Skip to content

Commit d8dcc06

Browse files
depryfdepryf
committed
Fix sex staging input variable name,
1 parent f29cc1a commit d8dcc06

12 files changed

Lines changed: 118 additions & 121 deletions

File tree

‎CHANGELOG.md‎

Lines changed: 5 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,10 @@
11
## Validation Framework Version History
22

3+
**Version 4.8**
4+
5+
- Updated staging client.
6+
- Fixed staging context methods to use 'sexAssignedAtBirth' instead of deprecated 'sex' NAACCR variable.
7+
38
**Version 4.7**
49

510
- Added new differenceInDays methods to the edits context.

‎build.gradle‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -20,7 +20,7 @@ repositories {
2020
}
2121

2222
dependencies {
23-
api 'com.imsweb:staging-client-java:11.8.1'
23+
api 'com.imsweb:staging-client-java:11.9.0'
2424
api 'org.apache.groovy:groovy:4.0.29'
2525
api 'com.thoughtworks.xstream:xstream:1.4.21'
2626

‎src/main/java/com/imsweb/validation/ValidationStagingUtils.java‎

Lines changed: 15 additions & 22 deletions
Original file line numberDiff line numberDiff line change
@@ -19,7 +19,7 @@ public final class ValidationStagingUtils {
1919
public static final String INPUT_PROP_SITE = "primarySite";
2020
public static final String INPUT_PROP_HIST = "histologicTypeIcdO3";
2121
public static final String INPUT_PROP_SSF25 = "csSiteSpecificFactor25";
22-
public static final String INPUT_PROP_SEX = "sex";
22+
public static final String INPUT_PROP_SEX_ASSIGNED_AT_BIRTH = "sexAssignedAtBirth";
2323
public static final String INPUT_PROP_DISC_1 = "schemaDiscriminator1";
2424
public static final String INPUT_PROP_DISC_2 = "schemaDiscriminator2";
2525
public static final String INPUT_PROP_BEHAV = "behaviorCodeIcdO3";
@@ -43,7 +43,7 @@ public static String computeCsSchemaId(Staging stagingInstance, Map<String, Stri
4343
lkup.setInput("ssf25", ssf25);
4444
List<Schema> info = stagingInstance.lookupSchema(lkup);
4545
if (info.size() == 1) {
46-
Schema schema = stagingInstance.getSchema(info.get(0).getId());
46+
Schema schema = stagingInstance.getSchema(info.getFirst().getId());
4747
return schema.getId();
4848
}
4949
return null;
@@ -56,15 +56,15 @@ public static String computeTnmSchemaId(Staging stagingInstance, Map<String, Str
5656
String site = input.get(INPUT_PROP_SITE);
5757
String hist = input.get(INPUT_PROP_HIST);
5858
String ssf25 = input.get(INPUT_PROP_SSF25);
59-
String sex = input.get(INPUT_PROP_SEX);
59+
String sex = input.get(INPUT_PROP_SEX_ASSIGNED_AT_BIRTH);
6060

6161
// get the TNM schema ID
6262
SchemaLookup lkup = new SchemaLookup(site, hist);
6363
lkup.setInput("ssf25", ssf25);
64-
lkup.setInput("sex", sex);
64+
lkup.setInput("sex_at_birth", sex);
6565
List<Schema> info = stagingInstance.lookupSchema(lkup);
6666
if (info.size() == 1) {
67-
Schema schema = stagingInstance.getSchema(info.get(0).getId());
67+
Schema schema = stagingInstance.getSchema(info.getFirst().getId());
6868
return schema.getId();
6969
}
7070
return null;
@@ -78,19 +78,19 @@ public static String computeEodSchemaId(Staging stagingInstance, Map<String, Str
7878
String hist = input.get(INPUT_PROP_HIST);
7979
String disc1 = input.get(INPUT_PROP_DISC_1);
8080
String disc2 = input.get(INPUT_PROP_DISC_2);
81-
String sex = input.get(INPUT_PROP_SEX);
81+
String sex = input.get(INPUT_PROP_SEX_ASSIGNED_AT_BIRTH);
8282
String behav = input.get(INPUT_PROP_BEHAV);
8383
String dxYear = input.get(INPUT_PROP_DX_YEAR);
8484

8585
SchemaLookup lkup = new SchemaLookup(site, hist);
8686
lkup.setInput("discriminator_1", disc1);
8787
lkup.setInput("discriminator_2", disc2);
88-
lkup.setInput("sex", sex);
88+
lkup.setInput("sex_at_birth", sex);
8989
lkup.setInput("behavior", behav);
9090
lkup.setInput("year_dx", dxYear);
9191
List<Schema> info = stagingInstance.lookupSchema(lkup);
9292
if (info.size() == 1) {
93-
Schema schema = stagingInstance.getSchema(info.get(0).getId());
93+
Schema schema = stagingInstance.getSchema(info.getFirst().getId());
9494
return schema.getId();
9595
}
9696
return null;
@@ -110,20 +110,13 @@ public static String getSsf25FromSex(String ssf25, String sex, String hist, Stri
110110
if (sex == null)
111111
return "009";
112112

113-
switch (sex) {
114-
case "2":
115-
case "6":
116-
return "002";
117-
case "1":
118-
case "5":
119-
return "001";
120-
case "3":
121-
return "003";
122-
case "4":
123-
return "004";
124-
default:
125-
return "009";
126-
}
113+
return switch (sex) {
114+
case "2", "6" -> "002";
115+
case "1", "5" -> "001";
116+
case "3" -> "003";
117+
case "4" -> "004";
118+
default -> "009";
119+
};
127120
}
128121

129122
return ssf25;

‎src/main/java/com/imsweb/validation/functions/StagingContextFunctions.java‎

Lines changed: 84 additions & 85 deletions
Large diffs are not rendered by default.

‎src/test/java/com/imsweb/validation/TestingUtils.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -48,9 +48,9 @@ public static void init() {
4848
if (_CS_STAGING == null)
4949
_CS_STAGING = loadStagingInstance("cs-02.05.50.zip");
5050
if (_TNM_STAGING == null)
51-
_TNM_STAGING = loadStagingInstance("tnm-2.0.zip");
51+
_TNM_STAGING = loadStagingInstance("tnm-2.1.zip");
5252
if (_EOD_STAGING == null)
53-
_EOD_STAGING = loadStagingInstance("eod_public-3.2.zip");
53+
_EOD_STAGING = loadStagingInstance("eod_public-3.3.zip");
5454
}
5555

5656
private static Staging loadStagingInstance(String data) {

‎src/test/java/com/imsweb/validation/ValidationStagingUtilsTest.java‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -31,7 +31,7 @@ public void testComputeCsShemaId() {
3131
input.put("histologicTypeIcdO3", "8000");
3232
Assert.assertNull(ValidationStagingUtils.computeCsSchemaId(TestingUtils.getCsStaging(), input));
3333

34-
input.put("sex", "1");
34+
input.put("sexAssignedAtBirth", "1");
3535
Assert.assertNull(ValidationStagingUtils.computeCsSchemaId(TestingUtils.getCsStaging(), input)); // peritoneum
3636

3737
input.put("dateOfDiagnosisYear", "2016");
@@ -62,7 +62,7 @@ public void testComputeTnmShemaId() {
6262
input.put("histologicTypeIcdO3", "8000");
6363
Assert.assertNull(ValidationStagingUtils.computeTnmSchemaId(TestingUtils.getTnmStaging(), input));
6464

65-
input.put("sex", "1");
65+
input.put("sexAssignedAtBirth", "1");
6666
Assert.assertNotNull(ValidationStagingUtils.computeTnmSchemaId(TestingUtils.getTnmStaging(), input)); // peritoneum
6767

6868
input.put("csSiteSpecificFactor25", "010");
@@ -90,7 +90,7 @@ public void testComputeEodShemaId() {
9090
input.put("histologicTypeIcdO3", "8000");
9191
Assert.assertNull(ValidationStagingUtils.computeEodSchemaId(TestingUtils.getEodStaging(), input));
9292

93-
input.put("sex", "1");
93+
input.put("sexAssignedAtBirth", "1");
9494
Assert.assertNotNull(ValidationStagingUtils.computeEodSchemaId(TestingUtils.getEodStaging(), input)); // retroperitoneum
9595

9696
input.put("schemaDiscriminator1", "1");

‎src/test/java/com/imsweb/validation/entities/SimpleNaaccrLinesValidatableTest.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -131,7 +131,7 @@ public void testGetCsSchemaId() throws IllegalAccessException {
131131
rec.put("primarySite", "C481");
132132
rec.put("csSiteSpecificFactor25", null);
133133
rec.put("schemaDiscriminator1", null);
134-
rec.put("sex", "1");
134+
rec.put("sexAssignedAtBirth", "1");
135135
v = new SimpleNaaccrLinesValidatable(rec);
136136
validatables = v.followCollection("line");
137137
line = (Map<String, String>)validatables.getFirst().getScope().get("line");

‎src/test/java/com/imsweb/validation/functions/StagingContextFunctionsTest.java‎

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -312,7 +312,7 @@ public void testGetTnmSchema() {
312312
input.put("csSiteSpecificFactor25", null);
313313
Assert.assertNull(_functions.getTnmStagingSchema(input));
314314

315-
input.put("sex", "1");
315+
input.put("sexAssignedAtBirth", "1");
316316
Assert.assertNotNull(_functions.getTnmStagingSchema(input));
317317

318318
input.put("csSiteSpecificFactor25", "010");
@@ -374,9 +374,9 @@ public void testGetTnmSchemaId() {
374374
input.put("primarySite", "C481");
375375
input.put("histologicTypeIcdO3", "8000");
376376
input.put("csSiteSpecificFactor25", null);
377-
input.put("sex", "2");
377+
input.put("sexAssignedAtBirth", "2");
378378
Assert.assertEquals("peritoneum_female_gen", _functions.getTnmSchemaId(input));
379-
input.put("sex", null);
379+
input.put("sexAssignedAtBirth", null);
380380
Assert.assertNull(_functions.getTnmSchemaId(input));
381381
}
382382

@@ -475,7 +475,7 @@ public void testGetEodSchema() {
475475
input.put("histologicTypeIcdO3", "8000");
476476
Assert.assertNull(_functions.getEodStagingSchema(input));
477477

478-
input.put("sex", "1");
478+
input.put("sexAssignedAtBirth", "1");
479479
Assert.assertNotNull(_functions.getEodStagingSchema(input)); // retroperitoneum
480480

481481
input.put("schemaDiscriminator1", "1");
@@ -547,9 +547,9 @@ public void testGetEodSchemaId() {
547547
input.put("primarySite", "C481");
548548
input.put("histologicTypeIcdO3", "8000");
549549
input.put("schemaDiscriminator1", null);
550-
input.put("sex", "2");
550+
input.put("sexAssignedAtBirth", "2");
551551
Assert.assertEquals("primary_peritoneal_carcinoma", _functions.getEodSchemaId(input));
552-
input.put("sex", null);
552+
input.put("sexAssignedAtBirth", null);
553553
Assert.assertNull(_functions.getEodSchemaId(input));
554554

555555
input.clear();
@@ -619,7 +619,7 @@ public void testIsNeededForStagingEodField() {
619619
input.put("histologicTypeIcdO3", "8000");
620620
input.put("schemaDiscriminator1", null);
621621

622-
Assert.assertTrue(_functions.isNeededForStagingEodField(input, "psaLabValue"));
622+
Assert.assertFalse(_functions.isNeededForStagingEodField(input, "psaLabValue"));
623623
Assert.assertFalse(_functions.isNeededForStagingEodField(input, "gleasonPatternsClinical"));
624624
Assert.assertTrue(_functions.isNeededForStagingEodField(input, "prostatePathologicalExtension"));
625625
Assert.assertFalse(_functions.isNeededForStagingEodField(input, "regionalNodesPositive"));

‎src/test/resources/staging/eod_public-3.2.zip‎

-2.14 MB
Binary file not shown.

‎src/test/resources/staging/eod_public-3.3.zip‎

1.85 MB
Binary file not shown.

0 commit comments

Comments
 (0)