Fix to allow robot merges in parallel

Author: bherr2

src/utils/robot.js

@@ -8,21 +8,15 @@ export function query(input, query, output, useDb = false) {
       `Querying ${input} failed.`
     );
   } else {
-    throwOnError(
-      `robot query -i ${input} --query ${query} ${output}`,
-      `Querying ${input} failed.`
-    );
+    throwOnError(`robot query -i ${input} --query ${query} ${output}`, `Querying ${input} failed.`);
   }
 }
 
 export function materialize(input, output) {
-  throwOnError(
-    `robot query -i ${input} --create-tdb true --tdb-directory ${output}`,
-    'Materialization failed.'
-  );
+  throwOnError(`robot query -i ${input} --create-tdb true --tdb-directory ${output}`, 'Materialization failed.');
 }
 
-export function extract(input, upperTerm, lowerTerms, output, intermediates = "all", outputFormat = "owl") {
+export function extract(input, upperTerm, lowerTerms, output, intermediates = 'all', outputFormat = 'owl') {
   throwOnError(
     `robot extract -i ${input} \
               --method MIREOT \
@@ -34,7 +28,7 @@ export function extract(input, upperTerm, lowerTerms, output, intermediates = "a
   );
 }
 
-export function subset(input, seedTerms, output, outputFormat = "owl") {
+export function subset(input, seedTerms, output, outputFormat = 'owl') {
   throwOnError(
     `robot extract -i ${input} \
                 --method subset \
@@ -44,7 +38,7 @@ export function subset(input, seedTerms, output, outputFormat = "owl") {
   );
 }
 
-export function module(input, seedTerms, output, method = "BOT", outputFormat = "owl") {
+export function module(input, seedTerms, output, method = 'BOT', outputFormat = 'owl') {
   throwOnError(
     `robot extract -i ${input} \
                 --method ${method} \
@@ -54,8 +48,8 @@ export function module(input, seedTerms, output, method = "BOT", outputFormat =
   );
 }
 
-export function filter(input, anyTerms, annotationTerms = ['rdfs:label'], output, outputFormat = "owl") {
-  const termArguments = annotationTerms.map(term => `--term ${term}`).join(" ");
+export function filter(input, anyTerms, annotationTerms = ['rdfs:label'], output, outputFormat = 'owl') {
+  const termArguments = annotationTerms.map((term) => `--term ${term}`).join(' ');
   throwOnError(
     `robot filter -i ${input} \
                   --include-terms ${anyTerms} \
@@ -65,45 +59,36 @@ export function filter(input, anyTerms, annotationTerms = ['rdfs:label'], output
   );
 }
 
-export function merge(inputs, output, outputFormat = "owl") {
+export function merge(inputs, output, outputFormat = 'owl') {
   // Convert the inputs to OWL/XML format to avoid blank node collisions
   const owlInputs = [];
-  for (const input of inputs) {
-    const output = `${input}.owl`;
-    throwOnError(
-      `robot convert -i ${input} --format owl -o ${output}`,
-      'Convert to OWL during merging failed.'
-    );
-    owlInputs.push(output);
-  }
+  inputs.forEach((input, index) => {
+    const owlOutput = `${output}.merge_${index}.owl`;
+    throwOnError(`robot convert -i ${input} --format owl -o ${owlOutput}`, 'Convert to OWL during merging failed.');
+    owlInputs.push(owlOutput);
+  });
   // Merge the OWL input files
-  const inputParams = owlInputs.reduce(
-    (collector, owlInput) => (`${collector} --input ${owlInput}`), "");
+  const inputParams = owlInputs.reduce((collector, owlInput) => `${collector} --input ${owlInput}`, '');
   try {
     throwOnError(
       `robot merge ${inputParams} \
              convert --format ${outputFormat} -o ${output}`,
       'Merge ontologies failed. See errors above.'
     );
-  } finally { // Clean up the generated OWL inputs
+  } finally {
+    // Clean up the generated OWL inputs
     for (const owlInput of owlInputs) {
       sh.rm('-f', owlInput);
     }
   }
 }
 
 export function convert(input, output, outputFormat) {
-  throwOnError(
-    `robot convert -i ${input} --format ${outputFormat} -o ${output}`,
-    'Data conversion failed.'
-  );
+  throwOnError(`robot convert -i ${input} --format ${outputFormat} -o ${output}`, 'Data conversion failed.');
 }
 
 export function remove(input, output, subsetSelector) {
-  throwOnError(
-    `robot remove --input ${input} --select ${subsetSelector} -o ${output}`,
-    'Data removal failed.'
-  );
+  throwOnError(`robot remove --input ${input} --select ${subsetSelector} -o ${output}`, 'Data removal failed.');
 }
 
 export function exclude(input, exclude_file, output) {
@@ -112,4 +97,3 @@ export function exclude(input, exclude_file, output) {
     'Data exclusion failed.'
   );
 }
-