Moving the SRA tests to a separate env (#1272)

- moving the SRA tests to a separate test target
- moving the ENA tests to a separate test target

.travis.yml

@@ -14,13 +14,19 @@ jdk:
 matrix:
   fast_finish: true
   allow_failures: 
+     - env: TEST_TYPE=EXTERNAL_APIS
      - env: TEST_TYPE=FTP
   include:
+     - jdk: oraclejdk8
+       env: TEST_TYPE=EXTERNAL_APIS
      - jdk: oraclejdk8
        env: TEST_TYPE=FTP
+
 script:
   - if [[ $TEST_TYPE == "FTP" ]]; then
         ./gradlew testFTP jacocoTestReport;
+    elif [[ $TEST_TYPE == "EXTERNAL_APIS" ]]; then
+        ./gradlew testExternalApis jacocoTestReport;
     else
         ./gradlew test jacocoTestReport;
     fi

build.gradle

@@ -104,16 +104,14 @@ test {
         events "failed", "skipped"
     }
 
-    if (System.env.CI == "true") {
-        jvmArgs += '-Dsamjdk.sra_libraries_download=true'
-    }
-
     tags {
         exclude "slow"
         exclude "broken"
         exclude "defaultReference"
         exclude "ftp"
-        if (System.env.CI == "false") exclude "sra"
+        exclude "sra"
+        exclude "ena"
+
         if (!OperatingSystem.current().isUnix()) exclude "unix"
     }
 } dependsOn findScalaAndJavaTypes, testWithDefaultReference
@@ -128,11 +126,13 @@ task testFTP(type: Test) {
     }
 }
 
-task testSRA(type: Test) {
-    description = "Run the SRA tests"
+task testExternalApis(type: Test) {
+    description = "Run the SRA and ENA tests (tests that interact with external APIs)"
     jvmArgs += '-Dsamjdk.sra_libraries_download=true'
 
     tags {
+        include "sra"
+        include "ena"
         exclude "slow"
         exclude "broken"
     }

src/test/java/htsjdk/TestClassDependenceTest.java

@@ -21,8 +21,7 @@
  */
 public class TestClassDependenceTest extends HtsjdkTest {
 
-
-    // since there are assertions inside the dataprovider, this test check that the dataprovider completes succeessfully.
+    // since there are assertions inside the dataprovider, this test checks that the dataprovider completes succeessfully.
     // This is needed since a failing data-provider will result in silently skipping the tests that rely on it.
 
     // This idea led to the creation of {@link TestDataProviders}, which renders it no-longer needed....

src/test/java/htsjdk/samtools/cram/ref/EnaRefServiceTest.java

@@ -7,6 +7,7 @@
 
 import java.io.IOException;
 
+@Test(groups="ena")
 public class EnaRefServiceTest extends HtsjdkTest {
 
     @DataProvider(name="testEnaRefServiceData")

src/test/java/htsjdk/samtools/sra/SRAQueryTest.java

@@ -68,6 +68,4 @@ public void testQueryCounts(String acc, String reference, int referenceStart, in
 
         assertCorrectCountsOfMappedAndUnmappedRecords(samRecordIterator, expectedNumMapped, expectedNumUnmapped);
     }
-
-
 }