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How to use _is_magic method in autotest

Best Python code snippet using autotest_python

sniffer.py

Source:sniffer.py

...83        if len(line) == 0:84            return True85        else:86            return False87    def _is_magic(self, filename, magic):88        """Figure out whether magic number of the file fits the argument."""89        data = open(filename, "rb")90        buff = data.read(56)91        L = len(magic)92        # we need at least L + 1 values93        if len(buff) <= L:94            return False95        # then, each magic number should fit the first bytes96        ret = [buff[i] == magic[i] for i in range(0, L)]97        # _log.debug("magic number: {}".format([hex(buff[i]) for i in range(0, L)]))98        # _log.debug("expected number: {}".format(magic))99        if False in ret:100            return False101        else:102            return True103    def is_abi(self, filename):104        try:105            data = open(filename, "rb")106            buff = data.read(4)107            if buff[0:4].decode() == "ABIF":108                return True109        except: #pragma: no cover110            return False111    def is_bam(self, filename):112        try:113            d = pysam.AlignmentFile(filename)114            return d.is_bam115        except:116            return False117    def is_bai(self, filename):118        try:119            data = open(filename, "rb").read()[0:4]120            if data.startswith(b"BAI"):121                return True122            else:123                return False124        except: #pragma: no cover125            return False126    def is_bcf(self, filename):127        try:128            d = pysam.VariantFile(filename)129            return d.is_bcf130        except: #pragma: no cover131            return False132    def is_binary_bed(self, filename):133        # This could be a BED binary file from plink134        # https://www.cog-genomics.org/plink2/formats#bed135        try:136            return self._is_magic(filename, [0x6C, 0x1B, 0x1])137        except:138            return False139    def is_bed(self, filename):140        try:141            data = open(filename, "r")142            line = data.readline()143            if len(line.split()) < 4:144                return False145            else:146                # reads 10 lines if possible. They should all be tab delimited147                # with same number of columns:148                L = len(line)149                for i in range(10):150                    line = data.readline().strip()151                    if len(line) != 4:152                        return False153                # let us assume it is a TSV-like file154                return True155        except:156            return False157    def is_bedgraph(self, filename):158        return self.is_bed(filename)159    def is_bigwig(self, filename):160        try:161            return self._is_magic(filename, [0x26, 0xFC, 0x8F])162        except:163            return False164    def is_bigbed(self, filename):165        try:166            return self._is_magic(filename, [0xEB, 0xF2, 0x89])167        except:168            return False169    def is_bplink(self, filename):170        raise NotImplementedError171    def is_bz2(self, filename):172        try:173            return self._is_magic(filename, [0x42, 0x5A, 0x68])174        except:175            return False176    def is_csv(self, filename):177        try:178            df = pd.read_csv(filename, sep=",")179            if len(df.columns) > 1:180                return True181        except:182            pass183    def is_cram(self, filename):184        try:185            d = pysam.AlignmentFile(filename)186            return d.is_cram187        except:188            return False189    def is_clustal(self, filename):190        with open(filename, "r") as fin:191            try:192                line = fin.readline().strip()193                if self._is_blank_line(line):194                    pass195            except:196                return False197    def is_dsrc(self, filename):198        try:199            # FIXME not sure whether we need more characters ?200            return self._is_magic(filename, [0xAA, 0x2])201        except:202            return False203    def is_embl(self, filename):204        # FIXME205        # here we naively read 20 lines and extract the first 2 letters checking206        # whether there are within the list of authorised values207        # non exhaustive list208        valid_ids = [209            "ID",210            "XX",211            "AC",212            "DE",213            "KW",214            "OS",215            "OC",216            "RN",217            "RA",218            "RT",219            "FT",220            "FH",221        ]222        try:223            with open(filename, "r") as fin:224                data = fin.readlines(200000)  # 200000 characters should be enough225            ids = [x.split()[0] for x in data if x[0:2] in valid_ids]226            # can be only of length 2227            ids = [x for x in ids if len(x) == 2]228            if len(ids) > 0:229                return True230            else:231                return False232        except:233            return False234    def is_ena(self, filename):235        try:236            data = open(filename, "r")237            L1 = data.readline()238            if L1.startswith("ID"):239                return True240            else:241                return False242        except:243            return False244    def is_fasta(self, filename):245        # FIXME this is valid for FASTA246        try:247            data = open(filename, "r")248            line1 = data.readline()249            line2 = data.readline()250            if line1.startswith(">") and line2[0] in "ABCDEFGHIKLMNPQRSTUVWYZX*-":251                return True252            else:253                return False254        except:255            return False256    def is_fastq(self, filename):257        try:258            data = open(filename, "r")259            line1 = data.readline()260            line2 = data.readline()261            line3 = data.readline()262            line4 = data.readline()263            if line1.startswith("@") and line3.startswith("+"):264                return True265            else:266                return False267        except:268            return False269    def is_genbank(self, filename):270        with open(filename, "r") as fin:271            try:272                line = fin.readline().strip()273                data = line.split()274                if data[0] == "LOCUS":275                    return True276                else:277                    return False278            except:279                return False280    def is_gfa(self, filename):281        # GFA1282        # Type descr283        # #   Comment284        # H   Header285        # S   Segment286        # L   Link287        # C   Containment288        # P   Path289        # optional fields are also possible: A, i, f, Z, J, H, B290        # GFA2291        # There is an integer length field in S-lines.292        # The L- and C-lines have been replaced by a consolidated E-line.293        # The P-line has been replaced with U- and O-lines that encode subgraphs and294        # paths, respectively, and can take edge idâs, obviating the need for orientation295        # signs and alignments between segments.296        # There is a new F-line for describing multi-alignments and a new G-line for297        # describing scaffolds.298        # Alignments can be trace length sequences as well as CIGAR strings.299        # Positions have been extended to include a postfix $ symbol for positions300        # representing the end of a read.301        # Segments, edges, and paths all have an orientation that is specified with a302        # postfix + or - symbol in contexts where the orientation is needed.303        try:304            # gfa1305            is_gfa1 = self._is_gfa1(filename)306            is_gfaXX = self._is_gfaXX(filename)307            if is_gfa1 or is_gfaXX:308                return True309            else:310                return False311        except Exception as err:312            print(err)313            return False314    def _is_gfa1(self, filename):315        with open(filename, "r") as fin:316            data = fin.readlines(200000)  # 200000 characters should be enough317        ids = [x.split()[0] for x in data]318        if "H" in ids and "S" in ids and "L" in ids:319            return True320        else:321            return False322    def _is_gfaXX(self, filename):323        # FIXME: need to be sure the test files are correct.324        # there are two right now one GFA1 the other is unclear since starting325        # values can be S but also a326        with open(filename, "r") as fin:327            data = fin.readlines(200000)  # 200000 characters should be enough328        ids = [x.split()[0] for x in data]329        if "a" in ids and "S":330            return True331        else:332            return False333    def is_gff2(self, filename):334        try:335            with open(filename, "r") as fin:336                data = fin.readline()337                if "gff-version 2" in data.strip():338                    return True339                else:340                    return False341        except:342            return False343    def is_gff3(self, filename):344        try:345            with open(filename, "r") as fin:346                data = fin.readline()347                if "gff-version 3" in data.strip():348                    return True349                else:350                    return False351        except:352            return False353    def is_gz(self, filename):354        try:355            return self._is_magic(filename, [0x1F, 0x8B])356        except:357            return False358    def is_json(self, filename):359        try:360            with open(filename) as fin:361                data = fin.read()362                json.loads(data)363                return True364        except:365            return False366    def is_maf(self, filename):367        with open(filename, "r") as fin:368            try:369                # read at most 50 lines and figure out whether370                # some lines starts with a or s371                # we get rid of the comments.372                # Read 5000 characters at most.373                data = fin.readlines(5000)374                comments = [line for line in data if line.startswith("#")]375                data = [line.strip() for line in data if line.startswith("#") is False]376                # get rid of blank lines377                data = [line for line in data if len(line.strip()) != 0]378                starts = [line[0:2] for line in data]379                if len(starts) == 0:380                    return False381                # line must start with one of i, e, q, a, s letter382                for x in starts:383                    assert x in ["a ", "s ", "e ", "q ", "i "]384                return True385            except Exception as err:386                _log.debug(err)387                return False388    def is_newick(self, filename):389        try:390            with open(filename, "r") as fin:391                data = fin.readlines()392                if data[0].strip()[0] == "(" and data[-1].strip()[-1] == ";":393                    return True394                else:395                    return False396        except:397            return False398    def is_nexus(self, filename):399        try:400            with open(filename, "r") as fin:401                line = fin.readline()402                if line.startswith("#NEXUS"):403                    return True404                else:405                    return False406        except:407            return False408    def is_ods(self, filename):409        try:410            return self._is_magic(filename, [0x50, 0x4B, 0x03, 0x04])411        except:412            return False413    def is_paf(self, filename):414        try:415            df = pd.read_csv(filename, sep=r"\s+", header=None)416            if len(df.columns) >= 12:417                if set(df.loc[:, 4]) == set(["+", "-"]):418                    return True419            return False420        except Exception as err:421            return False422    def is_phylip(self, filename):423        with open(filename, "r") as fin:424            # First, we figure out the dimensions of the alignemnt.425            # we should find 2 integers426            # blank lines are forbidden in  principle between header an427            # alignment428            try:429                header = fin.readline().strip()430                first = fin.readline().strip()431                m, n = header.split()432                m = int(m)433                n = int(n)434                name, seq = first.split(" ", 1)435                seq = seq.replace(" ", "")436                # we identify each alignement and check that the length are437                # identical and equal to n438                for this in range(1, m - 1):  # -1 since we already read 1 line439                    nextline = fin.readline().strip()440                    name, seq2 = nextline.split(" ", 1)441                    seq2 = seq2.replace(" ", "")442                    assert len(seq) == len(seq2), "not same length"443                return True444            except Exception as err:445                # print(err)446                return False447    def is_phyloxml(self, filename):448        try:449            tree = ET.parse(filename)450            tree.getroot()451            root = tree.getroot()452            if "phyloxml" in root.tag:453                return True454            else:455                return False456        except:457            return False458    def is_plink(self, filename):459        raise NotImplementedError460    def is_qual(self, filename):461        # if line1.startswith(">") and line2[0] in "ABCDEFGHIKLMNPQRSTUVWYZX*-":462        try:463            data = open(filename, "r")464            line1 = data.readline()465            line2 = data.readline()466            # we check the first line identifier.467            # then, we scan the entire line searching of encoding qualities468            # hoping that values between 33 and 126 will be enough to469            # differentiate them from the standard nucleotides and protein470            # characters.471            scores = [x for x in line2 if x not in "ABCDEFGHIKLMNPQRSTUVWYZX*-"]472            # if we find a character (e.g !, #ietc) it means is a quality file473            # however, if we do not find such a value, it does not mean it is474            # not a quality.475            # For instance, there is no way to say that ::476            #    >ID477            #    AACCTTGG478            # is a qual or fasta file479            if line1.startswith(">") and len(scores) > 1:480                return True481            else:482                return False483        except:484            return False485    def is_sam(self, filename):486        try:487            d = pysam.AlignmentFile(filename)488            return d.is_sam489        except:490            return False491    def is_scf(self, filename):492        try:493            data = open(filename, "rb")494            buff = data.read(56)495            if buff[0:4].decode() == ".scf":496                return True497        except:498            return False499    def is_stockholm(self, filename):500        with open(filename, "r") as fin:501            try:502                header = fin.readline().strip()503                assert "STOCKHOLM" in header504                return True505            except:506                return False507    def is_rar(self, filename):508        try:509            c1 = self._is_magic(filename, [0x52, 0x61, 0x72, 0x21, 0x1A, 0x7, 0x0])510            c2 = self._is_magic(filename, [0x52, 0x61, 0x72, 0x21, 0x1A, 0x7, 0x0])511            if c1 or c2:512                return True513            else:514                return False515        except:516            return False517    def is_twobit(self, filename):518        try:519            data = open(filename, "rb")520            buff = data.read(16)521            if 0x43 in buff and 0x27 in buff:522                return True523            else:524                return False525        except:526            return False527    def is_tsv(self, filename):528        try:529            df = pd.read_csv(filename, sep=r"\s+")530            if len(df.columns) > 1:531                return True532        except:533            pass534    def is_vcf(self, filename):535        try:536            d = pysam.VariantFile(filename)537            return d.is_vcf538        except:539            return False540    def is_wiggle(self, filename):541        return self.is_wig(filename)542    def is_wig(self, filename):543        try:544            with open(filename, "r") as fin:545                line = fin.readline()546                if "track" in line and "type=wiggle" in line:547                    return True548                else:549                    return False550        except:551            return False552    def is_xls(self, filename):553        try:554            return self._is_magic(filename, [0xD0, 0xCF, 0x11])555        except:556            return False557    def is_xlsx(self, filename):558        try:559            # FIXME only second case should be used most probably560            case1 = self._is_magic(filename, [0xD0, 0xCF, 0x11])561            case2 = self._is_magic(filename, [0x50, 0x4B, 0x3, 0x4])562            if case1 or case2:563                return True564            else:565                return False566        except:567            return False568    def is_xmfa(self, filename):569        try:570            with open(filename, "r") as fin:571                line = fin.readline()572                if "FormatVersion" in line and "Mauve" in line:573                    return True574                else:575                    return False576        except:577            return False578    def is_yaml(self, filename):579        try:580            data = yaml.load(open(filename, "r"), Loader=yaml.FullLoader)581            if data.keys():582                return True583        except:584            return False585    def is_zip(self, filename):586        try:587            c1 = self._is_magic(filename, [0x50, 0x4B, 0x3, 0x4])588            c2 = self._is_magic(filename, [0x50, 0x4B, 0x3, 0x4])589            c3 = self._is_magic(filename, [0x50, 0x4B, 0x3, 0x4])590            if c1 or c2 or c3:591                return True592            else:593                return False594        except:595            return False596    def is_7zip(self, filename):597        try:598            return self._is_magic(filename, [0x37, 0x7A, 0xBC, 0xAF, 0x27, 0x1C])599        except:600            return False601    def is_xz(self, filename):602        try:603            return self._is_magic(filename, [0xFD, 0x37, 0x7A, 0x58, 0x5A, 0x00])604        except:...

ultramock.py

Source:ultramock.py

1# -*- coding: utf-8 -*-2#3# This file is part of Invenio.4# Copyright (C) 2015 CERN.5#6# Invenio is free software; you can redistribute it7# and/or modify it under the terms of the GNU General Public License as8# published by the Free Software Foundation; either version 2 of the9# License, or (at your option) any later version.10#11# Invenio is distributed in the hope that it will be12# useful, but WITHOUT ANY WARRANTY; without even the implied warranty of13# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU14# General Public License for more details.15#16# You should have received a copy of the GNU General Public License17# along with Invenio; if not, write to the18# Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston,19# MA 02111-1307, USA.20#21# In applying this license, CERN does not22# waive the privileges and immunities granted to it by virtue of its status23# as an Intergovernmental Organization or submit itself to any jurisdiction.24"""Hijacks `mock` to fake as many non-available modules as possible."""25import sys26import types27try:28    import unittest.mock as mock29except ImportError:30    import mock31# skip `_is_magic` check.32orig_is_magic = mock._is_magic33def always_false(*args, **kwargs):34    return False35# avoid spec configuration for mocked classes with super classes.36# honestly this does not happen very often and is kind of a tricky case.37orig_mock_add_spec = mock.NonCallableMock._mock_add_spec38def mock_add_spec_fake(self, spec, spec_set):39    orig_mock_add_spec(self, None, None)40# special MagicMock with empty docs41class MyMagicMock(mock.MagicMock):42    """"""43# set up a fake class-metaclass hierarchy44class SuperMockMetaMeta(MyMagicMock):45    __metaclass__ = MyMagicMock()46class SuperMockMeta(MyMagicMock):47    __metaclass__ = SuperMockMetaMeta48class SuperMock(MyMagicMock):49    __metaclass__ = SuperMockMeta50class MockedModule(types.ModuleType):51    def __init__(self, name):52        super(types.ModuleType, self).__init__(name)53        self.__name__ = super.__name__54        self.__file__ = self.__name__.replace('.', '/') + '.py'55        sys.modules[self.__name__] = self56    def __getattr__(self, key):57        obj = SuperMock58        setattr(self, key, obj)59        return obj60# overwrite imports61orig_import = __import__62def import_mock(name, *args, **kwargs):63    try:64        return orig_import(name, *args, **kwargs)65    except ImportError:66        return MockedModule(name)67import_patch = mock.patch('__builtin__.__import__', side_effect=import_mock)68# public methods69def activate():70    mock._is_magic = always_false71    mock.NonCallableMock._mock_add_spec = mock_add_spec_fake72    import_patch.start()73def deactivate():74    import_patch.stop()75    mock.NonCallableMock._mock_add_spec = orig_mock_add_spec...

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