Merge pull request #140 from P2GX/cleanup

mabeckwith · web-flow · commit 3044286fe57a · 2025-12-17T14:26:06.000-05:00
Cleanup
diff --git a/maxodiff-cli/src/main/java/org/monarchinitiative/maxodiff/cli/cmd/BatchDiagnosisCommand.java b/maxodiff-cli/src/main/java/org/monarchinitiative/maxodiff/cli/cmd/BatchDiagnosisCommand.java
@@ -13,9 +13,7 @@
 import org.monarchinitiative.maxodiff.core.service.BiometadataService;
 import org.monarchinitiative.maxodiff.phenomizer.IcMicaData;
 import org.monarchinitiative.maxodiff.phenomizer.PhenomizerDifferentialDiagnosisEngine;
-import org.monarchinitiative.maxodiff.phenomizer.ScoringMode;
 import org.monarchinitiative.phenol.annotations.formats.hpo.HpoDiseases;
-import org.monarchinitiative.phenol.ontology.data.TermId;
 import org.monarchinitiative.phenol.ontology.similarity.TermPair;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
diff --git a/maxodiff-cli/src/main/java/org/monarchinitiative/maxodiff/cli/cmd/BenchmarkCommand.java b/maxodiff-cli/src/main/java/org/monarchinitiative/maxodiff/cli/cmd/BenchmarkCommand.java
@@ -43,7 +43,6 @@
 import java.util.*;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
-import java.util.stream.Collectors;
 import java.util.stream.Stream;
 import java.util.zip.GZIPOutputStream;
 
diff --git a/maxodiff-cli/src/main/java/org/monarchinitiative/maxodiff/cli/cmd/DifferentialDiagnosisCommand.java b/maxodiff-cli/src/main/java/org/monarchinitiative/maxodiff/cli/cmd/DifferentialDiagnosisCommand.java
@@ -11,15 +11,12 @@
 import org.monarchinitiative.maxodiff.core.analysis.*;
 import org.monarchinitiative.maxodiff.core.analysis.refinement.DiffDiagRefiner;
 import org.monarchinitiative.maxodiff.core.analysis.refinement.MaxodiffResult;
-import org.monarchinitiative.maxodiff.core.analysis.refinement.RefinementOptions;
-import org.monarchinitiative.maxodiff.core.analysis.refinement.RefinementResults;
 import org.monarchinitiative.maxodiff.core.diffdg.DifferentialDiagnosisEngine;
 import org.monarchinitiative.maxodiff.html.results.HtmlResults;
 import org.monarchinitiative.maxodiff.core.model.*;
 import org.monarchinitiative.maxodiff.core.service.BiometadataService;
 import org.monarchinitiative.maxodiff.phenomizer.IcMicaData;
 import org.monarchinitiative.maxodiff.phenomizer.PhenomizerDifferentialDiagnosisEngine;
-import org.monarchinitiative.maxodiff.phenomizer.ScoringMode;
 import org.monarchinitiative.phenol.annotations.formats.hpo.HpoDiseases;
 import org.monarchinitiative.phenol.ontology.data.TermId;
 import org.monarchinitiative.phenol.ontology.similarity.TermPair;
@@ -61,6 +58,9 @@ public class DifferentialDiagnosisCommand extends BaseCommand {
     protected Path outputDir = Path.of(".");
 
 
+    @CommandLine.Option(names = {"--csv"},
+            description = "Output results as CSV.")
+    private boolean writeCsv = false;
 
     @CommandLine.Option(names = {"--diseaseProbModel"},
             paramLabel = "{ranked}",
@@ -121,9 +121,7 @@ protected int runSingleMaxodiffAnalysis(Path phenopacketPath) throws Exception {
                     engine,
                     maxoDiffRefiner,
                     biometadataService);
-
-            boolean writeCsvFile = false;
-            if (writeCsvFile) {
+            if (writeCsv) {
                 MaxoDiffAnalysisResultRow row = runner.batchAnalysis(phenopacketData);
                 writeCsvResults(sample.id(), row);
             } else {
diff --git a/maxodiff-config/src/main/java/org/monarchinitiative/maxodiff/config/MaxoDiffLoader.java b/maxodiff-config/src/main/java/org/monarchinitiative/maxodiff/config/MaxoDiffLoader.java
@@ -12,7 +12,7 @@ public interface MaxoDiffLoader {
     MinimalOntology hpo();
     HpoDiseases hpoDiseases() throws MaxodiffDataException;
     IcMicaData icMicaData() throws MaxodiffDataException;
-    public static MaxoDiffLoader fileLoader(Path maxoPAth) throws MaxodiffDataException {
+    static MaxoDiffLoader fileLoader(Path maxoPAth) throws MaxodiffDataException {
         return new MaxoDiffFileLoader(maxoPAth);
     }
 }
diff --git a/maxodiff-config/src/main/java/org/monarchinitiative/maxodiff/config/MaxodiffPropsConfiguration.java b/maxodiff-config/src/main/java/org/monarchinitiative/maxodiff/config/MaxodiffPropsConfiguration.java
@@ -53,7 +53,7 @@ public DiffDiagRefiner diffDiagRefiner(String refiner) {
         DiffDiagRefiner diffDiagRefiner = null;
 
         if (refiner.equals("score")) {
-            diffDiagRefiner = new MaxoDiffRefiner(hpoDiseases, hpoToMaxoIdMap, maxoAnnotsMap, minHpo, hpo);
+            diffDiagRefiner = new MaxoDiffRefiner(hpoDiseases, hpoToMaxoIdMap, maxoAnnotsMap, hpo);
         }
         return diffDiagRefiner;
     }
diff --git a/maxodiff-core/src/main/java/org/monarchinitiative/maxodiff/core/analysis/impl/DiseaseTermCountImpl.java b/maxodiff-core/src/main/java/org/monarchinitiative/maxodiff/core/analysis/impl/DiseaseTermCountImpl.java
@@ -1,7 +1,6 @@
 package org.monarchinitiative.maxodiff.core.analysis.impl;
 
 import org.monarchinitiative.maxodiff.core.analysis.DiseaseTermCount;
-import org.monarchinitiative.maxodiff.core.analysis.HTMLFrequencyMap;
 import org.monarchinitiative.maxodiff.core.analysis.HpoFrequency;
 import org.monarchinitiative.phenol.annotations.base.Ratio;
 import org.monarchinitiative.phenol.annotations.formats.hpo.HpoDisease;
diff --git a/maxodiff-core/src/main/java/org/monarchinitiative/maxodiff/core/analysis/refinement/BaseDiffDiagRefiner.java b/maxodiff-core/src/main/java/org/monarchinitiative/maxodiff/core/analysis/refinement/BaseDiffDiagRefiner.java
@@ -6,7 +6,6 @@
 import org.monarchinitiative.maxodiff.core.model.*;
 import org.monarchinitiative.phenol.annotations.formats.hpo.HpoDisease;
 import org.monarchinitiative.phenol.annotations.formats.hpo.HpoDiseases;
-import org.monarchinitiative.phenol.ontology.data.MinimalOntology;
 import org.monarchinitiative.phenol.ontology.data.Ontology;
 import org.monarchinitiative.phenol.ontology.data.TermId;
 
@@ -18,18 +17,15 @@ public class BaseDiffDiagRefiner implements DiffDiagRefiner {
     private final HpoDiseases hpoDiseases;
     private final Map<TermId, Set<TermId>> fullHpoToMaxoTermIdMap;
     private final Map<SimpleTerm, Set<SimpleTerm>> hpoToMaxoTermMap;
-    private final MinimalOntology minHpo;
     private final Ontology hpo;
 
     public BaseDiffDiagRefiner(HpoDiseases hpoDiseases,
                                Map<TermId, Set<TermId>> fullHpoToMaxoTermIdMap,
                                Map<SimpleTerm, Set<SimpleTerm>> hpoToMaxoTermMap,
-                               MinimalOntology minHpo,
                                Ontology hpo) {
         this.hpoDiseases = hpoDiseases;
         this.fullHpoToMaxoTermIdMap = fullHpoToMaxoTermIdMap;
         this.hpoToMaxoTermMap = hpoToMaxoTermMap;
-        this.minHpo = minHpo;
         this.hpo = hpo;
     }
 
diff --git a/maxodiff-core/src/main/java/org/monarchinitiative/maxodiff/core/analysis/refinement/DiffDiagRefiner.java b/maxodiff-core/src/main/java/org/monarchinitiative/maxodiff/core/analysis/refinement/DiffDiagRefiner.java
@@ -15,7 +15,6 @@
 import java.util.Set;
 
 /**
- * TODO: insert description
  * Differential diagnosis results come from some source.
  * We don't expect to get differential diagnosis results for all possible diseases, e.g. the entire OMIM corpus.
  * We don't expect the collection of differential diagnoses to be in any particular order.
diff --git a/maxodiff-core/src/main/java/org/monarchinitiative/maxodiff/core/analysis/refinement/MaxoDiffRefiner.java b/maxodiff-core/src/main/java/org/monarchinitiative/maxodiff/core/analysis/refinement/MaxoDiffRefiner.java
diff --git a/maxodiff-core/src/main/java/org/monarchinitiative/maxodiff/core/analysis/refinement/RefinementOptions.java b/maxodiff-core/src/main/java/org/monarchinitiative/maxodiff/core/analysis/refinement/RefinementOptions.java
@@ -1,14 +1,12 @@
 package org.monarchinitiative.maxodiff.core.analysis.refinement;
 
-import org.monarchinitiative.maxodiff.core.analysis.refinement.RefinementOptionsImpl;
+public record RefinementOptions (
+        int nDiseases,
+        int nRepetitions) {
 
-public interface RefinementOptions {
-
-    static RefinementOptions of(int nDiseases, int nRepetitions) {
-        return new RefinementOptionsImpl(nDiseases, nRepetitions);
+    static public RefinementOptions of(int nDiseases, int nRepetitions) {
+        return new RefinementOptions(nDiseases, nRepetitions);
     }
 
-    int nDiseases();
-    int nRepetitions();
 
 }
diff --git a/maxodiff-core/src/main/java/org/monarchinitiative/maxodiff/core/analysis/refinement/RefinementOptionsImpl.java b/maxodiff-core/src/main/java/org/monarchinitiative/maxodiff/core/analysis/refinement/RefinementOptionsImpl.java
diff --git a/maxodiff-core/src/main/java/org/monarchinitiative/maxodiff/core/model/GeneralMaxoTerms.java b/maxodiff-core/src/main/java/org/monarchinitiative/maxodiff/core/model/GeneralMaxoTerms.java
@@ -0,0 +1,37 @@
+package org.monarchinitiative.maxodiff.core.model;
+
+import org.monarchinitiative.phenol.ontology.data.TermId;
+
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ * There are some diagnostic MAxO terms that are used as grouping terms. Sometimes, they have been used in the MAXO annotations
+ * to denote that a more specific diagnosic term was not available. For the purposes of MAxO-diff, we want to skip
+ * these terms. For instance, we have used "medical action" as an annotation to show that no other term is available.
+ * We do not expect this list to change much, if at all, in the future.
+ * @author peter robinson
+ */
+public class GeneralMaxoTerms {
+    private static TermId clinicalAssessment = TermId.of("MAXO:0000487");
+    private static TermId medicalAction = TermId.of("MAXO:0000001");
+    private static TermId medicalHistoryTaking = TermId.of("MAXO:0000574");
+    private static TermId magneticResonanceImagingProcedure = TermId.of("MAXO:0000424");
+    private static TermId clinicalBiopsy = TermId.of("MAXO:0001269");
+    private static TermId clinicalCoreNeedleBiopsy = TermId.of("MAXO:0001271");
+    private static Map<TermId, String> generalMaxoTerms = null;
+
+    public static Map<TermId, String> getGeneralMaxoTerms() {
+        if (generalMaxoTerms == null) {
+            generalMaxoTerms = new HashMap<>();
+            generalMaxoTerms.put(clinicalAssessment, "clinical Assessment");
+            generalMaxoTerms.put(medicalAction, "medical Action");
+            generalMaxoTerms.put(medicalHistoryTaking, "medical history taking");
+            generalMaxoTerms.put(magneticResonanceImagingProcedure, "magnetic resonance imaging procedure");
+            generalMaxoTerms.put(clinicalBiopsy, "clinical biopsy");
+            generalMaxoTerms.put(clinicalCoreNeedleBiopsy, "clinical core needle biopsy");
+        }
+        return generalMaxoTerms;
+
+    }
+}
diff --git a/maxodiff-core/src/main/java/org/monarchinitiative/maxodiff/core/model/RankMaxo.java b/maxodiff-core/src/main/java/org/monarchinitiative/maxodiff/core/model/RankMaxo.java
@@ -5,7 +5,6 @@
 import org.monarchinitiative.maxodiff.core.SimpleTerm;
 import org.monarchinitiative.maxodiff.core.analysis.*;
 import org.monarchinitiative.maxodiff.core.diffdg.DifferentialDiagnosisEngine;
-import org.monarchinitiative.phenol.ontology.data.MinimalOntology;
 import org.monarchinitiative.phenol.ontology.data.Ontology;
 import org.monarchinitiative.phenol.ontology.data.TermId;
 import org.slf4j.Logger;
diff --git a/maxodiff-core/src/test/java/org/monarchinitiative/maxodiff/core/analysis/RankMaxoTest.java b/maxodiff-core/src/test/java/org/monarchinitiative/maxodiff/core/analysis/RankMaxoTest.java
@@ -8,7 +8,6 @@
 import org.monarchinitiative.maxodiff.core.diffdg.DifferentialDiagnosisEngine;
 import org.monarchinitiative.maxodiff.core.model.*;
 import org.monarchinitiative.phenol.annotations.formats.hpo.HpoDiseases;
-import org.monarchinitiative.phenol.ontology.data.MinimalOntology;
 import org.monarchinitiative.phenol.ontology.data.Ontology;
 import org.monarchinitiative.phenol.ontology.data.TermId;
 
diff --git a/maxodiff-html-results/src/main/java/org/monarchinitiative/maxodiff/html/results/maxoHpo/MaxoHtmlResult.java b/maxodiff-html-results/src/main/java/org/monarchinitiative/maxodiff/html/results/maxoHpo/MaxoHtmlResult.java
@@ -5,11 +5,9 @@
 import org.monarchinitiative.maxodiff.core.analysis.RankMaxoScore;
 import org.monarchinitiative.maxodiff.core.analysis.refinement.MaxodiffResult;
 import org.monarchinitiative.maxodiff.core.service.BiometadataService;
-import org.monarchinitiative.maxodiff.html.results.HtmlResults;
 import org.monarchinitiative.maxodiff.html.results.SimpleTerm;
 import org.monarchinitiative.phenol.annotations.formats.hpo.HpoDiseases;
 import org.monarchinitiative.phenol.ontology.data.TermId;
-import org.monarchinitiative.phenol.ontology.similarity.TermPair;
 
 import java.util.*;
 
diff --git a/maxodiff-html/src/main/java/org/monarchinitiative/maxodiff/html/config/MaxodiffAutoConfiguration.java b/maxodiff-html/src/main/java/org/monarchinitiative/maxodiff/html/config/MaxodiffAutoConfiguration.java
@@ -130,7 +130,7 @@ public DiffDiagRefiner diffDiagRefiner(
             Map<TermId, Set<TermId>> hpoToMaxoIdMap,
             Map<SimpleTerm, Set<SimpleTerm>> maxoAnnotsMap) {
 
-        return new MaxoDiffRefiner(hpoDiseases, hpoToMaxoIdMap, maxoAnnotsMap, minHpo, hpo);
+        return new MaxoDiffRefiner(hpoDiseases, hpoToMaxoIdMap, maxoAnnotsMap, hpo);
     }
 
     @Bean
diff --git a/maxodiff-html/src/main/java/org/monarchinitiative/maxodiff/html/controller/MaxodiffController.java b/maxodiff-html/src/main/java/org/monarchinitiative/maxodiff/html/controller/MaxodiffController.java
@@ -41,8 +41,6 @@ public class MaxodiffController {
 
     private DiffDiagRefiner diffDiagRefiner;
 
-    private final MinimalOntology minHpo;
-
     private final Ontology hpo;
 
     private final HpoDiseases hpoDiseases;
@@ -59,7 +57,6 @@ public MaxodiffController(
             IcMicaData icMicaData,
             BiometadataService biometadataService,
             DiffDiagRefiner diffDiagRefiner,
-            MinimalOntology minHpo,
             Ontology hpo,
             HpoDiseases hpoDiseases,
             Map<TermId, Set<TermId>> hpoToMaxoIdMap,
@@ -68,7 +65,6 @@ public MaxodiffController(
         this.icMicaData = icMicaData;
         this.biometadataService = biometadataService;
         this.diffDiagRefiner = diffDiagRefiner;
-        this.minHpo = minHpo;
         this.hpo = hpo;
         this.hpoDiseases = hpoDiseases;
         this.hpoToMaxoIdMap = hpoToMaxoIdMap;
@@ -130,7 +126,7 @@ public String showResults(@RequestParam(value = "id", required = false) String s
         model.addAttribute("differentialDiagnoses", differentialDiagnoses);
 
         // Maxodiff refiner
-        diffDiagRefiner = new MaxoDiffRefiner(hpoDiseases, hpoToMaxoIdMap, hpoToMaxoTermMap, minHpo, hpo);
+        diffDiagRefiner = new MaxoDiffRefiner(hpoDiseases, hpoToMaxoIdMap, hpoToMaxoTermMap, hpo);
 
         // maxodiff analysis parameters: n diseases to use and n simulations to run
         Integer prevNDiseases = (Integer) model.getAttribute("nDiseases");

Original file line number	Diff line number	Diff line change
`@@ -12,7 +12,7 @@ public interface MaxoDiffLoader {`
`12`	`12`	`MinimalOntology hpo();`
`13`	`13`	`HpoDiseases hpoDiseases() throws MaxodiffDataException;`
`14`	`14`	`IcMicaData icMicaData() throws MaxodiffDataException;`
`15`		`- public static MaxoDiffLoader fileLoader(Path maxoPAth) throws MaxodiffDataException {`
	`15`	`+ static MaxoDiffLoader fileLoader(Path maxoPAth) throws MaxodiffDataException {`
`16`	`16`	`return new MaxoDiffFileLoader(maxoPAth);`
`17`	`17`	`}`
`18`	`18`	`}`
Original file line number	Diff line number	Diff line change
`@@ -53,7 +53,7 @@ public DiffDiagRefiner diffDiagRefiner(String refiner) {`
`53`	`53`	`DiffDiagRefiner diffDiagRefiner = null;`
`54`	`54`
`55`	`55`	`if (refiner.equals("score")) {`
`56`		`- diffDiagRefiner = new MaxoDiffRefiner(hpoDiseases, hpoToMaxoIdMap, maxoAnnotsMap, minHpo, hpo);`
	`56`	`+ diffDiagRefiner = new MaxoDiffRefiner(hpoDiseases, hpoToMaxoIdMap, maxoAnnotsMap, hpo);`
`57`	`57`	`}`
`58`	`58`	`return diffDiagRefiner;`
`59`	`59`	`}`