package htsjdk.beta.plugin.variants;

import htsjdk.beta.io.IOPathUtils;
import htsjdk.beta.io.bundle.*;
import htsjdk.io.HtsPath;
import htsjdk.io.IOPath;
import htsjdk.samtools.util.FileExtensions;
import htsjdk.samtools.util.Log;
import htsjdk.samtools.util.Tuple;
import htsjdk.utils.ValidationUtils;
import java.io.Serial;
import java.io.Serializable;
import java.nio.file.Files;
import java.util.*;
import java.util.function.Function;

/**
 * A {@link Bundle} for variants and variants-related resources that are backed by on disk files. A {@link
 * htsjdk.beta.plugin.variants.VariantsBundle} has a primary resource with content type {@link
 * BundleResourceType#CT_VARIANT_CONTEXTS}; and an optional index resource. A VariantsBundle can also
 * contain additional resources.
 *
 * Note that this class is merely a convenience class for the case where the variants are backed by files on disk.
 * A bundle that contains variants and related resources can be created manually using the {@link Bundle} class.
 * This class provides convenient constructors, and validation for JSON interconversions. To create a VariantsBundle
 * for variants sources that are backed by streams or other {@link BundleResource} types, the {@link Bundle} and
 * {@link BundleBuilder} classes can be used to construct such bundles directly.
 */
public class VariantsBundle extends Bundle implements Serializable {
    @Serial
    private static final long serialVersionUID = 1L;

    private static final Log LOG = Log.getInstance(VariantsBundle.class);

    /**
     * Create a {@link htsjdk.beta.plugin.variants.VariantsBundle} containing only a variants resource.
     *
     * @param vcfPath An {@link IOPath}-derived object that represents a source of variants.
     */
    public VariantsBundle(final IOPath vcfPath) {
        this(List.of(toInputResource(BundleResourceType.CT_VARIANT_CONTEXTS, vcfPath)));
    }

    /**
     * Create a {@link htsjdk.beta.plugin.variants.VariantsBundle} containing only variants and an index.
     *
     * @param vcfPath An {@link IOPath}-derived object that represents a source of variants.
     * @param indexPath An {@link IOPath}-derived object that represents the companion index for {@code vcfPath}.
     */
    public VariantsBundle(final IOPath vcfPath, final IOPath indexPath) {
        this(List.of(
                toInputResource(BundleResourceType.CT_VARIANT_CONTEXTS, vcfPath),
                toInputResource(BundleResourceType.CT_VARIANTS_INDEX, indexPath)));
    }

    /**
     * Create a {@link htsjdk.beta.plugin.variants.VariantsBundle} using the resources in an existing bundle. A
     * resource with content type {@link BundleResourceType#CT_VARIANT_CONTEXTS} must be present in the
     * resources, or this constructor will throw.
     *
     * @param resources collection of {@link BundleResource}. the collection must include a resource with
     *                 content type {@link BundleResourceType#CT_VARIANT_CONTEXTS}.
     * @throws IllegalArgumentException if no resource with content type
     * {@link BundleResourceType#CT_VARIANT_CONTEXTS} is included in the input {@link BundleResource}
     * collection.
     */
    public VariantsBundle(final Collection<BundleResource> resources) {
        super(BundleResourceType.CT_VARIANT_CONTEXTS, resources);
    }

    /**
     * @return the {@link BundleResourceType#CT_VARIANT_CONTEXTS} {@link BundleResource} for this
     * {@link htsjdk.beta.plugin.variants.VariantsBundle}
     */
    public BundleResource getVariants() {
        return getOrThrow(BundleResourceType.CT_VARIANT_CONTEXTS);
    }

    /**
     * Get the optional {@link BundleResourceType#CT_VARIANTS_INDEX} resource for this
     * {@link htsjdk.beta.plugin.variants.VariantsBundle}.
     *
     * @return the optional {@link BundleResourceType#CT_VARIANTS_INDEX} resource for this
     * {@link htsjdk.beta.plugin.variants.VariantsBundle}, or Optional.empty() if no index resource is present in
     * the bundle.
     */
    public Optional<BundleResource> getIndex() {
        return get(BundleResourceType.CT_VARIANTS_INDEX);
    }

    /**
     * Create a {@link VariantsBundle} from a JSON string contained in jsonPath.
     *
     * @param jsonPath the path to a file that contains a {@link Bundle} serialized to JSON. The bundle
     *                 must contain a resource with content type VARIANT_CONTEXTS.
     * @return a {@link VariantsBundle} created from jsonPath
     */
    public static VariantsBundle getVariantsBundleFromPath(final IOPath jsonPath) {
        return getVariantsBundleFromString(IOPathUtils.getStringFromPath(jsonPath));
    }

    /**
     * Create a {@link VariantsBundle} from a JSON string contained in jsonPath.
     *
     * @param <T> the IOPath-derived type of the IOPathResources to be used in the new bundle
     * @param jsonPath the path to a file that contains a {@link Bundle} serialized to JSON. The bundle
     *                 must contain a resource with content type VARIANT_CONTEXTS.
     * @param ioPathConstructor a function that takes a string and returns an IOPath-derived class of type {@code T}
     * @return a {@link VariantsBundle} created from jsonPath
     */
    public static <T extends IOPath> VariantsBundle getVariantsBundleFromPath(
            final IOPath jsonPath, final Function<String, T> ioPathConstructor) {
        return getVariantsBundleFromString(IOPathUtils.getStringFromPath(jsonPath), ioPathConstructor);
    }

    /**
     * Create a {@link htsjdk.beta.plugin.variants.VariantsBundle} from a JSON string.
     *
     * @param jsonString the jsonString to use to create the {@link htsjdk.beta.plugin.variants.VariantsBundle}
     * @return a {@link htsjdk.beta.plugin.variants.VariantsBundle}
     */
    public static VariantsBundle getVariantsBundleFromString(final String jsonString) {
        return getVariantsBundleFromString(jsonString, HtsPath::new);
    }

    /**
     * Create a {@link htsjdk.beta.plugin.variants.VariantsBundle} from a JSON string with all IOPathResources using
     * an IOPath-derived class of type {@code T}.
     *
     * @param <T> the IOPath-derived type of the IOPathResources to be used in the new bundle
     * @param jsonString the string to use to create the {@link htsjdk.beta.plugin.variants.VariantsBundle}
     * @param ioPathConstructor a function that takes a string and returns an IOPath-derived class of type {@code T}
     * @return a newly created {@link htsjdk.beta.plugin.variants.VariantsBundle}
     */
    public static <T extends IOPath> VariantsBundle getVariantsBundleFromString(
            final String jsonString, final Function<String, T> ioPathConstructor) {
        return new VariantsBundle(
                BundleJSON.toBundle(jsonString, ioPathConstructor).getResources());
    }

    /**
     * Find the companion index for a variants source, and create a new {@link htsjdk.beta.plugin.variants.VariantsBundle}
     * containing the variants and the companion index, if one can be found.
     *
     * @param variants the variants source to use
     * @return a {@link htsjdk.beta.plugin.variants.VariantsBundle} containing variants and companion index, if it can
     * be found.
     */
    public static Optional<IOPath> resolveIndex(final IOPath variants) {
        return resolveIndex(variants, HtsPath::new);
    }

    /**
     * Attempts to find the companion index for a variants source based on commonly used file extensions, and
     * create a new {@link htsjdk.beta.plugin.variants.VariantsBundle} containing the variants and the companion
     * index, if one can be found.
     *
     * An index can only be resolved for an IOPath that represents a file on a file system for which an NIO
     * provider is installed. Remote paths that use a protocol scheme for which no NIO file system is
     * available will (silently) not be resolved.
     *
     * @param <T> the IOPath-derived type of the IOPath to be returned
     * @param variantsHtsPath the IOPath-derived object representing the variants source to use
     * @param ioPathConstructor a function that takes a string and returns an IOPath-derived class of type <T>
     * @return a {@link IOPath}-derived object of type T containing the companion index for {@code variantsPath},
     * if it can be found
     */
    public static <T extends IOPath> Optional<T> resolveIndex(
            final T variantsHtsPath, final Function<String, T> ioPathConstructor) {
        final Set<String> indexExtensions = Set.of(FileExtensions.TRIBBLE_INDEX, FileExtensions.TABIX_INDEX);
        for (final String extension : indexExtensions) {
            final T putativeIndexPath = IOPathUtils.appendExtension(variantsHtsPath, extension, ioPathConstructor);
            if (Files.exists(putativeIndexPath.toPath())) {
                return Optional.of(putativeIndexPath);
            }
        }
        return Optional.empty();
    }

    private static <T extends IOPath> IOPathResource toInputResource(final String providedContentType, final T ioPath) {
        ValidationUtils.nonNull(ioPath, "ioPath");
        final Optional<Tuple<String, String>> typePair = getInferredContentTypes(ioPath);
        if (typePair.isPresent()) {
            if (providedContentType != null && !typePair.get().a.equals(providedContentType)) {
                LOG.warn(String.format(
                        "Provided content type \"%s\" for \"%s\" doesn't match derived content type \"%s\"",
                        providedContentType, ioPath.getRawInputString(), typePair.get().a));
            }
        }
        return new IOPathResource(ioPath, providedContentType);
    }

    // Try to infer the contentType/format, i.e., variants from an IOPath. Currently this
    // exists purely to check for logical inconsistencies. It can detect cases that are illogical
    // (an IOPath that has format CRAM, but file extension BAM), but it can't determinstically
    // and correctly infer the types in all cases without reproducing all the logic embedded in all the
    // codecs (i.e., an htsget IOPath ends in ".bam", but has format HTSGET_BAM, not BAM - detecting
    // that here would require parsing the entire IOPath structure, which is best left to the codecs
    // themselves). So for now its advisory, but maybe it should be abandoned altogether.
    private static <T extends IOPath> Optional<Tuple<String, String>> getInferredContentTypes(final T ioPath) {
        ValidationUtils.nonNull(ioPath, "ioPath");
        final Optional<String> extension = ioPath.getExtension();
        if (extension.isPresent()) {
            final String ext = extension.get();
            if (ext.equals(FileExtensions.VCF)) {
                return Optional.of(
                        new Tuple<>(BundleResourceType.CT_VARIANT_CONTEXTS, BundleResourceType.FMT_VARIANTS_VCF));
            } else if (ext.equals(FileExtensions.COMPRESSED_VCF) || ext.equals(FileExtensions.COMPRESSED_VCF_BGZ)) {
                return Optional.of(
                        new Tuple<>(BundleResourceType.CT_VARIANT_CONTEXTS, BundleResourceType.FMT_VARIANTS_VCF));
            }
        }
        return Optional.empty();
    }
}
