create.py

#!/usr/bin/env python
"""Creates a nf-core pipeline matching the current
organization's specification based on a template.
"""
import configparser
import imghdr
import logging
import os
import pathlib
import random
import re
import shutil
import subprocess
import sys
import time

import git
import jinja2
import questionary
import requests
import yaml

import nf_core
import nf_core.schema
import nf_core.utils

log = logging.getLogger(__name__)


class PipelineCreate(object):
    """Creates a nf-core pipeline a la carte from the nf-core best-practice template.

    Args:
        name (str): Name for the pipeline.
        description (str): Description for the pipeline.
        author (str): Authors name of the pipeline.
        version (str): Version flag. Semantic versioning only. Defaults to `1.0dev`.
        no_git (bool): Prevents the creation of a local Git repository for the pipeline. Defaults to False.
        force (bool): Overwrites a given workflow directory with the same name. Defaults to False.
            May the force be with you.
        outdir (str): Path to the local output directory.
    """

    def __init__(
        self,
        name,
        description,
        author,
        version="1.0dev",
        no_git=False,
        force=False,
        outdir=None,
        template_yaml_path=None,
        plain=False,
    ):
        self.template_params, skip_paths_keys = self.create_param_dict(
            name, description, author, version, template_yaml_path, plain
        )

        skippable_paths = {
            "github": [
                ".github/",
                ".gitignore",
            ],
            "ci": [".github/workflows/"],
            "igenomes": ["conf/igenomes.config"],
            "branded": [
                ".github/ISSUE_TEMPLATE/config",
                "CODE_OF_CONDUCT.md",
                ".github/workflows/awsfulltest.yml",
                ".github/workflows/awstest.yml",
            ],
        }
        # Get list of files we're skipping with the supplied skip keys
        self.skip_paths = set(sp for k in skip_paths_keys for sp in skippable_paths[k])

        # Set convenience variables
        self.name = self.template_params["name"]

        # Set fields used by the class methods
        self.no_git = (
            no_git if self.template_params["github"] else True
        )  # Set to True if template was configured without github hosting
        self.force = force
        if outdir is None:
            outdir = os.path.join(os.getcwd(), self.template_params["name_noslash"])
        self.outdir = outdir

    def create_param_dict(self, name, description, author, version, template_yaml_path, plain):
        """Creates a dictionary of parameters for the new pipeline.

        Args:
            template_yaml_path (str): Path to YAML file containing template parameters.
        """
        try:
            if template_yaml_path is not None:
                with open(template_yaml_path, "r") as f:
                    template_yaml = yaml.safe_load(f)
            else:
                template_yaml = {}
        except FileNotFoundError:
            raise UserWarning(f"Template YAML file '{template_yaml_path}' not found.")

        param_dict = {}
        # Get the necessary parameters either from the template or command line arguments
        param_dict["name"] = self.get_param("name", name, template_yaml, template_yaml_path)
        param_dict["description"] = self.get_param("description", description, template_yaml, template_yaml_path)
        param_dict["author"] = self.get_param("author", author, template_yaml, template_yaml_path)

        if "version" in template_yaml:
            if version is not None:
                log.info(f"Overriding --version with version found in {template_yaml_path}")
            version = template_yaml["version"]
        param_dict["version"] = version

        # Define the different template areas, and what actions to take for each
        # if they are skipped
        template_areas = {
            "github": {"name": "GitHub hosting", "file": True, "content": False},
            "ci": {"name": "GitHub CI", "file": True, "content": False},
            "github_badges": {"name": "GitHub badges", "file": False, "content": True},
            "igenomes": {"name": "iGenomes config", "file": True, "content": True},
            "nf_core_configs": {"name": "nf-core/configs", "file": False, "content": True},
        }

        # Once all necessary parameters are set, check if the user wants to customize the template more
        if template_yaml_path is None and not plain:
            customize_template = questionary.confirm(
                "Do you want to customize which parts of the template are used?",
                style=nf_core.utils.nfcore_question_style,
                default=False,
            ).unsafe_ask()
            if customize_template:
                template_yaml.update(self.customize_template(template_areas))

        # Now look in the template for more options, otherwise default to nf-core defaults
        param_dict["prefix"] = template_yaml.get("prefix", "nf-core")
        param_dict["branded"] = param_dict["prefix"] == "nf-core"

        skip_paths = [] if param_dict["branded"] else ["branded"]

        for t_area in template_areas:
            if t_area in template_yaml.get("skip", []):
                if template_areas[t_area]["file"]:
                    skip_paths.append(t_area)
                param_dict[t_area] = False
            else:
                param_dict[t_area] = True
        # If github is selected, exclude also github_badges
        if not param_dict["github"]:
            param_dict["github_badges"] = False

        # Set the last parameters based on the ones provided
        param_dict["short_name"] = (
            param_dict["name"].lower().replace(r"/\s+/", "-").replace(f"{param_dict['prefix']}/", "").replace("/", "-")
        )
        param_dict["name"] = f"{param_dict['prefix']}/{param_dict['short_name']}"
        param_dict["name_noslash"] = param_dict["name"].replace("/", "-")
        param_dict["prefix_nodash"] = param_dict["prefix"].replace("-", "")
        param_dict["name_docker"] = param_dict["name"].replace(param_dict["prefix"], param_dict["prefix_nodash"])
        param_dict["logo_light"] = f"{param_dict['name_noslash']}_logo_light.png"
        param_dict["logo_dark"] = f"{param_dict['name_noslash']}_logo_dark.png"
        param_dict["version"] = version

        return param_dict, skip_paths

    def customize_template(self, template_areas):
        """Customizes the template parameters.

        Args:
            name (str): Name for the pipeline.
            description (str): Description for the pipeline.
            author (str): Authors name of the pipeline.
        """
        template_yaml = {}
        prefix = questionary.text("Pipeline prefix", style=nf_core.utils.nfcore_question_style).unsafe_ask()
        while not re.match(r"^[a-zA-Z_][a-zA-Z0-9-_]*$", prefix):
            log.error("[red]Pipeline prefix cannot start with digit or hyphen and cannot contain punctuation.[/red]")
            prefix = questionary.text(
                "Please provide a new pipeline prefix", style=nf_core.utils.nfcore_question_style
            ).unsafe_ask()
        template_yaml["prefix"] = prefix

        choices = [{"name": template_areas[area]["name"], "value": area} for area in template_areas]
        template_yaml["skip"] = questionary.checkbox(
            "Skip template areas?", choices=choices, style=nf_core.utils.nfcore_question_style
        ).unsafe_ask()
        return template_yaml

    def get_param(self, param_name, passed_value, template_yaml, template_yaml_path):
        if param_name in template_yaml:
            if passed_value is not None:
                log.info(f"overriding --{param_name} with name found in {template_yaml_path}")
            passed_value = template_yaml[param_name]
        if passed_value is None:
            passed_value = getattr(self, f"prompt_wf_{param_name}")()
        return passed_value

    def prompt_wf_name(self):
        wf_name = questionary.text("Workflow name", style=nf_core.utils.nfcore_question_style).unsafe_ask()
        while not re.match(r"^[a-z]+$", wf_name):
            log.error("[red]Invalid workflow name: must be lowercase without punctuation.")
            wf_name = questionary.text(
                "Please provide a new workflow name", style=nf_core.utils.nfcore_question_style
            ).unsafe_ask()
        return wf_name

    def prompt_wf_description(self):
        wf_description = questionary.text("Description", style=nf_core.utils.nfcore_question_style).unsafe_ask()
        return wf_description

    def prompt_wf_author(self):
        wf_author = questionary.text("Author", style=nf_core.utils.nfcore_question_style).unsafe_ask()
        return wf_author

    def init_pipeline(self):
        """Creates the nf-core pipeline."""

        # Make the new pipeline
        self.render_template()

        # Init the git repository and make the first commit
        if not self.no_git:
            self.git_init_pipeline()

        if self.template_params["branded"]:
            log.info(
                "[green bold]!!!!!! IMPORTANT !!!!!!\n\n"
                + "[green not bold]If you are interested in adding your pipeline to the nf-core community,\n"
                + "PLEASE COME AND TALK TO US IN THE NF-CORE SLACK BEFORE WRITING ANY CODE!\n\n"
                + "[default]Please read: [link=https://nf-co.re/developers/adding_pipelines#join-the-community]https://nf-co.re/developers/adding_pipelines#join-the-community[/link]"
            )

    def render_template(self):
        """Runs Jinja to create a new nf-core pipeline."""
        log.info(f"Creating new nf-core pipeline: '{self.name}'")

        # Check if the output directory exists
        if os.path.exists(self.outdir):
            if self.force:
                log.warning(f"Output directory '{self.outdir}' exists - continuing as --force specified")
            else:
                log.error(f"Output directory '{self.outdir}' exists!")
                log.info("Use -f / --force to overwrite existing files")
                sys.exit(1)
        else:
            os.makedirs(self.outdir)

        # Run jinja2 for each file in the template folder
        env = jinja2.Environment(
            loader=jinja2.PackageLoader("nf_core", "pipeline-template"), keep_trailing_newline=True
        )
        template_dir = os.path.join(os.path.dirname(__file__), "pipeline-template")
        object_attrs = self.template_params
        object_attrs["nf_core_version"] = nf_core.__version__

        # Can't use glob.glob() as need recursive hidden dotfiles - https://stackoverflow.com/a/58126417/713980
        template_files = list(pathlib.Path(template_dir).glob("**/*"))
        template_files += list(pathlib.Path(template_dir).glob("*"))
        ignore_strs = [".pyc", "__pycache__", ".pyo", ".pyd", ".DS_Store", ".egg"]
        rename_files = {
            "workflows/pipeline.nf": f"workflows/{self.template_params['short_name']}.nf",
            "lib/WorkflowPipeline.groovy": f"lib/Workflow{self.template_params['short_name'][0].upper()}{self.template_params['short_name'][1:]}.groovy",
        }

        # Set the paths to skip according to customization
        for template_fn_path_obj in template_files:

            template_fn_path = str(template_fn_path_obj)

            # Skip files that are in the self.skip_paths list
            for skip_path in self.skip_paths:
                if os.path.relpath(template_fn_path, template_dir).startswith(skip_path):
                    break
            else:
                if os.path.isdir(template_fn_path):
                    continue
                if any([s in template_fn_path for s in ignore_strs]):
                    log.debug(f"Ignoring '{template_fn_path}' in jinja2 template creation")
                    continue

                # Set up vars and directories
                template_fn = os.path.relpath(template_fn_path, template_dir)
                output_path = os.path.join(self.outdir, template_fn)
                if template_fn in rename_files:
                    output_path = os.path.join(self.outdir, rename_files[template_fn])
                os.makedirs(os.path.dirname(output_path), exist_ok=True)

                try:
                    # Just copy binary files
                    if nf_core.utils.is_file_binary(template_fn_path):
                        raise AttributeError(f"Binary file: {template_fn_path}")

                    # Got this far - render the template
                    log.debug(f"Rendering template file: '{template_fn}'")
                    j_template = env.get_template(template_fn)
                    rendered_output = j_template.render(object_attrs)

                    # Write to the pipeline output file
                    with open(output_path, "w") as fh:
                        log.debug(f"Writing to output file: '{output_path}'")
                        fh.write(rendered_output)

                # Copy the file directly instead of using Jinja
                except (AttributeError, UnicodeDecodeError) as e:
                    log.debug(f"Copying file without Jinja: '{output_path}' - {e}")
                    shutil.copy(template_fn_path, output_path)

                # Something else went wrong
                except Exception as e:
                    log.error(f"Copying raw file as error rendering with Jinja: '{output_path}' - {e}")
                    shutil.copy(template_fn_path, output_path)

                # Mirror file permissions
                template_stat = os.stat(template_fn_path)
                os.chmod(output_path, template_stat.st_mode)

        # Remove all unused parameters in the nextflow schema
        if not self.template_params["igenomes"] or not self.template_params["nf_core_configs"]:
            self.update_nextflow_schema()

        if self.template_params["branded"]:
            # Make a logo and save it, if it is a nf-core pipeline
            self.make_pipeline_logo()
        else:
            if self.template_params["github"]:
                # Remove field mentioning nf-core docs
                # in the github bug report template
                self.remove_nf_core_in_bug_report_template()

            # Update the .nf-core.yml with linting configurations
            self.fix_linting()

    def update_nextflow_schema(self):
        """
        Removes unused parameters from the nextflow schema.
        """
        schema_path = os.path.join(self.outdir, "nextflow_schema.json")

        schema = nf_core.schema.PipelineSchema()
        schema.schema_filename = schema_path
        schema.no_prompts = True
        schema.load_schema()
        schema.get_wf_params()
        schema.remove_schema_notfound_configs()
        schema.save_schema(suppress_logging=True)

        # The schema is not guaranteed to follow Prettier standards
        # so we run prettier on the schema file
        try:
            subprocess.run(
                ["prettier", "--write", schema_path], stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL, check=False
            )
        except FileNotFoundError:
            log.warning("Prettier not found. Please install it and run it on the pipeline to fix linting issues.")

    def remove_nf_core_in_bug_report_template(self):
        """
        Remove the field mentioning nf-core documentation
        in the github bug report template
        """
        bug_report_path = os.path.join(self.outdir, ".github", "ISSUE_TEMPLATE", "bug_report.yml")

        with open(bug_report_path, "r") as fh:
            contents = yaml.load(fh, Loader=yaml.FullLoader)

        # Remove the first item in the body, which is the information about the docs
        contents["body"].pop(0)

        with open(bug_report_path, "w") as fh:
            yaml.dump(contents, fh, default_flow_style=False, sort_keys=False)

        # The dumped yaml file will not follow prettier formatting rules
        # so we run prettier on the file
        try:
            subprocess.run(
                ["prettier", "--write", bug_report_path],
                stdout=subprocess.DEVNULL,
                stderr=subprocess.DEVNULL,
                check=False,
            )
        except FileNotFoundError:
            log.warning("Prettier not found. Please install it and run it on the pipeline to fix linting issues.")

    def fix_linting(self):
        """
        Updates the .nf-core.yml with linting configurations
        for a customized pipeline.
        """
        # Create a lint config
        short_name = self.template_params["short_name"]
        lint_config = {
            "files_exist": [
                "CODE_OF_CONDUCT.md",
                f"assets/nf-core-{short_name}_logo_light.png",
                f"docs/images/nf-core-{short_name}_logo_light.png",
                f"docs/images/nf-core-{short_name}_logo_dark.png",
                ".github/ISSUE_TEMPLATE/config.yml",
                ".github/workflows/awstest.yml",
                ".github/workflows/awsfulltest.yml",
            ],
            "nextflow_config": [
                "manifest.name",
                "manifest.homePage",
            ],
            "multiqc_config": ["report_comment"],
        }

        # Add GitHub hosting specific configurations
        if not self.template_params["github"]:
            lint_config["files_exist"].extend(
                [
                    ".github/ISSUE_TEMPLATE/bug_report.yml",
                ]
            )
            lint_config["files_unchanged"] = [".github/ISSUE_TEMPLATE/bug_report.yml"]

        # Add CI specific configurations
        if not self.template_params["ci"]:
            lint_config["files_exist"].extend(
                [
                    ".github/workflows/branch.yml",
                    ".github/workflows/ci.yml",
                    ".github/workflows/linting_comment.yml",
                    ".github/workflows/linting.yml",
                ]
            )

        # Add custom config specific configurations
        if not self.template_params["nf_core_configs"]:
            lint_config["files_exist"].extend(["conf/igenomes.config"])
            lint_config["nextflow_config"].extend(
                [
                    "process.cpus",
                    "process.memory",
                    "process.time",
                    "custom_config",
                ]
            )

        # Add github badges specific configurations
        if not self.template_params["github_badges"] or not self.template_params["github"]:
            lint_config["readme"] = ["nextflow_badge"]

        # Add the lint content to the preexisting nf-core config
        nf_core_yml = nf_core.utils.load_tools_config(self.outdir)
        nf_core_yml["lint"] = lint_config
        with open(os.path.join(self.outdir, ".nf-core.yml"), "w") as fh:
            yaml.dump(nf_core_yml, fh, default_flow_style=False, sort_keys=False)

        # The dumped yaml file will not follow prettier formatting rules
        # so we run prettier on the file
        try:
            subprocess.run(
                ["prettier", "--write", os.path.join(self.outdir, ".nf-core.yml")],
                stdout=subprocess.DEVNULL,
                stderr=subprocess.DEVNULL,
                check=False,
            )
        except FileNotFoundError:
            log.warning(
                "Prettier is not installed. Please install it and run it on the pipeline to fix linting issues."
            )

    def make_pipeline_logo(self):
        """Fetch a logo for the new pipeline from the nf-core website"""

        logo_url = f"https://nf-co.re/logo/{self.template_params['short_name']}?theme=light"
        log.debug(f"Fetching logo from {logo_url}")

        email_logo_path = f"{self.outdir}/assets/{self.template_params['name_noslash']}_logo_light.png"
        self.download_pipeline_logo(f"{logo_url}&w=400", email_logo_path)
        for theme in ["dark", "light"]:
            readme_logo_url = f"{logo_url}?w=600&theme={theme}"
            readme_logo_path = f"{self.outdir}/docs/images/{self.template_params['name_noslash']}_logo_{theme}.png"
            self.download_pipeline_logo(readme_logo_url, readme_logo_path)

    def download_pipeline_logo(self, url, img_fn):
        """Attempt to download a logo from the website. Retry if it fails."""
        os.makedirs(os.path.dirname(img_fn), exist_ok=True)
        attempt = 0
        max_attempts = 10
        retry_delay = 0  # x up to 10 each time, so first delay will be 1-100 seconds
        while attempt < max_attempts:
            # If retrying, wait a while
            if retry_delay > 0:
                log.info(f"Waiting {retry_delay} seconds before next image fetch attempt")
                time.sleep(retry_delay)

            attempt += 1
            # Use a random number to avoid the template sync hitting the website simultaneously for all pipelines
            retry_delay = random.randint(1, 100) * attempt
            log.debug(f"Fetching logo '{img_fn}' (attempt {attempt})")
            try:
                # Try to fetch the logo from the website
                r = requests.get(url, timeout=180)
                if r.status_code != 200:
                    raise UserWarning(f"Got status code {r.status_code}")
                # Check that the returned image looks right

            except (ConnectionError, UserWarning) as e:
                # Something went wrong - try again
                log.warning(e)
                log.error("Connection error - retrying")
                continue

            # Write the new logo to the file
            with open(img_fn, "wb") as fh:
                fh.write(r.content)
            # Check that the file looks valid
            image_type = imghdr.what(img_fn)
            if image_type != "png":
                log.error(f"Logo from the website didn't look like an image: '{image_type}'")
                continue

            # Got this far, presumably it's good - break the retry loop
            break

    def git_init_pipeline(self):
        """Initialises the new pipeline as a Git repository and submits first commit.

        Raises:
            UserWarning: if Git default branch is set to 'dev' or 'TEMPLATE'.
        """
        # Check that the default branch is not dev
        try:
            default_branch = git.config.GitConfigParser().get_value("init", "defaultBranch")
        except configparser.Error:
            default_branch = None
            log.debug("Could not read init.defaultBranch")
        if default_branch == "dev" or default_branch == "TEMPLATE":
            raise UserWarning(
                f"Your Git defaultBranch is set to '{default_branch}', which is incompatible with nf-core.\n"
                "This can be modified with the command [white on grey23] git config --global init.defaultBranch <NAME> [/]\n"
                "Pipeline git repository is not initialised."
            )
        # Initialise pipeline
        log.info("Initialising pipeline git repository")
        repo = git.Repo.init(self.outdir)
        repo.git.add(A=True)
        repo.index.commit(f"initial template build from nf-core/tools, version {nf_core.__version__}")
        # Add TEMPLATE branch to git repository
        repo.git.branch("TEMPLATE")
        repo.git.branch("dev")
        log.info(
            "Done. Remember to add a remote and push to GitHub:\n"
            f"[white on grey23] cd {self.outdir} \n"
            " git remote add origin git@github.com:USERNAME/REPO_NAME.git \n"
            " git push --all origin                                       "
        )
        log.info("This will also push your newly created dev branch and the TEMPLATE branch for syncing.")