feat(reporter): add support for passing sample metadata to reporter

src/main/java/org/pharmgkb/pharmcat/BaseConfig.java

@@ -54,6 +54,7 @@ public class BaseConfig {
   boolean deleteIntermediateFiles;
   boolean verbose;
   SortedSet<String> samples = new TreeSet<>();
+  Path sampleMetadataFile;
 
 
   BaseConfig(CliHelper cliHelper) throws IOException, ReportableException {
@@ -94,6 +95,9 @@ public class BaseConfig {
         }
       }
     }
+    if (cliHelper.hasOption("sm")) {
+      sampleMetadataFile = cliHelper.getValidFile("sm", true);
+    }
 
     boolean researchMode = false;
     if (runMatcher) {

src/main/java/org/pharmgkb/pharmcat/BatchPharmCAT.java

@@ -49,6 +49,7 @@ public static void main(String[] args) {
           .addOption("i", "input-dir", "Directory containing source data files", false, "dir")
           .addOption("s", "samples", "Comma-separated list of samples", false, "samples")
           .addOption("S", "sample-file", "File containing a list of sample, one per line", false, "file")
+          .addOption("sm", "sample-metadata", "TSV containing sample metadata", false, "file")
 
           // named allele matcher args
           .addOption("matcher", "matcher", "Run named allele matcher independently")
@@ -401,7 +402,7 @@ public Pipeline build(Env env, int index, int totalTasks) throws ReportableExcep
           m_config.reporterSources, m_config.reporterCompact,
           m_config.reporterJson, m_config.reporterHtml, m_config.reporterCallsOnlyTsv,
           m_config.outputDir, m_config.baseFilename, m_config.deleteIntermediateFiles,
-          mode, (index + "/" + totalTasks), m_verbose);
+          mode, (index + "/" + totalTasks), m_verbose, null);
     }
 
 

src/main/java/org/pharmgkb/pharmcat/Constants.java

@@ -1,5 +1,6 @@
 package org.pharmgkb.pharmcat;
 
+import java.util.Collections;
 import java.util.List;
 import java.util.Set;
 import java.util.SortedSet;
@@ -97,7 +98,7 @@ public static boolean isActivityScoreGene(String gene, DataSource dataSource) {
     Set<String> genes = switch (dataSource) {
       case CPIC -> ACTIVITY_SCORE_GENES_CPIC;
       case DPWG -> ACTIVITY_SCORE_GENES_DPWG;
-      default -> throw new RuntimeException("No genes specified for " + dataSource);
+      default -> Collections.emptySet();
     };
     return gene != null && genes.contains(gene.toUpperCase());
   }

src/main/java/org/pharmgkb/pharmcat/Env.java

@@ -1,10 +1,13 @@
 package org.pharmgkb.pharmcat;
 
+import java.io.BufferedReader;
 import java.io.IOException;
+import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.HashMap;
 import java.util.Map;
 import java.util.Optional;
+import java.util.TreeMap;
 import com.google.common.collect.HashMultimap;
 import com.google.common.collect.Multimap;
 import org.checkerframework.checker.nullness.qual.Nullable;
@@ -33,6 +36,7 @@ public class Env {
   private MessageHelper m_messageHelper;
   private final Map<DataSource, Map<String, Map<String, Haplotype>>> m_haplotypeCache = new HashMap<>();
   private final Multimap<String, String> m_validHaplotypes = HashMultimap.create();
+  private final Map<Path, Map<String, Map<String, String>>> m_sampleDataMap = new HashMap<>();
 
 
   public Env() throws IOException, ReportableException {
@@ -189,4 +193,41 @@ public synchronized Haplotype makeHaplotype(String gene, String name, DataSource
           return haplotype;
         });
   }
+
+
+  public synchronized @Nullable Map<String, String> getSampleMetadata(Path sampleMetadataFile, String sampleId,
+      boolean cache) throws IOException {
+
+    Map<String, Map<String, String>> fileMap;
+    if (cache) {
+      fileMap = m_sampleDataMap.computeIfAbsent(sampleMetadataFile, f -> new TreeMap<>());
+      if (!fileMap.isEmpty()) {
+        return fileMap.get(sampleId);
+      }
+    } else {
+      fileMap = new TreeMap<>();
+    }
+    try (BufferedReader reader = Files.newBufferedReader(sampleMetadataFile)) {
+      String line;
+      while ((line = reader.readLine()) != null) {
+        String[] row = line.split("\t");
+        if (row.length >= 3) {
+          String sid = row[0];
+          if (cache) {
+            fileMap.computeIfAbsent(sid, k -> new HashMap<>())
+                .put(row[1], row[2]);
+          } else {
+            if (sid.equals(sampleId)) {
+              fileMap.computeIfAbsent(sid, k -> new HashMap<>())
+                  .put(row[1], row[2]);
+            } else if (fileMap.containsKey(sid)) {
+              // all values for a single sample must be consecutive
+              break;
+            }
+          }
+        }
+      }
+    }
+    return fileMap.get(sampleId);
+  }
 }

src/main/java/org/pharmgkb/pharmcat/PharmCAT.java

@@ -28,6 +28,7 @@ public static void main(String[] args) {
           // inputs
           .addOption("s", "samples", "Comma-separated list of samples", false, "samples")
           .addOption("S", "sample-file", "File containing a list of sample, one per line", false, "file")
+          .addOption("sm", "sample-metadata", "TSV containing sample metadata", false, "file")
 
           // named allele matcher args
           .addOption("matcher", "matcher", "Run named allele matcher independently")

src/main/java/org/pharmgkb/pharmcat/Pipeline.java

@@ -61,6 +61,7 @@ public enum Mode {
   private Path m_matcherHtmlFile;
   /** True if the VCF file only contains a single sample. */
   private final boolean m_singleSample;
+  private final Path m_sampleMetadataFile;
 
   private final boolean m_runPhenotyper;
   private Path m_phenotyperInputFile;
@@ -97,7 +98,8 @@ public Pipeline(Env env, BaseConfig config, @Nullable VcfFile vcfFile,
         config.reporterSources, config.reporterCompact,
         config.reporterJson, config.reporterHtml, config.reporterCallsOnlyTsv,
         config.outputDir, config.baseFilename, config.deleteIntermediateFiles,
-        Pipeline.Mode.CLI, null, config.verbose);
+        Pipeline.Mode.CLI, null, config.verbose,
+        config.sampleMetadataFile);
   }
 
 
@@ -109,11 +111,13 @@ public Pipeline(Env env,
       @Nullable List<PrescribingGuidanceSource> reporterSources, boolean reporterCompact,
       boolean reporterJson, boolean reporterHtml, boolean reporterCallsOnlyTsv,
       @Nullable Path outputDir, @Nullable String baseFilename, boolean deleteIntermediateFiles,
-      Mode mode, @Nullable String displayCount, boolean verbose) throws ReportableException {
+      Mode mode, @Nullable String displayCount, boolean verbose,
+      @Nullable Path sampleMetadataFile) throws ReportableException {
     m_env = env;
 
     m_runMatcher = runMatcher;
     m_baseDir = outputDir;
+    m_sampleMetadataFile = sampleMetadataFile;
     if (runMatcher) {
       m_vcfFile = Objects.requireNonNull(vcfFile);
       m_sampleId = sampleId;
@@ -268,7 +272,7 @@ public PipelineResult call() throws IOException {
         if (!batchDisplayMode) {
           namedAlleleMatcher.printWarnings();
         }
-        matcherResult = namedAlleleMatcher.call(m_vcfFile, m_sampleId);
+        matcherResult = namedAlleleMatcher.call(m_vcfFile, m_sampleId, m_sampleMetadataFile);
 
         if (matcherResult.getVcfWarnings() != null &&
             !matcherResult.getVcfWarnings().isEmpty()) {

src/main/java/org/pharmgkb/pharmcat/haplotype/AutogeneratedVcfTester.java

@@ -214,7 +214,7 @@ private void test(String gene, NamedAlleleMatcher namedAlleleMatcher, VcfFile vc
 
     boolean hasUnknownCall = expectedAlleles.contains("?");
     boolean hasComboCall = !hasUnknownCall && vcfFile.getFile().getFileName().toString().contains("noCall");
-    Result result = namedAlleleMatcher.call(vcfFile, null);
+    Result result = namedAlleleMatcher.call(vcfFile, null, null);
 
     if (isLowestFunctionGene(gene)) {
       if (result.getGeneCalls().get(0).getDiplotypes().isEmpty()) {

src/main/java/org/pharmgkb/pharmcat/haplotype/NamedAlleleMatcher.java

@@ -138,7 +138,7 @@ public static void main(String[] args) {
       NamedAlleleMatcher namedAlleleMatcher =
           new NamedAlleleMatcher(new Env(), definitionReader, findCombinations, topCandidateOnly, callCyp2d6)
               .printWarnings();
-      Result result = namedAlleleMatcher.call(new VcfFile(vcfFile), null);
+      Result result = namedAlleleMatcher.call(new VcfFile(vcfFile), null, null);
 
       Path jsonFile = CliUtils.getOutputFile(cliHelper, vcfFile, "json", BaseConfig.MATCHER_SUFFIX + ".json");
       ResultSerializer resultSerializer = new ResultSerializer();
@@ -182,10 +182,18 @@ private boolean getTopCandidateOnly(String gene) {
    * Calls diplotypes for the given VCF file for all genes for which a definition exists.
    */
   public Result call(VcfFile vcfFile, @Nullable String sampleId) throws IOException {
+    return call(vcfFile, sampleId, null);
+  }
+
+  /**
+   * Calls diplotypes for the given VCF file for all genes for which a definition exists.
+   */
+  public Result call(VcfFile vcfFile, @Nullable String sampleId, @Nullable Path sampleMetadataFile) throws IOException {
     VcfReader vcfReader = vcfFile.getReader(m_definitionReader, sampleId, m_findCombinations);
     SortedMap<String, SampleAllele> alleleMap = vcfReader.getAlleleMap();
     ResultBuilder resultBuilder = new ResultBuilder(m_definitionReader, m_topCandidateOnly, m_findCombinations, m_callCyp2d6)
-        .forFile(vcfFile, vcfReader.getWarnings().asMap());
+        .forFile(vcfFile, vcfReader.getWarnings().asMap(), vcfReader.getSampleId(), sampleMetadataFile);
+
     if (m_printWarnings) {
       vcfReader.getWarnings().keySet()
           .forEach(key -> {
@@ -207,7 +215,7 @@ public Result call(VcfFile vcfFile, @Nullable String sampleId) throws IOExceptio
         callAssumingReference(vcfReader.getSampleId(), alleleMap, gene, resultBuilder);
       }
     }
-    return resultBuilder.build();
+    return resultBuilder.build(m_env);
   }
 
   /**

src/main/java/org/pharmgkb/pharmcat/haplotype/ResultBuilder.java

@@ -1,5 +1,7 @@
 package org.pharmgkb.pharmcat.haplotype;
 
+import java.io.IOException;
+import java.nio.file.Path;
 import java.util.Collection;
 import java.util.Date;
 import java.util.List;
@@ -10,6 +12,7 @@
 import com.google.common.base.Preconditions;
 import org.checkerframework.checker.nullness.qual.Nullable;
 import org.pharmgkb.common.util.PathUtils;
+import org.pharmgkb.pharmcat.Env;
 import org.pharmgkb.pharmcat.VcfFile;
 import org.pharmgkb.pharmcat.definition.DefinitionReader;
 import org.pharmgkb.pharmcat.definition.model.DefinitionFile;
@@ -35,6 +38,7 @@ public class ResultBuilder {
   private final boolean m_topCandidatesOnly;
   private final boolean m_findCombinations;
   private final boolean m_callCyp2d6;
+  private Path m_sampleMetadataFile;
 
 
   public ResultBuilder(DefinitionReader definitionReader, boolean topCandidatesOnly, boolean findCombinations,
@@ -46,19 +50,30 @@ public ResultBuilder(DefinitionReader definitionReader, boolean topCandidatesOnl
     m_callCyp2d6 = callCyp2d6;
   }
 
-  public Result build() {
+  public Result build(Env env) throws IOException {
+    if (m_sampleMetadataFile != null) {
+      Metadata metadata = m_result.getMetadata();
+      Map<String, String> sampleData = env.getSampleMetadata(m_sampleMetadataFile, metadata.getSampleId(), true);
+      if (sampleData != null && !sampleData.isEmpty()) {
+        metadata.setSampleProps(sampleData);
+      }
+    }
     return m_result;
   }
 
 
-  public ResultBuilder forFile(VcfFile vcfFile, Map<String, Collection<String>> warnings) {
+  public ResultBuilder forFile(VcfFile vcfFile, Map<String, Collection<String>> warnings, String sampleId,
+      @Nullable Path sampleMetadataFile) {
     Preconditions.checkNotNull(vcfFile);
 
-    m_result.setMetadata(new Metadata(NamedAlleleMatcher.VERSION, m_definitionReader.getGenomeBuild(),
-        PathUtils.getFilename(vcfFile.getFile()), new Date(), m_topCandidatesOnly, m_findCombinations, m_callCyp2d6));
+    Metadata metadata = new Metadata(NamedAlleleMatcher.VERSION, m_definitionReader.getGenomeBuild(),
+        PathUtils.getFilename(vcfFile.getFile()), new Date(), m_topCandidatesOnly, m_findCombinations, m_callCyp2d6,
+        sampleId);
+    m_result.setMetadata(metadata);
     if (warnings != null) {
       m_result.setVcfWarnings(warnings);
     }
+    m_sampleMetadataFile = sampleMetadataFile;
     return this;
   }
 
@@ -74,15 +89,15 @@ protected ResultBuilder gene(String gene, MatchData matchData) {
 
 
   /**
-   * Adds diplotype results for specified gene.
+   * Adds diplotype results for a specified gene.
    */
   protected ResultBuilder diplotypes(String gene, MatchData matchData, SortedSet<DiplotypeMatch> matches) {
     Preconditions.checkNotNull(gene);
     return diplotypes(gene, matchData, matches, null);
   }
 
   /**
-   * Adds diplotype results for specified gene.
+   * Adds diplotype results for a specified gene.
    */
   protected ResultBuilder diplotypes(String gene, MatchData matchData, SortedSet<DiplotypeMatch> matches,
       @Nullable List<MessageAnnotation> warnings) {
@@ -100,7 +115,7 @@ protected ResultBuilder diplotypes(String gene, MatchData matchData, SortedSet<D
 
 
   /**
-   * Add haplotype results for specified gene.
+   * Add haplotype results for a specified gene.
    * <p>
    * This should only be used when we can't get diplotypes but still need to track potential haplotypes (e.g. DPYD).
    */
@@ -109,7 +124,7 @@ protected ResultBuilder haplotypes(String gene, MatchData matchData, List<Haplot
   }
 
   /**
-   * Add haplotype results for specified gene.
+   * Add haplotype results for a specified gene.
    * <p>
    * This should only be used when we can't get diplotypes but still need to track potential haplotypes (e.g. DPYD).
    */

src/main/java/org/pharmgkb/pharmcat/haplotype/VcfReader.java

@@ -122,7 +122,11 @@ public VcfReader(DefinitionReader definitionReader, Path vcfFile) throws IOExcep
   }
 
 
-  public @Nullable String getSampleId() {
+  /**
+   * Gets the Sample ID of the data to read.
+   */
+  public String getSampleId() {
+    // this should never be null after read() is called
     return m_sampleId;
   }
 

src/main/java/org/pharmgkb/pharmcat/haplotype/model/Metadata.java

@@ -2,8 +2,10 @@
 package org.pharmgkb.pharmcat.haplotype.model;
 
 import java.util.Date;
+import java.util.Map;
 import com.google.gson.annotations.Expose;
 import com.google.gson.annotations.SerializedName;
+import org.checkerframework.checker.nullness.qual.Nullable;
 
 
 public class Metadata {
@@ -18,7 +20,7 @@ public class Metadata {
   private String m_inputFilename;
   @Expose
   @SerializedName("timestamp")
-  private Date m_timetamp;
+  private Date m_timestamp;
   @Expose
   @SerializedName("topCandidatesOnly")
   private boolean m_topCandidatesOnly;
@@ -28,17 +30,24 @@ public class Metadata {
   @Expose
   @SerializedName("callCyp2d")
   private boolean m_callCyp2d6;
+  @Expose
+  @SerializedName("sampleId")
+  private String m_sampleId;
+  @Expose
+  @SerializedName("sampleProps")
+  private Map<String, String> m_sampleProps;
 
 
   public Metadata(String namedAlleleMatcherVersion, String genomeBuild, String vcfFilename, Date date,
-      boolean topCandidatesOnly, boolean findCombinations, boolean callCyp2d6) {
+      boolean topCandidatesOnly, boolean findCombinations, boolean callCyp2d6, String sampleId) {
     m_namedAlleleMatcherVersion = namedAlleleMatcherVersion;
     m_genomeBuild = genomeBuild;
     m_inputFilename = vcfFilename;
-    m_timetamp = date;
+    m_timestamp = date;
     m_topCandidatesOnly = topCandidatesOnly;
     m_findCombinations = findCombinations;
     m_callCyp2d6 = callCyp2d6;
+    m_sampleId = sampleId;
   }
 
 
@@ -54,8 +63,8 @@ public String getInputFilename() {
     return m_inputFilename;
   }
 
-  public Date getTimetamp() {
-    return m_timetamp;
+  public Date getTimestamp() {
+    return m_timestamp;
   }
 
   public boolean isTopCandidatesOnly() {
@@ -69,4 +78,21 @@ public boolean isFindCombinations() {
   public boolean isCallCyp2d6() {
     return m_callCyp2d6;
   }
+
+
+  public String getSampleId() {
+    return m_sampleId;
+  }
+
+  public void setSampleId(String sampleId) {
+    m_sampleId = sampleId;
+  }
+
+  public @Nullable Map<String, String> getSampleProps() {
+    return m_sampleProps;
+  }
+
+  public void setSampleProps(Map<String, String> sampleProps) {
+    m_sampleProps = sampleProps;
+  }
 }