def create_sips(cls, dump, deposit, files, recid):
"""Create submission information packages."""
if not recid or recid.status == PIDStatus.RESERVED:
return
first = True
for s in dump.sips:
# Create SIP
sip = SIP.create(
s['format'],
s['content'],
user_id=s['user_id'],
agent=s['agent'],
id_=s['id'],
)
sip.created = s['timestamp']
# Create SIP files only for first package.
if first:
first = False
for meta, f in files:
db.session.add(
SIPFile(sip_id=sip.id,
filepath=meta['key'],
file_id=f.id))
# PID - SIP relationship
db.session.add(RecordSIP(sip_id=sip.id, pid_id=recid.id))
def reconstruct_sipfiles_t(recid=None, pid=None):
"""Reconstruct SIPFiles from record metadata."""
if not pid:
pid = PersistentIdentifier.get('recid', recid)
recsip = RecordSIP.query.filter_by(pid_id=pid.id).order_by(
RecordSIP.created).first()
if recsip is None:
raise Exception("RecordSIP does not exist.")
sip = recsip.sip
record = Record.get_record(recsip.pid.object_uuid)
first_json_rec = \
next((rec for rec in record.revisions if '_files' in rec), None)
if first_json_rec is None:
raise Exception("Files information not found in SIPMetadata nor"
" in Record revision")
files_j = first_json_rec['_files']
ovs = [
ObjectVersion.query.filter_by(version_id=fj['version_id']).first()
for fj in files_j
]
for ov in ovs:
q = SIPFile.query.filter_by(sip_id=sip.id,
filepath=ov.key,
file_id=ov.file_id)
if not q.count():
obj = SIPFile(sip_id=sip.id,
filepath=ov.key,
file_id=ov.file_id,
created=sip.created)
db.session.add(obj)
db.session.commit()
def test_sip_file_model(app, db, sips):
"""Test the SIPFile model."""
sip = sips[0]
app.config['SIPSTORE_FILEPATH_MAX_LEN'] = 15
with pytest.raises(ValueError) as excinfo:
SIPFile(sip_id=sip.id,
filepath="way too long file name.zip",
file_id=sip.files[0].file_id)
assert 'Filepath too long' in str(excinfo.value)
def test_sip_file_model(db):
"""Test the SIPFile model."""
sip1 = SIP.create('json', '{}')
file1 = FileInstance.create()
sipfile1 = SIPFile(sip_id=sip1.id, filepath="foobar.zip", file_id=file1.id)
db.session.add(sipfile1)
db.session.commit()
assert SIP.query.count() == 1
assert SIPFile.query.count() == 1
def attach_file(self, file):
"""Add a file to the SIP.
:param file: the file to attach. It must at least implement a `key`
and a valid `file_id`. See
:py:class:`invenio_files_rest.models.ObjectVersion`.
:returns: the created SIPFile
:rtype: :py:class:`invenio_sipstore.models.SIPFile`
"""
sf = SIPFile(sip_id=self.id, filepath=file.key, file_id=file.file_id)
db.session.add(sf)
return sf
def load_sipfile(file_id, filepath, sip_id, created):
"""Load a single SIPFile from parameters into DB."""
q = SIPFile.query.filter_by(sip_id=sip_id,
filepath=filepath,
file_id=file_id)
dt_created = arrow.get(created).datetime.replace(tzinfo=None)
if not q.count():
obj = SIPFile(sip_id=sip_id,
filepath=filepath,
file_id=file_id,
created=dt_created)
db.session.add(obj)
db.session.commit()
def test_transfer_rsync(app, db, location):
"""Test factories.transfer_rsync function."""
# config
app.config['SIPSTORE_ARCHIVER_DIRECTORY_BUILDER'] = \
'helpers:archive_directory_builder'
app.config['SIPSTORE_ARCHIVER_METADATA_TYPES'] = ['test']
# SIP
sip = SIP.create()
# SIPMetadataType
mtype = SIPMetadataType(title='Test', name='test', format='json')
db.session.add(mtype)
# SIPMetadata
mcontent = {'title': 'title', 'author': 'me'}
meth = SIPMetadata(sip=sip, type=mtype, content=json.dumps(mcontent))
db.session.add(meth)
# SIPFile
f = FileInstance.create()
fcontent = b'weighted companion cube\n'
f.set_contents(BytesIO(fcontent), default_location=location.uri)
sfile = SIPFile(sip=sip, file=f, filepath='portal.txt')
db.session.add(sfile)
db.session.commit()
# EXPORT
folder = path.join(location.uri, 'lulz')
params = {
'server': '',
'user': '',
'destination': folder,
'args': '-az'
}
factories.transfer_rsync(sip.id, params)
# TEST
assert not path.exists(path.join(location.uri, 'test'))
assert path.isdir(folder)
assert path.isdir(path.join(folder, 'files'))
assert path.isfile(path.join(folder, 'files', 'portal.txt'))
assert path.isdir(path.join(folder, 'metadata'))
assert path.isfile(path.join(folder, 'metadata', 'test.json'))
with open(path.join(folder, 'files', 'portal.txt'), 'rb') as fp:
assert fp.read() == fcontent
with open(path.join(folder, 'metadata', 'test.json'), 'r') as fp:
assert json.loads(fp.read()) == mcontent
def create(cls,
pid,
record,
create_sip_files=True,
user_id=None,
agent=None):
"""Create a Zenodo SIP, from the PID and the Record.
Apart from the SIP itself, it also creates ``RecordSIP`` for the
SIP-PID-Record relationship, as well as ``SIPFile`` objects for each
the files in the record.
Those objects are not returned by this function but can be fetched by
the corresponding SIP relationships 'record_sips' and 'sip_files'.
:param pid: PID of the published record ('recid').
:type pid: `invenio_pidstore.models.PersistentIdentifier`
:param record: Record for which the SIP should be created.
:type record: `invenio_records.api.Record`
:param create_sip_files: If True the SIPFiles will be created.
:type create_sip_files: bool
:returns: A Zenodo-specifi SIP object.
:rtype: ``invenio_sipstore.models.SIP``
"""
if not user_id:
user_id = (None
if current_user.is_anonymous else current_user.get_id())
if not agent:
agent = cls._build_agent_info()
with db.session.begin_nested():
sip = SIP.create('json',
json.dumps(record.dumps()),
user_id=user_id,
agent=agent)
recsip = RecordSIP(sip_id=sip.id, pid_id=pid.id)
db.session.add(recsip)
if record.files and create_sip_files:
for f in record.files:
sf = SIPFile(sip_id=sip.id,
filepath=f.key,
file_id=f.file_id)
db.session.add(sf)
return sip
def sips(db, locations, sip_metadata_types):
"""Fixture for the SIP objects sharing multiple files.
Four SIPs are sharing three files in the following way:
SIP-1: File1
SIP-2: File1, File2
SIP-3: File2(renamed on SIPFile, but same FileInstance), File3
SIP-4: File4, File5, File6
"""
# A SIP with agent info
sip1 = SIP.create(
agent={
'email': '*****@*****.**',
'orcid': '1111-1111-1111-1111',
'ip_address': '1.1.1.1'
})
sip1api = SIPApi(sip1)
sip1api.attach_metadata('marcxml-test', '<p>XML 1</p>')
sip1api.attach_metadata('json-test', '{"title": "JSON 1"}')
# Metadata 'txt-test', although attached should not be archived
# (see conftest configuration)
sip1api.attach_metadata('txt-test', 'Title: TXT 1')
file1 = FileInstance.create()
file1.set_contents(BytesIO(b('test')),
default_location=locations['default'].uri)
sip1file1 = SIPFile(sip_id=sip1.id,
filepath="foobar.txt",
file_id=file1.id)
db_.session.add(sip1file1)
sip2 = SIP.create()
sip2api = SIPApi(sip2)
sip2api.attach_metadata('marcxml-test', '<p>XML 2</p>')
sip2api.attach_metadata('json-test', '{"title": "JSON 2"}')
file2 = FileInstance.create()
file2.set_contents(BytesIO(b'test-second'),
default_location=locations['default'].uri)
sip2file1 = SIPFile(sip_id=sip2.id,
filepath="foobar.txt",
file_id=file1.id)
sip2file2 = SIPFile(sip_id=sip2.id,
filepath="foobar2.txt",
file_id=file2.id)
db_.session.add(sip2file1)
db_.session.add(sip2file2)
sip3 = SIP.create()
sip3api = SIPApi(sip3)
sip3api.attach_metadata('marcxml-test', '<p>XML 3</p>')
sip3api.attach_metadata('json-test', '{"title": "JSON 3"}')
file3 = FileInstance.create()
file3.set_contents(BytesIO(b'test-third'),
default_location=locations['default'].uri)
sip3file2 = SIPFile(sip_id=sip3.id,
filepath="foobar2-renamed.txt",
file_id=file2.id)
sip3file3 = SIPFile(sip_id=sip3.id,
filepath="foobar3.txt",
file_id=file3.id)
db_.session.add(sip3file2)
db_.session.add(sip3file3)
# A SIP with naughty filenames
sip4 = SIP.create()
sip4api = SIPApi(sip4)
sip4api.attach_metadata('marcxml-test', '<p>XML 4 żółć</p>')
sip4api.attach_metadata('json-test', '{"title": "JSON 4 żółć"}')
file4 = FileInstance.create()
file4.set_contents(BytesIO('test-fourth żółć'.encode('utf-8')),
default_location=locations['default'].uri)
file5 = FileInstance.create()
file5.set_contents(BytesIO('test-fifth ąęćźə'.encode('utf-8')),
default_location=locations['default'].uri)
file6 = FileInstance.create()
file6.set_contents(BytesIO('test-sixth π'.encode('utf-8')),
default_location=locations['default'].uri)
sip5file4 = SIPFile(sip_id=sip4.id,
filepath="../../foobar.txt",
file_id=file4.id)
sip5file5 = SIPFile(sip_id=sip4.id,
filepath="http://maliciouswebsite.com/hack.js",
file_id=file5.id)
sip5file6 = SIPFile(sip_id=sip4.id,
filepath="łóżźćąę.dat",
file_id=file6.id)
db_.session.add(sip5file4)
db_.session.add(sip5file5)
db_.session.add(sip5file6)
# A SIP with metadata-only changes
sip5 = SIP.create()
sip5api = SIPApi(sip5)
sip5api.attach_metadata('marcxml-test', '<p>XML 5 Meta Only</p>')
db_.session.commit()
return [sip1api, sip2api, sip3api, sip4api, sip5api]
def create_files_and_sip(deposit, dep_pid):
"""Create deposit Bucket, Files and SIPs."""
from invenio_pidstore.errors import PIDDoesNotExistError
from invenio_pidstore.models import PersistentIdentifier
from invenio_sipstore.errors import SIPUserDoesNotExist
from invenio_sipstore.models import SIP, RecordSIP, SIPFile
from invenio_files_rest.models import Bucket, FileInstance, ObjectVersion
from invenio_records_files.models import RecordsBuckets
from invenio_db import db
buc = Bucket.create()
recbuc = RecordsBuckets(record_id=deposit.id, bucket_id=buc.id)
db.session.add(recbuc)
deposit.setdefault('_deposit', dict())
deposit.setdefault('_files', list())
files = deposit.get('files', [])
sips = deposit.get('sips', [])
recid = None
if sips:
recids = [int(sip['metadata']['recid']) for sip in sips]
if len(set(recids)) > 1:
logger.error('Multiple recids ({recids}) found in deposit {depid}'
' does not exists.'.format(recids=recids,
depid=dep_pid.pid_value))
raise DepositMultipleRecids(dep_pid.pid_value, list(set(recids)))
elif recids: # If only one recid
recid = recids[0]
# Store the path -> FileInstance mappings for SIPFile creation later
dep_file_instances = list()
for file_ in files:
fi = FileInstance.create()
fi.set_uri(file_['path'], file_['size'], file_['checksum'])
ov = ObjectVersion.create(buc, file_['name'], _file_id=fi.id)
file_meta = dict(
bucket=str(buc.id),
key=file_['name'],
checksum=file_['checksum'],
size=file_['size'],
version_id=str(ov.version_id),
)
deposit['_files'].append(file_meta)
dep_file_instances.append((file_['path'], fi))
for idx, sip in enumerate(sips):
agent = None
user_id = None
if sip['agents']:
agent = dict(
ip_address=sip['agents'][0].get('ip_address', ""),
email=sip['agents'][0].get('email_address', ""),
)
user_id = sip['agents'][0]['user_id']
content = sip['package']
sip_format = 'marcxml'
try:
sip = SIP.create(sip_format,
content,
user_id=user_id,
agent=agent)
except SIPUserDoesNotExist:
logger.exception('User ID {user_id} referred in deposit {depid} '
'does not exists.'.format(
user_id=user_id, depid=dep_pid.pid_value))
raise DepositSIPUserDoesNotExist(dep_pid.pid_value, user_id)
# If recid was found, attach it to SIP
# TODO: This is always uses the first recid, as we quit if multiple
# recids are found in the sips information
if recid:
try:
pid = PersistentIdentifier.get(pid_type='recid',
pid_value=recid)
record_sip = RecordSIP(sip_id=sip.id, pid_id=pid.id)
db.session.add(record_sip)
except PIDDoesNotExistError:
logger.exception('Record {recid} referred in '
'Deposit {depid} does not exists.'.format(
recid=recid, depid=dep_pid.pid_value))
raise DepositRecidDoesNotExist(dep_pid.pid_value, recid)
if idx == 0:
for fp, fi in dep_file_instances:
sipf = SIPFile(sip_id=sip.id, filepath=fp, file_id=fi.id)
db.session.add(sipf)
deposit.commit()
db.session.commit()
return deposit
def create_files_and_sip(deposit, dep_pid):
"""Create deposit Bucket, Files and SIPs."""
from invenio_pidstore.errors import PIDDoesNotExistError
from invenio_pidstore.models import PersistentIdentifier, PIDStatus
from invenio_sipstore.errors import SIPUserDoesNotExist
from invenio_sipstore.models import SIP, RecordSIP, SIPFile
from invenio_files_rest.models import Bucket, FileInstance, ObjectVersion
from invenio_records_files.models import RecordsBuckets
from invenio_db import db
buc = Bucket.create()
recbuc = RecordsBuckets(record_id=deposit.id, bucket_id=buc.id)
db.session.add(recbuc)
deposit.setdefault('_deposit', dict())
deposit.setdefault('_buckets', dict(deposit=str(buc.id)))
deposit.setdefault('_files', list())
files = deposit.get('files', [])
sips = deposit.get('sips', [])
# Look for prereserved DOI (and recid)
if 'drafts' in deposit:
drafts = list(deposit['drafts'].items())
if len(drafts) != 1:
logger.exception('Deposit {dep_pid} has multiple drafts'.format(
dep_pid=dep_pid))
if len(drafts) == 1:
draft_type, draft = drafts[0]
draft_v = draft['values']
if 'prereserve_doi' in draft_v:
pre_recid = str(draft_v['prereserve_doi']['recid'])
pre_doi = str(draft_v['prereserve_doi']['doi'])
# If pre-reserve info available, try to reserve 'recid'
try:
pid = PersistentIdentifier.get(pid_type='recid',
pid_value=str(pre_recid))
except PIDDoesNotExistError:
# Reserve recid
pid = PersistentIdentifier.create(
pid_type='recid',
pid_value=str(pre_recid),
object_type='rec',
status=PIDStatus.RESERVED)
# If pre-reserve info available, try to reserve 'doi'
try:
pid = PersistentIdentifier.get(pid_type='doi',
pid_value=str(pre_doi))
except PIDDoesNotExistError:
# Reserve DOI
pid = PersistentIdentifier.create(
pid_type='doi',
pid_value=str(pre_doi),
object_type='rec',
status=PIDStatus.RESERVED)
if RecordIdentifier.query.get(int(pre_recid)) is None:
RecordIdentifier.insert(int(pre_recid))
# Store the path -> FileInstance mappings for SIPFile creation later
dep_file_instances = list()
for file_ in files:
size = file_['size']
key = file_['name']
# Warning: Assumes all checksums are MD5!
checksum = 'md5:{0}'.format(file_['checksum'])
fi = FileInstance.create()
fi.set_uri(file_['path'], size, checksum)
ov = ObjectVersion.create(buc, key, _file_id=fi.id)
ext = splitext(ov.key)[1].lower()
if ext.startswith('.'):
ext = ext[1:]
file_meta = dict(
bucket=str(ov.bucket.id),
key=ov.key,
checksum=ov.file.checksum,
size=ov.file.size,
version_id=str(ov.version_id),
type=ext,
)
deposit['_files'].append(file_meta)
dep_file_instances.append((file_['path'], fi))
# Get a recid from SIP information
recid = None
if sips:
recids = [int(sip['metadata']['recid']) for sip in sips]
if len(set(recids)) > 1:
logger.error('Multiple recids ({recids}) found in deposit {depid}'
' does not exists.'.format(recids=recids,
depid=dep_pid.pid_value))
raise DepositMultipleRecids(dep_pid.pid_value, list(set(recids)))
elif recids: # If only one recid
recid = recids[0]
for idx, sip in enumerate(sips):
agent = None
user_id = None
if sip['agents']:
agent = dict(
ip_address=empty_str_if_none(sip['agents'][0].get(
'ip_address', "")),
email=empty_str_if_none(sip['agents'][0].get(
'email_address', "")),
)
user_id = sip['agents'][0]['user_id']
if user_id == 0:
user_id = None
content = sip['package']
sip_format = 'marcxml'
try:
sip = SIP.create(sip_format, content, user_id=user_id, agent=agent)
except SIPUserDoesNotExist:
logger.exception('User ID {user_id} referred in deposit {depid} '
'does not exists.'.format(
user_id=user_id, depid=dep_pid.pid_value))
sip = SIP.create(sip_format, content, agent=agent)
# Attach recid to SIP
if recid:
try:
pid = PersistentIdentifier.get(pid_type='recid',
pid_value=str(recid))
record_sip = RecordSIP(sip_id=sip.id, pid_id=pid.id)
db.session.add(record_sip)
except PIDDoesNotExistError:
logger.exception('Record {recid} referred in '
'Deposit {depid} does not exists.'.format(
recid=recid, depid=dep_pid.pid_value))
if deposit['_p']['submitted'] == True:
logger.exception('Pair {recid}/{depid} was submitted,'
' (should it be unpublished?).'.format(
recid=recid, depid=dep_pid.pid_value))
else:
logger.exception(
'Pair {recid}/{depid} was not submitted.'.format(
recid=recid, depid=dep_pid.pid_value))
# Reserve recid
pid = PersistentIdentifier.create(pid_type='recid',
pid_value=str(recid),
object_type='rec',
status=PIDStatus.RESERVED)
if RecordIdentifier.query.get(int(recid)) is None:
RecordIdentifier.insert(int(recid))
if idx == 0:
for fp, fi in dep_file_instances:
sipf = SIPFile(sip_id=sip.id, filepath=fp, file_id=fi.id)
db.session.add(sipf)
deposit.commit()
return deposit
