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author
eoberortner
committed
resolved conflicts
2 parents b1d1e48 + 661af53 commit 786a87c

5 files changed

Lines changed: 156 additions & 1 deletion

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

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@@ -238,6 +238,37 @@ public String dnaVarification(
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filenameSequences, vendor, sequencePatternsFilename));
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}
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/**
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* The partition() method Partitioning of large DNA sequences into synthesizable
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* building blocks with partial overlaps for an efficient assembly.
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*
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* @throws BOOSTClientException
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* @throws BOOSTBackEndException
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*/
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public String partition(
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String sequenceFileName,
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String fivePrimeVectorOverlap,
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String threePrimeVectorOverlap,
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String minLengthBB,
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String maxLengthBB,
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String minOverlapGC,
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String optOverlapGC,
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String maxOverlapGC,
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String minOverlapLength,
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String optOverlapLength,
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String maxOverlapLength)
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throws BOOSTClientException, BOOSTBackEndException {
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// construct the request's JSON object
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JSONObject requestData = RequestBuilder.buildPartation(sequenceFileName, fivePrimeVectorOverlap,
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threePrimeVectorOverlap, minLengthBB, maxLengthBB, minOverlapGC, optOverlapGC, maxOverlapGC,
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minOverlapLength, optOverlapLength, maxOverlapLength);
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return submitJob(requestData);
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}
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/**
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* The submitJob method submits a job to the BOOST back-end and returns
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* the UUID (as String) of the submitted job.

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

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@@ -277,6 +277,97 @@ public static JSONObject buildPolish(
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return modifiedData;
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}
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/**
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* The buildPartation wraps all required information for
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* BOOST's dna partition functionality into a JSON representation
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*
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* @return a JSONObject that represents the input values
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*
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* @throws BOOSTClientException ... if any given value is NULL or any given String value is empty
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* */
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public static JSONObject buildPartation(
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final String sequenceFileName,
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final String fivePrimeVectorOverlap,
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final String threePrimeVectorOverlap,
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String minLengthBB,
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String maxLengthBB,
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String minOverlapGC,
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String optOverlapGC,
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String maxOverlapGC,
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String minOverlapLength,
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String optOverlapLength,
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String maxOverlapLength)
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throws BOOSTClientException{
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//verify the values
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ParameterValueVerifier.verifyFilename(BOOSTConstants.INPUT_FILENAME, sequenceFileName);
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ParameterValueVerifier.verifyValue(BOOSTConstants.FIVE_PRIME_VECTOR_OVERLAP, fivePrimeVectorOverlap);
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ParameterValueVerifier.verifyValue(BOOSTConstants.THREE_PRIME_VECTOR_OVERLAP, threePrimeVectorOverlap);
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ParameterValueVerifier.verifyValue(BOOSTConstants.MIN_BB_LENGTH, minLengthBB);
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ParameterValueVerifier.verifyValue(BOOSTConstants.MAX_BB_LENGTH, maxLengthBB);
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ParameterValueVerifier.verifyValue(BOOSTConstants.MIN_OVERLAP_GC, minOverlapGC);
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ParameterValueVerifier.verifyValue(BOOSTConstants.OPT_OVERLAP_GC, optOverlapGC);
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ParameterValueVerifier.verifyValue(BOOSTConstants.MAX_OVERLAP_GC, maxOverlapGC);
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ParameterValueVerifier.verifyValue(BOOSTConstants.MIN_OVERLAP_LENGTH, minOverlapGC);
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ParameterValueVerifier.verifyValue(BOOSTConstants.OPT_OVERLAP_LENGTH, optOverlapGC);
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ParameterValueVerifier.verifyValue(BOOSTConstants.MAX_OVERLAP_LENGTH, maxOverlapLength);
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//----------------------------------------------
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// build the JSON representation of the input values
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JSONObject partationData = new JSONObject();
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//----------------------------------------------
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// JOB INFORMATION
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partationData.put(JSONKeys.JOB_INFORMATION,
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RequestBuilder.buildJobInformation(BOOSTFunctions.PARTITION));
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//----------------------------------------------
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// sequence information
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partationData.put(JSONKeys.SEQUENCE_INFORMATION,
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RequestBuilder.buildSequenceData(sequenceFileName, SequenceType.DNA, false));
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// partition information
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partationData.put(JSONKeys.PARTITIONING_INFORMATION,
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RequestBuilder.buildPartitionData(sequenceFileName, fivePrimeVectorOverlap,
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threePrimeVectorOverlap, minLengthBB, maxLengthBB, minOverlapGC, optOverlapGC,
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maxOverlapGC, minOverlapLength, optOverlapLength, maxOverlapLength));
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return partationData;
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}
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private static JSONObject buildPartitionData(final String sequenceFileName,
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final String fivePrimeVectorOverlap, final String threePrimeVectorOverlap,
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String minLengthBB, String maxLengthBB, String minOverlapGC, String optOverlapGC,
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String maxOverlapGC, String minOverlapLength, String optOverlapLength, String maxOverlapLength){
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JSONObject partationData = new JSONObject();
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//JSONObject subPartationData = new JSONObject();
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partationData.put(JSONKeys.FIVE_PRIME_VECTOR_OVERLAP, fivePrimeVectorOverlap);
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partationData.put(JSONKeys.THREE_PRIME_VECTOR_OVERLAP, threePrimeVectorOverlap);
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partationData.put(JSONKeys.MAX_BB_LENGTH, maxLengthBB);
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partationData.put(JSONKeys.MIN_BB_LENGTH, minLengthBB);
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partationData.put(JSONKeys.MAX_OVERLAP_GC, maxOverlapGC);
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partationData.put(JSONKeys.BATCH, "");
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partationData.put(JSONKeys.MIN_OVERLAP_GC, minOverlapGC);
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partationData.put(JSONKeys.MAX_OVERLAP_LENGTH, maxOverlapLength);
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partationData.put(JSONKeys.OPT_OVERLAP_GC, optOverlapGC);
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partationData.put(JSONKeys.OPT_OVERLAP_LENGTH, optOverlapLength);
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partationData.put(JSONKeys.MIN_OVERLAP_LENGTH, minOverlapLength);
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JSONObject partationParameters = new JSONObject();
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partationParameters.put(JSONKeys.PARTITIONING_INFORMATION, partationData);
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return partationData;
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}
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/**
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*
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* @param function

‎src/main/java/gov/doe/jgi/boost/client/constants/BOOSTConstants.java‎

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@@ -15,5 +15,19 @@ public class BOOSTConstants {
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// uri for signup
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public static final String SIGNUP_URI = "https://contacts.jgi.doe.gov/registration/new";
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// partitioning-related keys
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public static final String PARTITIONING_INFORMATION = "partitioning-parameters";
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public static final String MIN_BB_LENGTH = "min-BB-length";
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public static final String MAX_BB_LENGTH = "max-BB-length";
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public static final String MIN_OVERLAP_GC = "min-overlap-GC";
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public static final String OPT_OVERLAP_GC = "opt-overlap-GC";
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public static final String MAX_OVERLAP_GC = "max-overlap-GC";
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public static final String MIN_OVERLAP_LENGTH = "min-overlap-length";
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public static final String OPT_OVERLAP_LENGTH = "opt-overlap-length";
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public static final String MAX_OVERLAP_LENGTH = "max-overlap-length";
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public static final String FIVE_PRIME_VECTOR_OVERLAP = "5-prime-vector-overlap";
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public static final String THREE_PRIME_VECTOR_OVERLAP = "3-prime-vector-overlap";
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public static final String BATCH = "batch";
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}

‎src/main/java/gov/doe/jgi/boost/client/constants/JSONKeys.java‎

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@@ -49,6 +49,7 @@ public class JSONKeys {
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public static final String MAX_OVERLAP_LENGTH = "max-overlap-length";
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public static final String FIVE_PRIME_VECTOR_OVERLAP = "5-prime-vector-overlap";
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public static final String THREE_PRIME_VECTOR_OVERLAP = "3-prime-vector-overlap";
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public static final String BATCH = "batch";
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// output-related keys
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public static final String OUTPUT_INFORMATION = "output";

‎src/test/java/gov/doe/jgi/boost/client/DemoClient.java‎

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@@ -87,6 +87,24 @@ public static void main(String[] args)
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jobUUIDs.add(polishDNAJobUUID);
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}
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// partitioning of DNA
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String partitiongDNAJobUUID = client.partition(
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"./data/dna.fasta", // input sequence
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"aaacccgggttt", // 5-prime-vector-overlap
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"tttgggcccaaa", // 3-prime-vector-overlap
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Integer.toString(15), // min-BB-length
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Integer.toString(3000), // max-BB-length
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Double.toString(4.0), // minimum overlap GC
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Double.toString(40.0), // optimum overlap GC
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Double.toString(62.0), // maximum overlap GC
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Integer.toString(5), // minimum overlap length
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Integer.toString(25), // optimum overlap length
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Integer.toString(30) // maximum overlap length
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);
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if (null != partitiongDNAJobUUID) {
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jobUUIDs.add(polishDNAJobUUID);
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}
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// for all jobs, we check their status
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for(String jobUUID : jobUUIDs) {

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