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Template Rework #403

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merged 48 commits into from
Jun 25, 2019
Merged

Template Rework #403

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99927b2
First pass at template rework
Nov 5, 2018
a44b33b
Add tests for new template operation
Nov 7, 2018
e10c681
Update tests and docs for template
Nov 15, 2018
9e19d14
Add more details to template docs
Nov 15, 2018
4bbe022
Merge remote-tracking branch 'upstream/master' into template
Nov 15, 2018
364338c
Merge branch 'master' of https://github.com/ontodev/robot into template
jamesaoverton Mar 1, 2019
2e22b93
Partial fix from code review
Mar 1, 2019
0449588
Code review fixes, fix equivalent classes bug
Mar 2, 2019
df364ba
Remove old error message
Mar 2, 2019
2c3157a
Fix test cases for LABEL change
Mar 2, 2019
a62177c
Update docs
Mar 4, 2019
ec985ef
Add note to manchester error
Mar 4, 2019
59f68e0
Collect all exceptions and fail at the end
Mar 15, 2019
735fdec
Fix backwards compatibility
Mar 15, 2019
4c72438
Remove extra file
Mar 18, 2019
1aeeab7
Rework exceptions
Mar 18, 2019
49e5ccf
Rework --force
Mar 18, 2019
b4d8b28
Fix property assertion template strings
Apr 12, 2019
ea1252f
Add custom label-property option
May 6, 2019
a6bcc92
Use checker to resolve label property
May 7, 2019
8020ffb
Fix null pointer exception
May 7, 2019
4c0cc11
Revision updates
May 8, 2019
da2ab0b
Allow LABEL keyword to create labels
May 8, 2019
1633aad
Fix closing tag
May 8, 2019
80d7f1f
Change expression template strings
May 8, 2019
e94bc49
Fix property parsing bugs
May 9, 2019
0d1da47
Fix label checking
May 9, 2019
f93d2ab
Revert example files
Jun 6, 2019
77a1cf8
Remove extra white space
Jun 6, 2019
754b3a8
Remove extra newline
Jun 6, 2019
627c139
Remove extra newline
Jun 6, 2019
0ae4528
Merge branch 'master' into template
Jun 12, 2019
57ffd6b
Make ECs separate equivalent class statements
Jun 12, 2019
f17aa7f
Fix doc for EC
Jun 12, 2019
291bcda
Revise template docs
jamesaoverton Jun 12, 2019
962831b
Add CHARACTERISTIC for properties
Jun 13, 2019
e318d35
Add error docs
Jun 13, 2019
6d59871
Fix NI documentation
Jun 18, 2019
02fbd5d
Merge branch 'master' into template
Jun 18, 2019
f895de7
Code review updates
Jun 18, 2019
bdb38a3
Do not use single quotes for properties
Jun 18, 2019
6aebb31
Add test with new template strings
Jun 18, 2019
f51d8a4
Fix issue with new labels from multiple templates
Jun 19, 2019
d23e83c
Fix type resolution
Jun 19, 2019
3376622
Update tests for legacy and new formats
Jun 20, 2019
72c71d8
Remove import
Jun 20, 2019
94665c4
Remove unused var
Jun 21, 2019
4051527
Fix Javadocs
jamesaoverton Jun 25, 2019
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4 changes: 2 additions & 2 deletions docs/examples/reasoned.owl
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
<?xml version="1.0"?>
<rdf:RDF xmlns="http://purl.obolibrary.org/obo/go.owl#"
xml:base="http://purl.obolibrary.org/obo/go.owl"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:xml="http://www.w3.org/XML/1998/namespace"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
Expand Down Expand Up @@ -256,5 +256,5 @@



<!-- Generated by the OWL API (version 0.0.1-SNAPSHOT) https://github.com/owlcs/owlapi -->
<!-- Generated by the OWL API (version 4.5.6) https://github.com/owlcs/owlapi -->

11 changes: 6 additions & 5 deletions docs/examples/template.csv
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@@ -1,5 +1,6 @@
ID,Label,Definition,Definition Source,See Also,Editor,RDF Type,Class Type,Parent IRI
ID,A rdfs:label,A IAO:0000115,A IAO:0000119,AI rdfs:seeAlso,A IAO:0000117,TYPE,CLASS_TYPE,CI
ex:F344N,F 344/N,An inbred strain of rat used in many scientific investigations.,James A. Overton,http://www.informatics.jax.org/external/festing/rat/docs/F344.shtml,James A. Overton,owl:Class,subclass,NCBITaxon:10116
ex:B6C3F1,B6C3F1,An inbred strain of mouse used in many scientific investigations.,James A. Overton,http://jaxmice.jax.org/strain/100010.html,James A. Overton,owl:Class,subclass,NCBITaxon:10090
ex:rat-1234,rat 1234,,,F 344/N,,ex:F344N,,
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ID,Label,Definition,Definition Source,See Also,Editor,Type,Parent Class,Disjoint Class,Domain,Range,Individual Weight
ID,A rdfs:label,A IAO:0000115,>A IAO:0000119,AI rdfs:seeAlso,A IAO:0000117,TYPE,SC %,DC %,DOMAIN,RANGE,I weight in kilograms
ex:F344N,F 344/N,An inbred strain of rat used in many scientific investigations.,James A. Overton,http://www.informatics.jax.org/external/festing/rat/docs/F344.shtml,James A. Overton,class,NCBITaxon:10116,,,,
ex:B6C3F1,B6C3F1,An inbred strain of mouse used in many scientific investigations.,James A. Overton,http://jaxmice.jax.org/strain/100010.html,James A. Overton,class,NCBITaxon:10090,F 344/N,,,
ex:propery-1,weight in kilograms,Weight of a mouse or rat in kilograms (kg).,Rebecca C Jackson,,Rebecca C Jackson,data property,,,'F 344/N' or B6C3F1,xsd:decimal,
ex:rat-1234,rat 1234,,,,,F 344/N,,,,,0.2^^xsd:decimal
54 changes: 48 additions & 6 deletions docs/examples/template.owl
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Expand Up @@ -6,7 +6,8 @@
xmlns:xml="http://www.w3.org/XML/1998/namespace"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:obo="http://purl.obolibrary.org/obo/">
xmlns:obo="http://purl.obolibrary.org/obo/"
xmlns:example="http://example.com/">
<owl:Ontology rdf:about="https://github.com/ontodev/robot/examples/template.owl"/>


Expand Down Expand Up @@ -40,9 +41,39 @@



<!-- http://www.w3.org/1999/02/22-rdf-syntax-ns#type -->
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Data properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->

<owl:AnnotationProperty rdf:about="http://www.w3.org/1999/02/22-rdf-syntax-ns#type"/>



<!-- http://example.com/propery-1 -->

<owl:DatatypeProperty rdf:about="http://example.com/propery-1">
<rdfs:domain>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://example.com/B6C3F1"/>
<rdf:Description rdf:about="http://example.com/F344N"/>
</owl:unionOf>
</owl:Class>
</rdfs:domain>
<rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#decimal"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Weight of a mouse or rat in kilograms (kg).</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Rebecca C Jackson</obo:IAO_0000117>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">weight in kilograms</rdfs:label>
</owl:DatatypeProperty>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://example.com/propery-1"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Weight of a mouse or rat in kilograms (kg).</owl:annotatedTarget>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Rebecca C Jackson</obo:IAO_0000119>
</owl:Axiom>



Expand All @@ -61,12 +92,18 @@

<owl:Class rdf:about="http://example.com/B6C3F1">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_10090"/>
<owl:disjointWith rdf:resource="http://example.com/F344N"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An inbred strain of mouse used in many scientific investigations.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">James A. Overton</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">James A. Overton</obo:IAO_0000119>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">B6C3F1</rdfs:label>
<rdfs:seeAlso rdf:resource="http://jaxmice.jax.org/strain/100010.html"/>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://example.com/B6C3F1"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An inbred strain of mouse used in many scientific investigations.</owl:annotatedTarget>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">James A. Overton</obo:IAO_0000119>
</owl:Axiom>



Expand All @@ -76,10 +113,15 @@
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_10116"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An inbred strain of rat used in many scientific investigations.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">James A. Overton</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">James A. Overton</obo:IAO_0000119>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">F 344/N</rdfs:label>
<rdfs:seeAlso rdf:resource="http://www.informatics.jax.org/external/festing/rat/docs/F344.shtml"/>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://example.com/F344N"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An inbred strain of rat used in many scientific investigations.</owl:annotatedTarget>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">James A. Overton</obo:IAO_0000119>
</owl:Axiom>



Expand Down Expand Up @@ -110,8 +152,8 @@

<owl:NamedIndividual rdf:about="http://example.com/rat-1234">
<rdf:type rdf:resource="http://example.com/F344N"/>
<example:propery-1 rdf:datatype="http://www.w3.org/2001/XMLSchema#decimal">0.2</example:propery-1>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">rat 1234</rdfs:label>
<rdfs:seeAlso rdf:resource="http://example.com/F344N"/>
</owl:NamedIndividual>
</rdf:RDF>

Expand Down
2 changes: 1 addition & 1 deletion docs/examples/uberon_template.csv
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@@ -1,4 +1,4 @@
ID,Label,Definition,Definition Source,See Also,Editor,RDF Type,Class Type,Parent IRI
ID,A rdfs:label,A IAO:0000115,A IAO:0000119,AI rdfs:seeAlso,A IAO:0000117,TYPE,CLASS_TYPE,CI
UBERON:0000995,brain,The brain is the center of the nervous system in all vertebrate...,UBERON,http://en.wikipedia.org/wiki/Brain,Becky Tauber,owl:Class,subclass,UBERON:0000062
UBERON:0000211,ligament,Dense regular connective tissue...,UBERON,http://purl.obolibrary.org/obo/go/references/0000034,Becky Tauber,owl:Class,subclass,UBERON:0000062
UBERON:0000211,ligament,Dense regular connective tissue...,UBERON,http://purl.obolibrary.org/obo/go/references/0000034,Becky Tauber,owl:Class,subclass,UBERON:0000062
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