slice_constants.ts

import axios from "axios";


const config = require("config");
const _  = require('underscore');
import {Configs, ProjectConfigs} from "./types";
import path from "path";
export class SliceConstants {
    /**
     *
     * @private
     */
    public static REPLACE_PROJECT_NAMES = [
        'LEVEL4_LFC_COMBAT_*.csv',
        'LEVEL5_LFC_COMBAT_*.csv'
    ];

    /**
     * Rows with pert_ids in this project are retained
     * @type {string[]}
     */
    private static ROW_FILES_POST_FIX = [
        '_continuous_associations.csv',
        '_discrete_associations.csv',
        '_DRC_TABLE.csv',
         '_LEVEL3_LMFI_*.csv',
         '_LEVEL4_LFC_COMBAT_*.csv',
         '_LEVEL4_LFC_n*.csv',
         '_LEVEL5_LFC_COMBAT_*.csv',
         '_LEVEL5_LFC_n*.csv',
        '_model_table.csv'
        // '_RF_table.csv',
    ];

    /**
     * Files available from compound directories to be put into
     * the project data directory
     * @private
     */
    public static PROJECT_DATA_FILES = [
        'continuous_associations.csv',
        'discrete_associations.csv',
        'DRC_TABLE.csv',
        'LEVEL3_LMFI_*.csv',
        'LEVEL4_LFC_COMBAT_*.csv',
        'LEVEL5_LFC_COMBAT_*.csv',
        'model_table.csv',
        'RF_table.csv',
    ];

    /**
     * Rows with pert plates in this project are retained
     * @type {string[]}
     */
    private static QC_PLATE_FILES_POST_FIX = [
         '_QC_TABLE.csv'
    ];

    private static INST_INFO_FILES_POST_FIX: string[] = [
        '_inst_info.txt'
    ];
    /**
     * Rows with pert plates in this project are retained
     * @type {string[]}
     */
    private static PLATE_FILES_POST_FIX = [
        '_LEVEL2*.csv'
    ];
    /**
     * Files to copy from source to destination
     * @type {string[]}
     */
    private static COPY_FILES_POST_FIX = [
        '_cell_info.txt'
    ];
    /**
     * Columns with pert-ids not part of this project are removed from these files
     * @type {string[]}
     */
    private static COLUMN_FILES_POST_FIX = [
        '_IC50_MATRIX.csv',
        '_LFC_MATRIX.csv',
        '_AUC_MATRIX.csv'
    ];
    /**
     * Destination files to zip
     * @type {string[]}
     */
    private static FILES_TO_ZIP = [
        '_AUC_MATRIX.csv',
        '_continuous_associations.csv',
        '_discrete_associations.csv',
        '_DRC_TABLE.csv',
        '_IC50_MATRIX.csv',
        '_LEVEL3_LMFI_*.csv',
        '_LEVEL4_LFC_COMBAT_*.csv',
        '_LEVEL5_LFC_COMBAT_*.csv',
        '_LFC_MATRIX.csv',
        '_model_table.csv',
        '_RF_table.csv',
        '_QC_TABLE.csv'
    ];

    public constructor() {

    }
    /**
     * Executes a shell command and return it as a Promise.
     * @param cmd {string}
     * @return {Promise<string>}
     */
    public static execShellCommand(cmd:string) {
        const exec = require('child_process').exec;
        return new Promise((resolve, reject) => {
            exec(cmd, (error:any, stdout:any, stderr:any) => {
                if (error) {
                    console.log(error);
                }
                resolve(stdout? stdout : stderr);
            });
        });
    }
    public static matcher(pert_inames: string[],input: string) {
        const g = pert_inames.join("|");
        const PERT_INAMES_REG_EXP = new RegExp(g);
        return PERT_INAMES_REG_EXP.test(input);
    }
    private static async fetchData (screen:string) {
        const BASE_API_URL = config.get("base_url");
        const API_KEY = config.get("api_key");
        const filter = {where: {screen: screen}, order: "project_id ASC"};
        const url = BASE_API_URL + "/v_mts_projects_per_plates?filter=" + JSON.stringify(filter);
        const response = await axios.get(url, {
            headers: {
                'user_key': API_KEY,
                'Content-Type': 'application/json'
            }
        });
        return response.data;
    }
   public static  async fetchDataByScreen(screen:string){
        const projectData = await SliceConstants.fetchData(screen);
        const projects = _.uniq(_.pluck(projectData, "project_id"));
        let fileInfos: Configs[] = [];
        for (let project of projects) {
            const currentProjects = _.where(projectData, {project_id: project})  as string[]
            const pert_plates = _.uniq(_.pluck(currentProjects, "pert_plate"))  as string[]
            const pert_ids = _.uniq(_.pluck(currentProjects, "pert_id")) as string[]
            const pert_inames = _.uniq(_.pluck(currentProjects, "pert_iname"))  as string[]
            //TODO type this
            fileInfos.push({
                SCREEN: screen,
                DATA_SRC_DIR : "data-to-extract",
                PARENT_SRC_PROJECT_DIR: "data-to-extract/build",
                PARENT_DEST_PROJECT_DIR: project.toLowerCase(),
                PERT_INAMES: pert_inames,
                PERT_IDS: pert_ids,
                PERT_PLATES: pert_plates,
                PROJECT: project
            });
        }
        return fileInfos;
    }
    public static getOutputFileName(file:string,projectConfigs: ProjectConfigs){
        let outputFileName = file.replace(projectConfigs.SOURCE_DATA_DIR, projectConfigs.DESTINATION_DATA_DIR);
        outputFileName = outputFileName.replace(projectConfigs.OLD_PROJECT_PREFIX, projectConfigs.NEW_PROJECT_PREFIX);
        const fileName = path.basename(outputFileName);
        const nFileName = fileName.replace(projectConfigs.SCREEN,projectConfigs.PROJECT)
        return outputFileName.replace(fileName,nFileName);
    }
    public static prepareConstants(configs: Configs): ProjectConfigs {

        const OLD_PROJECT_DIR = configs.PARENT_SRC_PROJECT_DIR.toUpperCase();
        //The directory to host the source files
        const SOURCE_DIR = configs.PARENT_SRC_PROJECT_DIR;
        //The new project prefix
        const NEW_PROJECT_DIR = configs.PARENT_DEST_PROJECT_DIR.toUpperCase();

        //The directory that would host the processed files
        const DESTINATION_DIR = configs.PARENT_DEST_PROJECT_DIR + '/' + NEW_PROJECT_DIR;

        //pert-inames that should be retained
        const PERT_INAMES = configs.PERT_INAMES;

        //The pert ids that should be retained
        const PERT_IDS = configs.PERT_IDS;

        //The pert plates that should be retained
        const PERT_PLATES = configs.PERT_PLATES;


        //The directory to host the source files
        const SOURCE_DATA_DIR = SOURCE_DIR;

        //The directory that would host the processed files
        const DESTINATION_DATA_DIR = DESTINATION_DIR + "/data";

        //The old project prefix
        const OLD_PROJECT_PREFIX = OLD_PROJECT_DIR + "_";

        //The new project prefix
        const NEW_PROJECT_PREFIX = NEW_PROJECT_DIR + "_";

            //TODO. add downloads file

        return {
            SCREEN: configs.SCREEN,
            INST_INFO_FILES_POST_FIX: SliceConstants.INST_INFO_FILES_POST_FIX,
            QC_PLATE_FILES_POST_FIX: SliceConstants.QC_PLATE_FILES_POST_FIX,
            COLUMN_FILES_POST_FIX: SliceConstants.COLUMN_FILES_POST_FIX,
            ROW_FILES_POST_FIX: SliceConstants.ROW_FILES_POST_FIX,
            NEW_PROJECT_PREFIX: NEW_PROJECT_PREFIX,
            OLD_PROJECT_PREFIX: OLD_PROJECT_PREFIX,
            SOURCE_DATA_DIR: SOURCE_DATA_DIR,
            DESTINATION_DATA_DIR: DESTINATION_DATA_DIR,
            PERT_INAMES: PERT_INAMES,
            PERT_IDS: PERT_IDS,
            PERT_PLATES: PERT_PLATES,
            PLATE_FILES_POST_FIX: SliceConstants.PLATE_FILES_POST_FIX,
            COPY_FILES_POST_FIX: SliceConstants.COPY_FILES_POST_FIX,
            FILES_TO_ZIP: SliceConstants.FILES_TO_ZIP,
            DESTINATION_DIR: DESTINATION_DIR,
            SOURCE_DIR: SOURCE_DIR,
            OLD_PROJECT_DIR: OLD_PROJECT_DIR,
            NEW_PROJECT_DIR: NEW_PROJECT_DIR,
            PROJECT: configs.PROJECT
        }
    }
}