DiscvrLabKeyModules/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceReadsetHandlerInitTask.java at d98b42fd910895b76fb45e21547b35478ed7ecf0 · LabKey/DiscvrLabKeyModules · 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
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
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
package org.labkey.sequenceanalysis.pipeline;

import org.jetbrains.annotations.NotNull;
import org.labkey.api.pipeline.AbstractTaskFactory;
import org.labkey.api.pipeline.AbstractTaskFactorySettings;
import org.labkey.api.pipeline.PipelineJob;
import org.labkey.api.pipeline.PipelineJobException;
import org.labkey.api.pipeline.RecordedAction;
import org.labkey.api.pipeline.RecordedActionSet;
import org.labkey.api.sequenceanalysis.SequenceOutputFile;
import org.labkey.api.sequenceanalysis.model.Readset;
import org.labkey.api.sequenceanalysis.pipeline.ParameterizedOutputHandler;
import org.labkey.api.sequenceanalysis.pipeline.SequenceOutputHandler;
import org.labkey.api.sequenceanalysis.pipeline.ToolParameterDescriptor;
import org.labkey.api.util.FileType;
import org.labkey.sequenceanalysis.SequenceAnalysisServiceImpl;
import org.labkey.sequenceanalysis.SequenceReadsetImpl;

import java.util.ArrayList;
import java.util.Collections;
import java.util.List;

/**
 * Created by bimber on 1/16/2015.
 */
public class SequenceReadsetHandlerInitTask extends PipelineJob.Task<SequenceReadsetHandlerInitTask.Factory>
{
    protected SequenceReadsetHandlerInitTask(Factory factory, PipelineJob job)
    {
        super(factory, job);
    }

    public static class Factory extends AbstractTaskFactory<AbstractTaskFactorySettings, Factory>
    {
        public Factory()
        {
            super(SequenceReadsetHandlerInitTask.class);
            setLocation("webserver-high-priority");
        }

        @Override
        public List<FileType> getInputTypes()
        {
            return Collections.emptyList();
        }

        @Override
        public String getStatusName()
        {
            return PipelineJob.TaskStatus.running.toString();
        }

        @Override
        public List<String> getProtocolActionNames()
        {
            List<String> allowableNames = new ArrayList<>();
            for (SequenceOutputHandler handler : SequenceAnalysisServiceImpl.get().getFileHandlers(SequenceOutputHandler.TYPE.Readset))
            {
                allowableNames.add(handler.getName());
            }

            return allowableNames;
        }

        @Override
        public PipelineJob.Task createTask(PipelineJob job)
        {
            return new SequenceReadsetHandlerInitTask(this, job);
        }

        @Override
        public boolean isJobComplete(PipelineJob job)
        {
            return false;
        }
    }

    private SequenceReadsetHandlerJob getPipelineJob()
    {
        return (SequenceReadsetHandlerJob)getJob();
    }

    @NotNull @Override
    public RecordedActionSet run() throws PipelineJobException
    {
        List<RecordedAction> actions = new ArrayList<>();

        SequenceOutputHandler<SequenceOutputHandler.SequenceReadsetProcessor> handler = getPipelineJob().getHandler();
        List<SequenceOutputFile> outputsToCreate = new ArrayList<>();

        for (Readset f : getPipelineJob().getReadsets())
        {
            if (!(f instanceof SequenceReadsetImpl))
            {
                throw new PipelineJobException("Readset not instanceof SequenceReadsetImpl");
            }


            getPipelineJob().getSequenceSupport().cacheReadset(f.getReadsetId(), getJob().getUser(), handler.supportsSraArchivedData());
        }

        getJob().getLogger().info("total readsets: " + getPipelineJob().getReadsets().size());

        if (getPipelineJob().getParameterJson() != null)
        {
            getJob().getLogger().debug("job parameters:");
            getJob().getLogger().debug(getPipelineJob().getParameterJson().toString(1));
        }

        if (handler instanceof ParameterizedOutputHandler)
        {
            for (ToolParameterDescriptor pd : ((ParameterizedOutputHandler<SequenceOutputHandler.SequenceReadsetProcessor>)handler).getParameters())
            {
                if (pd instanceof ToolParameterDescriptor.CachableParam)
                {
                    Object val = getPipelineJob().getParameterJson().opt(pd.getName());
                    ((ToolParameterDescriptor.CachableParam)pd).doCache(getJob(), val, getPipelineJob().getSequenceSupport());
                }
            }
        }

        handler.getProcessor().init(getJob(), getPipelineJob().getSequenceSupport(), getPipelineJob().getReadsets(), getPipelineJob().getParameterJson(), getPipelineJob().getAnalysisDirectory(), actions, outputsToCreate);

        if (!outputsToCreate.isEmpty())
        {
            getJob().getLogger().info(outputsToCreate.size() + " to create");
            for (SequenceOutputFile o : outputsToCreate)
            {
                getPipelineJob().addOutputToCreate(o);
            }
        }

        return new RecordedActionSet(actions);
    }
}