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Add phyloref type to phyloreferences #61

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Feb 12, 2021
Merged

Add phyloref type to phyloreferences #61

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a074398
Added phylorefType to Brochu 2003 example.
gaurav Feb 9, 2021
254a36d
Added phyloref type generation and to expected JSON-LD and NQ output.
gaurav Feb 9, 2021
f4476bf
Removed phyloref:MalformedPhyloreference.
gaurav Feb 9, 2021
ce4f352
Added possible phylorefTypes to the JSON Schema.
gaurav Feb 9, 2021
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8 changes: 8 additions & 0 deletions docs/context/development/schema.json
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Expand Up @@ -285,6 +285,14 @@
"description": "The identifier of this clade definition in the Regnum database",
"minLength": 1
},
"phylorefType": {
"description": "The type of this phyloreference.",
"enum": [
"phyloref:PhyloreferenceUsingMaximumClade",
"phyloref:PhyloreferenceUsingMinimumClade",
"phyloref:PhyloreferenceUsingApomorphy"
]
},
"label": {
"type": "string",
"description": "The name or label of this phyloreference."
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17 changes: 15 additions & 2 deletions src/wrappers/PhylorefWrapper.js
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Expand Up @@ -680,13 +680,18 @@ class PhylorefWrapper {
PhylorefWrapper.componentClassesByLabel = {};
phylorefAsJSONLD.hasComponentClass = [];

// The type of this phyloreference.
let calculatedPhylorefType;

// The list of logical expressions generated for this phyloref.
let logicalExpressions = [];

if (internalSpecifiers.length === 0) {
// We can't handle phyloreferences without at least one internal specifier.
phylorefAsJSONLD.malformedPhyloreference = 'No internal specifiers provided';
} else if (externalSpecifiers.length > 0) {
calculatedPhylorefType = 'phyloref:PhyloreferenceUsingMaximumClade';

// If the phyloreference has at least one external specifier, we
// can provide a simplified expression for the internal specifier,
// in the form:
Expand All @@ -711,6 +716,8 @@ class PhylorefWrapper {
);
}
} else {
calculatedPhylorefType = 'phyloref:PhyloreferenceUsingMinimumClade';

// We only have internal specifiers. We therefore need to use the algorithm in
// PhylorefWrapper.createClassExpressionsForInternals() to create this expression.
logicalExpressions = PhylorefWrapper.createClassExpressionsForInternals(
Expand Down Expand Up @@ -772,8 +779,14 @@ class PhylorefWrapper {
}
phylorefAsJSONLD.subClassOf.push('phyloref:Phyloreference');

// Metadata.

// If the this Phyloref has a phylorefType that differs from the calculated
// phyloref type, throw an error.
if (has(phylorefAsJSONLD, 'phylorefType') && phylorefAsJSONLD.phylorefType !== calculatedPhylorefType) {
throw new Error(
`Phyloref ${this.label} has phylorefType set to '${phylorefAsJSONLD.phylorefType}', but it appears to be a '${calculatedPhylorefType}'.`
);
}
phylorefAsJSONLD.subClassOf.push(calculatedPhylorefType);

return phylorefAsJSONLD;
}
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6 changes: 6 additions & 0 deletions test/examples/correct/brochu_2003.json
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Expand Up @@ -45,6 +45,7 @@
"phylorefs": [
{
"label": "Alligatoridae",
"phylorefType": "phyloref:PhyloreferenceUsingMinimumClade",
"definition": "Alligatoridae (Cuvier 1807).\n\nLast common ancestor of Alligator mississippiensis and Caiman crocodilus and all of its descendents.",
"definitionSource": {
"type": "article",
Expand Down Expand Up @@ -121,6 +122,7 @@
},
{
"label": "Alligatorinae",
"phylorefType": "phyloref:PhyloreferenceUsingMaximumClade",
"definition": "Alligatorinae (Kälin 1940).\n\nAlligator mississippiensis and all crocodylians closer to it than to Caiman crocodilus.",
"definitionSource": {
"type": "article",
Expand Down Expand Up @@ -203,6 +205,7 @@
},
{
"label": "Caimaninae",
"phylorefType": "phyloref:PhyloreferenceUsingMaximumClade",
"definition": "Caimaninae (Norell 1988).\n\nCaiman crocodilus and all crocodylians closer to it than to Alligator mississippiensis.",
"definitionSource": {
"type": "article",
Expand Down Expand Up @@ -284,6 +287,7 @@
},
{
"label": "Crocodyloidea",
"phylorefType": "phyloref:PhyloreferenceUsingMaximumClade",
"definition": "Crocodyloidea (Fitzinger 1826).\n\nCrocodylus niloticus and all crocodylians closer to it than to Alligator mississippiensis or Gavialis gangeticus.",
"internalSpecifiers": [
{
Expand Down Expand Up @@ -343,6 +347,7 @@
},
{
"label": "Crocodylidae",
"phylorefType": "phyloref:PhyloreferenceUsingMinimumClade",
"definition": "Crocodylidae (Cuvier 1807). Definition dependent on phylogenetic context.\n\nLast common ancestor of Crocodylus niloticus, Osteolaemus tetraspis, and Tomistoma schlegelii and all of its descendents.",
"definitionSource": {
"type": "article",
Expand Down Expand Up @@ -431,6 +436,7 @@
},
{
"label": "Diplocynodontinae",
"phylorefType": "phyloref:PhyloreferenceUsingMaximumClade",
"definition": "Diplocynodontinae (Brochu 1999).\n\nDiplocynodon ratelii and all crocodylians closer to it than to Alligator mississippiensis.",
"definitionSource": {
"type": "article",
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24 changes: 18 additions & 6 deletions test/examples/correct/brochu_2003.jsonld
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Expand Up @@ -1286,6 +1286,7 @@
"phylorefs": [
{
"label": "Alligatoridae",
"phylorefType": "phyloref:PhyloreferenceUsingMinimumClade",
"definition": "Alligatoridae (Cuvier 1807).\n\nLast common ancestor of Alligator mississippiensis and Caiman crocodilus and all of its descendents.",
"definitionSource": {
"type": "article",
Expand Down Expand Up @@ -1403,11 +1404,13 @@
}
},
"subClassOf": [
"phyloref:Phyloreference"
"phyloref:Phyloreference",
"phyloref:PhyloreferenceUsingMinimumClade"
]
},
{
"label": "Alligatorinae",
"phylorefType": "phyloref:PhyloreferenceUsingMaximumClade",
"definition": "Alligatorinae (Kälin 1940).\n\nAlligator mississippiensis and all crocodylians closer to it than to Caiman crocodilus.",
"definitionSource": {
"type": "article",
Expand Down Expand Up @@ -1527,11 +1530,13 @@
]
},
"subClassOf": [
"phyloref:Phyloreference"
"phyloref:Phyloreference",
"phyloref:PhyloreferenceUsingMaximumClade"
]
},
{
"label": "Caimaninae",
"phylorefType": "phyloref:PhyloreferenceUsingMaximumClade",
"definition": "Caimaninae (Norell 1988).\n\nCaiman crocodilus and all crocodylians closer to it than to Alligator mississippiensis.",
"definitionSource": {
"type": "article",
Expand Down Expand Up @@ -1650,11 +1655,13 @@
]
},
"subClassOf": [
"phyloref:Phyloreference"
"phyloref:Phyloreference",
"phyloref:PhyloreferenceUsingMaximumClade"
]
},
{
"label": "Crocodyloidea",
"phylorefType": "phyloref:PhyloreferenceUsingMaximumClade",
"definition": "Crocodyloidea (Fitzinger 1826).\n\nCrocodylus niloticus and all crocodylians closer to it than to Alligator mississippiensis or Gavialis gangeticus.",
"internalSpecifiers": [
{
Expand Down Expand Up @@ -1934,11 +1941,13 @@
}
],
"subClassOf": [
"phyloref:Phyloreference"
"phyloref:Phyloreference",
"phyloref:PhyloreferenceUsingMaximumClade"
]
},
{
"label": "Crocodylidae",
"phylorefType": "phyloref:PhyloreferenceUsingMinimumClade",
"definition": "Crocodylidae (Cuvier 1807). Definition dependent on phylogenetic context.\n\nLast common ancestor of Crocodylus niloticus, Osteolaemus tetraspis, and Tomistoma schlegelii and all of its descendents.",
"definitionSource": {
"type": "article",
Expand Down Expand Up @@ -2682,11 +2691,13 @@
}
],
"subClassOf": [
"phyloref:Phyloreference"
"phyloref:Phyloreference",
"phyloref:PhyloreferenceUsingMinimumClade"
]
},
{
"label": "Diplocynodontinae",
"phylorefType": "phyloref:PhyloreferenceUsingMaximumClade",
"definition": "Diplocynodontinae (Brochu 1999).\n\nDiplocynodon ratelii and all crocodylians closer to it than to Alligator mississippiensis.",
"definitionSource": {
"type": "article",
Expand Down Expand Up @@ -2806,7 +2817,8 @@
]
},
"subClassOf": [
"phyloref:Phyloreference"
"phyloref:Phyloreference",
"phyloref:PhyloreferenceUsingMaximumClade"
]
}
],
Expand Down
6 changes: 6 additions & 0 deletions test/examples/correct/brochu_2003.nq
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Expand Up @@ -261,6 +261,7 @@
<http://example.org/brochu_2003.json#phyloref0> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Class> .
<http://example.org/brochu_2003.json#phyloref0> <http://www.w3.org/2000/01/rdf-schema#label> "Alligatoridae" .
<http://example.org/brochu_2003.json#phyloref0> <http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://ontology.phyloref.org/phyloref.owl#Phyloreference> .
<http://example.org/brochu_2003.json#phyloref0> <http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://ontology.phyloref.org/phyloref.owl#PhyloreferenceUsingMinimumClade> .
<http://example.org/brochu_2003.json#phyloref0> <http://www.w3.org/2002/07/owl#equivalentClass> _:b141 .
<http://example.org/brochu_2003.json#phyloref1> <http://purl.obolibrary.org/obo/IAO_0000115> "Alligatorinae (Kälin 1940).\n\nAlligator mississippiensis and all crocodylians closer to it than to Caiman crocodilus." .
<http://example.org/brochu_2003.json#phyloref1> <http://purl.obolibrary.org/obo/IAO_0000119> _:b149 .
Expand All @@ -270,6 +271,7 @@
<http://example.org/brochu_2003.json#phyloref1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Class> .
<http://example.org/brochu_2003.json#phyloref1> <http://www.w3.org/2000/01/rdf-schema#label> "Alligatorinae" .
<http://example.org/brochu_2003.json#phyloref1> <http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://ontology.phyloref.org/phyloref.owl#Phyloreference> .
<http://example.org/brochu_2003.json#phyloref1> <http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://ontology.phyloref.org/phyloref.owl#PhyloreferenceUsingMaximumClade> .
<http://example.org/brochu_2003.json#phyloref1> <http://www.w3.org/2002/07/owl#equivalentClass> _:b156 .
<http://example.org/brochu_2003.json#phyloref2> <http://purl.obolibrary.org/obo/IAO_0000115> "Caimaninae (Norell 1988).\n\nCaiman crocodilus and all crocodylians closer to it than to Alligator mississippiensis." .
<http://example.org/brochu_2003.json#phyloref2> <http://purl.obolibrary.org/obo/IAO_0000119> _:b163 .
Expand All @@ -279,6 +281,7 @@
<http://example.org/brochu_2003.json#phyloref2> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Class> .
<http://example.org/brochu_2003.json#phyloref2> <http://www.w3.org/2000/01/rdf-schema#label> "Caimaninae" .
<http://example.org/brochu_2003.json#phyloref2> <http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://ontology.phyloref.org/phyloref.owl#Phyloreference> .
<http://example.org/brochu_2003.json#phyloref2> <http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://ontology.phyloref.org/phyloref.owl#PhyloreferenceUsingMaximumClade> .
<http://example.org/brochu_2003.json#phyloref2> <http://www.w3.org/2002/07/owl#equivalentClass> _:b170 .
<http://example.org/brochu_2003.json#phyloref3> <http://purl.obolibrary.org/obo/IAO_0000115> "Crocodyloidea (Fitzinger 1826).\n\nCrocodylus niloticus and all crocodylians closer to it than to Alligator mississippiensis or Gavialis gangeticus." .
<http://example.org/brochu_2003.json#phyloref3> <http://purl.org/spar/pso/holdsStatusInTime> _:b177 .
Expand All @@ -294,6 +297,7 @@
<http://example.org/brochu_2003.json#phyloref3> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Class> .
<http://example.org/brochu_2003.json#phyloref3> <http://www.w3.org/2000/01/rdf-schema#label> "Crocodyloidea" .
<http://example.org/brochu_2003.json#phyloref3> <http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://ontology.phyloref.org/phyloref.owl#Phyloreference> .
<http://example.org/brochu_2003.json#phyloref3> <http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://ontology.phyloref.org/phyloref.owl#PhyloreferenceUsingMaximumClade> .
<http://example.org/brochu_2003.json#phyloref3_component1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Class> .
<http://example.org/brochu_2003.json#phyloref3_component1> <http://www.w3.org/2000/01/rdf-schema#label> "(Crocodylus niloticus ~ Alligator mississippiensis)" .
<http://example.org/brochu_2003.json#phyloref3_component1> <http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://ontology.phyloref.org/phyloref.owl#PhyloreferenceUsingMaximumClade> .
Expand Down Expand Up @@ -340,6 +344,7 @@
<http://example.org/brochu_2003.json#phyloref4> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Class> .
<http://example.org/brochu_2003.json#phyloref4> <http://www.w3.org/2000/01/rdf-schema#label> "Crocodylidae" .
<http://example.org/brochu_2003.json#phyloref4> <http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://ontology.phyloref.org/phyloref.owl#Phyloreference> .
<http://example.org/brochu_2003.json#phyloref4> <http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://ontology.phyloref.org/phyloref.owl#PhyloreferenceUsingMinimumClade> .
<http://example.org/brochu_2003.json#phyloref4_component1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Class> .
<http://example.org/brochu_2003.json#phyloref4_component1> <http://www.w3.org/2000/01/rdf-schema#label> "(Crocodylus niloticus & Osteolaemus tetraspis & Tomistoma schlegelii)" .
<http://example.org/brochu_2003.json#phyloref4_component1> <http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://example.org/brochu_2003.json#phyloref4> .
Expand Down Expand Up @@ -393,6 +398,7 @@
<http://example.org/brochu_2003.json#phyloref5> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Class> .
<http://example.org/brochu_2003.json#phyloref5> <http://www.w3.org/2000/01/rdf-schema#label> "Diplocynodontinae" .
<http://example.org/brochu_2003.json#phyloref5> <http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://ontology.phyloref.org/phyloref.owl#Phyloreference> .
<http://example.org/brochu_2003.json#phyloref5> <http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://ontology.phyloref.org/phyloref.owl#PhyloreferenceUsingMaximumClade> .
<http://example.org/brochu_2003.json#phyloref5> <http://www.w3.org/2002/07/owl#equivalentClass> _:b359 .
_:b0 <http://purl.org/dc/terms/bibliographicCitation> "Christopher A. Brochu (2003) Phylogenetic approaches toward crocodylian history Annual Review of Earth and Planetary Sciences 31 fig 1 doi: 10.1146/annurev.earth.31.100901.141308 URL: https://www.annualreviews.org/doi/10.1146/annurev.earth.31.100901.141308" .
_:b0 <http://purl.org/dc/terms/title> "Phylogenetic approaches toward crocodylian history" .
Expand Down