Initial Code for Schema to Release Migration

src/main/java/org/alliancegenome/agr_submission/dao/ReleaseVersionDAO.java

@@ -1,15 +1,35 @@
 package org.alliancegenome.agr_submission.dao;
 
+import java.util.List;
+import java.util.TreeSet;
+
 import javax.enterprise.context.ApplicationScoped;
 
 import org.alliancegenome.agr_submission.BaseSQLDAO;
 import org.alliancegenome.agr_submission.entities.ReleaseVersion;
 
+import lombok.extern.log4j.Log4j2;
+
+@Log4j2
 @ApplicationScoped
 public class ReleaseVersionDAO extends BaseSQLDAO<ReleaseVersion> {
 
 	public ReleaseVersionDAO() {
 		super(ReleaseVersion.class);
 	}
+
+	public ReleaseVersion getByName(String releaseVersion) {
+		return findByField("releaseVersion", releaseVersion);
+	}
+
+	public ReleaseVersion getCurrentReleaseVersion() {
+		List<ReleaseVersion> versions = findAll();
+		TreeSet<String> set = new TreeSet<>();
+		for(ReleaseVersion rv: versions) {
+			set.add(rv.getReleaseVersion());
+		}
+		log.debug("Return most current Release Version: " + set.pollFirst());
+		return getByName(set.pollLast());
+	}
 
 }

src/main/java/org/alliancegenome/agr_submission/main/S3Syncer.java

@@ -10,6 +10,7 @@ public class S3Syncer {
 
 	public static void main(String[] args) {
 		ConfigHelper.init();
+		boolean reportonly = false;
 
 		S3Helper s3 = new S3Helper();
 
@@ -39,12 +40,14 @@ public static void main(String[] args) {
 		System.out.println("List to Copy: " + copyList.size());
 		System.out.println("List to Delete: " + deleteList.size());
 
-		for(String s: copyList) {
-			s3.copyObject(s, srcBucket, dstBucket);
-		}
-
-		for(String s: deleteList) {
-			s3.deleteObject(s, dstBucket);
+		if(!reportonly) {
+			for(String s: copyList) {
+				s3.copyObject(s, srcBucket, dstBucket);
+			}
+
+			for(String s: deleteList) {
+				s3.deleteObject(s, dstBucket);
+			}
 		}
 
 

src/main/java/org/alliancegenome/agr_submission/services/SubmissionService.java

@@ -12,10 +12,12 @@
 import org.alliancegenome.agr_submission.dao.DataFileDAO;
 import org.alliancegenome.agr_submission.dao.DataSubTypeDAO;
 import org.alliancegenome.agr_submission.dao.DataTypeDAO;
+import org.alliancegenome.agr_submission.dao.ReleaseVersionDAO;
 import org.alliancegenome.agr_submission.dao.SchemaVersionDAO;
 import org.alliancegenome.agr_submission.entities.DataFile;
 import org.alliancegenome.agr_submission.entities.DataSubType;
 import org.alliancegenome.agr_submission.entities.DataType;
+import org.alliancegenome.agr_submission.entities.ReleaseVersion;
 import org.alliancegenome.agr_submission.entities.SchemaVersion;
 import org.alliancegenome.agr_submission.exceptions.GenericException;
 import org.alliancegenome.agr_submission.exceptions.SchemaDataTypeException;
@@ -39,7 +41,7 @@
 public class SubmissionService {
 
 	//@Inject private SnapShotDAO snapShotDAO;
-	//@Inject private ReleaseVersionDAO releaseDAO;
+	@Inject private ReleaseVersionDAO releaseVersionDAO;
 	@Inject private DataFileDAO dataFileDAO;
 	@Inject private SchemaVersionDAO schemaVersionDAO;
 	@Inject private DataTypeDAO dataTypeDAO;
@@ -54,30 +56,32 @@ public boolean submitAndValidateDataFile(String key, File inFile, boolean saveFi
 		// Split the keys by underscore
 		String[] keys = key.split("_");
 
-		String schemaLookup;
+		String releaseLookup;
 		String dataTypeLookup;
 		String dataSubTypeLookup;
 
 		if(keys.length == 3) {
 			log.debug("Key has 3 items: parse: (Schema-DataType-DataSubType): " + key);
-			schemaLookup = keys[0];
+			releaseLookup = keys[0];
 			dataTypeLookup = keys[1];
 			dataSubTypeLookup = keys[2];
 		} else if(keys.length == 2) { // DataType-TaxonId // Input a taxonId datatype file and validate against latest version of schema
 			log.debug("Key has 2 items: parse: (DataType-DataSubType): " + key);
-			schemaLookup = null;
+			releaseLookup = null;
 			dataTypeLookup = keys[0];
 			dataSubTypeLookup = keys[1];
 		} else {
 			throw new ValidataionException("Wrong Number of Args for File Data: " + key);
 		}
+
 
-		SchemaVersion schemaVersion = getSchemaVersion(schemaLookup);
+		SchemaVersion schemaVersion = getSchemaVersionFromReleaseVersion(releaseLookup);
+
 		DataType dataType = dataTypeDAO.findByField("name", dataTypeLookup);
 		DataSubType dataSubType = dataSubTypeDAO.findByField("name", dataSubTypeLookup);
 
 		if(schemaVersion == null) {
-			throw new SchemaDataTypeException("Could not Find schemaVersion: " + schemaLookup);
+			throw new SchemaDataTypeException("Could not Find releaseLookup: " + releaseLookup);
 		}
 		if(dataType == null) {
 			throw new SchemaDataTypeException("Could not Find dataType: " + dataTypeLookup);
@@ -139,6 +143,25 @@ private boolean validateData(SchemaVersion schemaVersionName, DataType dataType,
 		}
 
 	}
+
+	private SchemaVersion getSchemaVersionFromReleaseVersion(String releaseVersion) throws ValidataionException {
+		if(releaseVersion == null) {
+			ReleaseVersion rv = releaseVersionDAO.getCurrentReleaseVersion();
+			if(rv.getSchemaVersions().size() == 0) {
+				throw new ValidataionException("No Schema Versions found for Release Version: " + rv.getReleaseVersion());
+			}
+			return rv.getSchemaVersions().get(0);
+		} else {
+			ReleaseVersion rv = releaseVersionDAO.getByName(releaseVersion);
+			if(rv == null) {
+				throw new ValidataionException("Release Version not found: " + releaseVersion);
+			}
+			if(rv.getSchemaVersions().size() == 0) {
+				throw new ValidataionException("No Schema Versions found for Release Version: " + releaseVersion);
+			}
+			return rv.getSchemaVersions().get(0);
+		}
+	}
 
 	private SchemaVersion getSchemaVersion(String schemaString) throws ValidataionException {
 		if(schemaString == null) {