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Add named graphs to SPARQL interface. Add SPARQL diagnostics
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hsolbrig committed Feb 17, 2019
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285 changes: 285 additions & 0 deletions notebooks/PersistentResults.ipynb
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{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Using the SPARQL Slurper to build graphs\n",
"The following example uses a Wikidata ShEx definition to construct the minimal conforming graph from WikiData. The graph (`permagraph`) is then displayed\n",
"\n",
"Details:\n",
"* -ss - use the SparqlSlurper\n",
"* -sq - a query to find the first 100 items that are instances of wd:Q7397\n",
"* http://query.wikidata.org/sparql -- Wikidata SPARQL endpoint\n",
"* https://raw.githubusercontent.com/shexSpec/schemas/master/Wikidata/DigitalPreservation/SWIB/software.shex - ShEx\n",
"* --stopafter 1 -- only process one node (testing)\n",
"* -ps -- Print SPARQL queries"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"from pyshex.shex_evaluator import evaluate_cli as shexeval\n",
"from pyshex import shex_evaluator\n",
"from sparql_slurper import SlurpyGraph"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"SPARQL:\n",
"\n",
"PREFIX wdt: <http://www.wikidata.org/prop/direct/>\n",
"PREFIX wd: <http://www.wikidata.org/entity/>\n",
"\n",
"SELECT ?item WHERE { ?item (wdt:P31/wdt:P279*) wd:Q7397.} LIMIT 100\n",
"\n",
"SPARQL: (SELECT ?s ?p ?o {<http://www.wikidata.org/entity/Q2374> ?p ?o}) (0.32 secs) - 177 triples\n",
"Errors:\n",
" Focus: http://www.wikidata.org/entity/Q2374\n",
" Start: #wikidata-software\n",
" Reason: Testing <http://www.wikidata.org/entity/Q2374> against shape #wikidata-software\n",
" Triples:\n",
" <http://www.wikidata.org/entity/Q2374> p:P178 <http://www.wikidata.org/entity/statement/q2374-04C1F298-5F3D-4220-8714-B0C4587A0282> .\n",
" <http://www.wikidata.org/entity/Q2374> p:P178 <http://www.wikidata.org/entity/statement/q2374-66140209-9732-4C37-BFC4-BDB02A5D0803> .\n",
" <http://www.wikidata.org/entity/Q2374> p:P178 <http://www.wikidata.org/entity/statement/q2374-E713580E-6144-484C-9A86-42B3D7829ED3> .\n",
" 3 triples exceeds max {1,1}\n",
"\n",
"RESULT Graph:\n",
"@prefix ns1: <http://www.w3.org/2004/02/skos/core#> .\n",
"@prefix ns2: <http://wikiba.se/ontology#> .\n",
"@prefix ns3: <http://www.wikidata.org/prop/direct-normalized/> .\n",
"@prefix p: <http://www.wikidata.org/prop/> .\n",
"@prefix pq: <http://www.wikidata.org/prop/qualifier/> .\n",
"@prefix pr: <http://www.wikidata.org/prop/reference/> .\n",
"@prefix prov: <http://www.w3.org/ns/prov#> .\n",
"@prefix prv: <http://www.wikidata.org/prop/reference/value/> .\n",
"@prefix ps: <http://www.wikidata.org/prop/statement/> .\n",
"@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .\n",
"@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .\n",
"@prefix schema: <http://schema.org/> .\n",
"@prefix wd: <https://www.wikidata.org/wiki/> .\n",
"@prefix wdt: <http://www.wikidata.org/prop/direct/> .\n",
"@prefix xml: <http://www.w3.org/XML/1998/namespace> .\n",
"@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .\n",
"\n",
"<http://www.wikidata.org/entity/Q2374> rdfs:label \"Civilization III\",\n",
" \"Sid Meier's Civilization III\",\n",
" \"تمدن ۳\",\n",
" \"சிவிலைசேசன் மூன்று\",\n",
" \"シヴィライゼーションIII\",\n",
" \"文明III\",\n",
" \"문명 III\" ;\n",
" schema:dateModified \"2019-02-10T10:31:28+00:00\"^^xsd:dateTime ;\n",
" schema:description \"2001 video game\",\n",
" \"2001 videopeli\",\n",
" \"Computerspiel\",\n",
" \"computerspel van Firaxis Games\",\n",
" \"datorspel från 2001\",\n",
" \"gra wideo\",\n",
" \"jeu vidéo\",\n",
" \"joc video din 2001\",\n",
" \"jogo eletrônico\",\n",
" \"jogo eletrônico de 2001\",\n",
" \"tahová strategická počítačová hra\",\n",
" \"turn-based strategy video game\",\n",
" \"videogioco strategico\",\n",
" \"videoigra\",\n",
" \"videojoc de 2001\",\n",
" \"videojuego de estrategia por turnos ambientado en la construcción de imperios\",\n",
" \"videojáték\",\n",
" \"videospēle\",\n",
" \"βιντεοπαιχνίδι του 2001\",\n",
" \"видео-игра\",\n",
" \"відеогра 2001 року\",\n",
" \"компьютерная игра 2001 года\",\n",
" \"电脑游戏\" ;\n",
" schema:version 855058870 ;\n",
" ns2:identifiers 10 ;\n",
" ns2:sitelinks 27 ;\n",
" ns2:statements 50 ;\n",
" ns2:timestamp \"2019-02-10T10:31:36+00:00\"^^xsd:dateTime ;\n",
" ns1:altLabel \"CIV 3\",\n",
" \"CIV III\",\n",
" \"Civ 3\",\n",
" \"Civ3\",\n",
" \"Civilization 3\",\n",
" \"Sid Meier's Civilization III\",\n",
" \"Sid Meier’s Civilization III\",\n",
" \"Цивилизация III\",\n",
" \"Цивілізація 3\" ;\n",
" p:P1072 <http://www.wikidata.org/entity/statement/Q2374-3207a91f-4331-df8d-aaa3-218a543e2fde>,\n",
" <http://www.wikidata.org/entity/statement/Q2374-9213212a-4e43-82e7-a80c-a12b30b5981d> ;\n",
" p:P1073 <http://www.wikidata.org/entity/statement/Q2374-4600383a-4182-073c-8a6f-d7afad4719d8>,\n",
" <http://www.wikidata.org/entity/statement/Q2374-d979a7b9-4e35-4760-29ca-446fcd31a3e1> ;\n",
" p:P123 <http://www.wikidata.org/entity/statement/Q2374-7BA07BAB-BBBC-4A31-80BE-B4DBC51F880A>,\n",
" <http://www.wikidata.org/entity/statement/q2374-74F7A23E-B22F-453E-B308-D8A802C4E9C8>,\n",
" <http://www.wikidata.org/entity/statement/q2374-CA921CB5-04F5-4B39-A6E8-F9C316FDF1A7>,\n",
" <http://www.wikidata.org/entity/statement/q2374-CA960D7C-21FD-4797-83CD-3CA8D70D658F> ;\n",
" p:P136 <http://www.wikidata.org/entity/statement/Q2374-253BA882-87CE-468B-A3DC-B3D75F8BA608>,\n",
" <http://www.wikidata.org/entity/statement/Q2374-6dfd4af1-4ae3-a5fe-e871-848a98932cf5>,\n",
" <http://www.wikidata.org/entity/statement/Q2374-9F4BBFD4-D296-485C-A2D0-4F579BD32272>,\n",
" <http://www.wikidata.org/entity/statement/q2374-6155E97A-DBA3-4DA6-BD16-9CCFC672695C>,\n",
" <http://www.wikidata.org/entity/statement/q2374-E5C4ED7A-FCFE-4F1B-AF1A-58DFBC8DFF8C> ;\n",
" p:P138 <http://www.wikidata.org/entity/statement/Q2374-42919e13-40e2-f17a-7f10-0390ae1469dc> ;\n",
" p:P1476 <http://www.wikidata.org/entity/statement/Q2374-4f1f739f-4fa0-1413-f68d-a854b4e2b10a> ;\n",
" p:P1712 <http://www.wikidata.org/entity/statement/Q2374-b45613f5-418a-b6ee-9733-9b11fc58c2c5> ;\n",
" p:P1733 <http://www.wikidata.org/entity/statement/Q2374-b9420b21-4f85-a012-033c-dd6856ca63b5> ;\n",
" p:P178 <http://www.wikidata.org/entity/statement/q2374-04C1F298-5F3D-4220-8714-B0C4587A0282>,\n",
" <http://www.wikidata.org/entity/statement/q2374-66140209-9732-4C37-BFC4-BDB02A5D0803>,\n",
" <http://www.wikidata.org/entity/statement/q2374-E713580E-6144-484C-9A86-42B3D7829ED3> ;\n",
" p:P179 <http://www.wikidata.org/entity/statement/q2374-425EAD2F-7D43-4101-B33B-D6D7CF22AC19> ;\n",
" p:P1933 <http://www.wikidata.org/entity/statement/Q2374-C2D682C5-5582-4273-83E0-E0DCBA34EBD4> ;\n",
" p:P287 <http://www.wikidata.org/entity/statement/Q2374-404E4A0C-903E-4348-91A1-8B378B4B0AF2>,\n",
" <http://www.wikidata.org/entity/statement/Q2374-f3cd363f-4041-4e73-645b-059dfe9a735a> ;\n",
" p:P31 <http://www.wikidata.org/entity/statement/q2374-C160DF60-C748-4207-B56B-C46EA90003EE> ;\n",
" p:P345 <http://www.wikidata.org/entity/statement/Q2374-77A652CB-F006-4D9C-9F27-59BF9F5882E1> ;\n",
" p:P348 <http://www.wikidata.org/entity/statement/Q2374-C7AB2169-2E9A-488E-AB36-591790B96996> ;\n",
" p:P3984 <http://www.wikidata.org/entity/statement/Q2374-c0c7b27b-4cb7-260a-0db7-4fb2ef8d0776> ;\n",
" p:P400 <http://www.wikidata.org/entity/statement/Q2374-EB3D5380-EC39-4528-9417-9C4CBD125FDB>,\n",
" <http://www.wikidata.org/entity/statement/q2374-3970c8fb-4139-6452-e5f1-c90eef0c2cdf> ;\n",
" p:P404 <http://www.wikidata.org/entity/statement/q2374-1CAA47C8-482A-4C28-8078-05636FBD9CF4>,\n",
" <http://www.wikidata.org/entity/statement/q2374-34E775D5-88C3-4513-858D-CE01DCE42798> ;\n",
" p:P407 <http://www.wikidata.org/entity/statement/Q2374-C9E50C55-EB49-450B-A2ED-9EFD32ADF6DE> ;\n",
" p:P437 <http://www.wikidata.org/entity/statement/Q2374-2DFA500D-21D9-4748-A5A7-CB57CC54E332>,\n",
" <http://www.wikidata.org/entity/statement/Q2374-d12bda6a-4382-2c53-658d-64f557fd505c> ;\n",
" p:P4467 <http://www.wikidata.org/entity/statement/Q2374-a2e171c0-49a4-7445-5747-2f978003c910> ;\n",
" p:P479 <http://www.wikidata.org/entity/statement/Q2374-79c3887a-4b41-dc07-6e62-7dae438d97fc>,\n",
" <http://www.wikidata.org/entity/statement/Q2374-f27dc9b6-40ee-b343-ba6a-41c121d216e6> ;\n",
" p:P495 <http://www.wikidata.org/entity/statement/Q2374-4b6efcdd-487c-b148-b84e-64b31f9c24a7> ;\n",
" p:P5247 <http://www.wikidata.org/entity/statement/Q2374-1537c200-4c11-44db-0b98-e2c1dc107e01> ;\n",
" p:P527 <http://www.wikidata.org/entity/statement/Q2374-3b89c125-4a86-3982-eadb-736cb004b116>,\n",
" <http://www.wikidata.org/entity/statement/Q2374-9500f0ed-4254-d808-2741-9cf4a1c29050> ;\n",
" p:P57 <http://www.wikidata.org/entity/statement/Q2374-84179DF9-165B-49BD-BBF8-E7CBDFCB7AAD> ;\n",
" p:P577 <http://www.wikidata.org/entity/statement/Q2374-65964a78-4118-284e-916b-7ad483d29cf1>,\n",
" <http://www.wikidata.org/entity/statement/Q2374-91C6C335-A8C2-4A55-B37E-F3BBC888AAB7> ;\n",
" p:P5794 <http://www.wikidata.org/entity/statement/Q2374-76cd64e6-450d-cd7f-7289-b7698f5af7c6> ;\n",
" p:P6337 <http://www.wikidata.org/entity/statement/Q2374-2A621FA9-6D9E-4495-A964-FC22EABD8C12> ;\n",
" p:P646 <http://www.wikidata.org/entity/statement/Q2374-A1EED53E-942A-4CD3-9145-98A04A1B5119> ;\n",
" p:P856 <http://www.wikidata.org/entity/statement/Q2374-6F2AE23E-12BD-418B-BBC0-34A5B0C2DEF4> ;\n",
" p:P86 <http://www.wikidata.org/entity/statement/Q2374-93CE4466-DE8C-4CC2-B3F7-9D67B8AE26B8> ;\n",
" ns3:P646 <http://g.co/kg/m/01tl18> ;\n",
" wdt:P1072 <http://www.wikidata.org/entity/Q27979546>,\n",
" <http://www.wikidata.org/entity/Q27979555> ;\n",
" wdt:P1073 <http://www.wikidata.org/entity/Q27979546>,\n",
" <http://www.wikidata.org/entity/Q27979555> ;\n",
" wdt:P123 <http://www.wikidata.org/entity/Q1782700>,\n",
" <http://www.wikidata.org/entity/Q207922>,\n",
" <http://www.wikidata.org/entity/Q3123991>,\n",
" <http://www.wikidata.org/entity/Q738135> ;\n",
" wdt:P136 <http://www.wikidata.org/entity/Q1610017>,\n",
" <http://www.wikidata.org/entity/Q2176159>,\n",
" <http://www.wikidata.org/entity/Q3139142>,\n",
" <http://www.wikidata.org/entity/Q472055>,\n",
" <http://www.wikidata.org/entity/Q603555> ;\n",
" wdt:P138 <http://www.wikidata.org/entity/Q92616> ;\n",
" wdt:P1476 \"Sid Meier's Civilization III\" ;\n",
" wdt:P1712 \"game/pc/sid-meiers-civilization-iii\" ;\n",
" wdt:P1733 \"3910\" ;\n",
" wdt:P178 <http://www.wikidata.org/entity/Q3123991>,\n",
" <http://www.wikidata.org/entity/Q738135>,\n",
" <http://www.wikidata.org/entity/Q959759> ;\n",
" wdt:P179 <http://www.wikidata.org/entity/Q1868663> ;\n",
" wdt:P1933 \"sid-meiers-civilization-iii\" ;\n",
" wdt:P287 <http://www.wikidata.org/entity/Q5586418>,\n",
" <http://www.wikidata.org/entity/Q9284930> ;\n",
" wdt:P31 <http://www.wikidata.org/entity/Q7889> ;\n",
" wdt:P345 \"tt0299682\" ;\n",
" wdt:P348 \"1.29f\" ;\n",
" wdt:P3984 \"civ3\" ;\n",
" wdt:P400 <http://www.wikidata.org/entity/Q1406>,\n",
" <http://www.wikidata.org/entity/Q14116> ;\n",
" wdt:P404 <http://www.wikidata.org/entity/Q208850>,\n",
" <http://www.wikidata.org/entity/Q6895044> ;\n",
" wdt:P407 <http://www.wikidata.org/entity/Q1860> ;\n",
" wdt:P437 <http://www.wikidata.org/entity/Q337535>,\n",
" <http://www.wikidata.org/entity/Q7982> ;\n",
" wdt:P4467 \"Sid Meier's Civilization III\" ;\n",
" wdt:P479 <http://www.wikidata.org/entity/Q250>,\n",
" <http://www.wikidata.org/entity/Q7987> ;\n",
" wdt:P495 <http://www.wikidata.org/entity/Q30> ;\n",
" wdt:P5247 \"3030-1594\" ;\n",
" wdt:P527 <http://www.wikidata.org/entity/Q2633010>,\n",
" <http://www.wikidata.org/entity/Q548085> ;\n",
" wdt:P57 <http://www.wikidata.org/entity/Q92616> ;\n",
" wdt:P577 \"2001-10-30T00:00:00+00:00\"^^xsd:dateTime,\n",
" \"2006-10-25T00:00:00+00:00\"^^xsd:dateTime ;\n",
" wdt:P5794 \"sid-meier-s-civilization-iii\" ;\n",
" wdt:P6337 \"Civilization_III\" ;\n",
" wdt:P646 \"/m/01tl18\" ;\n",
" wdt:P856 <http://www.civ3.com/> ;\n",
" wdt:P86 <http://www.wikidata.org/entity/Q7357913> .\n",
"\n",
"\n"
]
}
],
"source": [
"permagraph = None\n",
"\n",
"def persistent_slurper(rdf: str) -> SlurpyGraph:\n",
" global permagraph\n",
" permagraph = SlurpyGraph(rdf)\n",
" return permagraph\n",
"\n",
"shex_evaluator.SlurpyGraph = persistent_slurper\n",
"\n",
"sparql_query = \"\"\"\n",
"PREFIX wdt: <http://www.wikidata.org/prop/direct/>\n",
"PREFIX wd: <http://www.wikidata.org/entity/>\n",
"\n",
"SELECT ?item WHERE { ?item (wdt:P31/wdt:P279*) wd:Q7397.} LIMIT 100\n",
"\"\"\"\n",
"\n",
"\n",
"x = [\"-ss\",\n",
" \"-sq\", sparql_query,\n",
" \"http://query.wikidata.org/sparql\",\n",
" \"https://raw.githubusercontent.com/shexSpec/schemas/master/Wikidata/DigitalPreservation/SWIB/software.shex\",\n",
" \"--stopafter\", \"1\",\n",
" \"-ps\"]\n",
"shexeval(x)\n",
"print()\n",
"print(\"RESULT Graph:\")\n",
"print(permagraph.serialize(format=\"turtle\").decode())\n"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.2"
}
},
"nbformat": 4,
"nbformat_minor": 2
}
5 changes: 5 additions & 0 deletions tests/test_cli/input/sparql.sparql
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PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX dbgraph: <https://w3id.org/data2services/graph/biolink/drugbank>
PREFIX drugbank: <http://identifiers.org/drugbank:>

SELECT ?g ?s ?p ?o {graph dbgraph: {?s rdf:type ?o}}

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