Examples of AnalysisBounds

com.infoclinika.mssharing.model.write.AnalysisBounds
@author Pavel Kaplin

Examples of com.infoclinika.mssharing.model.write.AnalysisBounds

        this.translationError = translationError;
    }


    public AnalysisBounds getBounds() {
        if (bounds == null) {
            bounds = new AnalysisBounds();
        }
        return bounds;
    }

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Examples of com.infoclinika.mssharing.model.write.AnalysisBounds

                    annotations = new Annotations(f.annotations.fractionNumber, f.annotations.sampleId);
                }
                return new FileItem(f.getFileMetaData().getId(), f.factorValues, Optional.fromNullable(annotations));
            }
        });
        final AnalysisBounds analysisBounds = experiment.getBounds();
        final List<Double> lockMasses = newLinkedList(experiment.getLockMasses());
        return newExperiment(userId, experiment.getProject().getId(), (experiment.getLab() == null) ? null : experiment.getLab().getId(), experimentInfo, experiment.getExperimentData().is2dLc(),
                restriction, factors, files, analysisBounds, lockMasses);
    }

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Examples of com.infoclinika.mssharing.model.write.AnalysisBounds

        final ImmutableSortedSet<DashboardReader.FileLine> fileLines = dashboardReader.readFiles(bob, DashboardReader.Filter.SHARED_WITH_ME);
        assertTrue(fileLines.size() == 1);
        final long id = fileLines.first().id;
        studyManagement.newExperiment(kate, publicProject, uc.getLab3(), new StudyManagement.ExperimentInfo("Duplicated title", "area", anyWorkflowType(), anySpecie())
                , false, restriction(kate), Collections.<StudyManagement.MetaFactor>emptyList(),
                ImmutableList.of(new StudyManagement.FileItem(id, Collections.<String>emptyList(), Optional.<StudyManagement.Annotations>absent())), new AnalysisBounds(), new ArrayList<Double>());
        assertTrue(dashboardReader.readFiles(bob, DashboardReader.Filter.SHARED_WITH_ME).size() == 0);
        assertTrue(dashboardReader.readFiles(bob, DashboardReader.Filter.PUBLIC).size() == 1);
    }

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Examples of com.infoclinika.mssharing.model.write.AnalysisBounds

abstract class AbstractStudyTest extends AbstractTest {


    protected long experimentInNewProject(long user, long lab) {
        final long project1 = uc.createProject(user, lab);
        final long file = uc.saveFile(user);
        return studyManagement.newExperiment(user, project1, lab, new StudyManagement.ExperimentInfo(anyStr(), "", anyWorkflowType(), anySpecie()), false, restriction(user), NO_FACTORS, noFactoredFile(file), new AnalysisBounds(), new ArrayList<Double>());
    }

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Examples of com.infoclinika.mssharing.model.write.AnalysisBounds

        final long bob = uc.createLab3AndBob();
        final long project = createPublicProject(bob);


        final long file1 = uc.saveFile(bob);
        final long experiment = studyManagement.newExperiment(bob, project, uc.getLab3(), experimentInfo(), false, restriction(bob),
                Collections.<StudyManagement.MetaFactor>emptyList(), noFactoredFile(file1), new AnalysisBounds(), new ArrayList<Double>());


        final  long file2 = uc.saveFile(bob);
        final String factorName = anyStr();
        final String factorValue = "2";
        addFilesToExperiment(bob, experiment,

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Examples of com.infoclinika.mssharing.model.write.AnalysisBounds

        instrument(bob, uc.getLab3(), anyInstrumentModel());
        long workflowType = anyWorkflowType();
        final long projectId = studyManagement.newProject(bob, uc.getLab3(), new StudyManagement.ProjectInfo(projectName, anyStr(), anyStr()));
        long specie = anySpecie();
        final long experimentId = studyManagement.newExperiment(bob, projectId, uc.getLab3(),
                new StudyManagement.ExperimentInfo(experimentName, experimentDescription, workflowType, specie), false, restriction(bob), NO_FACTORS, anyFile(bob), new AnalysisBounds(), new ArrayList<Double>());


        final DetailsReader.ExperimentItem experimentItem = detailsReader.readExperiment(bob, experimentId);
        assertNotNull(experimentItem.files);
        assertNotNull(experimentItem.factors);
        assertNotNull(experimentItem.factorValues);

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Examples of com.infoclinika.mssharing.model.write.AnalysisBounds

        final long file = uc.saveFile(bob);
        final long project = uc.createProject(bob, uc.getLab3());


         studyManagement.newExperiment(bob, project, uc.getLab3(), new StudyManagement.ExperimentInfo("", "", anyWorkflowType(), anySpecie())
                , true, restriction(bob), Collections.<StudyManagement.MetaFactor>emptyList(),
                of(new StudyManagement.FileItem(file, Collections.<String>emptyList(), Optional.<StudyManagement.Annotations>absent())), new AnalysisBounds(), new ArrayList<Double>());


    }

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Examples of com.infoclinika.mssharing.model.write.AnalysisBounds

        final long project = studyManagement.newProject(bob, uc.getLab3(), new StudyManagement.ProjectInfo("Title", "area", ""));
        final long file = uc.saveFile(bob);
        final long workflowType = anyWorkflowType();
        final long specie = anySpecie();
        studyManagement.newExperiment(bob, project, uc.getLab3(), new StudyManagement.ExperimentInfo("Duplicated title", "area", workflowType, specie),
                false, restriction(bob), Collections.<StudyManagement.MetaFactor>emptyList(), noFactoredFile(file), new AnalysisBounds(), new ArrayList<Double>());
        studyManagement.newExperiment(bob, project, uc.getLab3(), new StudyManagement.ExperimentInfo("Duplicated title", "another area", workflowType, specie),
                false, restriction(bob), Collections.<StudyManagement.MetaFactor>emptyList(), noFactoredFile(file), new AnalysisBounds(), new ArrayList<Double>());
    }

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Examples of com.infoclinika.mssharing.model.write.AnalysisBounds

        final long project = studyManagement.newProject(bob, uc.getLab3(), new StudyManagement.ProjectInfo("Title", "area", ""));
        final long file = uc.saveFile(bob);
        final long workflowType = anyWorkflowType();
        final long specie = anySpecie();
        studyManagement.newExperiment(bob, project, uc.getLab3(), new StudyManagement.ExperimentInfo("Duplicated title", "area", workflowType, specie)
                , false, restriction(bob), Collections.<StudyManagement.MetaFactor>emptyList(), noFactoredFile(file), new AnalysisBounds(), new ArrayList<Double>());
        final long experiment = studyManagement.newExperiment(bob, project, uc.getLab3(), new StudyManagement.ExperimentInfo("Title", "another area", workflowType, specie)
                , false, restriction(bob), Collections.<StudyManagement.MetaFactor>emptyList(), noFactoredFile(file), new AnalysisBounds(), new ArrayList<Double>());
        studyManagement.updateExperiment(bob, experiment, project, new StudyManagement.ExperimentInfo("Duplicated title", "another area", workflowType, specie)
                , false, restriction(bob), Collections.<StudyManagement.MetaFactor>emptyList(), noFactoredFile(file), new ArrayList<Double>());
    }

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Examples of com.infoclinika.mssharing.model.write.AnalysisBounds

    @Test(expectedExceptions = IllegalArgumentException.class)
    public void testDontAllowToCreateExperimentWithEmptyName() {
        final long bob = uc.createLab3AndBob();
        final long project = studyManagement.newProject(bob, uc.getLab3(), new StudyManagement.ProjectInfo("Title", "area", ""));
        studyManagement.newExperiment(bob, project, uc.getLab3(), new StudyManagement.ExperimentInfo("Duplicated title", "area", anyWorkflowType(), anySpecie())
                , false, restriction(bob), Collections.<StudyManagement.MetaFactor>emptyList(), noFactoredFile(uc.saveFile(bob)), new AnalysisBounds(), new ArrayList<Double>());
    }

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