ontodev · beckyjackson · Sep 30, 2022 · Sep 30, 2022 · Sep 30, 2022 · Sep 30, 2022
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 - Checking for empty strings in addition to missing ones in `missing_label.rq` [#1017]
+- Add new global option: `--input-format` [#1056]
 
 ## [1.9.0] - 2022-06-16
 
@@ -320,6 +321,7 @@ First official release of ROBOT!
 [`template`]: http://robot.obolibrary.org/template
 [`validate`]: http://robot.obolibrary.org/validate
 
+[#1056]: https://github.com/ontodev/robot/issues/1056
 [#1009]: https://github.com/ontodev/robot/issues/1009
 [#979]: https://github.com/ontodev/robot/pull/979
 [#978]: https://github.com/ontodev/robot/pull/978

diff --git a/docs/examples/ro-base-reasoned.owl b/docs/examples/ro-base-reasoned.owl
@@ -3687,15 +3687,6 @@ For example, protein A (transcription factor) indirectly increases by expression
 
 
 
-    <!-- http://xmlns.com/foaf/0.1/image -->
-
-    <owl:Class rdf:about="http://xmlns.com/foaf/0.1/image"/>
-    <rdf:Description>
-        <rdfs:seeAlso rdf:resource="https://github.com/oborel/obo-relations/issues/259"/>
-    </rdf:Description>
-
-
-
     <!-- 
     ///////////////////////////////////////////////////////////////////////////////////////
     //
@@ -3878,5 +3869,5 @@ For example, protein A (transcription factor) indirectly increases by expression
 
 
 
-<!-- Generated by the OWL API (version 1.8.4) https://github.com/owlcs/owlapi -->
+<!-- Generated by the OWL API (version 4.5.6) https://github.com/owlcs/owlapi -->
 
diff --git a/docs/examples/ro-base.owl b/docs/examples/ro-base.owl
@@ -3553,15 +3553,6 @@ For example, protein A (transcription factor) indirectly increases by expression
 
 
 
-    <!-- http://xmlns.com/foaf/0.1/image -->
-
-    <owl:Class rdf:about="http://xmlns.com/foaf/0.1/image"/>
-    <rdf:Description>
-        <rdfs:seeAlso rdf:resource="https://github.com/oborel/obo-relations/issues/259"/>
-    </rdf:Description>
-
-
-
     <!-- 
     ///////////////////////////////////////////////////////////////////////////////////////
     //

diff --git a/docs/global.md b/docs/global.md
@@ -8,6 +8,7 @@
 4. [Logging (`-v`, `-vv`, `-vvv`)](#logging)
 5. [XML Entities (`--xml-entities`)](#xml-entities)
 6. [Strict Parsing (`--strict`)](#strict-parsing)
+7. [Input Format (`--input-format`)](#input-format)
 
 ## Java Options
 
@@ -131,6 +132,22 @@ _:blank rdf:type rdf:Statement .
 _:blank rdf:type owl:Axiom .
 ```
 
+## Input Format
+
+When loading an ontology, OWLAPI will attempt to load with a variety of ontology format parsers. When all parsers fail, many error logs are printed (when using verbose mode). Finding the cause of the error based on parser can be difficult due to number of messages. For debugging purposes, you can specify the `--input-format` of the ontology as one of:
+
+| Format | Specification                                                                     |
+| ------ | --------------------------------------------------------------------------------- |
+| owl    | [RDF/XML](https://www.w3.org/TR/rdf-syntax-grammar/)                              |
+| obo    | [OBO Flat File](https://owlcollab.github.io/oboformat/doc/GO.format.obo-1_4.html) |
+| owx    | [OWL/XML](https://www.w3.org/TR/owl-xmlsyntax/)                                   |
+| ofn    | [OWL Functional](https://www.w3.org/TR/owl2-syntax/)                              |
+| omn    | [OWL Manchester](https://www.w3.org/TR/owl2-manchester-syntax/)                   |
+| ttl    | [Turtle](https://www.w3.org/TR/turtle/)                                           |
+| json   | [OBO Graphs JSON](https://github.com/geneontology/obographs/)                     |
+
+Be aware that the suffix of the ontology file does not always correspond to the format; OBO ontologies will often use the suffix `.owl` for both RDF/XML and functional syntax. Check the contents of the file using the format specifications for reference to be sure.
+
 ---
 
 ## Error Messages

diff --git a/docs/reason.md b/docs/reason.md
@@ -65,9 +65,9 @@ If the input module contains at least one import, axioms in the debug module wil
 
 ## Equivalent Class Axioms
 
-By default, ROBOT ignores one-to-one equivalent classes (e.g. `A EquivalentTo B`). But, in many cases, inferring equivalence between two classes is usually a sign that something has gone wrong. 
+By default, ROBOT ignores one-to-one equivalent classes (e.g. `A EquivalentTo B`). But, in many cases, inferring equivalence between two classes is usually a sign that something has gone wrong.
 
-Sometimes we want to avoid equivalence between named classes at all (in the case of OBO, where we strive for orthogonality). This can be done through `--equivalent-classes-allowed <arg>` (shorthand `-e`). 
+Sometimes we want to avoid equivalence between named classes at all (in the case of OBO, where we strive for orthogonality). This can be done through `--equivalent-classes-allowed <arg>` (shorthand `-e`).
 
 The `<arg>` options are:
 
@@ -77,16 +77,16 @@ The `<arg>` options are:
 
 ## Excluding tautologies
 
-A **tautology** is an axiom that would be true in any ontology, i.e., it's just a given due to the semantics of OWL. For example, every class is a subclass 
-of `owl:Thing`; it is not generally useful for an ontology to explicitly state this. Some reasoners may however include these kinds of statements as part 
+A **tautology** is an axiom that would be true in any ontology, i.e., it's just a given due to the semantics of OWL. For example, every class is a subclass
+of `owl:Thing`; it is not generally useful for an ontology to explicitly state this. Some reasoners may however include these kinds of statements as part
 of their output. The ROBOT `reason` command provides an option for filtering out tautologies generated by the reasoning process: `--exclude-tautologies <arg>`.
 
 The options for `<arg>` are:
 
  * `false` (default): allow any generated tautologies in the output.
  * `all` (recommended): use the HermiT reasoner to exclude any inferred axioms that would be entailed by an empty ontology.
  * `structural` (fast): exclude axioms matching a hard-coded set of tautological patterns (e.g., `X SubClassOf owl:Thing`, `owl:Nothing SubClassOf X`, `X SubClassOf X`). Much faster than `all`.
- 
+
 ## Generated Axioms
 
 By default, the `reason` operation will only assert inferred subclass axioms. This can be configured with the `--axiom-generators` option. OWLAPI provides the following inferred axiom generators:
@@ -113,27 +113,27 @@ By default, the `reason` operation will only assert inferred subclass axioms. Th
 One or more of these axiom generators can be passed into the option (separated by spaces). For example, to generate both subclass and disjoint class axioms:
 
 ```
-robot reason --input unreasoned.owl
-  --axiom-generators "SubClass DisjointClasses"
+robot reason --input unreasoned.owl \
+  --axiom-generators "SubClass DisjointClasses" \
   --output reasoned.owl
 ```
 
 Note that for some of the axiom generators you may need the Hermit reasoner
 to get meaningful results:
 
 
-    robot reason --input ro-base.owl --reasoner hermit
-      --axiom-generators "ObjectPropertyRange ObjectPropertyDomain"
+    robot reason --input ro-base.owl --reasoner hermit \
+      --axiom-generators "ObjectPropertyRange ObjectPropertyDomain" \
       --output ro-base-reasoned.owl
 
 
 If you are only passing one axiom generator, it does not need to be surrounded by double quotes.
 
 The axioms that are generated for subclasses, class assertions, and sub-object properties can be either direct or indirect. By default, the operation will only generate direct axioms (`--include-indirect false`). It is recommended to pipe to `reduce` after to remove any redundant axioms. For example, to generate all direct and indirect superclass expressions:
 ```
-robot reason --input unreasoned.owl
-  --reasoner emr
-  --include-indirect true
+robot reason --input unreasoned.owl \
+  --reasoner emr \
+  --include-indirect true \
   reduce --output reasoned.owl
 ```
 

diff --git a/docs/template.md b/docs/template.md
@@ -151,7 +151,7 @@ If the `TYPE` is a defined class, `owl:Individual`, or `owl:NamedIndividual`, an
 
 #### Example of Individual Template Strings
 
-| Label        | Entity Type | Individual Role      | Property Assertions | Different Individuals | 
+| Label        | Entity Type | Individual Role      | Property Assertions | Different Individuals |
 | ------------ | ----------- | -------------------- | ------------------- | --------------------- |
 | LABEL        | TYPE        | TI 'has role' some % | I part_of           | DI %                  |
 | Individual 1 | Class 1     | Role Class 1         | Individual 2        |                       |
@@ -188,7 +188,7 @@ If the command includes `--ancestors`, the result ontology will include the ance
 Create an output ontology that includes the input ontology and the terms defined in the template:
 
     robot template --merge-before --input edit.owl \
-     --template part_of_template.csv --output part_of_uberon.owl
+     --template part_of_template.csv --output results/part_of_uberon.owl
 
 
 Create two outputs -- the templated terms ([`uberon_template.owl`](/examples/uberon_template.owl)) and the input ontology merged with the output ontology with an annotation ([`uberon_v2.owl`](/examples/uberon_v2)):
@@ -311,7 +311,7 @@ AL rdfs:label@en
 
 The provided value cannot be parsed and may not be in proper Manchester syntax. See [Manchester Syntax](http://www.w3.org/2007/OWL/wiki/ManchesterSyntax) for more details. If you are using labels, make sure the labels are defined in the `--input` ontology or using the `LABEL` column. Also ensure that all properties use a label instead of a CURIE or IRI.
 
-When using a restriction (`some`, `only`, `min`, `max`, `exactly`, or `value`) the term that preceeds the restriction must be a property. 
+When using a restriction (`some`, `only`, `min`, `max`, `exactly`, or `value`) the term that preceeds the restriction must be a property.
 
 Terms joined using `and` or `or` must be of the same entity type, e.g., you cannot join an object property and a class in an expression.
 

diff --git a/robot-command/src/main/java/org/obolibrary/robot/CommandLineHelper.java b/robot-command/src/main/java/org/obolibrary/robot/CommandLineHelper.java
@@ -21,6 +21,8 @@
 import org.geneontology.reasoner.ExpressionMaterializingReasonerFactory;
 import org.geneontology.whelk.owlapi.WhelkOWLReasonerFactory;
 import org.semanticweb.elk.owlapi.ElkReasonerFactory;
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.io.OWLParserFactory;
 import org.semanticweb.owlapi.model.*;
 import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
 import org.slf4j.LoggerFactory;
@@ -66,7 +68,12 @@ public class CommandLineHelper {
 
   /** Error message when more than one --input is specified, excluding merge and unmerge. */
   private static final String multipleInputsError =
-      NS + "MULITPLE INPUTS ERROR only one --input is allowed";
+      NS + "MULTIPLE INPUTS ERROR only one --input is allowed";
+
+  /** Error message when --input-format is invalid. */
+  private static final String unknownInputFormatError =
+      NS
+          + "UNKNOWN INPUT FORMAT ERROR --input-format must be one of: owl, ofn, owx, omn, obo, ttl, or json";
 
   /** Error message when the --inputs pattern does not include * or ?, or is not quoted */
   private static final String wildcardError =
@@ -462,7 +469,7 @@ public static OWLOntology getInputOntology(IOHelper ioHelper, CommandLine line)
    * @param line the command line to use
    * @param catalogPath the catalog to use to load imports
    * @return the input ontology
-   * @throws IllegalArgumentException if requires options are missing
+   * @throws IllegalArgumentException if required options are missing
    * @throws IOException if the ontology cannot be loaded
    */
   public static OWLOntology getInputOntology(
@@ -476,17 +483,29 @@ public static OWLOntology getInputOntology(
       throw new IllegalArgumentException(multipleInputsError);
     }
 
+    // Create a manager to load ontology and maybe set parsers
+    // Otherwise, all parsers will be tried
+    OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
+    String inputFormat = getOptionalValue(line, "input-format");
+    if (inputFormat != null) {
+      Set<OWLParserFactory> parsers = IOHelper.getParsersByFormat(inputFormat);
+      if (parsers == null) {
+        throw new IllegalArgumentException(unknownInputFormatError);
+      }
+      manager.setOntologyParsers(parsers);
+    }
+
     if (!inputOntologyPaths.isEmpty()) {
       if (catalogPath != null) {
-        return ioHelper.loadOntology(inputOntologyPaths.get(0), catalogPath);
+        return ioHelper.loadOntology(manager, inputOntologyPaths.get(0), catalogPath);
       } else {
-        return ioHelper.loadOntology(inputOntologyPaths.get(0));
+        return ioHelper.loadOntology(manager, inputOntologyPaths.get(0));
       }
     } else if (!inputOntologyIRIs.isEmpty()) {
       if (catalogPath != null) {
-        return ioHelper.loadOntology(IRI.create(inputOntologyIRIs.get(0)), catalogPath);
+        return ioHelper.loadOntology(manager, IRI.create(inputOntologyIRIs.get(0)), catalogPath);
       } else {
-        return ioHelper.loadOntology(IRI.create(inputOntologyIRIs.get(0)));
+        return ioHelper.loadOntology(manager, IRI.create(inputOntologyIRIs.get(0)));
       }
     } else {
       // Both input options are empty
@@ -908,6 +927,11 @@ public static Options getCommonOptions() {
     o.addOption("v", "verbose", false, "increased logging");
     o.addOption("vv", "very-verbose", false, "high logging");
     o.addOption("vvv", "very-very-verbose", false, "maximum logging, including stack traces");
+    o.addOption(
+        null,
+        "input-format",
+        true,
+        "format of the input ontology: obo, owl, ttl, owx, omn, ofn, json");
     o.addOption(null, "catalog", true, "use catalog from provided file");
     o.addOption("p", "prefix", true, "add a prefix 'foo: http://bar'");
     o.addOption("P", "prefixes", true, "use prefixes from JSON-LD file");