feat(pharmcat): add FDA PGx association recommendations

- add FDA PGx Assocation recommendation data
- add new DataSourceType class to group recommendation datas
- rename recommendation data files to accommodate two FDA data types

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

@@ -14,7 +14,7 @@
 import org.apache.commons.io.FilenameUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.pharmgkb.common.util.CliHelper;
-import org.pharmgkb.pharmcat.reporter.model.DataSource;
+import org.pharmgkb.pharmcat.reporter.model.PrescribingGuidanceSource;
 
 
 /**
@@ -40,7 +40,7 @@ public class BaseConfig {
   boolean runReporter = true;
   String reporterTitle;
   boolean reporterCompact = true;
-  List<DataSource> reporterSources;
+  List<PrescribingGuidanceSource> reporterSources;
   boolean reporterJson;
   boolean reporterHtml = true;
   Path outputDir;
@@ -93,7 +93,6 @@ public class BaseConfig {
       topCandidateOnly = !cliHelper.hasOption("ma");
 
       if (cliHelper.hasOption("research")) {
-        //noinspection UnstableApiUsage
         List<String> types = sf_commaSplitter.splitToStream(Objects.requireNonNull(cliHelper.getValue("research")))
             .map(String::toLowerCase)
             .collect(Collectors.toList());
@@ -134,7 +133,7 @@ public class BaseConfig {
         reporterSources = new ArrayList<>();
         for (String src : sf_commaSplitter.splitToList(Objects.requireNonNull(cliHelper.getValue("rs")))) {
           try {
-            reporterSources.add(DataSource.valueOf(src.toUpperCase()));
+            reporterSources.add(PrescribingGuidanceSource.valueOf(src));
           } catch (IllegalArgumentException ex) {
             throw new ReportableException("Unknown source: " + src);
           }

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

@@ -13,6 +13,7 @@
 import org.pharmgkb.pharmcat.reporter.caller.Cyp2d6CopyNumberCaller;
 import org.pharmgkb.pharmcat.reporter.model.DataSource;
 import org.pharmgkb.pharmcat.reporter.model.MessageAnnotation;
+import org.pharmgkb.pharmcat.reporter.model.PrescribingGuidanceSource;
 import org.pharmgkb.pharmcat.reporter.model.result.Haplotype;
 
 
@@ -68,6 +69,10 @@ public String getReferenceAllele(String gene) {
     return m_phenotypeMap.getPhenotype(gene, source);
   }
 
+  public @Nullable GenePhenotype getPhenotype(String gene, PrescribingGuidanceSource source) {
+    return m_phenotypeMap.getPhenotype(gene, source.getPhenoSource());
+  }
+
 
   public PgkbGuidelineCollection getDrugs() {
     return m_drugs;

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

@@ -23,7 +23,7 @@
 import org.pharmgkb.pharmcat.reporter.ReportContext;
 import org.pharmgkb.pharmcat.reporter.format.HtmlFormat;
 import org.pharmgkb.pharmcat.reporter.format.JsonFormat;
-import org.pharmgkb.pharmcat.reporter.model.DataSource;
+import org.pharmgkb.pharmcat.reporter.model.PrescribingGuidanceSource;
 
 
 /**
@@ -64,7 +64,7 @@ public enum Mode {
   private Path m_reporterInputFile;
   private String m_reporterTitle;
   private boolean m_reporterCompact;
-  private List<DataSource> m_reporterSources;
+  private List<PrescribingGuidanceSource> m_reporterSources;
   private Path m_reporterJsonFile;
   private Path m_reporterHtmlFile;
   private ReportContext m_reportContext;
@@ -83,7 +83,7 @@ public Pipeline(Env env,
       boolean topCandidateOnly, boolean callCyp2d6, boolean findCombinations, boolean matcherHtml,
       boolean runPhenotyper, @Nullable Path phenotyperInputFile, @Nullable Path phenotyperOutsideCallsFile,
       boolean runReporter, @Nullable Path reporterInputFile, @Nullable String reporterTitle,
-      @Nullable List<DataSource> reporterSources, boolean reporterCompact, boolean reporterJson, boolean reporterHtml,
+      @Nullable List<PrescribingGuidanceSource> reporterSources, boolean reporterCompact, boolean reporterJson, boolean reporterHtml,
       @Nullable Path outputDir, @Nullable String baseFilename, boolean deleteIntermediateFiles,
       Mode mode, @Nullable String displayCount, boolean verbose) throws ReportableException {
     m_env = env;

src/main/java/org/pharmgkb/pharmcat/reporter/MessageHelper.java

@@ -19,6 +19,7 @@
 import org.pharmgkb.pharmcat.reporter.model.DataSource;
 import org.pharmgkb.pharmcat.reporter.model.MatchLogic;
 import org.pharmgkb.pharmcat.reporter.model.MessageAnnotation;
+import org.pharmgkb.pharmcat.reporter.model.PrescribingGuidanceSource;
 import org.pharmgkb.pharmcat.reporter.model.VariantReport;
 import org.pharmgkb.pharmcat.reporter.model.result.AnnotationReport;
 import org.pharmgkb.pharmcat.reporter.model.result.CallSource;
@@ -153,11 +154,11 @@ else if (!StringUtils.isBlank(match.getVariant()) &&
    * @param drugReport a {@link DrugReport} to add message annotations to
    * @param reportContext the report context to pull related information from
    */
-  public void addMatchingMessagesTo(DrugReport drugReport, ReportContext reportContext, DataSource source) {
+  public void addMatchingMessagesTo(DrugReport drugReport, ReportContext reportContext, PrescribingGuidanceSource source) {
     Collection<MessageAnnotation> allMessages = m_drugMap.get(drugReport.getName()).stream()
         .filter((ma) -> allowedForSource(ma, source))
         .toList();
-    if (allMessages.size() == 0) {
+    if (allMessages.isEmpty()) {
       return;
     }
     List<MessageAnnotation> reportAsGenotype = new ArrayList<>();
@@ -171,15 +172,15 @@ public void addMatchingMessagesTo(DrugReport drugReport, ReportContext reportCon
       }
     }
 
-    if (reportAsGenotype.size() > 0) {
+    if (!reportAsGenotype.isEmpty()) {
       for (MessageAnnotation msgAnn : reportAsGenotype) {
         String geneSymbol = msgAnn.getMatches().getGene();
         String genotype = null;
         for (GuidelineReport guidelineReport : drugReport.getGuidelines()) {
           if (geneSymbol == null || guidelineReport.getGenes().contains(geneSymbol)) {
             for (AnnotationReport annotationReport : guidelineReport.getAnnotations()) {
               if (genotype == null) {
-                genotype = computeGenotype(msgAnn, reportContext, source);
+                genotype = computeGenotype(msgAnn, reportContext, source.getPhenoSource());
               }
               annotationReport.addHighlightedVariant(genotype);
             }
@@ -189,18 +190,15 @@ public void addMatchingMessagesTo(DrugReport drugReport, ReportContext reportCon
     }
   }
 
-  private boolean allowedForSource(MessageAnnotation messageAnnotation, DataSource source) {
+  private boolean allowedForSource(MessageAnnotation messageAnnotation, PrescribingGuidanceSource source) {
     String key = messageAnnotation.getName();
-    if (key.contains("cpic-") && source != DataSource.CPIC) {
+    if (key.contains("cpic-") && source != PrescribingGuidanceSource.CPIC_GUIDELINE) {
       return false;
     }
-    if (key.contains("dpwg-") && source != DataSource.DPWG) {
+    if (key.contains("dpwg-") && source != PrescribingGuidanceSource.DPWG_GUIDELINE) {
       return false;
     }
-    if (key.contains("fda-") && source != DataSource.FDA) {
-      return false;
-    }
-    return true;
+    return !key.contains("fda-") || source == PrescribingGuidanceSource.FDA_LABEL;
   }
 
 
@@ -237,7 +235,7 @@ private String computeGenotype(MessageAnnotation msgAnn, ReportContext reportCon
    * @return true if the message is a match, false otherwise
    */
   private boolean matchDrugReport(MessageAnnotation message, ReportContext reportContext,
-      DataSource source) {
+      PrescribingGuidanceSource source) {
     String gene = message.getMatches().getGene();
     if (StringUtils.isBlank(gene)) {
       return true;

src/main/java/org/pharmgkb/pharmcat/reporter/PgkbGuidelineCollection.java

@@ -17,6 +17,7 @@
 import com.google.common.collect.TreeMultimap;
 import org.pharmgkb.common.util.PathUtils;
 import org.pharmgkb.pharmcat.reporter.model.DataSource;
+import org.pharmgkb.pharmcat.reporter.model.PrescribingGuidanceSource;
 import org.pharmgkb.pharmcat.reporter.model.pgkb.AccessionObject;
 import org.pharmgkb.pharmcat.reporter.model.pgkb.GuidelinePackage;
 import org.pharmgkb.pharmcat.util.DataSerializer;
@@ -41,7 +42,7 @@ public PgkbGuidelineCollection(Path dir) throws IOException {
         stream.filter(f -> f.getFileName().toString().endsWith(".json"))
             .forEach(annotationFiles::add);
     }}
-    if (annotationFiles.size() == 0) {
+    if (annotationFiles.isEmpty()) {
       throw new IOException("Cannot find annotations");
     }
 
@@ -60,9 +61,9 @@ public List<GuidelinePackage> getGuidelinePackages() {
     return f_guidelinePackages;
   }
 
-  public List<GuidelinePackage> findGuidelinePackages(String chemicalName, DataSource source) {
+  public List<GuidelinePackage> findGuidelinePackages(String chemicalName, PrescribingGuidanceSource source) {
     return f_guidelineMap.get(chemicalName).stream()
-        .filter(p -> p.getGuideline().getSource().equalsIgnoreCase(source.getPharmgkbName()))
+        .filter(p -> p.isDataSourceType(source))
         .collect(Collectors.toList());
   }
 

src/main/java/org/pharmgkb/pharmcat/reporter/ReportContext.java

@@ -10,13 +10,13 @@
 import java.util.Set;
 import java.util.SortedMap;
 import java.util.TreeMap;
-import com.google.common.collect.ImmutableList;
 import com.google.gson.annotations.Expose;
 import com.google.gson.annotations.SerializedName;
 import org.checkerframework.checker.nullness.qual.Nullable;
 import org.pharmgkb.pharmcat.Env;
 import org.pharmgkb.pharmcat.reporter.model.DataSource;
 import org.pharmgkb.pharmcat.reporter.model.MessageAnnotation;
+import org.pharmgkb.pharmcat.reporter.model.PrescribingGuidanceSource;
 import org.pharmgkb.pharmcat.reporter.model.pgkb.GuidelinePackage;
 import org.pharmgkb.pharmcat.reporter.model.result.DrugReport;
 import org.pharmgkb.pharmcat.reporter.model.result.GeneReport;
@@ -30,8 +30,6 @@
  * @author Ryan Whaley
  */
 public class ReportContext {
-  private static final List<DataSource> DRUG_REPORT_SOURCES = ImmutableList.of(DataSource.CPIC, DataSource.DPWG, DataSource.FDA);
-
   @Expose
   @SerializedName("title")
   private final String f_title;
@@ -52,7 +50,7 @@ public class ReportContext {
   private final SortedMap<DataSource, SortedMap<String, GeneReport>> m_geneReports;
   @Expose
   @SerializedName("drugs")
-  private final SortedMap<DataSource, SortedMap<String, DrugReport>> m_drugReports = new TreeMap<>();
+  private final SortedMap<PrescribingGuidanceSource, SortedMap<String, DrugReport>> m_drugReports = new TreeMap<>();
   @Expose
   @SerializedName("messages")
   private final List<MessageAnnotation> f_messages = new ArrayList<>();
@@ -70,12 +68,12 @@ public ReportContext(Env env, SortedMap<DataSource, SortedMap<String, GeneReport
     m_cpicVersion = validateVersions(env.getDrugs(), DataSource.CPIC);
     m_dpwgVersion = validateVersions(env.getDrugs(), DataSource.DPWG);
 
-    for (DataSource dataSource : DRUG_REPORT_SOURCES) {
-      Map<String, DrugReport> drugReports = m_drugReports.computeIfAbsent(dataSource, (s) -> new TreeMap<>());
+    for (PrescribingGuidanceSource dataSourceType : PrescribingGuidanceSource.values()) {
+      Map<String, DrugReport> drugReports = m_drugReports.computeIfAbsent(dataSourceType, (s) -> new TreeMap<>());
       // go through all drugs, we iterate this way because one guideline may have multiple chemicals/drugs
       for (String drugName : env.getDrugs().getGuidelineMap().keys()) {
-        List<GuidelinePackage> guidelinePackages = env.getDrugs().findGuidelinePackages(drugName, dataSource);
-        if (guidelinePackages != null && guidelinePackages.size() > 0) {
+        List<GuidelinePackage> guidelinePackages = env.getDrugs().findGuidelinePackages(drugName, dataSourceType);
+        if (guidelinePackages != null && !guidelinePackages.isEmpty()) {
           DrugReport newDrugReport = new DrugReport(drugName, guidelinePackages, this);
           drugReports.put(drugName.toLowerCase(), newDrugReport);
         }
@@ -89,7 +87,7 @@ public ReportContext(Env env, SortedMap<DataSource, SortedMap<String, GeneReport
         .flatMap((m) -> m.values().stream())
         .forEach(messageHelper::addMatchingMessagesTo);
     // to drug reports
-    for (DataSource source : m_drugReports.keySet()) {
+    for (PrescribingGuidanceSource source : m_drugReports.keySet()) {
       for (DrugReport drugReport : m_drugReports.get(source).values()) {
         messageHelper.addMatchingMessagesTo(drugReport, this, source);
 
@@ -150,7 +148,7 @@ private String validateVersions(PgkbGuidelineCollection guidelineCollection, Dat
    *
    * @return a map of {@link DrugReport} objects
    */
-  public Map<DataSource, SortedMap<String, DrugReport>> getDrugReports() {
+  public Map<PrescribingGuidanceSource, SortedMap<String, DrugReport>> getDrugReports() {
     return m_drugReports;
   }
 
@@ -168,8 +166,8 @@ public List<DrugReport> getDrugReports(String drug) {
         .toList();
   }
 
-  public @Nullable DrugReport getDrugReport(DataSource source, String drug) {
-    return m_drugReports.get(source).get(drug);
+  public @Nullable DrugReport getDrugReport(PrescribingGuidanceSource type, String drug) {
+    return m_drugReports.get(type).get(drug);
   }
 
   public List<GeneReport> getGeneReports(String gene) {
@@ -180,12 +178,13 @@ public List<GeneReport> getGeneReports(String gene) {
   }
 
   public @Nullable GeneReport getGeneReport(DataSource source, String gene) {
-    if (source == DataSource.FDA) {
-      return m_geneReports.get(DataSource.CPIC).get(gene);
-    }
     return m_geneReports.get(source).get(gene);
   }
 
+  public @Nullable GeneReport getGeneReport(PrescribingGuidanceSource source, String gene) {
+    return m_geneReports.get(source.getPhenoSource()).get(gene);
+  }
+
   /**
    * The user-freindly title for the report
    * @return the title string

src/main/java/org/pharmgkb/pharmcat/reporter/format/HtmlFormat.java

@@ -15,11 +15,12 @@
 import java.util.SortedSet;
 import java.util.TreeMap;
 import java.util.TreeSet;
+import java.util.stream.Collectors;
 import com.github.jknack.handlebars.Handlebars;
 import com.github.jknack.handlebars.helper.StringHelpers;
 import com.github.jknack.handlebars.io.ClassPathTemplateLoader;
 import com.google.common.collect.HashMultimap;
-import com.google.common.collect.Lists;
+import com.google.common.collect.ImmutableSet;
 import com.google.common.collect.Multimap;
 import com.google.common.collect.SortedSetMultimap;
 import com.google.common.collect.TreeMultimap;
@@ -31,6 +32,7 @@
 import org.pharmgkb.pharmcat.reporter.handlebars.ReportHelpers;
 import org.pharmgkb.pharmcat.reporter.model.DataSource;
 import org.pharmgkb.pharmcat.reporter.model.MessageAnnotation;
+import org.pharmgkb.pharmcat.reporter.model.PrescribingGuidanceSource;
 import org.pharmgkb.pharmcat.reporter.model.result.CallSource;
 import org.pharmgkb.pharmcat.reporter.model.result.DrugLink;
 import org.pharmgkb.pharmcat.reporter.model.result.DrugReport;
@@ -48,7 +50,8 @@ public class HtmlFormat extends AbstractFormat {
   private static final String sf_templatePrefix = "/org/pharmgkb/pharmcat/reporter";
   private static final String sf_handlebarTemplateName = "report";
   private static final boolean sf_compact_drugs = false;
-  private List<DataSource> m_sources = Lists.newArrayList(DataSource.CPIC, DataSource.DPWG, DataSource.FDA);
+  private Set<DataSource> m_geneSources = ImmutableSet.of(DataSource.CPIC, DataSource.DPWG);
+  private List<PrescribingGuidanceSource> m_sources = PrescribingGuidanceSource.listValues();
   private boolean m_compact;
   private final boolean f_testMode;
 
@@ -63,8 +66,11 @@ public HtmlFormat(Path outputPath, Env env, boolean testMode) {
     f_testMode = testMode;
   }
 
-  public HtmlFormat sources(List<DataSource> sources) {
+  public HtmlFormat sources(List<PrescribingGuidanceSource> sources) {
     if (sources != null) {
+      m_geneSources = sources.stream()
+          .map(PrescribingGuidanceSource::getPhenoSource)
+          .collect(Collectors.toSet());
       m_sources = sources;
     }
     return this;
@@ -122,7 +128,7 @@ private Map<String,Object> compile(ReportContext reportContext) {
     SortedSetMultimap<String, GeneReport> geneReportMap = TreeMultimap.create();
     Map<String, Map<String, String>> functionMap = new HashMap<>();
     for (DataSource source : new TreeSet<>(reportContext.getGeneReports().keySet())) {
-      if (!m_sources.contains(source)) {
+      if (!m_geneSources.contains(source)) {
         continue;
       }
       for (GeneReport geneReport : reportContext.getGeneReports().get(source).values()) {
@@ -151,7 +157,7 @@ private Map<String,Object> compile(ReportContext reportContext) {
         }
 
         // skip gene reports that aren't related to any drugs
-        if (geneReport.getRelatedDrugs().size() == 0) {
+        if (geneReport.getRelatedDrugs().isEmpty()) {
           continue;
         }
 
@@ -225,7 +231,7 @@ private Map<String,Object> compile(ReportContext reportContext) {
 
     // Section II: Prescribing Recommendations
     SortedMap<String, Recommendation> recommendationMap = new TreeMap<>();
-    for (DataSource source : reportContext.getDrugReports().keySet()) {
+    for (PrescribingGuidanceSource source : reportContext.getDrugReports().keySet()) {
       if (!m_sources.contains(source)) {
         continue;
       }