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Bugfix to Pipeline StepType when using a subclass (#139)
* Bugfix to Pipeline StepType when using a subclass
1 parent b970a7d commit 566bca1

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7 files changed

+181
-146
lines changed

7 files changed

+181
-146
lines changed

‎SequenceAnalysis/src/org/labkey/sequenceanalysis/SequencePipelineServiceImpl.java‎

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Original file line numberDiff line numberDiff line change
@@ -105,7 +105,6 @@ public <StepType extends PipelineStep> Set<PipelineStepProvider<StepType>> getPr
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{
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ParameterizedType parameterizedType = (ParameterizedType)provider.getClass().getGenericSuperclass();
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Class clazz = (Class)parameterizedType.getActualTypeArguments()[0];
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if (stepType.isAssignableFrom(clazz))
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{
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ret.add(provider);

‎singlecell/api-src/org/labkey/api/singlecell/pipeline/AbstractSingleCellStep.java‎

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@@ -0,0 +1,157 @@
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package org.labkey.api.singlecell.pipeline;
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import com.fasterxml.jackson.annotation.JsonIgnore;
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import org.jetbrains.annotations.Nullable;
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import org.labkey.api.pipeline.PipelineJobException;
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import org.labkey.api.sequenceanalysis.SequenceOutputFile;
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import org.labkey.api.sequenceanalysis.pipeline.PipelineStep;
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import org.labkey.api.sequenceanalysis.pipeline.PipelineStepOutput;
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import org.labkey.api.sequenceanalysis.pipeline.SequenceOutputHandler;
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import java.io.File;
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import java.io.Serializable;
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import java.util.Collection;
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import java.util.List;
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public interface AbstractSingleCellStep extends PipelineStep
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{
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public Collection<String> getRLibraries();
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public String getDockerContainerName();
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default void init(SequenceOutputHandler.JobContext ctx, List<SequenceOutputFile> inputFiles) throws PipelineJobException
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{
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}
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default boolean createsSeuratObjects()
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{
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return true;
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}
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public boolean requiresCiteSeq();
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public boolean requiresHashing();
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public boolean isIncluded(SequenceOutputHandler.JobContext ctx, List<SequenceOutputFile> inputs) throws PipelineJobException;
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default String getFileSuffix()
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{
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return getProvider().getName();
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}
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public Output execute(SequenceOutputHandler.JobContext ctx, List<SeuratObjectWrapper> inputObjects, String outputPrefix) throws PipelineJobException;
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public static interface Output extends PipelineStepOutput
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{
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/**
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* Returns the cached seurat object
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*/
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public List<SeuratObjectWrapper> getSeuratObjects();
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public File getMarkdownFile();
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public File getHtmlFile();
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}
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public static class SeuratObjectWrapper implements Serializable
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{
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private transient SequenceOutputFile _sequenceOutputFile;
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private Integer _sequenceOutputFileId;
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private Integer _readsetId;
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private File _file;
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private String _datasetId;
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private String _datasetName;
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//For serialization
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public SeuratObjectWrapper()
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{
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}
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public SeuratObjectWrapper(String datasetId, String datasetName, File file, SequenceOutputFile sequenceOutputFile)
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{
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_datasetId = datasetId;
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_datasetName = datasetName;
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_file = file;
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_sequenceOutputFileId = sequenceOutputFile.getRowid();
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_sequenceOutputFile = sequenceOutputFile;
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_readsetId = sequenceOutputFile.getReadset();
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}
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public SeuratObjectWrapper(String datasetId, String datasetName, File file, @Nullable Integer sequenceOutputFileId, @Nullable Integer readsetId)
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{
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_datasetId = datasetId;
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_datasetName = datasetName;
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_file = file;
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_sequenceOutputFileId = sequenceOutputFileId;
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_sequenceOutputFile = null;
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_readsetId = readsetId;
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}
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public File getFile()
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{
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return _file;
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}
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public void setFile(File file)
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{
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_file = file;
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}
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public String getDatasetId()
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{
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return _datasetId;
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}
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public void setDatasetId(String datasetId)
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{
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_datasetId = datasetId;
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}
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public String getDatasetName()
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{
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return _datasetName;
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}
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public void setDatasetName(String datasetName)
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{
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_datasetName = datasetName;
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}
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public Integer getReadsetId()
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{
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return _readsetId;
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}
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public void setReadsetId(Integer readsetId)
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{
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_readsetId = readsetId;
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}
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public Integer getSequenceOutputFileId()
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{
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return _sequenceOutputFileId;
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}
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public void setSequenceOutputFileId(Integer sequenceOutputFileId)
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{
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_sequenceOutputFileId = sequenceOutputFileId;
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}
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@JsonIgnore
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public SequenceOutputFile getSequenceOutputFile()
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{
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return _sequenceOutputFile;
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}
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@JsonIgnore
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public void setSequenceOutputFile(SequenceOutputFile sequenceOutputFile)
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{
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_sequenceOutputFile = sequenceOutputFile;
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}
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}
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}

‎singlecell/api-src/org/labkey/api/singlecell/pipeline/SingleCellRawDataStep.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,7 @@
33
/**
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* NOTE: this is a special class designed to encompass the steps related to processing raw count data from the 10x/loupe matrix
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*/
6-
public interface SingleCellRawDataStep extends SingleCellStep
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public interface SingleCellRawDataStep extends AbstractSingleCellStep
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{
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public final String STEP_TYPE = "singleCellRawData";
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}

‎singlecell/api-src/org/labkey/api/singlecell/pipeline/SingleCellStep.java‎

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Original file line numberDiff line numberDiff line change
@@ -13,147 +13,7 @@
1313
import java.util.Collection;
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import java.util.List;
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16-
public interface SingleCellStep extends PipelineStep
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public interface SingleCellStep extends AbstractSingleCellStep
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{
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public static final String STEP_TYPE = "singleCell";
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public Collection<String> getRLibraries();
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public String getDockerContainerName();
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default void init(SequenceOutputHandler.JobContext ctx, List<SequenceOutputFile> inputFiles) throws PipelineJobException
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{
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}
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default boolean createsSeuratObjects()
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{
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return true;
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}
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public boolean requiresCiteSeq();
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public boolean requiresHashing();
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public boolean isIncluded(SequenceOutputHandler.JobContext ctx, List<SequenceOutputFile> inputs) throws PipelineJobException;
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default String getFileSuffix()
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{
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return getProvider().getName();
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}
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public Output execute(SequenceOutputHandler.JobContext ctx, List<SeuratObjectWrapper> inputObjects, String outputPrefix) throws PipelineJobException;
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public static interface Output extends PipelineStepOutput
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{
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/**
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* Returns the cached seurat object
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*/
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public List<SeuratObjectWrapper> getSeuratObjects();
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public File getMarkdownFile();
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public File getHtmlFile();
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}
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public static class SeuratObjectWrapper implements Serializable
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{
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private transient SequenceOutputFile _sequenceOutputFile;
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private Integer _sequenceOutputFileId;
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private Integer _readsetId;
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private File _file;
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private String _datasetId;
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private String _datasetName;
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//For serialization
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public SeuratObjectWrapper()
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{
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}
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76-
public SeuratObjectWrapper(String datasetId, String datasetName, File file, SequenceOutputFile sequenceOutputFile)
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{
78-
_datasetId = datasetId;
79-
_datasetName = datasetName;
80-
_file = file;
81-
_sequenceOutputFileId = sequenceOutputFile.getRowid();
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_sequenceOutputFile = sequenceOutputFile;
83-
_readsetId = sequenceOutputFile.getReadset();
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85-
}
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public SeuratObjectWrapper(String datasetId, String datasetName, File file, @Nullable Integer sequenceOutputFileId, @Nullable Integer readsetId)
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{
89-
_datasetId = datasetId;
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_datasetName = datasetName;
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_file = file;
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_sequenceOutputFileId = sequenceOutputFileId;
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_sequenceOutputFile = null;
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_readsetId = readsetId;
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}
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public File getFile()
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{
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return _file;
100-
}
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public void setFile(File file)
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{
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_file = file;
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}
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public String getDatasetId()
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{
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return _datasetId;
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}
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public void setDatasetId(String datasetId)
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{
114-
_datasetId = datasetId;
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}
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public String getDatasetName()
118-
{
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return _datasetName;
120-
}
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public void setDatasetName(String datasetName)
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{
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_datasetName = datasetName;
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}
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public Integer getReadsetId()
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{
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return _readsetId;
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}
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public void setReadsetId(Integer readsetId)
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{
134-
_readsetId = readsetId;
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}
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public Integer getSequenceOutputFileId()
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{
139-
return _sequenceOutputFileId;
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}
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public void setSequenceOutputFileId(Integer sequenceOutputFileId)
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{
144-
_sequenceOutputFileId = sequenceOutputFileId;
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}
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@JsonIgnore
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public SequenceOutputFile getSequenceOutputFile()
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{
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return _sequenceOutputFile;
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}
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@JsonIgnore
154-
public void setSequenceOutputFile(SequenceOutputFile sequenceOutputFile)
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{
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_sequenceOutputFile = sequenceOutputFile;
157-
}
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}
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}

‎singlecell/src/org/labkey/singlecell/SingleCellController.java‎

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Original file line numberDiff line numberDiff line change
@@ -92,7 +92,7 @@ public SingleCellController()
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}
9393

9494
@RequiresPermission(InsertPermission.class)
95-
public class DownloadLoupeDataAction extends ExportAction<OutputFilesForm>
95+
public static class DownloadLoupeDataAction extends ExportAction<OutputFilesForm>
9696
{
9797
@Override
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public void export(OutputFilesForm form, HttpServletResponse response, BindException errors) throws Exception
@@ -461,7 +461,7 @@ else if (count > 1 && filter.getClauses().size() == FIELDS.size())
461461
}
462462

463463
@RequiresPermission(InsertPermission.class)
464-
public class SingleCellProcessingAction extends SimpleViewAction<Object>
464+
public static class SingleCellProcessingAction extends SimpleViewAction<Object>
465465
{
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public URLHelper getSuccessURL(Object form)
467467
{

‎singlecell/src/org/labkey/singlecell/SingleCellModule.java‎

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Original file line numberDiff line numberDiff line change
@@ -179,7 +179,8 @@ public static void registerPipelineSteps()
179179
public Set<Class> getUnitTests()
180180
{
181181
return PageFlowUtil.set(
182-
AbstractSingleCellHandler.TestCase.class
182+
AbstractSingleCellHandler.TestCase.class,
183+
PrepareRawCounts.TestCase.class
183184
);
184185
}
185186
}

‎singlecell/src/org/labkey/singlecell/pipeline/singlecell/PrepareRawCounts.java‎

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Original file line numberDiff line numberDiff line change
@@ -1,10 +1,18 @@
11
package org.labkey.singlecell.pipeline.singlecell;
22

3+
import org.apache.logging.log4j.Logger;
4+
import org.junit.Assert;
5+
import org.junit.Test;
6+
import org.labkey.api.pipeline.PipelineJob;
7+
import org.labkey.api.pipeline.WorkDirectory;
38
import org.labkey.api.sequenceanalysis.pipeline.AbstractPipelineStepProvider;
49
import org.labkey.api.sequenceanalysis.pipeline.PipelineContext;
10+
import org.labkey.api.sequenceanalysis.pipeline.SequenceAnalysisJobSupport;
11+
import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService;
512
import org.labkey.api.singlecell.pipeline.SeuratToolParameter;
613
import org.labkey.api.singlecell.pipeline.SingleCellRawDataStep;
714

15+
import java.io.File;
816
import java.util.Arrays;
917

1018
public class PrepareRawCounts extends AbstractCellMembraneStep
@@ -41,4 +49,14 @@ public String getFileSuffix()
4149
{
4250
return "counts";
4351
}
52+
53+
public static class TestCase extends Assert
54+
{
55+
@Test
56+
public void testStepClass()
57+
{
58+
assertEquals(SingleCellRawDataStep.STEP_TYPE, SequencePipelineService.get().getParamNameForStepType(SingleCellRawDataStep.class));
59+
assertEquals(SingleCellRawDataStep.class, new Provider().getStepClass());
60+
}
61+
}
4462
}

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