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cnathecnathe
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fixes post merge conflicts for classes moved to api for workflow
1 parent dc2e2d4 commit 8e58454

3 files changed

Lines changed: 155 additions & 1 deletion

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

Lines changed: 130 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -1,17 +1,29 @@
11
package org.labkey.api.workflow;
22

3+
import com.fasterxml.jackson.annotation.JsonIgnore;
34
import org.apache.commons.lang3.StringUtils;
5+
import org.json.JSONArray;
46
import org.json.JSONObject;
57
import org.labkey.api.data.CreatedModified;
8+
import org.labkey.api.exp.api.ExpProtocol;
9+
import org.labkey.api.exp.api.ExperimentService;
10+
import org.labkey.api.exp.api.SampleTypeService;
611
import org.labkey.api.util.GUID;
712

13+
import java.util.ArrayList;
14+
import java.util.Collections;
15+
import java.util.HashSet;
816
import java.util.LinkedHashMap;
17+
import java.util.List;
918
import java.util.Map;
19+
import java.util.Set;
1020

1121
public abstract class Action extends CreatedModified
1222
{
1323
public static final String ASSAY_TYPES_KEY = "assayTypes";
24+
public static final String NUM_PER_PARENT_KEY = "numPerParent";
1425
protected Long _rowId;
26+
protected int _ordinal;
1527
protected GUID _containerId;
1628
protected String _name;
1729
protected boolean _isUpdatable = false;
@@ -50,6 +62,16 @@ public void setName(String name)
5062
_name = name;
5163
}
5264

65+
public int getOrdinal()
66+
{
67+
return _ordinal;
68+
}
69+
70+
public void setOrdinal(int ordinal)
71+
{
72+
_ordinal = ordinal;
73+
}
74+
5375
public boolean getIsUpdatable()
5476
{
5577
return _isUpdatable;
@@ -90,6 +112,112 @@ public void setInputParameters(JSONObject inputParameters)
90112
_inputParameters = inputParameters;
91113
}
92114

115+
@JsonIgnore
116+
public List<String> validateInputParameters(int ordinal)
117+
{
118+
String prefix = "Action #" + ordinal + ": ";
119+
if (_type == WorkflowService.ActionType.AssayImport)
120+
{
121+
if (_inputParameters != null && _inputParameters.has(ASSAY_TYPES_KEY))
122+
{
123+
try
124+
{
125+
JSONArray assayTypes = _inputParameters.getJSONArray(ASSAY_TYPES_KEY);
126+
// When assay types are updatable, there may be none provided. Usually that means the inputParameters will
127+
// be empty or null, but it also works if the assay types array is empty.
128+
if (assayTypes.isEmpty())
129+
return Collections.emptyList();
130+
131+
Set<Object> invalidAssayIds = new HashSet<>();
132+
assayTypes.toList().forEach(assayId ->
133+
{
134+
try
135+
{
136+
int protocolId = (assayId instanceof String) ? Integer.valueOf((String) assayId) : (Integer) assayId;
137+
ExpProtocol assay = ExperimentService.get().getExpProtocol(protocolId);
138+
if (null == assay)
139+
invalidAssayIds.add(protocolId);
140+
}
141+
catch (Exception e)
142+
{
143+
invalidAssayIds.add(assayId);
144+
}
145+
});
146+
if (!invalidAssayIds.isEmpty())
147+
return List.of(prefix + "invalid assay IDs " + invalidAssayIds + ".");
148+
}
149+
catch (Exception e)
150+
{
151+
return List.of(prefix + ASSAY_TYPES_KEY + " must be an array.");
152+
}
153+
}
154+
155+
}
156+
else if (_type == WorkflowService.ActionType.AliquotSamples)
157+
{
158+
if (_inputParameters == null || !_inputParameters.has(NUM_PER_PARENT_KEY))
159+
return List.of(prefix + NUM_PER_PARENT_KEY + " is required for action of type " + _type + ".");
160+
else
161+
{
162+
try {
163+
int numPerParent = _inputParameters.getInt(NUM_PER_PARENT_KEY);
164+
if (numPerParent < 0)
165+
return List.of(prefix + NUM_PER_PARENT_KEY + " cannot be negative.");
166+
}
167+
catch (Exception e) {
168+
return List.of(prefix + NUM_PER_PARENT_KEY + " must be an integer.");
169+
}
170+
}
171+
}
172+
else
173+
{
174+
if (_inputParameters == null || _inputParameters.isEmpty())
175+
return List.of(prefix + "data about sample types and sample counts per parent is required for action of type " + _type + ".");
176+
if (_type == WorkflowService.ActionType.PoolSamples && _inputParameters.length() > 1)
177+
return List.of(prefix + "only one sample type can be specified for action of type " + _type + ".");
178+
SampleTypeService sampleTypeService = SampleTypeService.get();
179+
Set<String> invalidSampleTypeIds = new HashSet<>();
180+
List<Object> invalidCounts = new ArrayList<>();
181+
182+
_inputParameters.keys().forEachRemaining(id -> {
183+
try
184+
{
185+
if (sampleTypeService.getSampleType(Long.valueOf(id)) == null)
186+
invalidSampleTypeIds.add(id);
187+
}
188+
catch (NumberFormatException e)
189+
{
190+
invalidSampleTypeIds.add(id);
191+
}
192+
Object countObj = _inputParameters.get(id);
193+
if ((countObj instanceof String))
194+
try
195+
{
196+
if (Integer.parseInt((String) countObj) < 0)
197+
invalidCounts.add(countObj);
198+
}
199+
catch (NumberFormatException e)
200+
{
201+
invalidCounts.add(countObj);
202+
}
203+
else if (countObj instanceof Integer)
204+
{
205+
if (((Integer) countObj) < 0)
206+
invalidCounts.add(countObj);
207+
}
208+
else
209+
invalidCounts.add(countObj);
210+
});
211+
List<String> messages = new ArrayList<>();
212+
if (!invalidSampleTypeIds.isEmpty())
213+
messages.add(prefix + "invalid sample type IDs " + invalidSampleTypeIds + ".");
214+
if (!invalidCounts.isEmpty())
215+
messages.add(prefix + "invalid sample count values " + invalidCounts + ".");
216+
return messages;
217+
}
218+
return Collections.emptyList();
219+
}
220+
93221
@Override
94222
public boolean equals(Object o)
95223
{
@@ -103,6 +231,7 @@ public boolean equals(Object o)
103231
return false;
104232

105233
return _isUpdatable == action._isUpdatable &&
234+
_ordinal == action._ordinal &&
106235
java.util.Objects.equals(_rowId, action._rowId) &&
107236
java.util.Objects.equals(_taskId, action._taskId) &&
108237
java.util.Objects.equals(_type, action._type) &&
@@ -117,6 +246,7 @@ public Map<String, Object> toAuditDetailMap()
117246
Map<String, Object> map = new LinkedHashMap<>();
118247
map.put("rowId", _rowId);
119248
map.put("name", _name);
249+
map.put("ordinal", _ordinal);
120250
map.put("isUpdatable", _isUpdatable);
121251
map.put("taskId", _taskId);
122252
if (_type != null)

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

Lines changed: 10 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -10,6 +10,7 @@
1010
import org.labkey.api.util.GUID;
1111

1212
import java.util.Date;
13+
import java.util.HashMap;
1314
import java.util.LinkedHashMap;
1415
import java.util.List;
1516
import java.util.Map;
@@ -183,6 +184,15 @@ public void setContainer(Container container)
183184

184185
public abstract List<Action> getActions();
185186

187+
@JsonIgnore
188+
public Map<Long, Action> getActionsByRowId()
189+
{
190+
Map<Long, Action> map = new HashMap<>();
191+
for (Action action : getActions())
192+
map.put(action.getRowId(), action);
193+
return map;
194+
}
195+
186196
public void setActions(List<Action> actions)
187197
{
188198
_actions = actions;

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

Lines changed: 15 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -4,6 +4,7 @@
44
import com.fasterxml.jackson.annotation.JsonProperty;
55
import org.apache.commons.collections4.MapUtils;
66
import org.apache.commons.lang3.StringUtils;
7+
import org.jetbrains.annotations.Nullable;
78
import org.json.JSONObject;
89
import org.labkey.api.exp.api.ExpMaterial;
910
import org.labkey.api.security.User;
@@ -35,6 +36,7 @@ public enum EntityType
3536
protected Long _workRowId;
3637
protected EntityType _entityType;
3738
protected Long _entityValue;
39+
protected Long _actionId;
3840
protected Long _created;
3941
protected User _createdBy;
4042

@@ -54,6 +56,7 @@ public WorkEntity(Map<String, Object> map)
5456
else
5557
_entityType = (EntityType) map.get("entityType");
5658
_entityValue = MapUtils.getLong(map, "entityValue");
59+
_actionId = MapUtils.getLong(map, "actionId");
5760
if (map.get("Container") != null)
5861
this.setContainerId(new GUID((String) map.get("Container")));
5962
}
@@ -64,11 +67,12 @@ public WorkEntity(ExpMaterial sample)
6467
_entityValue = sample.getRowId();
6568
}
6669

67-
public WorkEntity(ExpMaterial sample, WorkType workType, Long workRowId)
70+
public WorkEntity(ExpMaterial sample, WorkType workType, Long workRowId, @Nullable Long actionId)
6871
{
6972
this(sample);
7073
_workType = workType;
7174
_workRowId = workRowId;
75+
_actionId = actionId;
7276
}
7377

7478

@@ -92,6 +96,16 @@ public void setContainerId(GUID containerId)
9296
_containerId = containerId;
9397
}
9498

99+
public Long getActionId()
100+
{
101+
return _actionId;
102+
}
103+
104+
public void setActionId(Long actionId)
105+
{
106+
_actionId = actionId;
107+
}
108+
95109
@JsonProperty("created")
96110
public Long getCreated()
97111
{

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