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components_command.py
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import logging
import mmap
import os
import shutil
from pathlib import Path
from typing import Dict, List, Optional, Union
import nf_core.utils
from nf_core.modules.modules_json import ModulesJson
from nf_core.modules.modules_repo import ModulesRepo
from .components_utils import get_repo_info
log = logging.getLogger(__name__)
class ComponentCommand:
"""
Base class for the 'nf-core modules' and 'nf-core subworkflows' commands
"""
def __init__(
self,
component_type: str,
directory: Union[str, Path] = ".",
remote_url: Optional[str] = None,
branch: Optional[str] = None,
no_pull: bool = False,
hide_progress: bool = False,
no_prompts: bool = False,
) -> None:
"""
Initialise the ComponentClass object
"""
self.component_type: str = component_type
self.directory: Path = Path(directory)
self.modules_repo = ModulesRepo(remote_url, branch, no_pull, hide_progress)
self.hide_progress: bool = hide_progress
self.no_prompts: bool = no_prompts
self.repo_type: Optional[str] = None
self.org: str = ""
self._configure_repo_and_paths()
def _configure_repo_and_paths(self, nf_dir_req: bool = True) -> None:
"""
Determine the repo type and set some default paths.
If this is a modules repo, determine the org_path too.
Args:
nf_dir_req (bool, optional): Whether this command requires being run in the nf-core modules repo or a nf-core pipeline repository. Defaults to True.
"""
try:
if self.directory:
if self.directory == Path(".") and not nf_dir_req:
self.no_prompts = True
self.directory, self.repo_type, self.org = get_repo_info(self.directory, use_prompt=not self.no_prompts)
except UserWarning:
if nf_dir_req:
raise
except FileNotFoundError:
raise
self.default_modules_path = Path("modules", self.org)
self.default_tests_path = Path("tests", "modules", self.org)
self.default_subworkflows_path = Path("subworkflows", self.org)
self.default_subworkflows_tests_path = Path("tests", "subworkflows", self.org)
def get_local_components(self) -> List[str]:
"""
Get the local modules/subworkflows in a pipeline
"""
local_component_dir = Path(self.directory, self.component_type, "local")
return [
str(path.relative_to(local_component_dir)) for path in local_component_dir.iterdir() if path.suffix == ".nf"
]
def get_components_clone_modules(self) -> List[str]:
"""
Get the modules/subworkflows repository available in a clone of nf-core/modules
"""
if self.component_type == "modules":
component_base_path = Path(self.directory, self.default_modules_path)
elif self.component_type == "subworkflows":
component_base_path = Path(self.directory, self.default_subworkflows_path)
return [
str(Path(directory).relative_to(component_base_path))
for directory, _, files in os.walk(component_base_path)
if "main.nf" in files
]
def has_valid_directory(self) -> bool:
"""Check that we were given a pipeline or clone of nf-core/modules"""
if self.repo_type == "modules":
return True
if not self.directory.exists():
log.error(f"Could not find directory: {self.directory}")
return False
main_nf = Path(self.directory, "main.nf")
nf_config = Path(self.directory, "nextflow.config")
if not main_nf.exists() and not nf_config.exists():
if self.directory.resolve().parts[-1].startswith("nf-core"):
raise UserWarning(f"Could not find a 'main.nf' or 'nextflow.config' file in '{self.directory}'")
log.warning(f"Could not find a 'main.nf' or 'nextflow.config' file in '{self.directory}'")
return True
def has_modules_file(self) -> None:
"""Checks whether a module.json file has been created and creates one if it is missing"""
modules_json_path = Path(self.directory, "modules.json")
if not modules_json_path.exists():
log.info("Creating missing 'module.json' file.")
ModulesJson(self.directory).create()
def clear_component_dir(self, component_name: str, component_dir: Union[str, Path]) -> bool:
"""
Removes all files in the module/subworkflow directory
Args:
component_name (str): The name of the module/subworkflow
component_dir (str, Path): The path to the module/subworkflow
"""
try:
shutil.rmtree(component_dir)
# remove all empty directories
for dir_path, dir_names, filenames in os.walk(self.directory, topdown=False):
if not dir_names and not filenames:
try:
Path(dir_path).rmdir()
except OSError:
pass
else:
log.debug(f"Deleted directory: '{dir_path}'")
log.debug(f"Successfully removed {self.component_type[:-1]} {component_name}")
return True
except OSError as e:
log.error(f"Could not remove {self.component_type[:-1]} {component_name}: {e}")
return False
def components_from_repo(self, install_dir: str) -> List[str]:
"""
Gets the modules/subworkflows installed from a certain repository
Args:
install_dir (str): The name of the directory where modules/subworkflows are installed
Returns:
[str]: The names of the modules/subworkflows
"""
repo_dir = Path(self.directory, self.component_type, install_dir)
if not repo_dir.exists():
raise LookupError(f"Nothing installed from {install_dir} in pipeline")
return [
str(Path(dir_path).relative_to(repo_dir)) for dir_path, _, files in os.walk(repo_dir) if "main.nf" in files
]
def install_component_files(
self, component_name: str, component_version: str, modules_repo: ModulesRepo, install_dir: Union[str, Path]
) -> bool:
"""
Installs a module/subworkflow into the given directory
Args:
component_name (str): The name of the module/subworkflow
component_version (str): Git SHA for the version of the module/subworkflow to be installed
modules_repo (ModulesRepo): A correctly configured ModulesRepo object
install_dir (str, Path): The path to where the module/subworkflow should be installed (should be the 'modules/' or 'subworkflows/' dir of the pipeline)
Returns:
(bool): Whether the operation was successful of not
"""
return modules_repo.install_component(component_name, install_dir, component_version, self.component_type)
def load_lint_config(self) -> None:
"""Parse a pipeline lint config file.
Load the '.nf-core.yml' config file and extract
the lint config from it
Add parsed config to the `self.lint_config` class attribute.
"""
_, tools_config = nf_core.utils.load_tools_config(self.directory)
if tools_config is None:
raise UserWarning("Could not load `.nf-core.yml` file.")
else:
self.lint_config = tools_config.get("lint", {})
def check_modules_structure(self) -> None:
"""
Check that the structure of the modules directory in a pipeline is the correct one:
modules/nf-core/TOOL/SUBTOOL
Prior to nf-core/tools release 2.6 the directory structure had an additional level of nesting:
modules/nf-core/modules/TOOL/SUBTOOL
"""
if self.repo_type == "pipeline":
wrong_location_modules: List[Path] = []
for directory, _, files in os.walk(Path(self.directory, "modules")):
if "main.nf" in files:
module_path = Path(directory).relative_to(Path(self.directory, "modules"))
parts = module_path.parts
# Check that there are modules installed directly under the 'modules' directory
if parts[1] == "modules":
wrong_location_modules.append(module_path)
# If there are modules installed in the wrong location
if len(wrong_location_modules) > 0:
log.info("The modules folder structure is outdated. Reinstalling modules.")
# Remove the local copy of the modules repository
log.info(f"Updating '{self.modules_repo.local_repo_dir}'")
self.modules_repo.setup_local_repo(
self.modules_repo.remote_url, self.modules_repo.branch, self.hide_progress
)
# Move wrong modules to the right directory
for module in wrong_location_modules:
modules_dir = Path("modules").resolve()
correct_dir = Path(modules_dir, self.modules_repo.repo_path, Path(*module.parts[2:]))
wrong_dir = Path(modules_dir, module)
shutil.move(str(wrong_dir), str(correct_dir))
log.info(f"Moved {wrong_dir} to {correct_dir}.")
shutil.rmtree(Path(self.directory, "modules", self.modules_repo.repo_path, "modules"))
# Regenerate modules.json file
modules_json = ModulesJson(self.directory)
modules_json.check_up_to_date()
def check_patch_paths(self, patch_path: Path, module_name: str) -> None:
"""
Check that paths in patch files are updated to the new modules path
"""
if patch_path.exists():
log.info(f"Modules {module_name} contains a patch file.")
rewrite = False
with open(patch_path) as fh:
lines = fh.readlines()
for index, line in enumerate(lines):
# Check if there are old paths in the patch file and replace
if f"modules/{self.modules_repo.repo_path}/modules/{module_name}/" in line:
rewrite = True
lines[index] = line.replace(
f"modules/{self.modules_repo.repo_path}/modules/{module_name}/",
f"modules/{self.modules_repo.repo_path}/{module_name}/",
)
if rewrite:
log.info(f"Updating paths in {patch_path}")
with open(patch_path, "w") as fh:
for line in lines:
fh.write(line)
# Update path in modules.json if the file is in the correct format
modules_json = ModulesJson(self.directory)
modules_json.load()
if (
modules_json.has_git_url_and_modules()
and self.modules_repo.repo_path is not None
and modules_json.modules_json is not None
):
modules_json.modules_json["repos"][self.modules_repo.remote_url]["modules"][
self.modules_repo.repo_path
][module_name]["patch"] = str(patch_path.relative_to(self.directory.resolve()))
modules_json.dump()
def check_if_in_include_stmts(self, component_path: str) -> Dict[str, List[Dict[str, Union[int, str]]]]:
"""
Checks for include statements in the main.nf file of the pipeline and a list of line numbers where the component is included
Args:
component_path (str): The path to the module/subworkflow
Returns:
(list): A list of dictionaries, with the workflow file and the line number where the component is included
"""
include_stmts: Dict[str, List[Dict[str, Union[int, str]]]] = {}
if self.repo_type == "pipeline":
workflow_files = Path(self.directory, "workflows").glob("*.nf")
for workflow_file in workflow_files:
with open(workflow_file) as fh:
# Check if component path is in the file using mmap
with mmap.mmap(fh.fileno(), 0, access=mmap.ACCESS_READ) as s:
if s.find(component_path.encode()) != -1:
# If the component path is in the file, check for include statements
for i, line in enumerate(fh):
if line.startswith("include") and component_path in line:
if str(workflow_file) not in include_stmts:
include_stmts[str(workflow_file)] = []
include_stmts[str(workflow_file)].append(
{"line_number": i + 1, "line": line.rstrip()}
)
return include_stmts
else:
log.debug("Not a pipeline repository, skipping check for include statements")
return include_stmts