core: improve Ontology downloader, #TASK-5775, #TASK-5564

opencb · Mar 7, 2024 · 50f7008 · 50f7008
1 parent fe05795
commit 50f7008
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Showing 2 changed files with 9 additions and 4 deletions.
diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/EtlCommons.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/EtlCommons.java
@@ -127,6 +127,7 @@ public class EtlCommons {
     public static final String HPO_VERSION_FILE = "hpoVersion.json";
     public static final String GO_VERSION_FILE = "goVersion.json";
     public static final String DO_VERSION_FILE = "doVersion.json";
+    public static final String MONDO_VERSION_FILE = "mondoVersion.json";
     public static final String HGMD_FILE = "hgmd.vcf";
     public static final String PUBMED_VERSION_FILENAME = "pubmedVersion.json";
 

diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/download/OntologyDownloadManager.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/download/OntologyDownloadManager.java
@@ -43,24 +43,28 @@ public List<DownloadFile> download() throws IOException, InterruptedException {
         Files.createDirectories(oboFolder);
 
         String url = configuration.getDownload().getHpoObo().getHost();
+        logger.info("Downloading {} ...", url);
         downloadFiles.add(downloadFile(url, oboFolder.resolve("hp.obo").toString()));
         saveVersionData(EtlCommons.OBO_DATA, "HPO", getTimeStamp(), getTimeStamp(),
-                Collections.singletonList(url), buildFolder.resolve(EtlCommons.HPO_VERSION_FILE));
+                Collections.singletonList(url), oboFolder.resolve(EtlCommons.HPO_VERSION_FILE));
 
         url = configuration.getDownload().getGoObo().getHost();
+        logger.info("Downloading {} ...", url);
         downloadFiles.add(downloadFile(url, oboFolder.resolve("go-basic.obo").toString()));
         saveVersionData(EtlCommons.OBO_DATA, "GO", getTimeStamp(), getTimeStamp(),
-                Collections.singletonList(url), buildFolder.resolve(EtlCommons.GO_VERSION_FILE));
+                Collections.singletonList(url), oboFolder.resolve(EtlCommons.GO_VERSION_FILE));
 
         url = configuration.getDownload().getDoidObo().getHost();
+        logger.info("Downloading {} ...", url);
         downloadFiles.add(downloadFile(url, oboFolder.resolve("doid.obo").toString()));
         saveVersionData(EtlCommons.OBO_DATA, "DO", getTimeStamp(), getTimeStamp(),
-                Collections.singletonList(url), buildFolder.resolve(EtlCommons.DO_VERSION_FILE));
+                Collections.singletonList(url), oboFolder.resolve(EtlCommons.DO_VERSION_FILE));
 
         url = configuration.getDownload().getMondoObo().getHost();
+        logger.info("Downloading {} ...", url);
         downloadFiles.add(downloadFile(url, oboFolder.resolve("mondo.obo").toString()));
         saveVersionData(EtlCommons.OBO_DATA, "MONDO", getTimeStamp(), getTimeStamp(),
-                Collections.singletonList(url), buildFolder.resolve(EtlCommons.DO_VERSION_FILE));
+                Collections.singletonList(url), oboFolder.resolve(EtlCommons.MONDO_VERSION_FILE));
 
         return downloadFiles;
     }