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Added support for SBOLDocument as well as filename for BOOST APIs (#34)
* accepting SBOLDocument for coding sequence * added support for SBOLDocument and filename * formatted some code * code refactoring
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4 files changed

Lines changed: 274 additions & 70 deletions

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

Lines changed: 207 additions & 18 deletions
Original file line numberDiff line numberDiff line change
@@ -1,9 +1,18 @@
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package gov.doe.jgi.boost.client;
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import java.io.IOException;
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import java.io.UnsupportedEncodingException;
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import javax.ws.rs.core.Response;
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import org.json.JSONException;
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import org.json.JSONObject;
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import org.sbolstandard.core2.SBOLConversionException;
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import org.sbolstandard.core2.SBOLDocument;
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import org.sbolstandard.core2.SBOLReader;
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import org.sbolstandard.core2.SBOLValidationException;
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import gov.doe.jgi.boost.client.constants.BOOSTConstants;
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import gov.doe.jgi.boost.client.constants.BOOSTResources;
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import gov.doe.jgi.boost.client.constants.JSONKeys;
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import gov.doe.jgi.boost.enums.FileFormat;
@@ -129,37 +138,98 @@ public String getToken() {
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}
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/**
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* The reverseTranslate method invokes BOOT's reverse-translate functionality.
141+
* The reverseTranslate method invokes BOOST's reverse-translate functionality.
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*
134-
* @param filenameSequences ... the name of the file that contains the input sequences
143+
* @param sequencesFilename ... the name of the file that contains the input sequences
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* @param strategy ... the codon selection strategy
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* @param filenameCodonUsageTable ... the name of the file that contains the codon usage table
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* @param outputFormat ... the desired output format
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*
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* @throws BOOSTClientException
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* @throws IOException
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* @throws SBOLConversionException
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* @throws SBOLValidationException
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* @throws BOOSTAPIsException
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*/
143154
public String reverseTranslate(
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final String filenameSequences,
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final String sequencesFilename,
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Strategy strategy, final String filenameCodonUsageTable,
146157
final FileFormat outputFormat)
147-
throws BOOSTClientException, BOOSTBackEndException, IOException {
158+
throws BOOSTClientException, BOOSTBackEndException, IOException,
159+
SBOLValidationException, SBOLConversionException {
160+
161+
// verify for filename
162+
ParameterValueVerifier.verifyFilename(BOOSTConstants.INPUT_FILENAME, sequencesFilename);
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164+
// read the file as SBOLDocument
165+
SBOLDocument document = SBOLReader.read(sequencesFilename);
166+
return this.reverseTranslate(document, strategy, filenameCodonUsageTable, outputFormat);
167+
}
168+
169+
/**
170+
* The reverseTranslate method invokes BOOST's reverse-translate functionality.
171+
*
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* @param designSequences ... sbol document that contains the input sequences
173+
* @param strategy ... the codon selection strategy
174+
* @param filenameCodonUsageTable ... the name of the file that contains the codon usage table
175+
* @param outputFormat ... the desired output format
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*
177+
* @throws BOOSTClientException
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* @throws IOException
179+
* @throws JSONException
180+
* @throws SBOLConversionException
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* @throws BOOSTAPIsException
182+
*/
183+
public String reverseTranslate(
184+
final SBOLDocument designSequences,
185+
Strategy strategy, final String filenameCodonUsageTable,
186+
final FileFormat outputFormat)
187+
throws BOOSTClientException, BOOSTBackEndException, IOException,
188+
JSONException, SBOLConversionException {
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149190
// construct the request's JSON object
150191
JSONObject requestData = RequestBuilder.buildReverseTranslate(
151-
filenameSequences, strategy, filenameCodonUsageTable, outputFormat);
152-
153-
System.out.println(requestData.toString(4));
192+
designSequences, strategy, filenameCodonUsageTable, outputFormat);
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155194
return this.submitJob(requestData);
195+
}
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197+
/**
198+
* The codonJuggle method invokes BOOST's codon-juggling functionality.
199+
*
200+
* @param sequencesFilename ... the name of the file that contains the input sequences
201+
* @param bAutoAnnotate ... true ... all sequences exclusively 5'-3' protein coding sequences (is only considered
202+
* when the sequences don't have feature annotations, e.g. FASTA or CSV)
203+
* @param strategy ... the codon replacement strategy
204+
* @param filenameCodonUsageTable ... the name of the file that contains the codon usage table
205+
* @param outputFormat ... the desired output format
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*
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* @throws BOOSTClientException
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* @throws IOException
209+
* @throws SBOLConversionException
210+
* @throws SBOLValidationException
211+
* @throws BOOSTAPIsException
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*/
213+
public String codonJuggle(
214+
final String sequencesFilename, boolean bAutoAnnotate,
215+
Strategy strategy, final String filenameCodonUsageTable,
216+
final FileFormat outputFormat)
217+
throws BOOSTClientException, BOOSTBackEndException, IOException,
218+
SBOLValidationException, SBOLConversionException {
219+
220+
// verify for filename
221+
ParameterValueVerifier.verifyFilename(BOOSTConstants.INPUT_FILENAME, sequencesFilename);
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223+
// read the file as SBOLDocument
224+
SBOLDocument document = SBOLReader.read(sequencesFilename);
225+
return this.codonJuggle(document, bAutoAnnotate, strategy, filenameCodonUsageTable, outputFormat);
157226
}
158227

228+
159229
/**
160230
* The codonJuggle method invokes BOOST's codon-juggling functionality.
161231
*
162-
* @param filenameSequences ... the name of the file that contains the input sequences
232+
* @param designSequences ... the sbol document that contains the input sequences
163233
* @param bAutoAnnotate ... true ... all sequences exclusively 5'-3' protein coding sequences (is only considered
164234
* when the sequences don't have feature annotations, e.g. FASTA or CSV)
165235
* @param strategy ... the codon replacement strategy
@@ -168,17 +238,20 @@ public String reverseTranslate(
168238
*
169239
* @throws BOOSTClientException
170240
* @throws IOException
241+
* @throws SBOLConversionException
242+
* @throws JSONException
171243
* @throws BOOSTAPIsException
172244
*/
173245
public String codonJuggle(
174-
final String filenameSequences, boolean bAutoAnnotate,
246+
final SBOLDocument designSequences, boolean bAutoAnnotate,
175247
Strategy strategy, final String filenameCodonUsageTable,
176248
final FileFormat outputFormat)
177-
throws BOOSTClientException, BOOSTBackEndException, IOException {
249+
throws BOOSTClientException, BOOSTBackEndException, IOException,
250+
JSONException, SBOLConversionException {
178251

179252
// construct the request's JSON object
180253
JSONObject requestData = RequestBuilder.buildCodonJuggle(
181-
filenameSequences, bAutoAnnotate, strategy, filenameCodonUsageTable, outputFormat);
254+
designSequences, bAutoAnnotate, strategy, filenameCodonUsageTable, outputFormat);
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183256
return this.submitJob(requestData);
184257
}
@@ -187,21 +260,56 @@ public String codonJuggle(
187260
* The verify method submits a job to BOOST that verifies
188261
* sequences against DNA synthesis constraints.
189262
*
190-
* @param codingSequence ... the name of the file that contains the sequences
263+
* @param sequencesFileName ... the name of the file that contains the sequences
264+
* @param constraintsFilename ... the name of the file that contains the DNA synthesis constraints
265+
* @param sequencePatternsFilename ... the name of the file that contains sequence patterns
266+
*
267+
* @return the UUID of the submitted job
268+
*
269+
* @throws BOOSTClientException
270+
* @throws SBOLConversionException
271+
* @throws SBOLValidationException
272+
* @throws BOOSTAPIsException
273+
*
274+
*/
275+
public String dnaVarification(
276+
final String sequencesFileName,
277+
Vendor vendor,
278+
final String sequencePatternsFilename)
279+
throws BOOSTClientException, BOOSTBackEndException,
280+
IOException, SBOLValidationException, SBOLConversionException {
281+
282+
// verify for filename
283+
ParameterValueVerifier.verifyFilename(BOOSTConstants.INPUT_FILENAME, sequencesFileName);
284+
285+
// read the file as SBOLDocument
286+
SBOLDocument document = SBOLReader.read(sequencesFileName);
287+
return this.dnaVarification(document, vendor, sequencePatternsFilename);
288+
289+
}
290+
291+
/**
292+
* The verify method submits a job to BOOST that verifies
293+
* sequences against DNA synthesis constraints.
294+
*
295+
* @param codingSequence ... the sbol document that contains the sequences
191296
* @param constraintsFilename ... the name of the file that contains the DNA synthesis constraints
192297
* @param sequencePatternsFilename ... the name of the file that contains sequence patterns
193298
*
194299
* @return the UUID of the submitted job
195300
*
196301
* @throws BOOSTClientException
302+
* @throws SBOLConversionException
303+
* @throws JSONException
197304
* @throws BOOSTAPIsException
198305
*
199306
*/
200307
public String dnaVarification(
201-
final String codingSequence,
308+
final SBOLDocument codingSequence,
202309
Vendor vendor,
203310
final String sequencePatternsFilename)
204-
throws BOOSTClientException, BOOSTBackEndException, IOException {
311+
throws BOOSTClientException, BOOSTBackEndException, IOException,
312+
JSONException, SBOLConversionException {
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206314
// represent the request data in JSON and
207315
// submit it to BOOST's Job Queue Management System (JQMS)
@@ -215,11 +323,14 @@ public String dnaVarification(
215323
*
216324
* @throws BOOSTClientException
217325
* @throws BOOSTBackEndException
326+
* @throws SBOLConversionException
327+
* @throws IOException
328+
* @throws SBOLValidationException
218329
* @throws BOOSTAPIsException
219330
*/
220331

221332
public String partition(
222-
String codingSequence,
333+
final String sequencesFilename,
223334
String fivePrimeVectorOverlap,
224335
String threePrimeVectorOverlap,
225336
String minLengthBB,
@@ -233,7 +344,37 @@ public String partition(
233344
String minPrimerLength,
234345
String maxPrimerLength,
235346
String maxPrimerTm)
236-
throws BOOSTClientException, BOOSTBackEndException {
347+
throws BOOSTClientException, BOOSTBackEndException,
348+
SBOLValidationException, IOException, SBOLConversionException {
349+
350+
// verify for filename
351+
ParameterValueVerifier.verifyFilename(BOOSTConstants.INPUT_FILENAME, sequencesFilename);
352+
353+
// read the file as SBOLDocument
354+
SBOLDocument document = SBOLReader.read(sequencesFilename);
355+
return this.partition(document, fivePrimeVectorOverlap, threePrimeVectorOverlap,
356+
minLengthBB, maxLengthBB, minOverlapGC, optOverlapGC, maxOverlapGC, minOverlapLength,
357+
optOverlapLength, maxOverlapLength, minPrimerLength, maxPrimerLength, maxPrimerTm);
358+
}
359+
360+
361+
public String partition(
362+
SBOLDocument codingSequence,
363+
String fivePrimeVectorOverlap,
364+
String threePrimeVectorOverlap,
365+
String minLengthBB,
366+
String maxLengthBB,
367+
String minOverlapGC,
368+
String optOverlapGC,
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String maxOverlapGC,
370+
String minOverlapLength,
371+
String optOverlapLength,
372+
String maxOverlapLength,
373+
String minPrimerLength,
374+
String maxPrimerLength,
375+
String maxPrimerTm)
376+
throws BOOSTClientException, BOOSTBackEndException, JSONException,
377+
UnsupportedEncodingException, SBOLConversionException {
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238379
// construct the request's JSON object
239380
JSONObject requestData = RequestBuilder.buildPartition(codingSequence, fivePrimeVectorOverlap,
@@ -356,16 +497,64 @@ public JSONObject getJobReport(final String jobUUID)
356497
*
357498
* @throws BOOSTClientException
358499
* @throws BOOSTBackEndException
500+
* @throws SBOLConversionException
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* @throws IOException
502+
* @throws SBOLValidationException
503+
* @throws BOOSTAPIsException
504+
*/
505+
public String polish(
506+
final String sequencesFilename,
507+
boolean bCodingSequences,
508+
Vendor vendor,
509+
Strategy strategy,
510+
final FileFormat outputFormat,
511+
final String codonUsageTable)
512+
throws BOOSTClientException, BOOSTBackEndException,
513+
SBOLValidationException, IOException, SBOLConversionException {
514+
515+
// verify for filename
516+
ParameterValueVerifier.verifyFilename(BOOSTConstants.INPUT_FILENAME, sequencesFilename);
517+
518+
// read the file as SBOLDocument
519+
SBOLDocument document = SBOLReader.read(sequencesFilename);
520+
return this.polish(document, bCodingSequences, vendor, strategy,
521+
outputFormat, codonUsageTable);
522+
}
523+
524+
525+
/**
526+
* The polish() method verifies the sequences in a given file against the
527+
* gene synthesis constraints of a commercial synthesis vendor.
528+
* In case of violations, the polish() method modifies the coding regions
529+
* of the sequence using the specified codon replacement strategy.
530+
*
531+
* @param codingSequence ... the sbol file that contains the sequences
532+
* @param type ... the type of the sequences, i.e. DNA, RNA, Protein
533+
* @param bCodingSequences ... if the sequences are encoded in a format that does not
534+
* support sequence feature annotations and if bCoding sequences is set to true,
535+
* then are all sequences are treated as coding sequences. If the sequences are
536+
* encoded in a format that does support sequence feature annotations, then the
537+
* bCodingSequences flag is ignored.
538+
* @param vendor ... the name of commercial synthesis provider
539+
* @param strategy ... the codon replacement strategy
540+
* @param codonUsageTableFilename ... the name of the file that contains the codon
541+
* usage table
542+
*
543+
* @throws BOOSTClientException
544+
* @throws BOOSTBackEndException
545+
* @throws SBOLConversionException
546+
* @throws UnsupportedEncodingException
547+
* @throws JSONException
359548
* @throws BOOSTAPIsException
360549
*/
361550
public String polish(
362-
final String codingSequence,
551+
final SBOLDocument codingSequence,
363552
boolean bCodingSequences,
364553
Vendor vendor,
365554
Strategy strategy,
366555
final FileFormat outputFormat,
367556
final String codonUsageTable)
368-
throws BOOSTClientException, BOOSTBackEndException {
557+
throws BOOSTClientException, BOOSTBackEndException, JSONException, UnsupportedEncodingException, SBOLConversionException {
369558

370559
// construct the request's JSON object
371560
JSONObject requestData = RequestBuilder.buildPolish( codingSequence,

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