refactor(wip): Upgrade to tawny-owl 2.3.3 and BFO 2020

build.gradle

@@ -19,7 +19,7 @@ dependencies {
     implementation 'org.clojure:clojure:1.11.1'
     testRuntimeOnly 'dev.clojurephant:jovial:0.4.2'
     devImplementation 'org.clojure:tools.namespace:1.3.0'
-    implementation 'uk.org.russet:tawny-owl:1.4.0'
+    implementation 'uk.org.russet:tawny-owl:2.3.3'
     implementation 'danlentz:clj-uuid:0.1.6'
 }
 

src/main/clojure/de/halbordnung/ontologies/tqme/base.clj

@@ -4,34 +4,44 @@
   (:require [clj-uuid :as uuid]
             [tawny.read :as r]
             [tawny.memorise]
-            [tawny.owl])
+            [tawny.owl :as o])
   (:use tawny.owl)
   (:import (org.semanticweb.owlapi.model IRI OWLOntology)))
 
 (defonce ^String bfo-iri  "http://purl.obolibrary.org/obo/bfo.owl")
 
-(defn resource-iri "Get a reference to the local BFO copy"  ^IRI []
+(defonce ^String tawny-iri  "http://www.purl.org/ontolink/tawny")
+
+
+(defn bfo-resource-iri "Get a reference to the local BFO copy"  ^IRI []
   (IRI/create (clojure.java.io/resource "bfo.owl")))
 
+(defn tawny-resource-iri "Get a reference to the local tawny.owl copy"  ^IRI []
+  (IRI/create (clojure.java.io/resource "tawny.owl")))
+
 (defn -scoped "Generate a v5 UUID in the tqme namespace" [^String n]
   ; The namespace here must be kept as is in order to keep IRIs stable
   (uuid/v5 (uuid/v5 uuid/+namespace-url+ "http://www.halbordnung.de/ontologies/tqc.owl")
            n))
-(defdontfn iri-generate
+(o/defno iri-generate
   "Generate IRIs for the determinist names"
   [o name]
-  (iri (str (.getOntologyIRI (.getOntologyID ^OWLOntology o)) "#" (-scoped name))))
+  (iri (str (.get (.getOntologyIRI (.getOntologyID ^OWLOntology o))) "#" (-scoped name))))
 
 (r/defread bfo
-  :location (resource-iri)
+  :location (bfo-resource-iri)
   :prefix "bfo"
   :iri bfo-iri
-  :viri "http://purl.obolibrary.org/obo/bfo/2014-05-03/bfo.owl"
+  :viri "http://purl.obolibrary.org/obo/bfo/2020/bfo.owl"
   :filter
   (clojure.core/partial tawny.read/iri-starts-with-filter "http://purl.obolibrary.org/obo/BFO")
   :transform
   (clojure.core/comp r/stop-characters-transform
                      r/exception-nil-label-transform))
+(tawny.memorise/remember bfo (clojure.java.io/resource "bfo_memo.clj"))
 
-(tawny.memorise/remember (clojure.java.io/resource "bfo_memo.clj"))
-
+(r/defread tawny
+  :location (tawny-resource-iri)
+  :prefix "tawny"
+  :iri  tawny-iri
+)

src/main/clojure/de/halbordnung/ontologies/tqme/core.clj

@@ -13,6 +13,7 @@
   :iri-gen b/iri-generate)
 
 (owl-import b/bfo)
+(owl-import b/tawny)
 
 (defclass tqme
   :label "temporally qualified material entity"
@@ -22,7 +23,7 @@
   )
 )
 
-(add-superclass b/material_entity tqme)
+(add-superclass tqme-ontology b/material_entity tqme)
 
 (defclass phase
   :label "minimal history segment"
@@ -40,12 +41,8 @@
                "    (they only occur at instants)"
                "  * They pertain to a single entity."))
 
-;; Match the history axiom
-(add-superclass phase (owl-only b/part_of_occurrent (owl-not b/process_profile)))
-
 (defoproperty phase-of
   :label "minimal history segment of"
-  :super b/specifically_depends_on_at_all_times
   :domain phase
   :range tqme
   :characteristic :functional)
@@ -55,12 +52,12 @@
   :inverse phase-of
   :characteristic :inversefunctional)
 
-(as-equivalent phase (owl-and (owl-some b/part_of_occurrent b/history)
+(as-equivalent phase (owl-and (owl-some b/occurrent_part_of b/history)
                               (owl-some b/exists_at b/zero-dimensional_temporal_region)))
 
-(add-superclass phase (owl-some phase-of o/owl-thing))
+(add-superclass tqme-ontology phase (owl-some phase-of o/owl-thing))
 
-(add-superclass b/material_entity (owl-some b/has_history b/history))
+(add-superclass tqme-ontology b/material_entity (owl-some b/has_history b/history))
 
 
 (defoproperty has-min-tqme
@@ -71,7 +68,7 @@
                             )
               )
 
-(add-subchain has-min-tqme [b/has_history b/has_occurrent_part phase-of])
+(add-subchain tqme-ontology has-min-tqme [b/has_history b/has_occurrent_part phase-of])
 
 (defoproperty min-tqme-of
               :label "minimal temporally qualified material entity of"
@@ -84,23 +81,47 @@
               :comment "the relation between a temporally qualified material entity and a maximal one"
               )
 
-(add-subchain has-max-tqme [has-phase b/part_of_occurrent b/history_of])
+(add-subchain tqme-ontology has-max-tqme [has-phase b/occurrent_part_of b/history_of])
 
 (defoproperty max-tqme-of
               :label "maximal material entity of"
               :domain b/material_entity
               :inverse has-max-tqme)
 
-(add-subproperty min-tqme-of has-max-tqme)
-(add-subproperty has-min-tqme max-tqme-of)
+(add-subproperty tqme-ontology min-tqme-of has-max-tqme)
+(add-subproperty tqme-ontology has-min-tqme max-tqme-of)
 
 ;; we steal a bit of stuff from tawny.owl to build our generators
-(defmontfn
+(defn
   guess-type-args
-  {:doc     "Broadcasting version of guess-type"
+  {:doc  "Broadcasting version of guess-type"
    :private true}
-  [o & args]
-  (guess-type o args))
+  ;; unwind to avoid variadic args for the most common calls.
+  ([a]
+   (guess-type a))
+  ([a b]
+   (or
+     (guess-type a)
+     (guess-type b)))
+  ([a b c]
+   (or
+     (guess-type a)
+     (guess-type b)
+     (guess-type c)))
+  ([a b c d]
+   (or
+     (guess-type a)
+     (guess-type b)
+     (guess-type c)
+     (guess-type d)))
+  ([a b c d & args]
+   (or
+     (guess-type a)
+     (guess-type b)
+     (guess-type c)
+     (guess-type d)
+     ;; guess-type already copes with collections
+     (guess-type args))))
 
 (defmulti phase-perm-spec
   "Returns a restriction on an phase that is scoped as permanently specific"
@@ -114,47 +135,80 @@
 (defmethod phase-perm-spec nil [& rest]
   (apply guess-type-error rest))
 
-(defmontfn ophase-perm-spec
+(defno ophase-perm-spec
   {:doc      "Returns a restriction on an phase that is scoped as permanently specific."
    :arglists '([& clazzes] [ontology & clazzes])}
   [o class]
-  (owl-some o phase-of class))
+  (owl-some phase-of class))
 
 (defmethod phase-perm-spec :tawny.owl/object [& rest]
   (apply ophase-perm-spec rest))
 
 
-(defmontfn object-perm-spec
+(defno object-perm-spec
   {:doc      "Returns a restriction on a material entity that is scoped as permanently specific."
    :arglists '([& clazzes] [ontology & clazzes])}
   [o class]
-  (owl-some o b/has_history (phase-perm-spec o class)))
+  (owl-some b/has_history (phase-perm-spec o class)))
 
 (defn perm-spec
-       [o class]
+       [class]
        class)
 
 (defn temp
-  [o ctor relation class]
-  (owl-some o
+  [ctor relation class]
+  (owl-some
             has-max-tqme
-            (owl-some o
+            (owl-some
                       has-min-tqme
-                      (ctor o
+                      (ctor
                             relation
-                            (owl-some o min-tqme-of class)
+                            (owl-some min-tqme-of class)
                             )
                       )
             )
   )
 
 (defn perm-gen
-  [o ctor relation class]
+  [ctor relation class]
   (owl-and
-    (owl-some o has-min-tqme
-              (ctor o relation (owl-some o min-tqme-of class)))
-    (owl-only o has-min-tqme
-              (ctor o relation (owl-some o min-tqme-of class)))
+    (owl-some has-min-tqme
+              (ctor relation (owl-some min-tqme-of class)))
+    (owl-only has-min-tqme
+              (ctor relation (owl-some min-tqme-of class)))
 
     )
-  )
+  )
+
+(defn perm-gen-full
+  [ctor relation class]
+  (owl-and
+    (owl-some b/has_history
+              (owl-some b/has_occurrent_part
+                        (owl-some has-phase
+                                  (ctor relation
+                                        (owl-some phase-of
+                                                  (owl-some b/occurrent_part_of
+                                                            (owl-some b/history_of class)
+                                                            )
+                                                  )
+                                        )
+                                  )
+                        )
+              )
+    (owl-only b/has_history
+              (owl-only b/has_occurrent_part
+                        (owl-only has-phase
+                                  (ctor relation
+                                        (owl-some phase-of
+                                                  (owl-some b/occurrent_part_of
+                                                            (owl-some b/history_of class)
+                                                            )
+                                                  )
+                                        )
+                                  )
+                        )
+              )
+
+    )
+  )