Merge pull request #315 from ontodev/more-consistent-query

More consistent query

docs/verify.md

@@ -22,4 +22,16 @@ Should output as a response:
 And the CSV file `results/equivalent.csv` should have:
 
     first,second,firstLabel,secondLabel
-    http://purl.obolibrary.org/obo/TEST_A,http://purl.obolibrary.org/obo/TEST_B,,
+    http://purl.obolibrary.org/obo/TEST_A,http://purl.obolibrary.org/obo/TEST_B,,
+
+---
+
+## Error Messages
+
+### Verification Failed
+
+At least one of the query you specifies returned results. The number of failures for each rule will be printed. A CSV file will be generated with the results that matched the rule.
+
+### Missing Query Error
+
+You must specify a query to execute with `--query` or `--queries`.

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

@@ -1,22 +1,12 @@
 package org.obolibrary.robot;
 
-import com.google.common.io.Files;
-import com.hp.hpl.jena.query.ResultSet;
-import com.hp.hpl.jena.query.ResultSetFactory;
-import com.hp.hpl.jena.query.ResultSetRewindable;
 import com.hp.hpl.jena.sparql.core.DatasetGraph;
 import java.io.File;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.OutputStream;
-import java.nio.charset.Charset;
-import java.util.HashMap;
-import java.util.Map;
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.Option;
 import org.apache.commons.cli.Options;
+import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.FilenameUtils;
-import org.obolibrary.robot.exceptions.CannotReadQuery;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -36,6 +26,10 @@ public class VerifyCommand implements Command {
   private static final String missingQueryError =
       NS + "MISSING QUERY ERROR at least one query is required";
 
+  /** Error message when no query is provided. */
+  private static final String verificationFailed =
+      NS + "VERIFICATION FAILED there were violations of at least one rule";
+
   /** Store the command-line options for the command. */
   private Options options;
 
@@ -122,44 +116,24 @@ public CommandState execute(CommandState state, String[] args) throws Exception
 
     File outputDir = new File(CommandLineHelper.getDefaultValue(line, "output-dir", "."));
 
-    Map<File, Tuple<ResultSetRewindable, OutputStream>> resultMap = new HashMap<>();
     String[] queryFilePaths = line.getOptionValues("queries");
-    if (queryFilePaths.length == 0) {
-      throw new IllegalArgumentException(missingQueryError);
-    }
+    boolean passing = true;
     for (String filePath : queryFilePaths) {
-      File query = new File(filePath);
-      ResultSet results = QueryOperation.execQuery(graph, fileContents(query));
-      ResultSetRewindable resultsCopy = ResultSetFactory.copyResults(results);
+      File queryFile = new File(filePath);
+      String queryString = FileUtils.readFileToString(queryFile);
       String csvPath = FilenameUtils.getBaseName(filePath).concat(".csv");
-      File resultCsv = outputDir.toPath().resolve(csvPath).toFile();
-      if (resultsCopy.size() > 0) {
-        resultMap.put(query, new Tuple<>(resultsCopy, new FileOutputStream(resultCsv)));
-      } else {
-        System.out.println("Rule " + resultCsv.getCanonicalPath() + ": 0 violations");
+      boolean result =
+          QueryOperation.runVerify(
+              graph, filePath, queryString, outputDir.toPath().resolve(csvPath), null);
+      if (result) {
+        passing = false;
       }
     }
 
-    boolean violationsExist = QueryOperation.execVerify(resultMap);
-    if (violationsExist) {
-      System.exit(1);
+    if (!passing) {
+      throw new Exception(verificationFailed);
     }
 
     return state;
   }
-
-  /**
-   * Utility function to get file contents.
-   *
-   * @param file the file to read
-   */
-  private static String fileContents(File file) {
-    try {
-      return Files.toString(file, Charset.defaultCharset());
-    } catch (IOException e) {
-      String message = "Cannot read from " + file + ": " + e.getMessage();
-      // TODO: Is this necessary?
-      throw new CannotReadQuery(message, e);
-    }
-  }
 }

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

@@ -5,6 +5,7 @@
 import com.hp.hpl.jena.sparql.core.DatasetGraph;
 import com.hp.hpl.jena.sparql.core.DatasetGraphFactory;
 import java.io.*;
+import java.nio.file.Path;
 import java.util.Map;
 import org.apache.jena.riot.Lang;
 import org.apache.jena.riot.RDFDataMgr;
@@ -427,6 +428,57 @@ public static boolean execVerify(
     return isViolation;
   }
 
+  /**
+   * Execute a SPARQL query and return true if there are any results, false otherwise. Prints
+   * violations to STDERR.
+   *
+   * @param dsg the graph to query over
+   * @param query the SPARQL query string
+   * @return true if the are results, false otherwise
+   */
+  public static boolean execVerify(DatasetGraph dsg, String ruleName, String query) {
+    ResultSetRewindable results = ResultSetFactory.copyResults(execQuery(dsg, query));
+    System.out.println("Rule " + ruleName + ": " + results.size() + " violation(s)");
+    if (results.size() == 0) {
+      System.out.println("PASS Rule " + ruleName + ": 0 violation(s)");
+      return false;
+    } else {
+      ResultSetMgr.write(System.err, results, Lang.CSV);
+      System.out.println("FAIL Rule " + ruleName + ": " + results.size() + " violation(s)");
+      return true;
+    }
+  }
+
+  /**
+   * Run a SELECT query and write the result to a file. Prints violations to STDERR.
+   *
+   * @param dsg The graph to query over.
+   * @param query The SPARQL query string.
+   * @param outputPath The file path to write to, if there are results
+   * @param outputFormat The file format.
+   * @throws FileNotFoundException if output file is not found
+   * @return true if the are results (so file is written), false otherwise
+   */
+  public static boolean runVerify(
+      DatasetGraph dsg, String ruleName, String query, Path outputPath, Lang outputFormat)
+      throws FileNotFoundException {
+    if (outputFormat == null) {
+      outputFormat = Lang.CSV;
+    }
+    ResultSetRewindable results = ResultSetFactory.copyResults(execQuery(dsg, query));
+    if (results.size() == 0) {
+      System.out.println("PASS Rule " + ruleName + ": 0 violation(s)");
+      return false;
+    } else {
+      System.out.println("FAIL Rule " + ruleName + ": " + results.size() + " violation(s)");
+      ResultSetMgr.write(System.err, results, Lang.CSV);
+      results.reset();
+      FileOutputStream csvFile = new FileOutputStream(outputPath.toFile());
+      writeResult(results, outputFormat, csvFile);
+      return true;
+    }
+  }
+
   /**
    * Count results.
    *