Merge pull request #1190 from ontodev/robot-header-update

ROBOT Header Update
ontodev · Mar 29, 2024 · 3d75b32 · 3d75b32
2 parents 7173c55 + f1b680b
commit 3d75b32
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Showing 5 changed files with 18 additions and 76 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,7 +8,7 @@ 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]
+- Added option to input template strings from external file [#1152]
 
 ### Fixed
 - '--annotate-with-source true' does not work with extract --method subset [#1160]
@@ -391,6 +391,7 @@ First official release of ROBOT!
 [#1171]: https://github.com/ontodev/robot/pull/1171
 [#1168]: https://github.com/ontodev/robot/pull/1168
 [#1160]: https://github.com/ontodev/robot/pull/1160
+[#1152]: https://github.com/ontodev/robot/issues/1152
 [#1148]: https://github.com/ontodev/robot/pull/1148
 [#1135]: https://github.com/ontodev/robot/pull/1135
 [#1119]: https://github.com/ontodev/robot/pull/1119
@@ -535,4 +536,3 @@ 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
diff --git a/docs/examples/animals_ext_template_error.tsv b/docs/examples/animals_ext_template_error.tsv
diff --git a/docs/template.md b/docs/template.md
@@ -232,7 +232,7 @@ ROBOT template data read from separate external file
 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 \
+robot template --template animals_template_error.tsv \
   --ext-template animals_ext_template.tsv \
   --output results/animals_ext_template.owl
 ```

diff --git a/results/animals_ext_template.owl b/results/animals_ext_template.owl
diff --git a/robot-command/src/main/java/org/obolibrary/robot/TemplateCommand.java b/robot-command/src/main/java/org/obolibrary/robot/TemplateCommand.java
@@ -155,21 +155,22 @@ public CommandState execute(CommandState state, String[] args) throws Exception
     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) {
+
+    // Handle external template files.
+    List<String> externalTemplatePath =
+        CommandLineHelper.getOptionValues(line, "external-template");
+    if (externalTemplatePath.size() > 0) {
+      List<List<String>> externalTemplate = new ArrayList<>();
+      externalTemplate = TemplateHelper.readTable(externalTemplatePath.get(0));
+      if (externalTemplate.size() == 0) {
         throw new IllegalArgumentException(missingRobotHeaderError);
       }
-      // Insert headerLine into all the template file data appropriately
+      // Insert externalTemplate 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));
+        // check that the first lines (headers) are the same
+        if (compareHeaders(template.get(0), externalTemplate.get(0))) {
+          template.add(1, externalTemplate.get(1));
         } else {
           throw new IllegalArgumentException(mismatchedRobotHeaderError);
         }
@@ -229,14 +230,14 @@ public CommandState execute(CommandState state, String[] args) throws Exception
   }
 
   /**
-   * Compare the headers for the template file and the external template file Return true or false
-   * for match and mismatch situations respectively
+   * Compare the headers for the template file and the external template file. Return true if they
+   * match, false otherwise.
    *
    * @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) {
+  private boolean compareHeaders(List<String> templateHeader, List<String> externalTemplateHeader) {
     if (templateHeader.size() == externalTemplateHeader.size()) {
       int numElements = templateHeader.size();
       for (int index = 0; index < numElements; index++) {