@stencila/dockter/dist/RGenerator.js

"use strict";
var __importDefault = (this && this.__importDefault) || function (mod) {
    return (mod && mod.__esModule) ? mod : { "default": mod };
};
Object.defineProperty(exports, "__esModule", { value: true });
const PackageGenerator_1 = __importDefault(require("./PackageGenerator"));
/**
 * A Dockerfile generator for R packages
 */
class RGenerator extends PackageGenerator_1.default {
    constructor(urlFetcher, pkg, folder) {
        super(urlFetcher, pkg, folder);
        // Default to yesterday's date (to ensure MRAN is available for the date)
        // Set here as it is required in two methods below
        let date = this.package.datePublished;
        if (!date)
            date = (new Date(Date.now() - 24 * 3600 * 1000)).toISOString().substring(0, 10);
        this.date = date;
    }
    // Methods that override those in `Generator`.
    // See that class for documentation on what each function does
    applies() {
        return this.package.runtimePlatform === 'R';
    }
    envVars(sysVersion) {
        return [
            // Set the timezone to avoid warning from Sys.timezone()
            // See https://github.com/rocker-org/rocker-versioned/issues/89
            ['TZ', 'Etc/UTC']
        ];
    }
    aptKeysCommand(sysVersion) {
        return 'apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 51716619E084DAB9';
    }
    aptRepos(base) {
        let version = this.baseVersionName(base);
        // At time of writing, MRAN did not have an ubuntu:18.04(bionic) repo which supported R 3.4 (only bionic_3.5)
        // See https://cran.microsoft.com/snapshot/2018-11-05/bin/linux/ubuntu/
        // So append that to the deb line
        if (version === 'bionic')
            version += '-cran35';
        return [
            `deb https://mran.microsoft.com/snapshot/${this.date}/bin/linux/ubuntu ${version}/`
        ];
    }
    aptPackages(sysVersion) {
        let pkgs = [
            'r-base'
        ];
        /**
         * Recurse through `softwareRequirements` and find any deb packages
         */
        function find(pkg) {
            if (pkg.runtimePlatform !== 'R' || !pkg.softwareRequirements)
                return;
            for (let subpkg of pkg.softwareRequirements) {
                if (subpkg.runtimePlatform === 'deb')
                    pkgs.push(subpkg.name || '');
                else
                    find(subpkg);
            }
        }
        find(this.package);
        return pkgs;
    }
    stencilaInstall(sysVersion) {
        return `apt-get update \\
 && apt-get install -y  zlib1g-dev libxml2-dev pkg-config \\
 && apt-get autoremove -y \\
 && apt-get clean \\
 && rm -rf /var/lib/apt/lists/* \\
 && Rscript -e 'install.packages("devtools")' \\
 && Rscript -e 'source("https://bioconductor.org/biocLite.R"); biocLite("graph")' \\
 && Rscript -e 'devtools::install_github("r-lib/pkgbuild")' \\
 && Rscript -e 'devtools::install_github("stencila/r")'`;
    }
    installFiles(sysVersion) {
        // Copy user defined files if they exist
        if (this.exists('install.R'))
            return [['install.R', 'install.R']];
        if (this.exists('DESCRIPTION'))
            return [['DESCRIPTION', 'DESCRIPTION']];
        // Generate a .DESCRIPTION with valid name to copy into image
        const name = (this.package.name || 'unnamed').replace(/[^a-zA-Z0-9]/, '');
        const pkgs = this.filterPackages('R').map(pkg => pkg.name);
        let desc = `Package: ${name}
Version: 1.0.0
Date: ${this.date}
Description: Generated by Dockter ${new Date().toISOString()}.
  To stop Dockter generating this file and start editing it yourself, rename it to "DESCRIPTION".
`;
        if (pkgs.length)
            desc += `Imports:\n  ${pkgs.join(',\n  ')}\n`;
        this.write('.DESCRIPTION', desc);
        return [['.DESCRIPTION', 'DESCRIPTION']];
    }
    installCommand(sysVersion) {
        if (this.exists('install.R')) {
            // Run the user supplied installation script
            return `Rscript install.R`;
        }
        else if (this.exists('DESCRIPTION') || this.exists('.DESCRIPTION')) {
            // To keep the Dockerfile as simple as possible, download and
            // execute the installation-from-DESCRIPTION script.
            return `bash -c "Rscript <(curl -sL https://unpkg.com/@stencila/dockter/src/install.R)"`;
        }
    }
    /**
     * The files to copy into the Docker image
     *
     * Copies all `*.R` files to the container
     */
    projectFiles() {
        const rfiles = this.glob('**/*.R');
        return rfiles.map(file => [file, file]);
    }
    /**
     * The command to execute in a container created from the Docker image
     *
     * If there is a top-level `main.R` or `cmd.R` then that will be used,
     * otherwise, the first `*.R` files by alphabetical order will be used.
     */
    runCommand() {
        const rfiles = this.glob('**/*.R');
        if (rfiles.length === 0)
            return;
        let script;
        if (rfiles.includes('main.R'))
            script = 'main.R';
        else if (rfiles.includes('cmd.R'))
            script = 'cmd.R';
        else
            script = rfiles[0];
        return `Rscript ${script}`;
    }
}
exports.default = RGenerator;