Merge pull request #1154 from pk-mitre/robot-header

Robot header

CHANGELOG.md

@@ -7,6 +7,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+### Added
+-- Added option to input template strings from external file [#1152]
+
 ### Fixed
 - '--annotate-with-source true' does not work with extract --method subset [#1160]
 - Fix how Template adds entities to the QuotedEntityChecker [#1104]
@@ -532,3 +535,4 @@ First official release of ROBOT!
 [#246]: https://github.com/ontodev/robot/issues/246
 [#174]: https://github.com/ontodev/robot/issues/174
 [#158]: https://github.com/ontodev/robot/issues/158
+[#1152]: https://github.com/ontodev/robot/issues/1152

docs/examples/animals_ext_template.owl

@@ -0,0 +1,55 @@
+<?xml version="1.0"?>
+<rdf:RDF xmlns="http://www.w3.org/2002/07/owl#"
+     xml:base="http://www.w3.org/2002/07/owl"
+     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#">
+    <Ontology/>
+
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Classes
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+
+
+
+    <!-- http://purl.obolibrary.org/obo/0000001 -->
+
+    <Class rdf:about="http://purl.obolibrary.org/obo/0000001">
+        <rdfs:comment>Any animal in the world.</rdfs:comment>
+        <rdfs:label>animal</rdfs:label>
+    </Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/0000002 -->
+
+    <Class rdf:about="http://purl.obolibrary.org/obo/0000002">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/0000001"/>
+        <rdfs:comment>A member of the genus Canis.</rdfs:comment>
+        <rdfs:label>canine</rdfs:label>
+    </Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/0000003 -->
+
+    <Class rdf:about="http://purl.obolibrary.org/obo/0000003">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/0000001"/>
+        <rdfs:comment>A member of the genus Felis.</rdfs:comment>
+        <rdfs:label>feline</rdfs:label>
+    </Class>
+</rdf:RDF>
+
+
+
+<!-- Generated by the OWL API (version 4.5.25) https://github.com/owlcs/owlapi -->
+

docs/examples/animals_ext_template.tsv

@@ -0,0 +1,2 @@
+CURIE	Label	Parent	Comment
+ID	LABEL	SC %	A rdfs:comment

docs/examples/animals_ext_template_error.tsv

@@ -0,0 +1,4 @@
+CURIE	Label	Parent	Comment
+obo:0000001	animal		Any animal in the world.
+0000002	canine	animal	A member of the genus Canis.
+obo:0000003	feline	animal	A member of the genus Felis.

docs/examples/animals_template.tsv

@@ -0,0 +1,4 @@
+CURIE	Label	Parent	Comment
+obo:0000001	animal		Any animal in the world.
+obo:0000002	canine	animal	A member of the genus Canis.
+obo:0000003	feline	animal	A member of the genus Felis.

docs/examples/animals_template_error.tsv

@@ -0,0 +1,5 @@
+CURIE	Label	Parent	Comment
+ID	LABEL	SC %	A rdfs:comment
+obo:0000001	animal		Any animal in the world.
+0000002	canine	animal	A member of the genus Canis.
+obo:0000003	feline	animal	A member of the genus Felis.

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        |                       |
@@ -223,6 +223,21 @@ robot template --merge-before \
   --output results/test_template.owl
 ```
 
+ROBOT template data read from separate external file
+
+    robot template --template animals_template.tsv \
+        --external-template animals_ext_template.tsv \
+        --output results/animals_ext_template.owl
+
+Adjusted line numbers for error reporting for template data read from separate external file
+<!-- DO NOT TEST -->
+```
+robot template --template animals_ext_template_error.tsv \
+  --ext-template animals_ext_template.tsv \
+  --output results/animals_ext_template.owl
+```
+
+
 \* NOTE: the imports would be merged into the output if `--collapse-import-closure true` is included instead.
 
 Further examples can be found [in the OBI repository](https://github.com/obi-ontology/obi/tree/master/src/ontology/templates)
@@ -313,7 +328,7 @@ 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.
 
@@ -366,3 +381,4 @@ An invalid `CHARACTERISTIC` value was passed. If you are providing multiple char
 ### Unknown Template Error
 
 Valid template strings are limited to the [described above](#template-strings). If a different template string is provided, this error message will be returned.
+

results/animals_ext_template.owl

@@ -0,0 +1,55 @@
+<?xml version="1.0"?>
+<rdf:RDF xmlns="http://www.w3.org/2002/07/owl#"
+     xml:base="http://www.w3.org/2002/07/owl"
+     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#">
+    <Ontology/>
+
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Classes
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+
+
+
+    <!-- http://purl.obolibrary.org/obo/0000001 -->
+
+    <Class rdf:about="http://purl.obolibrary.org/obo/0000001">
+        <rdfs:comment>Any animal in the world.</rdfs:comment>
+        <rdfs:label>animal</rdfs:label>
+    </Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/0000002 -->
+
+    <Class rdf:about="http://purl.obolibrary.org/obo/0000002">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/0000001"/>
+        <rdfs:comment>A member of the genus Canis.</rdfs:comment>
+        <rdfs:label>canine</rdfs:label>
+    </Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/0000003 -->
+
+    <Class rdf:about="http://purl.obolibrary.org/obo/0000003">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/0000001"/>
+        <rdfs:comment>A member of the genus Felis.</rdfs:comment>
+        <rdfs:label>feline</rdfs:label>
+    </Class>
+</rdf:RDF>
+
+
+
+<!-- Generated by the OWL API (version 4.5.26) https://github.com/owlcs/owlapi -->
+

robot-command/src/main/java/org/obolibrary/robot/TemplateCommand.java

@@ -28,6 +28,14 @@ public class TemplateCommand implements Command {
   private static final String missingTemplateError =
       NS + "MISSING TEMPLATE ERROR at least one template is required";
 
+  /** Error message when the header file is not provided */
+  private static final String missingRobotHeaderError =
+      NS + "MISSING ROBOT HEADER ERROR header is required";
+
+  private static final String mismatchedRobotHeaderError =
+      NS
+          + "MISMATCHED ROBOT HEADER mismatched template file header and external template file header";
+
   /** Store the command-line options for the command. */
   private Options options;
 
@@ -49,6 +57,7 @@ public TemplateCommand() {
         "A", "include-annotations", true, "if true, include ontology annotations from merge input");
     o.addOption("f", "force", true, "if true, do not exit on error");
     o.addOption("e", "errors", true, "write errors to this path (TSV or CSV)");
+    o.addOption("E", "external-template", true, "external robot template data file");
 
     options = o;
   }
@@ -143,6 +152,30 @@ public CommandState execute(CommandState state, String[] args) throws Exception
       tables.put(templatePath, TemplateHelper.readTable(templatePath));
     }
 
+    for (String templatePath : templatePaths) {
+      tables.put(templatePath, TemplateHelper.readTable(templatePath));
+    }
+    // Read the robot header line in
+    List<String> robotHeaderPath = CommandLineHelper.getOptionValues(line, "external-template");
+    if (robotHeaderPath.size() > 0) {
+      // For now only a single header line file is considered
+      List<List<String>> headerLine = new ArrayList<>();
+      headerLine = TemplateHelper.readTable(robotHeaderPath.get(0));
+      if (headerLine.size() == 0) {
+        throw new IllegalArgumentException(missingRobotHeaderError);
+      }
+      // Insert headerLine into all the template file data appropriately
+      for (String templatePath : templatePaths) {
+        List<List<String>> template = tables.get(templatePath);
+        // check that header lines match
+        if (checkHeaders(template.get(0), headerLine.get(0))) {
+          template.add(1, headerLine.get(1));
+        } else {
+          throw new IllegalArgumentException(mismatchedRobotHeaderError);
+        }
+      }
+    }
+
     // Process the templates
     OWLOntology outputOntology =
         TemplateOperation.template(inputOntology, ioHelper, tables, templateOptions);
@@ -194,4 +227,23 @@ public CommandState execute(CommandState state, String[] args) throws Exception
 
     return state;
   }
+
+  /**
+   * Compare the headers for the template file and the external template file Return true or false
+   * for match and mismatch situations respectively
+   *
+   * @param templateHeader header from template file
+   * @param externalTemplateHeader header from external template file
+   * @return true for match, false for mismatch
+   */
+  private boolean checkHeaders(List<String> templateHeader, List<String> externalTemplateHeader) {
+    if (templateHeader.size() == externalTemplateHeader.size()) {
+      int numElements = templateHeader.size();
+      for (int index = 0; index < numElements; index++) {
+        if (!templateHeader.get(index).equals(externalTemplateHeader.get(index))) return false;
+      }
+      return true;
+    }
+    return false;
+  }
 }

robot-core/src/main/java/org/obolibrary/robot/Template.java

@@ -422,6 +422,13 @@ public OWLOntology generateOutputOntology(String outputIRI, boolean force, Strin
     return outputOntology;
   }
 
+  public int getRowNum() {
+    return rowNum;
+  }
+
+  public void setRowNum(int rowNum) {
+    this.rowNum = rowNum;
+  }
   /**
    * Given a list of rows for a table, first validate the headers and template strings. Then, get
    * the location of important columns (e.g. IDs and labels). Finally, add all template rows to the

robot-core/src/main/java/org/obolibrary/robot/TemplateOperation.java

@@ -109,6 +109,7 @@ public static Map<String, String> getDefaultOptions() {
     Map<String, String> options = new HashMap<>();
     options.put("force", "false");
     options.put("errors", null);
+    options.put("external-template", null);
     return options;
   }
 
@@ -176,6 +177,10 @@ public static OWLOntology template(
     List<OWLOntology> outputOntologies = new ArrayList<>();
     for (Map.Entry<String, List<List<String>>> t : tables.entrySet()) {
       Template template = new Template(t.getKey(), t.getValue(), intermediate, ioHelper, checker);
+      // sufficient to check if ext-template option has a not null value
+      if (options.get("ext-template") != null) {
+        template.setRowNum(1);
+      }
       // Update the checker with new labels
       checker = template.getChecker();
       boolean force = OptionsHelper.optionIsTrue(options, "force");