Merge pull request #606 from TheJacksonLaboratory/fix_disease_databas…

…es_bug Fix pretest probability calculation.
TheJacksonLaboratory · Apr 7, 2023 · bfcfef7 · bfcfef7
2 parents d71ebdf + 7282b29
commit bfcfef7
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Showing 10 changed files with 31 additions and 21 deletions.
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -10,6 +10,7 @@ v2.0.0 (TBD)
 - Enhance HTML report, add `JSON` output format
 - Add ``prioritize`` command for running LIRICAL entirely from CLI
 - Add support for phenopacket schema ``v2``
+- Host documentation and API docs on github.io
 
 -------------------
 v1.3.3 (2021-05-14)

diff --git a/README.md b/README.md
@@ -4,7 +4,7 @@
 # LIRICAL
 LIRICAL (LIkelihood Ratio Interpretation of Clinical AbnormaLities) 
 is designed to provide clinically interpretable computational analysis of phenotypic
-abnormalities (encoded using the [Human Phenotype Ontology](http://www.human-phenotyope-ontology.org)),
+abnormalities (encoded using the [Human Phenotype Ontology](http://www.human-phenotype-ontology.org)),
 optionally combined with an analysis of variants and genotypes if a VCF file is provided with the
 results of diagnostic gene panel, exome, or genome sequencing.
 

diff --git a/lirical-cli/src/main/java/org/monarchinitiative/lirical/cli/cmd/BaseCommand.java b/lirical-cli/src/main/java/org/monarchinitiative/lirical/cli/cmd/BaseCommand.java
@@ -39,8 +39,7 @@ private void setupLoggingAndPrintBanner() {
         LoggerContext context = (LoggerContext) LoggerFactory.getILoggerFactory();
         context.getLogger(Logger.ROOT_LOGGER_NAME).setLevel(level);
 
-        if (!(level.equals(Level.WARN) || level.equals(Level.ERROR)))
-            printBanner();
+        printBanner();
     }
 
     private static String readBanner() {
@@ -59,10 +58,9 @@ private Level parseVerbosityLevel() {
         }
 
         return switch (verbosity) {
-            case 0 -> Level.WARN;
-            case 1 -> Level.INFO;
-            case 2 -> Level.DEBUG;
-            case 3 -> Level.TRACE;
+            case 0 -> Level.INFO;
+            case 1 -> Level.DEBUG;
+            case 2 -> Level.TRACE;
             default -> Level.ALL;
         };
     }

diff --git a/...-cli/src/main/java/org/monarchinitiative/lirical/cli/cmd/LiricalConfigurationCommand.java b/...-cli/src/main/java/org/monarchinitiative/lirical/cli/cmd/LiricalConfigurationCommand.java
@@ -116,20 +116,21 @@ public static class RunConfiguration {
 
     protected List<String> checkInput() {
         List<String> errors = new LinkedList<>();
+
+        Path codeHomeParent = codeHomeDir();
         // resources
         if (dataSection.liricalDataDirectory == null) {
-            Path codeHomeParent = codeHomeDir();
-            LOGGER.debug("Data directory is unset, searching in the code home directory at: {}", codeHomeParent);
+            LOGGER.debug("Data directory is unset, searching next to the LIRICAL file");
             Path codeHomeDataDir = codeHomeParent.resolve("data");
             if (Files.isDirectory(codeHomeDataDir)) {
-                LOGGER.debug("Found data folder at: {}", codeHomeDataDir.toAbsolutePath());
                 dataSection.liricalDataDirectory = codeHomeDataDir;
             } else {
-                String msg = "Path to Lirical data directory must be provided via `-d | --data` option";
+                String msg = "Path to LIRICAL data directory must be provided via `-d | --data` option";
                 LOGGER.error(msg);
                 errors.add(msg);
             }
         }
+        LOGGER.info("Using data folder at {}", dataSection.liricalDataDirectory.toAbsolutePath());
 
         // Obsolete options must/should not be used
         if (dataSection.exomiserDatabase != null) {
@@ -250,7 +251,7 @@ protected AnalysisOptions prepareAnalysisOptions(Lirical lirical, GenomeBuild ge
 
         List<TermId> diseaseIds = lirical.phenotypeService().diseases().stream()
                 .map(Identified::id)
-                .filter(diseaseId -> Collections.binarySearch(diseaseDatabasePrefixes, diseaseId.getPrefix()) > 0)
+                .filter(diseaseId -> diseaseDatabasePrefixes.contains(diseaseId.getPrefix()))
                 .toList();
         PretestDiseaseProbability pretestDiseaseProbability = PretestDiseaseProbabilities.uniform(diseaseIds);
         builder.pretestProbability(pretestDiseaseProbability);
@@ -335,7 +336,7 @@ else if (elapsedTime>59) {
 
     private static Path codeHomeDir() {
         String codePath = LiricalConfigurationCommand.class.getProtectionDomain().getCodeSource().getLocation().getFile();
-        LOGGER.debug("Found code path at {}", codePath);
+        LOGGER.info("Running LIRICAL from {}", codePath);
         return Path.of(codePath).toAbsolutePath().getParent();
     }
 

diff --git a/lirical-cli/src/main/java/org/monarchinitiative/lirical/cli/cmd/PhenopacketCommand.java b/lirical-cli/src/main/java/org/monarchinitiative/lirical/cli/cmd/PhenopacketCommand.java
@@ -47,7 +47,7 @@ public class PhenopacketCommand extends AbstractPrioritizeCommand {
     public Path phenopacketPath;
 
     @CommandLine.Option(names = {"--vcf"},
-            description = "Path to VCF file. This path has priority over any VCF files described in phenopacket.")
+            description = "Path to a VCF file. This path has priority over any VCF files described in phenopacket.")
     public Path vcfPath;
 
     @Override
@@ -59,23 +59,23 @@ protected String getGenomeBuild() {
     protected AnalysisData prepareAnalysisData(Lirical lirical,
                                                GenomeBuild genomeBuild,
                                                TranscriptDatabase transcriptDb) throws LiricalParseException {
-        LOGGER.info("Reading phenopacket from {}.", phenopacketPath.toAbsolutePath());
+        LOGGER.info("Reading phenopacket from {}", phenopacketPath.toAbsolutePath());
 
         PhenopacketData data = null;
         try (InputStream is = new BufferedInputStream(new FileInputStream(phenopacketPath.toFile()))) {
             PhenopacketImporter v2 = PhenopacketImporters.v2();
             data = v2.read(is);
             LOGGER.info("Success!");
         } catch (PhenopacketImportException | IOException e) {
-            LOGGER.info("Unable to parse as v2 phenopacket, trying v1.");
+            LOGGER.info("Unable to parse as v2 phenopacket, trying v1");
         }
 
         if (data == null) {
             try (InputStream is = new BufferedInputStream(new FileInputStream(phenopacketPath.toFile()))) {
                 PhenopacketImporter v1 = PhenopacketImporters.v1();
                 data = v1.read(is);
             } catch (PhenopacketImportException | IOException e) {
-                LOGGER.info("Unable to parser as v1 phenopacket.");
+                LOGGER.info("Unable to parse as v1 phenopacket");
                 throw new LiricalParseException("Unable to parse phenopacket from " + phenopacketPath.toAbsolutePath());
             }
         }

diff --git a/lirical-core/pom.xml b/lirical-core/pom.xml
@@ -27,6 +27,17 @@
         <dependency>
             <groupId>de.charite.compbio</groupId>
             <artifactId>jannovar-core</artifactId>
+            <exclusions>
+                <!-- We do not use parts of Jannovar that use the following libs: -->
+                <exclusion>
+                    <groupId>commons-net</groupId>
+                    <artifactId>commons-net</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.ini4j</groupId>
+                    <artifactId>ini4j</artifactId>
+                </exclusion>
+            </exclusions>
         </dependency>
         <dependency>
             <groupId>commons-lang</groupId>

diff --git a/lirical-core/src/main/java/org/monarchinitiative/lirical/core/analysis/AnalysisOptions.java b/lirical-core/src/main/java/org/monarchinitiative/lirical/core/analysis/AnalysisOptions.java
@@ -184,7 +184,7 @@ public Builder addDiseaseDatabases(DiseaseDatabase... diseaseDatabases) {
 
         public Builder addDiseaseDatabases(Collection<DiseaseDatabase> diseaseDatabases) {
             if (diseaseDatabases == null) {
-                LOGGER.warn("Disease databases should not be `null`!");
+                LOGGER.warn("Disease databases must not be `null`!");
                 return this;
             }
             this.diseaseDatabases.addAll(diseaseDatabases);

diff --git a/...main/java/org/monarchinitiative/lirical/core/analysis/impl/LiricalAnalysisRunnerImpl.java b/...main/java/org/monarchinitiative/lirical/core/analysis/impl/LiricalAnalysisRunnerImpl.java
@@ -61,7 +61,7 @@ public AnalysisResults run(AnalysisData data, AnalysisOptions options) throws Li
         ProgressReporter progressReporter = new ProgressReporter(1_000, "diseases");
         Stream<TestResult> testResultStream = phenotypeService.diseases().hpoDiseases()
                 .parallel() // why not?
-                .filter(d -> diseaseDatabasePrefixes.contains(d.id().getPrefix()))
+                .filter(disease -> diseaseDatabasePrefixes.contains(disease.id().getPrefix()))
                 .peek(d -> progressReporter.log())
                 .map(disease -> analyzeDisease(genotypeLikelihoodRatio.get(), disease, data, options, diseaseToGenotype))
                 .flatMap(Optional::stream);

diff --git a/lirical-core/src/main/resources/org/monarchinitiative/lirical/core/output/liricalHTML.ftl b/lirical-core/src/main/resources/org/monarchinitiative/lirical/core/output/liricalHTML.ftl
@@ -769,7 +769,7 @@
                 itself. The
                 results of LIRICAL should not be construed as medical advice and should always be reviewed by medical
                 professionals.</p>
-            <p>See LIRICAL's <a href="https://lirical.readthedocs.io/en/latest/" target="_blank">online
+            <p>See LIRICAL's <a href="https://thejacksonlaboratory.github.io/LIRICAL/stable" target="_blank">online
                     documentation</a>.</p>
 
             <h4><i>This LIRICAL run had the following configuration:</i></h4>

diff --git a/lirical-io/src/main/java/org/monarchinitiative/lirical/io/LiricalDataResolver.java b/lirical-io/src/main/java/org/monarchinitiative/lirical/io/LiricalDataResolver.java
@@ -22,7 +22,6 @@ public static LiricalDataResolver of(Path dataDirectory) throws LiricalDataExcep
 
     private LiricalDataResolver(Path dataDirectory) throws LiricalDataException {
         this.dataDirectory = Objects.requireNonNull(dataDirectory, "Data directory must not be null!");
-        LOGGER.debug("Using Lirical directory at `{}`.", dataDirectory.toAbsolutePath());
         checkV1Resources();
     }