<commit_before>/*
 * Copyright (c) 2007-2012 The Broad Institute, Inc.
 * SOFTWARE COPYRIGHT NOTICE
 * This software and its documentation are the copyright of the Broad Institute, Inc. All rights are reserved.
 *
 * This software is supplied without any warranty or guaranteed support whatsoever. The Broad Institute is not responsible for its use, misuse, or functionality.
 *
 * This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
 * Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
 */
package org.broad.igv.util;

import org.apache.log4j.Logger;
import org.broad.igv.gs.GSUtils;

import java.awt.*;
import java.io.File;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.Map;

/**
 * Represents a data file or other resource, which might be local file or remote resource.
 *
 * @author jrobinso
 */
public class ResourceLocator {

    private static Logger log = Logger.getLogger(ResourceLocator.class);

    /**
     * Display name
     */
    String name;

    /**
     * The local path or url (http, https, or ftp) for the resource.
     */
    String path;

    /**
     * URL to a database server
     */
    String dbURL;


    /**
     * Optional path to an associated index file
     */
    String indexPath;


    String trackInforURL; // A hyperlink to general information about the track.

    String featureInfoURL; //A URL pattern (UCSC convention) to a specific URL applicable to each feature

    String description; //Descriptive text

    /**
     * The type of resource (generally this refers to the file format)
     */
    String type;

    /**
     * Path to an associated density file.  This is used primarily for sequence alignments
     */
    String coverage;

    /**
     * A UCSC style track line.  Overrides value in file, if any.
     */
    String trackLine;  //

    /**
     * Color for features or data.  Somewhat redundant with trackLine.
     */
    Color color;


    String sampleId;

    String username;

    String password;

    /**
     * Constructor for local files
     *
     * @param path
     */
    public ResourceLocator(String path) {
        this.setPath(path);
    }

    /**
     * Constructor for database resources
     *
     * @param dbURL
     * @param path
     */
    public ResourceLocator(String dbURL, String path) {
        this.dbURL = dbURL;
        this.setPath(path);
    }

    /**
     * Determines if the resource actually exists.
     *
     * @return true if resource was found.
     */
    public boolean exists() {
        return ParsingUtils.pathExists(path);
    }


    public void setType(String type) {
        this.type = type;
    }

    public String getType() {
        return type;
    }

    public String getTypeString() {
        if (type != null) {
            return type;
        } else {

            String typeString = path.toLowerCase();
            if (path.startsWith("http://") || path.startsWith("https://")) {
                try {
                    URL url = new URL(path);

                    typeString = url.getPath().toLowerCase();
                    String query = url.getQuery();
                    if (query != null) {
                        Map<String, String> queryMap = HttpUtils.parseQueryString(query);
                        // If type is set explicitly use it
                        if (queryMap.containsKey("format")) {
                            String format = queryMap.get("dataformat");
                            if (format.contains("genomespace")) {
                                typeString = GSUtils.parseDataFormatString(format);
                            } else {
                                typeString = format;
                            }
                        } else if (queryMap.containsKey("file")) {
                            typeString = queryMap.get("file");
                        }
                    }

                } catch (MalformedURLException e) {
                    log.error("Error interpreting url: " + path, e);
                    typeString = path;
                }
            }

            // Strip .txt, .gz, and .xls extensions.  (So  foo.cn.gz => a .cn file)
            if (!typeString.endsWith("_sorted.txt") &&
                    (typeString.endsWith(".txt") || typeString.endsWith(
                            ".xls") || typeString.endsWith(".gz"))) {
                typeString = typeString.substring(0, typeString.lastIndexOf("."));
            }

            return typeString;

        }
    }

    public String toString() {
        return path + (dbURL == null ? "" : " " + dbURL);
    }

    public String getPath() {
        return path;
    }

    public String getFileName() {
        return (new File(path)).getName();
    }


    public String getDBUrl() {
        return dbURL;
    }

    public boolean isLocal() {
        return !(FileUtils.isRemote(path));
    }

    public void setTrackInforURL(String trackInforURL) {
        this.trackInforURL = trackInforURL;
    }

    public String getTrackInforURL() {
        return trackInforURL;
    }

    public String getDescription() {
        return description;
    }

    public void setDescription(String description) {
        this.description = description;
    }

    public String getTrackName() {
        return name != null ? name : new File(getPath()).getName();
    }


    public void setName(String name) {
        this.name = name;
    }

    public String getName() {
        return name;
    }

    public String getCoverage() {
        return coverage;
    }

    public void setCoverage(String coverage) {
        this.coverage = coverage;
    }

    public Color getColor() {
        return color;
    }

    public void setColor(Color color) {
        this.color = color;
    }


    public String getFeatureInfoURL() {
        return featureInfoURL;
    }

    public void setFeatureInfoURL(String featureInfoURL) {
        this.featureInfoURL = featureInfoURL;
    }

    public void setPath(String path) {
        if (path != null && path.startsWith("file://")) {
            this.path = path.substring(7);
        } else {
            this.path = path;
        }
    }

    public String getTrackLine() {
        return trackLine;
    }

    public void setTrackLine(String trackLine) {
        this.trackLine = trackLine;
    }

    public String getSampleId() {
        return sampleId;
    }

    public void setSampleId(String sampleId) {
        this.sampleId = sampleId;
    }

    public String getIndexPath() {
        return indexPath;
    }

    public void setIndexPath(String indexPath) {
        this.indexPath = indexPath;
    }

    public String getUsername() {
        return username;
    }

    public void setUsername(String username) {
        this.username = username;
    }

    public String getPassword() {
        return password;
    }

    public void setPassword(String password) {
        this.password = password;
    }

    @Override
    public boolean equals(Object o) {
        if (this == o) return true;
        if (o == null || getClass() != o.getClass()) return false;

        ResourceLocator that = (ResourceLocator) o;

        if (dbURL != null ? !dbURL.equals(that.dbURL) : that.dbURL != null) return false;
        if (!path.equals(that.path)) return false;

        return true;
    }

    @Override
    public int hashCode() {
        int result = path.hashCode();
        result = 31 * result + (dbURL != null ? dbURL.hashCode() : 0);
        return result;
    }


    public String getBamIndexPath() {

        if (indexPath != null) return indexPath;

        if (path.toLowerCase().startsWith("http://") || path.toLowerCase().startsWith("https://")) {
            // See if bam file is specified by parameter
            try {
                URL url = new URL(path);
                String queryString = url.getQuery();
                if (queryString != null) {
                    Map<String, String> parameters = HttpUtils.parseQueryString(queryString);
                    if (parameters.containsKey("index")) {
                        return parameters.get("index");
                    } else if (parameters.containsKey("file")) {
                        String bamFile = parameters.get("file");
                        String bamIndexFile = bamFile + ".bai";
                        String newQueryString = queryString.replace(bamFile, bamIndexFile);
                        return path.replace(queryString, newQueryString);
                    }
                }
            } catch (MalformedURLException e) {
                log.error(e);
            }

        }

        return path + ".bai";
    }


    /**
     * FOR LOAD FROM SERVER
     */
    public static enum AttributeType {

        DB_URL("serverURL"),
        PATH("path"),
        DESCRIPTION("description"),
        HYPERLINK("hyperlink"),
        INFOLINK("infolink"),
        ID("id"),
        SAMPLE_ID("sampleId"),
        NAME("name"),
        URL("url"),
        RESOURCE_TYPE("resourceType"),
        TRACK_LINE("trackLine"),
        COVERAGE("coverage"),
        COLOR("color");

        private String name;

        AttributeType(String name) {
            this.name = name;
        }

        public String getText() {
            return name;
        }

        @Override
        public String toString() {
            return getText();
        }

    }
}
<commit_msg>Use "file" parameter, if present, to determine data format typeString in ResourceLocator<commit_after>/*
 * Copyright (c) 2007-2012 The Broad Institute, Inc.
 * SOFTWARE COPYRIGHT NOTICE
 * This software and its documentation are the copyright of the Broad Institute, Inc. All rights are reserved.
 *
 * This software is supplied without any warranty or guaranteed support whatsoever. The Broad Institute is not responsible for its use, misuse, or functionality.
 *
 * This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
 * Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
 */
package org.broad.igv.util;

import org.apache.log4j.Logger;
import org.broad.igv.gs.GSUtils;

import java.awt.*;
import java.io.File;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.Map;

/**
 * Represents a data file or other resource, which might be local file or remote resource.
 *
 * @author jrobinso
 */
public class ResourceLocator {

    private static Logger log = Logger.getLogger(ResourceLocator.class);

    /**
     * Display name
     */
    String name;

    /**
     * The local path or url (http, https, or ftp) for the resource.
     */
    String path;

    /**
     * URL to a database server
     */
    String dbURL;


    /**
     * Optional path to an associated index file
     */
    String indexPath;


    String trackInforURL; // A hyperlink to general information about the track.

    String featureInfoURL; //A URL pattern (UCSC convention) to a specific URL applicable to each feature

    String description; //Descriptive text

    /**
     * The type of resource (generally this refers to the file format)
     */
    String type;

    /**
     * Path to an associated density file.  This is used primarily for sequence alignments
     */
    String coverage;

    /**
     * A UCSC style track line.  Overrides value in file, if any.
     */
    String trackLine;  //

    /**
     * Color for features or data.  Somewhat redundant with trackLine.
     */
    Color color;


    String sampleId;

    String username;

    String password;

    /**
     * Constructor for local files
     *
     * @param path
     */
    public ResourceLocator(String path) {
        this.setPath(path);
    }

    /**
     * Constructor for database resources
     *
     * @param dbURL
     * @param path
     */
    public ResourceLocator(String dbURL, String path) {
        this.dbURL = dbURL;
        this.setPath(path);
    }

    /**
     * Determines if the resource actually exists.
     *
     * @return true if resource was found.
     */
    public boolean exists() {
        return ParsingUtils.pathExists(path);
    }


    public void setType(String type) {
        this.type = type;
    }

    public String getType() {
        return type;
    }

    public String getTypeString() {
        if (type != null) {
            return type;
        } else {

            String typeString = path.toLowerCase();
            if (path.startsWith("http://") || path.startsWith("https://")) {
                try {
                    URL url = new URL(path);

                    typeString = url.getPath().toLowerCase();
                    String query = url.getQuery();
                    if (query != null) {
                        Map<String, String> queryMap = HttpUtils.parseQueryString(query);
                        // If type is set explicitly use it
                        if (queryMap.containsKey("dataformat")) {
                            String format = queryMap.get("dataformat");
                            if (format.contains("genomespace")) {
                                typeString = GSUtils.parseDataFormatString(format);
                            } else {
                                typeString = format;
                            }
                        } else if (queryMap.containsKey("file")) {
                            typeString = queryMap.get("file");
                        }
                    }

                } catch (MalformedURLException e) {
                    log.error("Error interpreting url: " + path, e);
                    typeString = path;
                }
            }

            // Strip .txt, .gz, and .xls extensions.  (So  foo.cn.gz => a .cn file)
            if (!typeString.endsWith("_sorted.txt") &&
                    (typeString.endsWith(".txt") || typeString.endsWith(
                            ".xls") || typeString.endsWith(".gz"))) {
                typeString = typeString.substring(0, typeString.lastIndexOf("."));
            }

            return typeString;

        }
    }

    public String toString() {
        return path + (dbURL == null ? "" : " " + dbURL);
    }

    public String getPath() {
        return path;
    }

    public String getFileName() {
        return (new File(path)).getName();
    }


    public String getDBUrl() {
        return dbURL;
    }

    public boolean isLocal() {
        return !(FileUtils.isRemote(path));
    }

    public void setTrackInforURL(String trackInforURL) {
        this.trackInforURL = trackInforURL;
    }

    public String getTrackInforURL() {
        return trackInforURL;
    }

    public String getDescription() {
        return description;
    }

    public void setDescription(String description) {
        this.description = description;
    }

    public String getTrackName() {
        return name != null ? name : new File(getPath()).getName();
    }


    public void setName(String name) {
        this.name = name;
    }

    public String getName() {
        return name;
    }

    public String getCoverage() {
        return coverage;
    }

    public void setCoverage(String coverage) {
        this.coverage = coverage;
    }

    public Color getColor() {
        return color;
    }

    public void setColor(Color color) {
        this.color = color;
    }


    public String getFeatureInfoURL() {
        return featureInfoURL;
    }

    public void setFeatureInfoURL(String featureInfoURL) {
        this.featureInfoURL = featureInfoURL;
    }

    public void setPath(String path) {
        if (path != null && path.startsWith("file://")) {
            this.path = path.substring(7);
        } else {
            this.path = path;
        }
    }

    public String getTrackLine() {
        return trackLine;
    }

    public void setTrackLine(String trackLine) {
        this.trackLine = trackLine;
    }

    public String getSampleId() {
        return sampleId;
    }

    public void setSampleId(String sampleId) {
        this.sampleId = sampleId;
    }

    public String getIndexPath() {
        return indexPath;
    }

    public void setIndexPath(String indexPath) {
        this.indexPath = indexPath;
    }

    public String getUsername() {
        return username;
    }

    public void setUsername(String username) {
        this.username = username;
    }

    public String getPassword() {
        return password;
    }

    public void setPassword(String password) {
        this.password = password;
    }

    @Override
    public boolean equals(Object o) {
        if (this == o) return true;
        if (o == null || getClass() != o.getClass()) return false;

        ResourceLocator that = (ResourceLocator) o;

        if (dbURL != null ? !dbURL.equals(that.dbURL) : that.dbURL != null) return false;
        if (!path.equals(that.path)) return false;

        return true;
    }

    @Override
    public int hashCode() {
        int result = path.hashCode();
        result = 31 * result + (dbURL != null ? dbURL.hashCode() : 0);
        return result;
    }


    public String getBamIndexPath() {

        if (indexPath != null) return indexPath;

        if (path.toLowerCase().startsWith("http://") || path.toLowerCase().startsWith("https://")) {
            // See if bam file is specified by parameter
            try {
                URL url = new URL(path);
                String queryString = url.getQuery();
                if (queryString != null) {
                    Map<String, String> parameters = HttpUtils.parseQueryString(queryString);
                    if (parameters.containsKey("index")) {
                        return parameters.get("index");
                    } else if (parameters.containsKey("file")) {
                        String bamFile = parameters.get("file");
                        String bamIndexFile = bamFile + ".bai";
                        String newQueryString = queryString.replace(bamFile, bamIndexFile);
                        return path.replace(queryString, newQueryString);
                    }
                }
            } catch (MalformedURLException e) {
                log.error(e);
            }

        }

        return path + ".bai";
    }


    /**
     * FOR LOAD FROM SERVER
     */
    public static enum AttributeType {

        DB_URL("serverURL"),
        PATH("path"),
        DESCRIPTION("description"),
        HYPERLINK("hyperlink"),
        INFOLINK("infolink"),
        ID("id"),
        SAMPLE_ID("sampleId"),
        NAME("name"),
        URL("url"),
        RESOURCE_TYPE("resourceType"),
        TRACK_LINE("trackLine"),
        COVERAGE("coverage"),
        COLOR("color");

        private String name;

        AttributeType(String name) {
            this.name = name;
        }

        public String getText() {
            return name;
        }

        @Override
        public String toString() {
            return getText();
        }

    }
}

{'fraction_non_alphanumeric': 0.10260714473063001, 'fraction_numerical': 0.0018884750563919635, 'mean_word_length': 1.7320149039839496, 'pattern_counts': {'":': 0, '<': 7, '<?xml version=': 0, '>': 9, 'https://': 4, 'lorem ipsum': 0, 'www.': 2, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '5618635', 'n_tokens_mistral': 5216, 'n_tokens_neox': 4957, 'n_words': 1413}