def test_find_executable_path():
with tempdir() as d:
f = d / "foo"
with open(f, "wt") as out:
out.write("foo")
os.chmod(f, stat.S_IRUSR)
assert find_executable_path("foo", [d]) is None
make_executable(f)
assert find_executable_path("foo", [d]) == f
def test_find_executable_path_system():
with tempdir() as d:
f = d / "foo"
with open(f, "wt") as out:
out.write("foo")
os.chmod(f, stat.S_IRUSR)
with setenv({"PATH": str(d)}):
assert find_executable_path("foo") is None
make_executable(f)
assert find_executable_path("foo") == f
def __init__(self,
project_root: Path,
import_dirs: Optional[List[Path]] = None,
java_bin: Optional[Union[str, Path]] = None,
java_args: Optional[str] = None,
cromwell_jar_file: Optional[Union[str, Path]] = None,
cromwell_config_file: Optional[Union[str, Path]] = None,
cromwell_args: Optional[str] = None):
self.project_root = project_root
self.import_dirs = import_dirs
if not java_bin:
java_home = os.environ.get(ENV_JAVA_HOME)
if java_home:
java_bin = Path(java_home) / "bin" / "java"
else:
java_bin = find_executable_path("java")
if not java_bin:
raise FileNotFoundError("Could not find java executable")
self.java_bin = ensure_path(java_bin,
exists=True,
is_file=True,
executable=True)
if not cromwell_jar_file:
cromwell_jar = os.environ.get(ENV_CROMWELL_JAR)
if cromwell_jar:
cromwell_jar_file = ensure_path(cromwell_jar)
else:
cromwell_jar_file = find_in_classpath("cromwell*.jar")
if not cromwell_jar_file:
raise FileNotFoundError("Could not find Cromwell JAR file")
self.cromwell_jar_file = ensure_path(cromwell_jar_file,
is_file=True,
exists=True)
if not cromwell_config_file:
config_file = os.environ.get(ENV_CROMWELL_CONFIG)
if config_file:
cromwell_config_file = ensure_path(config_file)
if cromwell_config_file:
self.cromwell_config_file = ensure_path(cromwell_config_file,
is_file=True,
exists=True)
else:
self.cromwell_config_file = None
if not java_args and self.cromwell_config_file:
java_args = f"-Dconfig.file={self.cromwell_config_file}"
self.java_args = java_args
self.cromwell_args = cromwell_args or os.environ.get(ENV_CROMWELL_ARGS)
def __init__(self,
java_bin: Optional[Union[str, Path]] = None,
java_args: Optional[str] = None):
if not java_bin:
java_home = os.environ.get(ENV_JAVA_HOME)
if java_home:
java_bin = Path(java_home) / "bin" / "java"
else:
java_bin = find_executable_path("java")
if not java_bin:
raise FileNotFoundError("Could not find java executable")
self.java_bin = ensure_path(java_bin,
exists=True,
is_file=True,
executable=True)
self.java_args = java_args or os.environ.get(ENV_JAVA_ARGS)
