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Fix for issue #41 -- don't ignore CLOSED error
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This issue only appeared when using the `evaluate` call.
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hsolbrig committed Mar 5, 2019
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2 changes: 2 additions & 0 deletions README.md
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[![DOI](https://zenodo.org/badge/116042298.svg)](https://zenodo.org/badge/latestdoi/116042298)

https://mybinder.org/v2/gh/hsolbrig/pyshex/master


This package is a reasonably literal implementation of the [Shape Expressions Language 2.0](http://shex.io/shex-semantics/). It can parse and "execute" ShExC and ShExJ source.
Expand Down Expand Up @@ -36,6 +37,7 @@ This package is a reasonably literal implementation of the [Shape Expressions La
* 0.7.2 -- Upgrade error reporting
* 0.7.3 -- Report using namespaces, enhance PrefixLib to inject into a module
* 0.7.4 -- Added '-ps', '-pr', '-gn', '-pb' options to CLI
* 0.7.5 -- Fix CLOSED issue in evaluate call (issue 41)

## Installation
```bash
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4 changes: 2 additions & 2 deletions notebooks/CLI.ipynb
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Expand Up @@ -76,11 +76,11 @@
{
"ename": "SystemExit",
"evalue": "0",
"output_type": "error",
"traceback": [
"An exception has occurred, use %tb to see the full traceback.\n",
"\u001b[0;31mSystemExit\u001b[0m\u001b[0;31m:\u001b[0m 0\n"
]
],
"output_type": "error"
}
],
"source": [
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Expand Up @@ -73,7 +73,7 @@ def satisfiesShape(cntxt: Context, n: Node, S: ShExJ.Shape, c: DebugContext) ->
f"{len(non_matchables)} non-matching triples on a closed shape"))
print(c.i(1, "", list(non_matchables)))
print()
rslt = False
return False


# Evaluate the actual expression. Start assuming everything matches...
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2 changes: 1 addition & 1 deletion setup.py
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Expand Up @@ -8,7 +8,7 @@

setup(
name='PyShEx',
version='0.7.4',
version='0.7.5',
packages = find_packages(exclude=['tests']),
url="http://github.com/hsolbrig/PyShEx",
license='Apache 2.0',
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2 changes: 1 addition & 1 deletion tests/__init__.py
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refresh_files = False

# True means skip the disease test
skip_diseases = False
skip_diseases = True

datadir = os.path.abspath(os.path.join(os.path.dirname(__file__), 'data'))

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4,052 changes: 2,026 additions & 2,026 deletions tests/data/earl_report.ttl

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221 changes: 79 additions & 142 deletions tests/test_cli/output/evaluate/dbsparql6

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16 changes: 8 additions & 8 deletions tests/test_issues/data/wikidata/disease/Q36855.ttl
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@@ -1,8 +1,8 @@
@prefix do: <http://purl.obolibrary.org/obo/DOID_> .
@prefix doio: <http://identifiers.org/doid/> .
@prefix mir: <http://www.ebi.ac.uk/miriam/main/collections/> .
@prefix ns1: <http://www.wikidata.org/prop/direct-normalized/> .
@prefix ns2: <http://wikiba.se/ontology#> .
@prefix ns1: <http://wikiba.se/ontology#> .
@prefix ns2: <http://www.wikidata.org/prop/direct-normalized/> .
@prefix p: <http://www.wikidata.org/prop/> .
@prefix pq: <http://www.wikidata.org/prop/qualifier/> .
@prefix pr: <http://www.wikidata.org/prop/reference/> .
Expand Down Expand Up @@ -116,10 +116,10 @@ wd:Q36855 rdfs:label "Cúm lợn",
"مرض جهاز تنفسي",
"സൂക്ഷ്മാണുവിനാൽ ആതിഥേയജീവിയിൽ ഉണ്ടാവുന്ന രോഗബാധ" ;
schema:version 853810717 ;
ns2:identifiers 10 ;
ns2:sitelinks 98 ;
ns2:statements 23 ;
ns2:timestamp "2019-02-08T13:09:31+00:00"^^xsd:dateTime ;
ns1:identifiers 10 ;
ns1:sitelinks 98 ;
ns1:statements 23 ;
ns1:timestamp "2019-02-08T13:09:31+00:00"^^xsd:dateTime ;
skos:altLabel "2009 H1N1 grip salgını",
"A",
"A(H1N1)",
Expand Down Expand Up @@ -289,8 +289,8 @@ wd:Q36855 rdfs:label "Cúm lợn",
p:P699 <http://www.wikidata.org/entity/statement/Q36855-251AFEFE-9357-4819-9345-8658A5817D72>,
<http://www.wikidata.org/entity/statement/Q36855-C725609A-6F51-4A2F-B451-897C76F77DCD> ;
p:P910 <http://www.wikidata.org/entity/statement/Q36855-FF9EC242-3136-4C46-8597-0772CDD86794> ;
ns1:P227 <http://d-nb.info/gnd/7679861-6> ;
ns1:P646 <http://g.co/kg/m/057c6k> ;
ns2:P227 <http://d-nb.info/gnd/7679861-6> ;
ns2:P646 <http://g.co/kg/m/057c6k> ;
wdt:P1225 "10644087" ;
wdt:P1296 "0517808" ;
wdt:P1417 "science/swine-flu" ;
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31 changes: 17 additions & 14 deletions tests/test_issues/data/wikidata/disease/Q36956.ttl
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@@ -1,8 +1,8 @@
@prefix do: <http://purl.obolibrary.org/obo/DOID_> .
@prefix doio: <http://identifiers.org/doid/> .
@prefix mir: <http://www.ebi.ac.uk/miriam/main/collections/> .
@prefix ns1: <http://wikiba.se/ontology#> .
@prefix ns2: <http://www.wikidata.org/prop/direct-normalized/> .
@prefix ns1: <http://www.wikidata.org/prop/direct-normalized/> .
@prefix ns2: <http://wikiba.se/ontology#> .
@prefix p: <http://www.wikidata.org/prop/> .
@prefix pq: <http://www.wikidata.org/prop/qualifier/> .
@prefix pr: <http://www.wikidata.org/prop/reference/> .
Expand Down Expand Up @@ -134,10 +134,10 @@ wd:Q36956 rdfs:label "Abïl",
"ᅟinfekta malsano kaŭzata de bakterio",
"らい菌の感染によって起こる病気" ;
schema:version 856153650 ;
ns1:identifiers 36 ;
ns1:sitelinks 121 ;
ns1:statements 96 ;
ns1:timestamp "2019-02-11T22:10:55+00:00"^^xsd:dateTime ;
ns2:identifiers 36 ;
ns2:sitelinks 121 ;
ns2:statements 96 ;
ns2:timestamp "2019-02-11T22:10:55+00:00"^^xsd:dateTime ;
skos:altLabel "Aussatz",
"Aussätzige",
"Bélpoklosság",
Expand Down Expand Up @@ -387,14 +387,14 @@ wd:Q36956 rdfs:label "Abïl",
p:P902 <http://www.wikidata.org/entity/statement/Q36956-227BA989-0DB8-4851-9FA9-8D0B9A5C2CCC> ;
p:P910 <http://www.wikidata.org/entity/statement/Q36956-3CA8A7C7-D284-43C0-BF0F-FE7F4C5D4D1D> ;
p:P935 <http://www.wikidata.org/entity/statement/Q36956-FC3919F8-A2D9-4660-AD53-A3E555AAEF18> ;
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ns2:P486 <http://id.nlm.nih.gov/mesh/D007918> ;
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wdt:P1051 "12585" ;
wdt:P1060 wd:Q15304512 ;
wdt:P1193 1.0,
Expand Down Expand Up @@ -497,6 +497,9 @@ wd:Q36956 rdfs:label "Abïl",
<http://www.wikidata.org/entity/statement/Q36956-1D3F6BDB-83D6-48A7-BE2D-CAD8BDF89494> prov:wasDerivedFrom <http://www.wikidata.org/reference/557ea321a4d4a5ee6ffff781bbbdd07ce0a5f12b> ;
ps:P279 wd:Q3041498 .

<http://www.wikidata.org/entity/statement/Q36956-1E2367F1-AFF6-4C84-A142-D59EA2C6006A> prov:wasDerivedFrom <http://www.wikidata.org/reference/557ea321a4d4a5ee6ffff781bbbdd07ce0a5f12b> ;
ps:P279 wd:Q18556979 .

<http://www.wikidata.org/entity/statement/Q36956-2583C4D4-43BC-4CCB-9D54-4D5C06E276A3> prov:wasDerivedFrom <http://www.wikidata.org/reference/557ea321a4d4a5ee6ffff781bbbdd07ce0a5f12b> ;
ps:P1550 "548" .

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22 changes: 11 additions & 11 deletions tests/test_issues/data/wikidata/disease/Q49989.ttl
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@@ -1,8 +1,8 @@
@prefix do: <http://purl.obolibrary.org/obo/DOID_> .
@prefix doio: <http://identifiers.org/doid/> .
@prefix mir: <http://www.ebi.ac.uk/miriam/main/collections/> .
@prefix ns1: <http://wikiba.se/ontology#> .
@prefix ns2: <http://www.wikidata.org/prop/direct-normalized/> .
@prefix ns1: <http://www.wikidata.org/prop/direct-normalized/> .
@prefix ns2: <http://wikiba.se/ontology#> .
@prefix p: <http://www.wikidata.org/prop/> .
@prefix pq: <http://www.wikidata.org/prop/qualifier/> .
@prefix pr: <http://www.wikidata.org/prop/reference/> .
Expand Down Expand Up @@ -71,10 +71,10 @@ wd:Q49989 rdfs:label "Boala Creutzfeldt-Jacob",
"Наиболее распространенная прионная болезнь",
"退行性神經系統疾病" ;
schema:version 851698859 ;
ns1:identifiers 25 ;
ns1:sitelinks 45 ;
ns1:statements 41 ;
ns1:timestamp "2019-02-05T20:46:37+00:00"^^xsd:dateTime ;
ns2:identifiers 25 ;
ns2:sitelinks 45 ;
ns2:statements 41 ;
ns2:timestamp "2019-02-05T20:46:37+00:00"^^xsd:dateTime ;
skos:altLabel "CJD",
"CJD (Creutzfeldt Jakob disease)",
"CJK",
Expand Down Expand Up @@ -131,11 +131,11 @@ wd:Q49989 rdfs:label "Boala Creutzfeldt-Jacob",
p:P673 <http://www.wikidata.org/entity/statement/q49989-E83E1327-5C13-4B3F-BB49-1DF65926A1EA> ;
p:P699 <http://www.wikidata.org/entity/statement/Q49989-161C34D8-88A3-4C6C-A153-02ED13E38DCF>,
<http://www.wikidata.org/entity/statement/Q49989-DD691227-8D8E-4836-8D6A-3FCDECAB8F62> ;
ns2:P349 <http://id.ndl.go.jp/auth/ndlna/00575235> ;
ns2:P486 <http://id.nlm.nih.gov/mesh/D007562> ;
ns2:P508 <http://purl.org/bncf/tid/54342> ;
ns2:P646 <http://g.co/kg/m/01ptn> ;
ns2:P672 <https://id.nlm.nih.gov/mesh/C10.228.140.380.165>,
ns1:P349 <http://id.ndl.go.jp/auth/ndlna/00575235> ;
ns1:P486 <http://id.nlm.nih.gov/mesh/D007562> ;
ns1:P508 <http://purl.org/bncf/tid/54342> ;
ns1:P646 <http://g.co/kg/m/01ptn> ;
ns1:P672 <https://id.nlm.nih.gov/mesh/C10.228.140.380.165>,
<https://id.nlm.nih.gov/mesh/C10.228.228.800.230> ;
wdt:P1296 "0262750" ;
wdt:P138 wd:Q62474,
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175 changes: 175 additions & 0 deletions tests/test_issues/data/wikidata/disease/Q819207.ttl
Original file line number Diff line number Diff line change
@@ -0,0 +1,175 @@
@prefix do: <http://purl.obolibrary.org/obo/DOID_> .
@prefix doio: <http://identifiers.org/doid/> .
@prefix mir: <http://www.ebi.ac.uk/miriam/main/collections/> .
@prefix ns1: <http://www.wikidata.org/prop/direct-normalized/> .
@prefix ns2: <http://wikiba.se/ontology#> .
@prefix p: <http://www.wikidata.org/prop/> .
@prefix pq: <http://www.wikidata.org/prop/qualifier/> .
@prefix pr: <http://www.wikidata.org/prop/reference/> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix prv: <http://www.wikidata.org/prop/reference/value/> .
@prefix ps: <http://www.wikidata.org/prop/statement/> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix schema: <http://schema.org/> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@prefix wd: <http://www.wikidata.org/entity/> .
@prefix wdt: <http://www.wikidata.org/prop/direct/> .
@prefix xml: <http://www.w3.org/XML/1998/namespace> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

wd:Q819207 rdfs:label "Pseudohipoparatireoidizam",
"Pseudohypoparathyreoidismus",
"pseudohipoparatiroidismo",
"pseudohypoparathyroidism",
"pseudohypoparathyroïdie",
"pseŭdohipoparatiroidismo",
"rzekoma niedoczynność przytarczyc",
"قصور جارات الدرق الكاذب",
"کم‌کاری کاذب غده پاراتیروئید",
"偽性副甲状腺機能低下症",
"거짓부갑상샘저하증" ;
schema:dateModified "2019-03-05T00:26:18+00:00"^^xsd:dateTime ;
schema:description "Krankheit",
"human disease",
"مرض يصيب الإنسان" ;
schema:version 874554328 ;
ns2:identifiers 28 ;
ns2:sitelinks 10 ;
ns2:statements 41 ;
ns2:timestamp "2019-03-05T00:26:22+00:00"^^xsd:dateTime ;
skos:altLabel "osteodystrofia Albrighta",
"zespół Albrighta",
"가부갑상선기능저하증",
"가성 부갑상샘 기능저하증",
"가성부갑상선기능저하증" ;
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ns1:P2581 <http://babelnet.org/rdf/s02883542n> ;
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ns1:P646 <http://g.co/kg/m/09k1w5> ;
ns1:P672 <https://id.nlm.nih.gov/mesh/C05.116.198.709>,
<https://id.nlm.nih.gov/mesh/C16.320.565.618.815>,
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<https://id.nlm.nih.gov/mesh/C18.452.174.766>,
<https://id.nlm.nih.gov/mesh/C18.452.648.618.815> ;
wdt:P1550 "97593" ;
wdt:P1692 "275.49" ;
wdt:P1748 "C99027" ;
wdt:P1995 wd:Q162606 ;
wdt:P2581 "02883542n" ;
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wd:Q55785986 ;
wdt:P2888 <http://identifiers.org/doid/DOID:4184>,
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<http://purl.obolibrary.org/obo/HP_0000852>,
<http://www.orpha.net/ORDO/Orphanet_97593> ;
wdt:P2892 "C0033806" ;
wdt:P31 wd:Q12136,
wd:Q42303753 ;
wdt:P373 "Pseudohypoparathyroidism" ;
wdt:P3827 "pseudohypoparathyroidism" ;
wdt:P3841 "HP:0000852" ;
wdt:P4229 "E20.1" ;
wdt:P4317 "10758" ;
wdt:P486 "D011547" ;
wdt:P492 "603233",
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wdt:P557 "10835",
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wdt:P604 "000364" ;
wdt:P646 "/m/09k1w5" ;
wdt:P672 "C05.116.198.709",
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