liftover: minor improvements

opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/executors/DockerWrapperAnalysisExecutor.java

@@ -23,6 +23,9 @@
 
 public abstract class DockerWrapperAnalysisExecutor  extends OpenCgaToolExecutor {
 
+//    protected String study;
+    protected Logger logger;
+
     public final static String DOCKER_INPUT_PATH = "/data/input";
     public final static String DOCKER_OUTPUT_PATH = "/data/output";
 
@@ -31,6 +34,10 @@ public abstract class DockerWrapperAnalysisExecutor  extends OpenCgaToolExecutor
 
     public static final String DOCKER_CLI_MSG = "Docker CLI: ";
 
+    public DockerWrapperAnalysisExecutor() {
+        logger = LoggerFactory.getLogger(this.getClass());
+    }
+
     public String getDockerImageName() {
         return "opencb/opencga-ext-tools";
     }

opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/liftover/LiftoverWrapperAnalysis.java

@@ -102,24 +102,31 @@ protected List<String> getSteps() {
         return Arrays.asList(PREPARE_RESOURCES_STEP, ID);
     }
 
-    protected void run() throws ToolException {
+    protected void run() throws ToolException, IOException {
         // Download and copy liftover resource files in the job dir
         step(PREPARE_RESOURCES_STEP, this::prepareResources);
 
         // Run liftover script
         step(ID, this::runLiftover);
 
         // Do we have to clean the liftover resource folder
+//        Files.newDirectoryStream(resourcePath).forEach(file -> {
+//            try {
+//                Files.delete(file);
+//            } catch (IOException e) {
+//                logger.warn("Error deleting file '{}': {}", file, e.getMessage());
+//            }
+//        });
     }
 
 
-    protected void prepareResources() throws IOException, ToolException {
+    private void prepareResources() throws IOException, ToolException {
         // Create folder where the liftover resources will be saved (within the job dir, aka outdir)
         resourcePath = Files.createDirectories(getOutDir().resolve(RESOURCES_FOLDER));
 
         // Identify Liftover resources to download only the required ones
         Map<String, List<String>> mapResources = new HashMap<>();
-        switch (analysisParams.getTargetAssembly()) {
+        switch (analysisParams.getTargetAssembly().toUpperCase()) {
             case LIFTOVER_GRCH38: {
                 mapResources.put(ID, Collections.singletonList("GRCh37_to_GRCh38.chain.gz"));
                 mapResources.put("reference-genome", Arrays.asList("Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz",
@@ -148,7 +155,7 @@ protected void prepareResources() throws IOException, ToolException {
         }
     }
 
-    protected void runLiftover() throws Exception {
+    private void runLiftover() throws Exception {
         // Get executor
         LiftoverWrapperAnalysisExecutor executor = getToolExecutor(LiftoverWrapperAnalysisExecutor.class);
 

opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/liftover/LiftoverWrapperAnalysisExecutor.java

@@ -43,7 +43,7 @@ public class LiftoverWrapperAnalysisExecutor extends DockerWrapperAnalysisExecut
     private String vcfDest;
     private Path resourcePath;
 
-    private Logger logger = LoggerFactory.getLogger(this.getClass());
+//    private Logger logger = LoggerFactory.getLogger(this.getClass());
 
     @Override
     protected void run() throws Exception {
@@ -91,7 +91,7 @@ private void runLiftover(File file, Path outPath) throws ToolExecutorException {
                     + " " + VIRTUAL_RESOURCES_FOLDER;
 
             // Execute Pythong script in docker
-            String dockerImage = "opencb/opencga-ext-tools:" + GitRepositoryState.getInstance().getBuildVersion();
+            String dockerImage = getDockerImageName() + GitRepositoryState.getInstance().getBuildVersion();
 
             String dockerCli = buildCommandLine(dockerImage, inputBindings, outputBinding, params, null);
             addEvent(Event.Type.INFO, "Docker command line: " + dockerCli);

opencga-app/app/analysis/liftover/liftover.sh

@@ -19,7 +19,7 @@
 INPUT_FILE=$1
 TARGET_ASSEMBLY=$2  ## Values accepted are: GRCh38, hg38
 OUTPUT_DIR=$3
-RESOURCES_DIR=$4
+LOCAL_RESOURCES_DIR=$4
 
 if [ -z "$INPUT_FILE" ] || [ -z "$TARGET_ASSEMBLY" ] || [ -z "$OUTPUT_DIR" ] || [ -z "$RESOURCES_DIR" ]; then
     echo "Usage: $0 <vcf_file> <target_assembly> <output_dir> <resources_dir>"
@@ -39,26 +39,26 @@ fi
 
 if [ $TARGET_ASSEMBLY == "GRCh38" ]; then
     echo "Liftover from GRCh37 to $TARGET_ASSEMBLY"
-#
-#    ## Prepare GRCh37 and GRCh38 reference genomes
-#    if [ ! -f Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz ]; then
+
+    ## Prepare GRCh37 and GRCh38 reference genomes
+#    if [ ! -f "${LOCAL_RESOURCES_DIR}/Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz" ]; then
 #      wget --no-check-certificate https://resources.opencb.org/opencb/opencga/analysis/commons/reference-genomes/Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz
 #    fi
 #
 #    if [ ! -f Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz ]; then
 #      wget --no-check-certificate https://resources.opencb.org/opencb/opencga/analysis/commons/reference-genomes/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
 #    fi
-#
-    echo "gunzip ${RESOURCES_DIR}/Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz"
-    gunzip ${RESOURCES_DIR}/Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz
-    SOURCE_REFERENCE_FILE="${RESOURCES_DIR}/Homo_sapiens.GRCh37.dna.primary_assembly.fa"
 
-    echo "gunzip ${RESOURCES_DIR}/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz"
-    gunzip ${RESOURCES_DIR}/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
-    TARGET_REFERENCE_FILE="${RESOURCES_DIR}/Homo_sapiens.GRCh38.dna.primary_assembly.fa"
+    echo "gunzip ${LOCAL_RESOURCES_DIR}/Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz"
+    gunzip ${LOCAL_RESOURCES_DIR}/Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz
+    SOURCE_REFERENCE_FILE="${LOCAL_RESOURCES_DIR}/Homo_sapiens.GRCh37.dna.primary_assembly.fa"
+
+    echo "gunzip ${LOCAL_RESOURCES_DIR}/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz"
+    gunzip ${LOCAL_RESOURCES_DIR}/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
+    TARGET_REFERENCE_FILE="${LOCAL_RESOURCES_DIR}/Homo_sapiens.GRCh38.dna.primary_assembly.fa"
 
 #    wget http://ftp.ensembl.org/pub/assembly_mapping/homo_sapiens/GRCh37_to_GRCh38.chain.gz
-    CHAIN_FILE="${RESOURCES_DIR}/GRCh37_to_GRCh38.chain.gz"
+    CHAIN_FILE="${LOCAL_RESOURCES_DIR}/GRCh37_to_GRCh38.chain.gz"
 elif [ $TARGET_ASSEMBLY == "hg38" ]; then
     echo "Liftover from hg19 to $TARGET_ASSEMBLY"
 #
@@ -71,16 +71,16 @@ elif [ $TARGET_ASSEMBLY == "hg38" ]; then
 #      wget https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz
 #    fi
 #
-    echo "gunzip ${RESOURCES_DIR}/hg19.fa.gz"
-    gunzip ${RESOURCES_DIR}/hg19.fa.gz
-    SOURCE_REFERENCE_FILE="${RESOURCES_DIR}/hg19.fa"
+    echo "gunzip ${LOCAL_RESOURCES_DIR}/hg19.fa.gz"
+    gunzip ${LOCAL_RESOURCES_DIR}/hg19.fa.gz
+    SOURCE_REFERENCE_FILE="${LOCAL_RESOURCES_DIR}/hg19.fa"
 
-    echo "gunzip ${RESOURCES_DIR}/hg38.fa.gz"
-    gunzip ${RESOURCES_DIR}/hg38.fa.gz
-    TARGET_REFERENCE_FILE="${RESOURCES_DIR}/hg38.fa"
+    echo "gunzip ${LOCAL_RESOURCES_DIR}/hg38.fa.gz"
+    gunzip ${LOCAL_RESOURCES_DIR}/hg38.fa.gz
+    TARGET_REFERENCE_FILE="${LOCAL_RESOURCES_DIR}/hg38.fa"
 
 #    wget http://hgdownload.cse.ucsc.edu/goldenpath/hg19/liftOver/hg19ToHg38.over.chain.gz
-    CHAIN_FILE="${RESOURCES_DIR}/hg19ToHg38.over.chain.gz"
+    CHAIN_FILE="${LOCAL_RESOURCES_DIR}/hg19ToHg38.over.chain.gz"
 else
     echo "Unsupported target assembly $TARGET_ASSEMBLY"
     exit 1

opencga-core/src/main/java/org/opencb/opencga/core/api/FieldConstants.java

@@ -567,14 +567,14 @@ public class FieldConstants {
     public static final String EXOMISER_CLINICAL_ANALYSIS_TYPE_DESCRIPTION = "Clinical analysis type: SINGLE or FAMILY.";
 
     // Liftover
-    public static final String LIFTOVER_GRCH38 = "GRCh38";
-    public static final String LIFTOVER_HG38 = "hg38";
+    public static final String LIFTOVER_GRCH38 = "GRCH38";
+    public static final String LIFTOVER_HG38 = "HG38";
     public static final String LIFTOVER_VCF_INPUT_FOLDER = "OPENCGA_VCF_INPUT_FOLDER";
     public static final String LIFTOVER_FILES_DESCRIPTION = "List of VCF files to lift over";
     public static final String LIFTOVER_TARGET_ASSEMBLY_DESCRIPTION = "Target assembly for lift over. Valid values: " + LIFTOVER_GRCH38
             + " (for Ensembl) or " + LIFTOVER_HG38 + " (for NCBI)";
     public static final String LIFTOVER_VCF_DESTINATION_DESCRIPTION = "Destination path where the lifted-over VCF files will be stored."
             + " If left empty, the VCF files will be stored in the job folder. If the keyword " + LIFTOVER_VCF_INPUT_FOLDER
-            + " is used, they will be stored in the same folder as the input VCF files. Otherwise, they will be stored in the specified"
+            + " is used, then VCF files be stored in the same folder as the input VCF files. Otherwise, they will be stored in the specified"
             + " destination path";
 }

opencga-core/src/main/java/org/opencb/opencga/core/models/variant/LiftoverWrapperParams.java

@@ -24,7 +24,7 @@
 
 public class LiftoverWrapperParams extends ToolParams {
 
-    public static final String DESCRIPTION = "BCFtools +liftover plugin parameterss";
+    public static final String DESCRIPTION = "BCFtools +liftover plugin parameters";
 
     @DataField(id = "files", description = FieldConstants.LIFTOVER_FILES_DESCRIPTION, required = true)
     private List<String> files;