def call_sessionmaker( root ):
from sqlalchemy.orm import sessionmaker
from sqlalchemy import create_engine
from esgcet.config import loadConfig, initLogging, registerHandlers
# init_file = "../scripts/esg.ini"
init_file = None # Load installed init file
echoSql = True
# Load the configuration and set up a database connection
config = loadConfig(init_file)
root.engine = create_engine(config.getdburl('extract'), echo=root.echoSql, pool_recycle=3600)
initLogging('extract', override_sa=root.engine)
Session = sessionmaker(bind=root.engine, autoflush=True, autocommit=False)
# Register project handlers
registerHandlers()
root.config = config
root.Session = Session
root.projectName = None
root.firstFile = None
root.dmap = None
root.extraFields = None
root.directoryMap = None
root.datasetMapfile = None
root.filefilt = None
def call_sessionmaker(root):
from sqlalchemy.orm import sessionmaker
from sqlalchemy import create_engine
from esgcet.config import loadConfig, initLogging, registerHandlers
# init_file = "../scripts/esg.ini"
init_file = None # Load installed init file
echoSql = True
# Load the configuration and set up a database connection
config = loadConfig(init_file)
root.engine = create_engine(config.getdburl('extract'),
echo=root.echoSql,
pool_recycle=3600)
initLogging('extract', override_sa=root.engine)
Session = sessionmaker(bind=root.engine, autoflush=True, autocommit=False)
# Register project handlers
registerHandlers()
root.config = config
root.Session = Session
root.projectName = None
root.firstFile = None
root.dmap = None
root.extraFields = None
root.directoryMap = None
root.datasetMapfile = None
root.filefilt = None
def publishCatalogs(threddsCatalogDictionary, parentDatasetIdDictionary, thredds=True, las=True, publish=True):
"""
Add one or more THREDDS catalogs to the THREDDS catalog directory, reinitialize THREDDS, and publish the catalogs to the gateway.
Returns a dictionary mapping (datasetName, version) => status, as returned from ``publish.publishDatasetList``. If ``publish`` is False, the return dictionary is empty.
threddsCatalogDictionary
Dictionary of THREDDS catalogs, as returned from ``generateReplicaThreddsCatalog``. The dictionary maps datasetId => String THREDDS catalog.
parentDatasetIdDictionary
Dictionary mapping datasetId => parent dataset identifier in the gateway hierarchy.
thredds=True
Boolean flag. If True, copy the catalogs to the THREDDS catalog directory and reinitialize the TDS server.
las=True
Boolean flag. If True, reinitialize the LAS server.
publish=True
Boolean flag. If True, publish the catalog(s) to the gateway.
"""
# Load the configuration and set up a database connection
config, Session = initdb()
# Register project handlers
registerHandlers()
datasetNames = threddsCatalogDictionary.keys()
result = publishDatasetList(datasetNames, Session, publish=publish, thredds=thredds, las=las, parentId=parentDatasetIdDictionary, threddsCatalogDictionary=threddsCatalogDictionary, reinitThredds=None, readFromCatalog=True)
return result
def load_configuration(parent):
import os
import pub_controls
from esgcet.config import getHandler, getHandlerByName, registerHandlers, CFHandler
from sqlalchemy.orm import sessionmaker
from esgcet.publish import multiDirectoryIterator, datasetMapIterator
offline = parent.offline
firstFile = parent.firstFile
projectName = parent.projectName
config = parent.config
Session = parent.Session
dmap = parent.dmap
datasetNames = parent.datasetNames
datasetMapfile = parent.datasetMapfile
for datasetName in datasetNames:
# Get a file iterator and sample file
if datasetMapfile is not None:
firstFile = dmap[datasetName][0][0]
fileiter = datasetMapIterator(dmap, datasetName)
else:
direcTuples = parent.directoryMap[datasetName]
firstDirec, sampleFile = direcTuples[0]
firstFile = os.path.join(firstDirec, sampleFile)
fileiter = multiDirectoryIterator(
[direc for direc, sampfile in direcTuples], parent.filefilt)
# Register project handlers
registerHandlers()
# If the project is not specified, try to read it from the first file
validate = True
if projectName is not None:
handler = getHandlerByName(projectName,
firstFile,
Session,
validate=validate,
offline=offline)
else:
handler = getHandler(firstFile, Session, validate=validate)
parent.handler = handler
# View the collection of datasets
tab_name = "Collection %i" % parent.top_ct
parent.ntk.new_page(parent, tab_name)
def publishCatalogs(threddsCatalogDictionary,
parentDatasetIdDictionary,
thredds=True,
las=True,
publish=True):
"""
Add one or more THREDDS catalogs to the THREDDS catalog directory, reinitialize THREDDS, and publish the catalogs to the gateway.
Returns a dictionary mapping (datasetName, version) => status, as returned from ``publish.publishDatasetList``. If ``publish`` is False, the return dictionary is empty.
threddsCatalogDictionary
Dictionary of THREDDS catalogs, as returned from ``generateReplicaThreddsCatalog``. The dictionary maps datasetId => String THREDDS catalog.
parentDatasetIdDictionary
Dictionary mapping datasetId => parent dataset identifier in the gateway hierarchy.
thredds=True
Boolean flag. If True, copy the catalogs to the THREDDS catalog directory and reinitialize the TDS server.
las=True
Boolean flag. If True, reinitialize the LAS server.
publish=True
Boolean flag. If True, publish the catalog(s) to the gateway.
"""
# Load the configuration and set up a database connection
config, Session = initdb()
# Register project handlers
registerHandlers()
datasetNames = threddsCatalogDictionary.keys()
result = publishDatasetList(
datasetNames,
Session,
publish=publish,
thredds=thredds,
las=las,
parentId=parentDatasetIdDictionary,
threddsCatalogDictionary=threddsCatalogDictionary,
reinitThredds=None,
readFromCatalog=True)
return result
def load_configuration( parent ):
import os
import pub_controls
from esgcet.config import getHandler, getHandlerByName, registerHandlers, CFHandler
from sqlalchemy.orm import sessionmaker
from esgcet.publish import multiDirectoryIterator, datasetMapIterator
offline = parent.offline
firstFile = parent.firstFile
projectName = parent.projectName
config = parent.config
Session = parent.Session
dmap = parent.dmap
datasetNames = parent.datasetNames
datasetMapfile = parent.datasetMapfile
for datasetName in datasetNames:
# Get a file iterator and sample file
if datasetMapfile is not None:
firstFile = dmap[datasetName][0][0]
fileiter = datasetMapIterator(dmap, datasetName)
else:
direcTuples = parent.directoryMap[datasetName]
firstDirec, sampleFile = direcTuples[0]
firstFile = os.path.join(firstDirec, sampleFile)
fileiter = multiDirectoryIterator([direc for direc, sampfile in direcTuples],parent.filefilt)
# Register project handlers
registerHandlers()
# If the project is not specified, try to read it from the first file
validate = True
if projectName is not None:
handler = getHandlerByName(projectName,firstFile,Session,validate=validate,offline=offline)
else:
handler = getHandler(firstFile, Session, validate=validate)
parent.handler = handler
# View the collection of datasets
tab_name= "Collection %i" % parent.top_ct
parent.ntk.new_page( parent, tab_name )
def main(argv):
try:
args, lastargs = getopt.getopt(argv, "a:ehi:o:p:", ['dataset=', 'dataset-tech-notes=', 'dataset-tech-notes-title=',\
'filter=', 'help', 'max-threads=', 'offline', 'output=', 'project=', 'property=', 'read-directories', 'read-files',\
'service=', 'use-version-dir', 'version='])
except getopt.error:
print sys.exc_value
return
if len(lastargs)==0:
print 'No directory specified'
return
appendMap = None
datasetName = None
datasetTechNotesURL = None
datasetTechNotesTitle = None
filefilt = '.*\.nc$'
init_file = None
offline = False
output = sys.stdout
projectName = None
properties = {}
readFiles = False
service = None
max_threads = 4
version_dir = False
use_version = None
for flag, arg in args:
if flag=='-a':
if os.path.exists(arg):
appendMap = readDatasetMap(arg)
else:
appendMap = {}
output = open(arg, 'a')
elif flag=='--dataset':
datasetName = arg
elif flag=='--dataset-tech-notes':
datasetTechNotesURL = arg
elif flag=='--dataset-tech-notes-title':
datasetTechNotesTitle = arg
elif flag=='--filter':
filefilt = arg
elif flag in ['-h', '--help']:
print usage
sys.exit(0)
elif flag=='-i':
init_file = arg
elif flag=='--max-threads':
max_threads = int(arg)
elif flag in ['-o', '--output']:
output = open(arg, 'w')
elif flag=='--offline':
offline = True
elif flag=='--project':
projectName = arg
elif flag in ['-p', '--property']:
name, value = arg.split('=')
properties[name] = value
elif flag in ['-e', '--read-directories']:
readFiles = False
elif flag=='--read-files':
readFiles = True
elif flag=='--service':
service = arg
elif flag=='--use-version-dir':
version_dir = True
elif flag=='--version':
version_dir = True
if not re.match('^[0-9]+$', arg[0]): # e.g. 'vYYYYMMDD'
use_version = arg[1:]
else:
use_version = arg
# Load the configuration and set up a database connection
config = loadConfig(init_file)
engine = create_engine(config.getdburl('extract'), echo=False, pool_recycle=3600)
initLogging('extract', override_sa=engine)
Session = sessionmaker(bind=engine, autoflush=True, autocommit=False)
# Register project handlers
registerHandlers()
if not offline:
# Determine if checksumming is enabled
line = config.get('DEFAULT', 'checksum', default=None)
if line is not None:
checksumClient, checksumType = splitLine(line)
else:
checksumClient = None
if projectName is not None:
handler = getHandlerByName(projectName, None, Session)
else:
warning("No project name specified!")
multiIter = multiDirectoryIterator(lastargs, filefilt=filefilt)
firstFile, size = multiIter.next()
handler = getHandler(firstFile, Session, validate=True)
if handler is None:
raise ESGPublishError("No project found in file %s, specify with --project."%firstFile)
projectName = handler.name
if not readFiles:
datasetMap = handler.generateDirectoryMap(lastargs, filefilt, initContext=properties, datasetName=datasetName, use_version=version_dir)
else:
datasetMap = handler.generateDirectoryMapFromFiles(lastargs, filefilt, initContext=properties, datasetName=datasetName)
# Output the map
keys = datasetMap.keys()
keys.sort()
datasetMapVersion = {}
if version_dir:
# check for version directory
for dataset_id in keys:
ds_id_version = dataset_id.split('#')
if len(ds_id_version) == 2:
ds_id, ds_version = ds_id_version
if not re.match('^[0-9]+$', ds_version):
warning("Version must be an integer. Skipping version %s of dataset %s."%(ds_version, ds_id))
continue
if use_version and ds_version != use_version:
continue
if ds_id in datasetMapVersion:
datasetMapVersion[ds_id].append(ds_version)
else:
datasetMapVersion[ds_id] = [ds_version]
else:
error("No version directory found. Skipping dataset %s."%dataset_id)
if datasetMapVersion:
keys = datasetMapVersion.keys()
keys.sort()
else:
if use_version:
error("Version %s not found. No datasets to process."%use_version)
else:
error("No datasets to process.")
return
for dataset_id in keys:
skip_dataset = False
dataset_id_version = dataset_id
path_version = None
# if multiple versions of the same dataset available use latest version
if version_dir:
path_version = sorted(datasetMapVersion[dataset_id])[-1]
if len(datasetMapVersion[dataset_id]) > 1:
info("Multiple versions for %s (%s), processing latest (%s)"%(dataset_id, datasetMapVersion[dataset_id], path_version))
dataset_id_version = '%s#%s'%(dataset_id, path_version)
direcTuple = datasetMap[dataset_id_version]
direcTuple.sort()
mapfile_md = {}
for nodepath, filepath in direcTuple:
# If readFiles is not set, generate a map entry for each file in the directory
# that matches filefilt ...
if not readFiles:
itr = directoryIterator(nodepath, filefilt=filefilt, followSubdirectories=False)
# ... otherwise if readFiles is set, generate a map entry for each file
else:
itr = fnIterator([filepath])
for filepath, sizet in itr:
size, mtime = sizet
mapfile_md[filepath] = [size]
mapfile_md[filepath].append("mod_time=%f"%float(mtime))
extraStuff = "mod_time=%f"%float(mtime)
if datasetTechNotesURL is not None:
mapfile_md[filepath].append('dataset_tech_notes=%s'%datasetTechNotesURL)
if datasetTechNotesURL is not None:
mapfile_md[filepath].append('dataset_tech_notes_title=%s'%datasetTechNotesTitle)
if checksumClient is not None:
pool = ThreadPool(processes=max_threads)
args = [(filepath, checksumClient) for filepath in mapfile_md]
checksum_list = pool.map(calc_checksum_wrapper, args)
for entry in checksum_list:
if not entry[1]:
error('Calculation of checksum for file %s failed. Skipping dataset %s ...'%(entry[0], dataset_id))
skip_dataset = True # skip entire dataset if we have one file without checksum
break
mapfile_md[entry[0]].append('checksum=%s'%entry[1])
mapfile_md[entry[0]].append('checksum_type=%s'%checksumType)
for fpath in mapfile_md:
mapfile_line = '%s | %s | %d'%(dataset_id_version, fpath, mapfile_md[fpath][0])
for md in mapfile_md[fpath][1:]:
mapfile_line+=' | %s'%md
# Print the map entry if:
# - Checksum exists for all files of dataset (in case checksumming is enabled)
# - The map is being created, not appended, or
# - The existing map does not have the dataset, or
# - The existing map has the dataset, but not the file.
if path_version:
ds_id = (dataset_id, int(path_version))
else:
ds_id = (dataset_id, -1)
if not skip_dataset and ( (appendMap is None) or (not appendMap.has_key(ds_id)) or (( fpath, "%d"% mapfile_md[fpath][1]) not in appendMap[ds_id]) ):
print >>output, mapfile_line
else: # offline
if projectName is not None:
handler = getHandlerByName(projectName, None, Session, offline=True)
else:
raise ESGPublishError("Must specify --project for offline datasets.")
listerSection = getOfflineLister(config, "project:%s"%projectName, service)
offlineLister = config.get(listerSection, 'offline_lister_executable')
commandArgs = "--config-section %s "%listerSection
commandArgs += " ".join(lastargs)
for dsetName, filepath, sizet in processNodeMatchIterator(offlineLister, commandArgs, handler, filefilt=filefilt, datasetName=datasetName, offline=True):
size, mtime = sizet
extrastuff = ""
if mtime is not None:
extrastuff = "| mod_time=%f"%float(mtime)
if (appendMap is None) or (not appendMap.has_key(dsetName)) or ((filepath, "%d"%size) not in appendMap[dsetName]):
print >>output, "%s | %s | %d %s"%(dsetName, filepath, size, extrastuff)
if output is not sys.stdout:
output.close()
def esgpublishWrapper(**kw):
from esgcet.query import queryDatasetMap
aggregateDimension = kw.get("aggregateDimension", "time")
datasetMapfile = kw.get("datasetMapfile", None)
datasetName = kw.get("datasetName", None)
directoryList = kw.get("directoryList", None)
echoSql = kw.get("echoSql", False)
filefilt = kw.get("filefilt", '.*\.nc$')
init_file = kw.get("init_file", None)
initcontext = kw.get("initcontext", {})
keepVersion = kw.get("keepVersion", False)
las = kw.get("las", False)
log_filename = kw.get("log_filename", None)
masterGateway = kw.get("masterGateway", None)
message = kw.get("message", None)
offline = kw.get("offline", False)
parent = kw.get("parent", None)
perVariable = kw.get("perVariable", None)
projectName = kw.get("projectName", None)
properties = kw.get("properties", {})
publish = kw.get("publish", False)
publishOnly = kw.get("publishOnly", False)
publishOp = kw.get("publishOp", CREATE_OP)
readFiles = kw.get("readFiles", False)
readFromCatalog = kw.get("readFromCatalog", False)
reinitThredds = kw.get("reinitThredds", None)
rescan = kw.get("rescan", False)
rescanDatasetName = kw.get("rescanDatasetName", [])
resultThreddsDictionary = None
service = kw.get("service", None)
summarizeErrors = kw.get("summarizeErrors", False)
testProgress1 = kw.get("testProgress1", None)
testProgress2 = kw.get("testProgress2", None)
thredds = kw.get("thredds", False)
threddsCatalogDictionary = kw.get("threddsCatalogDictionary", None)
version = kw.get("version", None)
# If offline, the project must be specified
if offline and (projectName is None):
raise ESGPublishError(
"Must specify project with --project for offline datasets")
# Must specify version for replications
if masterGateway is not None and version is None:
raise ESGPublishError(
"Must specify version with --new-version for replicated datasets")
# Load the configuration and set up a database connection
config, Session = initdb(init_file=init_file,
echoSql=echoSql,
log_filename=log_filename)
# Register project handlers
registerHandlers()
# If the dataset map is input, just read it ...
dmap = None
directoryMap = None
extraFields = None
if datasetMapfile is not None:
dmap, extraFields = readDatasetMap(datasetMapfile,
parse_extra_fields=True)
datasetNames = dmap.keys()
elif rescan:
# Note: No need to get the extra fields, such as mod_time, since
# they are already in the database, and will be used for file comparison if necessary.
dmap, offline = queryDatasetMap(rescanDatasetName, Session)
datasetNames = dmap.keys()
# ... otherwise generate the directory map.
else:
# Online dataset(s)
if not offline:
if projectName is not None:
handler = getHandlerByName(projectName, None, Session)
else:
multiIter = multiDirectoryIterator(directoryList,
filefilt=filefilt)
firstFile, size = multiIter.next()
listIter = list(multiIter)
handler = getHandler(firstFile, Session, validate=True)
if handler is None:
raise ESGPublishError(
"No project found in file %s, specify with --project."
% firstFile)
projectName = handler.name
props = properties.copy()
props.update(initcontext)
if not readFiles:
directoryMap = handler.generateDirectoryMap(
directoryList,
filefilt,
initContext=props,
datasetName=datasetName)
else:
directoryMap = handler.generateDirectoryMapFromFiles(
directoryList,
filefilt,
initContext=props,
datasetName=datasetName)
datasetNames = [(item, -1) for item in directoryMap.keys()]
# Offline dataset. Format the spec as a dataset map : dataset_name => [(path, size), (path, size), ...]
else:
handler = getHandlerByName(projectName,
None,
Session,
offline=True)
dmap = {}
listerSection = getOfflineLister(config,
"project:%s" % projectName,
service)
offlineLister = config.get(listerSection,
'offline_lister_executable')
commandArgs = "--config-section %s " % listerSection
commandArgs += " ".join(directoryList)
for dsetName, filepath, sizet in processNodeMatchIterator(
offlineLister,
commandArgs,
handler,
filefilt=filefilt,
datasetName=datasetName,
offline=True):
size, mtime = sizet
if dmap.has_key((dsetName, -1)):
dmap[(dsetName, -1)].append((filepath, str(size)))
else:
dmap[(dsetName, -1)] = [(filepath, str(size))]
datasetNames = dmap.keys()
datasetNames.sort()
if len(datasetNames) == 0:
warning("No datasets found.")
# Iterate over datasets
if not publishOnly:
datasets = iterateOverDatasets(projectName,
dmap,
directoryMap,
datasetNames,
Session,
aggregateDimension,
publishOp,
filefilt,
initcontext,
offline,
properties,
keepVersion=keepVersion,
newVersion=version,
extraFields=extraFields,
masterGateway=masterGateway,
comment=message,
readFiles=readFiles)
result = publishDatasetList(
datasetNames,
Session,
publish=publish,
thredds=thredds,
las=las,
parentId=parent,
service=service,
perVariable=perVariable,
threddsCatalogDictionary=threddsCatalogDictionary,
reinitThredds=reinitThredds,
readFromCatalog=readFromCatalog)
return result
def esgscanWrapper(directoryList, **kw):
if len(directoryList) == 0:
raise ESGPublishError('No directory specified')
output = sys.stdout
appendMap = None
appendPath = kw.get("appendPath", None)
if appendPath is not None:
if os.path.exists(appendPath):
appendMap = readDatasetMap(appendPath)
else:
appendMap = {}
output = open(appendPath, 'a')
datasetName = kw.get("datasetName", None)
filefilt = kw.get("fileFilt", '.*\.nc$')
init_file = kw.get("initFile", None)
offline = kw.get("offline", False)
outputPath = kw.get("outputPath", None)
if outputPath is not None:
output = open(outputPath, 'w')
else:
output = sys.stdout
projectName = kw.get("projectName", None)
readFiles = kw.get("readFiles", False)
service = kw.get("service", None)
# Load the configuration and set up a database connection
config, Session = initdb(init_file=init_file)
# Register project handlers
registerHandlers()
if not offline:
# Determine if checksumming is enabled
line = config.get('DEFAULT', 'checksum', default=None)
if line is not None:
checksumClient, checksumType = splitLine(line)
else:
checksumClient = None
if projectName is not None:
handler = getHandlerByName(projectName, None, Session)
else:
multiIter = multiDirectoryIterator(directoryList,
filefilt=filefilt)
firstFile, size = multiIter.next()
handler = getHandler(firstFile, Session, validate=True)
if handler is None:
raise ESGPublishError(
"No project found in file %s, specify with --project." %
firstFile)
projectName = handler.name
if not readFiles:
datasetMap = handler.generateDirectoryMap(directoryList,
filefilt,
datasetName=datasetName)
else:
datasetMap = handler.generateDirectoryMapFromFiles(
directoryList, filefilt, datasetName=datasetName)
# Output the map
keys = datasetMap.keys()
keys.sort()
for datasetId in keys:
direcTuple = datasetMap[datasetId]
direcTuple.sort()
for nodepath, filepath in direcTuple:
# If readFiles is not set, generate a map entry for each file in the directory
# that matches filefilt ...
if not readFiles:
itr = directoryIterator(nodepath,
filefilt=filefilt,
followSubdirectories=False)
# ... otherwise if readFiles is set, generate a map entry for each file
else:
itr = fnIterator([filepath])
for filepath, sizet in itr:
size, mtime = sizet
extraStuff = "mod_time=%f" % float(mtime)
if checksumClient is not None:
csum = checksum(filepath, checksumClient)
extraStuff += " | checksum=%s | checksum_type=%s" % (
csum, checksumType)
# Print the map entry if:
# - The map is being created, not appended, or
# - The existing map does not have the dataset, or
# - The existing map has the dataset, but not the file.
if (appendMap is
None) or (not appendMap.has_key(datasetId)) or (
(filepath, "%d" % size)
not in appendMap[datasetId]):
print >> output, "%s | %s | %d | %s" % (
datasetId, filepath, size, extraStuff)
else: # offline
if projectName is not None:
handler = getHandlerByName(projectName,
None,
Session,
offline=True)
else:
raise ESGPublishError(
"Must specify --project for offline datasets.")
listerSection = getOfflineLister(config, "project:%s" % projectName,
service)
offlineLister = config.get(listerSection, 'offline_lister_executable')
commandArgs = "--config-section %s " % listerSection
commandArgs += " ".join(directoryList)
for dsetName, filepath, sizet in processNodeMatchIterator(
offlineLister,
commandArgs,
handler,
filefilt=filefilt,
datasetName=datasetName,
offline=True):
size, mtime = sizet
extrastuff = ""
if mtime is not None:
extrastuff = "| mod_time=%f" % float(mtime)
if (appendMap is None) or (not appendMap.has_key(dsetName)) or (
(filepath, "%d" % size) not in appendMap[dsetName]):
print >> output, "%s | %s | %d %s" % (dsetName, filepath, size,
extrastuff)
if output is not sys.stdout:
output.close()
def esgpublishWrapper(**kw):
from esgcet.query import queryDatasetMap
aggregateDimension = kw.get("aggregateDimension", "time")
datasetMapfile = kw.get("datasetMapfile", None)
datasetName = kw.get("datasetName", None)
directoryList = kw.get("directoryList", None)
echoSql = kw.get("echoSql", False)
filefilt = kw.get("filefilt", ".*\.nc$")
init_file = kw.get("init_file", None)
initcontext = kw.get("initcontext", {})
keepVersion = kw.get("keepVersion", False)
las = kw.get("las", False)
log_filename = kw.get("log_filename", None)
masterGateway = kw.get("masterGateway", None)
message = kw.get("message", None)
offline = kw.get("offline", False)
parent = kw.get("parent", None)
perVariable = kw.get("perVariable", None)
projectName = kw.get("projectName", None)
properties = kw.get("properties", {})
publish = kw.get("publish", False)
publishOnly = kw.get("publishOnly", False)
publishOp = kw.get("publishOp", CREATE_OP)
readFiles = kw.get("readFiles", False)
readFromCatalog = kw.get("readFromCatalog", False)
reinitThredds = kw.get("reinitThredds", None)
rescan = kw.get("rescan", False)
rescanDatasetName = kw.get("rescanDatasetName", [])
resultThreddsDictionary = None
service = kw.get("service", None)
summarizeErrors = kw.get("summarizeErrors", False)
testProgress1 = kw.get("testProgress1", None)
testProgress2 = kw.get("testProgress2", None)
thredds = kw.get("thredds", False)
threddsCatalogDictionary = kw.get("threddsCatalogDictionary", None)
version = kw.get("version", None)
# If offline, the project must be specified
if offline and (projectName is None):
raise ESGPublishError("Must specify project with --project for offline datasets")
# Must specify version for replications
if masterGateway is not None and version is None:
raise ESGPublishError("Must specify version with --new-version for replicated datasets")
# Load the configuration and set up a database connection
config, Session = initdb(init_file=init_file, echoSql=echoSql, log_filename=log_filename)
# Register project handlers
registerHandlers()
# If the dataset map is input, just read it ...
dmap = None
directoryMap = None
extraFields = None
if datasetMapfile is not None:
dmap, extraFields = readDatasetMap(datasetMapfile, parse_extra_fields=True)
datasetNames = dmap.keys()
elif rescan:
# Note: No need to get the extra fields, such as mod_time, since
# they are already in the database, and will be used for file comparison if necessary.
dmap, offline = queryDatasetMap(rescanDatasetName, Session)
datasetNames = dmap.keys()
# ... otherwise generate the directory map.
else:
# Online dataset(s)
if not offline:
if projectName is not None:
handler = getHandlerByName(projectName, None, Session)
else:
multiIter = multiDirectoryIterator(directoryList, filefilt=filefilt)
firstFile, size = multiIter.next()
listIter = list(multiIter)
handler = getHandler(firstFile, Session, validate=True)
if handler is None:
raise ESGPublishError("No project found in file %s, specify with --project." % firstFile)
projectName = handler.name
props = properties.copy()
props.update(initcontext)
if not readFiles:
directoryMap = handler.generateDirectoryMap(
directoryList, filefilt, initContext=props, datasetName=datasetName
)
else:
directoryMap = handler.generateDirectoryMapFromFiles(
directoryList, filefilt, initContext=props, datasetName=datasetName
)
datasetNames = [(item, -1) for item in directoryMap.keys()]
# Offline dataset. Format the spec as a dataset map : dataset_name => [(path, size), (path, size), ...]
else:
handler = getHandlerByName(projectName, None, Session, offline=True)
dmap = {}
listerSection = getOfflineLister(config, "project:%s" % projectName, service)
offlineLister = config.get(listerSection, "offline_lister_executable")
commandArgs = "--config-section %s " % listerSection
commandArgs += " ".join(directoryList)
for dsetName, filepath, sizet in processNodeMatchIterator(
offlineLister, commandArgs, handler, filefilt=filefilt, datasetName=datasetName, offline=True
):
size, mtime = sizet
if dmap.has_key((dsetName, -1)):
dmap[(dsetName, -1)].append((filepath, str(size)))
else:
dmap[(dsetName, -1)] = [(filepath, str(size))]
datasetNames = dmap.keys()
datasetNames.sort()
if len(datasetNames) == 0:
warning("No datasets found.")
# Iterate over datasets
if not publishOnly:
datasets = iterateOverDatasets(
projectName,
dmap,
directoryMap,
datasetNames,
Session,
aggregateDimension,
publishOp,
filefilt,
initcontext,
offline,
properties,
keepVersion=keepVersion,
newVersion=version,
extraFields=extraFields,
masterGateway=masterGateway,
comment=message,
readFiles=readFiles,
)
result = publishDatasetList(
datasetNames,
Session,
publish=publish,
thredds=thredds,
las=las,
parentId=parent,
service=service,
perVariable=perVariable,
threddsCatalogDictionary=threddsCatalogDictionary,
reinitThredds=reinitThredds,
readFromCatalog=readFromCatalog,
)
return result
def esgscanWrapper(directoryList, **kw):
if len(directoryList) == 0:
raise ESGPublishError("No directory specified")
output = sys.stdout
appendMap = None
appendPath = kw.get("appendPath", None)
if appendPath is not None:
if os.path.exists(appendPath):
appendMap = readDatasetMap(appendPath)
else:
appendMap = {}
output = open(appendPath, "a")
datasetName = kw.get("datasetName", None)
filefilt = kw.get("fileFilt", ".*\.nc$")
init_file = kw.get("initFile", None)
offline = kw.get("offline", False)
outputPath = kw.get("outputPath", None)
if outputPath is not None:
output = open(outputPath, "w")
else:
output = sys.stdout
projectName = kw.get("projectName", None)
readFiles = kw.get("readFiles", False)
service = kw.get("service", None)
# Load the configuration and set up a database connection
config, Session = initdb(init_file=init_file)
# Register project handlers
registerHandlers()
if not offline:
# Determine if checksumming is enabled
line = config.get("DEFAULT", "checksum", default=None)
if line is not None:
checksumClient, checksumType = splitLine(line)
else:
checksumClient = None
if projectName is not None:
handler = getHandlerByName(projectName, None, Session)
else:
multiIter = multiDirectoryIterator(directoryList, filefilt=filefilt)
firstFile, size = multiIter.next()
handler = getHandler(firstFile, Session, validate=True)
if handler is None:
raise ESGPublishError("No project found in file %s, specify with --project." % firstFile)
projectName = handler.name
if not readFiles:
datasetMap = handler.generateDirectoryMap(directoryList, filefilt, datasetName=datasetName)
else:
datasetMap = handler.generateDirectoryMapFromFiles(directoryList, filefilt, datasetName=datasetName)
# Output the map
keys = datasetMap.keys()
keys.sort()
for datasetId in keys:
direcTuple = datasetMap[datasetId]
direcTuple.sort()
for nodepath, filepath in direcTuple:
# If readFiles is not set, generate a map entry for each file in the directory
# that matches filefilt ...
if not readFiles:
itr = directoryIterator(nodepath, filefilt=filefilt, followSubdirectories=False)
# ... otherwise if readFiles is set, generate a map entry for each file
else:
itr = fnIterator([filepath])
for filepath, sizet in itr:
size, mtime = sizet
extraStuff = "mod_time=%f" % float(mtime)
if checksumClient is not None:
csum = checksum(filepath, checksumClient)
extraStuff += " | checksum=%s | checksum_type=%s" % (csum, checksumType)
# Print the map entry if:
# - The map is being created, not appended, or
# - The existing map does not have the dataset, or
# - The existing map has the dataset, but not the file.
if (
(appendMap is None)
or (not appendMap.has_key(datasetId))
or ((filepath, "%d" % size) not in appendMap[datasetId])
):
print >> output, "%s | %s | %d | %s" % (datasetId, filepath, size, extraStuff)
else: # offline
if projectName is not None:
handler = getHandlerByName(projectName, None, Session, offline=True)
else:
raise ESGPublishError("Must specify --project for offline datasets.")
listerSection = getOfflineLister(config, "project:%s" % projectName, service)
offlineLister = config.get(listerSection, "offline_lister_executable")
commandArgs = "--config-section %s " % listerSection
commandArgs += " ".join(directoryList)
for dsetName, filepath, sizet in processNodeMatchIterator(
offlineLister, commandArgs, handler, filefilt=filefilt, datasetName=datasetName, offline=True
):
size, mtime = sizet
extrastuff = ""
if mtime is not None:
extrastuff = "| mod_time=%f" % float(mtime)
if (
(appendMap is None)
or (not appendMap.has_key(dsetName))
or ((filepath, "%d" % size) not in appendMap[dsetName])
):
print >> output, "%s | %s | %d %s" % (dsetName, filepath, size, extrastuff)
if output is not sys.stdout:
output.close()
def main(argv):
try:
args, lastargs = getopt.getopt(argv, "hi:", [
'database-delete', 'database-only', 'echo-sql', 'map=',
'no-republish', 'no-thredds-reinit', 'skip-gateway', 'skip-index',
'las', 'log=', 'rest-api', 'skip-thredds', 'sync-thredds',
'use-list='
])
except getopt.error:
print sys.exc_value
return
deleteAll = False
datasetMap = None
deleteDset = False
unpublishOnGateway = False
echoSql = False
init_file = None
gatewayOp = DELETE
las = False
log_filename = None
republish = True
restApi = None
thredds = True
syncThredds = False
useList = False
threddsReinit = True
for flag, arg in args:
if flag == '--database-delete':
deleteDset = True
elif flag == '--database-only':
gatewayOp = NO_OPERATION
thredds = False
deleteDset = True
elif flag == '--echo-sql':
echoSql = True
elif flag in ['-h', '--help']:
return
elif flag == '-i':
init_file = arg
elif flag == '--map':
datasetMap = readDatasetMap(arg)
elif flag == '--skip-gateway':
gatewayOp = NO_OPERATION
elif flag == '--skip-index':
gatewayOp = NO_OPERATION
elif flag == '--las':
las = True
elif flag == '--log':
log_filename = arg
elif flag == '--no-republish':
republish = False
elif flag == '--no-thredds-reinit':
threddsReinit = False
elif flag == '--rest-api':
restApi = True
elif flag == '--skip-thredds':
thredds = False
elif flag == '--sync-thredds':
syncThredds = True
elif flag == '--use-list':
useList = True
useListPath = arg
if gatewayOp != NO_OPERATION and unpublishOnGateway:
gatewayOp = UNPUBLISH
# Load the configuration and set up a database connection
config = loadConfig(init_file)
engine = create_engine(config.getdburl('extract'),
echo=echoSql,
pool_recycle=3600)
initLogging('extract', override_sa=engine, log_filename=log_filename)
Session = sessionmaker(bind=engine, autoflush=True, autocommit=False)
if config is None:
raise ESGPublishError("No configuration file found.")
threddsRoot = config.get('DEFAULT', 'thredds_root')
# Get the default publication interface (REST or Hessian)
if restApi is None:
restApi = config.getboolean('DEFAULT', 'use_rest_api', default=False)
if datasetMap is None:
if not useList:
datasetNames = [parseDatasetVersionId(item) for item in lastargs]
else:
if useListPath == '-':
namelist = sys.stdin
else:
namelist = open(useListPath)
datasetNames = []
for line in namelist.readlines():
versionId = parseDatasetVersionId(line.strip())
datasetNames.append(versionId)
else:
datasetNames = datasetMap.keys()
datasetNames.sort()
result = deleteDatasetList(datasetNames,
Session,
gatewayOp,
thredds,
las,
deleteDset,
deleteAll=deleteAll,
republish=republish,
reinitThredds=threddsReinit,
restInterface=restApi)
# Republish previous versions as needed. This will happen if the latest version
# was deleted from the database, and is not
# the only version. In this case the previous version will be rescanned to generate the aggregations.
if republish:
statusDict, republishList = result
if len(republishList) > 0:
# Register project handlers.
registerHandlers()
info("Republishing modified datasets:")
republishDatasetNames = [
generateDatasetVersionId(dsetTuple)
for dsetTuple in republishList
]
dmap, offline = queryDatasetMap(republishDatasetNames, Session)
datasetNames = dmap.keys()
datasets = iterateOverDatasets(None,
dmap,
None,
republishList,
Session,
"time",
UPDATE_OP,
None, {},
offline, {},
forceAggregate=True)
republishOp = (gatewayOp != NO_OPERATION
) # Don't republish if skipping the gateway op
result = publishDatasetList(datasetNames,
Session,
publish=republishOp,
thredds=thredds)
# Synchronize database and THREDDS catalogs
if syncThredds:
threddsRoot = config.get('DEFAULT', 'thredds_root')
# Make a dictionary of catalogs from the database
session = Session()
subcatalogs = session.query(Catalog).select_from(
join(Catalog, Dataset,
Catalog.dataset_name == Dataset.name)).all()
catdict = {}
for catalog in subcatalogs:
location = os.path.join(threddsRoot, catalog.location)
catdict[location] = 1
session.close()
# Scan all XML files in the threddsroot
os.path.walk(threddsRoot, cleanupCatalogs, catdict)
def main(argv):
try:
args, lastargs = getopt.getopt(argv, "a:cdehi:m:p:ru", ['append', 'create', 'dataset=', 'delete-files', 'echo-sql', 'experiment=', 'filter=', 'help', 'keep-version', 'log=', 'map=', 'message=', 'model=', 'offline', 'parent=', 'per-time', 'per-variable', 'project=', 'property=', 'publish', 'new-version=', 'no-thredds-reinit', 'noscan', 'read-directories', 'read-files', 'rename-files', 'replace', 'replica=', 'rest-api', 'service=', 'set-replica', 'summarize-errors', 'thredds', 'thredds-reinit', 'update', 'use-existing=', 'use-list=', 'validate=', 'version-list=', 'nodbwrite'])
except getopt.error:
print sys.exc_value
return
aggregateDimension = "time"
datasetMapfile = None
datasetName = None
echoSql = False
filefilt = '.*\.nc$'
init_file = None
initcontext = {}
keepVersion = False
las = False
log_filename = None
masterGateway = None
message = None
offline = False
parent = None
perVariable = None
projectName = None
properties = {}
publish = False
publishOnly = False
publishOp = CREATE_OP
readFiles = False
rescan = False
rescanDatasetName = []
restApi = None
schema = None
service = None
summarizeErrors = False
testProgress1 = testProgress2 = None
thredds = False
threddsReinit = None
version = None
versionList = None
nodbwrite = False
for flag, arg in args:
if flag=='-a':
aggregateDimension = arg
elif flag=='--append':
publishOp = UPDATE_OP
elif flag in ['-c', '--create']:
publishOp = CREATE_OP
elif flag=='--dataset':
datasetName = arg
elif flag in ['-d', '--delete-files']:
publishOp = DELETE_OP
elif flag=='--echo-sql':
echoSql = True
elif flag=='--experiment':
initcontext['experiment'] = arg
elif flag=='--filter':
filefilt = arg
elif flag in ['-h', '--help']:
print usage
sys.exit(0)
elif flag=='-i':
init_file = arg
elif flag=='--keep-version':
keepVersion = True
elif flag=='--log':
log_filename = arg
elif flag=='--map':
datasetMapfile = arg
elif flag in ['-m', '--message']:
message = arg
elif flag=='--model':
initcontext['model'] = arg
elif flag=='--nodbwrite':
nodbwrite = True
elif flag=='--new-version':
try:
version = string.atoi(arg)
if version <=0:
raise ValueError
except ValueError:
raise ESGPublishError("Version number must be a positive integer: %s"%arg)
elif flag=='--no-thredds-reinit':
threddsReinit = False
elif flag=='--noscan':
publishOnly = True
elif flag=='--offline':
offline = True
elif flag=='--parent':
parent = arg
elif flag=='--per-time':
perVariable = False
elif flag=='--per-variable':
perVariable = True
elif flag=='--project':
projectName = arg
elif flag in ['-p', '--property']:
name, value = arg.split('=')
properties[name] = value
elif flag=='--publish':
publish = True
elif flag in ['-e', '--read-directories']:
readFiles = False
elif flag=='--read-files':
readFiles = True
elif flag=='--rename-files':
publishOp = RENAME_OP
elif flag in ['-r', '--replace']:
publishOp = REPLACE_OP
elif flag=='--replica':
masterGateway = arg
warning("The --replica option is deprecated. Use --set-replica instead")
elif flag=='--rest-api':
restApi = True
elif flag=='--service':
service = arg
elif flag=='--set-replica':
masterGateway = 'DEFAULT'
elif flag=='--summarize-errors':
summarizeErrors = True
elif flag=='--thredds':
thredds = True
elif flag=='--thredds-reinit':
threddsReinit = True
elif flag in ['-u', '--update']:
publishOp = UPDATE_OP
elif flag=='--use-existing':
rescan = True
rescanDatasetName.append(arg)
elif flag=='--use-list':
rescan = True
if arg=='-':
namelist=sys.stdin
else:
namelist = open(arg)
for line in namelist.readlines():
line = line.strip()
if line[0]!='#':
rescanDatasetName.append(line)
elif flag=='--validate':
schema = arg
restApi = True
elif flag=='--version-list':
versionList = arg
# If offline, the project must be specified
if offline and (projectName is None):
raise ESGPublishError("Must specify project with --project for offline datasets")
if version is not None and versionList is not None:
raise ESGPublishError("Cannot specify both --new-version and --version-list")
if versionList is not None:
version = {}
f = open(versionList)
lines = f.readlines()
f.close()
for line in lines:
line = line.strip()
dsid, vers = line.split('|')
dsid = dsid.strip()
vers = int(vers.strip())
version[dsid] = vers
# Load the configuration and set up a database connection
config = loadConfig(init_file)
engine = create_engine(config.getdburl('extract'), echo=echoSql, pool_recycle=3600)
initLogging('extract', override_sa=engine, log_filename=log_filename)
Session = sessionmaker(bind=engine, autoflush=True, autocommit=False)
# Register project handlers
registerHandlers()
# Get the default publication interface (REST or Hessian)
if restApi is None:
restApi = config.getboolean('DEFAULT', 'use_rest_api', default=False)
# If the dataset map is input, just read it ...
dmap = None
directoryMap = None
extraFields = None
if datasetMapfile is not None:
dmap, extraFields = readDatasetMap(datasetMapfile, parse_extra_fields=True)
datasetNames = dmap.keys()
elif rescan:
# Note: No need to get the extra fields, such as mod_time, since
# they are already in the database, and will be used for file comparison if necessary.
dmap, offline = queryDatasetMap(rescanDatasetName, Session)
datasetNames = dmap.keys()
# ... otherwise generate the directory map.
else:
# Online dataset(s)
if not offline:
if len(lastargs)==0:
print "No directories specified."
return
if projectName is not None:
handler = getHandlerByName(projectName, None, Session)
else:
multiIter = multiDirectoryIterator(lastargs, filefilt=filefilt)
firstFile, size = multiIter.next()
listIter = list(multiIter)
handler = getHandler(firstFile, Session, validate=True)
if handler is None:
raise ESGPublishError("No project found in file %s, specify with --project."%firstFile)
projectName = handler.name
props = properties.copy()
props.update(initcontext)
if not readFiles:
directoryMap = handler.generateDirectoryMap(lastargs, filefilt, initContext=props, datasetName=datasetName)
else:
directoryMap = handler.generateDirectoryMapFromFiles(lastargs, filefilt, initContext=props, datasetName=datasetName)
datasetNames = [(item,-1) for item in directoryMap.keys()]
# Offline dataset. Format the spec as a dataset map : dataset_name => [(path, size), (path, size), ...]
else:
handler = getHandlerByName(projectName, None, Session, offline=True)
dmap = {}
listerSection = getOfflineLister(config, "project:%s"%projectName, service)
offlineLister = config.get(listerSection, 'offline_lister_executable')
commandArgs = "--config-section %s "%listerSection
commandArgs += " ".join(lastargs)
for dsetName, filepath, sizet in processNodeMatchIterator(offlineLister, commandArgs, handler, filefilt=filefilt, datasetName=datasetName, offline=True):
size, mtime = sizet
if dmap.has_key((dsetName,-1)):
dmap[(dsetName,-1)].append((filepath, str(size)))
else:
dmap[(dsetName,-1)] = [(filepath, str(size))]
datasetNames = dmap.keys()
datasetNames.sort()
if len(datasetNames)==0:
warning("No datasets found.")
min_version = -1
else:
min_version = sorted(datasetNames, key=lambda x: x[1])[0][1]
# Must specify version for replications
if min_version == -1 and masterGateway is not None and version is None and versionList is None:
raise ESGPublishError("Must specify version with --new-version (or --version-list) for replicated datasets")
# Iterate over datasets
if not publishOnly:
# pdb.set_trace()
datasets = iterateOverDatasets(projectName, dmap, directoryMap, datasetNames, Session, aggregateDimension, publishOp, filefilt, initcontext, offline, properties, keepVersion=keepVersion, newVersion=version, extraFields=extraFields, masterGateway=masterGateway, comment=message, readFiles=readFiles, nodbwrite=nodbwrite)
if (not nodbwrite):
result = publishDatasetList(datasetNames, Session, publish=publish, thredds=thredds, las=las, parentId=parent, service=service, perVariable=perVariable, reinitThredds=threddsReinit, restInterface=restApi, schema=schema)
# print `result`
if summarizeErrors:
print 'Summary of errors:'
for name,versionno in datasetNames:
dset = Dataset.lookup(name, Session)
print dset.get_name(Session), dset.get_project(Session), dset.get_model(Session), dset.get_experiment(Session), dset.get_run_name(Session)
if dset.has_warnings(Session):
print '=== Dataset: %s ==='%dset.name
for line in dset.get_warnings(Session):
print line