Implement dbSNP file download as 'variation' TASK-5794

Author: imedina

cellbase-lib/src/main/java/org/opencb/cellbase/lib/download/VariationDownloadManager.java

@@ -0,0 +1,61 @@
+/*
+ * Copyright 2015-2020 OpenCB
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.opencb.cellbase.lib.download;
+
+import org.opencb.cellbase.core.config.CellBaseConfiguration;
+import org.opencb.cellbase.core.config.DownloadProperties;
+import org.opencb.cellbase.core.exception.CellBaseException;
+import org.opencb.cellbase.lib.EtlCommons;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.Collections;
+import java.util.List;
+
+public class VariationDownloadManager extends AbstractDownloadManager {
+
+    private static final String DBSNP_NAME = "dbSNP";
+    public VariationDownloadManager(String species, String assembly, Path targetDirectory, CellBaseConfiguration configuration)
+            throws IOException, CellBaseException {
+        super(species, assembly, targetDirectory, configuration);
+    }
+
+    @Override
+    public List<DownloadFile> download() throws IOException, InterruptedException {
+        return Collections.singletonList(downloadCaddScores());
+    }
+
+    public DownloadFile downloadCaddScores() throws IOException, InterruptedException {
+        if (!speciesHasInfoToDownload(speciesConfiguration, "variation")) {
+            return null;
+        }
+        if (speciesConfiguration.getScientificName().equals("Homo sapiens")) {
+            logger.info("Downloading dbSNP scores information ...");
+
+            Path variation = downloadFolder.resolve("variation");
+            Files.createDirectories(variation);
+
+            DownloadProperties.URLProperties dbSNP = configuration.getDownload().getDbSNP();
+            String url = dbSNP.getHost();
+            saveVersionData(EtlCommons.VARIATION_DATA, DBSNP_NAME, dbSNP.getVersion(), getTimeStamp(),
+                    Collections.singletonList(url), variation.resolve("dbSnpVersion.json"));
+            return downloadFile(url, variation.resolve(EtlCommons.DBSNP_FILE).toString());
+        }
+        return null;
+    }
+}