def find_extension(source_file, sourcecache: SourceCache):
for ext in EXTENSIONS:
if source_file.get_filename().endswith("wrapper{}".format(ext)):
return source_file
for ext in EXTENSIONS:
script = source_file.join("wrapper{}".format(ext))
if sourcecache.exists(script):
return script
def wrapper(
path,
input,
output,
params,
wildcards,
threads,
resources,
log,
config,
rulename,
conda_env,
conda_base_path,
container_img,
singularity_args,
env_modules,
bench_record,
prefix,
jobid,
bench_iteration,
cleanup_scripts,
shadow_dir,
runtime_sourcecache_path,
):
"""
Load a wrapper from https://github.com/snakemake/snakemake-wrappers under
the given path + wrapper.(py|R|Rmd) and execute it.
"""
path = get_script(path,
SourceCache(runtime_cache_path=runtime_sourcecache_path),
prefix=prefix)
script(
path,
"",
input,
output,
params,
wildcards,
threads,
resources,
log,
config,
rulename,
conda_env,
conda_base_path,
container_img,
singularity_args,
env_modules,
bench_record,
jobid,
bench_iteration,
cleanup_scripts,
shadow_dir,
runtime_sourcecache_path,
)
def find_extension(path,
sourcecache: SourceCache,
extensions=[".py", ".R", ".Rmd", ".jl"]):
for ext in extensions:
if path.endswith("wrapper{}".format(ext)):
return path
path = infer_source_file(path)
for ext in extensions:
script = path.join("wrapper{}".format(ext))
if sourcecache.exists(script):
return script
def wrapper(
path,
input,
output,
params,
wildcards,
threads,
resources,
log,
config,
rulename,
conda_env,
conda_base_path,
container_img,
singularity_args,
env_modules,
bench_record,
prefix,
jobid,
bench_iteration,
cleanup_scripts,
shadow_dir,
runtime_sourcecache_path,
):
"""
Load a wrapper from https://github.com/snakemake/snakemake-wrappers under
the given path + wrapper.(py|R|Rmd) and execute it.
"""
assert path is not None
script_source = get_script(
path, SourceCache(runtime_cache_path=runtime_sourcecache_path), prefix=prefix
)
if script_source is None:
raise WorkflowError(
f"Unable to locate wrapper script for wrapper {path}. "
"This can be a network issue or a mistake in the wrapper URL."
)
script(
script_source.get_path_or_uri(),
"",
input,
output,
params,
wildcards,
threads,
resources,
log,
config,
rulename,
conda_env,
conda_base_path,
container_img,
singularity_args,
env_modules,
bench_record,
jobid,
bench_iteration,
cleanup_scripts,
shadow_dir,
runtime_sourcecache_path,
)
def notebook(
path,
basedir,
input,
output,
params,
wildcards,
threads,
resources,
log,
config,
rulename,
conda_env,
conda_base_path,
container_img,
singularity_args,
env_modules,
bench_record,
jobid,
bench_iteration,
cleanup_scripts,
shadow_dir,
edit,
runtime_sourcecache_path,
):
"""
Load a script from the given basedir + path and execute it.
"""
draft = False
if edit is not None:
if is_local_file(path):
if not os.path.isabs(path):
local_path = os.path.join(basedir, path)
else:
local_path = path
if not os.path.exists(local_path):
# draft the notebook, it does not exist yet
language = None
draft = True
path = "file://{}".format(os.path.abspath(local_path))
if path.endswith(".py.ipynb"):
language = "jupyter_python"
elif path.endswith(".r.ipynb"):
language = "jupyter_r"
else:
raise WorkflowError(
"Notebook to edit has to end on .py.ipynb or .r.ipynb in order "
"to decide which programming language shall be used.")
else:
raise WorkflowError(
"Notebook {} is not local, but edit mode is only allowed for "
"local notebooks.".format(path))
if not draft:
path, source, language, is_local = get_source(
path, SourceCache(runtime_sourcecache_path), basedir, wildcards,
params)
else:
source = None
is_local = True
exec_class = get_exec_class(language)
executor = exec_class(
path,
source,
basedir,
input,
output,
params,
wildcards,
threads,
resources,
log,
config,
rulename,
conda_env,
conda_base_path,
container_img,
singularity_args,
env_modules,
bench_record,
jobid,
bench_iteration,
cleanup_scripts,
shadow_dir,
is_local,
)
if draft:
executor.draft(listen=edit)
else:
executor.evaluate(edit=edit)
def notebook(
path,
basedir,
input,
output,
params,
wildcards,
threads,
resources,
log,
config,
rulename,
conda_env,
conda_base_path,
container_img,
singularity_args,
env_modules,
bench_record,
jobid,
bench_iteration,
cleanup_scripts,
shadow_dir,
edit,
runtime_sourcecache_path,
):
"""
Load a script from the given basedir + path and execute it.
"""
draft = False
if edit is not None:
if is_local_file(path):
if not os.path.isabs(path):
local_path = os.path.join(basedir, path)
else:
local_path = path
if not os.path.exists(local_path):
# draft the notebook, it does not exist yet
language = None
draft = True
path = "file://{}".format(os.path.abspath(local_path))
if path.endswith(".py.ipynb"):
language = "jupyter_python"
elif path.endswith(".r.ipynb"):
language = "jupyter_r"
else:
raise WorkflowError(
"Notebook to edit has to end on .py.ipynb or .r.ipynb in order "
"to decide which programming language shall be used.")
else:
raise WorkflowError(
"Notebook {} is not local, but edit mode is only allowed for "
"local notebooks.".format(path))
if not draft:
path, source, language, is_local = get_source(
path, SourceCache(runtime_sourcecache_path), basedir, wildcards,
params)
else:
source = None
is_local = True
path = infer_source_file(path)
exec_class = get_exec_class(language)
executor = exec_class(
path,
source,
basedir,
input,
output,
params,
wildcards,
threads,
resources,
log,
config,
rulename,
conda_env,
conda_base_path,
container_img,
singularity_args,
env_modules,
bench_record,
jobid,
bench_iteration,
cleanup_scripts,
shadow_dir,
is_local,
)
if edit is None:
executor.evaluate(edit=edit)
elif edit.draft_only:
executor.draft()
msg = "Generated skeleton notebook:\n{} ".format(path)
if conda_env and not container_img:
msg += (
"\n\nEditing with VSCode:\nOpen notebook, run command 'Select notebook kernel' (Ctrl+Shift+P or Cmd+Shift+P), and choose:"
"\n{}\n".format(
str(
Path(conda_env) / "bin" /
executor.get_interpreter_exec())))
msg += ("\nEditing with Jupyter CLI:"
"\nconda activate {}\njupyter notebook {}\n".format(
conda_env, path))
logger.info(msg)
elif draft:
executor.draft_and_edit(listen=edit)
else:
executor.evaluate(edit=edit)
def script(
path,
basedir,
input,
output,
params,
wildcards,
threads,
resources,
log,
config,
rulename,
conda_env,
conda_base_path,
container_img,
singularity_args,
env_modules,
bench_record,
jobid,
bench_iteration,
cleanup_scripts,
shadow_dir,
runtime_sourcecache_path,
):
"""
Load a script from the given basedir + path and execute it.
"""
path, source, language, is_local = get_source(
path, SourceCache(runtime_sourcecache_path), basedir, wildcards, params
)
exec_class = {
"python": PythonScript,
"r": RScript,
"rmarkdown": RMarkdown,
"julia": JuliaScript,
"rust": RustScript,
}.get(language, None)
if exec_class is None:
raise ValueError(
"Unsupported script: Expecting either Python (.py), R (.R), RMarkdown (.Rmd) or Julia (.jl) script."
)
executor = exec_class(
path,
source,
basedir,
input,
output,
params,
wildcards,
threads,
resources,
log,
config,
rulename,
conda_env,
conda_base_path,
container_img,
singularity_args,
env_modules,
bench_record,
jobid,
bench_iteration,
cleanup_scripts,
shadow_dir,
is_local,
)
executor.evaluate()