jdk is now an optional dependency; when install-jdk is not installed,…

… RNAlysis searches for java in PATH by default

rnalysis/utils/installs.py

@@ -2,56 +2,69 @@
 import platform
 import shutil
 import subprocess
+import warnings
 from pathlib import Path
 from shutil import copyfileobj
 from typing import Union, Literal
 from urllib.request import urlopen
 
-import jdk
-
 from rnalysis.utils import io
 
-PICARD_JAR = Path(os.environ.get('PICARDTOOLS_JAR', io.get_data_dir().joinpath('picard.jar')))
-JDK_ROOT = io.get_data_dir().joinpath('jdk17')
-
-
-def get_jdk_path():
-    # List all files and directories in the given directory
-    items = os.listdir(JDK_ROOT)
-
-    # Filter for directories starting with 'jdk-'
-    jdk_directories = sorted([item for item in items if
-                              item.startswith('jdk-') and os.path.isdir(os.path.join(JDK_ROOT, item))], reverse=True)
-    if len(jdk_directories) == 0:
-        raise FileNotFoundError('No JDK directory found')
+try:
+    import jdk
+except ImportError:  # pragma: no cover
+    warnings.warn("'install-jdk' not found. To use PicardTools, you would need to install JDK manually.")
 
-    base_dir = JDK_ROOT.joinpath(f'{jdk_directories[0]}')
 
-    if platform.system() == 'Windows':
-        pattern = "java.exe"
-    else:
-        pattern = "java"
+    class jdk:  # pragma: no cover
+        @staticmethod
+        def install(version):
+            warnings.warn("Cannot install JDK.")
 
-    # Filter for files starting with 'java' or 'java.exe'
-    matches = list(base_dir.rglob(pattern))
-    if len(matches) == 0:
-        raise FileNotFoundError(f'No java executable found in {base_dir}')
+PICARD_JAR = Path(os.environ.get('PICARDTOOLS_JAR', io.get_data_dir().joinpath('picard.jar')))
+JDK_VERSION = "21"
+JDK_ROOT = io.get_data_dir().joinpath(f'jdk{JDK_VERSION}')
 
-    return matches[0].parent
 
+def get_jdk_path():
+    try:
+        if platform.system() == 'Windows':
+            pattern = "java.exe"
+        else:
+            pattern = "java"
+        # List all files and directories in the given directory
+        items = os.listdir(JDK_ROOT)
+        # Filter for directories starting with 'jdk-'
+        jdk_directories = sorted([item for item in items if
+                                  item.startswith('jdk-') and os.path.isdir(os.path.join(JDK_ROOT, item))],
+                                 reverse=True)
+        if len(jdk_directories) == 0:
+            raise FileNotFoundError('No JDK directory found')
+        base_dir = JDK_ROOT.joinpath(f'{jdk_directories[0]}')
+
+        # Filter for files starting with 'java' or 'java.exe'
+        matches = list(base_dir.rglob(pattern))
+        if len(matches) == 0:
+            raise FileNotFoundError(f'No java executable found in {base_dir}')
+        return matches[0].parent
+    except FileNotFoundError:
+        # find jdk installation in PATH
+        return ""
 
 def is_jdk_installed():
     try:
         if not JDK_ROOT.exists():
             return False
         # Run the "java -version" command and capture the output
         jdk_path = get_jdk_path()
-        output = subprocess.check_output([f'{jdk_path}/java', "-version"], stderr=subprocess.STDOUT, text=True)
-        # Check if the output contains "version 17" or "17." (for Java 17)
-        if "version 17" in output or " 17." in output:
+        output = subprocess.check_output(
+            [Path(jdk_path).joinpath("java").as_posix(), "-version"],
+            stderr=subprocess.STDOUT, text=True)
+        # Check if the output contains "version X" or "X." (for Java X)
+        if f"version {JDK_VERSION}" in output or f" {JDK_VERSION}." in output:
             return True
     except (subprocess.CalledProcessError, FileNotFoundError):
-        # If the "java -version" command returns an error, Java 17 is not installed.
+        # If the "java -version" command returns an error, Java X is not installed.
         return False
     return False
 
@@ -62,7 +75,7 @@ def install_jdk():
         if JDK_ROOT.exists():
             shutil.rmtree(JDK_ROOT)
         JDK_ROOT.mkdir(parents=True, exist_ok=True)
-        jdk.install('17', path=JDK_ROOT.as_posix())
+        jdk.install(str(JDK_VERSION), path=JDK_ROOT.as_posix())
         print('Done')
 
 

tests/test_installs.py

@@ -6,8 +6,8 @@
 from rnalysis.utils.installs import *
 
 # Constants for mocking
-MOCK_JDK_DIRS = ['jdk-17.0.1', 'jdk-16', 'jdk-15']
-MOCK_JDK_VERSION_OUTPUT = "java version 17"
+MOCK_JDK_DIRS = [f'jdk-{installs.JDK_VERSION}.0.1', 'jdk-16', 'jdk-15']
+MOCK_JDK_VERSION_OUTPUT = f"java version {installs.JDK_VERSION}"
 
 
 @pytest.fixture
@@ -28,8 +28,7 @@ def test_get_jdk_path_success(monkeypatch):
 
 def test_get_jdk_path_failure(monkeypatch):
     monkeypatch.setattr('os.listdir', lambda x: [])
-    with pytest.raises(FileNotFoundError):
-        get_jdk_path()
+    assert get_jdk_path() == ""
 
 
 # Test is_jdk_installed
@@ -44,7 +43,8 @@ def test_is_jdk_installed_failure_no_dir(monkeypatch):
 
 def test_is_jdk_installed_failure_wrong_version(monkeypatch):
     monkeypatch.setattr('pathlib.Path.exists', lambda self: True)
-    monkeypatch.setattr('subprocess.check_output', lambda *args, **kwargs: MOCK_JDK_VERSION_OUTPUT.replace('17', '15'))
+    monkeypatch.setattr('subprocess.check_output',
+                        lambda *args, **kwargs: MOCK_JDK_VERSION_OUTPUT.replace(str(installs.JDK_VERSION), '15'))
     assert not is_jdk_installed()