Is there a limit on the size of the query you can use with with a SELECT query? I have a long SELECT query (posted below) that keeps throwing a QueryBadFormed error. I have validated the query on sparql.org and I have ran the query on the triple store. I am using GraphDB 8.6 SE. The query runs fine. Code: from SPARQLWrapper import SPARQLWrapper, SPARQLWrapper2, JSON, CSV, TSV # set endpoint and query endpoint = r"http://localhost:7200/repositories/EDR" query = get_dental_procedures_query() # return query below # get results from endpoint sparql = SPARQLWrapper(endpoint) setReturnFormat(JSON) # I've also tried CSV and TSV sparql.setQuery(query) results = sparql.query().convert() Error returned: SPARQLWrapper.SPARQLExceptions.QueryBadFormed: QueryBadFormed: a bad request has been sent to the endpoint, probably the sparql query is bad formed. Here is the query: BASE <http://purl.regenstrief.org/NDPBRN/dental-practice/> PREFIX mesial_surface: <http://purl.obolibrary.org/obo/FMA_no_fmaid_Mesial_surface_enamel_of_tooth> PREFIX exception: <http://purl.obolibrary.org/obo/OHD_0000404> PREFIX ada_num: <http://purl.obolibrary.org/obo/OHD_0000065> PREFIX occurrence_date: <http://purl.obolibrary.org/obo/OHD_0000015> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX resin_filling_proc: <http://purl.obolibrary.org/obo/OHD_0000042> PREFIX birth_date: <http://purl.obolibrary.org/obo/OHD_0000050> PREFIX restored_buccal: <http://purl.obolibrary.org/obo/OHD_0000222> PREFIX caries_finding: <http://purl.obolibrary.org/obo/OHD_0000024> PREFIX dental_finding: <http://purl.obolibrary.org/obo/OHD_0000010> PREFIX molar: <http://purl.obolibrary.org/obo/FMA_55638> PREFIX male_gender_role: <http://purl.obolibrary.org/obo/OMRSE_00000007> PREFIX endodontically_restored_tooth: <http://purl.obolibrary.org/obo/0000236> PREFIX root_canal_treatment: <http://purl.obolibrary.org/obo/OHD_0000230> PREFIX has_part: <http://purl.obolibrary.org/obo/BFO_0000051> PREFIX gender_role: <http://purl.obolibrary.org/obo/OMRSE_00000007> PREFIX part_of: <http://purl.obolibrary.org/obo/BFO_0000050> PREFIX inheres_in: <http://purl.obolibrary.org/obo/BFO_0000052> PREFIX missing_tooth_finding: <http://purl.obolibrary.org/obo/OHD_0000026> PREFIX pbrn_id: <http://purl.obolibrary.org/obo/OHD_0000273> PREFIX distal_surface: <http://purl.obolibrary.org/obo/FMA_no_fmaid_Distal_surface_enamel_of_tooth> PREFIX has_output: <http://purl.obolibrary.org/obo/OBI_0000299> PREFIX occlusal_surface: <http://purl.obolibrary.org/obo/FMA_no_fmaid_Occlusal_surface_enamel_of_tooth> PREFIX incisor: <http://purl.obolibrary.org/obo/FMA_12823> PREFIX graph: <http://purl.regenstrief.org/NDPBRN/dental-practice#> PREFIX patient_role: <http://purl.obolibrary.org/obo/OHD_0000190> PREFIX anterior_tooth: <http://purl.obolibrary.org/obo/OHD_0000307> PREFIX resin: <http://purl.obolibrary.org/obo/OHD_0000036> PREFIX restored_lingual: <http://purl.obolibrary.org/obo/OHD_0000226> PREFIX dental_proc: <http://purl.obolibrary.org/obo/OHD_0000002> PREFIX restored_surface: <http://purl.obolibrary.org/obo/OHD_0000208> PREFIX extracoronally_restored_tooth: <http://purl.obolibrary.org/obo/0000238> PREFIX lingual_surface: <http://purl.obolibrary.org/obo/FMA_no_fmaid_Lingual_surface_enamel_of_tooth> PREFIX dentition: <http://purl.obolibrary.org/obo/FMA_75152> PREFIX sesame: <http://www.openrdf.org/schema/sesame#> PREFIX lesion: <http://purl.obolibrary.org/obo/OHD_0000021> PREFIX labial_surface: <http://purl.obolibrary.org/obo/FMA_no_fmaid_Labial_surface_enamel_of_tooth> PREFIX has_input: <http://purl.obolibrary.org/obo/OBI_0000293> PREFIX posterior_tooth: <http://purl.obolibrary.org/obo/OHD_0000308> PREFIX extraction_proc: <http://purl.obolibrary.org/obo/OHD_0000057> PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX restored_occlusal: <http://purl.obolibrary.org/obo/OHD_0000228> PREFIX is_about: <http://purl.obolibrary.org/obo/IAO_0000136> PREFIX restored_labial: <http://purl.obolibrary.org/obo/OHD_0000225> PREFIX coronally_restored_tooth: <http://purl.obolibrary.org/obo/0000237> PREFIX patient: <http://purl.obolibrary.org/obo/OHD_0000012> PREFIX prop: <http://purl.regenstrief.org/NDPBRN/property/> PREFIX restoration_proc: <http://purl.obolibrary.org/obo/OHD_0000004> PREFIX last_visit_date: <http://purl.obolibrary.org/obo/OHD_0000219> PREFIX tooth: <http://purl.obolibrary.org/obo/FMA_12516> PREFIX intracoronally_restored_tooth: <http://purl.obolibrary.org/obo/0000239> PREFIX bearer_of: <http://purl.obolibrary.org/obo/BFO_0000053> PREFIX first_visit_date: <http://purl.obolibrary.org/obo/OHD_0000218> PREFIX surgically_modified_tooth: <http://purl.obolibrary.org/obo/0000231> PREFIX canine: <http://purl.obolibrary.org/obo/FMA_55636> PREFIX facial_surface: <http://purl.obolibrary.org/obo/FMA_no_fmaid_Facial_surface_enamel_of_tooth> PREFIX restored_distal: <http://purl.obolibrary.org/obo/OHD_0000223> PREFIX premolar: <http://purl.obolibrary.org/obo/FMA_55637> PREFIX restored_tooth: <http://purl.obolibrary.org/obo/OHD_0000189> PREFIX restored_facial: <http://purl.obolibrary.org/obo/OHD_0000235> PREFIX material: <http://purl.obolibrary.org/obo/OHD_0000000> PREFIX missing_tooth_num: <http://purl.obolibrary.org/obo/OHD_0000234> PREFIX buccal_surface: <http://purl.obolibrary.org/obo/FMA_no_fmaid_Buccal_surface_enamel_of_tooth> PREFIX realizes: <http://purl.obolibrary.org/obo/BFO_0000055> PREFIX female_gender_role: <http://purl.obolibrary.org/obo/OMRSE_00000008> PREFIX restored_mesial: <http://purl.obolibrary.org/obo/OHD_0000227> PREFIX restored_incisal: <http://purl.obolibrary.org/obo/OHD_0000224> PREFIX visit: <http://purl.obolibrary.org/obo/OHD_0000009> PREFIX obo: <http://purl.obolibrary.org/obo/> PREFIX incisal_surface: <http://purl.obolibrary.org/obo/FMA_no_fmaid_Incisal_surface_enamel_of_tooth> SELECT DISTINCT ?practice ?patient_id ?gender ?dob ?first_visit ?last_visit ?tooth_id ?tooth_num ?first_PCR ?first_RCT ?event_name ?ada_code ?event_date ?extract_date ?missing_date (if(bound(?surface_m), 1, 0) AS ?m) (if(bound(?surface_o), 1, 0) AS ?o) (if(bound(?surface_d), 1, 0) AS ?d) (if(bound(?surface_b), 1, 0) AS ?b) (if(bound(?surface_l), 1, 0) AS ?l) (if(bound(?surface_f), 1, 0) AS ?f) (if(bound(?surface_incisal), 1, 0) AS ?i) WHERE { ?patient_i a patient: ; birth_date: ?dob ; pbrn_id: ?pbrn_id OPTIONAL { ?gender_t rdfs:subClassOf male_gender_role: ; rdfs:label ?gender_name . ?gender_i sesame:directType ?gender_t ; inheres_in: ?patient_i } ?patient_i first_visit_date: ?first_visit ; last_visit_date: ?last_visit . ?tooth_t rdfs:subClassOf tooth: ; ada_num: ?ada_num . ?tooth_i sesame:directType ?tooth_t OPTIONAL { ?tooth_i prop:first_PCR_date ?first_PCR } OPTIONAL { ?tooth_i prop:first_RCT_date ?first_RCT } OPTIONAL { ?tooth_i prop:extraction_date ?extract_date } OPTIONAL { ?tooth_i prop:missing_tooth_finding_date ?missing_date } ?event_t rdfs:subClassOf dental_proc: ; rdfs:label ?event_name . ?event_i sesame:directType ?event_t ; has_input: ?patient_i ; has_output: ?tooth_i ; occurrence_date: ?event_date ; prop:ada_code ?ada_code OPTIONAL { ?event_i has_output: ?surface_m . ?surface_m sesame:directType restored_mesial: ; part_of: ?tooth_i } OPTIONAL { ?event_i has_output: ?surface_o . ?surface_o sesame:directType restored_occlusal: ; part_of: ?tooth_i } OPTIONAL { ?event_i has_output: ?surface_d . ?surface_d sesame:directType restored_distal: ; part_of: ?tooth_i } OPTIONAL { ?event_i has_output: ?surface_b . ?surface_b sesame:directType restored_buccal: ; part_of: ?tooth_i } OPTIONAL { ?event_i has_output: ?surface_l . ?surface_l sesame:directType restored_lingual: ; part_of: ?tooth_i } OPTIONAL { ?event_i has_output: ?surface_f . ?surface_f sesame:directType restored_facial: ; part_of: ?tooth_i } OPTIONAL { ?event_i has_output: ?surface_incisal . ?surface_incisal sesame:directType restored_incisal: ; part_of: ?tooth_i } BIND(strafter(str(?tooth_i), "tooth/") AS ?tooth_id) BIND(strafter(str(?patient_i), "patient/") AS ?patient_id) BIND(strbefore(str(?gender_name), " ") AS ?gender) BIND(strafter(str(?ada_num), "Tooth ") AS ?tooth_num) BIND(strafter(str(?pbrn_id), "NDPBRN practice ") AS ?practice) } limit 5 Continue reading...
