def handle_collection(self, collection, *args, **options):
for index_file_name in args:
try:
# TODO: print number of records ingested
ingest(collection.mission, collection.file_type,
options["url"], index_file_name)
except Exception as exc:
raise CommandError(
"Failed to ingest index file '%s'. Error was: %s" %
(index_file_name, exc))
def handle_location(self, collection, location):
tmp_dir = tempfile.mkdtemp()
shutil.copytree(collection.data_dir, join(tmp_dir, "backup"))
annotations_file = tempfile.TemporaryFile()
ingested_dir = join(collection.data_dir, "ingested", location.slug)
pending_dir = join(collection.data_dir, "pending", location.slug)
safe_makedirs(ingested_dir)
safe_makedirs(pending_dir)
try:
# move all files from ingested dir to pending dir
for path in glob.iglob(join(ingested_dir, "*")):
os.rename(path, join(pending_dir, basename(path)))
# save all annotations to a CSV
writer = csv.writer(annotations_file, delimiter="\t")
writer.writerow(["filename", "annotation"])
for record in location.records.filter():
for annotation in record.annotations.all():
writer.writerow([record.filename, annotation.text])
annotations_file.seek(0)
# delete all index file records in database
location.index_files.all().delete()
# re-ingest all index files in pending
for path in glob.iglob(join(pending_dir, "*")):
ingest(
collection.mission, collection.file_type, location.url,
basename(path)
)
# restore annotations and remove temporary file
reader = csv.reader(annotations_file, delimiter="\t")
next(reader) # skip header
for row in reader:
models.Annotation.objects.create(
record=location.records.get(filename=row[0]),
text=row[1]
)
except:
# restore backups
shutil.rmtree(collection.data_dir)
shutil.move(join(tmp_dir, "backup"), collection.data_dir)
raise
finally:
shutil.rmtree(tmp_dir)
def handle_collection(self, collection, *args, **options):
for index_file_name in args:
try:
# TODO: print number of records ingested
ingest(
collection.mission, collection.file_type, options["url"],
index_file_name
)
except Exception as exc:
raise CommandError(
"Failed to ingest index file '%s'. Error was: %s"
% (index_file_name, exc)
)
def handle_location(self, collection, location):
tmp_dir = tempfile.mkdtemp()
shutil.copytree(collection.data_dir, join(tmp_dir, "backup"))
annotations_file = tempfile.TemporaryFile()
ingested_dir = join(collection.data_dir, "ingested", location.slug)
pending_dir = join(collection.data_dir, "pending", location.slug)
safe_makedirs(ingested_dir)
safe_makedirs(pending_dir)
try:
# move all files from ingested dir to pending dir
for path in glob.iglob(join(ingested_dir, "*")):
os.rename(path, join(pending_dir, basename(path)))
# save all annotations to a CSV
writer = csv.writer(annotations_file, delimiter="\t")
writer.writerow(["filename", "annotation"])
for record in location.records.filter():
for annotation in record.annotations.all():
writer.writerow([record.filename, annotation.text])
annotations_file.seek(0)
# delete all index file records in database
location.index_files.all().delete()
# re-ingest all index files in pending
for path in glob.iglob(join(pending_dir, "*")):
ingest(collection.mission, collection.file_type, location.url,
basename(path))
# restore annotations and remove temporary file
reader = csv.reader(annotations_file, delimiter="\t")
next(reader) # skip header
for row in reader:
models.Annotation.objects.create(
record=location.records.get(filename=row[0]), text=row[1])
except:
# restore backups
shutil.rmtree(collection.data_dir)
shutil.move(join(tmp_dir, "backup"), collection.data_dir)
raise
finally:
shutil.rmtree(tmp_dir)
def _harvest_locked(collection, url, reschedule):
location = collection.locations.get(url=url)
if location.location_type == "oads":
harvester = OADSHarvester(location)
elif location.location_type == "nga":
harvester = NGAHarvester(location)
else:
raise HarvestingError(
"Invalid location type '%s'." % location.location_type
)
# scan the source
logger.debug("Scanning location %s." % location)
available_index_files = harvester.scan()
logger.debug("Successfully scanned location %s." % location)
# categorize files
inserted, updated, deleted = select_index_files(
(base for base, url in available_index_files),
location.index_files.values_list("filename", flat=True)
)
# directories for index files
pending_dir = join(collection.data_dir, "pending", location.slug)
ingested_dir = join(collection.data_dir, "ingested", location.slug)
safe_makedirs(pending_dir)
safe_makedirs(ingested_dir)
failed_retrieve = []
updated_to_retrieve = [u[1] for u in updated]
# perform actual harvesting
for index_file_name in itertools.chain(inserted, updated_to_retrieve):
try:
harvester.retrieve(
join(url, index_file_name), index_file_name, pending_dir
)
logger.debug("Retrieved %s." % index_file_name)
except:
failed_retrieve.append(index_file_name)
logger.debug("Failed to retrieve %s." % index_file_name)
updated_to_delete = [u[0] for u in updated]
# delete index files that are deleted or updated
for index_file_name in itertools.chain(updated_to_delete, deleted):
# delete model
location.index_files.get(filename=index_file_name).delete()
# remove ingested index file
os.remove(join(ingested_dir, index_file_name))
failed_ingest = []
# finally ingest the updated and newly inserted index files
for index_file_name in itertools.chain(updated_to_retrieve, inserted):
try:
index_file_name = extract_zipped_index_file(
join(pending_dir, index_file_name)
)
ingest(
collection.mission, collection.file_type, url,
basename(index_file_name)
)
logger.debug("Ingested %s." % basename(index_file_name))
except:
failed_ingest.append(basename(index_file_name))
logger.debug("Failed to ingest %s." % basename(index_file_name))
logger.info("Finished harvesting for %s: %s" % (collection, location))
if failed_retrieve:
logger.error("Failed to retrieve %s" % ", ".join(failed_retrieve))
if failed_ingest:
logger.error("Failed to ingest %s" % ", ".join(failed_ingest))
# if this was a scheduled harvest, reschedule it again
if reschedule:
try:
interval = collection.configuration.harvest_interval
schedule("harvest", now() + interval, {
"mission": collection.mission,
"file_type": collection.file_type,
"url": location.url,
"reschedule": True
})
except Exception as exc:
logger.error(
"Failed to reschedule harvest for %s %s. Error was '%s'." % (
collection, location, exc
)
)
return failed_retrieve, failed_ingest
def import_collection(filename, mission=None, file_type=None):
""" Import a previously exported archive.
"""
collections_qs = models.Collection.objects.filter(
mission=mission, file_type=file_type
)
if collections_qs.exists():
raise ImportException("Collection %s/%s already exists." % (
mission, file_type
))
if not zipfile.is_zipfile(filename):
raise ImportException("File %s is not a ZIP file." % filename)
with closing(zipfile.ZipFile(filename, "r")) as archive:
manifest = json.loads(archive.read("manifest.json"))
# TODO: better version check
mission = mission or manifest["mission"]
file_type = file_type or manifest["file_type"]
collection = models.Collection.objects.create(
mission=mission, file_type=file_type
)
if minv.__version__ != manifest["version"]:
raise ImportException(
"Cannot import file %s due to version mismatch: %r != %r"
% (filename, minv.__version__, manifest["version"])
)
locations = json.loads(archive.read("locations.json"))
for url, values in locations.items():
models.Location.objects.create(
collection=collection, url=url, location_type=values["type"]
)
try:
archive.extract("collection.conf", collection.config_dir)
except KeyError:
pass
slug_to_location = dict(
(location.slug, location)
for location in collection.locations.all()
)
# create a temporary directory tree to extract files to
tmp_dir = tempfile.mkdtemp()
# extract index files and ingest them
members = [
member for member in archive.namelist()
if member.startswith("locations/") and
basename(member) != "annotations.csv"
]
try:
for member in members:
slug, _, index_filename = member[10:].partition("/")
url = slug_to_location[slug].url
directory = join(collection.data_dir, "pending", slug)
safe_makedirs(directory)
path = archive.extract(member, tmp_dir)
move(path, directory)
ingest(mission, file_type, url, index_filename)
finally:
rmtree(tmp_dir)
# read annotations
members = [
member for member in archive.namelist()
if member.startswith("locations/") and
member.endswith("annotations.csv")
]
for member in members:
slug, _, index_filename = member[10:].partition("/")
location = slug_to_location[slug]
with closing(archive.open(member)) as annotations:
reader = csv.reader(annotations)
next(reader) # skip header
for record_filename, text in reader:
models.Annotation.objects.create(
record=models.Record.objects.get(
location=location, filename=record_filename
),
text=text
)
return collection
