Merge pull request #13 from eoberortner/GSoC18

revert Pull request hash code- b4a6fb2

Author: prem0862

README.md

@@ -21,16 +21,16 @@ by providing a method for each functionality of the BOOST REST API.
 
 As a first step, you have to instantiate the BOOSTClient class using one of the following alternatives:
 
-* providing your BOOST username and password.
+* providing your BOOST username and password.You can provide these in LoginCredentials class.
 
 ```
-BOOSTClient client = new BOOSTClient("your-username", "your-password");
+BOOSTClient client = new BOOSTClient(LoginCredentials.mUserName, LoginCredentials.mPassword);
 ```
 
-* providing your BOOST JSON Web Token (JWT)
+* providing your BOOST JSON Web Token (JWT). You can provide your BOOST-JWT token in LoginCredentials class.
 
 ```
-BOOSTClient client = new BOOSTClient("your-BOOST-JWT");
+BOOSTClient client = new BOOSTClient(LoginCredentials.mJWT);
 ```
 
 ### Supported methods of the BOOST Client
@@ -56,6 +56,27 @@ client.codonJuggle(
 	FileFormat.GENBANK);           // the desired output format
 ```
 
+* dnaVerification
+
+```
+client.dnaVarification(
+	"./data/dna.fasta",           // a FASTA file containing the input sequence
+	Vendor.GEN9                   // vendor
+	"./data/patterns.fasta");     // sequence patterns
+```
+	
+* polish
+
+```
+client.polish(
+        "./data/dna.fasta",           // a FASTA file containing input sequence
+        true,                         // encoding sequences support sequence feature annotations
+        Vendor.JGI,                   // vendor
+        Strategy.Balanced2Random,     // codon selection strategy
+        FileFormat.SBOL,              // the desired output format
+        "Saccharomyces cerevisiae");  // predefined host
+ ```      
+       
 ## Examples 
 
 An example of invoking every supported method is provided in the [DemoClient](https://github.com/eoberortner/BOOST-REST-Client/blob/master/src/test/java/gov/doe/jgi/boost/client/DemoClient.java) 
@@ -70,4 +91,4 @@ Please contact ```eoberortner (at) lbl (dot) gov```
 
 
 
-     
+     

src/main/java/gov/doe/jgi/boost/client/BOOSTClient.java

@@ -9,7 +9,9 @@
 import gov.doe.jgi.boost.client.constants.BOOSTResources;
 import gov.doe.jgi.boost.client.constants.JSONKeys;
 import gov.doe.jgi.boost.enums.FileFormat;
+import gov.doe.jgi.boost.enums.SequenceType;
 import gov.doe.jgi.boost.enums.Strategy;
+import gov.doe.jgi.boost.enums.Vendor;
 import gov.doe.jgi.boost.exception.BOOSTBackEndException;
 import gov.doe.jgi.boost.exception.BOOSTClientException;
 
@@ -224,18 +226,49 @@ public String codonJuggle(
 	 * 
 	 * @throws BOOSTClientException
 	 */
-	public String verify(
+	public String dnaVarification(
 			final String filenameSequences, 
-			final String constraintsFilename, 
+			Vendor vendor, 
 			final String sequencePatternsFilename)
 				throws BOOSTClientException, BOOSTBackEndException, IOException {
 
 		// represent the request data in JSON and
 		// submit it to BOOST's Job Queue Management System (JQMS)
 		return submitJob(RequestBuilder.buildVerify(
-				filenameSequences, constraintsFilename, sequencePatternsFilename));
+				filenameSequences, vendor, sequencePatternsFilename));
 	}
 
+	/**
+	 * The partition() method Partitioning of large DNA sequences into synthesizable
+	 * building blocks with partial overlaps for an efficient assembly.
+	 *  
+	 * @throws BOOSTClientException
+	 * @throws BOOSTBackEndException 
+	 */
+
+	public String partition(
+			String sequenceFileName, 
+			String fivePrimeVectorOverlap, 
+			String threePrimeVectorOverlap,
+			String minLengthBB, 
+			String maxLengthBB, 
+			String minOverlapGC, 
+			String optOverlapGC, 
+			String maxOverlapGC, 
+			String minOverlapLength, 
+			String optOverlapLength,
+			String maxOverlapLength) 
+					throws BOOSTClientException, BOOSTBackEndException {
+		
+		// construct the request's JSON object
+		JSONObject requestData = RequestBuilder.buildPartation(sequenceFileName, fivePrimeVectorOverlap,
+				threePrimeVectorOverlap, minLengthBB, maxLengthBB, minOverlapGC, optOverlapGC, maxOverlapGC,
+				minOverlapLength, optOverlapLength, maxOverlapLength);
+		
+		return submitJob(requestData);
+	}
+	
+	
 	/**
 	 * The submitJob method submits a job to the BOOST back-end and returns 
 	 * the UUID (as String) of the submitted job. 
@@ -383,33 +416,48 @@ public JSONObject getJobReport(final String jobUUID)
 //			throw new BOOSTClientException(e.getLocalizedMessage());
 //		}
 //	}
-//	
-//	
-//	/**
-//	 * The polish() method verifies the sequences in a given file against the 
-//	 * gene synthesis constraints of a commercial synthesis vendor. 
-//	 * In case of violations, the polish() method modifies the coding regions 
-//	 * of the sequence using the specified codon replacement strategy.
-//	 *  
-//	 * @param sequencesFilename ... the name of the file that contains the sequences
-//	 * @param type ... the type of the sequences, i.e. DNA, RNA, Protein
-//	 * @param bCodingSequences ... if the sequences are encoded in a format that does not 
-//	 * support sequence feature annotations and if bCoding sequences is set to true, 
-//	 * then are all sequences are treated as coding sequences. If the sequences are 
-//	 * encoded in a format that does support sequence feature annotations, then the 
-//	 * bCodingSequences flag is ignored. 
-//	 * @param vendor ... the name of commercial synthesis provider
-//	 * @param strategy ... the codon replacement strategy
-//	 * @param codonUsageTableFilename ... the name of the file that contains the codon 
-//	 * usage table
-//	 * 
-//	 * @throws BOOSTClientException
-//	 */
-//	public void polish(final String sequencesFilename, SequenceType type, boolean bCodingSequences,
-//			Vendor vendor, Strategy strategy, final String codonUsageTableFilename) 
-//				throws BOOSTClientException {
-//		
-//		// check if the user did a login previously
+	
+	
+	/**
+	 * The polish() method verifies the sequences in a given file against the 
+	 * gene synthesis constraints of a commercial synthesis vendor. 
+	 * In case of violations, the polish() method modifies the coding regions 
+	 * of the sequence using the specified codon replacement strategy.
+	 *  
+	 * @param sequencesFilename ... the name of the file that contains the sequences
+	 * @param type ... the type of the sequences, i.e. DNA, RNA, Protein
+	 * @param bCodingSequences ... if the sequences are encoded in a format that does not 
+	 * support sequence feature annotations and if bCoding sequences is set to true, 
+	 * then are all sequences are treated as coding sequences. If the sequences are 
+	 * encoded in a format that does support sequence feature annotations, then the 
+	 * bCodingSequences flag is ignored. 
+	 * @param vendor ... the name of commercial synthesis provider
+	 * @param strategy ... the codon replacement strategy
+	 * @param codonUsageTableFilename ... the name of the file that contains the codon 
+	 * usage table
+	 * 
+	 * @throws BOOSTClientException
+	 * @throws BOOSTBackEndException 
+	 */
+	public String polish(
+			final String sequencesFilename, 
+			boolean bCodingSequences,
+			Vendor vendor, 
+			Strategy strategy, 
+			final FileFormat outputFormat,
+			final String codonUsageTable) 
+				throws BOOSTClientException, BOOSTBackEndException {
+		
+		// construct the request's JSON object
+		JSONObject requestData = RequestBuilder.buildPolish( sequencesFilename, 
+			bCodingSequences, vendor, strategy, outputFormat, codonUsageTable);
+				
+		 return submitJob(requestData);
+		
+	}
+	
+		
+		// check if the user did a login previously
 //		if(null == token) {
 //			throw new BOOSTClientException("You must authenticate first!");
 //		}

src/main/java/gov/doe/jgi/boost/client/RequestBuilder.java

@@ -165,14 +165,14 @@ public static JSONObject buildCodonJuggle(
 	 */
 	public static JSONObject buildVerify(
 			final String filenameSequences, 
-			final String constraintsFilename,
+			Vendor vendor,
 			final String sequencePatternsFilename)
 				throws BOOSTClientException, IOException {
 
 		//---------------------------------
 		// verify the given values
 		ParameterValueVerifier.verifyFilename(JSONKeys.SEQUENCE_INFORMATION, filenameSequences);
-		ParameterValueVerifier.verifyFilename(JSONKeys.CONSTRAINTS_INFORMATION, constraintsFilename);
+		ParameterValueVerifier.verifyNull(BOOSTConstants.VENDOR, vendor);
 		// the sequence patterns filename is optional
 		if(null != sequencePatternsFilename && !sequencePatternsFilename.trim().isEmpty()) {
 			ParameterValueVerifier.verifyFilename(JSONKeys.PATTERN_INFORMATION, sequencePatternsFilename);
@@ -202,14 +202,172 @@ public static JSONObject buildVerify(
 
 		//---------------------------------
 		// CONSTRAINTS
-		requestData.put(JSONKeys.CONSTRAINTS_INFORMATION,
-				RequestBuilder.buildConstraints(constraintsFilename));
+		requestData.put(JSONKeys.VENDOR_NAME, vendor);
 		//---------------------------------
 
 
 		return requestData;
 	}
 
+	
+	/**
+	 *  
+	 * @param sequencesFilename ... the name of the file that contains the sequences
+	 * @param type ... the type of the sequences, i.e. DNA, RNA, Protein
+	 * @param bCodingSequences ... if the sequences are encoded in a format that does not 
+	 * support sequence feature annotations and if bCoding sequences is set to true, 
+	 * then are all sequences are treated as coding sequences. If the sequences are 
+	 * encoded in a format that does support sequence feature annotations, then the 
+	 * bCodingSequences flag is ignored. 
+	 * @param vendor ... the name of commercial synthesis provider
+	 * @param strategy ... the codon replacement strategy
+	 * @param codonUsageTableFilename ... the name of the file that contains the codon 
+	 * usage table
+	 * 
+	 * @throws BOOSTClientException
+	 */
+	public static JSONObject buildPolish(
+			final String sequencesFilename, 
+			boolean bCodingSequences,
+			Vendor vendor, 
+			Strategy strategy, 
+			final FileFormat outputFormat,
+			final String codonUsageTable) 
+				throws BOOSTClientException {
+		
+		//-------------------------------------
+		// verify the given values
+		ParameterValueVerifier.verifyFilename(BOOSTConstants.INPUT_FILENAME, sequencesFilename);
+		ParameterValueVerifier.verifyNull(BOOSTConstants.VENDOR, vendor);
+		try {
+			ParameterValueVerifier.verifyFilename(BOOSTConstants.CODON_USAGE_TABLE, codonUsageTable);
+		} catch(Exception e) {}
+		ParameterValueVerifier.verifyNull(BOOSTConstants.OUTPUT_FORMAT, outputFormat);
+		ParameterValueVerifier.verifyNull(BOOSTConstants.STRATEGY, strategy);
+		//----------------------------------------
+		
+		JSONObject modifiedData = new JSONObject();
+		
+		//-----------------------------------------
+		//JOB INFORMATION
+		modifiedData.put(JSONKeys.JOB_INFORMATION,
+				RequestBuilder.buildJobInformation(BOOSTFunctions.POLISH));
+		//-----------------------------------------
+		
+		// sequence information
+		modifiedData.put(JSONKeys.SEQUENCE_INFORMATION,
+				RequestBuilder.buildSequenceData(sequencesFilename, SequenceType.DNA, bCodingSequences ));
+		//-----------------------------------------
+		
+		// constraints
+		modifiedData.put(JSONKeys.VENDOR_NAME, vendor);
+		//------------------------------------------
+		
+		// modification information
+		modifiedData.put(JSONKeys.MODIFICATION_INFORMATION,
+				RequestBuilder.buildModificationData(strategy, codonUsageTable));
+		//-------------------------------------------
+		
+		// output information
+		modifiedData.put(JSONKeys.OUTPUT_INFORMATION, 
+				RequestBuilder.buildOutputData(outputFormat));
+		//-------------------------------------------------
+		
+		
+		return modifiedData;
+	}
+	
+	/**
+	 * The buildPartation wraps all required information for  
+	 * BOOST's dna partition functionality into a JSON representation  
+	 * 
+	 * @return a JSONObject that represents the input values
+	 * 
+	 * @throws BOOSTClientException ... if any given value is NULL or any given String value is empty
+	 * */
+	
+	public static JSONObject buildPartation(
+			final String sequenceFileName,
+			final String fivePrimeVectorOverlap,
+			final String threePrimeVectorOverlap,
+			String minLengthBB,
+			String maxLengthBB,
+			String minOverlapGC,
+			String optOverlapGC,
+			String maxOverlapGC,
+			String minOverlapLength,
+			String optOverlapLength,
+			String maxOverlapLength)
+					throws BOOSTClientException{
+					
+		//verify the values
+		ParameterValueVerifier.verifyFilename(BOOSTConstants.INPUT_FILENAME, sequenceFileName);
+		ParameterValueVerifier.verifyValue(BOOSTConstants.FIVE_PRIME_VECTOR_OVERLAP, fivePrimeVectorOverlap);
+		ParameterValueVerifier.verifyValue(BOOSTConstants.THREE_PRIME_VECTOR_OVERLAP, threePrimeVectorOverlap);
+		ParameterValueVerifier.verifyValue(BOOSTConstants.MIN_BB_LENGTH, minLengthBB);
+		ParameterValueVerifier.verifyValue(BOOSTConstants.MAX_BB_LENGTH, maxLengthBB);
+		ParameterValueVerifier.verifyValue(BOOSTConstants.MIN_OVERLAP_GC, minOverlapGC);
+		ParameterValueVerifier.verifyValue(BOOSTConstants.OPT_OVERLAP_GC, optOverlapGC);
+		ParameterValueVerifier.verifyValue(BOOSTConstants.MAX_OVERLAP_GC, maxOverlapGC);
+		ParameterValueVerifier.verifyValue(BOOSTConstants.MIN_OVERLAP_LENGTH, minOverlapGC);
+		ParameterValueVerifier.verifyValue(BOOSTConstants.OPT_OVERLAP_LENGTH, optOverlapGC);
+		ParameterValueVerifier.verifyValue(BOOSTConstants.MAX_OVERLAP_LENGTH, maxOverlapLength);
+		
+		//----------------------------------------------
+		
+		// build the JSON representation of the input values
+		JSONObject partationData = new JSONObject();
+				
+		//----------------------------------------------
+		
+		
+		// JOB INFORMATION
+		partationData.put(JSONKeys.JOB_INFORMATION, 
+				RequestBuilder.buildJobInformation(BOOSTFunctions.PARTITION));
+		//----------------------------------------------
+		
+
+		// sequence information
+		partationData.put(JSONKeys.SEQUENCE_INFORMATION,  
+				RequestBuilder.buildSequenceData(sequenceFileName, SequenceType.DNA, false));
+		
+		// partition information
+		partationData.put(JSONKeys.PARTITIONING_INFORMATION, 
+				RequestBuilder.buildPartitionData(sequenceFileName, fivePrimeVectorOverlap,
+						threePrimeVectorOverlap, minLengthBB, maxLengthBB, minOverlapGC, optOverlapGC, 
+						maxOverlapGC, minOverlapLength, optOverlapLength, maxOverlapLength));
+	    
+		
+		return partationData;	
+		
+	}
+
+	private static JSONObject buildPartitionData(final String sequenceFileName,
+			final String fivePrimeVectorOverlap, final String threePrimeVectorOverlap,
+			String minLengthBB, String maxLengthBB, String minOverlapGC, String optOverlapGC,
+			String maxOverlapGC, String minOverlapLength, String optOverlapLength, String maxOverlapLength){
+		
+		JSONObject partationData = new JSONObject();
+		//JSONObject subPartationData = new JSONObject();
+		partationData.put(JSONKeys.FIVE_PRIME_VECTOR_OVERLAP, fivePrimeVectorOverlap);
+		partationData.put(JSONKeys.THREE_PRIME_VECTOR_OVERLAP, threePrimeVectorOverlap);
+		partationData.put(JSONKeys.MAX_BB_LENGTH, maxLengthBB);
+		partationData.put(JSONKeys.MIN_BB_LENGTH, minLengthBB);
+		partationData.put(JSONKeys.MAX_OVERLAP_GC, maxOverlapGC);
+		partationData.put(JSONKeys.BATCH, "");
+		partationData.put(JSONKeys.MIN_OVERLAP_GC, minOverlapGC);
+		partationData.put(JSONKeys.MAX_OVERLAP_LENGTH, maxOverlapLength);
+		partationData.put(JSONKeys.OPT_OVERLAP_GC, optOverlapGC);
+		partationData.put(JSONKeys.OPT_OVERLAP_LENGTH, optOverlapLength);
+		partationData.put(JSONKeys.MIN_OVERLAP_LENGTH, minOverlapLength);
+		
+		JSONObject partationParameters = new JSONObject();
+		partationParameters.put(JSONKeys.PARTITIONING_INFORMATION, partationData);
+		
+		return partationData;
+	}
+	
+	
 	/**
 	 * 
 	 * @param function