diff --git a/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/ColumnMeta.java b/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/ColumnMeta.java index 3243a9db..681102a4 100644 --- a/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/ColumnMeta.java +++ b/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/ColumnMeta.java @@ -2,14 +2,13 @@ import com.fasterxml.jackson.annotation.JsonIgnore; import com.fasterxml.jackson.annotation.JsonInclude; -import com.fasterxml.jackson.databind.annotation.JsonSerialize; import java.io.Serializable; import java.util.List; @JsonInclude(JsonInclude.Include.NON_NULL) -public class ColumnMeta implements Serializable{ +public class ColumnMeta implements Serializable { private static final long serialVersionUID = -124111104912063811L; private String name; diff --git a/docker/pic-sure-hpds-etl/Dockerfile b/docker/pic-sure-hpds-etl/Dockerfile index a0aea075..b375fc13 100644 --- a/docker/pic-sure-hpds-etl/Dockerfile +++ b/docker/pic-sure-hpds-etl/Dockerfile @@ -7,6 +7,7 @@ RUN apk add --no-cache --purge -uU curl wget unzip gnupg openssl ADD create_key.sh . ADD SQLLoader-jar-with-dependencies.jar . ADD CSVLoader-jar-with-dependencies.jar . +ADD CSVLoaderNewSearch-jar-with-dependencies.jar . ADD CSVDumper-jar-with-dependencies.jar . ADD VCFLocalLoader-jar-with-dependencies.jar . ADD VariantMetadataLoader-jar-with-dependencies.jar . diff --git a/etl/pom.xml b/etl/pom.xml index b388883e..c218d06a 100644 --- a/etl/pom.xml +++ b/etl/pom.xml @@ -130,6 +130,26 @@ single + + buildCSVLoaderNewSearch + + + + edu.harvard.hms.dbmi.avillach.hpds.etl.phenotype.CSVLoaderNewSearch + + + ${project.basedir}/../docker/pic-sure-hpds-etl + + jar-with-dependencies + + CSVLoaderNewSearch + CSVLoaderNewSearch + + package + + single + + buildCSVLoader diff --git a/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/LoadingStore.java b/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/LoadingStore.java index 91c8d605..2373e80e 100644 --- a/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/LoadingStore.java +++ b/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/LoadingStore.java @@ -161,7 +161,7 @@ public void dumpStats() { */ public void dumpStatsAndColumnMeta(String hpdsDirectory) { try (ObjectInputStream objectInputStream = - new ObjectInputStream(new GZIPInputStream(new FileInputStream(hpdsDirectory + "columnMeta.javabin")));){ + new ObjectInputStream(new GZIPInputStream(new FileInputStream(hpdsDirectory + "columnMeta.javabin")))){ TreeMap metastore = (TreeMap) objectInputStream.readObject(); try(BufferedWriter writer = Files.newBufferedWriter(Paths.get(hpdsDirectory + "columnMeta.csv"), StandardOpenOption.CREATE, StandardOpenOption.TRUNCATE_EXISTING)) { CSVPrinter printer = new CSVPrinter(writer, CSVFormat.DEFAULT);