downloader: add MONDO ontology

opencb · Jan 2, 2024 · 7e72929 · 7e72929
1 parent 0004be6
commit 7e72929
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Showing 2 changed files with 10 additions and 4 deletions.
diff --git a/cellbase-core/src/main/resources/configuration.yml b/cellbase-core/src/main/resources/configuration.yml
@@ -173,12 +173,16 @@ download:
     version: "2.1.1"
   hpoObo:
     host: http://purl.obolibrary.org/obo/hp.obo
+    version: "2023-12-01"
   goObo:
     host: http://purl.obolibrary.org/obo/go/go-basic.obo
+    version: "2023-12-01"
   doidObo:
     host: http://purl.obolibrary.org/obo/doid.obo
+    version: "2023-12-01"
   mondoObo:
     host: http://purl.obolibrary.org/obo/mondo.obo
+    version: "2023-12-01"
   goAnnotation:
     host: http://geneontology.org/gene-associations/goa_human.gaf.gz
   revel:

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
@@ -36,30 +36,32 @@ public OntologyDownloadManager(String species, String assembly, Path targetDirec
 
 
     public List<DownloadFile> download() throws IOException, InterruptedException {
-        logger.info("Downloading obo files ...");
+        logger.info("Downloading OBO files ...");
 
         List<DownloadFile> downloadFiles = new ArrayList<>();
         Path oboFolder = downloadFolder.resolve("ontology");
         Files.createDirectories(oboFolder);
 
         String url = configuration.getDownload().getHpoObo().getHost();
         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));
 
         url = configuration.getDownload().getGoObo().getHost();
         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));
 
         url = configuration.getDownload().getDoidObo().getHost();
         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));
 
+        url = configuration.getDownload().getMondoObo().getHost();
+        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));
+
         return downloadFiles;
     }
 }