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Merge pull request nf-core#1447 from ewels/modules-info
New modules command: nf-core modules info <tool>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,194 @@ | ||
| import base64 | ||
| import logging | ||
| import os | ||
| import requests | ||
| import yaml | ||
|
|
||
| from rich import box | ||
| from rich.text import Text | ||
| from rich.console import Group | ||
| from rich.markdown import Markdown | ||
| from rich.panel import Panel | ||
| from rich.table import Table | ||
|
|
||
| from .modules_command import ModuleCommand | ||
| from .module_utils import get_repo_type, get_installed_modules, get_module_git_log, module_exist_in_repo | ||
| from .modules_repo import ModulesRepo | ||
|
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| log = logging.getLogger(__name__) | ||
|
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|
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| class ModuleInfo(ModuleCommand): | ||
| def __init__(self, pipeline_dir, tool): | ||
|
|
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| self.module = tool | ||
| self.meta = None | ||
| self.local_path = None | ||
| self.remote_location = None | ||
|
|
||
| # Quietly check if this is a pipeline or not | ||
| if pipeline_dir: | ||
| try: | ||
| pipeline_dir, repo_type = get_repo_type(pipeline_dir, use_prompt=False) | ||
| log.debug(f"Found {repo_type} repo: {pipeline_dir}") | ||
| except UserWarning as e: | ||
| log.debug(f"Only showing remote info: {e}") | ||
| pipeline_dir = None | ||
|
|
||
| super().__init__(pipeline_dir) | ||
|
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| def get_module_info(self): | ||
| """Given the name of a module, parse meta.yml and print usage help.""" | ||
|
|
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| # Running with a local install, try to find the local meta | ||
| if self.dir: | ||
| self.meta = self.get_local_yaml() | ||
|
|
||
| # Either failed locally or in remote mode | ||
| if not self.meta: | ||
| self.meta = self.get_remote_yaml() | ||
|
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| # Could not find the meta | ||
| if self.meta == False: | ||
| raise UserWarning(f"Could not find module '{self.module}'") | ||
|
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| return self.generate_module_info_help() | ||
|
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||
| def get_local_yaml(self): | ||
| """Attempt to get the meta.yml file from a locally installed module. | ||
| Returns: | ||
| dict or bool: Parsed meta.yml found, False otherwise | ||
| """ | ||
|
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||
| # Get installed modules | ||
| self.get_pipeline_modules() | ||
|
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||
| # Try to find and load the meta.yml file | ||
| module_base_path = f"{self.dir}/modules/" | ||
| if self.repo_type == "modules": | ||
| module_base_path = f"{self.dir}/" | ||
| for dir, mods in self.module_names.items(): | ||
| for mod in mods: | ||
| if mod == self.module: | ||
| mod_dir = os.path.join(module_base_path, dir, mod) | ||
| meta_fn = os.path.join(mod_dir, "meta.yml") | ||
| if os.path.exists(meta_fn): | ||
| log.debug(f"Found local file: {meta_fn}") | ||
| with open(meta_fn, "r") as fh: | ||
| self.local_path = mod_dir | ||
| return yaml.safe_load(fh) | ||
|
|
||
| log.debug(f"Module '{self.module}' meta.yml not found locally") | ||
| return False | ||
|
|
||
| def get_remote_yaml(self): | ||
| """Attempt to get the meta.yml file from a remote repo. | ||
| Returns: | ||
| dict or bool: Parsed meta.yml found, False otherwise | ||
| """ | ||
| # Fetch the remote repo information | ||
| self.modules_repo.get_modules_file_tree() | ||
|
|
||
| # Check if our requested module is there | ||
| if self.module not in self.modules_repo.modules_avail_module_names: | ||
| return False | ||
|
|
||
| # Get the remote path | ||
| meta_url = None | ||
| for file_dict in self.modules_repo.modules_file_tree: | ||
| if file_dict.get("path") == f"modules/{self.module}/meta.yml": | ||
| meta_url = file_dict.get("url") | ||
|
|
||
| if not meta_url: | ||
| return False | ||
|
|
||
| # Download and parse | ||
| log.debug(f"Attempting to fetch {meta_url}") | ||
| response = requests.get(meta_url) | ||
| result = response.json() | ||
| file_contents = base64.b64decode(result["content"]) | ||
| self.remote_location = self.modules_repo.name | ||
| return yaml.safe_load(file_contents) | ||
|
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||
| def generate_module_info_help(self): | ||
| """Take the parsed meta.yml and generate rich help. | ||
| Returns: | ||
| rich renderable | ||
| """ | ||
|
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||
| renderables = [] | ||
|
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||
| # Intro panel | ||
| intro_text = Text() | ||
| if self.local_path: | ||
| intro_text.append(Text.from_markup(f"Location: [blue]{self.local_path}\n")) | ||
| elif self.remote_location: | ||
| intro_text.append( | ||
| Text.from_markup( | ||
| f":globe_with_meridians: Repository: [link=https://github.com/{self.remote_location}]{self.remote_location}[/]\n" | ||
| ) | ||
| ) | ||
|
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||
| if self.meta.get("tools"): | ||
| tools_strings = [] | ||
| for tool in self.meta["tools"]: | ||
| for tool_name, tool_meta in tool.items(): | ||
| tools_strings.append(f"[link={tool_meta['homepage']}]{tool_name}") | ||
| intro_text.append(Text.from_markup(f":wrench: Tools: {', '.join(tools_strings)}\n", style="dim")) | ||
|
|
||
| if self.meta.get("description"): | ||
| intro_text.append(Text.from_markup(f":book: Description: {self.meta['description']}", style="dim")) | ||
|
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| renderables.append( | ||
| Panel( | ||
| intro_text, | ||
| title=f"[bold]Module: [green]{self.module}\n", | ||
| title_align="left", | ||
| ) | ||
| ) | ||
|
|
||
| # Inputs | ||
| if self.meta.get("input"): | ||
| inputs_table = Table(expand=True, show_lines=True, box=box.MINIMAL_HEAVY_HEAD, padding=0) | ||
| inputs_table.add_column(":inbox_tray: Inputs") | ||
| inputs_table.add_column("Description") | ||
| inputs_table.add_column("Pattern", justify="right", style="green") | ||
| for input in self.meta["input"]: | ||
| for key, info in input.items(): | ||
| inputs_table.add_row( | ||
| f"[orange1 on black] {key} [/][dim i] ({info['type']})", | ||
| Markdown(info["description"] if info["description"] else ""), | ||
| info.get("pattern", ""), | ||
| ) | ||
|
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| renderables.append(inputs_table) | ||
|
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||
| # Outputs | ||
| if self.meta.get("output"): | ||
| outputs_table = Table(expand=True, show_lines=True, box=box.MINIMAL_HEAVY_HEAD, padding=0) | ||
| outputs_table.add_column(":outbox_tray: Outputs") | ||
| outputs_table.add_column("Description") | ||
| outputs_table.add_column("Pattern", justify="right", style="green") | ||
| for output in self.meta["output"]: | ||
| for key, info in output.items(): | ||
| outputs_table.add_row( | ||
| f"[orange1 on black] {key} [/][dim i] ({info['type']})", | ||
| Markdown(info["description"] if info["description"] else ""), | ||
| info.get("pattern", ""), | ||
| ) | ||
|
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| renderables.append(outputs_table) | ||
|
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||
| # Installation command | ||
| if self.remote_location: | ||
| cmd_base = "nf-core modules" | ||
| if self.remote_location != "nf-core/modules": | ||
| cmd_base = f"nf-core modules --github-repository {self.remote_location}" | ||
| renderables.append( | ||
| Text.from_markup(f"\n :computer: Installation command: [magenta]{cmd_base} install {self.module}\n") | ||
| ) | ||
|
|
||
| return Group(*renderables) |
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