self.__link(intGroup, '0', group[record.getName()])
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f.flush()
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if logger.isEnabledFor(logging.DEBUG):
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logger.debug("Stored group " + str(record.getGroup()) + " to group " + str(group))
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return ss
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return ss
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def __writeHDFDataset(self, f, data, dims, szDims, dataset, group, props, dataType, storeOp, rec):
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nDims = len(szDims)
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szDims1 = [None,] * nDims
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@ -150,16 +151,16 @@ class H5pyDataStore(IDataStore.IDataStore):
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if recMaxDims == None or recMaxDims[i] == 0:
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maxDims[i] = None
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else:
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maxDims[i] = recMaxDims[i]
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maxDims[i] = recMaxDims[i]
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if type(data) is numpy.ndarray and data.shape != tuple(szDims1):
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data = data.reshape(szDims1)
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data = data.reshape(szDims1)
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ss = {}
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if dataset in group.keys():
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if dataset in group.keys():
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ds = group[dataset]
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if storeOp == 'STORE_ONLY':
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raise StorageException('Dataset ' + str(dataset) + ' already exists in group ' + str(group))
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raise StorageException('Dataset ' + str(dataset) + ' already exists in group ' + str(group))
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elif storeOp == 'APPEND':
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if dims == 1:
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newSize = [ds.shape[0] + szDims1[0]]
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@ -178,35 +179,35 @@ class H5pyDataStore(IDataStore.IDataStore):
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elif storeOp == 'REPLACE' or storeOp == 'OVERWRITE':
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if ds.shape != data.shape:
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ds.resize(data.shape)
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ds[()] = data
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ds[()] = data
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ss['op'] = 'REPLACE'
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else:
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chunk = self.__calculateChunk(nDims, dataType, storeOp, maxDims)
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else:
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chunk = self.__calculateChunk(nDims, dataType, storeOp, maxDims)
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compression = None
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if props:
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compression = props.getCompression()
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compression = props.getCompression()
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fillValue = rec.getFillValue()
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ds = self.__createDatasetInternal(group, dataset, dataType, szDims1, maxDims, chunk, compression, fillValue)
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#ds = group.create_dataset(dataset, szDims1, dataType, maxshape=maxDims, chunks=chunk, compression=compression)
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ds[()] = data
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ss['op'] = 'STORE_ONLY'
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self.__writeProperties(rec, ds)
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return ss
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def __getHdf5Datatype(self, record):
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dtype = dataRecordMap[record.__class__]
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if dtype == types.StringType:
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from h5py import h5t
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size = record.getMaxLength()
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if size > 0:
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dtype = h5t.py_create('S' + str(size))
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size = record.getMaxLength()
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if size > 0:
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dtype = h5t.py_create('S' + str(size))
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else:
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dtype = vlen_str_type
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#dtype.set_strpad(h5t.STR_NULLTERM)
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return dtype
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return dtype
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def __calculateChunk(self, nDims, dataType, storeOp, maxDims):
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if nDims == 1:
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chunk = [DEFAULT_CHUNK_SIZE]
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@ -222,13 +223,13 @@ class H5pyDataStore(IDataStore.IDataStore):
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# So fixed dimension gets chunk size of:
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# blocksize / (fixed dimension size * bytesize)
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# For example, float of dimensions (infinite, 6) would be
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# (int(4096 / (6 * 4)), 6)
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# (int(4096 / (6 * 4)), 6)
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if dataType != vlen_str_type:
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sizeOfEntry = numpy.dtype(dataType).itemsize
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else:
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sizeOfEntry = None
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secondDim = maxDims[1]
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secondDim = maxDims[1]
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if sizeOfEntry:
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chunkSize = int(FILESYSTEM_BLOCK_SIZE / (secondDim * sizeOfEntry))
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chunk = [chunkSize, secondDim]
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@ -239,111 +240,113 @@ class H5pyDataStore(IDataStore.IDataStore):
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"data with mode " + storeOp + " not supported yet")
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chunk = tuple(chunk)
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return chunk
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def __writeProperties(self, dr, dataset):
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attrs = dr.getDataAttributes()
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if attrs:
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for key in attrs:
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for key in attrs:
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dataset.attrs[key] = attrs[key]
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def __storeInterpolated(self, f, rec, op):
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if op != 'REPLACE' and op != 'STORE_ONLY':
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raise StorageException("Only replace and store modes are supported with interpolation enabled")
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# store the base product
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ss = self.__writeHDF(f, rec, op)
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sizes = rec.getSizes()
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ss = self.__writeHDF(f, rec, op)
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sizes = rec.getSizes()
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newSzX = sizes[1]
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newSzY = sizes[0]
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originalName = rec.getName()
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originalGroup = rec.getGroup()
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level = 0
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# avoid recursive links by turning off downscaling
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rec.getProps().setDownscaled(False)
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rec.getProps().setDownscaled(False)
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from PIL import Image
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import time
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while newSzX > DOWNSCALE_THRESHOLD or newSzY > DOWNSCALE_THRESHOLD:
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data = rec.retrieveDataObject()
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# data is potentially 1-dimensional from serialization, ensure it goes to correct 2 dimensions
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data = data.reshape([newSzX, newSzY])
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newSzX = newSzX / 2
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newSzY = newSzY / 2
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newSzY = newSzY / 2
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level += 1
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rec.setName(str(level))
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rec.setGroup(originalGroup + '/' + originalName + '-interpolated')
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rec.setGroup(originalGroup + '/' + originalName + '-interpolated')
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# satellite data comes in as signed bytes but pil requires unsigned bytes
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data = numpy.array(data + 127, dtype=numpy.uint8)
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data = numpy.array(data + 127, dtype=numpy.uint8)
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image = Image.fromarray(data)
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image = image.resize((newSzY, newSzX))
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downsized = numpy.array(image)
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# transform back to signed bytes
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downsized = numpy.array(downsized - 127, dtype=numpy.int8)
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rec.putDataObject(downsized)
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rec.setSizes([newSzY, newSzX])
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rec.setSizes([newSzY, newSzX])
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self.__writeHDF(f, rec, op)
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return ss
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def __writePartialHDFDataset(self, f, data, dims, szDims, datasetName, group, props,
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minIndex):
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def __writePartialHDFDataset(self, f, data, dims, szDims, ds, props,
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minIndex):
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# reverse sizes for hdf5
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szDims1 = [None, ] * len(szDims)
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for i in range(len(szDims)):
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szDims1[i] = szDims[len(szDims) - i - 1]
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szDims1[i] = szDims[len(szDims) - i - 1]
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offset = [None, ] * len(minIndex)
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for i in range(len(minIndex)):
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offset[i] = minIndex[len(minIndex) - i - 1]
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ds = group[datasetName]
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# process chunking
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offset[i] = minIndex[len(minIndex) - i - 1]
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# process chunking
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# chunkSize = None
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# if data.dtype != numpy._string and data.dtype != numpy._object:
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# chunkSize = DEFAULT_CHUNK_SIZE
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# chunkSize = DEFAULT_CHUNK_SIZE
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# else:
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# chunkSize = 1
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# chunk = [chunkSize] * len(szDims)
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data = data.reshape(szDims1)
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endIndex = [offset[0] + szDims1[0], offset[1] + szDims1[1]]
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ds[offset[0]:endIndex[0], offset[1]:endIndex[1]] = data
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return {'op':'REPLACE'}
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def delete(self, request):
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fn = request.getFilename()
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f, lock = self.__openFile(fn, 'w')
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resp = DeleteResponse()
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resp.setSuccess(True)
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deleteFile = False
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try:
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locs = request.getLocations()
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for dataset in locs:
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ds = self.__getGroup(f, dataset)
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ds = self.__getNode(f, None, dataset)
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grp = ds.parent
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grp.id.unlink(ds.name)
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finally:
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# check if file has any remaining data sets
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# if no data sets, flag file for deletion
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f.flush()
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deleteFile = not self.__hasDataSet(f)
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finally:
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deleteFile = False
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try:
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f.flush()
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deleteFile = not self.__hasDataSet(f)
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except Exception, e:
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logger.error('Error occurred checking for dataSets in file [' + str(fn) + ']: ' + IDataStore._exc())
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t0=time.time()
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f.close()
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t1=time.time()
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timeMap['closeFile']=t1-t0
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if deleteFile:
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try:
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os.remove(fn)
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except Exception, e:
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logger.error('Error occurred deleting file [' + str(fn) + ']: ' + IDataStore._exc())
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LockManager.releaseLock(lock)
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return resp
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@ -358,18 +361,20 @@ class H5pyDataStore(IDataStore.IDataStore):
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if self.__hasDataSet(child):
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return True
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return False
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def retrieve(self, request):
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fn = request.getFilename()
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fn = request.getFilename()
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f, lock = self.__openFile(fn, 'r')
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try:
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group = request.getGroup()
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group = request.getGroup()
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req = request.getRequest()
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rootNode=f['/']
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if req:
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grp = self.__getGroup(f, group)
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result = [self.__retrieveInternal(grp, request.getDataset(), req)]
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ds = self.__getNode(rootNode, group, request.getDataset())
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result = [self.__retrieveInternal(ds, req)]
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else:
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result = self.__retrieve(f, group, request.getIncludeInterpolated())
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groupNode = self.__getNode(rootNode, group)
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result = self.__retrieve(groupNode, request.getIncludeInterpolated())
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resp = RetrieveResponse()
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resp.setRecords(result)
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return resp
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@ -379,32 +384,29 @@ class H5pyDataStore(IDataStore.IDataStore):
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t1=time.time()
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timeMap['closeFile']=t1-t0
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LockManager.releaseLock(lock)
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def __retrieve(self, f, group, includeInterpolated=False):
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def __retrieve(self, group, includeInterpolated=False):
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records = []
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if type(group) is str:
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group = self.__getGroup(f, group)
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datasets = group.keys()
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for ds in datasets:
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interpDs = ds.endswith('-interpolated')
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if includeInterpolated and interpDs:
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subresults = self.__retrieve(f, group.name + '/' + ds, False)
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subresults = self.__retrieve(group[ds], False)
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if subresults:
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records += subresults
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elif not interpDs:
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rec = self.__retrieveInternal(group, ds, REQUEST_ALL)
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elif not interpDs:
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rec = self.__retrieveInternal(group[ds], REQUEST_ALL)
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records.append(rec)
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return records
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def __retrieveInternal(self, grp, dsName, req):
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ds = grp[dsName]
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def __retrieveInternal(self, ds, req):
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rawData = HDF5OpManager.read(ds, req)
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rec = DataStoreFactory.createStorageRecord(rawData, ds)
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return rec
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return rec
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|
||||
def retrieveDatasets(self, request):
|
||||
t6 = time.time()
|
||||
fn = request.getFilename()
|
||||
|
|
@ -420,8 +422,9 @@ class H5pyDataStore(IDataStore.IDataStore):
|
|||
names = request.getDatasetGroupPath()
|
||||
req = request.getRequest()
|
||||
result = []
|
||||
rootNode=f['/']
|
||||
for dsName in names:
|
||||
ds = self.__getGroup(f, dsName)
|
||||
ds = self.__getNode(rootNode, None, dsName)
|
||||
t2 = time.time()
|
||||
rawData = HDF5OpManager.read(ds, req)
|
||||
t3 = time.time()
|
||||
|
|
@ -430,7 +433,7 @@ class H5pyDataStore(IDataStore.IDataStore):
|
|||
paramMap[dsName] = ('%.3f' % (diff))
|
||||
rec = DataStoreFactory.createStorageRecord(rawData, ds)
|
||||
result.append(rec)
|
||||
|
||||
|
||||
resp = RetrieveResponse()
|
||||
resp.setRecords(result)
|
||||
return resp
|
||||
|
|
@ -439,7 +442,7 @@ class H5pyDataStore(IDataStore.IDataStore):
|
|||
t4 = time.time()
|
||||
LockManager.releaseLock(lock)
|
||||
t5 = time.time()
|
||||
if logger.isEnabledFor(logging.DEBUG):
|
||||
if logger.isEnabledFor(logging.DEBUG):
|
||||
logger.debug("pid=" + str(os.getpid()) + " filename=" + fn + \
|
||||
", numberOfDatasets/Parameters=" + str(len(names)) + \
|
||||
", getLockTime=" + ('%.3f' % (t1-t0)) + \
|
||||
|
|
@ -447,7 +450,7 @@ class H5pyDataStore(IDataStore.IDataStore):
|
|||
", releaseLockTime=" + ('%.3f' % (t5-t4)) + \
|
||||
", retrieveDatasetsTotal=" + ('%.3f' % (t4-t6)) + \
|
||||
", perParamRead=" + str(paramMap))
|
||||
|
||||
|
||||
def retrieveGroups(self, request):
|
||||
fn = request.getFilename()
|
||||
f, lock = self.__openFile(fn, 'r')
|
||||
|
|
@ -455,12 +458,14 @@ class H5pyDataStore(IDataStore.IDataStore):
|
|||
groups = request.getGroups()
|
||||
req = request.getRequest()
|
||||
recs = []
|
||||
rootNode=f['/']
|
||||
for group in groups:
|
||||
grp = self.__getGroup(f, group)
|
||||
grp = self.__getNode(rootNode, group)
|
||||
datasets = grp.keys()
|
||||
for ds in datasets:
|
||||
rawData = HDF5OpManager.read(grp[ds], req)
|
||||
rec = DataStoreFactory.createStorageRecord(rawData, grp[ds])
|
||||
dsNode=grp[ds]
|
||||
rawData = HDF5OpManager.read(dsNode, req)
|
||||
rec = DataStoreFactory.createStorageRecord(rawData, dsNode)
|
||||
recs.append(rec)
|
||||
resp = RetrieveResponse()
|
||||
resp.setRecords(recs)
|
||||
|
|
@ -471,13 +476,13 @@ class H5pyDataStore(IDataStore.IDataStore):
|
|||
t1=time.time()
|
||||
timeMap['closeFile']=t1-t0
|
||||
LockManager.releaseLock(lock)
|
||||
|
||||
def getDatasets(self, request):
|
||||
fn = request.getFilename()
|
||||
|
||||
def getDatasets(self, request):
|
||||
fn = request.getFilename()
|
||||
f, lock = self.__openFile(fn, 'r')
|
||||
try:
|
||||
grpName = request.getGroup()
|
||||
grp = self.__getGroup(f, grpName)
|
||||
grp = self.__getNode(f['/'], grpName)
|
||||
ds = grp.keys()
|
||||
return ds
|
||||
finally:
|
||||
|
|
@ -486,7 +491,7 @@ class H5pyDataStore(IDataStore.IDataStore):
|
|||
t1=time.time()
|
||||
timeMap['closeFile']=t1-t0
|
||||
LockManager.releaseLock(lock)
|
||||
|
||||
|
||||
def deleteFiles(self, request):
|
||||
fn = request.getFilename()
|
||||
if os.path.exists(fn):
|
||||
|
|
@ -494,40 +499,40 @@ class H5pyDataStore(IDataStore.IDataStore):
|
|||
self.__recursiveDeleteFiles(fn,request.getDatesToDelete())
|
||||
else:
|
||||
self.__removeFile(fn)
|
||||
|
||||
|
||||
# if it didn't succeed, an exception will be thrown and therefore
|
||||
# an error response returned
|
||||
resp = DeleteResponse()
|
||||
resp = DeleteResponse()
|
||||
resp.setSuccess(True)
|
||||
return resp
|
||||
|
||||
|
||||
def createDataset(self, request):
|
||||
fn = request.getFilename()
|
||||
f, lock = self.__openFile(fn, 'w')
|
||||
try:
|
||||
rec = request.getRecord()
|
||||
rec = request.getRecord()
|
||||
props = rec.getProps()
|
||||
if props and not props.getChunked() and props.getCompression != 'NONE':
|
||||
if props and not props.getChunked() and props.getCompression != 'NONE':
|
||||
raise StorageException("Data must be chunked to be compressed")
|
||||
grp = rec.getGroup()
|
||||
group = self.__getGroup(f, grp, create=True)
|
||||
|
||||
group = self.__getNode(f['/'], grp, None, create=True)
|
||||
|
||||
# reverse sizes for hdf5
|
||||
szDims = rec.getSizes()
|
||||
szDims1 = [None, ] * len(szDims)
|
||||
for i in range(len(szDims)):
|
||||
szDims1[i] = szDims[len(szDims) - i - 1]
|
||||
szDims = tuple(szDims1)
|
||||
|
||||
|
||||
chunks = None
|
||||
if props and props.getChunked():
|
||||
chunks = (DEFAULT_CHUNK_SIZE,) * len(szDims)
|
||||
|
||||
|
||||
compression = None
|
||||
if props:
|
||||
compression = props.getCompression()
|
||||
|
||||
dtype = self.__getHdf5Datatype(rec)
|
||||
compression = props.getCompression()
|
||||
|
||||
dtype = self.__getHdf5Datatype(rec)
|
||||
datasetName = rec.getName()
|
||||
fillValue = rec.getFillValue()
|
||||
ds = self.__createDatasetInternal(group, datasetName, dtype, szDims,
|
||||
|
|
@ -542,9 +547,9 @@ class H5pyDataStore(IDataStore.IDataStore):
|
|||
t1=time.time()
|
||||
timeMap['closeFile']=t1-t0
|
||||
LockManager.releaseLock(lock)
|
||||
|
||||
|
||||
def __createDatasetInternal(self, group, datasetName, dtype, szDims,
|
||||
maxDims=None, chunks=None, compression=None, fillValue=None):
|
||||
maxDims=None, chunks=None, compression=None, fillValue=None):
|
||||
plc = h5py.h5p.create(h5py.h5p.DATASET_CREATE)
|
||||
if fillValue is not None:
|
||||
fVal = numpy.zeros(1, dtype)
|
||||
|
|
@ -556,21 +561,21 @@ class H5pyDataStore(IDataStore.IDataStore):
|
|||
if compression == 'LZF':
|
||||
plc.set_shuffle()
|
||||
plc.set_filter(h5py.h5z.FILTER_LZF, h5py.h5z.FLAG_OPTIONAL)
|
||||
|
||||
|
||||
szDims = tuple(szDims)
|
||||
if maxDims is not None:
|
||||
maxDims = tuple(x if x is not None else h5py.h5s.UNLIMITED for x in maxDims)
|
||||
maxDims = tuple(x if x is not None else h5py.h5s.UNLIMITED for x in maxDims)
|
||||
|
||||
space_id = h5py.h5s.create_simple(szDims, maxDims)
|
||||
type_id = h5py.h5t.py_create(dtype, logical=True)
|
||||
|
||||
|
||||
id = h5py.h5d.create(group.id, datasetName, type_id, space_id, plc)
|
||||
ds = group[datasetName]
|
||||
return ds
|
||||
|
||||
|
||||
def __recursiveDeleteFiles(self, dir, datesToDelete):
|
||||
if os.path.exists(dir) and os.path.isdir(dir):
|
||||
|
||||
|
||||
if datesToDelete is None:
|
||||
self.__removeDir(dir)
|
||||
else:
|
||||
|
|
@ -598,11 +603,11 @@ class H5pyDataStore(IDataStore.IDataStore):
|
|||
if gotLock:
|
||||
os.remove(path)
|
||||
else:
|
||||
raise StorageException('Unable to acquire lock on file ' + path + ' for deleting')
|
||||
raise StorageException('Unable to acquire lock on file ' + path + ' for deleting')
|
||||
finally:
|
||||
if gotLock:
|
||||
LockManager.releaseLock(lock)
|
||||
|
||||
LockManager.releaseLock(lock)
|
||||
|
||||
def __removeDir(self, path):
|
||||
gotLock = False
|
||||
try:
|
||||
|
|
@ -610,14 +615,14 @@ class H5pyDataStore(IDataStore.IDataStore):
|
|||
if gotLock:
|
||||
shutil.rmtree(path)
|
||||
else:
|
||||
raise StorageException('Unable to acquire lock on file ' + path + ' for deleting')
|
||||
raise StorageException('Unable to acquire lock on file ' + path + ' for deleting')
|
||||
finally:
|
||||
if gotLock:
|
||||
LockManager.releaseLock(lock)
|
||||
|
||||
def __openFile(self, filename, mode='r'):
|
||||
LockManager.releaseLock(lock)
|
||||
|
||||
def __openFile(self, filename, mode='r'):
|
||||
if mode == 'r' and not os.path.exists(filename):
|
||||
raise StorageException('File ' + filename + ' does not exist')
|
||||
raise StorageException('File ' + filename + ' does not exist')
|
||||
gotLock, fd = LockManager.getLock(filename, mode)
|
||||
t0=time.time()
|
||||
if not gotLock:
|
||||
|
|
@ -635,39 +640,89 @@ class H5pyDataStore(IDataStore.IDataStore):
|
|||
t1=time.time()
|
||||
timeMap['openFile']=t1-t0
|
||||
|
||||
return f, fd
|
||||
|
||||
def __getGroup(self, f, name, create=False):
|
||||
return f, fd
|
||||
|
||||
def __getNode(self, rootNode, groupName, dsName=None, create=False):
|
||||
t0=time.time()
|
||||
if create:
|
||||
parts = name.split('/')
|
||||
grp = None
|
||||
for s in parts:
|
||||
if not grp:
|
||||
if not s:
|
||||
s = '/'
|
||||
if s == '/' or s in f.keys():
|
||||
grp = f[s]
|
||||
else:
|
||||
grp = f.create_group(s)
|
||||
else:
|
||||
if s:
|
||||
if s in grp.keys():
|
||||
grp = grp[s]
|
||||
else:
|
||||
grp = grp.create_group(s)
|
||||
else:
|
||||
if name is None or len(name.strip()) == 0:
|
||||
# if no group is specific default to base group
|
||||
grp = f['/']
|
||||
|
||||
# expected output to be node for /group1::group2::group3/dataSet
|
||||
# expected output of /group1::group2::group3/dataSet-interpolated/1
|
||||
if groupName:
|
||||
if dsName:
|
||||
toNormalize=groupName + '/' + dsName
|
||||
else:
|
||||
try:
|
||||
group=name
|
||||
if not group.startswith('/'):
|
||||
group = '/' + group
|
||||
grp = f[group]
|
||||
except:
|
||||
raise StorageException("No group " + name + " found")
|
||||
toNormalize=groupName
|
||||
elif dsName:
|
||||
toNormalize=dsName
|
||||
else:
|
||||
# both None, return root node as default
|
||||
return rootNode
|
||||
|
||||
tokens=toNormalize.split('/')
|
||||
|
||||
# remove any empty tokens
|
||||
tokens = filter(None, tokens)
|
||||
|
||||
dsNameToken=None
|
||||
if dsName:
|
||||
# data set name was given, keep last token for ds name
|
||||
dsNameToken = tokens.pop()
|
||||
|
||||
# need to check final token for -interpolated
|
||||
isInterpToken = None
|
||||
if tokens:
|
||||
isInterpToken = tokens[-1]
|
||||
if isInterpToken.endswith('-interpolated'):
|
||||
del tokens[-1]
|
||||
if dsNameToken:
|
||||
dsNameToken = isInterpToken + '/' + dsNameToken
|
||||
else:
|
||||
dsNameToken = isInterpToken
|
||||
|
||||
if tokens:
|
||||
basePath='::'.join(tokens)
|
||||
else:
|
||||
basePath=None
|
||||
|
||||
node = None
|
||||
if create:
|
||||
if basePath is None:
|
||||
node = rootNode
|
||||
if basePath in rootNode.keys():
|
||||
node = rootNode[basePath]
|
||||
else:
|
||||
node = rootNode.create_group(basePath)
|
||||
|
||||
if dsNameToken:
|
||||
for token in dsNameToken.split('/'):
|
||||
if token in node.keys():
|
||||
node = node[token]
|
||||
else:
|
||||
node = node.create_group(token)
|
||||
else:
|
||||
if dsNameToken:
|
||||
if basePath:
|
||||
basePath += '/' + dsNameToken
|
||||
else:
|
||||
basePath = dsNameToken
|
||||
|
||||
|
||||
try:
|
||||
if basePath:
|
||||
node = rootNode[basePath]
|
||||
else:
|
||||
node = rootNode
|
||||
except:
|
||||
group = None
|
||||
if groupName:
|
||||
group = groupName
|
||||
if dsName:
|
||||
group += '/' + dsName
|
||||
elif dsName:
|
||||
group = dsName
|
||||
|
||||
# check old group structure
|
||||
node = self.__getGroup(rootNode, group)
|
||||
|
||||
t1=time.time()
|
||||
if timeMap.has_key('getGroup'):
|
||||
|
|
@ -675,16 +730,32 @@ class H5pyDataStore(IDataStore.IDataStore):
|
|||
else:
|
||||
timeMap['getGroup']=t1-t0
|
||||
|
||||
return node
|
||||
|
||||
# deprecated, should only be called in transition period
|
||||
def __getGroup(self, rootNode, name):
|
||||
if name is None or len(name.strip()) == 0:
|
||||
# if no group is specific default to base group
|
||||
grp = rootNode
|
||||
else:
|
||||
try:
|
||||
group=name
|
||||
if group.startswith('/'):
|
||||
group = group[1:]
|
||||
grp = rootNode[group]
|
||||
except:
|
||||
raise StorageException("No group " + name + " found")
|
||||
|
||||
return grp
|
||||
|
||||
|
||||
def __link(self, group, linkName, dataset):
|
||||
# this is a hard link
|
||||
group[linkName] = dataset
|
||||
|
||||
|
||||
# untested code, this would be if we went with symbolic links, this is unpublished h5py API
|
||||
#id = group.id
|
||||
#id.link(dataset.name, linkName, h5py.h5g.LINK_SOFT)
|
||||
|
||||
|
||||
def copy(self, request):
|
||||
resp = FileActionResponse()
|
||||
file = request.getFilename()
|
||||
|
|
@ -693,12 +764,12 @@ class H5pyDataStore(IDataStore.IDataStore):
|
|||
action = self.__doCopy if not repack else self.__doRepack
|
||||
self.__doFileAction(file, pth, request.getOutputDir(), action, resp, request.getRepackCompression(), request.getTimestampCheck())
|
||||
return resp
|
||||
|
||||
|
||||
def __doCopy(self, filepath, basePath, outputDir, compression):
|
||||
shutil.copy(filepath, outputDir)
|
||||
success = (os.path.isfile(os.path.join(outputDir, os.path.basename(filepath))))
|
||||
return success
|
||||
|
||||
|
||||
def repack(self, request):
|
||||
resp = FileActionResponse()
|
||||
pth = request.getFilename()
|
||||
|
|
@ -714,17 +785,17 @@ class H5pyDataStore(IDataStore.IDataStore):
|
|||
goodfiles = fnmatch.filter(files, '*.h5')
|
||||
results.extend(os.path.join(base, f) for f in goodfiles)
|
||||
return results
|
||||
|
||||
|
||||
def __doRepack(self, filepath, basePath, outDir, compression):
|
||||
t0=time.time()
|
||||
# call h5repack to repack the file
|
||||
if outDir is None:
|
||||
repackedFullPath = filepath + '.repacked'
|
||||
repackedFullPath = filepath + '.repacked'
|
||||
else:
|
||||
repackedFullPath = filepath.replace(basePath, outDir)
|
||||
cmd = ['h5repack', '-f', compression, filepath, repackedFullPath]
|
||||
ret = subprocess.call(cmd)
|
||||
|
||||
|
||||
success = (ret == 0)
|
||||
if success:
|
||||
# repack was successful, replace the old file if we did it in the
|
||||
|
|
@ -747,7 +818,7 @@ class H5pyDataStore(IDataStore.IDataStore):
|
|||
else:
|
||||
timeMap['repack']=t1-t0
|
||||
return success
|
||||
|
||||
|
||||
def __doFileAction(self, filepath, basePath, outputDir, fileAction, response, compression='NONE', timestampCheck=None):
|
||||
lock = None
|
||||
try:
|
||||
|
|
@ -766,23 +837,23 @@ class H5pyDataStore(IDataStore.IDataStore):
|
|||
if timestampCheck:
|
||||
f.attrs[timestampCheck] = time.time() + 30
|
||||
f.close()
|
||||
|
||||
|
||||
success = fileAction(filepath, basePath, outputDir, compression)
|
||||
|
||||
|
||||
# update response
|
||||
if success:
|
||||
getter = response.getSuccessfulFiles
|
||||
setter = response.setSuccessfulFiles
|
||||
else:
|
||||
getter = response.getFailedFiles
|
||||
setter = response.setFailedFiles
|
||||
setter = response.setFailedFiles
|
||||
responseList = getter()
|
||||
if responseList:
|
||||
responseList += [filepath]
|
||||
else:
|
||||
responseList = [filepath]
|
||||
setter(responseList)
|
||||
except Exception, e:
|
||||
except Exception, e:
|
||||
logger.warn("Error repacking file " + filepath + ": " + str(e))
|
||||
failed = response.getFailedFiles()
|
||||
if failed:
|
||||
|
|
@ -793,5 +864,3 @@ class H5pyDataStore(IDataStore.IDataStore):
|
|||
finally:
|
||||
if lock:
|
||||
LockManager.releaseLock(lock)
|
||||
|
||||
|
||||
|
|
|
|||
Loading…
Add table
Reference in a new issue