Revert "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.You can provide these in LoginCredentials class.
+* providing your BOOST username and password.
 
 ```
-BOOSTClient client = new BOOSTClient(LoginCredentials.mUserName, LoginCredentials.mPassword);
+BOOSTClient client = new BOOSTClient("your-username", "your-password");
 ```
 
-* providing your BOOST JSON Web Token (JWT). You can provide your BOOST-JWT token in LoginCredentials class.
+* providing your BOOST JSON Web Token (JWT)
 
 ```
-BOOSTClient client = new BOOSTClient(LoginCredentials.mJWT);
+BOOSTClient client = new BOOSTClient("your-BOOST-JWT");
 ```
 
 ### Supported methods of the BOOST Client
@@ -56,27 +56,6 @@ 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) 
@@ -91,4 +70,4 @@ Please contact ```eoberortner (at) lbl (dot) gov```
 
 
 
-     
+     

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

@@ -9,9 +9,7 @@
 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;
 
@@ -226,49 +224,18 @@ public String codonJuggle(
 	 * 
 	 * @throws BOOSTClientException
 	 */
-	public String dnaVarification(
+	public String verify(
 			final String filenameSequences, 
-			Vendor vendor, 
+			final String constraintsFilename, 
 			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, vendor, sequencePatternsFilename));
+				filenameSequences, constraintsFilename, 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. 
@@ -416,48 +383,33 @@ 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
-	 * @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
+//	
+//	
+//	/**
+//	 * 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
 //		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, 
-			Vendor vendor,
+			final String constraintsFilename,
 			final String sequencePatternsFilename)
 				throws BOOSTClientException, IOException {
 
 		//---------------------------------
 		// verify the given values
 		ParameterValueVerifier.verifyFilename(JSONKeys.SEQUENCE_INFORMATION, filenameSequences);
-		ParameterValueVerifier.verifyNull(BOOSTConstants.VENDOR, vendor);
+		ParameterValueVerifier.verifyFilename(JSONKeys.CONSTRAINTS_INFORMATION, constraintsFilename);
 		// the sequence patterns filename is optional
 		if(null != sequencePatternsFilename && !sequencePatternsFilename.trim().isEmpty()) {
 			ParameterValueVerifier.verifyFilename(JSONKeys.PATTERN_INFORMATION, sequencePatternsFilename);
@@ -202,172 +202,14 @@ public static JSONObject buildVerify(
 
 		//---------------------------------
 		// CONSTRAINTS
-		requestData.put(JSONKeys.VENDOR_NAME, vendor);
+		requestData.put(JSONKeys.CONSTRAINTS_INFORMATION,
+				RequestBuilder.buildConstraints(constraintsFilename));
 		//---------------------------------
 
 
 		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