diff --git a/.gitignore b/.gitignore index 72a7aac..ad84ea9 100644 --- a/.gitignore +++ b/.gitignore @@ -6,7 +6,7 @@ __pycache__/ ontologytimemachine/utils/archivo_ontologies_download.txt ontologytimemachine/utils/archivo_ontologies_hash.txt - +experiments/downloads* # C extensions *.so diff --git a/experiments/aggregate_results.py b/experiments/aggregate_results.py new file mode 100644 index 0000000..88e7763 --- /dev/null +++ b/experiments/aggregate_results.py @@ -0,0 +1,187 @@ +import json +from collections import defaultdict +import csv + +# Content type mapping for each format +content_type_mapping = { + "ttl": "text/turtle", + "nt": "application/n-triples", + "rdfxml": ["application/rdf+xml", "application/xml"], # Updated to include multiple accepted types +} + +# rdf_mimtetypes = ['text/turtle', 'application/n-triples', 'application/rdf+xml', 'application/xml'] +rdf_mimtetypes = [ + 'text/turtle', 'application/n-triples', 'application/rdf+xml', 'application/xml', + 'application/owl+xml', 'application/ld+json', 'text/owl-functional', 'text/owl-manchester', + 'text/n3', 'application/trig', 'application/x-turtle', 'application/x-trig', + 'application/x-nquads' , 'application/n-quads' +] + + +# File paths for the logs +no_proxy_file_path = 'downloads-200ms-shuffled/download_log_extended_fixshort.json' +proxy_file_path = 'downloads_proxy_requests/download_proxy_log_extended_fix.json' + +# Load the JSON data for no-proxy and with-proxy scenarios +with open(no_proxy_file_path, 'r') as f: + no_proxy_data = json.load(f) + +with open(proxy_file_path, 'r') as f: + proxy_data = json.load(f) + +# Initialize the aggregation dictionary for both proxy and no-proxy scenarios +aggregation = { + "w/o proxy": defaultdict(lambda: defaultdict(int)), + "with proxy": defaultdict(lambda: defaultdict(int)), +} + +# Define categories for table +categories = [ + "unsuccessful payload retrieval", + "DNS issue", + "Con. / transport issue", + "TLS cert issue", + "Too many redirects", + "Non-200 HTTP code", + "Successful request (code 200)", + "0 bytes content", + "no rdf content (0 triples parsable)", + "partially parsable rdf-content", + # "pp describes requested ont.", + "fully parsable rdf-content", + # "describes requested ont.", + "no RDF mimetype", + "confused RDF mimetype", + "correct mimetype", + "correct for all 3 formats", +] + +# Error type to category mapping logic +def map_error_to_category(error_type, type_more_specific): + if error_type == "TooManyRedirects": + return "Too many redirects" + elif error_type == "SSLError": + return "TLS cert issue" + elif error_type == "ConnectionError": + if type_more_specific == "NameResolutionError": + return "DNS issue" + else: + return "Con. / transport issue" + elif error_type == "ConnectTimeout": + return "Con. / transport issue" + else: + return "Con. / transport issue" + +# Check if MIME type is valid for the format +def is_correct_mimetype(format, content_type): + expected_types = content_type_mapping.get(format, []) + if isinstance(expected_types, list): + for expected_type in expected_types: + if expected_type in content_type: + return True + return False + return expected_types in content_type + +def is_rdf_mimetype(content_type): + for rdf_mimetype in rdf_mimtetypes: + if rdf_mimetype in content_type: + return True + return False + +# Process data for aggregation +def process_data(data, proxy_key): + for entry in data: + url = entry.get("url", "") + downloads = entry.get("downloads", {}) + formats_correct = set() + + for format, details in downloads.items(): + # Extract details + status_code = details.get("status_code") + parsed_triples = details.get("parsed_triples", 0) + content_length = details.get("content_lenght_measured", 0) + content_type = details.get("content_type", "").lower() if details.get("content_type") else None + uri_in_subject_position = details.get("uri_in_subject_position", False) + rapper_error = details.get("rapper_error") + error = details.get("error", {}) + + # Check for errors and categorize them + if error and error.get("type"): + error_type = error["type"] + type_more_specific = error.get("type_more_specific") + category = map_error_to_category(error_type, type_more_specific) + aggregation[proxy_key][category][format] += 1 + aggregation[proxy_key]["unsuccessful payload retrieval"][format] += 1 + continue + + # Handle non-200 status codes + if status_code != 200: + aggregation[proxy_key]["Non-200 HTTP code"][format] += 1 + aggregation[proxy_key]["unsuccessful payload retrieval"][format] += 1 + continue + + # Successful request (status code 200) + aggregation[proxy_key]["Successful request (code 200)"][format] += 1 + + # Categorize successful ontologies + if content_length == 0: + aggregation[proxy_key]["0 bytes content"][format] += 1 + elif parsed_triples == 0: + aggregation[proxy_key]["no rdf content (0 triples parsable)"][format] += 1 + elif parsed_triples > 0 and rapper_error: + aggregation[proxy_key]["partially parsable rdf-content"][format] += 1 + # if uri_in_subject_position: + # aggregation[proxy_key]["pp describes requested ont."][format] += 1 + elif parsed_triples > 0 and not rapper_error: + aggregation[proxy_key]["fully parsable rdf-content"][format] += 1 + if True: + # aggregation[proxy_key]["describes requested ont."][format] += 1 + + # Check MIME types only for ontologies that describe the requested ontology + if content_type and is_correct_mimetype(format, content_type): + aggregation[proxy_key]["correct mimetype"][format] += 1 + formats_correct.add(format) + elif content_type and is_rdf_mimetype(content_type): + aggregation[proxy_key]["confused RDF mimetype"][format] += 1 + else: + aggregation[proxy_key]["no RDF mimetype"][format] += 1 + + # Check if ontology is correct for all 3 formats + if formats_correct == {"ttl", "nt", "rdfxml"}: + aggregation[proxy_key]["correct for all 3 formats"]["all"] += 1 + +# Function to write aggregation results to TSV file +def write_to_tsv(filename, proxy_key): + with open(filename, 'w', newline='') as tsvfile: + writer = csv.writer(tsvfile, delimiter='\t') + writer.writerow(["Accessibility Status", "turtle", "ntriples", "rdfxml"]) + for category in categories: + row = [category] + for format in ["ttl", "nt", "rdfxml"]: + row.append(aggregation[proxy_key][category].get(format, 0)) + writer.writerow(row) + # Write total for "correct for all 3 formats" + correct_all = aggregation[proxy_key]["correct for all 3 formats"]["all"] + writer.writerow(["correct for all 3 formats", correct_all]) + +# Process both datasets +process_data(no_proxy_data, "w/o proxy") +process_data(proxy_data, "with proxy") + +# Write results to TSV files +write_to_tsv('no_proxy_results.tsv', "w/o proxy") +write_to_tsv('proxy_results.tsv', "with proxy") + +# Print the table +table_headers = ["Accessibility Status", "turtle", "ntriples", "rdfxml"] +for proxy_key in ["w/o proxy", "with proxy"]: + print(f"\nRequested format {proxy_key}") + print(f"{table_headers[0]:<40} {table_headers[1]:<10} {table_headers[2]:<10} {table_headers[3]:<10}") + for category in categories: + row = [category] + for format in ["ttl", "nt", "rdfxml"]: + row.append(aggregation[proxy_key][category].get(format, 0)) + print(f"{row[0]:<40} {row[1]:<10} {row[2]:<10} {row[3]:<10}") + # Print total for "correct for all 3 formats" + correct_all = aggregation[proxy_key]["correct for all 3 formats"]["all"] + print(f"{'correct for all 3 formats':<40} {correct_all:<10}") diff --git a/experiments/aggregate_results_NIRcheck.py b/experiments/aggregate_results_NIRcheck.py new file mode 100644 index 0000000..8dcd035 --- /dev/null +++ b/experiments/aggregate_results_NIRcheck.py @@ -0,0 +1,187 @@ +import json +from collections import defaultdict +import csv + +# Content type mapping for each format +content_type_mapping = { + "ttl": "text/turtle", + "nt": "application/n-triples", + "rdfxml": ["application/rdf+xml", "application/xml"], # Updated to include multiple accepted types +} + +# rdf_mimtetypes = ['text/turtle', 'application/n-triples', 'application/rdf+xml', 'application/xml'] +rdf_mimtetypes = [ + 'text/turtle', 'application/n-triples', 'application/rdf+xml', 'application/xml', + 'application/owl+xml', 'application/ld+json', 'text/owl-functional', 'text/owl-manchester', + 'text/n3', 'application/trig', 'application/x-turtle', 'application/x-trig', + 'application/x-nquads' , 'application/n-quads' +] + + +# File paths for the logs +no_proxy_file_path = 'downloads-200ms-shuffled/download_log_extended_fixshort.json' +proxy_file_path = 'downloads_proxy_requests/download_proxy_log_extended_fix.json' + +# Load the JSON data for no-proxy and with-proxy scenarios +with open(no_proxy_file_path, 'r') as f: + no_proxy_data = json.load(f) + +with open(proxy_file_path, 'r') as f: + proxy_data = json.load(f) + +# Initialize the aggregation dictionary for both proxy and no-proxy scenarios +aggregation = { + "w/o proxy": defaultdict(lambda: defaultdict(int)), + "with proxy": defaultdict(lambda: defaultdict(int)), +} + +# Define categories for table +categories = [ + "unsuccessful payload retrieval", + "DNS issue", + "Con. / transport issue", + "TLS cert issue", + "Too many redirects", + "Non-200 HTTP code", + "Successful request (code 200)", + "0 bytes content", + "no rdf content (0 triples parsable)", + "partially parsable rdf-content", + "pp describes requested ont.", + "fully parsable rdf-content", + "describes requested ont.", + "no RDF mimetype", + "confused RDF mimetype", + "correct mimetype", + "correct for all 3 formats", +] + +# Error type to category mapping logic +def map_error_to_category(error_type, type_more_specific): + if error_type == "TooManyRedirects": + return "Too many redirects" + elif error_type == "SSLError": + return "TLS cert issue" + elif error_type == "ConnectionError": + if type_more_specific == "NameResolutionError": + return "DNS issue" + else: + return "Con. / transport issue" + elif error_type == "ConnectTimeout": + return "Con. / transport issue" + else: + return "Con. / transport issue" + +# Check if MIME type is valid for the format +def is_correct_mimetype(format, content_type): + expected_types = content_type_mapping.get(format, []) + if isinstance(expected_types, list): + for expected_type in expected_types: + if expected_type in content_type: + return True + return False + return expected_types in content_type + +def is_rdf_mimetype(content_type): + for rdf_mimetype in rdf_mimtetypes: + if rdf_mimetype in content_type: + return True + return False + +# Process data for aggregation +def process_data(data, proxy_key): + for entry in data: + url = entry.get("url", "") + downloads = entry.get("downloads", {}) + formats_correct = set() + + for format, details in downloads.items(): + # Extract details + status_code = details.get("status_code") + parsed_triples = details.get("parsed_triples", 0) + content_length = details.get("content_lenght_measured", 0) + content_type = details.get("content_type", "").lower() if details.get("content_type") else None + uri_in_subject_position = details.get("uri_in_subject_position", False) + rapper_error = details.get("rapper_error") + error = details.get("error", {}) + + # Check for errors and categorize them + if error and error.get("type"): + error_type = error["type"] + type_more_specific = error.get("type_more_specific") + category = map_error_to_category(error_type, type_more_specific) + aggregation[proxy_key][category][format] += 1 + aggregation[proxy_key]["unsuccessful payload retrieval"][format] += 1 + continue + + # Handle non-200 status codes + if status_code != 200: + aggregation[proxy_key]["Non-200 HTTP code"][format] += 1 + aggregation[proxy_key]["unsuccessful payload retrieval"][format] += 1 + continue + + # Successful request (status code 200) + aggregation[proxy_key]["Successful request (code 200)"][format] += 1 + + # Categorize successful ontologies + if content_length == 0: + aggregation[proxy_key]["0 bytes content"][format] += 1 + elif parsed_triples == 0: + aggregation[proxy_key]["no rdf content (0 triples parsable)"][format] += 1 + elif parsed_triples > 0 and rapper_error: + aggregation[proxy_key]["partially parsable rdf-content"][format] += 1 + if uri_in_subject_position: + aggregation[proxy_key]["pp describes requested ont."][format] += 1 + elif parsed_triples > 0 and not rapper_error: + aggregation[proxy_key]["fully parsable rdf-content"][format] += 1 + if uri_in_subject_position: + aggregation[proxy_key]["describes requested ont."][format] += 1 + + # Check MIME types only for ontologies that describe the requested ontology + if content_type and is_correct_mimetype(format, content_type): + aggregation[proxy_key]["correct mimetype"][format] += 1 + formats_correct.add(format) + elif content_type and is_rdf_mimetype(content_type): + aggregation[proxy_key]["confused RDF mimetype"][format] += 1 + else: + aggregation[proxy_key]["no RDF mimetype"][format] += 1 + + # Check if ontology is correct for all 3 formats + if formats_correct == {"ttl", "nt", "rdfxml"}: + aggregation[proxy_key]["correct for all 3 formats"]["all"] += 1 + +# Function to write aggregation results to TSV file +def write_to_tsv(filename, proxy_key): + with open(filename, 'w', newline='') as tsvfile: + writer = csv.writer(tsvfile, delimiter='\t') + writer.writerow(["Accessibility Status", "turtle", "ntriples", "rdfxml"]) + for category in categories: + row = [category] + for format in ["ttl", "nt", "rdfxml"]: + row.append(aggregation[proxy_key][category].get(format, 0)) + writer.writerow(row) + # Write total for "correct for all 3 formats" + correct_all = aggregation[proxy_key]["correct for all 3 formats"]["all"] + writer.writerow(["correct for all 3 formats", correct_all]) + +# Process both datasets +process_data(no_proxy_data, "w/o proxy") +process_data(proxy_data, "with proxy") + +# Write results to TSV files +write_to_tsv('no_proxy_results.tsv', "w/o proxy") +write_to_tsv('proxy_results.tsv', "with proxy") + +# Print the table +table_headers = ["Accessibility Status", "turtle", "ntriples", "rdfxml"] +for proxy_key in ["w/o proxy", "with proxy"]: + print(f"\nRequested format {proxy_key}") + print(f"{table_headers[0]:<40} {table_headers[1]:<10} {table_headers[2]:<10} {table_headers[3]:<10}") + for category in categories: + row = [category] + for format in ["ttl", "nt", "rdfxml"]: + row.append(aggregation[proxy_key][category].get(format, 0)) + print(f"{row[0]:<40} {row[1]:<10} {row[2]:<10} {row[3]:<10}") + # Print total for "correct for all 3 formats" + correct_all = aggregation[proxy_key]["correct for all 3 formats"]["all"] + print(f"{'correct for all 3 formats':<40} {correct_all:<10}") diff --git a/experiments/archivo_ontologies.txt b/experiments/archivo_ontologies.txt new file mode 100644 index 0000000..83c00ae --- /dev/null +++ b/experiments/archivo_ontologies.txt @@ -0,0 +1,1817 @@ +http://rdf.insee.fr/def/geo +http://deductions.github.io/biological-collections.owl.ttl# +http://def.seegrid.csiro.au/isotc211/iso19150/-2/2012/basic +http://openenergy-platform.org/ontology/oeo/oeo-shared/ +http://www.w3.org/ns/ssn/ext +http://vocab.deri.ie/fingal +http://semanticscience.org/resource/SIO_000275.rdf +https://privatealpha.com/ontology/process-model/1# +http://www.w3.org/2006/timezone +https://w3id.org/ldes#Vocabulary +http://semanticscience.org/resource/SIO_000856.rdf +https://spec.edmcouncil.org/fibo/ontology/FND/Agreements/Agreements/ +http://vocab.linkeddata.es/datosabiertos/kos/sector-publico/empleo/empleado-publico +https://www.auto.tuwien.ac.at/downloads/thinkhome/ontology/WeatherOntology.owl +http://purl.obolibrary.org/obo/MFOEM.owl +http://www.agfa.com/w3c/2009/clinicalEvaluation +http://deductions.github.io/doas.owl.ttl# +http://lod.taxonconcept.org/ontology/txn.owl +http://semanticscience.org/resource/SIO_001331.rdf +http://archivi.ibc.regione.emilia-romagna.it/ontology/eac-cpf/eac-cpf.rdf +http://semanticscience.org/resource/SIO_000053.rdf +http://def.seegrid.csiro.au/isotc211/iso19107/2003/geometry +http://www.openlinksw.com/ontology/features +http://semanticscience.org/resource/SIO_001276.rdf +http://njh.me/ +http://semanticscience.org/resource/SIO_000838.rdf +https://d-nb.info/standards/elementset/agrelon# +http://ontologi.es/doap-deps# +http://open-services.net/ns/core# +http://purl.org/metainfo/terms/dsp +http://www.bioassayontology.org/bao/bao_complete.owl +http://edamontology.org +http://purl.allotrope.org/voc/afo/REC/2020/12/aft +https://mdcs.monumentenkennis.nl/damageatlas/ontology +http://colin.maudry.com/ontologies/dgfr# +http://lod.taxonconcept.org/ontology/sci_people.owl +http://semanticscience.org/resource/SIO_000832.rdf +http://semanticscience.org/resource/SIO_010071.rdf +http://purl.org/linked-data/sdmx/2009/concept#cog +http://purl.obolibrary.org/obo/go.owl +https://id.parliament.uk/schema +https://dataid.dbpedia.org/databus# +http://rds.posccaesar.org/2008/02/OWL/ISO-15926-2_2003 +http://www.w3.org/ns/prov-links +http://eulersharp.sourceforge.net/2003/03swap/foster +http://vocab.linkeddata.es/datosabiertos/kos/sector-publico/empleo/grupo-profesional +http://swpatho.ag-nbi.de/context/meta.owl +http://semanticscience.org/resource/SIO_000652.rdf +http://semanticscience.org/resource/SIO_001167.rdf +https://w3id.org/sbeo +http://purl.obolibrary.org/obo/chiro.owl +http://purl.bdrc.io/ontology/core/ +http://semanticscience.org/resource/SIO_000483.rdf +http://www.openlinksw.com/ontology/shop +http://purl.org/xro/ns +http://semanticscience.org/resource/SIO_000498.rdf +http://ns.inria.fr/ludo/v1/gamemodel +http://www.w3.org/ns/prov-dc-directmappings +https://saref.etsi.org/saref4syst/ +https://w3id.org/ops +https://spec.edmcouncil.org/fibo/ontology/FND/Utilities/AnnotationVocabulary/ +http://www.w3.org/TR/2003/CR-owl-guide-20030818/wine +http://purl.obolibrary.org/obo/cio.owl +http://www.bl.uk/schemas/bibliographic/blterms +http://semanticscience.org/resource/SIO_000915.rdf +https://privatealpha.com/ontology/content-inventory/1# +https://w3id.org/icon/ontology/ +http://purl.org/spar/tvc +http://semanticscience.org/resource/SIO_000405.rdf +http://purl.org/uF/hCard/terms/ +http://semanticscience.org/resource/SIO_010038.rdf +http://xmlns.com/foaf/0.1/ +http://purl.allotrope.org/voc/afo/WD/2020/03/afo +http://linked.data.gov.au/def/asgs +http://lod.taxonconcept.org/ontology/taxnomen/index.owl +http://protege.stanford.edu/plugins/owl/dc/protege-dc.owl +http://ns.inria.fr/prissma/v1 +http://akswnc7.informatik.uni-leipzig.de/dstreitmatter/archivo/archivo-test-ontology.ttl# +https://ontologies.semanticarts.com/o/gistCore +https://w3id.org/pfeepsa# +http://www.tele.pw.edu.pl/~sims-onto/ConnectivityType.owl +http://www.molmod.info/semantics/pims-ii.ttl +http://semanticscience.org/resource/SIO_001318.rdf +http://purl.org/net/bel-epa/ccy +http://spinrdf.org/spin +https://www.gleif.org/ontology/ReportingException/ +http://dataid.dbpedia.org/ns/mods +http://purl.obolibrary.org/obo/iao.owl +http://purl.org/datajourneys/ +http://qudt.org/vocab/unit/acoustics +http://vocab.deri.ie/pdo +http://semanticscience.org/resource/SIO_000837.rdf +http://purl.org/foodontology +https://www.omg.org/spec/LCC/Countries/Regions/AboutRegions/ +http://vocab.deri.ie/ppo +https://w3id.org/won/core +http://data.ign.fr/id/codes/topo/typederelief/liste +https://w3id.org/affectedBy +http://assemblee-virtuelle.github.io/grands-voisins-v2/thesaurus.ttl +https://w3id.org/scholarlydata/ontology/conference-ontology.owl +http://vocabularies.wikipathways.org/wpTypes# +http://purl.obolibrary.org/obo/peco.owl +http://purl.obolibrary.org/obo/obcs.owl +http://swat.cse.lehigh.edu/resources/onto/aigp.owl +http://purl.org/net/wf-invocation +http://gadm.geovocab.org/ontology +http://kmi.open.ac.uk/projects/smartproducts/ontologies/food.owl +http://vocab.ciudadesabiertas.es/def/sector-publico/empleo +http://semweb.mmlab.be/ns/fnml +https://w3id.org/GConsent +http://purl.allotrope.org/voc/afo/perspective/REC/2020/12/molecular-scale +http://purl.org/imbi/ru-meta.owl +http://semanticscience.org/resource/SIO_011125.rdf +http://www.omg.org/techprocess/ab/SpecificationMetadata/ +http://purl.obolibrary.org/obo/hao.owl +http://www.openlinksw.com/ontology/acl# +http://rdf.insee.fr/def/demo +http://openenergy-platform.org/ontology/oeo/oeo-physical/ +http://www.sealitproject.eu/ontology/ +http://purl.org/NET/acc +http://data.ign.fr/id/codes/topo/typedelaisse/liste +http://catalogus-professorum.org/cpm/2/ +http://semanticscience.org/resource/SIO_000600.rdf +http://mmoon.org/core/ +http://purl.obolibrary.org/obo/uberon.owl +http://semanticscience.org/resource/SIO_010379.rdf +https://d-nb.info/standards/vocab/gnd/gnd-sc# +http://purl.allotrope.org/voc/afo/REC/2021/06/afo 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+http://semanticscience.org/resource/SIO_000338.rdf +http://purl.org/ppeo/PPEO.owl +https://raw.githubusercontent.com/enpadasi/Ontology-for-Nutritional-Studies/master/src/ontology/imports/ONS_imports.owl +https://id.kb.se/vocab/ +https://spec.edmcouncil.org/fibo/ontology/FND/ProductsAndServices/PaymentsAndSchedules/ +http://www.daml.org/services/owl-s/1.2/Service.owl +https://saref.etsi.org/saref4wear/ +http://semanticscience.org/resource/SIO_001000.rdf +http://www.ontologydesignpatterns.org/cp/owl/countingas.owl +https://w3id.org/sao +http://semanticscience.org/resource/SIO_000115.rdf +http://purl.allotrope.org/voc/qb/REC/2018/10/cube +http://semanticscience.org/resource/SIO_000822.rdf +https://w3id.org/dpv# +http://publications.europa.eu/resource/authority/asset-classification +http://vocab.linkeddata.es/datosabiertos/def/medio-ambiente/contaminacion-acustica +http://qudt.org/2.1/vocab/prefix +https://purl.org/heals/sco/ +http://purl.obolibrary.org/obo/trans.owl +http://ns.softwiki.de/req/2/ +http://biohackathon.org/resource/faldo +http://purl.allotrope.org/voc/afo/perspective/REC/2020/09/molecular-scale +http://def.seegrid.csiro.au/isotc211/iso19115/2003/citation +http://purl.obolibrary.org/obo/ro/subsets/ro-interaction.owl +http://semanticscience.org/resource/SIO_000162.rdf +http://purl.obolibrary.org/obo/po/imports/ncbitaxon_import.owl +http://semanticscience.org/resource/SIO_000295.rdf +https://spec.edmcouncil.org/fibo/ontology/FND/Arrangements/Documents/ +http://www.ontologydesignpatterns.org/cp/owl/semiotics.owl +http://www.w3.org/ns/formats/ +http://purl.allotrope.org/voc/afo/REC/2018/11/aft +http://purl.org/NET/decimalised#d +http://data.posccaesar.org/rdl/ +http://purl.org/ontology/ao/core# +http://purl.org/poso/ +http://purl.org/spar/pso +http://purl.obolibrary.org/obo/oarcs.owl +http://purl.org/NET/ssnext/electricmeters# +http://semanticscience.org/resource/SIO_001007.rdf +http://geovocab.org/geometry +http://bblfish.net/work/atom-owl/2006-06-06/ +http://vocab.deri.ie/scovo +https://w3id.org/seas/OperatingOntology +http://www.opmw.org/ontology/ +http://www.w3.org/ns/spec#AdvisementLevel +http://purl.org/net/hifm/ontology# +http://semanticscience.org/resource/SIO_001373.rdf +http://vocab.ciudadesabiertas.es/def/transporte/autobus +http://purl.allotrope.org/voc/afo/domain/REC/2021/03/class-coordination +http://purl.org/wf4ever/roterms# +https://w3id.org/eep +http://mged.sourceforge.net/ontologies/MGEDOntology.owl +https://w3id.org/seas/EvaluationOntology +http://datafoodconsortium.org/ontologies/DFC_FullModel.owl +http://eunis.eea.europa.eu/rdf/species-schema.rdf +http://securitytoolbox.appspot.com/securityAlgorithms# +http://publications.europa.eu/resource/authority/dataset-type +http://purl.org/olia/ubyCat.owl +http://purl.org/ccf/ccf.owl +http://semanticscience.org/resource/SIO_000852.rdf +http://www.w3.org/TR/2003/PR-owl-guide-20031209/wine +http://semanticscience.org/resource/SIO_000429.rdf +http://purl.obolibrary.org/obo/sibo.owl +http://brt.basisregistraties.overheid.nl/def/top10nl +http://www.w3.org/ns/regorg +http://vocab.linkeddata.es/datosabiertos/def/urbanismo-infraestructuras/equipamiento +http://w3id.org/semiot/ontologies/semiot# +http://w3id.org/gaia-x/core# +https://w3id.org/seas/FeatureOfInterestOntology +http://ontologies.geohive.ie/osi +http://purl.org/NET/dc_owl2dl/terms_od +https://w3id.org/example +http://semanticscience.org/resource/SIO_000106.rdf +http://purl.org/procurement/public-contracts-authority-kinds# +https://w3id.org/rdfp/ +http://www.w3.org/ns/odrl/2/ +http://purl.org/spar/pro/ +https://saref.etsi.org/saref4ehaw/ +https://w3id.org/arco/ontology/catalogue +http://vocabularies.wikipathways.org/wp# +http://w3id.org/roh +http://emmo.info/emmo +http://geni-orca.renci.org/owl/topology.owl +http://timbus.teco.edu/ontologies/DIO.owl +http://purl.org/ontology/prv/core# +https://w3id.org/arco/ontology/denotative-description +http://semanticscience.org/resource/SIO_000107.rdf +http://purl.jp/bio/11/mbgd +https://w3id.org/todo/tododfa +http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-ma.owl +http://www.mygrid.org.uk/mygrid-moby-service +http://dati.san.beniculturali.it/SAN/TesauroSAN +http://www.agfa.com/w3c/2009/infectiousDisorder# +https://spec.edmcouncil.org/fibo/ontology/FND/DatesAndTimes/Occurrences/ +http://www.data-knowledge.org/dk/ +https://w3id.org/fdof/ontology +http://d3fend.mitre.org/ontologies/d3fend.owl +http://www.yso.fi/onto/allars/ +http://www.w3.org/ns/radion# +http://semanticscience.org/resource/SIO_001396.rdf \ No newline at end of file diff --git a/experiments/download_ontologies.py b/experiments/download_ontologies.py new file mode 100644 index 0000000..34190f9 --- /dev/null +++ b/experiments/download_ontologies.py @@ -0,0 +1,178 @@ +import os +import requests +import json +import traceback +import time +from urllib.parse import urlparse +from requests.adapters import HTTPAdapter +from requests.packages.urllib3.util.retry import Retry + +def ensure_directory(path): + """Ensure the directory exists.""" + if not os.path.exists(path): + os.makedirs(path) + +def save_file(content, file_path): + """Save content to a file.""" + with open(file_path, "wb") as file: + file.write(content) + +def read_ontologies_from_file(file_path): + """Read ontology URLs from a file where each line is an ontology URL.""" + if not os.path.exists(file_path): + raise FileNotFoundError(f"The file {file_path} does not exist.") + + with open(file_path, "r") as file: + return [line.strip() for line in file if line.strip()] + +def get_causal_chain(exception): + """Get the causal chain of exceptions.""" + chain = [] + while exception: + chain.append({ + "type": type(exception).__name__, + "message": str(exception), + }) + exception = exception.__context__ + return chain + +def get_type_chain(chain): + """Get the type chain as a string separated by '||'.""" + return ' || '.join([entry['type'] for entry in chain]) + +def get_more_specific_type(chain): + """Get the more specific type from the causal chain.""" + if len(chain) > 1: + if chain[1]['type'] == 'MaxRetryError' and len(chain) > 2: + return chain[2]['type'] + return chain[1]['type'] + return None + +def download_ontology(url, formats, base_folder): + """Download an ontology in specified formats and log details.""" + ontology_info = { + "url": url, + "downloads": {}, + } + + headers = { + "Accept": "", + } + + proxies = { + "http": f"http://localhost:8898", + "https": f"http://localhost:8898", + } + + cacert_path = "ca-cert.pem" + + # session = requests.Session() + # session.max_redirects = 10 + # retries = Retry(total=0, backoff_factor=1, status_forcelist=[427]) # wanted to use for 429 originally, but backoff is als applied to connection timeouts and such + # session.mount('http://', HTTPAdapter(max_retries=retries)) + # session.mount('https://', HTTPAdapter(max_retries=retries)) + + for format_name, mime_type in formats.items(): + try: + headers["Accept"] = mime_type + start_time = time.time() + #response = session.get(url, proxies=proxies, headers=headers, verify=cacert_path, timeout=10) + response = requests.get(url, headers=headers, timeout=10) + request_duration = time.time() - start_time + + file_path = "" + if response.status_code == 200: + parsed_url = urlparse(url) + ontology_name = os.path.basename(parsed_url.path) or "ontology" + ontology_url = url.replace('/', '_').replace(':', '_').replace('.', '_') + filename = f"{ontology_url}.{format_name}" + folder_path = os.path.join(base_folder, format_name) + ensure_directory(folder_path) + file_path = os.path.join(folder_path, filename) + + download_start_time = time.time() + save_file(response.content, file_path) + download_duration = time.time() - download_start_time + + ontology_info["downloads"][format_name] = { + "status_code": response.status_code, + "file_path": file_path, + "request_start_time": start_time, + "request_duration": request_duration, + "error": { + "type": None, + "type_more_specific": None, + "type_chain": None, + "message": None, + "traceback": None, + "chain_details": None, + }, + "content_length": response.headers.get('Content-Length'), + "content_lenght_measured": len(response.content), + "content_type": response.headers.get('Content-Type'), + "headers": dict(response.headers), + # "download_duration": download_duration, + } + # else: + # ontology_info["downloads"][format_name] = { + # "status_code": response.status_code, + # "headers": dict(response.headers), + # "error": "Failed to fetch the ontology", + # "request_start_time": start_time, + # "request_duration": request_duration, + # } + + except Exception as e: + request_duration = time.time() - start_time + chain_details = get_causal_chain(e) + ontology_info["downloads"][format_name] = { + "status_code": None, + "file_path": None, + "request_start_time": start_time, + "request_duration": request_duration, + "content_length": None, + "content_lenght_measured": None, + "content_type": None, + "error": { + "type": type(e).__name__, + "type_more_specific": get_more_specific_type(chain_details), + "type_chain": get_type_chain(chain_details), + "message": str(e), + "traceback": traceback.format_exc(), + "chain_details": chain_details, + }, + "headers": None + } + + + return ontology_info + +def main(): + ontology_file = "archivo_ontologies.txt" + urls = read_ontologies_from_file(ontology_file) + + formats = { + "ttl": "text/turtle", + "nt": "application/n-triples", + "rdfxml": "application/rdf+xml", + } + + base_folder = "downloads" + ensure_directory(base_folder) + + log = [] + + for url in urls: + print(f'URL: {url}') + ontology_log = download_ontology(url, formats, base_folder) + time.sleep(0.2) + log.append(ontology_log) + + log_file = os.path.join(base_folder, "download_log.json") + with open(log_file, "w") as file: + json.dump(log, file, indent=4) + + print(f"Download complete. Log saved to {log_file}") + +if __name__ == "__main__": + main() diff --git a/experiments/download_ontologies_proxy.py b/experiments/download_ontologies_proxy.py new file mode 100644 index 0000000..9695587 --- /dev/null +++ b/experiments/download_ontologies_proxy.py @@ -0,0 +1,178 @@ +import os +import requests +import json +import traceback +import time +from urllib.parse import urlparse +from requests.adapters import HTTPAdapter +from requests.packages.urllib3.util.retry import Retry + +def ensure_directory(path): + """Ensure the directory exists.""" + if not os.path.exists(path): + os.makedirs(path) + +def save_file(content, file_path): + """Save content to a file.""" + with open(file_path, "wb") as file: + file.write(content) + +def read_ontologies_from_file(file_path): + """Read ontology URLs from a file where each line is an ontology URL.""" + if not os.path.exists(file_path): + raise FileNotFoundError(f"The file {file_path} does not exist.") + + with open(file_path, "r") as file: + return [line.strip() for line in file if line.strip()] + +def get_causal_chain(exception): + """Get the causal chain of exceptions.""" + chain = [] + while exception: + chain.append({ + "type": type(exception).__name__, + "message": str(exception), + }) + exception = exception.__context__ + return chain + +def get_type_chain(chain): + """Get the type chain as a string separated by '||'.""" + return ' || '.join([entry['type'] for entry in chain]) + +def get_more_specific_type(chain): + """Get the more specific type from the causal chain.""" + if len(chain) > 1: + if chain[1]['type'] == 'MaxRetryError' and len(chain) > 2: + return chain[2]['type'] + return chain[1]['type'] + return None + +def download_ontology(url, formats, base_folder): + """Download an ontology in specified formats and log details.""" + ontology_info = { + "url": url, + "downloads": {}, + } + + headers = { + "Accept": "", + } + + proxies = { + "http": f"http://localhost:8898", + "https": f"http://localhost:8898", + } + + cacert_path = "ca-cert.pem" + + # session = requests.Session() + # session.max_redirects = 10 + # retries = Retry(total=0, backoff_factor=1, status_forcelist=[427]) # wanted to use for 429 originally, but backoff is als applied to connection timeouts and such + # session.mount('http://', HTTPAdapter(max_retries=retries)) + # session.mount('https://', HTTPAdapter(max_retries=retries)) + + for format_name, mime_type in formats.items(): + try: + headers["Accept"] = mime_type + start_time = time.time() + #response = session.get(url, proxies=proxies, headers=headers, verify=cacert_path, timeout=10) + response = requests.get(url, proxies=proxies, headers=headers, verify=cacert_path, timeout=10) + request_duration = time.time() - start_time + + file_path = "" + if response.status_code == 200: + parsed_url = urlparse(url) + ontology_name = os.path.basename(parsed_url.path) or "ontology" + ontology_url = url.replace('/', '_').replace(':', '_').replace('.', '_') + filename = f"{ontology_url}.{format_name}" + folder_path = os.path.join(base_folder, format_name) + ensure_directory(folder_path) + file_path = os.path.join(folder_path, filename) + + download_start_time = time.time() + save_file(response.content, file_path) + download_duration = time.time() - download_start_time + + ontology_info["downloads"][format_name] = { + "status_code": response.status_code, + "file_path": file_path, + "request_start_time": start_time, + "request_duration": request_duration, + "error": { + "type": None, + "type_more_specific": None, + "type_chain": None, + "message": None, + "traceback": None, + "chain_details": None, + }, + "content_length": response.headers.get('Content-Length'), + "content_lenght_measured": len(response.content), + "content_type": response.headers.get('Content-Type'), + "headers": dict(response.headers), + # "download_duration": download_duration, + } + # else: + # ontology_info["downloads"][format_name] = { + # "status_code": response.status_code, + # "headers": dict(response.headers), + # "error": "Failed to fetch the ontology", + # "request_start_time": start_time, + # "request_duration": request_duration, + # } + + except Exception as e: + request_duration = time.time() - start_time + chain_details = get_causal_chain(e) + ontology_info["downloads"][format_name] = { + "status_code": None, + "file_path": None, + "request_start_time": start_time, + "request_duration": request_duration, + "content_length": None, + "content_lenght_measured": None, + "content_type": None, + "error": { + "type": type(e).__name__, + "type_more_specific": get_more_specific_type(chain_details), + "type_chain": get_type_chain(chain_details), + "message": str(e), + "traceback": traceback.format_exc(), + "chain_details": chain_details, + }, + "headers": None + } + + + return ontology_info + +def main(): + ontology_file = "archivo_ontologies.txt" + urls = read_ontologies_from_file(ontology_file) + + formats = { + "ttl": "text/turtle", + "nt": "application/n-triples", + "rdfxml": "application/rdf+xml", + } + + base_folder = "downloads_proxy_requests" + ensure_directory(base_folder) + + log = [] + + for url in urls: + print(f'URL: {url}') + ontology_log = download_ontology(url, formats, base_folder) + time.sleep(0.2) + log.append(ontology_log) + + log_file = os.path.join(base_folder, "download_proxy_log.json") + with open(log_file, "w") as file: + json.dump(log, file, indent=4) + + print(f"Download complete. Log saved to {log_file}") + +if __name__ == "__main__": + main() diff --git a/experiments/downloads/download_log.json b/experiments/downloads/download_log.json new file mode 100644 index 0000000..0a6c210 --- /dev/null +++ b/experiments/downloads/download_log.json @@ -0,0 +1,75 @@ +[ + { + "url": "http://babelnet.org/rdf/", + "downloads": { + "ttl": { + "status_code": 503, + "error": "Failed to fetch the ontology" + }, + "nt": { + "status_code": 503, + "error": "Failed to fetch the ontology" + }, + "rdfxml": { + "status_code": 503, + "error": "Failed to fetch the ontology" + } + } + }, + { + "url": "http://bag.basisregistraties.overheid.nl/def/bag", + "downloads": { + "ttl": { + "status_code": 200, + "headers": { + "vary": "Origin,Access-Control-Request-Method,Access-Control-Request-Headers", + "x-envoy-upstream-service-time": "21", + "Set-Cookie": "b92febf50d71b9ccc8184dfcf4ae480b=8bb862a4db465e2ec78dc36e4519d647; Path=/def; HttpOnly; Domain=bag.basisregistraties.overheid.nl", + "Strict-Transport-Security": "max-age=31536000; includeSubDomains; preload", + "Content-Encoding": "gzip", + "Content-Type": "text/turtle", + "Transfer-Encoding": "chunked", + "Date": "Fri, 13 Dec 2024 05:21:18 GMT", + "Keep-Alive": "timeout=20", + "Connection": "keep-alive", + "Server": "unspecified" + }, + "file_path": "downloads/ttl/http___bag_basisregistraties_overheid_nl_def_bag.ttl" + }, + "nt": { + "status_code": 200, + "headers": { + "vary": "Origin,Access-Control-Request-Method,Access-Control-Request-Headers", + "x-envoy-upstream-service-time": "15", + "Set-Cookie": "b92febf50d71b9ccc8184dfcf4ae480b=590194453cdff47017f98c1dc79192d7; Path=/def; HttpOnly; Domain=bag.basisregistraties.overheid.nl", + "Strict-Transport-Security": "max-age=31536000; includeSubDomains; preload", + "Content-Encoding": "gzip", + "Content-Type": "application/n-triples", + "Transfer-Encoding": "chunked", + "Date": "Fri, 13 Dec 2024 05:21:18 GMT", + "Keep-Alive": "timeout=20", + "Connection": "keep-alive", + "Server": "unspecified" + }, + "file_path": "downloads/nt/http___bag_basisregistraties_overheid_nl_def_bag.nt" + }, + "rdfxml": { + "status_code": 200, + "headers": { + "vary": "Origin,Access-Control-Request-Method,Access-Control-Request-Headers", + "x-envoy-upstream-service-time": "11", + "Set-Cookie": "b92febf50d71b9ccc8184dfcf4ae480b=590194453cdff47017f98c1dc79192d7; Path=/def; HttpOnly; Domain=bag.basisregistraties.overheid.nl", + "Strict-Transport-Security": "max-age=31536000; includeSubDomains; preload", + "Content-Encoding": "gzip", + "Content-Type": "application/rdf+xml", + "Transfer-Encoding": "chunked", + "Date": "Fri, 13 Dec 2024 05:21:19 GMT", + "Keep-Alive": "timeout=20", + "Connection": "keep-alive", + "Server": "unspecified" + }, + "file_path": "downloads/rdfxml/http___bag_basisregistraties_overheid_nl_def_bag.rdfxml" + } + } + } +] \ No newline at end of file diff --git a/experiments/parse_ontologies.py b/experiments/parse_ontologies.py new file mode 100644 index 0000000..d101633 --- /dev/null +++ b/experiments/parse_ontologies.py @@ -0,0 +1,102 @@ +import json +import subprocess +import os +import re + +ontology_map = { + 'nt': 'ntriples', + 'ttl': 'turtle', + 'rdfxml': 'rdfxml' +} + +def process_ontologies(json_file_path, output_file_path): + def is_uri_in_subject(triples, ontology_uri): + """ + Check if the ontology URI appears in the subject position of any triple. + """ + subject_pattern = re.compile(rf"^<{re.escape(ontology_uri)}>") + return any(subject_pattern.match(triple) for triple in triples) + + def format_error_message(error_message): + lines = error_message.splitlines() + if len(lines) > 20: + return "\n".join(lines[:10] + ["\n\n\n............\n\n\n"] + lines[-10:]) + return error_message + + # Load the JSON file + with open(json_file_path, 'r') as f: + ontologies = json.load(f) + + base_folder = os.path.dirname(json_file_path) + input_base_folder = os.path.basename(base_folder) + + for ontology in ontologies: + ontology_url = ontology["url"] + print(f'URL: {ontology_url}') + for format_type, format_data in ontology["downloads"].items(): + # Extract the file path and format + file_path = format_data.get("file_path") + status_code = format_data.get("status_code") + if not file_path: + format_data["parsed_triples"] = None + format_data["uri_in_subject_position"] = None + format_data["rapper_error"] = None + elif file_path and status_code == 200: + file_path_parts = file_path.split(os.sep) + file_path_parts[0] = input_base_folder + file_path = os.sep.join(file_path_parts) + # Prepare the command + command = [ + "cat", + file_path, + "|", + "rapper", + f"-i {ontology_map[format_type]}", + f"-o ntriples", + "-", + ontology_url + ] + print(" ".join(command)) + + # Execute the command + try: + result = subprocess.run( + " ".join(command), + shell=True, + capture_output=True, + text=True + ) + + # Check the result and update the JSON + output = result.stdout + triples = output.splitlines() + num_triples = output.count("\n") + + uri_in_subject = is_uri_in_subject(triples, ontology_url) + format_data["uri_in_subject_position"] = uri_in_subject + format_data["parsed_triples"] = num_triples + + if result.returncode == 0: + format_data["rapper_error"] = None + else: + format_data["rapper_error"] = format_error_message(result.stderr.strip()) + + except Exception as e: + format_data["parsed_triples"] = 0 + format_data["uri_in_subject_position"] = False + format_data["rapper_error"] = str(e) + + # Save the updated JSON + with open(output_file_path, 'w') as f: + json.dump(ontologies, f, indent=4) + +if __name__ == "__main__": + # Replace these paths with your actual file paths + input_json_path = "downloads_direct_requests/download_log.json" + output_json_path = "downloads_direct_requests/download_log_fixshort.json" + + if os.path.exists(input_json_path): + process_ontologies(input_json_path, output_json_path) + print(f"Processed ontologies. Updated JSON saved to {output_json_path}") + else: + print(f"Input file {input_json_path} not found.") diff --git a/experiments/transform_json.py b/experiments/transform_json.py new file mode 100644 index 0000000..706369e --- /dev/null +++ b/experiments/transform_json.py @@ -0,0 +1,36 @@ +import json +import os + +def transform_json(input_file_path, output_file_path): + if not os.path.exists(input_file_path): + raise FileNotFoundError(f"The file {input_file_path} does not exist.") + + with open(input_file_path, "r") as file: + data = json.load(file) + + for entry in data: + for download in entry.get("downloads", {}).values(): + if "headers" in download and isinstance(download["headers"], dict): + download["headers"] = "\n".join(f"{k}: {v}" for k, v in download["headers"].items()) + if "error" in download and download["error"] and "chain_details" in download["error"]: + chain_details = download["error"]["chain_details"] + if isinstance(chain_details, list): + download["error"]["chain_details"] = "\n".join( + f"{item['type']}: {item['message']}" for item in chain_details + ) + if "rapper_error" in download and download["rapper_error"]: + rapper_error_lines = download["rapper_error"].splitlines() + if len(rapper_error_lines) > 11: + download["rapper_error"] = "\n".join(rapper_error_lines[:6] + ["..."] + rapper_error_lines[-5:]) + + with open(output_file_path, "w") as file: + json.dump(data, file, indent=4) + +def main(): + input_json_file = "downloads-200ms-shuffled/download_log_extended.json" + output_json_file = "downloads-200ms-shuffled/download_log_extended_flattened.json" + transform_json(input_json_file, output_json_file) + print(f"Transformation complete. File saved to {output_json_file}") + +if __name__ == "__main__": + main() diff --git a/ontologytimemachine/utils/config.py b/ontologytimemachine/utils/config.py index b18e207..ae49c33 100644 --- a/ontologytimemachine/utils/config.py +++ b/ontologytimemachine/utils/config.py @@ -90,9 +90,9 @@ class Config: logLevelTimeMachine: LogLevel = LogLevel.DEBUG logLevelBase: LogLevel = LogLevel.INFO ontoFormatConf: OntoFormatConfig = field(default_factory=OntoFormatConfig) - ontoVersion: OntoVersion = OntoVersion.ORIGINAL_FAILOVER_LIVE_LATEST + ontoVersion: OntoVersion = OntoVersion.LATEST_ARCHIVED restrictedAccess: bool = False - clientConfigViaProxyAuth: ClientConfigViaProxyAuth = ClientConfigViaProxyAuth.REQUIRED + clientConfigViaProxyAuth: ClientConfigViaProxyAuth = ClientConfigViaProxyAuth.IGNORE httpsInterception: HttpsInterception = HttpsInterception.ALL disableRemovingRedirects: bool = False timestamp: str = ""