Release progV3.5.3

hivdb · Jan 6, 2025 · e0443f5 · e0443f5
1 parent c18e673
commit e0443f5
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Showing 12 changed files with 7,597 additions and 5,694 deletions.
diff --git a/.latest-version b/.latest-version
@@ -1 +1 @@
-20241110055209
+20250106053346
diff --git a/build.gradle b/build.gradle
@@ -6,7 +6,7 @@ plugins {
 }
 
 group = 'edu.stanford.hivdb'
-version = '3.5.2'
+version = '3.5.3'
 
 sourceCompatibility = 15
 targetCompatibility = 15

diff --git a/hivfacts b/hivfacts
diff --git a/sierra-tests/build.gradle b/sierra-tests/build.gradle
@@ -5,7 +5,7 @@ plugins {
 }
 
 group = 'edu.stanford.hivdb'
-version = '3.5.2'
+version = '3.5.3'
 
 description = """Sierra Unit Tests"""
 

diff --git a/.../java/edu/stanford/hivdb/drugresistance/algorithm/GeneDRASIResultHandlerDrugSuscTest.java b/.../java/edu/stanford/hivdb/drugresistance/algorithm/GeneDRASIResultHandlerDrugSuscTest.java
@@ -223,6 +223,7 @@ public void testGetTotalDrugScores() {
 		expected.put(hiv.getDrug("DOR"), 0.0);
 		expected.put(hiv.getDrug("NVP"), 0.0);
 		expected.put(hiv.getDrug("RPV"), 0.0);
+		expected.put(hiv.getDrug("DPV"), 0.0);
 		expected.put(hiv.getDrug("ETR"), 0.0);
 		expected.put(hiv.getDrug("EFV"), 0.0);
 		assertEquals(expected, geneDR.getTotalDrugScores());
@@ -243,6 +244,7 @@ public void testGetTotalDrugScores() {
 		expectedNNRTI.put(hiv.getDrug("DOR"), 0.0);
 		expectedNNRTI.put(hiv.getDrug("NVP"), 0.0);
 		expectedNNRTI.put(hiv.getDrug("RPV"), 0.0);
+		expectedNNRTI.put(hiv.getDrug("DPV"), 0.0);
 		expectedNNRTI.put(hiv.getDrug("ETR"), 0.0);
 		expectedNNRTI.put(hiv.getDrug("EFV"), 0.0);
 		 assertEquals(
@@ -328,6 +330,12 @@ public void testDrugSuscGetPartialScores() {
 		mutScores.put(hiv.newMutationSet("RT100I"), 60.);
 		expected.put(hiv.getDrug("RPV"), mutScores);
 
+		mutScores = new TreeMap<>();
+		mutScores.put(hiv.newMutationSet("RT100I"), 60.);
+		mutScores.put(hiv.newMutationSet("RT101E"), 45.);
+		mutScores.put(hiv.newMutationSet("RT181C"), 60.);
+		expected.put(hiv.getDrug("DPV"), mutScores);
+
 		mutScores = new TreeMap<>();
 		mutScores.put(hiv.newMutationSet("RT181C"), 30.);
 		mutScores.put(hiv.newMutationSet("RT101E"), 10.);

diff --git a/sierra-tests/src/test/java/edu/stanford/hivdb/drugs/DrugClassTest.java b/sierra-tests/src/test/java/edu/stanford/hivdb/drugs/DrugClassTest.java
@@ -32,7 +32,7 @@ public void testGetSynonyms() {
 	@Test
 	public void testGetDrugs() {
 		DrugClass<HIV> drugClass = hiv.getDrugClass("NNRTI");
-		assertEquals(drugClass.getDrugs().size(), 5);
+		assertEquals(drugClass.getDrugs().size(), 6);
 	}
 
 	@Test
@@ -175,6 +175,7 @@ public void testGetDrugsFullDrugClass() {
 
 		List<Drug<HIV>> NNRTIDrugs = new ArrayList<>();
 		NNRTIDrugs.add(hiv.getDrug("DOR"));
+		NNRTIDrugs.add(hiv.getDrug("DPV"));
 		NNRTIDrugs.add(hiv.getDrug("EFV"));
 		NNRTIDrugs.add(hiv.getDrug("ETR"));
 		NNRTIDrugs.add(hiv.getDrug("NVP"));

diff --git a/sierra-tests/src/test/java/edu/stanford/hivdb/drugs/DrugTest.java b/sierra-tests/src/test/java/edu/stanford/hivdb/drugs/DrugTest.java
@@ -18,7 +18,7 @@ public class DrugTest {
     @Test
     public void testLoadJSON() {
     	// WARNING: This test would fail each time new drug is added.
-    	assertEquals(26, hiv.getDrugs().size());
+    	assertEquals(hiv.getDrugs().size(), 27);
     }
 
     @Test
@@ -111,7 +111,7 @@ public void testCompareTo() {
     public void testFullDrugs() {
 		// WARNING: This test would fail every time a drug is added.
     	// INFO: You should update all the fullDrugs test below adding new drug and also update this test.
-  		assertEquals(26, hiv.getDrugs().size());
+  		assertEquals(hiv.getDrugs().size(), 27);
 
     }
 

diff --git a/sierra-tests/src/test/java/edu/stanford/hivdb/hivfacts/HIVTest.java b/sierra-tests/src/test/java/edu/stanford/hivdb/hivfacts/HIVTest.java
@@ -180,7 +180,7 @@ public void testGetDrugClass() {
     @Test
     public void testGetDrugs() {
     	assertNotNull(hiv.getDrugs());
-    	assertEquals(26, hiv.getDrugs().size());
+    	assertEquals(hiv.getDrugs().size(), 27);
     }
 
 	@Test
@@ -229,8 +229,8 @@ public void testGetDrugSynonymMapWithException() {
 	@Test
 	public void testGetDrugResistAlgorithms() {
 		assertNotNull(hiv.getDrugResistAlgorithms());
-		// 20241109, 47 algorithms
-		assertEquals(47, hiv.getDrugResistAlgorithms().size());
+		// 20250105, 48 algorithms
+		assertEquals(48, hiv.getDrugResistAlgorithms().size());
 	}
 
 	@Test

diff --git a/sierra-tests/src/test/java/edu/stanford/hivdb/hivfacts/hiv2/HIV2Test.java b/sierra-tests/src/test/java/edu/stanford/hivdb/hivfacts/hiv2/HIV2Test.java
@@ -164,7 +164,7 @@ public void testGetDrugClass() {
     @Test
     public void testGetDrugs() {
     	assertNotNull(hiv2.getDrugs());
-    	assertEquals(26, hiv2.getDrugs().size());
+    	assertEquals(hiv2.getDrugs().size(), 27);
     }
 
 	@Test

diff --git a/sierra-tests/src/test/java/edu/stanford/hivdb/viruses/VirusTest.java b/sierra-tests/src/test/java/edu/stanford/hivdb/viruses/VirusTest.java
@@ -47,13 +47,13 @@ public void testExtractMutationGenesInvaid() {
 
 	@Test
 	public void testGetLatestDrugResistAlgorithm() {
-		assertEquals("9.7", hiv.getLatestDrugResistAlgorithm("HIVDB").getVersion());
+		assertEquals("9.8", hiv.getLatestDrugResistAlgorithm("HIVDB").getVersion());
 		assertEquals("34", hiv.getLatestDrugResistAlgorithm("ANRS").getVersion());
 		assertEquals("10.0", hiv.getLatestDrugResistAlgorithm("Rega").getVersion());
 	}
 
 	@Test
 	public void testGetDefaultDrugResistAlgorithm() {
-		assertEquals("9.7", hiv.getDefaultDrugResistAlgorithm().getVersion());
+		assertEquals("9.8", hiv.getDefaultDrugResistAlgorithm().getVersion());
 	}
 }
+4,438 −0		data/algorithms/HIVDB_9.8.xml
+1 −1		data/algorithms/HIVDB_latest.xml
+5 −0		data/algorithms/versions.json
+1 −0		data/algorithms/versions.yml
+2 −1		data/drms_hiv1.csv
+6 −1		data/drms_hiv1.json
+6 −0		data/drugs.json
+4 −0		data/drugs.yml
+9,780 −0		data/patterns-hiv1/patterns-NNRTI.json
+1 −1		scripts/build_drms.py