package net.sourceforge.seqware.pipeline.plugins.filelinker;

import au.com.bytecode.opencsv.CSVReader;
import au.com.bytecode.opencsv.bean.CsvToBean;
import au.com.bytecode.opencsv.bean.HeaderColumnNameTranslateMappingStrategy;
import com.google.common.annotations.VisibleForTesting;
import static com.google.common.base.Preconditions.checkElementIndex;
import static com.google.common.base.Preconditions.checkNotNull;
import com.google.common.collect.Lists;
import com.google.common.collect.Maps;
import com.google.common.collect.Sets;
import java.io.BufferedReader;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.InputStreamReader;
import java.io.Reader;
import java.io.UnsupportedEncodingException;
import java.util.Arrays;
import java.util.List;
import java.util.Map;
import java.util.Set;
import net.sourceforge.seqware.common.module.FileMetadata;
import org.apache.commons.lang3.StringUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

public class FileLinkerParser {

    private static final String UTF8 = "UTF8";

    private static final Logger LOG = LoggerFactory.getLogger(FileLinkerParser.class);

    public static Map<Integer, List<FileMetadata>> parse(String filename, char separator) throws FileNotFoundException,
            UnsupportedEncodingException {
        checkNotNull(filename);
        checkElementIndex(0, filename.length());
        checkNotNull(separator);
        BufferedReader br = new BufferedReader(new InputStreamReader(new FileInputStream(filename), UTF8));
        List<FileLinkerLine> lines = getFileInfo(br, separator);
        requiredValuesPresent(lines);
        return fileMetadataFromFileInfo(lines);
    }

    @VisibleForTesting
    static List<FileLinkerLine> getFileInfo(Reader reader) {
        return getFileInfo(reader, '\t');
    }

    @VisibleForTesting
    static List<FileLinkerLine> getFileInfo(Reader reader, char separator) {
        CSVReader csvReader = new CSVReader(reader, separator);
        HeaderColumnNameTranslateMappingStrategy<FileLinkerLine> strat = new HeaderColumnNameTranslateMappingStrategy<>();
        strat.setType(FileLinkerLine.class);
        Map<String, String> map = Maps.newHashMap();
        map.put("sequencer_run", "sequencerRun");
        map.put("sample", "sample");
        map.put("lane", "laneString");
        map.put("ius_sw_accession", "seqwareAccessionString");
        map.put("file_status", "fileStatus");
        map.put("mime_type", "mimeType");
        map.put("size", "sizeString");
        map.put("md5sum", "md5sum");
        map.put("file", "filename");
        strat.setColumnMapping(map);

        CsvToBean<FileLinkerLine> csvToBean = new CsvToBean<>();
        List<FileLinkerLine> defaultUsers = csvToBean.parse(strat, csvReader);

        return defaultUsers;
    }

    private static Map<Integer, List<FileMetadata>> fileMetadataFromFileInfo(List<FileLinkerLine> lines) {
        Map<Integer, List<FileMetadata>> result = Maps.newHashMap();
        for (FileLinkerLine line : lines) {
            FileMetadata fileMetadata = new FileMetadata();
            fileMetadata.setMetaType(line.getMimeType());
            fileMetadata.setFilePath(line.getFilename());
            if (!StringUtils.isBlank(line.getMd5sum())) {
                fileMetadata.setMd5sum(line.getMd5sum());
            }
            if (line.getSize() != null) {
                fileMetadata.setSize(line.getSize());
            }
            if (result.containsKey(line.getSeqwareAccession())) {
                result.get(line.getSeqwareAccession()).add(fileMetadata);
            } else {
                List<FileMetadata> fileMetadataList = Lists.newArrayList();
                fileMetadataList.add(fileMetadata);
                result.put(line.getSeqwareAccession(), fileMetadataList);
            }
        }
        return result;
    }

    static void requiredValuesPresent(List<FileLinkerLine> lines) {
        boolean hasRequiredValues = true;
        Set<Integer> badLines = Sets.newHashSet();
        for (int i = 0; i < lines.size(); i++) {
            FileLinkerLine line = lines.get(i);
            if (!line.hasRequiredValues()) {
                hasRequiredValues = false;
                badLines.add(i + 2);
                LOG.error(
                        "Required value(s) missing in csv file at line number [{}]. ius_sw_accession, seqwareAccession, mime_type and file are required. {}",
                        i + 2, line);
            }
        }
        if (!hasRequiredValues) {
            throw new FileLinkerLineException("Csv file missing required values on the following lines: "
                    + Arrays.toString(badLines.toArray()));
        }
    }

}