Excise SRA support from htsjdk (#1774)

The NCBI SRA reader, backed by the gov.nih.nlm.ncbi:ngs-java native
library, has been a recurring source of build/runtime friction and is
being removed for v5.0.0. Downstream consumers that need SRA must
implement it themselves or use a different library.

Removed:
- gov.nih.nlm.ncbi:ngs-java api dependency from build.gradle.
- The "sra" TestNG group from build.gradle's test and testExternalApis
  tasks (and from htsjdk.TestDataProviders.EXCLUDED_GROUPS).
- The -Dsamjdk.sra_libraries_download=true JVM arg from
  testExternalApis. The corresponding Defaults.SRA_LIBRARIES_DOWNLOAD
  field is removed.
- 10 main sources under htsjdk/samtools and htsjdk/samtools/sra/
  (SRAFileReader, SRAIterator, SRAIndex, SRAAccession, SRALazyRecord,
  SRAAlignmentIterator, SRAUnalignmentIterator, SRAUtils, ReferenceCache,
  SRAIndexedSequenceFile).
- 7 test classes under htsjdk/samtools/sra/ and the test_archive.sra
  resource.
- SamReader.Type.SRA_TYPE.
- The README's SRA license-attribution sentence.

Modified (SRA hooks removed):
- SamInputResource: drops InputResource.Type.SRA_ACCESSION, the
  abstract asSRAAccession() method and all its overrides, the
  SRAInputResource inner class, and the SamInputResource.of(SRAAccession)
  factory.
- SamReaderFactory: drops the SRA dispatch in the resource type switch,
  the isSra() autodetection branch, the abstract
  applyTo(SRAFileReader, ...) method on Option and all five overrides
  of it, plus the instanceof SRAFileReader branch.
- SamReaderFactoryTest, SamReaderTest, ReadsBundle (TODO comment): minor
  follow-on edits where these referenced the removed types.

Verification:
- ./gradlew compileJava compileTestJava: passes.
- ./gradlew test: 21,877 / 21,877 pass (down from 21,936 on dev; the
  difference is the removed sra test classes plus DataProvider-discovered
  test paths that referenced the sra group).
- ./gradlew spotbugsMain spotbugsTest: clean, no new findings.
- ./gradlew spotlessCheck: clean (autoformat applied during compile).
- Stragglers: grep'd src/, build.gradle, README, CONTRIBUTING, CHANGELOG,
  and .github/ for "SRA" tokens, "import ngs.", "sra" string literals,
  "ngs-java", and "sra_libraries" -- no remaining references.

CHANGELOG entry deferred to the dedicated v5.0.0 CHANGELOG task.

Author: tfenne

README.md

@@ -96,7 +96,6 @@ Broadly speaking the majority of the code is covered under the MIT license with
 
 * Much of the CRAM code is under the Apache License, Version 2
 * Core `tribble` code (underlying VCF reading/writing amongst other things) is under LGPL
-* Code supporting the reading/writing of SRA format is uncopyrighted & public domain
 
 ### Java Minimum Version Support Policy
 

build.gradle

@@ -51,7 +51,6 @@ dependencies {
     implementation "org.json:json:20231013"
     implementation 'org.openjdk.nashorn:nashorn-core:15.4'
 
-    api "gov.nih.nlm.ncbi:ngs-java:2.9.0"
     api "org.apache.commons:commons-jexl:2.1.1"
 
     testImplementation 'org.testng:testng:7.8.0'
@@ -225,13 +224,13 @@ tasks.register('testWithOptimisticVCF4_4', Test) {
 }
 
 test {
-    description = "Runs the unit tests other than the SRA tests"
+    description = "Runs the unit tests other than external-API tests"
 
    useTestNG {
        if (OperatingSystem.current().isUnix()) {
-           excludeGroups "slow", "broken", "defaultReference", "optimistic_vcf_4_4", "ftp", "http", "sra", "ena", "htsget"
+           excludeGroups "slow", "broken", "defaultReference", "optimistic_vcf_4_4", "ftp", "http", "ena", "htsget"
        } else {
-           excludeGroups "slow", "broken", "defaultReference", "optimistic_vcf_4_4", "ftp", "http", "sra", "ena", "htsget", "unix"
+           excludeGroups "slow", "broken", "defaultReference", "optimistic_vcf_4_4", "ftp", "http", "ena", "htsget", "unix"
        }
        parallel = "classes"
        threadCount = Runtime.runtime.availableProcessors()
@@ -250,13 +249,12 @@ tasks.register('testFTP', Test) {
 }
 
 tasks.register('testExternalApis', Test) {
-    description = "Run the SRA, ENA, and HTTP tests (tests that interact with external APIs)"
+    description = "Run the ENA and HTTP tests (tests that interact with external APIs)"
     testClassesDirs = sourceSets.test.output.classesDirs
     classpath = sourceSets.test.runtimeClasspath
-    jvmArgs += '-Dsamjdk.sra_libraries_download=true'
 
     useTestNG {
-        includeGroups "sra", "http", "ena"
+        includeGroups "http", "ena"
         excludeGroups "slow", "broken"
     }
 }

src/main/java/htsjdk/beta/plugin/reads/ReadsBundle.java

@@ -201,7 +201,7 @@ private static <T extends IOPath> Optional<Tuple<String, String>> getInferredCon
             } else if (ext.equals((FileExtensions.SAM))) {
                 return Optional.of(new Tuple<>(BundleResourceType.CT_ALIGNED_READS, BundleResourceType.FMT_READS_SAM));
             }
-            // TODO: finish this, else SRA, htsget,...
+            // TODO: finish this, else htsget,...
         }
         return Optional.empty();
     }

src/main/java/htsjdk/samtools/Defaults.java

@@ -95,12 +95,6 @@ public class Defaults {
      */
     public static final String EBI_REFERENCE_SERVICE_URL_MASK;
 
-    /**
-     * Boolean describing whether downloading of SRA native libraries is allowed,
-     * in case such native libraries are not found locally.  Default = false.
-     */
-    public static final boolean SRA_LIBRARIES_DOWNLOAD;
-
     /**
      * Whether to attempt to use jlibdeflate (libdeflate via JNI) for DEFLATE compression and decompression.
      * When true, the default deflater/inflater factories will try to load the native library and fall back
@@ -143,7 +137,6 @@ public class Defaults {
         CUSTOM_READER_FACTORY = getStringProperty("custom_reader", "");
         SAM_FLAG_FIELD_FORMAT =
                 SamFlagField.valueOf(getStringProperty("sam_flag_field_format", SamFlagField.DECIMAL.name()));
-        SRA_LIBRARIES_DOWNLOAD = getBooleanProperty("sra_libraries_download", false);
         USE_LIBDEFLATE = getBooleanProperty("use_libdeflate", true);
         DISABLE_SNAPPY_COMPRESSOR = getBooleanProperty(DISABLE_SNAPPY_PROPERTY_NAME, false);
         OPTIMISTIC_VCF_4_4 = getBooleanProperty(OPTIMISTIC_VCF_4_4_PROPERTY, false);