Python GraphUtils.addComment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 addComment [as 别名]

#.........这里部分代码省略.........

        sex_specific_genotype_id = '_'+'-'.join((re.sub(r':', '', strain_id),
                                                 sex, 'genotype'))
        if strain_label is not None:
            sex_specific_genotype_label = strain_label + ' (' + sex + ')'
        else:
            sex_specific_genotype_label = strain_id + '(' + sex + ')'

        if self.nobnodes:
            genotype_id = ':'+genotype_id
            sex_specific_genotype_id = ':'+sex_specific_genotype_id

        genotype_type = Genotype.genoparts['sex_qualified_genotype']
        if sex == 'm':
            genotype_type = Genotype.genoparts['male_genotype']
        elif sex == 'f':
            genotype_type = Genotype.genoparts['female_genotype']

        # add the genotype to strain connection
        self.geno.addGenotype(
            genotype_id, genotype_label,
            Genotype.genoparts['genomic_background'])
        self.gu.addTriple(
            g, strain_id,
            Genotype.object_properties['has_genotype'], genotype_id)

        self.geno.addGenotype(
            sex_specific_genotype_id, sex_specific_genotype_label,
            genotype_type)

        # add the strain as the background for the genotype
        self.gu.addTriple(
            g, sex_specific_genotype_id,
            Genotype.object_properties['has_sex_agnostic_genotype_part'],
            genotype_id)

        # #############    BUILD THE G2P ASSOC    #############
        # TODO add more provenance info when that model is completed

        if phenotypes is not None:
            for phenotype_id in phenotypes:
                assoc = G2PAssoc(
                    self.name, sex_specific_genotype_id, phenotype_id)
                assoc.add_evidence(assay_id)
                assoc.add_evidence(eco_id)
                assoc.add_association_to_graph(g)
                assoc_id = assoc.get_association_id()
                self.gu.addComment(g, assoc_id, comment)

        return

    def getTestSuite(self):
        import unittest
        from tests.test_mpd import MPDTestCase

        test_suite = unittest.TestLoader().loadTestsFromTestCase(MPDTestCase)

        return test_suite

    @staticmethod
    def normalise_units(units):
        # todo:
        return units

    @staticmethod
    def build_measurement_description(row):
        (assay_id, projsym, varname, descrip, units, cat1, cat2, cat3,
         intervention, intparm, appmeth, panelsym, datatype, sextested,
         nstrainstested, ageweeks) = row

        if sextested == 'f':
            sextested = 'female'
        elif sextested == 'm':
            sextested = 'male'
        elif sextested == 'fm':
            sextested = 'male and female'
        else:
            logger.warning("Unknown sex tested key: %s", sextested)
        description = "This is an assay of [" + descrip + "] shown as a [" + \
                      datatype + "] measured in [" + units + "]"

        if intervention is not None and intervention != "":
            description += " in response to [" + intervention + "]"
        if intparm is not None and intervention != "":
            description += \
                ". This represents the [" + intparm + \
                "] arm, using materials and methods that included [" +\
                appmeth + "]"

        description += \
            ".  The overall experiment is entitled [" + projsym + "].  "

        description += \
            "It was conducted in [" + sextested + "] mice at [" + \
            ageweeks + "] of age in" + " [" + nstrainstested + \
            "] different mouse strains. "
        description += "Keywords: " + cat1 + \
                       ((", " + cat2) if cat2.strip() is not "" else "") + \
                       ((", " + cat3) if cat3.strip() is not "" else "") + "."
        return description

# 需要导入模块: from dipper.utils.GraphUtils import GraphUtils [as 别名]
# 或者: from dipper.utils.GraphUtils.GraphUtils import addComment [as 别名]
    def _process_nlx_157874_1_view(self, raw, limit=None):
        """
        This table contains the Elements of Morphology data that has been
        screen-scraped into DISCO.
        Note that foaf:depiction is inverse of foaf:depicts relationship.

        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'])

#.........这里部分代码省略.........

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

#.........这里部分代码省略.........
                                 self.stored_omia_mol_gen[phene]['mol_gen'],
                                 self.stored_omia_mol_gen[phene]['map_info'],
                                 self.stored_omia_mol_gen[phene]['species']))

        logger.info(
            "Wrote %d potential G2P descriptions for curation to %s",
            len(self.stored_omia_mol_gen), f)

        return

    def _process_article_row(self, row):

        # don't bother in test mode
        if self.testMode:
            return

        iarticle_id = self._make_internal_id('article', row['article_id'])
        self.id_hash['article'][row['article_id']] = iarticle_id
        rtype = None
        if row['journal'] != '':
            rtype = Reference.ref_types['journal_article']
        r = Reference(iarticle_id, rtype)

        if row['title'] is not None:
            r.setTitle(row['title'].strip())
        if row['year'] is not None:
            r.setYear(row['year'])
        r.addRefToGraph(self.g)

        if row['pubmed_id'] is not None:
            pmid = 'PMID:'+str(row['pubmed_id'])
            self.id_hash['article'][row['article_id']] = pmid
            self.gu.addSameIndividual(self.g, iarticle_id, pmid)
            self.gu.addComment(self.g, pmid, iarticle_id)

        return

    def _process_omia_group_row(self, row):
        omia_id = 'OMIA:'+row['omia_id']

        if self.testMode and omia_id not in self.test_ids['disease']:
            return

        group_name = row['group_name']
        group_summary = row['group_summary']

        disease_id = None
        group_category = row.get('group_category')
        disease_id = \
            self.map_omia_group_category_to_ontology_id(group_category)
        if disease_id is not None:
            self.gu.addClassToGraph(self.g, disease_id, None)
            if disease_id == 'MP:0008762':  # embryonic lethal
                # add this as a phenotype association
                # add embryonic onset
                assoc = D2PAssoc(self.name, omia_id, disease_id)
                assoc.add_association_to_graph(self.g)
                disease_id = None
        else:
            logger.info(
                "No disease superclass defined for %s:  %s",
                omia_id, group_name)
            # default to general disease  FIXME this may not be desired
            disease_id = 'DOID:4'

        if group_summary == '':