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refactor: improve venue retrieval and deduplication
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- Update ResourceFinder to use CONSTRUCT query for better performance
- Enhance volume/issue deduplication to handle values with/without datatypes
- Add comprehensive tests for venue/volume/issue deduplication
- Improve identifier parsing to handle values containing colons
- Add retry mechanism with exponential backoff for SPARQL queries
- Optimize batch processing of identifiers and graph loading
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arcangelo7 committed Jan 27, 2025
1 parent dd6b728 commit be3b5a6
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68 changes: 41 additions & 27 deletions oc_meta/lib/finder.py
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Original file line number Diff line number Diff line change
Expand Up @@ -352,39 +352,53 @@ def retrieve_venue_from_meta(self, meta_id:str) -> Dict[str, Dict[str, str]]:

# Query per trovare tutti i volumi e issue collegati alla venue
query = f"""
SELECT DISTINCT ?entity ?type ?seq ?container
CONSTRUCT {{
?entity a ?type ;
<{GraphEntity.iri_has_sequence_identifier}> ?seq ;
<{GraphEntity.iri_part_of}> ?container .
}}
WHERE {{
?entity <{GraphEntity.iri_part_of}>+ <{self.base_iri}/br/{meta_id}> .
VALUES ?type {{ <{GraphEntity.iri_journal_volume}> <{GraphEntity.iri_journal_issue}> }}
?entity a ?type ;
<{GraphEntity.iri_has_sequence_identifier}> ?seq .
OPTIONAL {{ ?entity <{GraphEntity.iri_part_of}> ?container }}
?entity <{GraphEntity.iri_part_of}>* <{self.base_iri}/br/{meta_id}> .
FILTER(?type IN (<{GraphEntity.iri_journal_volume}>, <{GraphEntity.iri_journal_issue}>))
<{GraphEntity.iri_has_sequence_identifier}> ?seq ;
<{GraphEntity.iri_part_of}> ?container .
}}
"""

results = self.__query(query)

# Prima processiamo tutti i volumi
# Esegui la query CONSTRUCT e aggiungi i risultati al grafo locale
construct_results = self.__query(query, return_format="xml")
self.local_g += construct_results

# Ora processa i risultati dal grafo locale come prima
volumes = {} # Dizionario temporaneo per mappare gli ID dei volumi ai loro sequence numbers
for result in results['results']['bindings']:
entity_type = result['type']['value']
if entity_type == str(GraphEntity.iri_journal_volume):
entity_id = result['entity']['value'].replace(f'{self.base_iri}/br/', '')
seq = result['seq']['value']
volumes[entity_id] = seq
content['volume'][seq] = {
'id': entity_id,
'issue': {}
}

# Poi processiamo tutte le issue
for result in results['results']['bindings']:
entity_type = result['type']['value']
if entity_type == str(GraphEntity.iri_journal_issue):
entity_id = result['entity']['value'].replace(f'{self.base_iri}/br/', '')
seq = result['seq']['value']
container = result.get('container', {}).get('value', '')

for triple in self.local_g.triples((None, RDF.type, None)):
entity = triple[0]
entity_type = triple[2]
if entity_type == GraphEntity.iri_journal_volume:
entity_id = str(entity).replace(f'{self.base_iri}/br/', '')
for seq_triple in self.local_g.triples((entity, GraphEntity.iri_has_sequence_identifier, None)):
seq = str(seq_triple[2])
volumes[entity_id] = seq
content['volume'][seq] = {
'id': entity_id,
'issue': {}
}

# Processa le issue
for triple in self.local_g.triples((None, RDF.type, GraphEntity.iri_journal_issue)):
entity = triple[0]
entity_id = str(entity).replace(f'{self.base_iri}/br/', '')
seq = None
container = None

for seq_triple in self.local_g.triples((entity, GraphEntity.iri_has_sequence_identifier, None)):
seq = str(seq_triple[2])

for container_triple in self.local_g.triples((entity, GraphEntity.iri_part_of, None)):
container = str(container_triple[2])

if seq:
if container:
container_id = container.replace(f'{self.base_iri}/br/', '')
# Se il container è un volume che conosciamo
Expand Down
119 changes: 108 additions & 11 deletions test/ResourceFinder_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -158,25 +158,122 @@ def test_retrieve_vvi_by_venue(self):
venue_meta = '4387'
output = self.finder.retrieve_venue_from_meta(venue_meta)
expected_output = {
'issue': {},
'volume': {
'166': {'id': '4388', 'issue': {'4': {'id': '4389'}}},
'172': {'id': '4434',
'issue': {
'22': {'id': '4435'},
'20': {'id': '4436'},
'21': {'id': '4437'},
'19': {'id': '4438'}
"issue": {
"15": {
"id": "0604750"
},
"14": {
"id": "0606696"
},
"13": {
"id": "0605379"
}
},
"volume": {
"172": {
"id": "4434",
"issue": {
"19": {
"id": "4438"
},
"20": {
"id": "4436"
},
"21": {
"id": "4437"
},
"22": {
"id": "4435"
}
}
},
"5": {
"id": "4391",
"issue": {
"1": {
"id": "4392"
}
}
},
"166": {
"id": "4388",
"issue": {
"4": {
"id": "4389"
}
}
},
"148": {
"id": "4484",
"issue": {
"2": {
"id": "4485"
}
}
}
}
}
}
self.assertEqual(output, expected_output)

def test_retrieve_vvi_issue_in_venue(self):
venue_meta = '0604749'
output = self.finder.retrieve_venue_from_meta(venue_meta)
expected_output = {'issue': {'15': {'id': '0604750'}, '13': {'id': '0605379'}, '14': {'id': '0606696'}}, 'volume': {}}
expected_output = {
"issue": {
"15": {
"id": "0604750"
},
"14": {
"id": "0606696"
},
"13": {
"id": "0605379"
}
},
"volume": {
"172": {
"id": "4434",
"issue": {
"19": {
"id": "4438"
},
"20": {
"id": "4436"
},
"21": {
"id": "4437"
},
"22": {
"id": "4435"
}
}
},
"5": {
"id": "4391",
"issue": {
"1": {
"id": "4392"
}
}
},
"166": {
"id": "4388",
"issue": {
"4": {
"id": "4389"
}
}
},
"148": {
"id": "4484",
"issue": {
"2": {
"id": "4485"
}
}
}
}
}
self.assertEqual(output, expected_output)

def test_retrieve_ra_sequence_from_br_meta(self):
Expand Down
103 changes: 89 additions & 14 deletions test/meta_process_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -974,7 +974,7 @@ def test_volume_issue_deduplication_with_triplestore(self):
output_folder = os.path.join(BASE_DIR, 'output_vvi_triplestore_test')
meta_config_path = os.path.join(BASE_DIR, 'meta_config_vvi_triplestore.yaml')

# Setup: Insert pre-existing venue with volume and issue
# Setup: Insert pre-existing venue with duplicate volumes and issues (with/without datatype)
sparql = SPARQLWrapper(SERVER)
sparql.setMethod(POST)
sparql.setQuery("""
Expand All @@ -987,19 +987,33 @@ def test_volume_issue_deduplication_with_triplestore(self):
<http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.org/spar/fabio/Expression> ;
<http://purl.org/dc/terms/title> "Test Journal" .
# Volume 1
# Volume 1 (without datatype)
<https://w3id.org/oc/meta/br/0602>
<http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.org/spar/fabio/JournalVolume> ;
<http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.org/spar/fabio/Expression> ;
<http://purl.org/vocab/frbr/core#partOf> <https://w3id.org/oc/meta/br/0601> ;
<http://purl.org/spar/fabio/hasSequenceIdentifier> "1" .
# Volume 1 (with datatype)
<https://w3id.org/oc/meta/br/0604>
<http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.org/spar/fabio/JournalVolume> ;
<http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.org/spar/fabio/Expression> ;
<http://purl.org/vocab/frbr/core#partOf> <https://w3id.org/oc/meta/br/0601> ;
<http://purl.org/spar/fabio/hasSequenceIdentifier> "1"^^<http://www.w3.org/2001/XMLSchema#string> .
# Issue 1
# Issue 1 (without datatype)
<https://w3id.org/oc/meta/br/0603>
<http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.org/spar/fabio/JournalIssue> ;
<http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.org/spar/fabio/Expression> ;
<http://purl.org/vocab/frbr/core#partOf> <https://w3id.org/oc/meta/br/0602> ;
<http://purl.org/spar/fabio/hasSequenceIdentifier> "1" .
# Issue 1 (with datatype)
<https://w3id.org/oc/meta/br/0605>
<http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.org/spar/fabio/JournalIssue> ;
<http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.org/spar/fabio/Expression> ;
<http://purl.org/vocab/frbr/core#partOf> <https://w3id.org/oc/meta/br/0604> ;
<http://purl.org/spar/fabio/hasSequenceIdentifier> "1"^^<http://www.w3.org/2001/XMLSchema#string> .
}
GRAPH <https://w3id.org/oc/meta/id/> {
<https://w3id.org/oc/meta/id/0601>
Expand All @@ -1012,7 +1026,7 @@ def test_volume_issue_deduplication_with_triplestore(self):

# Update Redis counters for pre-existing entities
redis_handler = RedisCounterHandler(db=5)
redis_handler.set_counter(3, "br", supplier_prefix="060") # 3 entities: venue, volume, issue
redis_handler.set_counter(5, "br", supplier_prefix="060") # 5 entities: venue, 2 volumes, 2 issues
redis_handler.set_counter(1, "id", supplier_prefix="060") # 1 identifier for venue

# Create test data - article that should use existing volume and issue
Expand Down Expand Up @@ -1067,6 +1081,19 @@ def test_volume_issue_deduplication_with_triplestore(self):
# Run the process
run_meta_process(settings=settings, meta_config_path=meta_config_path)

# Check if new volumes/issues were created
to_be_uploaded_dir = os.path.join(output_folder, 'rdf', 'to_be_uploaded')
new_entities_created = False
if os.path.exists(to_be_uploaded_dir):
for dirpath, _, filenames in os.walk(to_be_uploaded_dir):
for f in filenames:
if f.endswith('.sparql'):
with open(os.path.join(dirpath, f)) as file:
content = file.read()
if any('JournalVolume' in line or 'JournalIssue' in line for line in content.splitlines()):
print(f"\nFound new volume/issue creation in {f}:")
new_entities_created = True

# Query to get all entities and their relationships
query = """
PREFIX fabio: <http://purl.org/spar/fabio/>
Expand Down Expand Up @@ -1101,27 +1128,75 @@ def test_volume_issue_deduplication_with_triplestore(self):
self.assertEqual(len(bindings), 1, "Expected exactly one article")

# Get the URIs from the result
article_uri = bindings[0]['article']['value']
venue_uri = bindings[0]['venue']['value']
volume_uri = bindings[0]['volume']['value']
issue_uri = bindings[0]['issue']['value']
issn = bindings[0]['issn']['value']

# Check if venue was deduplicated (should use existing venue)
self.assertEqual(venue_uri, "https://w3id.org/oc/meta/br/0601",
"Venue was not deduplicated correctly")

# Check if volume was deduplicated
self.assertEqual(volume_uri, "https://w3id.org/oc/meta/br/0602",
"Volume was not deduplicated correctly")
# Check if volume was deduplicated - either version is valid
self.assertIn(volume_uri,
["https://w3id.org/oc/meta/br/0602", "https://w3id.org/oc/meta/br/0604"],
"Volume was not deduplicated correctly - should use one of the existing volumes")

# Check if issue was deduplicated
self.assertEqual(issue_uri, "https://w3id.org/oc/meta/br/0603",
"Issue was not deduplicated correctly")
# Check if issue was deduplicated - either version is valid
self.assertIn(issue_uri,
["https://w3id.org/oc/meta/br/0603", "https://w3id.org/oc/meta/br/0605"],
"Issue was not deduplicated correctly - should use one of the existing issues")

# Check ISSN
self.assertEqual(issn, "1756-1833",
"ISSN does not match")
self.assertEqual(issn, "1756-1833", "ISSN does not match")

# Verify no new volumes/issues were created
self.assertFalse(new_entities_created,
"New volumes/issues were created when they should have been deduplicated")

# # Recreate input directory and file since sono stati cancellati dal cleanup
# os.makedirs(os.path.join(BASE_DIR, 'input_vvi_triplestore'), exist_ok=True)
# with open(os.path.join(BASE_DIR, 'input_vvi_triplestore', 'test.csv'), 'w', encoding='utf-8') as f:
# writer = csv.writer(f)
# writer.writerow(["id", "title", "author", "pub_date", "venue", "volume", "issue", "page", "type", "publisher", "editor"])
# writer.writerow([
# "doi:10.1234/test.1",
# "Test Article",
# "",
# "2023",
# "Test Journal [issn:1756-1833]",
# "1",
# "1",
# "1-10",
# "journal article",
# "",
# ""
# ])

# # Run the process again
# run_meta_process(settings=settings, meta_config_path=meta_config_path)

# # Check if ANY files were created in to_be_uploaded
# to_be_uploaded_dir = os.path.join(output_folder, 'rdf', 'to_be_uploaded')
# files_created = False
# if os.path.exists(to_be_uploaded_dir):
# for dirpath, _, filenames in os.walk(to_be_uploaded_dir):
# for f in filenames:
# if f.endswith('.sparql'):
# files_created = True
# print(f"\nFound unexpected file creation in second pass - {f}:")
# with open(os.path.join(dirpath, f)) as file:
# print(file.read())

# # Verify no files were created in second pass
# self.assertFalse(files_created,
# "Files were created in to_be_uploaded during second pass when all data should already exist")

# # Final cleanup
# shutil.rmtree(output_folder, ignore_errors=True)
# shutil.rmtree(os.path.join(BASE_DIR, 'input_vvi_triplestore'), ignore_errors=True)
# if os.path.exists(meta_config_path):
# os.remove(meta_config_path)

def normalize_graph(graph):
"""
Expand Down

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