added -v option to --remove-axioms-about to invert choice

preserve replaced-by when removing annotation assertions if deprecated preserved added docs for module option
owlcollab · Dec 13, 2017 · 178e1f9 · 178e1f9
1 parent f90176d
commit 178e1f9
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Showing 2 changed files with 23 additions and 6 deletions.
diff --git a/OWLTools-Core/src/main/java/owltools/mooncat/Mooncat.java b/OWLTools-Core/src/main/java/owltools/mooncat/Mooncat.java
@@ -736,16 +736,20 @@ public void removeClassesNotInIDSpace(String idspace, boolean removeDangling) {
     }
 
     public void removeAxiomsAboutIdSpace(String idspace, boolean removeDangling) {
-        removeAxiomsAboutIdSpace(idspace, removeDangling, true);
+        removeAxiomsAboutIdSpace(idspace, removeDangling, true, false);
     }
-    public void removeAxiomsAboutIdSpace(String idspace, boolean removeDangling, boolean removeAnnotations) {
+    public void removeAxiomsAboutIdSpace(String idspace, boolean removeDangling, boolean removeAnnotations, boolean isInvert) {
         LOG.info("Removing classes not in: "+idspace);
         idspace = idspace.toLowerCase()+":";
         Set<OWLAxiom> rmAxioms = new HashSet<>();
         int n=0;
         for (OWLClass c : graph.getSourceOntology().getClassesInSignature()) {
             String id = graph.getIdentifier(c).toLowerCase();
-            if (id.startsWith(idspace)) {
+            boolean isRm = id.startsWith(idspace);
+            if (isInvert) {
+                isRm = !isRm;
+            }
+            if (isRm) {
                 n++;
                 rmAxioms.addAll(graph.getSourceOntology().getAxioms(c));
                 if (removeAnnotations) {

diff --git a/OWLTools-Runner/src/main/java/owltools/cli/CommandRunner.java b/OWLTools-Runner/src/main/java/owltools/cli/CommandRunner.java
@@ -1122,6 +1122,7 @@ else if (opts.nextEq("--remove-annotation-assertions")) {
                 boolean isPreserveSynonyms = false;
                 boolean isPreserveRelations = false;
                 boolean isPreserveDeprecations = true;
+                boolean isPreserveDeprecationAxioms = true;
                 Set<IRI> preserveAnnotationPropertyIRIs = new HashSet<IRI>();
                 while (opts.hasOpts()) {
                     if (opts.nextEq("-l|--preserve-labels")) {
@@ -1170,6 +1171,12 @@ else if (opts.nextEq("-p|--preserve-property")) {
                             if (aaa.getProperty().isDeprecated()) {
                                 keepAxioms.add(aaa);
                             }
+                            if (isPreserveDeprecationAxioms) {
+                                if (piri.equals(Obo2OWLVocabulary.IRI_OIO_consider.getIRI()) ||
+                                        piri.equals(Obo2OWLVocabulary.IRI_IAO_0100001.getIRI())) {
+                                    keepAxioms.add(aaa);
+                                }
+                            }
                         }
                         if (isPreserveDefinitions) {
                             if (piri.equals(Obo2OWLVocabulary.IRI_IAO_0000115.getIRI())) {
@@ -2788,7 +2795,7 @@ else if (opts.nextEq("--reason-subontologies")) {
                 }
             }
             else if (opts.nextEq("--run-reasoner")) {
-                opts.info("[-r reasonername] [--assert-implied] [--indirect] [-u]", "infer new relationships");
+                opts.info("[-r reasonername] [--assert-implied] [--indirect] [-u] [-m UNSATMODFILE]", "infer new relationships");
                 boolean isAssertImplied = false;
                 boolean isDirect = true;
                 boolean isShowUnsatisfiable = false;
@@ -3691,20 +3698,26 @@ else if (opts.nextEq("--remove-subset")) {
                 m.removeSubsetClasses(cset, isRemoveDangling);
             }
             else if (opts.nextEq("--remove-axioms-about")) {
-                opts.info("[-d] IDSPACES", "Removes axioms that are about the specified ID space");
+                opts.info("[-v] [-d] IDSPACES", "Removes axioms that are about the specified ID space");
                 boolean isRemoveDangling = true;
+                boolean isInvert = false;
                 while (opts.hasOpts()) {
                     if (opts.nextEq("-d|--keep-dangling")) {
                         opts.info("",
                                 "if specified, dangling axioms (ie pointing to removed classes) are preserved");
                         isRemoveDangling = false;
                     }
+                    else if (opts.nextEq("-v|--invert")) {
+                        opts.info("",
+                                "invert - remove axioms NOT about");
+                        isInvert = true;
+                    }
                     else
                         break;
                 }
                 String idspace = opts.nextOpt();
                 Mooncat m = new Mooncat(g);
-                m.removeAxiomsAboutIdSpace(idspace, isRemoveDangling);
+                m.removeAxiomsAboutIdSpace(idspace, isRemoveDangling, true, isInvert);
             }
             else if (opts.nextEq("--remove-classes-in-idspace")) {
                 opts.info("[-d] [-s IDSPACE]", "Removes classes in an ID space from ontology");