test: fix JUnit tests by updating configuration files, #TASK-5564

opencb · Aug 13, 2024 · 344e92e · 344e92e
1 parent 162f34d
commit 344e92e
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Showing 5 changed files with 15 additions and 11 deletions.
diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/utils/DatabaseNameUtils.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/utils/DatabaseNameUtils.java
@@ -57,7 +57,7 @@ public static String cleanAssembly(String assembly) {
             throw new InvalidParameterException("Assembly is empty");
         }
 
-        return assembly.replace("\\.", "")
+        return assembly.replace(".", "")
                 .replace("-", "")
                 .replace("_", "").toLowerCase(Locale.ROOT);
     }

diff --git a/cellbase-core/src/main/resources/configuration.yml b/cellbase-core/src/main/resources/configuration.yml
@@ -335,7 +335,7 @@ species:
         - variation
         - variation_functional_score
         - missense_variation_functional_score
-        - clinical_variant
+        - clinical_variants
         - splice_score
         - ontology
         - pubmed

diff --git a/cellbase-core/src/test/resources/configuration.yml b/cellbase-core/src/test/resources/configuration.yml
@@ -334,13 +334,15 @@ species:
         - conservation
         - repeats
         - gene
-        - regulation
         - protein
-        - clinical_variant
-        - missense_variation_functional_score
-        - ontology
+        - regulation
+        - variation
         - variation_functional_score
+        - missense_variation_functional_score
+        - clinical_variants
         - splice_score
+        - ontology
+        - pubmed
         - pharmacogenomics
     - id: mmusculus
       scientificName: Mus musculus

diff --git a/cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/MongoDBAdaptorFactoryTest.java b/cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/MongoDBAdaptorFactoryTest.java
@@ -55,7 +55,7 @@ public void testGetDatabaseName() {
                 assertThrows(InvalidParameterException.class,
                         () -> DatabaseNameUtils.getDatabaseName("speciesName", null, cellBaseConfiguration.getVersion()),
                         "Expected getDatabaseName() to throw an exception, but it didn't");
-        assertTrue(thrown.getMessage().contains("Species and assembly are required"));
+        assertTrue(thrown.getMessage().contains("species and assembly are required"));
 
         // handle special characters
         databaseName = DatabaseNameUtils.getDatabaseName("speciesName", "my_funny.assembly--name", cellBaseConfiguration.getVersion());

diff --git a/cellbase-lib/src/test/resources/configuration.test.yaml b/cellbase-lib/src/test/resources/configuration.test.yaml
@@ -321,13 +321,15 @@ species:
         - conservation
         - repeats
         - gene
-        - regulation
         - protein
-        - clinical_variant
-        - missense_variation_functional_score
-        - ontology
+        - regulation
+        - variation
         - variation_functional_score
+        - missense_variation_functional_score
+        - clinical_variants
         - splice_score
+        - ontology
+        - pubmed
         - pharmacogenomics
     - id: mmusculus
       scientificName: Mus musculus