Python ProvDocument.add_bundle方法代码示例

# 需要导入模块: from prov.model import ProvDocument [as 别名]
# 或者: from prov.model.ProvDocument import add_bundle [as 别名]

#.........这里部分代码省略.........

    def _get_model_parameters_estimations(self, error_model):
        """
        Infer model estimation method from the 'error_model'. Return an object
        of type ModelParametersEstimation.
        """
        if error_model.dependance == NIDM_INDEPEDENT_ERROR:
            if error_model.variance_homo:
                estimation_method = STATO_OLS
            else:
                estimation_method = STATO_WLS
        else:
            estimation_method = STATO_GLS

        mpe = ModelParametersEstimation(estimation_method, self.software.id)

        return mpe

    def use_prefixes(self, ttl):
        prefix_file = os.path.join(os.path.dirname(__file__), 'prefixes.csv')
        context = dict()
        with open(prefix_file, encoding="ascii") as csvfile:
            reader = csv.reader(csvfile)
            next(reader, None)  # skip the headers
            for alphanum_id, prefix, uri in reader:
                if alphanum_id in ttl:
                    context[prefix] = uri
                    ttl = "@prefix " + prefix + ": <" + uri + "> .\n" + ttl
                    ttl = ttl.replace(alphanum_id, prefix + ":")
                    if uri in ttl:
                        ttl = ttl.replace(alphanum_id, prefix + ":")
                elif uri in ttl:
                    context[prefix] = uri
                    ttl = "@prefix " + prefix + ": <" + uri + "> .\n" + ttl
                    ttl = ttl.replace(alphanum_id, prefix + ":")
        return (ttl, context)

    def save_prov_to_files(self, showattributes=False):
        """
        Write-out provn serialisation to nidm.provn.
        """
        self.doc.add_bundle(self.bundle)
        # provn_file = os.path.join(self.export_dir, 'nidm.provn')
        # provn_fid = open(provn_file, 'w')
        # # FIXME None
        # # provn_fid.write(self.doc.get_provn(4).replace("None", "-"))
        # provn_fid.close()

        ttl_file = os.path.join(self.export_dir, 'nidm.ttl')
        ttl_txt = self.doc.serialize(format='rdf', rdf_format='turtle')
        ttl_txt, json_context = self.use_prefixes(ttl_txt)

        # Add namespaces to json-ld context
        for namespace in self.doc._namespaces.get_registered_namespaces():
            json_context[namespace._prefix] = namespace._uri
        for namespace in \
                list(self.doc._namespaces._default_namespaces.values()):
            json_context[namespace._prefix] = namespace._uri
        json_context["xsd"] = "http://www.w3.org/2000/01/rdf-schema#"

        # Work-around to issue with INF value in rdflib (reported in
        # https://github.com/RDFLib/rdflib/pull/655)
        ttl_txt = ttl_txt.replace(' inf ', ' "INF"^^xsd:float ')
        with open(ttl_file, 'w') as ttl_fid:
            ttl_fid.write(ttl_txt)

        # print(json_context)
        jsonld_file = os.path.join(self.export_dir, 'nidm.json')
        jsonld_txt = self.doc.serialize(format='rdf', rdf_format='json-ld',
                                        context=json_context)
        with open(jsonld_file, 'w') as jsonld_fid:
            jsonld_fid.write(jsonld_txt)

        # provjsonld_file = os.path.join(self.export_dir, 'nidm.provjsonld')
        # provjsonld_txt = self.doc.serialize(format='jsonld')
        # with open(provjsonld_file, 'w') as provjsonld_fid:
        #     provjsonld_fid.write(provjsonld_txt)

        # provn_file = os.path.join(self.export_dir, 'nidm.provn')
        # provn_txt = self.doc.serialize(format='provn')
        # with open(provn_file, 'w') as provn_fid:
        #     provn_fid.write(provn_txt)

        # Post-processing
        if not self.zipped:
            # Just rename temp directory to output_path
            os.rename(self.export_dir, self.out_dir)
        else:
            # Create a zip file that contains the content of the temp directory
            os.chdir(self.export_dir)
            zf = zipfile.ZipFile(os.path.join("..", self.out_dir), mode='w')
            try:
                for root, dirnames, filenames in os.walk("."):
                    for filename in filenames:
                        zf.write(os.path.join(filename))
            finally:
                zf.close()
                # Need to move up before deleting the folder
                os.chdir("..")
                shutil.rmtree(os.path.join("..", self.export_dir))