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Workflow: Add Update Sample Status Action #7667

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106 changes: 77 additions & 29 deletions api/src/org/labkey/api/workflow/Action.java
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@

import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedHashMap;
import java.util.List;
Expand Down Expand Up @@ -126,6 +127,37 @@ public void setInputParameters(JSONObject inputParameters)
_inputParameters = inputParameters;
}

private List<String> validateStatus(Container container, String prefix, boolean updateKeyExpected)
{
boolean updateStatus = true;

if (updateKeyExpected)
{
updateStatus = _inputParameters.getBoolean(UPDATE_STATUS_KEY);
if (updateStatus && !_inputParameters.has(STATUS_KEY))
return List.of(prefix + STATUS_KEY + " is required for action of type " + _type + " when " + UPDATE_STATUS_KEY + " is true.");
if (!updateStatus && _inputParameters.has(STATUS_KEY))
return List.of(prefix + STATUS_KEY + " is not allowed for action of type " + _type + " when " + UPDATE_STATUS_KEY + " is false.");
}

if (updateStatus && container != null)
{
try
{
long statusId = _inputParameters.getLong(STATUS_KEY);
SampleStatusService sampleStatusService = SampleStatusService.get();
if (sampleStatusService.getStateForRowId(container, statusId) == null)
return List.of(prefix + "Invalid " + STATUS_KEY + " (" + statusId + ").");
}
catch (Exception e)
{
return List.of(prefix + "Invalid " + STATUS_KEY + ".");
}
}

return Collections.emptyList();
}

@JsonIgnore
public List<String> validateInputParameters(int ordinal, Container container)
{
Expand Down Expand Up @@ -185,15 +217,34 @@ else if (_type == WorkflowService.ActionType.AliquotSamples)
}
else if (_type == WorkflowService.ActionType.DeriveSamples || _type == WorkflowService.ActionType.PoolSamples)
{
if (_inputParameters == null || _inputParameters.isEmpty())
return List.of(prefix + "data about sample types and sample counts per parent is required for action of type " + _type + ".");
if (_type == WorkflowService.ActionType.PoolSamples && _inputParameters.length() > 1)
String emptyMessage = prefix + "data about sample types and sample counts per parent is required for action of type " + _type + ".";

if (_inputParameters == null) return List.of(emptyMessage);

// We can't just check _inputParameters size because it may include sample status keys, so we extract the
// sample type IDs and validate against those.
List<String> sampleTypeIds = new ArrayList<>();
_inputParameters.keys().forEachRemaining(id -> {
if (id.equals(UPDATE_STATUS_KEY) || id.equals(STATUS_KEY)) return;
sampleTypeIds.add(id);
});

if (sampleTypeIds.isEmpty())
return List.of(emptyMessage);

if (_type == WorkflowService.ActionType.PoolSamples && sampleTypeIds.size() > 1)
return List.of(prefix + "only one sample type can be specified for action of type " + _type + ".");

SampleTypeService sampleTypeService = SampleTypeService.get();
Set<String> invalidSampleTypeIds = new HashSet<>();
List<Object> invalidCounts = new ArrayList<>();
List<String> messages = new ArrayList<>();

for (String id : sampleTypeIds)
{
// validated above
if (id.equals(UPDATE_STATUS_KEY) || id.equals(STATUS_KEY)) continue;

_inputParameters.keys().forEachRemaining(id -> {
try
{
if (sampleTypeService.getSampleType(Long.valueOf(id)) == null)
Expand All @@ -204,54 +255,51 @@ else if (_type == WorkflowService.ActionType.DeriveSamples || _type == WorkflowS
invalidSampleTypeIds.add(id);
}
Object countObj = _inputParameters.get(id);
if ((countObj instanceof String))
if (countObj instanceof String countStr)
try
{
if (Integer.parseInt((String) countObj) < 0)
if (Integer.parseInt(countStr) < 0)
invalidCounts.add(countObj);
}
catch (NumberFormatException e)
{
invalidCounts.add(countObj);
}
else if (countObj instanceof Integer)
else if (countObj instanceof Integer count)
{
if (((Integer) countObj) < 0)
if (count < 0)
invalidCounts.add(countObj);
}
else
invalidCounts.add(countObj);
});
List<String> messages = new ArrayList<>();
}

if (!invalidSampleTypeIds.isEmpty())
messages.add(prefix + "invalid sample type IDs " + invalidSampleTypeIds + ".");
if (!invalidCounts.isEmpty())
messages.add(prefix + "invalid sample count values " + invalidCounts + ".");

if (_inputParameters.has(UPDATE_STATUS_KEY) || _inputParameters.has(STATUS_KEY))
{
List<String> statusMessages = validateStatus(container, prefix, true);

if (!statusMessages.isEmpty())
messages.addAll(statusMessages);
}

return messages;
}
else if (_type == WorkflowService.ActionType.RemoveFromStorage)
{
if (_inputParameters == null || _inputParameters.isEmpty())
return Collections.emptyList();
boolean updateStatus = _inputParameters.getBoolean(UPDATE_STATUS_KEY);
if (updateStatus && !_inputParameters.has(STATUS_KEY))
return List.of(prefix + STATUS_KEY + " is required for action of type " + _type + " when " + UPDATE_STATUS_KEY + " is true.");
if (!updateStatus && _inputParameters.has(STATUS_KEY))
return List.of(prefix + STATUS_KEY + " is not allowed for action of type " + _type + " when " + UPDATE_STATUS_KEY + " is false.");
if (updateStatus && container != null)
{
try
{
long statusId = _inputParameters.getLong(STATUS_KEY);
SampleStatusService sampleStatusService = SampleStatusService.get();
if (sampleStatusService.getStateForRowId(container, statusId) == null)
return List.of(prefix + "Invalid " + STATUS_KEY + " (" + statusId + ").");
}
catch (Exception e)
{
return List.of(prefix + "Invalid " + STATUS_KEY + ".");
}
}

return validateStatus(container, prefix, true);
} else if (_type == WorkflowService.ActionType.UpdateSampleStatus) {
if (_inputParameters == null || _inputParameters.isEmpty())
return Collections.emptyList();

return validateStatus(container, prefix, false);
} else {
if (_inputParameters != null && !_inputParameters.isEmpty())
return List.of(prefix + "input parameters are not allowed for action of type " + _type + ".");
Expand Down
3 changes: 2 additions & 1 deletion api/src/org/labkey/api/workflow/WorkflowService.java
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Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,8 @@ enum ActionType
MoveInStorage("input parameters", "Moved samples in storage"),
CheckOut("input parameters", "Checked out samples"),
CheckIn("input parameters", "Checked in samples"),
RemoveFromStorage("sample status value", "Removed samples from storage");
RemoveFromStorage("sample status value", "Removed samples from storage"),
UpdateSampleStatus("sample status value", "Updated sample status");

private final String _inputDescription;
private final String _auditMessage;
Expand Down