Merge pull request #638 from TheJacksonLaboratory/move-html-and-tsv-t…

…o-lirical-io

Move the HTML and TSV writers into the I/O module

lirical-configuration/src/main/java/org/monarchinitiative/lirical/configuration/AnalysisResultWriterFactoryImpl.java

@@ -3,8 +3,8 @@
 import org.monarchinitiative.lirical.core.output.AnalysisResultWriterFactory;
 import org.monarchinitiative.lirical.core.output.AnalysisResultsWriter;
 import org.monarchinitiative.lirical.core.output.OutputFormat;
-import org.monarchinitiative.lirical.core.output.TemplateBasedAnalysisResultsWriter;
 import org.monarchinitiative.lirical.io.output.JsonAnalysisResultWriter;
+import org.monarchinitiative.lirical.io.output.TemplateBasedAnalysisResultsWriter;
 import org.monarchinitiative.phenol.annotations.formats.hpo.HpoDiseases;
 import org.monarchinitiative.phenol.ontology.data.Ontology;
 

lirical-core/pom.xml

@@ -48,10 +48,6 @@
             <groupId>org.apache.commons</groupId>
             <artifactId>commons-lang3</artifactId>
         </dependency>
-        <dependency>
-            <groupId>org.freemarker</groupId>
-            <artifactId>freemarker</artifactId>
-        </dependency>
 
         <dependency>
             <groupId>org.monarchinitiative.phenol</groupId>

lirical-core/src/main/java/org/monarchinitiative/lirical/core/likelihoodratio/LrWithExplanationFactory.java

@@ -1,13 +1,14 @@
 package org.monarchinitiative.lirical.core.likelihoodratio;
 
-import org.monarchinitiative.phenol.ontology.data.Ontology;
+import org.monarchinitiative.phenol.ontology.data.MinimalOntology;
+import org.monarchinitiative.phenol.ontology.data.Term;
 import org.monarchinitiative.phenol.ontology.data.TermId;
 
 public class LrWithExplanationFactory {
 
-    private final Ontology ontology;
+    private final MinimalOntology ontology;
 
-    public LrWithExplanationFactory(Ontology ontology) {
+    public LrWithExplanationFactory(MinimalOntology ontology) {
         this.ontology = ontology;
     }
 
@@ -20,8 +21,8 @@ public LrWithExplanation create(TermId queryTerm, TermId matchingTerm, LrMatchTy
     }
 
     private String getExplanation(TermId queryTerm, TermId matchingTerm, LrMatchType matchType, double lr) {
-        String queryTermLabel = String.format("%s[%s]", ontology.getTermMap().get(queryTerm).getName(), queryTerm.getValue());
-        String matchTermLabel = String.format("%s[%s]", ontology.getTermMap().get(matchingTerm).getName(), matchingTerm.getValue());
+        String queryTermLabel = String.format("%s[%s]", ontology.termForTermId(queryTerm).map(Term::getName).orElse("UNKNOWN"), queryTerm.getValue());
+        String matchTermLabel = String.format("%s[%s]", ontology.termForTermId(matchingTerm).map(Term::getName).orElse("UNKNOWN"), matchingTerm.getValue());
         double log10LR = Math.log10(lr);
         return switch (matchType) {
             case EXACT_MATCH -> String.format("E:%s[%.3f]", queryTermLabel, log10LR);

lirical-core/src/main/java/org/monarchinitiative/lirical/core/output/package-info.java

@@ -1,4 +1,4 @@
 /**
- * Classes for creating HTML or TSV output files for LIRICAL.
+ * Base data model for writing out the results of LIRICAL analysis.
  */
 package org.monarchinitiative.lirical.core.output;

lirical-io/pom.xml

@@ -33,6 +33,10 @@
             <groupId>com.fasterxml.jackson.datatype</groupId>
             <artifactId>jackson-datatype-jdk8</artifactId>
         </dependency>
+        <dependency>
+            <groupId>org.freemarker</groupId>
+            <artifactId>freemarker</artifactId>
+        </dependency>
         <dependency>
             <groupId>com.google.protobuf</groupId>
             <artifactId>protobuf-java</artifactId>

lirical-core/src/main/java/org/monarchinitiative/lirical/core/output/BaseDifferential.java → lirical-io/src/main/java/org/monarchinitiative/lirical/io/output/BaseDifferential.java

@@ -1,7 +1,7 @@
-package org.monarchinitiative.lirical.core.output;
+package org.monarchinitiative.lirical.io.output;
 
-import org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLrWithExplanation;
 import org.monarchinitiative.lirical.core.analysis.TestResult;
+import org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLrWithExplanation;
 import org.monarchinitiative.phenol.annotations.formats.GeneIdentifier;
 import org.monarchinitiative.phenol.ontology.data.TermId;
 

lirical-core/src/main/java/org/monarchinitiative/lirical/core/output/DifferentialDiagnosis.java → lirical-io/src/main/java/org/monarchinitiative/lirical/io/output/DifferentialDiagnosis.java

@@ -1,9 +1,8 @@
-package org.monarchinitiative.lirical.core.output;
+package org.monarchinitiative.lirical.io.output;
 
 import org.monarchinitiative.lirical.core.analysis.TestResult;
 import org.monarchinitiative.phenol.ontology.data.TermId;
 
-
 import java.util.List;
 import java.util.Objects;
 

lirical-core/src/main/java/org/monarchinitiative/lirical/core/output/HtmlTemplate.java → lirical-io/src/main/java/org/monarchinitiative/lirical/io/output/HtmlTemplate.java

@@ -1,12 +1,13 @@
-package org.monarchinitiative.lirical.core.output;
+package org.monarchinitiative.lirical.io.output;
 
 import freemarker.template.Template;
 import freemarker.template.TemplateException;
 import org.monarchinitiative.lirical.core.analysis.AnalysisData;
 import org.monarchinitiative.lirical.core.analysis.AnalysisResults;
 import org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLrWithExplanation;
 import org.monarchinitiative.lirical.core.model.Gene2Genotype;
-import org.monarchinitiative.lirical.core.output.svg.Lr2Svg;
+import org.monarchinitiative.lirical.core.output.*;
+import org.monarchinitiative.lirical.io.output.svg.Lr2Svg;
 import org.monarchinitiative.phenol.annotations.formats.GeneIdentifier;
 import org.monarchinitiative.phenol.annotations.formats.hpo.HpoDisease;
 import org.monarchinitiative.phenol.annotations.formats.hpo.HpoDiseases;

lirical-core/src/main/java/org/monarchinitiative/lirical/core/output/ImprobableDifferential.java → lirical-io/src/main/java/org/monarchinitiative/lirical/io/output/ImprobableDifferential.java

@@ -1,4 +1,4 @@
-package org.monarchinitiative.lirical.core.output;
+package org.monarchinitiative.lirical.io.output;
 
 import java.text.DecimalFormat;
 

lirical-core/src/main/java/org/monarchinitiative/lirical/core/output/LiricalTemplate.java → lirical-io/src/main/java/org/monarchinitiative/lirical/io/output/LiricalTemplate.java

@@ -1,11 +1,13 @@
-package org.monarchinitiative.lirical.core.output;
+package org.monarchinitiative.lirical.io.output;
 
 import freemarker.template.Configuration;
 import freemarker.template.Version;
 import org.monarchinitiative.lirical.core.analysis.AnalysisData;
 import org.monarchinitiative.lirical.core.exception.LiricalRuntimeException;
 import org.monarchinitiative.lirical.core.model.Gene2Genotype;
 import org.monarchinitiative.lirical.core.model.LiricalVariant;
+import org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata;
+import org.monarchinitiative.lirical.core.output.OutputOptions;
 import org.monarchinitiative.phenol.ontology.data.Ontology;
 import org.monarchinitiative.phenol.ontology.data.Term;
 import org.monarchinitiative.phenol.ontology.data.TermId;
@@ -120,7 +122,7 @@ protected static void mkdirIfNotExist(Path dir) {
     }
 
     protected Function<LiricalVariant, VisualizableVariant> toVisualizableVariant() {
-        return lv -> new VisualizableVariantDefault(analysisData.sampleId(), lv, isPassingPathogenicThreshold(lv));
+        return lv -> VisualizableVariant.of(analysisData.sampleId(), lv, isPassingPathogenicThreshold(lv));
     }
 
     private boolean isPassingPathogenicThreshold(LiricalVariant lv) {

lirical-core/src/main/java/org/monarchinitiative/lirical/core/output/SparklinePacket.java → lirical-io/src/main/java/org/monarchinitiative/lirical/io/output/SparklinePacket.java

@@ -1,10 +1,10 @@
-package org.monarchinitiative.lirical.core.output;
+package org.monarchinitiative.lirical.io.output;
 
 
-import org.monarchinitiative.lirical.core.output.svg.Sparkline2Svg;
 import org.monarchinitiative.lirical.core.analysis.AnalysisResults;
-import org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLrWithExplanation;
 import org.monarchinitiative.lirical.core.analysis.TestResult;
+import org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLrWithExplanation;
+import org.monarchinitiative.lirical.io.output.svg.Sparkline2Svg;
 import org.monarchinitiative.phenol.annotations.formats.GeneIdentifier;
 import org.monarchinitiative.phenol.annotations.formats.hpo.HpoDisease;
 import org.monarchinitiative.phenol.annotations.formats.hpo.HpoDiseases;

lirical-core/src/main/java/org/monarchinitiative/lirical/core/output/TemplateBasedAnalysisResultsWriter.java → lirical-io/src/main/java/org/monarchinitiative/lirical/io/output/TemplateBasedAnalysisResultsWriter.java

@@ -1,7 +1,11 @@
-package org.monarchinitiative.lirical.core.output;
+package org.monarchinitiative.lirical.io.output;
 
 import org.monarchinitiative.lirical.core.analysis.AnalysisData;
 import org.monarchinitiative.lirical.core.analysis.AnalysisResults;
+import org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata;
+import org.monarchinitiative.lirical.core.output.AnalysisResultsWriter;
+import org.monarchinitiative.lirical.core.output.OutputFormat;
+import org.monarchinitiative.lirical.core.output.OutputOptions;
 import org.monarchinitiative.phenol.annotations.formats.hpo.HpoDiseases;
 import org.monarchinitiative.phenol.ontology.data.Ontology;
 

lirical-core/src/main/java/org/monarchinitiative/lirical/core/output/TsvDifferential.java → lirical-io/src/main/java/org/monarchinitiative/lirical/io/output/TsvDifferential.java

@@ -1,4 +1,4 @@
-package org.monarchinitiative.lirical.core.output;
+package org.monarchinitiative.lirical.io.output;
 
 import org.monarchinitiative.lirical.core.analysis.TestResult;
 import org.monarchinitiative.lirical.core.model.TranscriptAnnotation;

lirical-core/src/main/java/org/monarchinitiative/lirical/core/output/TsvTemplate.java → lirical-io/src/main/java/org/monarchinitiative/lirical/io/output/TsvTemplate.java

@@ -1,10 +1,12 @@
-package org.monarchinitiative.lirical.core.output;
+package org.monarchinitiative.lirical.io.output;
 
 import freemarker.template.Template;
 import freemarker.template.TemplateException;
 import org.monarchinitiative.lirical.core.analysis.AnalysisData;
 import org.monarchinitiative.lirical.core.analysis.AnalysisResults;
 import org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLrWithExplanation;
+import org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata;
+import org.monarchinitiative.lirical.core.output.OutputOptions;
 import org.monarchinitiative.phenol.annotations.formats.hpo.HpoDisease;
 import org.monarchinitiative.phenol.annotations.formats.hpo.HpoDiseases;
 import org.monarchinitiative.phenol.ontology.data.Ontology;

lirical-core/src/main/java/org/monarchinitiative/lirical/core/output/VisualizableVariant.java → lirical-io/src/main/java/org/monarchinitiative/lirical/io/output/VisualizableVariant.java

@@ -1,5 +1,6 @@
-package org.monarchinitiative.lirical.core.output;
+package org.monarchinitiative.lirical.io.output;
 
+import org.monarchinitiative.lirical.core.model.LiricalVariant;
 import org.monarchinitiative.lirical.core.model.TranscriptAnnotation;
 
 import java.util.List;
@@ -10,6 +11,10 @@
 public interface VisualizableVariant {
     // Note: the interface MUST be public, otherwise FreeMarker will not work.
 
+    static VisualizableVariant of(String sampleId, LiricalVariant lv, boolean isPassingPathogenicityThreshold) {
+        return new VisualizableVariantDefault(sampleId, lv, isPassingPathogenicityThreshold);
+    }
+
     String contigName();
 
     int pos();

lirical-core/src/main/java/org/monarchinitiative/lirical/core/output/VisualizableVariantDefault.java → lirical-io/src/main/java/org/monarchinitiative/lirical/io/output/VisualizableVariantDefault.java

@@ -1,4 +1,4 @@
-package org.monarchinitiative.lirical.core.output;
+package org.monarchinitiative.lirical.io.output;
 
 import org.monarchinitiative.lirical.core.model.*;
 import org.monarchinitiative.svart.CoordinateSystem;

lirical-io/src/main/java/org/monarchinitiative/lirical/io/output/package-info.java

@@ -0,0 +1,4 @@
+/**
+ * Classes for writing out LIRICAL analysis results into HTML, TSV, and JSON files.
+ */
+package org.monarchinitiative.lirical.io.output;

lirical-core/src/main/java/org/monarchinitiative/lirical/core/output/svg/Lirical2Svg.java → lirical-io/src/main/java/org/monarchinitiative/lirical/io/output/svg/Lirical2Svg.java

@@ -1,4 +1,4 @@
-package org.monarchinitiative.lirical.core.output.svg;
+package org.monarchinitiative.lirical.io.output.svg;
 
 import java.io.IOException;
 import java.io.Writer;

lirical-core/src/main/java/org/monarchinitiative/lirical/core/output/svg/Lr2Svg.java → lirical-io/src/main/java/org/monarchinitiative/lirical/io/output/svg/Lr2Svg.java

@@ -1,4 +1,4 @@
-package org.monarchinitiative.lirical.core.output.svg;
+package org.monarchinitiative.lirical.io.output.svg;
 
 
 import org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLrWithExplanation;

lirical-core/src/main/java/org/monarchinitiative/lirical/core/output/svg/Posttest2Svg.java → lirical-io/src/main/java/org/monarchinitiative/lirical/io/output/svg/Posttest2Svg.java

@@ -1,4 +1,4 @@
-package org.monarchinitiative.lirical.core.output.svg;
+package org.monarchinitiative.lirical.io.output.svg;
 
 import org.monarchinitiative.lirical.core.analysis.AnalysisResults;
 import org.monarchinitiative.phenol.annotations.formats.hpo.HpoDisease;

lirical-core/src/main/java/org/monarchinitiative/lirical/core/output/svg/Sparkline2Svg.java → lirical-io/src/main/java/org/monarchinitiative/lirical/io/output/svg/Sparkline2Svg.java

@@ -1,4 +1,4 @@
-package org.monarchinitiative.lirical.core.output.svg;
+package org.monarchinitiative.lirical.io.output.svg;
 
 import org.monarchinitiative.lirical.core.analysis.AnalysisResults;
 import org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLrWithExplanation;

lirical-core/src/main/java/org/monarchinitiative/lirical/core/output/svg/package-info.java → lirical-io/src/main/java/org/monarchinitiative/lirical/io/output/svg/package-info.java

@@ -1,4 +1,4 @@
 /** Classes to create an SVG graphic representing the result of likelihood raio analysis of one HPO Case.
  * @author <a href="mailto:[email protected]">Peter Robinson</a>
  */
-package org.monarchinitiative.lirical.core.output.svg;
+package org.monarchinitiative.lirical.io.output.svg;

lirical-core/src/test/java/org/monarchinitiative/lirical/core/output/DifferentialDiagnosisTest.java → lirical-io/src/test/java/org/monarchinitiative/lirical/io/output/DifferentialDiagnosisTest.java

@@ -1,4 +1,4 @@
-package org.monarchinitiative.lirical.core.output;
+package org.monarchinitiative.lirical.io.output;
 
 import org.junit.jupiter.api.BeforeAll;
 import org.junit.jupiter.api.Test;

lirical-io/src/test/java/org/monarchinitiative/lirical/io/output/JsonAnalysisResultWriterTest.java

@@ -27,7 +27,6 @@
 import java.util.List;
 import java.util.stream.Collectors;
 
-import static org.junit.jupiter.api.Assertions.*;
 import static org.hamcrest.MatcherAssert.*;
 import static org.hamcrest.Matchers.*;
 

lirical-core/src/test/java/org/monarchinitiative/lirical/core/output/svg/Posttest2SvgTest.java → lirical-io/src/test/java/org/monarchinitiative/lirical/io/output/svg/Posttest2SvgTest.java

@@ -1,9 +1,9 @@
-package org.monarchinitiative.lirical.core.output.svg;
+package org.monarchinitiative.lirical.io.output.svg;
 
 
 import org.junit.jupiter.api.BeforeAll;
 import org.junit.jupiter.api.Test;
-import org.monarchinitiative.lirical.core.TestResources;
+import org.mockito.Mockito;
 import org.monarchinitiative.lirical.core.analysis.AnalysisResults;
 import org.monarchinitiative.lirical.core.analysis.TestResult;
 import org.monarchinitiative.lirical.core.likelihoodratio.LrMatchType;
@@ -12,12 +12,16 @@
 import org.monarchinitiative.phenol.annotations.formats.hpo.HpoDisease;
 import org.monarchinitiative.phenol.annotations.formats.hpo.HpoDiseaseAnnotation;
 import org.monarchinitiative.phenol.annotations.formats.hpo.HpoDiseases;
+import org.monarchinitiative.phenol.ontology.data.MinimalOntology;
+import org.monarchinitiative.phenol.ontology.data.Term;
 import org.monarchinitiative.phenol.ontology.data.TermId;
 
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Optional;
 
 import static org.junit.jupiter.api.Assertions.*;
+import static org.mockito.Mockito.when;
 
 
 public class Posttest2SvgTest {
@@ -27,13 +31,20 @@ public class Posttest2SvgTest {
     private static List<HpoDisease> DISEASES;
     private static AnalysisResults RESULTS;
 
+    public static MinimalOntology HPO;
+
     @BeforeAll
     public static void setup() throws NullPointerException {
+        TermId some = TermId.of("HP:0000006");
+
+        HPO = Mockito.mock(MinimalOntology.class);
+        when(HPO.termForTermId(some)).thenReturn(Optional.of(Term.of(some, "Some term")));
+
         double PRETEST_PROB = 0.001;
-        FACTORY = new LrWithExplanationFactory(TestResources.hpo());
+        FACTORY = new LrWithExplanationFactory(HPO);
         List<TestResult> results = new ArrayList<>();
         //result 1
-        TermId some = TermId.of("HP:0000006");
+
         List<LrWithExplanation> reslist = createTestList(some, 1d, 10d, 100d);
         List<LrWithExplanation> excluded = List.of();
         List<HpoDiseaseAnnotation> annotations = List.of();