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Issue 43241: reintroduce test coverage
1 parent eea2a4d commit 84408c8

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+84
-103
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2 files changed

+84
-103
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‎experiment/src/org/labkey/experiment/api/ExpSampleTypeTestCase.jsp‎

Lines changed: 79 additions & 98 deletions
Original file line numberDiff line numberDiff line change
@@ -25,7 +25,6 @@
2525
<%@ page import="org.labkey.api.data.CompareType" %>
2626
<%@ page import="org.labkey.api.data.Container" %>
2727
<%@ page import="org.labkey.api.data.ContainerManager" %>
28-
<%@ page import="org.labkey.api.data.DbScope" %>
2928
<%@ page import="org.labkey.api.data.JdbcType" %>
3029
<%@ page import="org.labkey.api.data.SQLFragment" %>
3130
<%@ page import="org.labkey.api.data.SimpleFilter" %>
@@ -70,9 +69,7 @@
7069
<%@ page import="org.labkey.api.util.PageFlowUtil" %>
7170
<%@ page import="org.labkey.api.util.TestContext" %>
7271
<%@ page import="org.labkey.experiment.api.ExpProvisionedTableTestHelper" %>
73-
<%@ page import="org.labkey.experiment.api.ExpSampleTypeImpl" %>
7472
<%@ page import="org.labkey.experiment.api.ExperimentServiceImpl" %>
75-
<%@ page import="org.labkey.experiment.api.SampleTypeServiceImpl" %>
7673
<%@ page import="java.io.StringBufferInputStream" %>
7774
<%@ page import="java.util.ArrayList" %>
7875
<%@ page import="java.util.Arrays" %>
@@ -91,6 +88,13 @@
9188
<%@ page import="org.labkey.api.dataiterator.MapDataIterator" %>
9289
<%@ page import="static org.labkey.api.exp.api.ExperimentService.asInteger" %>
9390
<%@ page import="static org.labkey.api.exp.api.ExperimentService.asLong" %>
91+
<%@ page import="static java.util.Collections.emptyList" %>
92+
<%@ page import="org.jetbrains.annotations.Nullable" %>
93+
<%@ page import="org.labkey.api.view.ActionURL" %>
94+
<%@ page import="org.labkey.api.query.QueryParam" %>
95+
<%@ page import="org.labkey.api.view.ViewServlet" %>
96+
<%@ page import="org.labkey.api.util.JsonUtil" %>
97+
<%@ page import="org.labkey.api.settings.LookAndFeelProperties" %>
9498
<%@ page extends="org.labkey.api.jsp.JspTest.BVT" %>
9599

96100
<%!
@@ -128,16 +132,12 @@ private void assertExpectedName(ExpSampleType st, String expectedName)
128132
@Test
129133
public void nameNotNull() throws Exception
130134
{
131-
final User user = TestContext.get().getUser();
132-
133135
try
134136
{
135137
List<GWTPropertyDescriptor> props = new ArrayList<>();
136138
props.add(new GWTPropertyDescriptor("name", "string"));
137139
138-
final ExpSampleType st = SampleTypeService.get().createSampleType(c, user,
139-
null, null, props, Collections.emptyList(),
140-
-1, -1, -1, -1, null, null);
140+
createSampleType(null, props, null);
141141
}
142142
catch (ApiUsageException ee)
143143
{
@@ -148,16 +148,12 @@ public void nameNotNull() throws Exception
148148
@Test // Issue 51321
149149
public void reservedNameFirst() throws Exception
150150
{
151-
final User user = TestContext.get().getUser();
152-
153151
try
154152
{
155153
List<GWTPropertyDescriptor> props = new ArrayList<>();
156154
props.add(new GWTPropertyDescriptor("name", "string"));
157155
158-
final ExpSampleType st = SampleTypeService.get().createSampleType(c, user,
159-
"First", null, props, Collections.emptyList(),
160-
-1, -1, -1, -1, null, null);
156+
createSampleType("First", props, null);
161157
}
162158
catch (ApiUsageException ee)
163159
{
@@ -168,16 +164,12 @@ public void reservedNameFirst() throws Exception
168164
@Test // Issue 51321
169165
public void reservedNameAll() throws Exception
170166
{
171-
final User user = TestContext.get().getUser();
172-
173167
try
174168
{
175169
List<GWTPropertyDescriptor> props = new ArrayList<>();
176170
props.add(new GWTPropertyDescriptor("name", "string"));
177171
178-
final ExpSampleType st = SampleTypeService.get().createSampleType(c, user,
179-
"All", null, props, Collections.emptyList(),
180-
-1, -1, -1, -1, null, null);
172+
createSampleType("All", props, null);
181173
}
182174
catch (ApiUsageException ee)
183175
{
@@ -189,18 +181,12 @@ public void reservedNameAll() throws Exception
189181
@Test
190182
public void nameScale() throws Exception
191183
{
192-
final User user = TestContext.get().getUser();
193-
194184
try
195185
{
196186
List<GWTPropertyDescriptor> props = new ArrayList<>();
197187
props.add(new GWTPropertyDescriptor("name", "string"));
198188
199-
String name = StringUtils.repeat("a", 1000);
200-
201-
final ExpSampleType st = SampleTypeService.get().createSampleType(c, user,
202-
name, null, props, Collections.emptyList(),
203-
-1, -1, -1, -1, null, null);
189+
createSampleType(StringUtils.repeat("a", 1000), props, null);
204190
}
205191
catch (ApiUsageException ee)
206192
{
@@ -212,20 +198,14 @@ public void nameScale() throws Exception
212198
@Test
213199
public void nameExpressionScale() throws Exception
214200
{
215-
final User user = TestContext.get().getUser();
216-
217201
try
218202
{
219203
List<GWTPropertyDescriptor> props = new ArrayList<>();
220204
props.add(new GWTPropertyDescriptor("name", "string"));
221205
props.add(new GWTPropertyDescriptor("prop", "string"));
222206
props.add(new GWTPropertyDescriptor("age", "int"));
223207
224-
String nameExpression = StringUtils.repeat("a", 1000);
225-
226-
final ExpSampleType st = SampleTypeService.get().createSampleType(c, user,
227-
"Samples", null, props, Collections.emptyList(),
228-
-1, -1, -1, -1, nameExpression, null);
208+
createSampleType("Samples", props, StringUtils.repeat("a", 1000));
229209
}
230210
catch (ApiUsageException ee)
231211
{
@@ -237,17 +217,13 @@ public void nameExpressionScale() throws Exception
237217
@Test
238218
public void idColsUnset_nameExpressionNull_noNameProperty() throws Exception
239219
{
240-
final User user = TestContext.get().getUser();
241-
242220
try
243221
{
244222
List<GWTPropertyDescriptor> props = new ArrayList<>();
245223
props.add(new GWTPropertyDescriptor("notName", "string"));
246224
props.add(new GWTPropertyDescriptor("age", "int"));
247225
248-
final ExpSampleType st = SampleTypeService.get().createSampleType(c, user,
249-
"Samples", null, props, Collections.emptyList(),
250-
-1, -1, -1, -1, null, null);
226+
createSampleType("Samples", props, null);
251227
fail("Expected exception");
252228
}
253229
catch (ApiUsageException ee)
@@ -260,15 +236,11 @@ public void idColsUnset_nameExpressionNull_noNameProperty() throws Exception
260236
@Test
261237
public void idColsUnset_nameExpressionNull_hasNameProperty() throws Exception
262238
{
263-
final User user = TestContext.get().getUser();
264-
265239
List<GWTPropertyDescriptor> props = new ArrayList<>();
266240
props.add(new GWTPropertyDescriptor("name", "string"));
267241
props.add(new GWTPropertyDescriptor("age", "int"));
268242
269-
final ExpSampleType st = SampleTypeService.get().createSampleType(c, user,
270-
"Samples", null, props, Collections.emptyList(),
271-
-1, -1, -1, -1, null, null);
243+
final ExpSampleType st = createSampleType("Samples", props, null);
272244
273245
ExpMaterial sample = st.getSample(c, "bob");
274246
assertNull(sample);
@@ -285,18 +257,12 @@ public void idColsUnset_nameExpressionNull_hasNameProperty() throws Exception
285257
@Test
286258
public void idColsUnset_nameExpression_hasNameProperty() throws Exception
287259
{
288-
final User user = TestContext.get().getUser();
289-
290260
List<GWTPropertyDescriptor> props = new ArrayList<>();
291261
props.add(new GWTPropertyDescriptor("name", "string"));
292262
props.add(new GWTPropertyDescriptor("prop", "string"));
293263
props.add(new GWTPropertyDescriptor("age", "int"));
294264
295-
final String nameExpression = "S-${prop}.${age}";
296-
297-
final ExpSampleType st = SampleTypeService.get().createSampleType(c, user,
298-
"Samples", null, props, Collections.emptyList(),
299-
-1, -1, -1, -1, nameExpression, null);
265+
createSampleType("Samples", props, "S-${prop}.${age}");
300266
}
301267
302268
// idCols not null, nameExpression null, no 'name' property -- ok
@@ -364,9 +330,7 @@ public void idColsSet_nameExpressionNull_hasNameProperty() throws Exception
364330
props.add(new GWTPropertyDescriptor("prop", "string"));
365331
props.add(new GWTPropertyDescriptor("age", "int"));
366332
367-
final ExpSampleType st = SampleTypeService.get().createSampleType(c, user,
368-
"Samples", null, props, Collections.emptyList(),
369-
0, -1, -1, -1, null, null);
333+
final ExpSampleType st = createSampleType("Samples", props, null);
370334
371335
final String expectedName1 = "bob";
372336
ExpMaterial sample1 = st.getSample(c, expectedName1);
@@ -428,11 +392,7 @@ public void testNameExpression() throws Exception
428392
props.add(new GWTPropertyDescriptor("age", "int"));
429393
430394
final String sampleTypeName = "Samples";
431-
final String nameExpression = "S-${prop}.${age}.${genId:number('000')}";
432-
433-
final ExpSampleType st = SampleTypeService.get().createSampleType(c, user,
434-
sampleTypeName, null, props, Collections.emptyList(),
435-
-1, -1, -1, -1, nameExpression, null);
395+
final ExpSampleType st = createSampleType(sampleTypeName, props, "S-${prop}.${age}.${genId:number('000')}");
436396
437397
final String expectedName1 = "bob";
438398
final String expectedName2 = "S-red.11.002";
@@ -547,16 +507,12 @@ public void testNameExpression() throws Exception
547507
@Test
548508
public void testAliases() throws Exception
549509
{
550-
final User user = TestContext.get().getUser();
551-
552510
// setup
553511
List<GWTPropertyDescriptor> props = new ArrayList<>();
554512
props.add(new GWTPropertyDescriptor("name", "string"));
555513
props.add(new GWTPropertyDescriptor("age", "int"));
556514
557-
final ExpSampleType st = SampleTypeService.get().createSampleType(c, user,
558-
"Samples", null, props, Collections.emptyList(),
559-
-1, -1, -1, -1, null, null);
515+
final ExpSampleType st = createSampleType("Samples", props, null);
560516
561517
List<Map<String, Object>> rows = new ArrayList<>();
562518
Map<String, Object> row = new CaseInsensitiveHashMap<>();
@@ -584,11 +540,7 @@ public void testBlankRows() throws Exception
584540
props.add(new GWTPropertyDescriptor("name", "string"));
585541
props.add(new GWTPropertyDescriptor("age", "int"));
586542
587-
final String nameExpression = "S-${now:date}-${dailySampleCount}";
588-
589-
final ExpSampleTypeImpl st = SampleTypeServiceImpl.get().createSampleType(c, user,
590-
"Samples", null, props, Collections.emptyList(),
591-
-1, -1, -1, -1, nameExpression, null);
543+
final ExpSampleType st = createSampleType("Samples", props, "S-${now:date}-${dailySampleCount}");
592544
593545
List<? extends ExpMaterial> allSamples = st.getSamples(c);
594546
assertTrue("Expected no samples", allSamples.isEmpty());
@@ -685,18 +637,9 @@ public void testUpdateSomeParents() throws Exception
685637
List<GWTPropertyDescriptor> props = new ArrayList<>();
686638
props.add(new GWTPropertyDescriptor("name", "string"));
687639
props.add(new GWTPropertyDescriptor("age", "int"));
688-
final ExpSampleTypeImpl childType = SampleTypeServiceImpl.get().createSampleType(c, user,
689-
"ChildSamples", null, props, Collections.emptyList(),
690-
-1, -1, -1, -1, null, null);
691-
692-
final ExpSampleTypeImpl parent1Type = SampleTypeServiceImpl.get().createSampleType(c, user,
693-
"Parent1Samples", null, props, Collections.emptyList(),
694-
-1, -1, -1, -1, null, null);
695-
696-
final ExpSampleTypeImpl parent2Type = SampleTypeServiceImpl.get().createSampleType(c, user,
697-
"Parent2Samples", null, props, Collections.emptyList(),
698-
-1, -1, -1, -1, null, null);
699-
640+
final ExpSampleType childType = createSampleType("ChildSamples", props, null);
641+
final ExpSampleType parent1Type = createSampleType("Parent1Samples", props, null);
642+
final ExpSampleType parent2Type = createSampleType("Parent2Samples", props, null);
700643
701644
UserSchema schema = QueryService.get().getUserSchema(user, c, SchemaKey.fromParts("Samples"));
702645
List<Map<String, Object>> rows = new ArrayList<>();
@@ -827,13 +770,12 @@ public void testParentColAndDataInputDerivation() throws Exception
827770
props.add(new GWTPropertyDescriptor("data", "int"));
828771
props.add(new GWTPropertyDescriptor("parent", "string"));
829772
830-
final ExpSampleTypeImpl st = SampleTypeServiceImpl.get().createSampleType(c, user,
831-
"Samples", null, props, Collections.emptyList(),
832-
0, -1, -1, 2, null, null);
773+
String sampleTypeName = "Samples";
774+
final ExpSampleType st = createSampleType(sampleTypeName, props, null);
833775
834776
// insert and derive with both 'parent' column and 'DataInputs/Samples'
835-
UserSchema schema = QueryService.get().getUserSchema(user, c, SchemaKey.fromParts("Samples"));
836-
TableInfo table = schema.getTable("Samples");
777+
UserSchema schema = QueryService.get().getUserSchema(user, c, SamplesSchema.SCHEMA_SAMPLES);
778+
TableInfo table = schema.getTable(sampleTypeName);
837779
QueryUpdateService svc = table.getUpdateService();
838780
839781
List<Map<String, Object>> rows = new ArrayList<>();
@@ -955,6 +897,48 @@ public void testParentColAndDataInputDerivation() throws Exception
955897
assertFalse(oldDerivationRun.getMaterialInputs().containsKey(E));
956898
assertFalse(oldDerivationRun.getMaterialOutputs().contains(D));
957899
assertTrue(oldDerivationRun.getMaterialOutputs().contains(E));
900+
901+
// Issue 43241: Display of dates from Input/Output columns for sample types does not use the project date format
902+
{
903+
var folderProps = LookAndFeelProperties.getWriteableInstance(c);
904+
folderProps.setDefaultDateTimeFormat("'kevink' dd-MM-yyyy");
905+
folderProps.save();
906+
907+
var multiValueColumn = "Outputs/Materials/" + sampleTypeName + "/Created";
908+
var url = new ActionURL("query", "selectRows", c);
909+
url.addParameter(QueryParam.schemaName, schema.getName());
910+
url.addParameter("query." + QueryParam.queryName, sampleTypeName);
911+
url.addParameter("query." + QueryParam.columns, "Name, " + multiValueColumn);
912+
url.addFilter("query", FieldKey.fromParts("Name"), CompareType.EQUAL, "A");
913+
url.addParameter("includeMetadata", false);
914+
url.addParameter("apiVersion", "17.1");
915+
916+
var response = ViewServlet.GET(url, user, null);
917+
assertEquals(200, response.getStatus());
918+
919+
var json = JsonUtil.DEFAULT_MAPPER.readTree(response.getContentAsString());
920+
var resultRows = json.get("rows");
921+
assertEquals(1, resultRows.size());
922+
923+
var createdValues = resultRows.get(0).get("data").get(multiValueColumn);
924+
assertEquals(4, createdValues.size());
925+
926+
for (var data : createdValues)
927+
{
928+
var value = data.get("value").asText();
929+
assertNotNull(value);
930+
931+
// Formatted with container date format
932+
var formattedValue = data.get("formattedValue").asText();
933+
assertTrue("Expected date format not applied", formattedValue.startsWith("kevink "));
934+
935+
// Do not care what the JSON format looks like, as long as it is different
936+
assertNotEquals(value, formattedValue);
937+
}
938+
939+
folderProps.clearDefaultDateTimeFormat();
940+
folderProps.save();
941+
}
958942
}
959943
960944
@Test
@@ -971,12 +955,8 @@ public void testSampleTypeWithVocabularyProperties() throws Exception
971955
Domain mockDomain = helper.createVocabularyTestDomain(user, c);
972956
Map<String, String> vocabularyPropertyURIs = helper.getVocabularyPropertyURIS(mockDomain);
973957
974-
//create sample type
975-
ExpSampleTypeImpl st = SampleTypeServiceImpl.get().createSampleType(c, user,
976-
sampleName, null, List.of(new GWTPropertyDescriptor("name", "string")), Collections.emptyList(),
977-
-1, -1, -1, -1, null, null);
978-
979-
assertNotNull(st);
958+
// create a sample type
959+
createSampleType(sampleName, List.of(new GWTPropertyDescriptor("name", "string")), null);
980960
981961
UserSchema schema = QueryService.get().getUserSchema(user, c, SchemaKey.fromParts("Samples"));
982962
@@ -1038,9 +1018,7 @@ public void testDetailedAuditLog() throws Exception
10381018
props.add(new GWTPropertyDescriptor("Name", "string"));
10391019
props.add(new GWTPropertyDescriptor("Measure", "string"));
10401020
props.add(new GWTPropertyDescriptor("Value", "float"));
1041-
final ExpSampleTypeImpl st = SampleTypeServiceImpl.get().createSampleType(c, user,
1042-
"SamplesDAL", null, props, Collections.emptyList(),
1043-
-1, -1, -1, -1, null, null);
1021+
final ExpSampleType st = createSampleType("SamplesDAL", props, null);
10441022
10451023
QuerySchema samplesSchema = DefaultSchema.get(user, c, "samples");
10461024
assertNotNull(samplesSchema);
@@ -1130,10 +1108,8 @@ public void testExpMaterialPermissions() throws Exception
11301108
User user = TestContext.get().getUser();
11311109
var schema = QueryService.get().getUserSchema(user, c, ExpSchema.SCHEMA_EXP);
11321110
1133-
// create sample type
1134-
ExpSampleTypeImpl st = SampleTypeServiceImpl.get().createSampleType(c, user,
1135-
"MySamples", null, List.of(new GWTPropertyDescriptor("name", "string")), Collections.emptyList(),
1136-
-1, -1, -1, -1, null, null);
1111+
// create a sample type
1112+
ExpSampleType st = createSampleType("MySamples", List.of(new GWTPropertyDescriptor("name", "string")), null);
11371113
11381114
// insert a sample
11391115
var errors = new BatchValidationException();
@@ -1214,7 +1190,7 @@ public void testInsertOptionUpdate() throws Exception
12141190
props.add(new GWTPropertyDescriptor(longFieldName, "string"));
12151191
12161192
final String sampleTypeName = "TestSamplesWithRequired";
1217-
ExpSampleType sampleType = SampleTypeService.get().createSampleType(c, user, sampleTypeName, null, props, Collections.emptyList(), -1, -1, -1, -1, null);
1193+
ExpSampleType sampleType = createSampleType(sampleTypeName, props, null);
12181194
12191195
TableInfo table = getSampleTypeTable(sampleTypeName);
12201196
QueryUpdateService qus = table.getUpdateService();
@@ -1353,6 +1329,11 @@ public void testInsertOptionUpdate() throws Exception
13531329
assertNull(rows.get(2).get("AliquotedFromLSID"));
13541330
}
13551331
1332+
private ExpSampleType createSampleType(String sampleTypeName, List<GWTPropertyDescriptor> props, @Nullable String nameExpression) throws Exception
1333+
{
1334+
return SampleTypeService.get().createSampleType(c, TestContext.get().getUser(), sampleTypeName, null, props, emptyList(), -1, -1, -1, -1, nameExpression, null);
1335+
}
1336+
13561337
private @NotNull TableInfo getSampleTypeTable(String sampleType)
13571338
{
13581339
UserSchema schema = QueryService.get().getUserSchema(TestContext.get().getUser(), c, SamplesSchema.SCHEMA_SAMPLES);

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