Package uk.ac.bbsrc.tgac.miso.core.data

Examples of uk.ac.bbsrc.tgac.miso.core.data.SequencerReference

138
139
140
141
142
143
144
145
    return sequencerReference.getId();
  }

  public SequencerReference get(long id) throws IOException {
    List eResults = template.query(SEQUENCER_REFERENCE_SELECT_BY_ID, new Object[]{id}, new SequencerReferenceMapper());
    SequencerReference e = eResults.size() > 0 ? (SequencerReference) eResults.get(0) : null;
    return e;
  }
View Full Code Here
144
145
146
147
148
149
150
151
    return e;
  }

  public SequencerReference getByRunId(long runId) throws IOException {
    List eResults = template.query(SEQUENCER_REFERENCE_SELECT_BY_RELATED_RUN, new Object[]{runId}, new SequencerReferenceMapper());
    SequencerReference e = eResults.size() > 0 ? (SequencerReference) eResults.get(0) : null;
    return e;
  }
View Full Code Here
150
151
152
153
154
155
156
157
    return e;
  }

  public SequencerReference getByName(String referenceName) throws IOException {
    List eResults = template.query(SEQUENCER_REFERENCE_SELECT_BY_NAME, new Object[]{referenceName}, new SequencerReferenceMapper());
    SequencerReference e = eResults.size() > 0 ? (SequencerReference) eResults.get(0) : null;
    return e;
  }
View Full Code Here
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
                                 new MapSqlParameterSource().addValue("referenceId", r.getId())) == 1));
  }

  public class SequencerReferenceMapper implements RowMapper<SequencerReference> {
    public SequencerReference mapRow(ResultSet rs, int rowNum) throws SQLException {
      SequencerReference c = dataObjectFactory.getSequencerReference();

      try {
        if (c != null) {
          c.setId(rs.getLong("referenceId"));
          c.setName(rs.getString("name"));
          c.setPlatform(platformDAO.get(rs.getLong("platformId")));
          c.setAvailable(rs.getBoolean("available"));

          Blob ipBlob = rs.getBlob("ipAddress");
          if (ipBlob != null) {
            if (ipBlob.length() > 0) {
              byte[] rbytes = ipBlob.getBytes(1, (int)ipBlob.length());
              c.setIpAddress(InetAddress.getByAddress(rbytes));
            }
          }
        }
      }
      catch (IOException e1) {
View Full Code Here
90
91
92
93
94
95
96
97
98
99
100
101
102
103
    return new ModelAndView("/pages/viewStats.jsp", model);
  }

  @RequestMapping(value = "/sequencer/{referenceId}", method = RequestMethod.GET)
  public ModelAndView viewSequencer(@PathVariable(value = "referenceId") Long referenceId, ModelMap model) throws IOException {
    SequencerReference sr = requestManager.getSequencerReferenceById(referenceId);
    if (sr != null) {
      model.put("sequencerReference", sr);
      String ip = sr.getIpAddress().toString();
      if (ip.startsWith("/")) {
        model.put("trimmedIpAddress", ip.substring(1));
      }
      else {
        model.put("trimmedIpAddress", ip);
View Full Code Here
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
  }

  @RequestMapping(value = "/ls454/{referenceId}", method = RequestMethod.GET)
  public ModelAndView ls454Stats(@PathVariable(value = "referenceId") Long referenceId, ModelMap model) throws IOException {
    model.put("platformtype", PlatformType.LS454);
    SequencerReference sr = requestManager.getSequencerReferenceById(referenceId);
    if (sr != null) {
      if (!sr.getPlatform().getPlatformType().equals(PlatformType.LS454)) {
        throw new IOException("Trying to interrogate a " + sr.getPlatform().getPlatformType().getKey() + " sequencer reference with a 454 strategy");
      }
      try {
        SequencerInterrogator context = SequencerInterrogatorFactory.getSequencerInterrogator(sr);

        model.put("stats", context.listAllStatus());
        model.put("referenceName", sr.getName());
        model.put("referenceId", sr.getId());
      }
      catch (InterrogationException e) {
        model.put("error", MisoWebUtils.generateErrorDivMessage("Cannot retrieve status information for the given sequencer reference: " + sr.getName(), e.getMessage()));
        log.info(e.getMessage());
        e.printStackTrace();
      }
    }
    else {
View Full Code Here
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
  }

  @RequestMapping(value = "/ls454/{referenceId}/{runName}", method = RequestMethod.GET)
  public ModelAndView ls454Stats(@PathVariable(value = "referenceId") Long referenceId, @PathVariable(value = "runName") String runName, ModelMap model) throws IOException {
    model.put("platformtype", PlatformType.LS454);
    SequencerReference sr = requestManager.getSequencerReferenceById(referenceId);
    if (sr != null) {
      if (!sr.getPlatform().getPlatformType().equals(PlatformType.LS454)) {
        throw new IOException("Trying to interrogate a " + sr.getPlatform().getPlatformType().getKey() + " sequencer reference with a 454 strategy");
      }
      try {
        SequencerInterrogator context = SequencerInterrogatorFactory.getSequencerInterrogator(sr);
        Status status = context.getRunStatus(runName);
        if (status != null) {
          model.put("referenceName", sr.getName());
          model.put("referenceId", sr.getId());
          model.put("runId", requestManager.getRunByAlias(runName).getId());
          model.put("runName", runName);
          model.put("runStatus", status);
        }
        else {
          model.put("error", MisoWebUtils.generateErrorDivMessage("Cannot consume the xml file for the given run name: " + runName));
        }
      }
      catch (InterrogationException e) {
        model.put("error", MisoWebUtils.generateErrorDivMessage("Cannot retrieve status information for the given sequencer reference: " + sr.getName(), e.getMessage()));
        log.info(e.getMessage());
        e.printStackTrace();
      }
    }
    else {
View Full Code Here
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
  }

  @RequestMapping(value = "/illumina/{referenceId}", method = RequestMethod.GET)
  public ModelAndView illuminaStats(@PathVariable(value = "referenceId") Long referenceId, ModelMap model) throws IOException {
    model.put("platformtype", PlatformType.ILLUMINA.getKey().toLowerCase());
    SequencerReference sr = requestManager.getSequencerReferenceById(referenceId);
    if (sr != null) {
      if (!sr.getPlatform().getPlatformType().equals(PlatformType.ILLUMINA)) {
        throw new IOException("Trying to interrogate a " + sr.getPlatform().getPlatformType().getKey() + " sequencer reference with an Illumina strategy");
      }
      model.put("stats", requestManager.listAllStatusBySequencerName(sr.getName()));
      model.put("referenceName", sr.getName());
      model.put("referenceId", sr.getId());
    }
    else {
      model.put("error", "Cannot retrieve the given sequencer reference: " + referenceId);
    }
    return new ModelAndView("/pages/viewStats.jsp", model);
View Full Code Here
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
  }

  @RequestMapping(value = "/illumina/{referenceId}/{runName}", method = RequestMethod.GET)
  public ModelAndView illuminaStats(@PathVariable(value = "referenceId") Long referenceId, @PathVariable(value = "runName") String runName, ModelMap model) throws IOException {
    model.put("platformtype", PlatformType.ILLUMINA);
    SequencerReference sr = requestManager.getSequencerReferenceById(referenceId);
    if (sr != null) {
      if (!sr.getPlatform().getPlatformType().equals(PlatformType.ILLUMINA)) {
        throw new IOException("Trying to interrogate a " + sr.getPlatform().getPlatformType().getKey() + " sequencer reference with an Illumina strategy");
      }
     
      try {
        Status status = requestManager.getStatusByRunName(runName);
        if (status != null) {
          model.put("referenceName", sr.getName());
          model.put("referenceId", sr.getId());
          model.put("runId", requestManager.getRunByAlias(runName).getId());
          model.put("runName", runName);
          model.put("runStatus", status);

          InputStream in = StatsController.class.getResourceAsStream("/status/xsl/illumina/statusXml.xsl");
View Full Code Here
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
  }

  @RequestMapping(value = "/solid/{referenceId}", method = RequestMethod.GET)
  public ModelAndView solidStats(@PathVariable(value = "referenceId") Long referenceId, ModelMap model) throws IOException {
    model.put("platformtype", PlatformType.SOLID);
    SequencerReference sr = requestManager.getSequencerReferenceById(referenceId);

    if (!sr.getPlatform().getPlatformType().equals(PlatformType.SOLID)) {
      throw new IOException("Trying to interrogate a " + sr.getPlatform().getPlatformType().getKey() + " sequencer reference with a SOLiD strategy");
    }

    if (!sr.getPlatform().getInstrumentModel().contains("5500xl")) {
      SolidService ss = new SolidService(new URL("http://"+sr.getFQDN()+":8080/sets/webservice/solid?wsdl"), new QName("http://solid.aga.appliedbiosystems.com", "SolidService"));
      StringBuilder sb = new StringBuilder();
      try {
        InputStream in = StatsController.class.getResourceAsStream("/integration/solid/xsl/clusterStatus.xsl");
        if (in != null) {
          String xsl = LimsUtils.inputStreamToString(in);
          sb.append(SubmissionUtils.xslTransform(ss.getSolidPort().getClusterStatus().getXml(), xsl));
        }
      }
      catch (TransformerException e) {
        sb.append("Unable to transform Cluster Status XML: " + e.getMessage());
        e.printStackTrace();
      }
      model.put("clusterStatus", sb.toString());
    }
   
    model.put("stats", requestManager.listAllStatusBySequencerName(sr.getName()));
    model.put("referenceName", sr.getName());
    model.put("referenceId", sr.getId());

    return new ModelAndView("/pages/viewStats.jsp", model);
  }
View Full Code Here
TOP

Related Classes of uk.ac.bbsrc.tgac.miso.core.data.SequencerReference

  • uk.ac.bbsrc.tgac.miso.spring.ajax.SequencerReferenceControllerHelperService
  • uk.ac.bbsrc.tgac.miso.sqlstore.SQLSequencerReferenceDAO
  • uk.ac.bbsrc.tgac.miso.sqlstore.SQLSequencerReferenceDAO$SequencerReferenceMapper
  • uk.ac.bbsrc.tgac.miso.webapp.controller.StatsController
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.