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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,159 @@ | ||
| import logging | ||
| import os | ||
| import shutil | ||
| from pathlib import Path | ||
|
|
||
| import yaml | ||
|
|
||
| from nf_core.modules.modules_json import ModulesJson | ||
| from nf_core.modules.modules_repo import ModulesRepo | ||
|
|
||
| from .components_utils import get_repo_type | ||
|
|
||
| log = logging.getLogger(__name__) | ||
|
|
||
|
|
||
| class ComponentCommand: | ||
| """ | ||
| Base class for the 'nf-core modules' and 'nf-core subworkflows' commands | ||
| """ | ||
|
|
||
| def __init__(self, component_type, dir, remote_url=None, branch=None, no_pull=False, hide_progress=False): | ||
| """ | ||
| Initialise the ComponentClass object | ||
| """ | ||
| self.component_type = component_type | ||
| self.dir = dir | ||
| self.modules_repo = ModulesRepo(remote_url, branch, no_pull, hide_progress) | ||
| self.hide_progress = hide_progress | ||
| self.default_modules_path = Path("modules", "nf-core") | ||
| self.default_tests_path = Path("tests", "modules", "nf-core") | ||
| self.default_subworkflows_path = Path("subworkflows", "nf-core") | ||
| self.default_subworkflows_tests_path = Path("tests", "subworkflows", "nf-core") | ||
| try: | ||
| if self.dir: | ||
| self.dir, self.repo_type = get_repo_type(self.dir) | ||
| else: | ||
| self.repo_type = None | ||
| except LookupError as e: | ||
| raise UserWarning(e) | ||
|
|
||
| def get_local_components(self): | ||
| """ | ||
| Get the local modules/subworkflows in a pipeline | ||
| """ | ||
| local_component_dir = Path(self.dir, 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): | ||
| """ | ||
| Get the modules/subworkflows repository available in a clone of nf-core/modules | ||
| """ | ||
| if self.component_type == "modules": | ||
| component_base_path = Path(self.dir, self.default_modules_path) | ||
| elif self.component_type == "subworkflows": | ||
| component_base_path = Path(self.dir, self.default_subworkflows_path) | ||
| return [ | ||
| str(Path(dir).relative_to(component_base_path)) | ||
| for dir, _, files in os.walk(component_base_path) | ||
| if "main.nf" in files | ||
| ] | ||
|
|
||
| def has_valid_directory(self): | ||
| """Check that we were given a pipeline or clone of nf-core/modules""" | ||
| if self.repo_type == "modules": | ||
| return True | ||
| if self.dir is None or not os.path.exists(self.dir): | ||
| log.error(f"Could not find directory: {self.dir}") | ||
| return False | ||
| main_nf = os.path.join(self.dir, "main.nf") | ||
| nf_config = os.path.join(self.dir, "nextflow.config") | ||
| if not os.path.exists(main_nf) and not os.path.exists(nf_config): | ||
| if Path(self.dir).resolve().parts[-1].startswith("nf-core"): | ||
| raise UserWarning(f"Could not find a 'main.nf' or 'nextflow.config' file in '{self.dir}'") | ||
| log.warning(f"Could not find a 'main.nf' or 'nextflow.config' file in '{self.dir}'") | ||
| return True | ||
|
|
||
| def has_modules_file(self): | ||
| """Checks whether a module.json file has been created and creates one if it is missing""" | ||
| modules_json_path = os.path.join(self.dir, "modules.json") | ||
| if not os.path.exists(modules_json_path): | ||
| log.info("Creating missing 'module.json' file.") | ||
| ModulesJson(self.dir).create() | ||
|
|
||
| def clear_component_dir(self, component_name, component_dir): | ||
| """Removes all files in the module/subworkflow directory""" | ||
| try: | ||
| shutil.rmtree(component_dir) | ||
| if self.component_type == "modules": | ||
| # Try cleaning up empty parent if tool/subtool and tool/ is empty | ||
| if component_name.count("/") > 0: | ||
| parent_dir = os.path.dirname(component_dir) | ||
| try: | ||
| os.rmdir(parent_dir) | ||
| except OSError: | ||
| log.debug(f"Parent directory not empty: '{parent_dir}'") | ||
| else: | ||
| log.debug(f"Deleted orphan tool directory: '{parent_dir}'") | ||
| log.debug(f"Successfully removed {component_name} {self.component_type[:-1]}") | ||
| return True | ||
| except OSError as e: | ||
| log.error(f"Could not remove {self.component_type[:-1]}: {e}") | ||
| return False | ||
|
|
||
| def components_from_repo(self, install_dir): | ||
| """ | ||
| 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.dir, 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, component_version, modules_repo, install_dir): | ||
| """ | ||
| 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): 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): | ||
| """Parse a pipeline lint config file. | ||
| Look for a file called either `.nf-core-lint.yml` or | ||
| `.nf-core-lint.yaml` in the pipeline root directory and parse it. | ||
| (`.yml` takes precedence). | ||
| Add parsed config to the `self.lint_config` class attribute. | ||
| """ | ||
| config_fn = os.path.join(self.dir, ".nf-core-lint.yml") | ||
|
|
||
| # Pick up the file if it's .yaml instead of .yml | ||
| if not os.path.isfile(config_fn): | ||
| config_fn = os.path.join(self.dir, ".nf-core-lint.yaml") | ||
|
|
||
| # Load the YAML | ||
| try: | ||
| with open(config_fn, "r") as fh: | ||
| self.lint_config = yaml.safe_load(fh) | ||
| except FileNotFoundError: | ||
| log.debug(f"No lint config file found: {config_fn}") |
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