Package org.cipres.treebase.domain.study

Examples of org.cipres.treebase.domain.study.Analysis

81
82
83
84
85
86
87
88
89
90
91
92
    /*
     * retrieve list of anlysisSteps for an analysis
     */
    // TODO: check if value is null
    String analysis_id = ServletRequestUtils.getStringParameter(request, "id", null);
    Analysis analysis = mAnalysisService.findByID(Long.parseLong(analysis_id));
    List<AnalysisStep> steps = analysis.getAnalysisStepsReadOnly();
    // send selected analysis info to session
    ControllerUtil.saveAnalysis(request, analysis);
    /*
     * map AnalysisStep to AnalysisStepCommand so we can print the algorithm type and the order
     */
 
View Full Code Here
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
    StudyStatus inprogress = getStudyStatusHome().findStatusInProgress();

    Citation c = new ArticleCitation();
    c.setTitle(newName);

    Analysis a1 = new Analysis();
    a1.setName("1 " + newName);
    Analysis a2 = new Analysis();
    a2.setName("2 " + newName);

    Study s = new Study();
    s.setName(newName);
    s.setStudyStatus(inprogress);
    s.setCitation(c);
    c.setStudy(s);
    s.addAnalysis(a1);
    s.addAnalysis(a2);

    TaxonLabel label = new TaxonLabel();
    label.setTaxonLabel(newName);
    label.setStudy(s);

    getStudyHome().store(label);
    getStudyHome().store(s);

    // force commit immeidately, important:
    setComplete();
    endTransaction();

    onSetUp();

    // Notes: this is important: why?? there are two copies of s in the same session.
    // how???
    s = (Study) hibernateTemplate.merge(s);

    Long studyID = s.getId();
    Long citationID = c.getId();
    logger.info("study created: " + s.getName() + "id = " + studyID);
    logger.info("citation created: " + c.getTitle() + "id = " + citationID);
    logger.info("analysis created: " + a1.getName() + "id = " + a1.getId());
    logger.info("analysis created: " + a2.getName() + "id = " + a2.getId());
    logger.info("taxonLabel created: " + label.getTaxonLabel() + "id = " + label.getId());

    // 2. verify
    String sqlStr = "select count(*) from Study where study_id=" + s.getId();
    int count = jdbcTemplate.queryForInt(sqlStr);
View Full Code Here
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
    Long studyID = s.getId();
    Long citationID = c.getId();
    logger.info("study created: " + s.getName() + "id = " + studyID);
    logger.info("citation created: " + c.getTitle() + "id = " + citationID);

    Analysis a1 = new Analysis();
    a1.setName("1 " + newName);
    Analysis a2 = new Analysis();
    a2.setName("2 " + newName);

    // NOTES: this will fail to add analysis to studyu!!
    // s.addAnalysis(a1);
    // s.addAnalysis(a2);

    Analysis updatedA1 = getFixture().update(a1);
    Analysis updatedA2 = getFixture().update(a2);

    s.addAnalysis(updatedA1);
    s.addAnalysis(updatedA2);
    Study updatedS = getFixture().update(s);

    // Note: a1.getID() and a2.getID() will return false.
    logger.info("analysis created: " + a1.getName() + "id = " + updatedA1.getId());
    logger.info("analysis created: " + a2.getName() + "id = " + updatedA2.getId());

    // 2. verify
    String sqlStr = "select count(*) from Study where study_id=" + s.getId();
    int count = jdbcTemplate.queryForInt(sqlStr);
    assertTrue(count == 1);

    // assertTrue("need to return Analysis ID.", a1.getId() != null);

    // 3. delete
    // Note: this one will fail: getFixture().deleteStudy(s);
    getFixture().deleteStudy(updatedS);
    setComplete();

    // 4. verify delete:
    int countVerify = jdbcTemplate.queryForInt(sqlStr);
    assertTrue("Deletion failed.", countVerify == 0);

    String sqlStrAnalysis = "select count(*) from analysis where analysis_id="
      + updatedA2.getId();
    count = jdbcTemplate.queryForInt(sqlStrAnalysis);
    assertTrue("cascade Delete analysis failed.", count == 0);

    if (logger.isInfoEnabled()) {
      logger.info(testName + " - end "); //$NON-NLS-1$
View Full Code Here
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
    s.setName(newName);
    s.setStudyStatus(inprogress);
    s.setCitation(c);
    c.setStudy(s);

    Analysis a1 = new Analysis();
    a1.setName("1 " + newName);
    Analysis a2 = new Analysis();
    a2.setName("2 " + newName);
    s.addAnalysis(a1);
    s.addAnalysis(a2);

    getStudyHome().store(s);

    // force commit immeidately, important:
    setComplete();
    endTransaction();

    Long studyID = s.getId();
    Long citationID = c.getId();
    Long a1ID = a1.getId();
    Long a2ID = a2.getId();

    logger.info("study created: " + s.getName() + "id = " + studyID);
    logger.info("citation created: " + c.getTitle() + "id = " + citationID);
    logger.info("2 analyses created: id= " + a1ID + ", " + a2ID);
View Full Code Here
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
        warn("  Couldn't find creation date");
      }
    }

    for (ValueAnalysisSection an : aux.getAnalysisSections()) {
      Analysis theAnalysis = new Analysis();
      theAnalysis.setStudy(theStudy);
      theAnalysis.setName(an.getString("analysis_name"));
     
      // TODO: TB_ANALYSISID

      AnalysisStep theAnalysisStep = new AnalysisStep();
      theAnalysisStep.setAnalysis(theAnalysis);
      theAnalysis.addAnalysisStep(theAnalysisStep);
      ContextManager.getAnalysisService().save(theAnalysis);
      ContextManager.getAnalysisStepService().save(theAnalysisStep);
     
      Algorithm theAlgorithm;
      String tb1Algorithm = an.getString("algorithm");
View Full Code Here
101
102
103
104
105
106
107
108
109
110
111
112
113
    if (pAnalysisStep == null) {
      return false;
    }

    // manage bi-directional relationships:
    Analysis analysis = pAnalysisStep.getAnalysis();
    if (analysis != null) {
      analysis.removeAnalysisStep(pAnalysisStep);
    }

    // Cascade delete:
    // * software
    // * algorithm:
 
View Full Code Here
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
    s.setName(newName);
    s.setStudyStatus(inprogress);
    s.setCitation(c);
    c.setStudy(s);

    Analysis a1 = new Analysis();
    a1.setName("1 " + newName);
    Analysis a2 = new Analysis();
    a2.setName("2 " + newName);
    s.addAnalysis(a1);
    s.addAnalysis(a2);

    getStudyHome().store(s);

    // force commit immediately, important:
    setComplete();
    endTransaction();

    Long studyID = s.getId();
    Long citationID = c.getId();
    Long a1ID = a1.getId();
    Long a2ID = a2.getId();

    logger.info("study created: " + s.getName() + "id = " + studyID);
    logger.info("citation created: " + c.getTitle() + "id = " + citationID);
    logger.info("2 analyses created: id= " + a1ID + ", " + a2ID);
    assertTrue("need to return Analysis ID.", a1.getId() != null && a2.getId() != null);

    // 2. verify
    String sqlStr = "select count(*) from analysis where study_id=" + s.getId();
    int count = jdbcTemplate.queryForInt(sqlStr);
    assertTrue(count == 2);
View Full Code Here
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
    block.addPhyloTree(tree);
    block.addPhyloTree(tree2);

    // Create an analysis step and associate w/ tree.
    Study s = getTestStudy();
    Analysis a1 = new Analysis();
    a1.setName("1 " + newName);
    AnalysisStep step1 = new AnalysisStep();
    step1.setName("step1 " + newName);
    s.addAnalysis(a1);
    a1.addAnalysisStep(step1);

    AnalyzedTree treeData = new AnalyzedTree();
    treeData.setTree(tree);
    treeData.setInput(Boolean.FALSE);
    step1.addAnalyzedData(treeData);

    getFixture().store(tree);
    getFixture().store(tree2);
    getFixture().store(block);

    // force commit immediately, important:
    setComplete();
    endTransaction();
    logger.info("tree1 created: " + tree.getLabel() + "id = " + tree.getId());
    logger.info("tree2 created: " + tree2.getLabel() + "id = " + tree2.getId());
    logger.info("treeBlock created: " + block.getTitle() + "id = " + block.getId());
    logger.info("analysis step created: " + step1.getName() + "id = " + step1.getId()
      + " associated data count=" + step1.getDataSetReadOnly().size());
    // logger.info("treeBlock created: " + block.getTitle() + "id = " + block.getId());

    // 2. verify
    String treeSql = "select count(*) from phylotree where treeBlock_id=" + block.getId();
    String blockSql = "select count(*) from treeblock where treeBlock_id=" + block.getId();
    String analyzedDataSql = "select count(*) from analyzedData where analysisstep_id="
      + step1.getId();
    String a1Sql = "select count(*) from analysis where analysis_id=" + a1.getId();
    int count = jdbcTemplate.queryForInt(treeSql);
    assertTrue(count == 2);
    count = jdbcTemplate.queryForInt(blockSql);
    assertTrue(count == 1);
    count = jdbcTemplate.queryForInt(a1Sql);
    assertTrue(count == 1);
    count = jdbcTemplate.queryForInt(analyzedDataSql);
    assertTrue(count == 1);

    onSetUp();

    // 3. delete
    getFixture().refresh(block);
    getFixture().refresh(a1);
    getFixture().refreshAll(a1.getAnalysisStepsReadOnly());

    getFixture().deleteTreeBlock(block);
    setComplete();
    endTransaction();

    // 3.2: have to separate the deleting of analysis, due to
    // analysisstep -->analyzedData.
    onSetUp();
    // getFixture().refresh(a1);
    a1 = (Analysis) loadObject(Analysis.class, a1.getId());
    getAnalysisService().deleteAnalysis(a1);

    setComplete();
    endTransaction();

View Full Code Here
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
      return false;
    }

    // Need to make sure the object belongs to the current session:
    // Analysis currentAnalysis = update(pAnalysis);
    Analysis currentAnalysis = pAnalysis;

    // manage bi-directional relationships:
    Study study = currentAnalysis.getStudy();
    if (study != null) {
      study.removeAnalysis(currentAnalysis);
    }

    // Cascade delete:
    // * analysis step:
    getAnalysisStepService().deleteAnalysisSteps(currentAnalysis.getAnalysisStepsReadOnly());

    getAnalysisHome().deletePersist(currentAnalysis);

    return true;
  }
View Full Code Here
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
   *
   * @see org.cipres.treebase.domain.study.AnalysisService#getPermission(java.lang.String,
   *      java.lang.Long)
   */
  public TBPermission getPermission(String pUsername, Long pAnalysisId) {
    Analysis a = findByID(pAnalysisId);
    // Long submissionID = null;
    Submission sub = null;

    if (a != null) {
      sub = a.getStudy().getSubmission();
    }

    if (sub == null) {
      return TBPermission.NONE;
    }
View Full Code Here
TOP

Related Classes of org.cipres.treebase.domain.study.Analysis

  • org.cipres.treebase.auxdata.CommitStudy
  • org.cipres.treebase.dao.tree.PhyloTreeDAOTest
  • org.cipres.treebase.domain.matrix.Matrix
  • org.cipres.treebase.domain.tree.PhyloTree
  • org.cipres.treebase.framework.ExecutionResult
  • org.cipres.treebase.service.study.AnalysisServiceImpl
  • org.cipres.treebase.service.study.AnalysisServiceImplTest
  • org.cipres.treebase.service.study.AnalysisStepServiceImpl
  • org.cipres.treebase.service.study.StudyServiceImplTest
  • org.cipres.treebase.web.controllers.AnalysisFormController
    • 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.