# This code is part of the Biopython distribution and governed by its
# license.  Please see the LICENSE file that should have been included
# as part of this package.

"""Common code for SeqRecord object tests."""

from Bio.Seq import UnknownSeq
from Bio.SeqUtils.CheckSum import seguid
from Bio.SeqFeature import ExactPosition, UnknownPosition
from Bio.SeqFeature import FeatureLocation, CompoundLocation, SeqFeature
from Bio.SeqRecord import SeqRecord


def checksum_summary(record):
    """Abbreviated string showing sequence, checksum, and length."""
    if isinstance(record.seq, UnknownSeq):
        return repr(record.seq)
    if len(record.seq) < 25:
        short = str(record.seq)
    else:
        short = str(record.seq)[:19] + "..." + str(record.seq)[-3:]
    return "%s [%s] len %i" % (short, seguid(record.seq), len(record.seq))


def compare_reference(old_r, new_r):
    """Compare two Reference objects.

    Note new_r is assumed to be a BioSQL DBSeqRecord, due to limitations
    of the BioSQL table structure.
    """
    assert old_r.title == new_r.title, "%s vs %s" % (old_r.title, new_r.title)
    assert old_r.authors == new_r.authors, "%s vs %s" % (old_r.authors, new_r.authors)
    assert old_r.journal == new_r.journal, "%s vs %s" % (old_r.journal, new_r.journal)
    assert old_r.medline_id == new_r.medline_id, "%s vs %s" % (
        old_r.medline_id,
        new_r.medline_id,
    )

    if old_r.pubmed_id and new_r.pubmed_id:
        assert old_r.pubmed_id == new_r.pubmed_id
        # Looking at BioSQL/BioSeq.py function _retrieve_reference
        # it seems that it will get either the MEDLINE or PUBMED,
        # but not both.  I *think* the current schema does not allow
        # us to store both... must confirm this.

    # TODO - assert old_r.comment == new_r.comment
    # Looking at the tables, I *think* the current schema does not
    # allow us to store a reference comment.  Must confirm this.
    assert old_r.comment == new_r.comment or new_r.comment == "", "%r vs %r" % (
        old_r.comment,
        new_r.comment,
    )

    # TODO - assert old_r.consrtm == new_r.consrtm
    # Looking at the tables, I *think* the current schema does not
    # allow us to store a consortium.
    assert old_r.consrtm == new_r.consrtm or new_r.consrtm == ""

    if len(old_r.location) == 0:
        assert len(new_r.location) == 0
    else:
        # BioSQL can only store ONE location!
        # TODO - Check BioPerl with a GenBank file with multiple ref locations
        assert isinstance(old_r.location[0], FeatureLocation)
        assert isinstance(new_r.location[0], FeatureLocation)
        assert (
            old_r.location[0].start == new_r.location[0].start
            and old_r.location[0].end == new_r.location[0].end
        )

    return True


def compare_feature(old_f, new_f):
    """Compare two SeqFeature objects."""
    assert isinstance(old_f, SeqFeature)
    assert isinstance(new_f, SeqFeature)

    assert old_f.type == new_f.type, "%s -> %s" % (old_f.type, new_f.type)

    assert old_f.strand == new_f.strand, "%s -> %s" % (old_f.strand, new_f.strand)

    assert old_f.ref == new_f.ref, "%s -> %s" % (old_f.ref, new_f.ref)

    assert old_f.ref_db == new_f.ref_db, "%s -> %s" % (old_f.ref_db, new_f.ref_db)

    # TODO - BioSQL does not store/retrieve feature's id (Bug 2526)
    assert old_f.id == new_f.id or new_f.id == "<unknown id>"

    # TODO - Work out how the location_qualifier_value table should
    # be used, given BioPerl seems to ignore it (Bug 2766)
    # assert old_f.location_operator == new_f.location_operator, \
    #        "%s -> %s" % (old_f.location_operator, new_f.location_operator)

    # We dont store fuzzy locations:
    assert old_f.location.start == new_f.location.start or (
        isinstance(old_f.location.start, UnknownPosition)
        and isinstance(new_f.location.start, UnknownPosition)
    ), "%s -> %s" % (old_f.location.start, new_f.location.start)
    assert old_f.location.end == new_f.location.end or (
        isinstance(old_f.location.end, UnknownPosition)
        and isinstance(new_f.location.end, UnknownPosition)
    ), "%s -> %s" % (old_f.location.end, new_f.location.end)

    assert isinstance(old_f.location, CompoundLocation) == isinstance(
        new_f.location, CompoundLocation
    )
    if isinstance(old_f.location, CompoundLocation):
        assert len(old_f.location.parts) == len(new_f.location.parts)
        for old_l, new_l in zip(old_f.location.parts, new_f.location.parts):
            assert old_l.start == new_l.start
            assert old_l.end == new_l.end
            assert old_l.strand == new_l.strand
            assert old_l.ref == new_l.ref
            assert old_l.ref_db == new_l.ref_db

    assert len(old_f.location.parts) == len(new_f.location.parts)
    for old_sub, new_sub in zip(old_f.location.parts, new_f.location.parts):
        # These are FeatureLocation objects
        assert old_sub.nofuzzy_start == new_sub.nofuzzy_start
        assert old_sub.nofuzzy_end == new_sub.nofuzzy_end
        assert old_sub.strand == new_sub.strand

    assert len(old_f.qualifiers) == len(new_f.qualifiers)
    assert set(old_f.qualifiers) == set(new_f.qualifiers)
    for key in old_f.qualifiers:
        if isinstance(old_f.qualifiers[key], str):
            if isinstance(new_f.qualifiers[key], str):
                assert old_f.qualifiers[key] == new_f.qualifiers[key]
            elif isinstance(new_f.qualifiers[key], list):
                # Maybe a string turning into a list of strings?
                assert [old_f.qualifiers[key]] == new_f.qualifiers[key], "%r -> %r" % (
                    old_f.qualifiers[key],
                    new_f.qualifiers[key],
                )
            else:
                raise ValueError("Problem with feature's '%s' qualifier" % key)
        else:
            # Should both be lists of strings...
            assert old_f.qualifiers[key] == new_f.qualifiers[key], "%s -> %s" % (
                old_f.qualifiers[key],
                new_f.qualifiers[key],
            )
    return True


def compare_sequence(old, new):
    """Compare two Seq or DBSeq objects."""
    assert len(old) == len(new), "%i vs %i" % (len(old), len(new))
    assert str(old) == str(new), "%s vs %s" % (old, new)

    if isinstance(old, UnknownSeq):
        assert isinstance(new, UnknownSeq)
    else:
        assert not isinstance(new, UnknownSeq)

    ln = len(old)
    s = str(old)
    assert isinstance(s, str)

    # Don't check every single element; for long sequences
    # this takes far far far too long to run!
    # Test both positive and negative indices
    if ln < 50:
        indices = list(range(-ln, ln))
    else:
        # A selection of end cases, and the mid point
        indices = [-ln, -ln + 1, -(ln // 2), -1, 0, 1, ln // 2, ln - 2, ln - 1]

    # Test element access,
    for i in indices:
        expected = s[i]
        assert expected == old[i]
        assert expected == new[i]

    # Test slices
    indices.append(ln)  # check copes with overflows
    indices.append(ln + 1000)  # check copes with overflows
    for i in indices:
        for j in indices:
            expected = s[i:j]
            assert expected == str(old[i:j]), "Slice %r vs %r" % (expected, old[i:j])
            assert expected == str(new[i:j]), "Slice %r vs %r" % (expected, new[i:j])
            # Slicing with step of 1 should make no difference.
            # Slicing with step 3 might be useful for codons.
            for step in [1, 3]:
                expected = s[i:j:step]
                assert expected == str(old[i:j:step])
                assert expected == str(new[i:j:step])

        # Check automatic end points
        expected = s[i:]
        assert expected == str(old[i:])
        assert expected == str(new[i:])

        expected = s[:i]
        assert expected == str(old[:i])
        assert expected == str(new[:i])

    # Check "copy" splice
    assert s == str(old[:])
    assert s == str(new[:])
    return True


def compare_features(old_list, new_list):
    """Compare two lists of SeqFeature objects."""
    assert isinstance(old_list, list)
    assert isinstance(new_list, list)
    assert len(old_list) == len(new_list)
    for old_f, new_f in zip(old_list, new_list):
        if not compare_feature(old_f, new_f):
            return False
    return True


def compare_record(old, new):
    """Compare two SeqRecord or DBSeqRecord objects."""
    assert isinstance(old, SeqRecord)
    assert isinstance(new, SeqRecord)
    # Sequence:
    compare_sequence(old.seq, new.seq)
    # Basics:
    assert old.id == new.id
    assert old.name == new.name
    assert old.description == new.description
    assert old.dbxrefs == new.dbxrefs, "dbxrefs mismatch\nOld: %s\nNew: %s" % (
        old.dbxrefs,
        new.dbxrefs,
    )
    # Features:
    if not compare_features(old.features, new.features):
        return False

    # Annotation:
    # We are expecting to see some "extra" annotations appearing,
    # such as 'cross_references', 'dates', 'data_file_division',
    # 'ncbi_taxon' and 'gi'.
    # TODO - address these, see Bug 2681?
    new_keys = set(new.annotations).difference(old.annotations)
    new_keys = new_keys.difference(
        ["cross_references", "date", "data_file_division", "ncbi_taxid", "gi"]
    )
    assert not new_keys, "Unexpected new annotation keys: %s" % ", ".join(new_keys)
    missing_keys = set(old.annotations).difference(new.annotations)
    missing_keys = missing_keys.difference(
        ["ncbi_taxid", "structured_comment"]  # Can't store chimeras
    )
    assert not missing_keys, "Unexpectedly missing annotation keys: %s" % ", ".join(
        missing_keys
    )

    # In the short term, just compare any shared keys:
    for key in set(old.annotations).intersection(new.annotations):
        if key == "references":
            assert len(old.annotations[key]) == len(new.annotations[key])
            for old_r, new_r in zip(old.annotations[key], new.annotations[key]):
                compare_reference(old_r, new_r)
        elif key == "comment":
            # Turn them both into containing strings for comparison - due to
            # line wrapping in GenBank etc we don't really expect the white
            # space to be 100% the same.
            if isinstance(old.annotations[key], list):
                old_comment = " ".join(old.annotations[key])
            else:
                old_comment = old.annotations[key]
            if isinstance(new.annotations[key], list):
                new_comment = " ".join(new.annotations[key])
            else:
                new_comment = new.annotations[key]
            old_comment = old_comment.replace("\n", " ").replace("  ", " ")
            new_comment = new_comment.replace("\n", " ").replace("  ", " ")
            assert old_comment == new_comment, (
                "Comment annotation changed by load/retrieve\n"
                "Was:%r\nNow:%r" % (old_comment, new_comment)
            )
        elif key in ["taxonomy", "organism", "source"]:
            # If there is a taxon id recorded, these fields get overwritten
            # by data from the taxon/taxon_name tables.  There is no
            # guarantee that they will be identical after a load/retrieve.
            assert isinstance(new.annotations[key], str) or isinstance(
                new.annotations[key], list
            )
        elif isinstance(old.annotations[key], type(new.annotations[key])):
            assert old.annotations[key] == new.annotations[key], (
                "Annotation '%s' changed by load/retrieve\nWas:%s\nNow:%s"
                % (key, old.annotations[key], new.annotations[key])
            )
        elif isinstance(old.annotations[key], str) and isinstance(
            new.annotations[key], list
        ):
            # Any annotation which is a single string gets turned into
            # a list containing one string by BioSQL at the moment.
            assert [old.annotations[key]] == new.annotations[key], (
                "Annotation '%s' changed by load/retrieve\nWas:%s\nNow:%s"
                % (key, old.annotations[key], new.annotations[key])
            )
        elif isinstance(old.annotations[key], list) and isinstance(
            new.annotations[key], str
        ):
            assert old.annotations[key] == [new.annotations[key]], (
                "Annotation '%s' changed by load/retrieve\nWas:%s\nNow:%s"
                % (key, old.annotations[key], new.annotations[key])
            )
    return True


def compare_records(old_list, new_list):
    """Compare two lists of SeqRecord objects."""
    assert isinstance(old_list, list)
    assert isinstance(new_list, list)
    assert len(old_list) == len(new_list)
    for old_r, new_r in zip(old_list, new_list):
        if not compare_record(old_r, new_r):
            return False
    return True
