MacCossLabModules/panoramapublic/src/org/labkey/panoramapublic/pipeline/PxDataValidationPipelineJob.java at b9ee7cd3017cf2f98666c6af7eb8c74e87665404 · LabKey/MacCossLabModules · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
package org.labkey.panoramapublic.pipeline;

import com.fasterxml.jackson.annotation.JsonCreator;
import com.fasterxml.jackson.annotation.JsonProperty;
import org.labkey.api.pipeline.PipeRoot;
import org.labkey.api.pipeline.PipelineJob;
import org.labkey.api.pipeline.PipelineJobService;
import org.labkey.api.pipeline.TaskId;
import org.labkey.api.pipeline.TaskPipeline;
import org.labkey.api.portal.ProjectUrls;
import org.labkey.api.util.FileUtil;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.view.ActionURL;
import org.labkey.api.view.ViewBackgroundInfo;
import org.labkey.panoramapublic.model.ExperimentAnnotations;

public class PxDataValidationPipelineJob extends PipelineJob implements PxDataValidationJobSupport
{
    private final ExperimentAnnotations _experimentAnnotations;
    private final int _validationId;
    private final String _description;

    @JsonCreator
    protected PxDataValidationPipelineJob(@JsonProperty("_experimentAnnotations") ExperimentAnnotations experiment,
                                          @JsonProperty("_validation") int validationId,
                                          @JsonProperty("_description") String description)
    {
        super();
        _experimentAnnotations = experiment;
        _validationId = validationId;
        _description = description;
    }

    public PxDataValidationPipelineJob(ViewBackgroundInfo info, PipeRoot root, ExperimentAnnotations experiment, int validationId)
    {
        super(PxValidationPipelineProvider.NAME, info, root);
        _experimentAnnotations = experiment;
        _validationId = validationId;
        _description = String.format("Validating data for experiment Id: %d, validation Id: %d", experiment.getId(), validationId);

        String baseLogFileName = FileUtil.makeFileNameWithTimestamp("Experiment_Validation_" + experiment.getExperimentId(), "log");
        setLogFile(root.getLogDirectory(true).resolveChild(baseLogFileName));

        header("Validating data for a ProteomeXchange submission.");
    }

    @Override
    public ActionURL getStatusHref()
    {
        if (getContainer() != null)
        {
            return PageFlowUtil.urlProvider(ProjectUrls.class).getBeginURL(getContainer());
        }
        return null;
    }

    @Override
    public String getDescription()
    {
        return _description;
    }

    @Override
    public TaskPipeline getTaskPipeline()
    {
        return PipelineJobService.get().getTaskPipeline(new TaskId(PxDataValidationPipelineJob.class));
    }

    @Override
    public ExperimentAnnotations getExpAnnotations()
    {
        return _experimentAnnotations;
    }

    @Override
    public int getValidationId()
    {
        return _validationId;
    }
}