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Merge remote-tracking branch 'origin/develop' into fb_urlProvider
2 parents 7b6cc78 + 163973e commit 7ae6f55

18 files changed

Lines changed: 3598 additions & 1152 deletions

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‎api/src/org/labkey/api/study/actions/ParticipantVisitResolverChooser.java‎

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@@ -168,7 +168,7 @@ public void renderInputHtml(RenderContext ctx, HtmlWriter out, Object value)
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return ret2;
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}
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),
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disabledInput ? InputBuilder.hidden().name(_typeInputName).value(finalSelected.getName()).appendTo(out) : null
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disabledInput ? InputBuilder.hidden().name(_typeInputName).value(finalSelected.getName()).getHtmlString() : null
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)
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).appendTo(out);
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}

‎api/src/org/labkey/api/workflow/Action.java‎

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package org.labkey.api.workflow;
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import com.fasterxml.jackson.annotation.JsonIgnore;
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import org.apache.commons.lang3.StringUtils;
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import org.json.JSONArray;
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import org.json.JSONObject;
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import org.labkey.api.data.Container;
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import org.labkey.api.data.ContainerManager;
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import org.labkey.api.data.CreatedModified;
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import org.labkey.api.exp.api.ExpProtocol;
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import org.labkey.api.exp.api.ExperimentService;
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import org.labkey.api.exp.api.SampleTypeService;
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import org.labkey.api.qc.SampleStatusService;
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import org.labkey.api.util.GUID;
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import java.util.ArrayList;
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import java.util.Collections;
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import java.util.HashSet;
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import java.util.LinkedHashMap;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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public abstract class Action extends CreatedModified
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{
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public static final String ASSAY_TYPES_KEY = "assayTypes";
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public static final String NUM_PER_PARENT_KEY = "numPerParent";
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public static final String UPDATE_STATUS_KEY = "updateStatus";
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public static final String STATUS_KEY = "sampleStatus";
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protected Long _rowId;
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protected int _ordinal;
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protected GUID _containerId;
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private Container _container;
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protected String _name;
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protected boolean _isUpdatable = false;
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protected Long _taskId;
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protected WorkflowService.ActionType _type;
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protected JSONObject _inputParameters;
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public Long getRowId()
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{
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return _rowId;
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}
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public void setRowId(Long rowId)
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{
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_rowId = rowId;
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}
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public GUID getContainerId()
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{
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return _containerId;
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}
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public void setContainerId(GUID containerId)
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{
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_containerId = containerId;
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}
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@JsonIgnore
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public Container getContainer()
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{
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if (_container == null && _containerId != null)
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_container = ContainerManager.getForId(_containerId);
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return _container;
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}
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public String getName()
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{
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return _name;
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}
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public void setName(String name)
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{
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_name = name;
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}
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public int getOrdinal()
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{
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return _ordinal;
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}
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public void setOrdinal(int ordinal)
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{
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_ordinal = ordinal;
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}
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public boolean getIsUpdatable()
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{
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return _isUpdatable;
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}
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public void setIsUpdatable(boolean updatable)
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{
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_isUpdatable = updatable;
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}
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public Long getTaskId()
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{
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return _taskId;
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}
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public void setTaskId(Long taskId)
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{
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_taskId = taskId;
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}
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public WorkflowService.ActionType getType()
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{
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return _type;
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}
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public void setType(WorkflowService.ActionType type)
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{
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_type = type;
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}
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public JSONObject getInputParameters()
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{
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return _inputParameters;
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}
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public void setInputParameters(JSONObject inputParameters)
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{
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_inputParameters = inputParameters;
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}
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@JsonIgnore
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public List<String> validateInputParameters(int ordinal, Container container)
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{
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String prefix = "Action #" + ordinal + ": ";
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if (_type == WorkflowService.ActionType.AssayImport)
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{
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if (_inputParameters != null && _inputParameters.has(ASSAY_TYPES_KEY))
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{
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try
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{
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JSONArray assayTypes = _inputParameters.getJSONArray(ASSAY_TYPES_KEY);
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// When assay types are updatable, there may be none provided. Usually that means the inputParameters will
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// be empty or null, but it also works if the assay types array is empty.
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if (assayTypes.isEmpty())
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return Collections.emptyList();
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Set<Object> invalidAssayIds = new HashSet<>();
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assayTypes.toList().forEach(assayId ->
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{
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try
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{
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int protocolId = (assayId instanceof String) ? Integer.valueOf((String) assayId) : (Integer) assayId;
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ExpProtocol assay = ExperimentService.get().getExpProtocol(protocolId);
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if (null == assay)
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invalidAssayIds.add(protocolId);
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}
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catch (Exception e)
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{
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invalidAssayIds.add(assayId);
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}
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});
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if (!invalidAssayIds.isEmpty())
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return List.of(prefix + "invalid assay IDs " + invalidAssayIds + ".");
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}
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catch (Exception e)
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{
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return List.of(prefix + ASSAY_TYPES_KEY + " must be an array.");
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}
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}
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}
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else if (_type == WorkflowService.ActionType.AliquotSamples)
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{
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if (_inputParameters == null || !_inputParameters.has(NUM_PER_PARENT_KEY))
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return List.of(prefix + NUM_PER_PARENT_KEY + " is required for action of type " + _type + ".");
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else
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{
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try {
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int numPerParent = _inputParameters.getInt(NUM_PER_PARENT_KEY);
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if (numPerParent < 0)
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return List.of(prefix + NUM_PER_PARENT_KEY + " cannot be negative.");
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}
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catch (Exception e) {
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return List.of(prefix + NUM_PER_PARENT_KEY + " must be an integer.");
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}
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}
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}
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else if (_type == WorkflowService.ActionType.DeriveSamples || _type == WorkflowService.ActionType.PoolSamples)
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{
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if (_inputParameters == null || _inputParameters.isEmpty())
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return List.of(prefix + "data about sample types and sample counts per parent is required for action of type " + _type + ".");
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if (_type == WorkflowService.ActionType.PoolSamples && _inputParameters.length() > 1)
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return List.of(prefix + "only one sample type can be specified for action of type " + _type + ".");
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SampleTypeService sampleTypeService = SampleTypeService.get();
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Set<String> invalidSampleTypeIds = new HashSet<>();
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List<Object> invalidCounts = new ArrayList<>();
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_inputParameters.keys().forEachRemaining(id -> {
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try
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{
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if (sampleTypeService.getSampleType(Long.valueOf(id)) == null)
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invalidSampleTypeIds.add(id);
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}
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catch (NumberFormatException e)
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{
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invalidSampleTypeIds.add(id);
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}
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Object countObj = _inputParameters.get(id);
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if ((countObj instanceof String))
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try
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{
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if (Integer.parseInt((String) countObj) < 0)
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invalidCounts.add(countObj);
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}
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catch (NumberFormatException e)
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{
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invalidCounts.add(countObj);
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}
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else if (countObj instanceof Integer)
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{
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if (((Integer) countObj) < 0)
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invalidCounts.add(countObj);
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}
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else
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invalidCounts.add(countObj);
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});
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List<String> messages = new ArrayList<>();
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if (!invalidSampleTypeIds.isEmpty())
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messages.add(prefix + "invalid sample type IDs " + invalidSampleTypeIds + ".");
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if (!invalidCounts.isEmpty())
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messages.add(prefix + "invalid sample count values " + invalidCounts + ".");
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return messages;
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}
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else if (_type == WorkflowService.ActionType.RemoveFromStorage)
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{
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if (_inputParameters == null || _inputParameters.isEmpty())
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return Collections.emptyList();
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boolean updateStatus = _inputParameters.getBoolean(UPDATE_STATUS_KEY);
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if (updateStatus && !_inputParameters.has(STATUS_KEY))
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return List.of(prefix + STATUS_KEY + " is required for action of type " + _type + " when " + UPDATE_STATUS_KEY + " is true.");
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if (!updateStatus && _inputParameters.has(STATUS_KEY))
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return List.of(prefix + STATUS_KEY + " is not allowed for action of type " + _type + " when " + UPDATE_STATUS_KEY + " is false.");
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if (updateStatus && container != null)
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{
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try
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{
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long statusId = _inputParameters.getLong(STATUS_KEY);
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SampleStatusService sampleStatusService = SampleStatusService.get();
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if (sampleStatusService.getStateForRowId(container, statusId) == null)
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return List.of(prefix + "Invalid " + STATUS_KEY + " (" + statusId + ").");
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}
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catch (Exception e)
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{
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return List.of(prefix + "Invalid " + STATUS_KEY + ".");
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}
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}
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} else {
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if (_inputParameters != null && !_inputParameters.isEmpty())
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return List.of(prefix + "input parameters are not allowed for action of type " + _type + ".");
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}
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return Collections.emptyList();
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}
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@Override
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public boolean equals(Object o)
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{
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if (this == o) return true;
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if (o == null || getClass() != o.getClass()) return false;
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Action action = (Action) o;
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// GitHub Issue 799: Workflow Automation: Attempting to add a sample filter on an existing template errors
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// Migration script generated action.name, but they are currently not used. Allow name to be changed to null or empty string.
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if (!java.util.Objects.equals(_name, action._name) && !StringUtils.isEmpty(action.getName()))
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return false;
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return _isUpdatable == action._isUpdatable &&
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_ordinal == action._ordinal &&
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java.util.Objects.equals(_rowId, action._rowId) &&
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java.util.Objects.equals(_taskId, action._taskId) &&
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java.util.Objects.equals(_type, action._type) &&
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java.util.Objects.equals(
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_inputParameters == null ? null : _inputParameters.toString(),
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action._inputParameters == null ? null : action._inputParameters.toString()
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);
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}
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public Map<String, Object> toAuditDetailMap()
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{
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Map<String, Object> map = new LinkedHashMap<>();
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map.put("rowId", _rowId);
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map.put("name", _name);
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map.put("ordinal", _ordinal);
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map.put("isUpdatable", _isUpdatable);
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map.put("taskId", _taskId);
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if (_type != null)
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map.put("type", _type.name());
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if (_inputParameters != null)
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map.put("inputParameters", _inputParameters.toString());
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return map;
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}
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public abstract Task getTask();
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}

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