Python GraphUtils.addPage方法代码示例

# 需要导入模块: from dipper.utils.GraphUtils import GraphUtils [as 别名]
# 或者: from dipper.utils.GraphUtils.GraphUtils import addPage [as 别名]
    def _process_collection(self, collection_id, label, page):
        """
        This function will process the data supplied internally
        about the repository from Coriell.

        Triples:
            Repository a ERO:collection
            rdf:label Literal(label)
            foaf:page Literal(page)

        :param collection_id:
        :param label:
        :param page:
        :return:
        """
        # #############    BUILD THE CELL LINE REPOSITORY    #############
        for g in [self.graph, self.testgraph]:
            # FIXME: How to devise a label for each repository?
            gu = GraphUtils(curie_map.get())
            repo_id = 'CoriellCollection:'+collection_id
            repo_label = label
            repo_page = page

            gu.addIndividualToGraph(
                g, repo_id, repo_label, self.terms['collection'])
            gu.addPage(g, repo_id, repo_page)

        return

# 需要导入模块: from dipper.utils.GraphUtils import GraphUtils [as 别名]
# 或者: from dipper.utils.GraphUtils.GraphUtils import addPage [as 别名]
    def _get_process_allelic_variants(self, entry, g):
        gu = GraphUtils(curie_map.get())
        geno = Genotype(g)
        du = DipperUtil()
        if entry is not None:
            publist = {}  # to hold the entry-specific publication mentions for the allelic variants
            entry_num = entry['mimNumber']

            # process the ref list just to get the pmids
            ref_to_pmid = self._get_pubs(entry, g)

            if 'allelicVariantList' in entry:
                allelicVariantList = entry['allelicVariantList']
                for al in allelicVariantList:
                    al_num = al['allelicVariant']['number']
                    al_id = 'OMIM:'+str(entry_num)+'.'+str(al_num).zfill(4)
                    al_label = None
                    al_description = None
                    if al['allelicVariant']['status'] == 'live':
                        publist[al_id] = set()
                        if 'mutations' in al['allelicVariant']:
                            al_label = al['allelicVariant']['mutations']
                        if 'text' in al['allelicVariant']:
                            al_description = al['allelicVariant']['text']
                            m = re.findall('\{(\d+)\:', al_description)
                            publist[al_id] = set(m)
                        geno.addAllele(al_id, al_label, geno.genoparts['variant_locus'], al_description)
                        geno.addAlleleOfGene(al_id, 'OMIM:'+str(entry_num),
                                             geno.object_properties['is_sequence_variant_instance_of'])
                        for r in publist[al_id]:
                            pmid = ref_to_pmid[int(r)]
                            gu.addTriple(g, pmid, gu.object_properties['is_about'], al_id)
                        # look up the pubmed id in the list of references
                        if 'dbSnps' in al['allelicVariant']:
                            dbsnp_ids = re.split(',', al['allelicVariant']['dbSnps'])
                            for dnum in dbsnp_ids:
                                did = 'dbSNP:'+dnum.strip()
                                gu.addIndividualToGraph(g, did, None)
                                gu.addEquivalentClass(g, al_id, did)
                        if 'clinvarAccessions' in al['allelicVariant']:
                            # clinvarAccessions triple semicolon delimited, each lik eRCV000020059;;1
                            rcv_ids = re.split(';;;', al['allelicVariant']['clinvarAccessions'])
                            rcv_ids = [(re.match('(RCV\d+)\;\;', r)).group(1) for r in rcv_ids]
                            for rnum in rcv_ids:
                                rid = 'ClinVar:'+rnum
                                gu.addXref(g, al_id, rid)
                        gu.addPage(g, al_id, "http://omim.org/entry/"+str(entry_num)+"#"+str(al_num).zfill(4))
                    elif re.search('moved', al['allelicVariant']['status']):
                        # for both 'moved' and 'removed'
                        moved_ids = None
                        if 'movedTo' in al['allelicVariant']:
                            moved_id = 'OMIM:'+al['allelicVariant']['movedTo']
                            moved_ids = [moved_id]
                        gu.addDeprecatedIndividual(g, al_id, moved_ids)
                    else:
                        logger.error('Uncaught alleleic variant status %s', al['allelicVariant']['status'])
                # end loop allelicVariantList

        return

# 需要导入模块: from dipper.utils.GraphUtils import GraphUtils [as 别名]
# 或者: from dipper.utils.GraphUtils.GraphUtils import addPage [as 别名]

#.........这里部分代码省略.........
        Since it is bad form to have two definitions,
        we concatenate the two into one string.

        Triples:
            <eom id> a owl:Class
                rdf:label Literal(eom label)
                OIO:hasRelatedSynonym Literal(synonym list)
                IAO:definition Literal(objective_def. subjective def)
                foaf:depiction Literal(small_image_url),
                               Literal(large_image_url)
                foaf:page Literal(page_url)
                rdfs:comment Literal(long commented text)


        :param raw:
        :param limit:
        :return:
        """

        gu = GraphUtils(curie_map.get())
        line_counter = 0
        with open(raw, 'r') as f1:
            f1.readline()  # read the header row; skip
            filereader = csv.reader(f1, delimiter='\t', quotechar='\"')
            for line in filereader:
                line_counter += 1
                (morphology_term_id, morphology_term_num,
                 morphology_term_label, morphology_term_url,
                 terminology_category_label, terminology_category_url,
                 subcategory, objective_definition, subjective_definition,
                 comments, synonyms, replaces, small_figure_url,
                 large_figure_url, e_uid, v_uid, v_uuid,
                 v_last_modified) = line

                # note:
                # e_uid v_uuid v_last_modified terminology_category_url
                # subcategory v_uid morphology_term_num
                # terminology_category_label hp_label notes
                # are currently unused.

                # Add morphology term to graph as a class
                # with label, type, and description.
                gu.addClassToGraph(self.graph, morphology_term_id,
                                   morphology_term_label)

                # Assemble the description text

                if subjective_definition != '' and not (
                        re.match(r'.+\.$', subjective_definition)):
                    # add a trailing period.
                    subjective_definition = subjective_definition.strip() + '.'
                if objective_definition != '' and not (
                        re.match(r'.+\.$', objective_definition)):
                    # add a trailing period.
                    objective_definition = objective_definition.strip() + '.'

                definition = \
                    '  '.join(
                        (objective_definition, subjective_definition)).strip()

                gu.addDefinition(self.graph, morphology_term_id, definition)

                # <term id> FOAF:depicted_by literal url
                # <url> type foaf:depiction

                # do we want both images?
                # morphology_term_id has depiction small_figure_url
                if small_figure_url != '':
                    gu.addDepiction(self.graph, morphology_term_id,
                                    small_figure_url)

                # morphology_term_id has depiction large_figure_url
                if large_figure_url != '':
                    gu.addDepiction(self.graph, morphology_term_id,
                                    large_figure_url)

                # morphology_term_id has comment comments
                if comments != '':
                    gu.addComment(self.graph, morphology_term_id,
                                  comments.strip())

                if synonyms != '':
                    for s in synonyms.split(';'):
                        gu.addSynonym(
                            self.graph, morphology_term_id, s.strip(),
                            gu.properties['hasExactSynonym'])

                # morphology_term_id hasRelatedSynonym replaces (; delimited)
                if replaces != '' and replaces != synonyms:
                    for s in replaces.split(';'):
                        gu.addSynonym(
                            self.graph, morphology_term_id, s.strip(),
                            gu.properties['hasRelatedSynonym'])

                # morphology_term_id has page morphology_term_url
                gu.addPage(self.graph, morphology_term_id, morphology_term_url)

                if limit is not None and line_counter > limit:
                    break
        return