def test_main(self):
loop_stub = Mock()
router_stub = Mock()
radio_stub = Mock()
gateway.Router.return_value = router_stub
gateway.Radio.return_value = radio_stub
gateway.Radio.send_packet = {}
gateway.asyncio.get_event_loop.return_value = loop_stub
router_stub.connect_to_message_queue.return_value = 'Future'
gateway.main()
gateway.initialize_gpio.assert_called_once_with()
gateway.Radio.assert_called_once_with()
gateway.Router.assert_called_once_with()
loop_stub.run_until_complete.assert_called_once_with('Future')
router_stub.set_send_packet.assert_called_once_with(
radio_stub.send_packet)
gateway.poll.assert_called_once_with(loop_stub, radio_stub,
router_stub)
loop_stub.run_forever.assert_called_once_with()
loop_stub.close.assert_called_once_with()
def test_main(self):
loop_stub = Mock()
router_stub = Mock()
radio_stub = Mock()
gateway.Router.return_value = router_stub
gateway.Radio.return_value = radio_stub
gateway.Radio.send_packet = {}
gateway.asyncio.get_event_loop.return_value = loop_stub
router_stub.connect_to_message_queue.return_value = 'Future'
gateway.main()
gateway.initialize_gpio.assert_called_once_with()
gateway.Radio.assert_called_once_with()
gateway.Router.assert_called_once_with()
loop_stub.run_until_complete.assert_called_once_with('Future')
router_stub.set_send_packet.assert_called_once_with(radio_stub.send_packet)
gateway.poll.assert_called_once_with(loop_stub, radio_stub, router_stub)
loop_stub.run_forever.assert_called_once_with()
loop_stub.close.assert_called_once_with()
def testIPSL():
import gateway
#connect to db
db = ReplicaDB('sqlite:///ipsl2.db')
#get datasets for replication
datasets = ["cmip5.output1.IPSL.IPSL-CM5A-LR.aqua4K.day.atmos.cfDay.r1i1p1","cmip5.output1.IPSL.IPSL-CM5A-LR.aqua4K.day.atmos.day.r1i1p1","cmip5.output1.IPSL.IPSL-CM5A-LR.aqua4K.fx.atmos.fx.r0i0p0","cmip5.output1.IPSL.IPSL-CM5A-LR.aqua4K.fx.land.fx.r0i0p0","cmip5.output1.IPSL.IPSL-CM5A-LR.aqua4K.fx.ocean.fx.r0i0p0","cmip5.output1.IPSL.IPSL-CM5A-LR.aqua4K.3hr.atmos.3hr.r1i1p1","cmip5.output1.IPSL.IPSL-CM5A-LR.aqua4K.6hr.atmos.6hrLev.r1i1p1","cmip5.output1.IPSL.IPSL-CM5A-LR.aqua4K.6hr.atmos.6hrPlev.r1i1p1"]
for ds in datasets:
cmd = '-g BADC -of --parent {0}'.format(ds)
files = gateway.main(cmd.split(' '))
print len(files)
print files[0]
db.add_all(files)
def setUp(self):
self.config = testing.setUp()
import ConfigParser
from gateway.models import DBSession
from gateway.models import initialize_sql
config = ConfigParser.ConfigParser()
config.readfp(open('testing.ini'))
db_string = config.get('app:gateway', 'db_string')
initialize_sql(db_string)
from gateway import main
from webtest import TestApp
app = main(None, **{'db_string': db_string,
'mako.directories': config.get('app:gateway', 'mako.directories')})
self.testapp = TestApp(app)
self.session = DBSession()
def updateCollections(gw_name):
import gateway
gw_server = gateway.getGatewayInfo()[gw_name]['server']
db = getSession()
datasets = {}
for col in db.query(Collection).filter(Collection.state=='published').filter(Collection.gateway==gw_server):
for dataset in gateway.main(('-g %s --parent %s -do' % (col.gateway, col.id)).split()):
datasets[dataset['id']] = col.id
#search for orphans of this gateway
for dataset in db.query(Dataset).filter(Dataset.parent_gateway==gw_server).filter(Dataset.parent_id==None):
if dataset.id in datasets:
dataset.parent_id = datasets[dataset.id]
else:
#perhaps the top level collection was retracted!
print "Dataset has no parent", dataset.id
db.commit()
def processGateway(gw_name):
import urllib2, re, xml, gateway
db = getSession()
gw_url = gateway.getGatewayInfo()[gw_name]['url']
gw_server = gateway.getGatewayInfo()[gw_name]['server']
hlog.debug("jfp gw_url=%s, gw_server=%s",gw_url,gw_server)
try:
cmip5_id = _getCMIP5Id(gw_url)
except:
if gw_name == 'NCI':
hlog.warn("_getCMIP5Id failed; but recognize gateway and will use 'cmip5'")
cmip5_id = 'cmip5'
else:
print 'No CMIP5 found for Gateway %s. Check manually.(3)' % gw_name
return
hlog.debug("jfp cmip5_id=%s",cmip5_id)
#get all toplevel collections from gateway
gw_top = {}
hlog.debug("jfp in processGateway, will call gateway.main with args %s",
('-g %s -co' % gw_name).split())
collections = gateway.main(('-g %s -co' % gw_name).split())
if collections==None: collections=[]
if collections==2: # quick fix; gateway.main should throw an exception instead
collections=[]
for tlc in collections:
gw_top[tlc['id']] = tlc
#get already known collections
db_col = {}
for col in db.query(Collection).filter(Collection.gateway==gw_server).all():
#within the gateway these are unique
db_col[col.id] = col
hlog.debug("jfp db_col=%s",db_col)
db_ds = {}
for ds in getLatestDatasetsQuery(gw_server).filter(Dataset.parent_gateway==gw_server).all():
db_ds[ds.id] = ds
#now get all CMIP5 datasets
page_url = '%s/project/%s/dataset/feed.atom' % (gw_url, cmip5_id)
hlog.debug("jfp in processGateway, about to open %s",page_url)
# jfp 2012.09.11 This url is unavailable at NCI; the harvest will always fail.
# if page_url.find('nci.org.au')>-1: # jfp unreliable site, try the url twice (doesn't help)
# try:
# print "first attempt..."
# page = urllib2.urlopen(page_url,None,120).read()
# except Exception as e:
# print "...failed: ",e
# print "second attempt..."
try:
page = urllib2.urlopen(page_url).read()
except Exception as e:
print "exception opening %s in processGateway: %s" % (page_url,e)
raise e
dom = xml.dom.minidom.parseString(page)
counter = 0 #commit after a bunch
existing_ds = {}
hlog.debug("jfp %s dom entries",len(dom.getElementsByTagName('entry')))
for entry in dom.getElementsByTagName('entry'):
id = entry.getElementsByTagName('title')[0].childNodes[0].data
timestamp = entry.getElementsByTagName('updated')[0].childNodes[0].data
last_update = datetime.datetime(*time.strptime(timestamp, "%Y-%m-%dT%H:%M:%SZ")[:6])
#top level and normal are mixed!
if id in gw_top:
#this is a top level for cmip5!
print "Top level found", id
if id in db_col:
#update
col = db_col[id]
if last_update > col.modtime:
#we know this collection was modified! (not that we car now...)
print "Collection modifed! was %s now is %s" % (col.modtime, last_update)
col.modtime = last_update
else:
#add new collection
metadata = gateway.main(('-g %s --parent %s -mo' % (gw_name, id)).split())
if metatdata==None: continue
db.add(Collection(gateway=gw_server,id=id,modtime=last_update,state=metadata['state']))
continue
#remember this dataset for later
existing_ds[id] = True
if id in db_ds:
#we know this normal dataset! Check if it has changed
if db_ds[id].modtime == last_update:
#old news...
hlog.debug("Unchanged dataset %s, modtime=%s",id,last_update)
continue
print "Changed dataset found", id, db_ds[id].modtime, last_update
hlog.info( "Changed dataset found %s %s %s", id, db_ds[id].modtime, last_update )
#something got changed!
old_ds = db_ds[id]
old_ds.modtime = last_update
else:
print "New dataset found", id, " on ", time.ctime()
hlog.info( "New dataset found %s on %s" %(id,time.ctime()) )
old_ds = None
#new dataset version or something changed!
metadata = gateway.main(('-g %s --parent %s -mo' % (gw_name, id)).split())
if metadata==None or metadata==2: continue
hlog.debug("version %s",metadata['version'])
#version work around
if metadata['state'] == 'retracted':
print "retracted dataset"
#this got retracted!
if old_ds and old_ds.state != metadata['state']:
#state changed!
old_ds.state = metadata['state']
continue
if not metadata['catalog'] or not metadata['version']:
print "Can't parse this, no catalog or version!!", metadata
continue
files = gateway.main(('-g %s --parent %s -fo' % (gw_name, id)).split())
if files==None: files=[]
filecount = len(files)
if filecount > 0:
size = sum([int(f['size']) for f in files])
#we assume this is per dataset defined, and not per file
ep = files[filecount/2]['endpoints']
if ep:
types = [e['type'] for e in ep]
else:
types = []
else:
#empty dataset?! There are some...
size = 0
types = []
if old_ds and int(metadata['version']) == old_ds.version:
print "Same version was updated!!"
to_check_update = [('access_http', 'HTTPServer' in types),
('access_gridftp', 'GridFTP' in types), ('access_opendap', 'OPeNDAP'in types),
('filecount', filecount), ('size', size)]
for var, value in to_check_update:
report = ""
old_value = old_ds.__dict__[var]
if old_value != value:
#report and update
report += "Changed %s from %s to %s, " % (var, old_value, value)
old_ds.__dict__[var] = value
continue #Use old_ds instead of creating a new one.
elif old_ds:
#new version
print "New version found %s, last one was %s; on %s" %\
(metadata['version'], old_ds.version, time.ctime())
hlog.info( "New version found %s, last one was %s; on %s" %\
(metadata['version'], old_ds.version, time.ctime()) )
#Definitely a new version of either an existing dataset or a new one.
try: #jfp added try/except
db.add(Dataset(id=id, version=int(metadata['version']), catalog=metadata['catalog'],\
state=metadata['state'], filecount=filecount, size=size, access_http=\
('HTTPServer' in types), access_gridftp=('GridFTP' in types),\
access_opendap=('OPeNDAP' in types), modtime=last_update, parent_gateway=gw_server))
db.flush() # jfp will slow things down, but we'll catch problems right away
except sqlalchemy.exc.IntegrityError: #jfp added try/except
print "exception adding dataset id=",id," version=",metadata['version']," state=",metadata['state']
print "catalog=",metadata['catalog']," modtime=",last_update," parent_gateway=",gw_server
print "access_http=",('HTTPServer' in types)," access_gridftp=",('GridFTP' in types)
print sys.exc_info()[:2]
db.rollback() # jfp mandatory after a failed flush!
# raise #jfp Now should be able to continue with other datasets.
if counter > 20:
#db.commit()
counter = 0
else:
counter += 1
#db.commit()
#Now we must find missing ones, so we delete them properly
for col in db_col.values():
for dataset in col.datasets:
if not dataset.id in existing_ds:
if dataset.state == 'published':
dataset.state = 'retracted'
print "dataset %s was removed by %s" % (dataset.id,time.ctime())
hlog.info( "dataset %s was removed by %s" %(dataset.id,time.ctime()) )
#db.commit()
# print "jfp finished with loop over db_col.values()"
datasets = {}
for col in db.query(Collection).filter(Collection.state=='published').filter(Collection.gateway==gw_server):
gdatasets = gateway.main(('-g %s --parent %s -do' % (col.gateway, col.id)).split())
if gdatasets==None: gdatasets=[]
for dataset in gdatasets:
datasets[dataset['id']] = col.id
for d in db.new:
if d.id in datasets:
d.parent_id = datasets[d.id]
else:
print "problem with", d
db.commit()
print "jfp committed"
def processGatewayOld(gw_name, fast=True):
"""Old method for harvesting gateways"""
import urllib2, re, xml, gateway
db = getSession()
gw_url = gateway.getGatewayInfo()[gw_name]['url']
gw_server = gateway.getGatewayInfo()[gw_name]['server']
#skip these
skip_top_level = []
try:
cmip5_id = _getCMIP5Id(gw_url)
except:
print 'No CMIP5 found for Gateway %s. Check manually.(2)' % gw_name
hlog.warn( 'No CMIP5 found for Gateway %s. Check manually.(2)' % gw_name )
return
#get already known collections
db_col = {}
for col in db.query(Collection).filter(Collection.gateway==gw_server).all():
#within the gateway these are unique
db_col[col.id] = col
#now get known datasets
db_ds = {}
for ds in getLatestDatasetsQuery(gw_server).filter(Dataset.parent_gateway==gw_server).all():
db_ds['%s#%s' % (ds.id, ds.version)] = ds
counter = 0
for col in _getCMIP5Collections(gw_url, cmip5_id):
hlog.info( "Processing Collection %s on %s" %(col,time.ctime()) )
if col in skip_top_level:
print "Skipping"
hlog.info( "Skipping, time is %s" % (time.ctime()) )
continue
if not col in db_col:
#new collection!
hlog.info("New collection %s on %s" % (col,time.ctime()))
md = gateway.main(('-g %s --parent %s -mo' % (gw_name, col)).split())
if md==None: continue
#use a fictional date for the update so we know later on which
#should be latered
db.add(Collection(id=col, gateway=gw_server,state=md['state'],
modtime=dummy_date))
existing_ds = {}
datasets = gateway.main(('-g %s --parent %s -do' % (gw_name,col)).split())
if datasets==None: datasets=[]
for dataset in datasets:
ds_key = '%s#%s' % (dataset['id'], dataset['version'])
#store for later
existing_ds[ds_key] = True
if ds_key in db_ds:
old_ds = db_ds[ds_key]
#should we update? (for now don't...)
#if int(dataset['version']) == old_ds.version:
#same version... we might want to check... but in the common case this won't be necessary
#and is extremely expensive for this old way of getting things
# continue
else:
old_ds = None
#Avoid reparsing already parsed datasets. The might change! e.g. they can be retracted.
#They should be parsed once in a while
if fast and old_ds: continue
print "Processing dataset", ds_key, " on ", time.ctime()
hlog.info( "Processing dataset %s on %s" %(ds_key,time.ctime()) )
metadata = gateway.main(('-g %s --parent %s -mo' % (gw_name, dataset['id'])).split())
if not metadata:
continue
#version work around
if metadata['state'] == 'retracted':
print "retracted dataset"
hlog.info( "retracted dataset" )
#this got retracted!
if old_ds and old_ds.state != metadata['state']:
#state changed!
old_ds.state = metadata['state']
continue
if not metadata['catalog'] or not metadata['version']:
print "Can't parse this, no catalog or version!!", metadata
hlog.info( "Can't parse this, no catalog or version!! %s" %s (metadata) )
continue
#this is new!
files = gateway.main(('-g %s --parent %s -fo' % (gw_name,dataset['id'])).split())
if files==None: files=[]
filecount = len(files)
if filecount > 0:
size = sum([int(f['size']) for f in files])
#we assume this is per dataset defined, and not per file
# use some file in the middle for this
ep = files[filecount/2]['endpoints']
if ep:
types = [e['type'] for e in ep]
else:
types = []
else:
#empty dataset?! There are some...
size = 0
types = []
if old_ds:
#we will need to update the existing one
old_ds.access_http=('HTTPServer' in types)
old_ds.access_gridftp=('GridFTP' in types)
old_ds.access_opendap=('OPeNDAP'in types)
else:
db.add(Dataset(id=dataset['id'], version=int(metadata['version']), catalog=metadata['catalog'],
state=metadata['state'], filecount=filecount, size=size, access_http=('HTTPServer' in types),
access_gridftp=('GridFTP' in types), access_opendap=('OPeNDAP' in types),
modtime=dummy_date, parent_gateway=gw_server, parent_id=col))
if counter > 20:
db.commit()
counter = 0
else:
counter += 1
# db.commit() #jfp temporary extra commit, to aid debugging
if col in db_col:
print col, len(db_col[col].datasets), len(existing_ds)
hlog.info( "collection,lengths: %s, %s, %s on %s" %\
( col, len(db_col[col].datasets), len(existing_ds), time.ctime() ) )
for dataset in db_col[col].datasets:
ds_key = '%s#%s' % (dataset.id, dataset.version)
if not ds_key in existing_ds:
print "dataset %s was deleted" % ds_key
hlog.info( "dataset %s was deleted" % ds_key )
db.delete(dataset)
#if dataset.state == 'published':
#dataset.state = 'retracted'
#commit the rest of the changes
db.commit()
def main(argv=None):
if argv is None: argv = sys.argv[1:]
import getopt
try:
args, lastargs = getopt.getopt(argv, "g:D:e:dvqh", ['help', 'gateway-url=', 'parent='])
except getopt.error:
print sys.exc_info()[:3]
return 1
#init values
db_name = 'replica.db'
gatewayURL = gatewayName = regex = None
parent_set = False
gw_args = "-o"
#parse arguments
for flag, arg in args:
if flag=='-g': gw_args = '%s -g %s' % (gw_args, arg)
elif flag=='--gateway-url': gw_args = '%s --gateway-url %s' % (gw_args, arg)
elif flag=='--parent':
gw_args = '%s --parent %s' % (gw_args, arg)
parent_set = True
elif flag=='-D': db_name = arg
elif flag=='-e':
import re
regex = re.compile(arg)
# elif flag=='-x': retrieve_xml = True
# elif flag=='-o': retrieve_object = True
elif flag=='-d': log.setLevel(logging.DEBUG)
elif flag=='-v': log.setLevel(logging.INFO)
elif flag=='-q': log.setLevel(logging.NONE)
elif flag=='-h' or flag=='--help': return 1
if not parent_set:
gw_args = '-A ' + gw_args
log.warn('Top level collection not set. Trying all known top-level collections (set with --parent)')
else: gw_args = '-d ' + gw_args
#Get datasets
log.info('Retrieving datasets from Gateway')
log.debug('cmd: %s', gw_args)
ds = gateway.main(gw_args.split(' '))
if ds: log.debug('Total datasets: %s', len(ds))
else:
log.error('No Dataset was found!')
return 0
if regex:
ds = [d['id'] for d in ds if regex.search(d['id'])]
#prepare DB
log.debug('DB: %s', db_name)
log.debug('Entries: %s', len(ds))
db = ReplicaDB('sqlite:///%s' % db_name)
db.open()
for d in ds:
cmd = '{0} -of --parent {1}'.format(gw_args[3:], d)
log.debug('getting files with %s', cmd)
files = gateway.main(cmd.split(' '))
if files:
log.info('Adding %s files for dataset %s', len(files), d)
db.add_all(files)
else:
log.error('no file found!')
return 0
def processGateway(gw_name):
import urllib2, re, xml, gateway
db = getSession()
gw_url = gateway.getGatewayInfo()[gw_name]['url']
gw_server = gateway.getGatewayInfo()[gw_name]['server']
try:
cmip5_id = _getCMIP5Id(gw_url)
except:
print 'No CMIP5 found for Gateway %s. Check manually.' % gw_name
return
#get all toplevel collections from gateway
gw_top = {}
for tlc in gateway.main(('-g %s -co' % gw_name).split()):
gw_top[tlc['id']] = tlc
#get already known collections
db_col = {}
for col in db.query(Collection).filter(Collection.gateway==gw_server).all():
#within the gateway these are unique
db_col[col.id] = col
db_ds = {}
for ds in getLatestDatasetsQuery(gw_server).filter(Dataset.parent_gateway==gw_server).all():
db_ds[ds.id] = ds
#now get all CMIP5 datasets
page = urllib2.urlopen('%s/project/%s/dataset/feed.atom' % (gw_url, cmip5_id)).read()
dom = xml.dom.minidom.parseString(page)
counter = 0 #commit after a bunch
existing_ds = {}
for entry in dom.getElementsByTagName('entry'):
id = entry.getElementsByTagName('title')[0].childNodes[0].data
timestamp = entry.getElementsByTagName('updated')[0].childNodes[0].data
last_update = datetime.datetime(*time.strptime(timestamp, "%Y-%m-%dT%H:%M:%SZ")[:6])
#top level and normal are mixed!
if id in gw_top:
#this is a top level for cmip5!
print "Top level found", id
if id in db_col:
#update
col = db_col[id]
if last_update > col.modtime:
#we know this collection was modified! (not that we car now...)
print "Collection modifed! was %s now is %s" % (col.modtime, last_update)
col.modtime = last_update
else:
#add new collection
metadata = gateway.main(('-g %s --parent %s -mo' % (gw_name, id)).split())
db.add(Collection(gateway=gw_server,id=id,modtime=last_update,state=metadata['state']))
continue
#remember this dataset for later
existing_ds[id] = True
if id in db_ds:
#we know this normal dataset! Check if it has changed
if db_ds[id].modtime == last_update:
#old news...
continue
print "Changed dataset found", id, db_ds[id].modtime, last_update
#something got changed!
old_ds = db_ds[id]
else:
print "New dataset found", id
old_ds = None
#new dataset version or something changed!
metadata = gateway.main(('-g %s --parent %s -mo' % (gw_name, id)).split())
#version work around
if metadata['state'] == 'retracted':
print "retracted dataset"
#this got retracted!
if old_ds and old_ds.state != metadata['state']:
#state changed!
old_ds.state = metadata['state']
continue
if not metadata['catalog'] or not metadata['version']:
print "Can't parse this, no catalog or version!!", metadata
continue
files = gateway.main(('-g %s --parent %s -fo' % (gw_name, id)).split())
filecount = len(files)
if filecount > 0:
size = sum([int(f['size']) for f in files])
#we assume this is per dataset defined, and not per file
ep = files[filecount/2]['endpoints']
if ep:
types = [e['type'] for e in ep]
else:
types = []
else:
#empty dataset?! There are some...
size = 0
types = []
if old_ds and int(metadata['version']) == old_ds.version:
print "Same version was updated!!"
to_check_update = [('access_http', 'HTTPServer' in types),
('access_gridftp', 'GridFTP' in types), ('access_opendap', 'OPeNDAP'in types),
('filecount', filecount), ('size', size)]
for var, value in to_check_update:
report = ""
old_value = old_ds.__dict__[var]
if old_value != value:
#report and update
report += "Changed %s from %s to %s, " % (var, old_value, value)
old_ds.__dict__[var] = value
continue #Use old_ds instead of creating a new one.
elif old_ds:
#new version
print "New version found %s, last one was %s" % (metadata['version'], old_ds.version)
#Definitely a new version of either an existing dataset or a new one.
db.add(Dataset(id=id, version=int(metadata['version']), catalog=metadata['catalog'], state=metadata['state'],
filecount=filecount, size=size, access_http=('HTTPServer' in types), access_gridftp=('GridFTP' in types),
access_opendap=('OPeNDAP' in types), modtime=last_update, parent_gateway=gw_server))
if counter > 20:
#db.commit()
counter = 0
else:
counter += 1
#db.commit()
#Now we must find missing ones, so we delete them properly
for col in db_col.values():
for dataset in col.datasets:
if not dataset.id in existing_ds:
if dataset.state == 'published':
dataset.state = 'retracted'
print "dataset %s was removed" % dataset.id
#db.commit()
datasets = {}
for col in db.query(Collection).filter(Collection.state=='published').filter(Collection.gateway==gw_server):
for dataset in gateway.main(('-g %s --parent %s -do' % (col.gateway, col.id)).split()):
datasets[dataset['id']] = col.id
for d in db.new:
if d.id in datasets:
d.parent_id = datasets[d.id]
else:
print "problem with", d
db.commit()