#!/usr/bin/env python
# Copyright 2010 by Andrea Pierleoni
# Revisions copyright 2010-2015 by Peter Cock.  All rights reserved.
# 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.
"""Test for the Uniprot parser on Uniprot XML files."""

import os
import unittest

from Bio import SeqIO
from Bio.SeqRecord import SeqRecord

from seq_tests_common import compare_reference, compare_record


# Left as None if the import within UniProtIO fails
if SeqIO.UniprotIO.ElementTree is None:
    from Bio import MissingPythonDependencyError
    # TODO: Can this fail on Python 2.7 onwards?
    raise MissingPythonDependencyError("No ElementTree module was found. "
                                       "Use Python 2.5+, lxml or elementtree "
                                       "if you want to use "
                                       "Bio.SeqIO.UniprotIO.")


class TestUniprot(unittest.TestCase):
    """Tests Uniprot XML parser."""

    def test_uni001(self):
        """Parsing Uniprot file uni001."""
        filename = "uni001"
        # test the record parser

        datafile = os.path.join("SwissProt", filename)

        with open(datafile) as test_handle:
            seq_record = SeqIO.read(test_handle, "uniprot-xml")

        self.assertTrue(isinstance(seq_record, SeqRecord))

        # test a couple of things on the record -- this is not exhaustive
        self.assertEqual(seq_record.id, "Q91G55")
        self.assertEqual(seq_record.name, "043L_IIV6")
        self.assertEqual(seq_record.description, "Uncharacterized protein 043L")
        self.assertEqual(repr(seq_record.seq), "Seq('MDLINNKLNIEIQKFCLDLEKKYNINYNNLIDLWFNKESTERLIKCEVNLENKI...IPI', ProteinAlphabet())")

        # self.assertEqual(seq_record.accessions, ['Q91G55']) #seq_record.accessions does not exist
        # self.assertEqual(seq_record.organism_classification, ['Eukaryota', 'Metazoa', 'Chordata', 'Craniata', 'Vertebrata', 'Mammalia', 'Eutheria', 'Primates', 'Catarrhini', 'Hominidae', 'Homo'])
        # self.assertEqual(record.seqinfo, (348, 39676, '75818910'))

        self.assertEqual(len(seq_record.features), 1)
        self.assertEqual(repr(seq_record.features[0]), "SeqFeature(FeatureLocation(ExactPosition(0), ExactPosition(116)), type='chain', id='PRO_0000377969')")

        self.assertEqual(len(seq_record.annotations["references"]), 2)
        self.assertEqual(seq_record.annotations["references"][0].authors, "Jakob N.J., Mueller K., Bahr U., Darai G.")
        self.assertEqual(seq_record.annotations["references"][0].title, "Analysis of the first complete DNA sequence of an invertebrate iridovirus: coding strategy of the genome of Chilo iridescent virus.")
        self.assertEqual(seq_record.annotations["references"][0].journal, "Virology 286:182-196(2001)")
        self.assertEqual(seq_record.annotations["references"][0].comment, "journal article | 2001 | Scope: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA] | ")

        self.assertEqual(len(seq_record.dbxrefs), 11)
        self.assertEqual(seq_record.dbxrefs[0], "DOI:10.1006/viro.2001.0963")

        self.assertEqual(seq_record.annotations["sequence_length"], 116)
        self.assertEqual(seq_record.annotations["sequence_checksum"], "4A29B35FB716523C")
        self.assertEqual(seq_record.annotations["modified"], "2009-07-07")
        self.assertEqual(seq_record.annotations["accessions"], ["Q91G55"])
        self.assertEqual(seq_record.annotations["taxonomy"], ["Viruses", "dsDNA viruses, no RNA stage", "Iridoviridae", "Iridovirus"])
        self.assertEqual(seq_record.annotations["sequence_mass"], 13673)
        self.assertEqual(seq_record.annotations["dataset"], "Swiss-Prot")
        self.assertEqual(seq_record.annotations["gene_name_ORF"], ["IIV6-043L"])
        self.assertEqual(seq_record.annotations["version"], 21)
        self.assertEqual(seq_record.annotations["sequence_modified"], "2001-12-01")
        self.assertEqual(seq_record.annotations["keywords"], ["Complete proteome", "Virus reference strain"])
        self.assertEqual(seq_record.annotations["organism_host"], ["Acheta domesticus", "House cricket", "Chilo suppressalis", "striped riceborer", "Gryllus bimaculatus", "Two-spotted cricket", "Gryllus campestris", "Spodoptera frugiperda", "Fall armyworm"])
        self.assertEqual(seq_record.annotations["created"], "2009-06-16")
        self.assertEqual(seq_record.annotations["organism_name"], ["Chilo iridescent virus"])
        self.assertEqual(seq_record.annotations["organism"], "Invertebrate iridescent virus 6 (IIV-6)")
        self.assertEqual(seq_record.annotations["recommendedName_fullName"], ["Uncharacterized protein 043L"])
        self.assertEqual(seq_record.annotations["sequence_version"], 1)
        self.assertEqual(seq_record.annotations["proteinExistence"], ["Predicted"])

    def test_uni003(self):
        """Parsing Uniprot file uni003."""
        filename = "uni003"
        # test the record parser

        datafile = os.path.join("SwissProt", filename)

        test_handle = open(datafile)
        seq_record = SeqIO.read(test_handle, "uniprot-xml")
        test_handle.close()

        self.assertTrue(isinstance(seq_record, SeqRecord))

        # test general record entries
        self.assertEqual(seq_record.id, "O44185")
        self.assertEqual(seq_record.name, "FLP13_CAEEL")
        self.assertEqual(seq_record.description,
                         "FMRFamide-like neuropeptides 13")
        self.assertEqual(repr(seq_record.seq),
                         "Seq('MMTSLLTISMFVVAIQAFDSSEIRMLDEQYDTKNPFFQF"
                         "LENSKRSDRPTRAMD...GRK', ProteinAlphabet())")

        self.assertEqual(len(seq_record.annotations["references"]), 7)
        self.assertEqual(seq_record.annotations["references"][5].authors,
                         "Kim K., Li C.")
        self.assertEqual(seq_record.annotations["references"][5].title,
                         "Expression and regulation of an FMRFamide-related "
                         "neuropeptide gene family in Caenorhabditis elegans.")
        self.assertEqual(seq_record.annotations["references"][5].journal,
                         "J. Comp. Neurol. 475:540-550(2004)")
        self.assertEqual(seq_record.annotations["references"][5].comment,
                         "journal article | 2004 | Scope: TISSUE SPECIFICITY, "
                         "DEVELOPMENTAL STAGE | ")

        self.assertEqual(seq_record.annotations["accessions"], ["O44185"])
        self.assertEqual(seq_record.annotations["created"], "2004-05-10")
        self.assertEqual(seq_record.annotations["dataset"], "Swiss-Prot")
        self.assertEqual(seq_record.annotations["gene_name_ORF"], ["F33D4.3"])
        self.assertEqual(seq_record.annotations["gene_name_primary"], "flp-13")
        self.assertEqual(seq_record.annotations["keywords"],
                         ["Amidation", "Cleavage on pair of basic residues",
                          "Complete proteome", "Direct protein sequencing",
                          "Neuropeptide", "Reference proteome", "Repeat",
                          "Secreted", "Signal"])
        self.assertEqual(seq_record.annotations["modified"], "2012-11-28")
        self.assertEqual(seq_record.annotations["organism"],
                         "Caenorhabditis elegans")
        self.assertEqual(seq_record.annotations["proteinExistence"],
                         ["evidence at protein level"])
        self.assertEqual(seq_record.annotations["recommendedName_fullName"],
                         ["FMRFamide-like neuropeptides 13"])
        self.assertEqual(seq_record.annotations["sequence_length"], 160)
        self.assertEqual(seq_record.annotations["sequence_checksum"],
                         "BE4C24E9B85FCD11")
        self.assertEqual(seq_record.annotations["sequence_mass"], 17736)
        self.assertEqual(seq_record.annotations["sequence_modified"], "1998-06-01")
        self.assertEqual(seq_record.annotations["sequence_precursor"], "true")
        self.assertEqual(seq_record.annotations["sequence_version"], 1)
        self.assertEqual(seq_record.annotations["taxonomy"],
                         ["Eukaryota", "Metazoa", "Ecdysozoa", "Nematoda",
                          "Chromadorea", "Rhabditida", "Rhabditoidea", "Rhabditidae",
                          "Peloderinae", "Caenorhabditis"])
        self.assertEqual(seq_record.annotations["type"],
                         ["ECO:0000006", "ECO:0000001"])
        self.assertEqual(seq_record.annotations["version"], 74)

        # test comment entries
        self.assertEqual(seq_record.annotations["comment_allergen"],
                         ["Causes an allergic reaction in human."])
        self.assertEqual(seq_record.annotations["comment_alternativeproducts_isoform"],
                         ["Q8W1X2-1", "Q8W1X2-2"])
        self.assertEqual(seq_record.annotations["comment_biotechnology"],
                         ["Green fluorescent protein has been engineered to "
                          "produce a vast number of variously colored "
                          "mutants, fusion proteins, and biosensors. "
                          "Fluorescent proteins and its mutated allelic "
                          "forms, blue, cyan and yellow have become a useful "
                          "and ubiquitous tool for making chimeric proteins, "
                          "where they function as a fluorescent protein tag. "
                          "Typically they tolerate N- and C-terminal fusion "
                          "to a broad variety of proteins. They have been "
                          "expressed in most known cell types and are used "
                          "as a noninvasive fluorescent marker in living "
                          "cells and organisms. They enable a wide range of "
                          "applications where they have functioned as a cell "
                          "lineage tracer, reporter of gene expression, or as "
                          "a measure of protein-protein interactions.",
                          "Can also be used as a molecular thermometer, "
                          "allowing accurate temperature measurements in "
                          "fluids. The measurement process relies on the "
                          "detection of the blinking of GFP using "
                          "fluorescence correlation spectroscopy."])
        self.assertEqual(seq_record.annotations["comment_catalyticactivity"],
                         ["ATP + acetyl-CoA + HCO(3)(-) = ADP + phosphate "
                          "+ malonyl-CoA.",
                          "ATP + biotin-[carboxyl-carrier-protein] "
                          "+ CO(2) = ADP + phosphate + "
                          "carboxy-biotin-[carboxyl-carrier-protein]."])
        self.assertEqual(seq_record.annotations["comment_caution"],
                         ["Could be the product of a pseudogene. The "
                          "existence of a transcript at this locus is "
                          "supported by only one sequence submission "
                          "(PubMed:2174397)."])
        self.assertEqual(seq_record.annotations["comment_cofactor"],
                         ["Biotin (By similarity).", "Binds 2 manganese ions "
                          "per subunit (By similarity)."])
        self.assertEqual(seq_record.annotations["comment_developmentalstage"],
                         ["Expressed from the comma stage of embryogenesis, "
                          "during all larval stages, and in low levels in "
                          "adults."])
        self.assertEqual(seq_record.annotations["comment_disease"],
                         ["Defects in MC2R are the cause of glucocorticoid "
                          "deficiency type 1 (GCCD1) [MIM:202200]; also known "
                          "as familial glucocorticoid deficiency type 1 "
                          "(FGD1). GCCD1 is an autosomal recessive disorder "
                          "due to congenital insensitivity or resistance to "
                          "adrenocorticotropin (ACTH). It is characterized by "
                          "progressive primary adrenal insufficiency, without "
                          "mineralocorticoid deficiency."])
        self.assertEqual(seq_record.annotations["comment_disruptionphenotype"],
                         ["Mice display impaired B-cell development which "
                          "does not progress pass the progenitor stage."])
        self.assertEqual(seq_record.annotations["comment_domain"],
                         ["Two regions, an N-terminal (aa 96-107) and a "
                          "C-terminal (aa 274-311) are required for binding "
                          "FGF2."])
        self.assertEqual(seq_record.annotations["comment_enzymeregulation"],
                         ["By phosphorylation. The catalytic activity is "
                          "inhibited by soraphen A, a polyketide isolated "
                          "from the myxobacterium Sorangium cellulosum and "
                          "a potent inhibitor of fungal growth."])
        self.assertEqual(seq_record.annotations["comment_function"],
                         ["FMRFamides and FMRFamide-like peptides are "
                          "neuropeptides. AADGAPLIRF-amide and "
                          "APEASPFIRF-amide inhibit muscle tension in somatic "
                          "muscle. APEASPFIRF-amide is a potent inhibitor of "
                          "the activity of dissected pharyngeal myogenic "
                          "muscle system."])
        self.assertEqual(seq_record.annotations["comment_induction"],
                         ["Repressed in presence of fatty acids. Repressed "
                          "3-fold by lipid precursors, inositol and "
                          "choline, and also controlled by regulatory "
                          "factors INO2, INO4 and OPI1."])
        self.assertEqual(seq_record.annotations["comment_interaction_intactId"],
                         ["EBI-356720", "EBI-746969", "EBI-720116"])
        self.assertEqual(seq_record.annotations["comment_massspectrometry"],
                         ["88..98:1032|MALDI", "100..110:1133.7|MALDI"])
        self.assertEqual(seq_record.annotations["comment_miscellaneous"],
                         ["Present with 20200 molecules/cell in log phase "
                          "SD medium."])
        self.assertEqual(seq_record.annotations["comment_onlineinformation"],
                         ["NIEHS-SNPs@http://egp.gs.washington.edu/data/api5/"])
        self.assertEqual(seq_record.annotations["comment_pathway"],
                         ["Lipid metabolism; malonyl-CoA biosynthesis; "
                         "malonyl-CoA from acetyl-CoA: step 1/1."])
        self.assertEqual(seq_record.annotations["comment_RNAediting"],
                         ["Partially edited. RNA editing generates receptor "
                          "isoforms that differ in their ability to interact "
                          "with the phospholipase C signaling cascade in a "
                          "transfected cell line, suggesting that this RNA "
                          "processing event may contribute to the modulation "
                          "of serotonergic neurotransmission in the central "
                          "nervous system."])
        self.assertEqual(seq_record.annotations["comment_PTM"],
                         ["Acetylation at Lys-251 impairs "
                          "antiapoptotic function."])
        self.assertEqual(seq_record.annotations["comment_pharmaceutical"],
                         ["Could be used as a possible therapeutic agent for "
                          "treating rheumatoid arthritis."])
        self.assertEqual(seq_record.annotations["comment_polymorphism"],
                         ["Position 23 is polymorphic; the frequencies in "
                          "unrelated Caucasians are 0.87 for Cys and 0.13 "
                          "for Ser."])
        self.assertEqual(seq_record.annotations["comment_similarity"],
                         ["Belongs to the FARP (FMRFamide related peptide) "
                          "family."])
        self.assertEqual(seq_record.annotations["comment_subcellularlocation_location"],
                         ["Secreted"])
        self.assertEqual(seq_record.annotations["comment_subunit"],
                         ["Homodimer."])
        self.assertEqual(seq_record.annotations["comment_tissuespecificity"],
                         ["Each flp gene is expressed in a distinct set of "
                          "neurons. Flp-13 is expressed in the ASE sensory "
                          "neurons, the DD motor neurons, the 15, M3 and M5 "
                          "cholinergic pharyngeal motoneurons, and the ASG, "
                          "ASK and BAG neurons."])
        self.assertEqual(seq_record.annotations["comment_toxicdose"],
                         ["LD(50) is 50 ug/kg in mouse by "
                          "intracerebroventricular injection "
                          "and 600 ng/g in Blatella germanica."])

    def test_sp016(self):
        """Parsing SwissProt file sp016."""
        filename = "sp016"
        # test the record parser

        datafile = os.path.join("SwissProt", filename)

        test_handle = open(datafile)
        seq_record = SeqIO.read(test_handle, "swiss")
        test_handle.close()

        self.assertTrue(isinstance(seq_record, SeqRecord))

        # test ProteinExistence (the numerical value describing the evidence for the existence of the protein)
        self.assertEqual(seq_record.annotations["protein_existence"], 1)
        # test Sequence version
        self.assertEqual(seq_record.annotations["sequence_version"], 1)
        # test Entry version
        self.assertEqual(seq_record.annotations["entry_version"], 93)

    def test_sp002(self):
        """Parsing SwissProt file sp002."""
        filename = "sp002"
        # test the record parser

        datafile = os.path.join("SwissProt", filename)

        test_handle = open(datafile)
        seq_record = SeqIO.read(test_handle, "swiss")
        test_handle.close()

        self.assertTrue(isinstance(seq_record, SeqRecord))

        # test Sequence version
        self.assertEqual(seq_record.annotations["sequence_version"], 34)
        # test Entry version
        self.assertEqual(seq_record.annotations["entry_version"], 36)

    def compare_txt_xml(self, old, new):
        """Compare text and XML based parser output."""
        self.assertEqual(old.id, new.id)
        self.assertEqual(old.name, new.name)
        self.assertEqual(len(old), len(new))
        self.assertEqual(str(old.seq), str(new.seq))
        for key in set(old.annotations).intersection(new.annotations):
            if key == "references":
                self.assertEqual(len(old.annotations[key]),
                                 len(new.annotations[key]))
                for r1, r2 in zip(old.annotations[key], new.annotations[key]):
                    # Tweak for line breaks in plain text SwissProt
                    r1.title = r1.title.replace("- ", "-")
                    r2.title = r2.title.replace("- ", "-")
                    r1.journal = r1.journal.rstrip(".")  # Should parser do this?
                    r1.medline_id = ""  # Missing in UniPort XML? TODO - check
                    # Lots of extra comments in UniProt XML
                    r1.comment = ""
                    r2.comment = ""
                    if not r2.journal:
                        r1.journal = ""
                    compare_reference(r1, r2)
            elif old.annotations[key] == new.annotations[key]:
                pass
            elif key in ["date"]:
                # TODO - Why is this a list vs str?
                pass
            elif not isinstance(old.annotations[key], type(new.annotations[key])):
                raise TypeError("%s gives %s vs %s" %
                                (key, old.annotations[key], new.annotations[key]))
            elif key in ["organism"]:
                if old.annotations[key] == new.annotations[key]:
                    pass
                elif old.annotations[key].startswith(new.annotations[key] + " "):
                    pass
                else:
                    raise ValueError(key)
            elif (isinstance(old.annotations[key], list) and
                  sorted(old.annotations[key]) == sorted(new.annotations[key])):
                pass
            else:
                raise ValueError("%s gives %s vs %s" %
                                 (key, old.annotations[key], new.annotations[key]))
        self.assertEqual(len(old.features), len(new.features),
                         "Features in %s, %i vs %i" %
                         (old.id, len(old.features), len(new.features)))
        for f1, f2 in zip(old.features, new.features):
            """
            self.assertEqual(f1.location.nofuzzy_start, f2.location.nofuzzy_start,
                             "%s %s vs %s %s" %
                             (f1.location, f1.type, f2.location, f2.type))
            self.assertEqual(f1.location.nofuzzy_end, f2.location.nofuzzy_end,
                             "%s %s vs %s %s" %
                             (f1.location, f1.type, f2.location, f2.type))
            """
            self.assertEqual(repr(f1.location), repr(f2.location),
                             "%s %s vs %s %s" %
                             (f1.location, f1.type, f2.location, f2.type))

    def test_Q13639(self):
        """Compare SwissProt text and uniprot XML versions of Q13639."""
        old = SeqIO.read("SwissProt/Q13639.txt", "swiss")
        new = SeqIO.read("SwissProt/Q13639.xml", "uniprot-xml")
        self.compare_txt_xml(old, new)

    def test_H2CNN8(self):
        """Compare SwissProt text and uniprot XML versions of H2CNN8."""
        old = SeqIO.read("SwissProt/H2CNN8.txt", "swiss")
        new = SeqIO.read("SwissProt/H2CNN8.xml", "uniprot-xml")
        self.compare_txt_xml(old, new)

    def test_F2CXE6(self):
        """Compare SwissProt text and uniprot XML versions of F2CXE6."""
        # This evil record has a semi-colon in the genem name,
        # GN   Name=HvPIP2;8 {ECO:0000313|EMBL:BAN04711.1};
        # <gene><name type="primary" evidence="3">HvPIP2;8</name></gene>
        old = SeqIO.read("SwissProt/F2CXE6.txt", "swiss")
        new = SeqIO.read("SwissProt/F2CXE6.xml", "uniprot-xml")
        self.compare_txt_xml(old, new)
        # TODO - Why the mismatch gene_name vs gene_name_primary?
        # TODO - Handle evidence codes on GN line (see GitHub isse #416)
        self.assertEqual(old.annotations["gene_name"], "Name=HvPIP2;8 {ECO:0000313|EMBL:BAN04711.1};")
        self.assertEqual(new.annotations["gene_name_primary"], "HvPIP2;8")
        self.assertEqual(old.name, "F2CXE6_HORVD")
        self.assertEqual(new.name, "F2CXE6_HORVD")

    def test_P84001(self):
        """Parse mass spec structured comment with unknown loc."""
        xml = list(SeqIO.parse("SwissProt/P84001.xml", "uniprot-xml"))[0]
        self.assertEqual(xml.id, "P84001")
        self.assertEqual(len(xml.annotations["comment_massspectrometry"]), 1)
        self.assertEqual(xml.annotations["comment_massspectrometry"][0], "undefined:9571|Electrospray")

    def test_multi_ex(self):
        """Compare SwissProt text and uniprot XML versions of several examples."""
        txt_list = list(SeqIO.parse("SwissProt/multi_ex.txt", "swiss"))
        xml_list = list(SeqIO.parse("SwissProt/multi_ex.xml", "uniprot-xml"))
        fas_list = list(SeqIO.parse("SwissProt/multi_ex.fasta", "fasta"))
        with open("SwissProt/multi_ex.list") as handle:
            ids = [x.strip() for x in handle]
        self.assertEqual(len(txt_list), len(ids))
        self.assertEqual(len(txt_list), len(fas_list))
        self.assertEqual(len(txt_list), len(xml_list))
        for txt, xml, fas, id in zip(txt_list, xml_list, fas_list, ids):
            self.assertEqual(txt.id, id)
            self.assertIn(txt.id, fas.id.split("|"))
            self.assertEqual(str(txt.seq), str(fas.seq))
            self.compare_txt_xml(txt, xml)

    def test_multi_ex_index(self):
        """Index SwissProt text and uniprot XML versions of several examples."""
        txt_list = list(SeqIO.parse("SwissProt/multi_ex.txt", "swiss"))
        xml_list = list(SeqIO.parse("SwissProt/multi_ex.xml", "uniprot-xml"))
        with open("SwissProt/multi_ex.list") as handle:
            ids = [x.strip() for x in handle]
        txt_index = SeqIO.index("SwissProt/multi_ex.txt", "swiss")
        xml_index = SeqIO.index("SwissProt/multi_ex.xml", "uniprot-xml")
        self.assertEqual(sorted(txt_index), sorted(ids))
        self.assertEqual(sorted(xml_index), sorted(ids))
        # Check SeqIO.parse() versus SeqIO.index() for plain text "swiss"
        for old in txt_list:
            new = txt_index[old.id]
            compare_record(old, new)
        # Check SeqIO.parse() versus SeqIO.index() for XML "uniprot-xml"
        for old in xml_list:
            new = xml_index[old.id]
            compare_record(old, new)
        txt_index.close()
        xml_index.close()

    def test_submittedName_allowed(self):
        """Checks if parser supports new XML Element (submittedName)."""
        for entry in SeqIO.parse(open("SwissProt/R5HY77.xml"), "uniprot-xml"):
            self.assertEqual(entry.id, "R5HY77")
            self.assertEqual(entry.description, "Elongation factor Ts")


if __name__ == "__main__":
    runner = unittest.TextTestRunner(verbosity=2)
    unittest.main(testRunner=runner)
