Coverage Report
File JPred4WSClient.java
Coverage histogram
54% of files have more coverage
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| JPred4WSClient | 23 | 42 | 21 |
Contributing tests
This file is covered by 41 tests.
.
Source view
| 1 | package jalview.ws2.client.jpred4; | |
| 2 | ||
| 3 | import java.io.ByteArrayOutputStream; | |
| 4 | import java.io.IOException; | |
| 5 | import java.util.List; | |
| 6 | ||
| 7 | import jalview.datamodel.SequenceI; | |
| 8 | import jalview.io.AlignFile; | |
| 9 | import jalview.io.DataSourceType; | |
| 10 | import jalview.io.FastaFile; | |
| 11 | import jalview.io.FileFormat; | |
| 12 | import jalview.io.FormatAdapter; | |
| 13 | import jalview.io.JPredFile; | |
| 14 | import jalview.ws.params.ArgumentI; | |
| 15 | import jalview.ws2.api.Credentials; | |
| 16 | import jalview.ws2.api.JobStatus; | |
| 17 | import jalview.ws2.api.WebServiceJobHandle; | |
| 18 | import jalview.ws2.client.api.SecStructPredWebServiceClientI; | |
| 19 | import uk.ac.dundee.compbio.jpred.JPredClient; | |
| 20 | import uk.ac.dundee.compbio.jpred.JPredRequest; | |
| 21 | import uk.ac.dundee.compbio.jpred.ResultTypes; | |
| 22 | ||
| 23 | public class JPred4WSClient implements SecStructPredWebServiceClientI | |
| 24 | { | |
| 25 | final JPredClient client; | |
| 26 | ||
| 27 | private final JPredRequest.Mode mode; | |
| 28 | ||
| 29 | private final JPredRequest.Format format; | |
| 30 | ||
| 31 | 116 |  JPred4WSClient(JPredClient client, boolean msaMode) |
| 32 | { | |
| 33 | 116 | this.mode = msaMode ? JPredRequest.Mode.MSA : JPredRequest.Mode.SINGLE; |
| 34 | 116 | this.format = msaMode ? JPredRequest.Format.FASTA : JPredRequest.Format.SEQ; |
| 35 | 116 | this.client = client; |
| 36 | } | |
| 37 | ||
| 38 | 0 | @Override |
| 39 | public String getUrl() | |
| 40 | { | |
| 41 | 0 | return client.getURL().toString(); |
| 42 | } | |
| 43 | ||
| 44 | 0 | @Override |
| 45 | public String getClientName() | |
| 46 | { | |
| 47 | 0 | return "jpred4"; |
| 48 | } | |
| 49 | ||
| 50 | 0 | @Override |
| 51 | public WebServiceJobHandle submit(List<SequenceI> sequences, | |
| 52 | List<ArgumentI> args, Credentials credentials) throws IOException | |
| 53 | { | |
| 54 | 0 | var input = mode == JPredRequest.Mode.MSA |
| 55 | ? FileFormat.Fasta | |
| 56 | .getWriter(null) | |
| 57 | .print(sequences.toArray(new SequenceI[sequences.size()]), false) | |
| 58 | : sequences.get(0).getSequenceAsString(); | |
| 59 | ||
| 60 | 0 | JPredRequest request = JPredRequest |
| 61 | .newBuilder() | |
| 62 | .mode(mode) | |
| 63 | .format(format) | |
| 64 | .input(input) | |
| 65 | .build(); | |
| 66 | 0 | var jobId = client.submit(request); |
| 67 | 0 | return new WebServiceJobHandle(getClientName(), "jpred4", getUrl(), jobId); |
| 68 | } | |
| 69 | ||
| 70 | 0 | @Override |
| 71 | public JobStatus getStatus(WebServiceJobHandle job) throws IOException | |
| 72 | { | |
| 73 | 0 | var status = client.getStatus(job.getJobId()); |
| 74 | 0 | switch (status) |
| 75 | { | |
| 76 | 0 | case PENDING: |
| 77 | 0 | return JobStatus.QUEUED; |
| 78 | 0 | case RUNNING: |
| 79 | 0 | return JobStatus.RUNNING; |
| 80 | 0 | case FINISHED: |
| 81 | 0 | return JobStatus.COMPLETED; |
| 82 | 0 | case NO_JOB: |
| 83 | 0 | return JobStatus.SERVER_ERROR; |
| 84 | 0 | case MALFORMED: |
| 85 | 0 | return JobStatus.INVALID; |
| 86 | 0 | case NOT_EXIST: |
| 87 | 0 | return JobStatus.SERVER_ERROR; |
| 88 | 0 | default: |
| 89 | 0 | return JobStatus.UNKNOWN; |
| 90 | } | |
| 91 | } | |
| 92 | ||
| 93 | 0 | @Override |
| 94 | public String getLog(WebServiceJobHandle job) throws IOException | |
| 95 | { | |
| 96 | 0 | var stream = client.getResultStream(job.getJobId(), ResultTypes.LOG); |
| 97 | // FIXME: potential OOM | |
| 98 | 0 | return new String(stream.readAllBytes()); |
| 99 | } | |
| 100 | ||
| 101 | 0 | @Override |
| 102 | public String getErrorLog(WebServiceJobHandle job) throws IOException | |
| 103 | { | |
| 104 | 0 | return ""; |
| 105 | } | |
| 106 | ||
| 107 | 0 | @Override |
| 108 | public void cancel(WebServiceJobHandle job) | |
| 109 | throws IOException, UnsupportedOperationException | |
| 110 | { | |
| 111 | ||
| 112 | } | |
| 113 | ||
| 114 | 0 | @Override |
| 115 | public AlignFile getAlignmentFile(WebServiceJobHandle job) throws IOException | |
| 116 | { | |
| 117 | 0 | var stream = client.getResultStream(job.getJobId(), ResultTypes.PSIBLAST_ALIGN); |
| 118 | 0 | var buffer = new byte[2048]; |
| 119 | 0 | var file = new ByteArrayOutputStream(); |
| 120 | 0 | var len = 0; |
| 121 | 0 | while ((len= stream.read(buffer)) >= 0) |
| 122 | 0 | file.write(buffer, 0, len); |
| 123 | 0 | return new FastaFile(file.toString("UTF-8"), DataSourceType.PASTE); |
| 124 | } | |
| 125 | ||
| 126 | 0 | @Override |
| 127 | public JPredFile getPredictionFile(WebServiceJobHandle job) throws IOException | |
| 128 | { | |
| 129 | 0 | var stream = client.getResultStream(job.getJobId(), ResultTypes.CONCISE); |
| 130 | 0 | var buffer = new byte[2048]; |
| 131 | 0 | var file = new ByteArrayOutputStream(); |
| 132 | 0 | var len = 0; |
| 133 | 0 | while ((len= stream.read(buffer)) >= 0) |
| 134 | 0 | file.write(buffer, 0, len); |
| 135 | 0 | return new JPredFile(file.toString("UTF-8"), DataSourceType.PASTE); |
| 136 | } | |
| 137 | } |