def preprocess_config(self, config):
if isinstance(config, str):
config = {'published_schema': config}
else:
config = {**config}
if 'draft_schema' not in config:
if not config['published_schema'].startswith('/'):
config['draft_schema'] = 'draft' + '/' + config[
'published_schema']
config['draft_schema_file'] = os.path.join(
self.app.config['INVENIO_RECORD_DRAFT_SCHEMAS_DIR'],
config['draft_schema'])
config['published_index'] = schema_to_index(
config['published_schema'])[0]
draft_index = schema_to_index(config['draft_schema'])[0]
config['draft_index'] = draft_index
config['published_mapping_file'] = current_search.mappings[
config['published_index']]
config['draft_mapping_file'] = os.path.join(
self.app.config['INVENIO_RECORD_DRAFT_MAPPINGS_DIR'],
f'{draft_index}.json')
return config
def schema_prefix(schema):
"""Get index prefix for a given schema."""
if not schema:
return None
index, doctype = schema_to_index(
schema, index_names=current_search.mappings.keys())
return index.split('-')[0]
def add_citation_counts(chunk_size=500, request_timeout=120):
def _get_records_to_update_generator(citations_lookup):
with click.progressbar(citations_lookup.iteritems()) as bar:
for uuid, citation_count in bar:
yield {
'_op_type': 'update',
'_index': index,
'_type': doc_type,
'_id': str(uuid),
'doc': {
'citation_count': citation_count
}
}
index, doc_type = schema_to_index('records/hep.json')
citations_lookup = Counter()
click.echo('Extracting all citations...')
with click.progressbar(
es_scan(es,
query={
'_source': 'references.recid',
'filter': {
'exists': {
'field': 'references.recid'
}
},
'size': LARGE_CHUNK_SIZE
},
scroll=u'2m',
index=index,
doc_type=doc_type)) as records:
for record in records:
unique_refs_ids = dedupe_list(
list(
chain.from_iterable(
map(force_list,
get_value(record, '_source.references.recid')))))
for unique_refs_id in unique_refs_ids:
citations_lookup[unique_refs_id] += 1
click.echo('... DONE.')
click.echo('Mapping recids to UUIDs...')
citations_lookup = _build_recid_to_uuid_map(citations_lookup)
click.echo('... DONE.')
click.echo('Adding citation numbers...')
success, failed = es_bulk(
es,
_get_records_to_update_generator(citations_lookup),
chunk_size=chunk_size,
raise_on_exception=False,
raise_on_error=False,
request_timeout=request_timeout,
stats_only=True,
)
click.echo(
'... DONE: {} records updated with success. {} failures.'.format(
success, failed))
def schema_prefix(schema):
"""Get index prefix for a given schema."""
if not schema:
return None
index, doctype = schema_to_index(
schema, index_names=current_search.mappings.keys())
return index.split('-')[0]
def test_schema_to_index_prefixes_indices(app):
"""Test that prefix is added to the index when creating it."""
new_conf = {'SEARCH_INDEX_PREFIX': 'prefix-'}
with patch.dict(app.config, new_conf):
result = schema_to_index('default-v1.0.0.json')
assert result == ('prefix-default-v1.0.0', 'default-v1.0.0')
def _record_to_index(record):
"""Get index/doctype given a record."""
index, doctype = schema_to_index(record.get('$schema', ''))
if index and doctype:
return index, doctype
else:
return current_app.config['INDEXER_DEFAULT_INDEX'], \
current_app.config['INDEXER_DEFAULT_DOCTYPE']
class Meta:
"""Configuration for CERN search."""
index = schema_to_index(Keyword._schema)[0]
doc_types = None
fields = ('*', )
default_filter = DefaultFilter(
Q('bool', filter=[Q('match', deleted=False)]))
def _record_to_index(record):
"""Get index/doctype given a record."""
index, doctype = schema_to_index(record.get('$schema', ''))
if index and doctype:
return index, doctype
else:
return current_app.config['INDEXER_DEFAULT_INDEX'], \
current_app.config['INDEXER_DEFAULT_DOCTYPE']
def get_search_index(json_schemas, url_prefix):
indices = [schema_to_index(x)[0] for x in json_schemas]
indices = [x for x in indices if x]
if len(indices) == 1:
return indices[0]
else:
raise Exception('Add "published_search_index" or "json_schemas" to '
'DRAFT_ENABLED_RECORDS_REST_ENDPOINTS["%s"]' %
url_prefix)
def _get_percolator_doc_type(index):
es_ver = ES_VERSION[0]
if es_ver == 2:
return '.percolator'
elif es_ver == 5:
return 'percolators'
elif es_ver == 6:
mapping_path = current_search.mappings[index]
_, doc_type = schema_to_index(mapping_path)
return doc_type
def _get_percolator_doc_type(index):
es_ver = ES_VERSION[0]
if es_ver == 2:
return '.percolator'
elif es_ver == 5:
return 'percolators'
elif es_ver in (6, 7):
mapping_path = current_search.mappings[index]
_, doc_type = schema_to_index(mapping_path)
return doc_type
def add_citation_counts(chunk_size=500, request_timeout=120):
def _get_records_to_update_generator(citations_lookup):
with click.progressbar(citations_lookup.iteritems()) as bar:
for uuid, citation_count in bar:
yield {
'_op_type': 'update',
'_index': index,
'_type': doc_type,
'_id': str(uuid),
'doc': {'citation_count': citation_count}
}
index, doc_type = schema_to_index('records/hep.json')
citations_lookup = Counter()
click.echo('Extracting all citations...')
with click.progressbar(es_scan(
es,
query={
'_source': 'references.recid',
'filter': {
'exists': {
'field': 'references.recid'
}
},
'size': LARGE_CHUNK_SIZE
},
scroll=u'2m',
index=index,
doc_type=doc_type)) as records:
for record in records:
unique_refs_ids = dedupe_list(list(chain.from_iterable(map(
force_list, get_value(record, '_source.references.recid')))))
for unique_refs_id in unique_refs_ids:
citations_lookup[unique_refs_id] += 1
click.echo('... DONE.')
click.echo('Mapping recids to UUIDs...')
citations_lookup = _build_recid_to_uuid_map(citations_lookup)
click.echo('... DONE.')
click.echo('Adding citation numbers...')
success, failed = es_bulk(
es,
_get_records_to_update_generator(citations_lookup),
chunk_size=chunk_size,
raise_on_exception=False,
raise_on_error=False,
request_timeout=request_timeout,
stats_only=True,
)
click.echo('... DONE: {} records updated with success. {} failures.'.format(
success, failed))
def _record_to_index(record):
"""Get index/doc_type given a record."""
index_names = current_search.mappings.keys()
schema = record.get('$schema', '')
if isinstance(schema, dict):
schema = schema.get('$ref', '')
index, doc_type = schema_to_index(schema, index_names=index_names)
if index and doc_type:
return index, doc_type
else:
return (current_app.config['INDEXER_DEFAULT_INDEX'],
current_app.config['INDEXER_DEFAULT_DOC_TYPE'])
def _record_to_index(record):
"""Get index/doc_type given a record."""
index_names = current_search.mappings.keys()
schema = record.get('$schema', '')
if isinstance(schema, dict):
schema = schema.get('$ref', '')
index, doc_type = schema_to_index(schema, index_names=index_names)
if index and doc_type:
return index, doc_type
else:
return (current_app.config['INDEXER_DEFAULT_INDEX'],
current_app.config['INDEXER_DEFAULT_DOC_TYPE'])
def preprocess_record(self, pid, record, links_factory=None, **kwargs):
"""Adds cached ACLs to the serialized record."""
ret = super().preprocess_record(pid, record, links_factory, **kwargs)
index_names = current_search.mappings.keys()
index, doc_type = schema_to_index(record['$schema'],
index_names=index_names)
search_class = None
if self.acl_rest_endpoint is None:
if has_request_context():
search_class = getattr(request._methodview, 'search_class')
if not search_class: # pragma no cover
raise AttributeError(
'Please set acl_rest_endpoint property with the key to RECORDS_REST_ENDPOINTS'
)
else:
rest_configuration = current_app.config['RECORDS_REST_ENDPOINTS'][
self.acl_rest_endpoint]
search_class = obj_or_import_string(rest_configuration.get(
'search_class', None),
default=ACLRecordsSearch)
sc = search_class(index=index, doc_type=doc_type)
rec = sc.acl_return_all(operation=self.acl_operations).get_record(
str(record.id))
rec = rec.execute()
if rec.hits:
matched_acls = getattr(rec.hits[0].meta, 'matched_queries', [])
matched_acls = [
x.replace(f'{ACL_MATCHED_QUERY}_', '') for x in matched_acls
]
else: # pragma no cover
logger.error(
'Should not happen, record %s not found in elasticsearch',
record.id)
matched_acls = []
ret['invenio_explicit_acls'] = matched_acls
return ret
def default_record_to_index(record):
"""Default function to get index/doc_type given a record.
It tries to extract from `record['$schema']` the index and doc_type.
If it fails, return the default values.
:param record: The record object.
:returns: Tuple (index, doc_type).
"""
index_names = current_search.mappings.keys()
schema = record.get('$schema', '')
if isinstance(schema, dict):
schema = schema.get('$ref', '')
index, doc_type = schema_to_index(schema, index_names=index_names)
if index and doc_type:
return index, doc_type
else:
return (current_app.config['INDEXER_DEFAULT_INDEX'],
current_app.config['INDEXER_DEFAULT_DOC_TYPE'])
def default_record_to_index(record):
"""Default function to get index/doc_type given a record.
It tries to extract from `record['$schema']` the index and doc_type.
If it fails, return the default values.
:param record: The record object.
:returns: Tuple (index, doc_type).
"""
index_names = current_search.mappings.keys()
schema = record.get('$schema', '')
if isinstance(schema, dict):
schema = schema.get('$ref', '')
index, doc_type = schema_to_index(schema, index_names=index_names)
if index and doc_type:
return index, doc_type
else:
return (current_app.config['INDEXER_DEFAULT_INDEX'],
current_app.config['INDEXER_DEFAULT_DOC_TYPE'])
def record_to_index(record):
"""Get index/doc_type given a record.
It tries to extract from `record['$schema']` the index and doc_type.
If it fails, return the default values.
:param record: The record object.
:returns: Tuple (index, doc_type).
"""
index_names = current_search.mappings.keys()
schema = record.get('$schema', '')
if isinstance(schema, dict):
schema = schema.get('$ref', '')
# put all document in the same index
if re.search(r'/documents/', schema):
schema = re.sub(r'-.*\.json', '.json', schema)
index, doc_type = schema_to_index(schema, index_names=index_names)
if index and doc_type:
return index, doc_type
else:
return (current_app.config['INDEXER_DEFAULT_INDEX'],
current_app.config['INDEXER_DEFAULT_DOC_TYPE'])
def test_schema_to_index(schema_url, result):
"""Test conversion of schema to index name and document type."""
assert result == schema_to_index(schema_url)
def test_schema_to_index(schema_url, result):
"""Test conversion of schema to index name and document type."""
assert result == schema_to_index(schema_url)
class Meta:
"""Configuration for CERN search."""
index = schema_to_index(Keyword._schema)[0]
doc_types = None
fields = ('*', )
def test_schema_to_index_with_names(app):
"""Test that prefix is added to the index when creating it."""
result = schema_to_index('default-v1.0.0.json',
index_names=['default-v1.0.0'])
doc_type = '_doc' if ES_VERSION[0] >= 7 else 'default-v1.0.0'
assert result == ('default-v1.0.0', doc_type)
def test_schema_to_index(schema, expected, index_names, app):
"""Test the expected value of schema to index."""
result = schema_to_index(schema, index_names=index_names)
if ES_VERSION[0] >= 7 and expected[0]:
expected = (expected[0], "_doc")
assert result == expected
def add_citation_counts(chunk_size=500, request_timeout=10):
index, doc_type = schema_to_index('records/hep.json')
def get_records_to_update_generator(citation_lookup):
for recid, citation_count in citation_lookup.iteritems():
try:
uuid = PersistentIdentifier.query.filter(PersistentIdentifier.object_type == "rec", PersistentIdentifier.pid_value == str(recid)).one().object_uuid
yield {'_op_type': 'update',
'_index': index,
'_type': doc_type,
'_id': str(uuid),
'doc': {'citation_count': citation_count}
}
except NoResultFound:
continue
click.echo("Extracting all citations...")
# lookup dictionary where key: recid of the record
# and value: number of records that cite that record
citations_lookup = Counter()
with click.progressbar(es_scan(
current_search_client,
query={
"_source": "references.recid",
"filter": {
"exists": {
"field": "references.recid"
}
},
"size": LARGE_CHUNK_SIZE
},
scroll=u'2m',
index=index,
doc_type=doc_type)) as records:
for record in records:
# update lookup dictionary based on references of the record
if 'references' in record['_source']:
unique_refs_ids = set()
references = record['_source']['references']
for reference in references:
recid = reference.get('recid')
if recid:
if isinstance(recid, list):
# Sometimes there is more than one recid in the
# reference.
recid = recid.pop()
unique_refs_ids.add(recid)
for unique_refs_id in unique_refs_ids:
citations_lookup[unique_refs_id] += 1
click.echo("... DONE.")
click.echo("Adding citation numbers...")
success, failed = es_bulk(
current_search_client,
get_records_to_update_generator(citations_lookup),
chunk_size=chunk_size,
raise_on_exception=True,
raise_on_error=True,
request_timeout=request_timeout,
stats_only=True)
click.echo("... DONE: {} records updated with success. {} failures.".format(success, failed))
def doc_type_should_be_sent_to_orcid(record):
index, doc_type = schema_to_index(record['$schema'])
return doc_type == 'hep'
def test_schema_to_index_with_names(app):
"""Test that prefix is added to the index when creating it."""
result = schema_to_index("default-v1.0.0.json", index_names=["default-v1.0.0"])
doc_type = "_doc" if ES_VERSION[0] >= 7 else "default-v1.0.0"
assert result == ("default-v1.0.0", doc_type)
def doc_type_should_be_sent_to_orcid(record):
"""Return ``True`` is a document type should be sent to ORCID."""
index, doc_type = schema_to_index(record['$schema'])
pushable_doc_types = current_app.config['ORCID_RECORDS_DOC_TYPES']
return doc_type in pushable_doc_types
def test_schema_to_index(schema, expected, index_names, app):
"""Test the expected value of schema to index."""
result = schema_to_index(schema, index_names=index_names)
assert result == expected
def doc_type_should_be_sent_to_orcid(record):
"""Return ``True`` is a document type should be sent to ORCID."""
index, doc_type = schema_to_index(record['$schema'])
return doc_type == 'hep'
def add_citation_counts(chunk_size=500, request_timeout=40):
index, doc_type = schema_to_index('records/hep.json')
def get_records_to_update_generator(citation_lookup):
for recid, citation_count in citation_lookup.iteritems():
try:
uuid = PersistentIdentifier.query.filter(PersistentIdentifier.object_type == "rec", PersistentIdentifier.pid_value == str(recid)).one().object_uuid
yield {'_op_type': 'update',
'_index': index,
'_type': doc_type,
'_id': str(uuid),
'doc': {'citation_count': citation_count}
}
except NoResultFound:
continue
click.echo("Extracting all citations...")
# lookup dictionary where key: recid of the record
# and value: number of records that cite that record
citations_lookup = Counter()
with click.progressbar(es_scan(
current_search_client,
query={
"_source": "references.recid",
"filter": {
"exists": {
"field": "references.recid"
}
},
"size": LARGE_CHUNK_SIZE
},
scroll=u'2m',
index=index,
doc_type=doc_type)) as records:
for record in records:
# update lookup dictionary based on references of the record
if 'references' in record['_source']:
unique_refs_ids = set()
references = record['_source']['references']
for reference in references:
recid = reference.get('recid')
if recid:
if isinstance(recid, list):
# Sometimes there is more than one recid in the
# reference.
recid = recid.pop()
unique_refs_ids.add(recid)
for unique_refs_id in unique_refs_ids:
citations_lookup[unique_refs_id] += 1
click.echo("... DONE.")
click.echo("Adding citation numbers...")
success, failed = es_bulk(
current_search_client,
get_records_to_update_generator(citations_lookup),
chunk_size=chunk_size,
raise_on_exception=True,
raise_on_error=True,
request_timeout=request_timeout,
stats_only=True)
click.echo("... DONE: {} records updated with success. {} failures.".format(success, failed))
def doc_type_should_be_sent_to_orcid(record):
index, doc_type = schema_to_index(record['$schema'])
return doc_type == 'hep'
