How to use get_config_from_file method in toolium

Best Python code snippet using toolium_python

batchassist_test.py

Source:batchassist_test.py

...232    with open(conffile) as f:233        for line in f:234            confdict = json.loads(line)235    assert refdict[key] == confdict236def get_config_from_file(conf_from_file):237    configfilepaths = []238    targets = conf_from_file.get_targets()239    nontargetlist = []240    targets.sort()241    for target in targets:242        (243            minsize, maxsize, mpprimer, exception, target, path,244            intermediate, qc_gene, mfold, skip_download,245            assemblylevel, skip_tree, nolist,246            offline, ignore_qc, mfethreshold, customdb,247            blastseqs, probe, blastdbv5248                ) = conf_from_file.get_config(target)249        config = CLIconf(250            minsize, maxsize, mpprimer, exception, target, path,251            intermediate, qc_gene, mfold, skip_download,252            assemblylevel, nontargetlist, skip_tree,253            nolist, offline, ignore_qc, mfethreshold, customdb,254            blastseqs, probe, blastdbv5)255        config.save_config()256        cfilepath = os.path.join(257                config.path, config.target, "config", "config.json")258        configfilepaths.append(cfilepath)259    print(configfilepaths)260    return configfilepaths261def test_sys_exit(monkeypatch):262    monkeypatch.setattr('builtins.input', fail_input)263    with pytest.raises(SystemExit):264        conf_from_file = Config()265    monkeypatch.setattr('builtins.input', fail_startinput)266    with pytest.raises(SystemExit):267        conf_from_file = Config()268# mockprimer_csv = os.path.join(path, "Summary", target, abbr + "_primer.csv")269def test_default_input(monkeypatch):270    monkeypatch.setattr('builtins.input', alldef_input)271    conf_from_file = Config()272    configpath = get_config_from_file(conf_from_file)[0]273    compare_configfiles(reference_dict, configpath, "0")274    defdir = os.path.join("/", "Lactobacillus_curvatus")275    if os.path.isdir(defdir):276        shutil.rmtree(defdir)277def test_offline(monkeypatch):278    monkeypatch.setattr('builtins.input', offline_input)279    conf_from_file = Config()280    configpath = get_config_from_file(conf_from_file)[0]281    compare_configfiles(reference_dict, configpath, "1")282    if os.path.isfile(configpath):283        os.remove(configpath)284    configpath = get_config_from_file(conf_from_file)[1]285    compare_configfiles(reference_dict, configpath, "2")286    if os.path.isfile(configpath):287        os.remove(configpath)288    monkeypatch.setattr('builtins.input', offline_input2)289    conf_from_file = Config()290    configpath = get_config_from_file(conf_from_file)[0]291    compare_configfiles(reference_dict, configpath, "1")292    if os.path.isfile(configpath):293        os.remove(configpath)294    configpath = get_config_from_file(conf_from_file)[1]295    compare_configfiles(reference_dict, configpath, "2")296    if os.path.isfile(configpath):297        os.remove(configpath)298def test_nodefault(monkeypatch):299    G.create_directory(tmpdir)300    dbpath_tmp = os.path.join(tmpdir, "customdb.fas.nsq")301    with open(dbpath_tmp, "w") as f:302        f.write(">mockDB")303    try:304        monkeypatch.setattr('builtins.input', nodef_input)305        conf_from_file = Config()306        configpath = get_config_from_file(conf_from_file)[0]307        compare_configfiles(reference_dict, configpath, "3")308        if os.path.isfile(configpath):309            os.remove(configpath)310        configpath = get_config_from_file(conf_from_file)[1]311        compare_configfiles(reference_dict, configpath, "4")312        if os.path.isfile(configpath):313            os.remove(configpath)314        monkeypatch.setattr('builtins.input', nodef_input2)315        conf_from_file = Config()316        configpath = get_config_from_file(conf_from_file)[0]317        compare_configfiles(reference_dict, configpath, "8")318        configpath = get_config_from_file(conf_from_file)[1]319        compare_configfiles(reference_dict, configpath, "9")320    finally:321        if os.path.isfile(dbpath_tmp):322            os.remove(dbpath_tmp)323def test_start_all(monkeypatch):324    monkeypatch.setattr('builtins.input', start_input)325    conf_from_file = Config()326    configpath = get_config_from_file(conf_from_file)[0]327    compare_configfiles(reference_dict, configpath, "8")328    if os.path.isfile(configpath):329        os.remove(configpath)330    configpath = get_config_from_file(conf_from_file)[1]331    compare_configfiles(reference_dict, configpath, "9")332    if os.path.isfile(configpath):333        os.remove(configpath)334def test_start_unknown(monkeypatch):335    print("Start unknown")336    mock = batchassist_mock(start_oneinput, start_unknown)337    monkeypatch.setattr('builtins.input', mock.prompt_input)338    conf_from_file = Config()339    configpath = get_config_from_file(conf_from_file)[0]340    compare_configfiles(reference_dict, configpath, "8")341def test_start_wrong(monkeypatch):342    print("Start wrong")343    mock = batchassist_mock(save_wronginput, start_wronginput)344    monkeypatch.setattr('builtins.input', mock.prompt_input)345    conf_from_file = Config()346    configpath = get_config_from_file(conf_from_file)[0]347    compare_configfiles(reference_dict, configpath, "8")348    if os.path.isfile(configpath):349        os.remove(configpath)350def test_not_valid_input(monkeypatch):351    print("test not valid input")352    dbpath_tmp = os.path.join(tmpdir, "customdb.fas.nsq")353    with open(dbpath_tmp, "w") as f:354        f.write(">mockDB")355    try:356        mock = batchassist_mock(nodef_input, wrong_input)357        monkeypatch.setattr('builtins.input', mock.prompt_input)358        conf_from_file = Config()359        configpath = get_config_from_file(conf_from_file)[0]360        compare_configfiles(reference_dict, configpath, "3")361        if os.path.isfile(configpath):362            os.remove(configpath)363        configpath = get_config_from_file(conf_from_file)[1]364        compare_configfiles(reference_dict, configpath, "4")365        if os.path.isfile(configpath):366            os.remove(configpath)367        mock = batchassist_mock(nodef_input, wrong_input2)368        monkeypatch.setattr('builtins.input', mock.prompt_input)369        conf_from_file = Config()370        configpath = get_config_from_file(conf_from_file)[0]371        compare_configfiles(reference_dict, configpath, "7")372        if os.path.isfile(configpath):373            os.remove(configpath)374    finally:375        if os.path.isfile(dbpath_tmp):376            os.remove(dbpath_tmp)377def test_incomplete_config(monkeypatch):378    testfile = os.path.join(379        "/", "primerdesign", "test", "Lactobacillus_curvatus",380        "config", "config.json")381    incomplete_dict = {382            "target": "lactobacillus_curvatus", "path": "/primerdesign/test"}383    with open(testfile, "w") as f:384        f.write(json.dumps(incomplete_dict))385    monkeypatch.setattr('builtins.input', start_input)386    conf_from_file = Config()387    configpath = get_config_from_file(conf_from_file)[0]388    compare_configfiles(reference_dict, configpath, "5")389def prepare_tmp_db():390    t = os.path.join(testfiles_dir, "tmp_config.json")391    tmp_path = os.path.join(pipe_dir, "tmp_config.json")392    if os.path.isfile(tmp_path):393        os.remove(tmp_path)394    shutil.copy(t, tmp_path)395def remove_tmp_db():396    tmp_path = os.path.join(pipe_dir, "tmp_config.json")397    if os.path.isfile(tmp_path):398        os.remove(tmp_path)399def change_tmp_db():400    tmp_path = os.path.join(pipe_dir, "tmp_config.json")401    tmp_dict = {402        "new_run": {403            'modus': "continue", "targets": None,404            "path": "/primerdesign/test"},405        "email": "biologger@protonmail.com"}406    with open(tmp_path, "w") as f:407        f.write(json.dumps(tmp_dict))408def change_db_again():409    tmp_path = os.path.join(pipe_dir, "tmp_config.json")410    tmp_dict = {411        "new_run": {412            'modus': "continue",413            "targets": ["Lactobacillus_curvatus", "Lactobacillus_sunkii"],414            "path": "/primerdesign/test"},415        "email": "biologger@protonmail.com"}416    with open(tmp_path, "w") as f:417        f.write(json.dumps(tmp_dict))418def test_autorun():419    from speciesprimer import auto_run420    prepare_tmp_db()421    targets, conf_from_file, use_configfile = auto_run()422    assert targets == ["Lactobacillus_curvatus"]423    configpath = get_config_from_file(conf_from_file)[0]424    compare_configfiles(reference_dict, configpath, "6")425    change_tmp_db()426    targets, conf_from_file, use_configfile = auto_run()427    targets.sort()428    assert targets == ["Lactobacillus_curvatus", "Lactobacillus_helveticus"]429    configpath = get_config_from_file(conf_from_file)[0]430    compare_configfiles(reference_dict, configpath, "6")431    change_db_again()432    targets, conf_from_file, use_configfile = auto_run()433    assert targets == ["Lactobacillus_curvatus"]434    configpath = get_config_from_file(conf_from_file)[0]435    compare_configfiles(reference_dict, configpath, "6")436    remove_tmp_db()437def test_shellrun(monkeypatch):438    nt_nal = os.path.join("/", "blastdb", "nt.nal")439    if os.path.isfile(nt_nal):440        conf1 = os.path.join(441            "/", "primerdesign", "test", "Lactobacillus_curvatus",442            "config", "config.json")443        conf2 = os.path.join(444            "/", "primerdesign", "test", "Lactobacillus_helveticus",445            "config", "config.json")446        test = os.path.join("/", "primerdesign", "test")447        if os.path.isdir(test):448            shutil.rmtree(test)...

__main__.py

Source:__main__.py

...65    for _, seq, threshold, score in l:66        results.append(search_bigsi(bigsi, seq, threshold, score))67    return results68API = hug.API("bigsi-%s" % str(__version__))69def get_config_from_file(config_file):70    if config_file is None:71        if os.environ.get("BIGSI_CONFIG"):72            config_file = os.environ.get("BIGSI_CONFIG")73        else:74            return DEFAULT_CONFIG75    with open(config_file, "r") as infile:76        config = yaml.load(infile, Loader=yaml.FullLoader)77    return config78def chunks(l, n):79    """Yield successive n-sized chunks from l."""80    for i in range(0, len(l), n):81        yield l[i : i + n]82@hug.object(name="bigsi", version="0.1.1", api=API)83@hug.object.urls("/", requires=())84class bigsi(object):85    @hug.object.cli86    @hug.object.post("/insert", output_format=hug.output_format.pretty_json)87    def insert(self, config: hug.types.text, bloomfilter, sample):88        """Inserts a bloom filter into the graph89        e.g. bigsi insert ERR1010211.bloom ERR101021190        """91        config = get_config_from_file(config)92        index = BIGSI(config)93        return insert(index=index, bloomfilter=bloomfilter, sample=sample)94    @hug.object.cli95    @hug.object.post("/bloom")96    def bloom(self, ctx, outfile, config=None):97        """Creates a bloom filter from a sequence file or cortex graph. (fastq,fasta,bam,ctx)98        e.g. index insert ERR1010211.ctx99        """100        config = get_config_from_file(config)101        bf = bloom(102            config=config,103            outfile=outfile,104            kmers=extract_kmers_from_ctx(ctx, config["k"]),105        )106    @hug.object.cli107    @hug.object.post("/build", output_format=hug.output_format.pretty_json)108    def build(109        self,110        bloomfilters: hug.types.multiple = [],111        samples: hug.types.multiple = [],112        from_file: hug.types.text = None,113        config: hug.types.text = None,114    ):115        config = get_config_from_file(config)116        if from_file and bloomfilters:117            raise ValueError(118                "You can only specify blooms via from_file or bloomfilters, but not both"119            )120        elif from_file:121            samples = []122            bloomfilters = []123            with open(from_file, "r") as tsvfile:124                reader = csv.reader(tsvfile, delimiter="\t")125                for row in reader:126                    bloomfilters.append(row[0])127                    samples.append(row[1])128        if samples:129            assert len(samples) == len(bloomfilters)130        else:131            samples = bloomfilters132        if config.get("max_build_mem_bytes"):133            max_memory_bytes = humanfriendly.parse_size(config["max_build_mem_bytes"])134        else:135            max_memory_bytes = None136        return build(137            config=config,138            bloomfilter_filepaths=bloomfilters,139            samples=samples,140            max_memory=max_memory_bytes,141        )142    @hug.object.cli143    @hug.object.post("/merge", output_format=hug.output_format.pretty_json)144    def merge(self, config: hug.types.text, merge_config: hug.types.text):145        config = get_config_from_file(config)146        merge_config = get_config_from_file(merge_config)147        index1 = BIGSI(config)148        index2 = BIGSI(merge_config)149        merge(index1, index2)150        return {"result": "merged %s into %s." % (merge_config, config)}151    @hug.object.cli152    @hug.object.post(153        "/search",154        response_headers={"Access-Control-Allow-Origin": "*"},155        output=hug.output_format.text,156    )157    @hug.object.get(158        "/search",159        examples="seq=ACACAAACCATGGCCGGACGCAGCTTTCTGA",160        response_headers={"Access-Control-Allow-Origin": "*"},161        output=hug.output_format.text,162    )163    def search(164        self,165        seq: hug.types.text,166        threshold: hug.types.float_number = 1.0,167        config: hug.types.text = None,168        score: hug.types.smart_boolean = False,169        format: hug.types.one_of(["json", "csv"]) = "json",170    ):171        config = get_config_from_file(config)172        bigsi = BIGSI(config)173        d = search_bigsi(bigsi, seq, threshold, score)174        if format == "csv":175            return d_to_csv(d)176        else:177            return json.dumps(d, indent=4)178    @hug.object.cli179    @hug.object.post(180        "/variant_search",181        response_headers={"Access-Control-Allow-Origin": "*"},182        output=hug.output_format.text,183    )184    @hug.object.get(185        "/variant_search",186        response_headers={"Access-Control-Allow-Origin": "*"},187        output=hug.output_format.text,188    )189    def variant_search(190        self,191        reference: hug.types.text,192        ref: hug.types.text,193        pos: hug.types.number,194        alt: hug.types.text,195        gene: hug.types.text = None,196        genbank: hug.types.text = None,197        config: hug.types.text = None,198        format: hug.types.one_of(["json", "csv"]) = "json",199    ):200        config = get_config_from_file(config)201        bigsi = BIGSI(config)202        if genbank and gene:203            d = BIGSIAminoAcidMutationSearch(bigsi, reference, genbank).search(204                gene, ref, pos, alt205            )206        elif genbank or gene:207            raise ValueError("genbank and gene must be supplied together")208        else:209            d = BIGSIVariantSearch(bigsi, reference).search(ref, pos, alt)210        d["citation"] = "http://dx.doi.org/10.1038/s41587-018-0010-1"211        if format == "csv":212            return d_to_csv(d)213        else:214            return json.dumps(d, indent=4)215    @hug.object.cli216    @hug.object.post(217        "/bulk_search",218        response_headers={"Access-Control-Allow-Origin": "*"},219        output=hug.output_format.text,220    )221    @hug.object.get(222        "/bulk_search",223        examples="seqfile=query.fasta",224        response_headers={"Access-Control-Allow-Origin": "*"},225        output=hug.output_format.text,226    )227    def bulk_search(228        self,229        fasta: hug.types.text,230        threshold: hug.types.float_number = 1.0,231        config: hug.types.text = None,232        score: hug.types.smart_boolean = False,233        format: hug.types.one_of(["json", "csv"]) = "json",234        stream: hug.types.smart_boolean = False,235    ):236        config = get_config_from_file(config)237        fasta = Fasta(fasta)238        if not stream:239            _config = copy.copy(config)240            _config["nproc"] = 1241            csv_combined = ""242            nproc = config.get("nproc", 1)243            with multiprocessing.Pool(processes=nproc) as pool:244                args = [(_config, str(seq), threshold, score) for seq in fasta.values()]245                dd = pool.map_async(246                    search_bigsi_parallel, chunks(args, math.ceil(len(args) / nproc))247                ).get()248                dd = [item for sublist in dd for item in sublist]249            if format == "csv":250                return "\n".join([d_to_csv(d, False, False) for d in dd])251            else:252                return json.dumps(dd, indent=4)253        else:254            bigsi = BIGSI(config)255            csv_combined = ""256            for i, seq in enumerate(fasta.values()):257                seq = str(seq)258                d = {259                    "query": seq,260                    "threshold": threshold,261                    "results": bigsi.search(seq, threshold, score),262                    "citation": "http://dx.doi.org/10.1038/s41587-018-0010-1",263                }264                if format == "csv":265                    if i == 0:266                        with_header = True267                        carriage_return = False268                    elif i == len(fasta) - 1:269                        carriage_return = True270                    else:271                        with_header = False272                        carriage_return = False273                    csv_result = d_to_csv(d, with_header, carriage_return)274                    csv_combined += csv_result275                    if stream:276                        print(csv_result)277                else:278                    if stream:279                        print(json.dumps(d))280    @hug.object.cli281    @hug.object.delete("/", output_format=hug.output_format.pretty_json)282    def delete(self, config: hug.types.text = None):283        config = get_config_from_file(config)284        get_storage(config).delete_all()285def main():286    API.cli()287if __name__ == "__main__":...

main.py

Source:main.py

1from PIInterface import PIInterface2from QSeeIntegrator import QSeeIntegrator3import json4def get_config_from_file(filepath):5  try:6    with open(filepath, 'r') as j:7      json_data = json.load(j)8      return json_data9  except FileNotFoundError as e:10    print("No configuration found")11    raise(e)12def main():13  #Initialize PI Interface and QSeeIntegrator  Configurations14  pi_config = get_config_from_file("configurations/pi.json")15  qsee_config = get_config_from_file("configurations/qsee.json")16  #Collect PI Data17  pi_interface = PIInterface(pi_config)18  pi_data = pi_interface.collect_data(params=pi_config.get("StreamSetParameters"))19  #Transform PI Data for QSEE Analytics POST API Request20  qsee_integrator = QSeeIntegrator(qsee_config)21  transform_data = qsee_integrator.transform_data(pi_data)22  for readings in transform_data:23    print("Performing QSEE analytics api call")24    resp = qsee_integrator.post_analysis(transform_data[readings])25    resp_data = get_config_from_file("configurations/sample_qsee_response.json") #sample response26    if resp.status_code == 200:27      resp_data = resp.json()28      print("Pushing analytics data to PI")29      try:30        pi_interface.post_analytics_result(resp_data)31      except Exception as e:32        raise(e)33    else:34      pass #TODO Exception35if __name__ == "__main__":...

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