def add_staged_file_to_dataset(rel_filepath, dataset_id, username,
mimetype="application/octet-stream"):
"""
add file in user's staging path to a dataset
may be replaced by main code functions.
quick and dirty hack to get it working
"""
originfilepath = os.path.join(get_full_staging_path(username), rel_filepath)
dataset = Dataset.objects.get(pk=dataset_id)
newDatafile = Dataset_File()
newDatafile.dataset = dataset
newDatafile.size = os.path.getsize(originfilepath)
newDatafile.protocol = "tardis"
newDatafile.mimetype = mimetype
file_dir = "/" + str(dataset.experiment.id) + "/" + str(dataset.id) + "/"
file_path = file_dir + rel_filepath
prelim_full_file_path = settings.FILE_STORE_PATH + file_path
full_file_path = duplicate_file_check_rename(prelim_full_file_path)
newDatafile.filename = os.path.basename(full_file_path)
newDatafile.url = "%s://%s" % (newDatafile.protocol,
full_file_path[
len(settings.FILE_STORE_PATH) + len(file_dir):])
if not os.path.exists(os.path.dirname(full_file_path)):
os.makedirs(os.path.dirname(full_file_path))
shutil.move(originfilepath, full_file_path)
newDatafile.save()
def _make_data_file(dataset, filename, content):
# TODO:
# create datasetfile
f = mktemp()
print "Inside make data file ", f
open(f, "w+b").write(content)
df = Dataset_File()
df.dataset = dataset
df.filename = filename
df.url = 'file://'+f
df.protocol = "staging"
df.size = len(content)
df.verify(allowEmptyChecksums=True)
df.save()
print "Df ---", df
def process_enclosure(self, dataset, enclosure):
filename = getattr(enclosure, 'title', basename(enclosure.href))
datafile = Dataset_File(url=enclosure.href, \
filename=filename, \
dataset=dataset)
datafile.protocol = enclosure.href.partition('://')[0]
try:
datafile.mimetype = enclosure.mime
except AttributeError:
pass
try:
datafile.size = enclosure.length
except AttributeError:
pass
try:
hash = enclosure.hash
# Split on white space, then ':' to get tuples to feed into dict
hashdict = dict([s.partition(':')[::2] for s in hash.split()])
# Set SHA-512 sum
datafile.sha512sum = hashdict['sha-512']
except AttributeError:
pass
datafile.save()
self.make_local_copy(datafile)
def process_enclosure(self, dataset, enclosure):
'''
Examines one "enclosure" from an entry, representing a datafile.
Determines whether to process it, and if so, starts the transfer.
'''
# TODO tjdett: This method needs a clean-up, as it's doing many more things than was originally intended. It now contains more more code about
# deciding whether to process the enclosure than it does about actually processing it. That decision, or the influencing factors, should be refactored into separate methods.
# Python has built-in time deltas and Django has time formatting functions, both of which would clean this code up considerably.
def _get_enclosure_url(enclosure):
''' Optionally manipulate datafile URL, eg: http://foo.edu/bar.txt -> file:////fooserver/bar.txt'''
if IngestOptions.USE_LOCAL_TRANSFERS:
return enclosure.href.replace(IngestOptions.URL_BASE_TO_REPLACE, IngestOptions.LOCAL_SOURCE_PATH)
else:
return enclosure.href
filename = getattr(enclosure, 'title', basename(enclosure.href))
# check if we were provided a full path, and hence a subdirectory for the file
if (IngestOptions.DATAFILE_DIRECTORY_DEPTH >= 1 and
getattr(enclosure, "path", "") != "" and
enclosure.path.split("/")[IngestOptions.DATAFILE_DIRECTORY_DEPTH:] != ""):
filename = "/".join(enclosure.path.split("/")[IngestOptions.DATAFILE_DIRECTORY_DEPTH:])
datafiles = dataset.dataset_file_set.filter(filename=filename)
def fromunix1000 (tstr):
return datetime.datetime.utcfromtimestamp(float(tstr)/1000)
if datafiles.count() > 0:
datafile = datafiles[0]
from django.db.models import Max
newest=datafiles.aggregate(Max('modification_time'))['modification_time__max']
if not newest:# datafile.modification_time:
### rethink this!
return # We have this file, it has no time/date, let's skip it.
def total_seconds(td): # exists on datetime.timedelta in Python 2.7
return (td.microseconds + (td.seconds + td.days * 24 * 3600) * 10**6) / 10**6
timediff = total_seconds(fromunix1000(enclosure.modified) - newest)
if timediff == 0:
return # We have this file already, same time/date.
elif timediff < 0:
logging.getLogger(__name__).warn("Skipping datafile. File to ingest '{0}' is {1} *older* than stored file. Are the system clocks correct?".
format(enclosure.href, self.human_time(-timediff)))
return
else:
if not IngestOptions.ALLOW_UPDATING_DATAFILES:
logging.getLogger(__name__).warn("Skipping datafile. ALLOW_UPDATING_DATAFILES is disabled, and '{0}' is {1}newer than stored file.".
format(enclosure.href, self.human_time(timediff)))
return
logging.getLogger(__name__).info("Ingesting updated datafile. File to ingest '{0}' is {1} newer than stored file. This will create an additional copy.".
format(enclosure.href, self.human_time(timediff)))
if IngestOptions.HIDE_REPLACED_DATAFILES:
# Mark all older versions of file as hidden. (!)
try:
from tardis.microtardis.models import Dataset_Hidden
Dataset_Hidden.objects.filter(datafile__dataset=dataset).update(hidden=True)
except ImportError:
logger.warn("The MicroTardis app must be installed in order to use the HIDE_REPLACED_DATAFILES option. Existing version of datafile {0} " +
"will not be hidden.".format(datafile.filename))
else: # no local copy already.
logging.getLogger(__name__).info("Ingesting datafile: '{0}'".format(enclosure.href))
# Create a record and start transferring.
datafile = Dataset_File(dataset=dataset,
url=_get_enclosure_url(enclosure),
filename=filename,
created_time=fromunix1000(enclosure.created),
modification_time=fromunix1000(enclosure.modified))
datafile.protocol = enclosure.href.partition('://')[0]
datafile.mimetype = getattr(enclosure, "mime", datafile.mimetype)
datafile.size = getattr(enclosure, "length", datafile.size)
try:
hash = enclosure.hash
# Split on white space, then ':' to get tuples to feed into dict
hashdict = dict([s.partition(':')[::2] for s in hash.split()])
# Set SHA-512 sum
datafile.sha512sum = hashdict['sha-512']
except AttributeError:
pass
datafile.save()
