Package org.cipres.treebase.domain.study

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

180
181
182
183
184
185
186
187
188
189
190
191
192
     
      TaxonLabelSet tSet=pTreeBlock.getTaxonLabelSet();
     
      // bi-directional relationships:
      // * submission -> treeblock
      Submission sub = getSubmissionHome().findByTreeBlock(pTreeBlock);
      if (sub != null) {
        sub.removePhyloTreeBlock(pTreeBlock);
      }

      // cascade delete all trees by hibernate:
      // bi-directional relationships:
      // * remove analysisStep --> phyloTree
View Full Code Here
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
    // 2. query
    Matrix m = (Matrix) loadObject(Matrix.class, matrixId);
    assertTrue(m != null);

    Submission s = getFixture().findByMatrix(m);
    assertTrue(s != null);

    // 3. verify
    String sqlStr = "select count(*) from sub_matrix where submission_id = " + s.getId()
      + " and matrix_id = " + m.getId();
    int count = jdbcTemplate.queryForInt(sqlStr);
    assertTrue(count == 1);

    if (logger.isInfoEnabled()) {
View Full Code Here
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
    // 2. query
    PhyloTree tree = (PhyloTree) loadObject(PhyloTree.class, treeId);
    assertTrue(tree != null);

    Submission s = getFixture().findByTree(tree);
    assertTrue(s != null);

    // 3. verify
    String sqlStr = "select count(*) from sub_treeblock st, phylotree t where st.submission_id = " + s.getId()
      + " and st.treeblock_id = t.treeblock_id and t.phylotree_id = " + tree.getId();
    int count = jdbcTemplate.queryForInt(sqlStr);
    assertTrue(count == 1);

    if (logger.isInfoEnabled()) {
View Full Code Here
49
50
51
52
53
54
55
56
57
58
59
60
61
    if (LOGGER.isInfoEnabled()) {
      LOGGER.info("NUMBER OF SUBMISSIONS: " + submissioncount);
    }

    while (submissionIterator.hasNext()) {
      Submission pSubmission = submissionIterator.next();
      if (LOGGER.isInfoEnabled()) {
        LOGGER.info("Submission ID: " + pSubmission.getId());
      }
      getSubmissionService().deleteSubmission(pSubmission);

    }
View Full Code Here
170
171
172
173
174
175
176
177
178
179
180
    if (files.isEmpty()) {
      return new ModelAndView(getCancelView());
    }

    Study study = ControllerUtil.findStudy(request, getStudyService());
    Submission submission = study.getSubmission();
    MyProgressionListener listener = new MyProgressionListener();

    getSubmissionService().addNexusFiles(submission, files, listener);
    getStudyService().addNexusFiles(study, files);
View Full Code Here
151
152
153
154
155
156
157
158
159
160
161
 
    }

    public ModelAndView GetRecord( OAIPMHCommand params, Map model){
     
      Submission submission = null; 
     
      try{
         long id = IdentifyUtil.parseID(params);
           submission = studyService.findByID(id).getSubmission();
      }catch(NumberFormatException nfe){
View Full Code Here
190
191
192
193
194
195
196
197
198
199
200
     
    }
   
    public ModelAndView ListMetadataFormats(OAIPMHCommand params, Map model){
   
      Submission submission = null; 
     
      try{
         long id = IdentifyUtil.parseID(params);
           submission = studyService.findByID(id).getSubmission();
      }catch(NumberFormatException nfe){
View Full Code Here
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
   */
  public ModelAndView handleRequest(HttpServletRequest request, HttpServletResponse response)
    throws Exception {

    Study study = ControllerUtil.findStudy(request, mStudyService);
    Submission submission = (Submission) study.getSubmission();

    StudyCommand studyCommand = new StudyCommand();
    // copy study information
    studyCommand.setStudy(study);
    // study from TBI do not contain submission_id
    if (submission != null) {
      studyCommand.setSubmission_id(submission.getId());
    }

    List<Analysis> analysisList = study.getAnalyses();
    List<AnalysisCommand> analysisCommandList = new ArrayList<AnalysisCommand>();
    List<Analysis> changedAnalyses = new ArrayList<Analysis>();
View Full Code Here
69
70
71
72
73
74
75
76
77
78
79
    // relationship managmenet:
    // * if the user has submission:
    Iterator<Submission> iter = pUser.getSubmissionIterator();
    while (iter.hasNext()) {
      Submission element = iter.next();
      element.setSubmitter(null);
    }

    super.deletePersist(pUser);
  }
View Full Code Here
110
111
112
113
114
115
116
117
118
119
120
121
122
123
      // study.setCitation(c);

      // retrieve Study object from session to be submitted with citation
      // Study study = (Study) request.getSession().getAttribute(Constants.STUDY_KEY);
      // citationCommand.getCitationMap(citationType).setStudy(study);
      Submission submission = mSubmissionService.createSubmission(user, study);

      // save Study object to session and remove
      ControllerUtil.saveStudy(request, submission.getStudy());

    } else if (request.getParameter(ACTION_UPDATE) != null) {
      mStudyService.update(study);
    } else if (request.getParameter(ACTION_DELETE) != null) {
View Full Code Here
TOP

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

  • org.cipres.treebase.auxdata.CommitStudy
  • org.cipres.treebase.dao.admin.UserDAO
  • org.cipres.treebase.dao.matrix.MatrixDAO
  • org.cipres.treebase.dao.study.SubmissionDAO
  • org.cipres.treebase.dao.study.SubmissionDAOTest
  • org.cipres.treebase.dao.taxon.TaxonLabelDAO
  • org.cipres.treebase.dao.tree.PhyloTreeDAO
  • org.cipres.treebase.domain.admin.UserRole.TBPermission
  • org.cipres.treebase.domain.tree.PhyloTreeTest
  • org.cipres.treebase.service.study.AnalysisServiceImpl
    • 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.