Python ProvDocument.used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 used [as 别名]
def ctfToProv():
    d1 = ProvDocument()
    dummy = ProvDocument()
    ex = Namespace('ex', 'http://example/')  # namespaces do not need to be explicitly added to a document
    #data = event_field(os.path.join(trace_path,'../config.yaml'))
    counter = 0
    counter_1 = 0
    relationships = []
    entities = []
    activities = []
    producer_events = {}
    for event in trace_collection.events:
        dataset = {'ex:'+k:event[k] for k in event.field_list_with_scope(
            babeltrace.CTFScope.EVENT_FIELDS)}
        dataset.update({'ex:'+'timestamp':(event['timestamp']/1000000000)})
        #dataset.update({'ex:'+'name':event.name})

        e1 = d1.entity(ex['event'+str(counter)],dataset)
        entities.append(e1)
        producer_agent = d1.agent('ex:'+event['producer_id'])
        if event['producer_id'] not in producer_events:
                producer_events[event['producer_id']] = []
        else:
                pel = producer_events[events['producer_id']]
                d1.wasAssociatedWith(pel[len(pel)-1], e1)
                pel.append(e1)
        controller_agent = d1.agent('ex:'+event['controller_id'])
        activity = d1.activity('ex:'+event['activity']+str(counter_1))
        activities.append(activity)
        d1.wasGeneratedBy(e1, activity)
        # strings used to detect if the relationship already exists in the d1 document
        association_relationship = str(dummy.wasAssociatedWith(activity, producer_agent))
        used_relationship = str(dummy.used(controller_agent, producer_agent))

        # Add activity to producer agent if it has not been added before.
        d1.wasAssociatedWith(activity, producer_agent)
        # if association_relationship not in relationships:
        #     d1.wasAssociatedWith(activity, producer_agent)
        #     relationships.append(association_relationship)

        # Add producer agent to controller agent if it has not been added yet.
        if used_relationship not in relationships:
            d1.used(controller_agent, producer_agent)
            relationships.append(used_relationship)

        # Add temporal relationship between this event and the previous one.
#        if counter > 0:
#            d1.wasAssociatedWith(entities[counter - 1], e1)

        counter+=1
        counter_1 +=1
    return d1

# 需要导入模块: from prov.model import ProvDocument [as 别名]
# 或者: from prov.model.ProvDocument import used [as 别名]
def to_prov(obj, namespace, service):
    """
    :type obj: dict
    :rtype: prov.model.ProvDocument
    """
    g = ProvDocument()
    ap = Namespace('aip', 'https://araport.org/provenance/')

    g.add_namespace("dcterms", "http://purl.org/dc/terms/")
    g.add_namespace("foaf", "http://xmlns.com/foaf/0.1/")

    vaughn = g.agent(ap['matthew_vaughn'], {
        'prov:type': PROV["Person"], 'foaf:givenName': "Matthew Vaughn",
        'foaf:mbox': "<mailto:[email protected]>"
    })
    # Hard coded for now
    walter = g.agent(ap['walter_moreira'], {
        'prov:type': PROV["Person"], 'foaf:givenName': "Walter Moreira",
        'foaf:mbox': "<mailto:[email protected]>"
    })
    utexas = g.agent(ap['university_of_texas'], {
        'prov:type': PROV["Organization"],
        'foaf:givenName': "University of Texas at Austin"
    })
    g.actedOnBehalfOf(walter, utexas)
    g.actedOnBehalfOf(vaughn, utexas)
    adama_platform = g.agent(
        ap['adama_platform'],
        {'dcterms:title': "ADAMA",
         'dcterms:description': "Araport Data And Microservices API",
         'dcterms:language': "en-US",
         'dcterms:identifier': "https://api.araport.org/community/v0.3/",
         'dcterms:updated': "2015-04-17T09:44:56"})
    g.wasGeneratedBy(adama_platform, walter)
    g.wasGeneratedBy(adama_platform, vaughn)

    iden = service_iden(namespace, service)
    srv = service_store[iden]['service']
    adama_microservice = g.agent(
        ap[iden],
        {'dcterms:title': srv.name.title(),
         'dcterms:description': srv.description,
         'dcterms:language': "en-US",
         'dcterms:identifier': api_url_for('service',
                                           namespace=namespace,
                                           service=service),
         'dcterms:source': srv.git_repository
         })

    g.used(adama_microservice, adama_platform, datetime.datetime.now())

    for author in getattr(srv, 'authors', []):
        try:
            author_name = author['name']
            author_email = author['email']
        except KeyError:
            raise APIException(
                'name and email are required in author field')
        author_agent = g.agent(
            ap[slugify(author_name)],
            {'prov:type': PROV['Person'],
             'foaf:givenName': author_name,
             'foaf:mbox': '<mailto:{}>'.format(author_email)})
        sponsor_name = author.get('sponsor_organization_name', None)
        if sponsor_name:
            sponsor_agent = g.agent(
                ap[slugify(sponsor_name)],
                {'prov:type': PROV['Organization'],
                 'foaf:givenName': sponsor_name,
                 'dcterms:identifier': author.get('sponsor_uri', '')})
            g.actedOnBehalfOf(author_agent, sponsor_agent)
        g.wasGeneratedBy(adama_microservice,
                         author_agent,
                         datetime.datetime.now())

    sources_entities = process_sources(srv.sources, g, ap)
    for src in sources_entities:
        g.used(adama_microservice, src, datetime.datetime.now())

    response = g.entity(ap['adama_response'])
    g.wasGeneratedBy(response, ap[srv.type], datetime.datetime.now())
    g.used(ap[srv.type], adama_microservice, datetime.datetime.now())

    return g

# 需要导入模块: from prov.model import ProvDocument [as 别名]
# 或者: from prov.model.ProvDocument import used [as 别名]
def primer_example():
    # https://github.com/lucmoreau/ProvToolbox/blob/master/prov-n/src/test/resources/prov/primer.pn
    #===========================================================================
    # document
    g = ProvDocument()

    #    prefix ex <http://example/>
    #    prefix dcterms <http://purl.org/dc/terms/>
    #    prefix foaf <http://xmlns.com/foaf/0.1/>
    ex = Namespace('ex', 'http://example/')  # namespaces do not need to be explicitly added to a document
    g.add_namespace("dcterms", "http://purl.org/dc/terms/")
    g.add_namespace("foaf", "http://xmlns.com/foaf/0.1/")

    #    entity(ex:article, [dcterms:title="Crime rises in cities"])
    # first time the ex namespace was used, it is added to the document automatically
    g.entity(ex['article'], {'dcterms:title': "Crime rises in cities"})
    #    entity(ex:articleV1)
    g.entity(ex['articleV1'])
    #    entity(ex:articleV2)
    g.entity(ex['articleV2'])
    #    entity(ex:dataSet1)
    g.entity(ex['dataSet1'])
    #    entity(ex:dataSet2)
    g.entity(ex['dataSet2'])
    #    entity(ex:regionList)
    g.entity(ex['regionList'])
    #    entity(ex:composition)
    g.entity(ex['composition'])
    #    entity(ex:chart1)
    g.entity(ex['chart1'])
    #    entity(ex:chart2)
    g.entity(ex['chart2'])
    #    entity(ex:blogEntry)
    g.entity(ex['blogEntry'])

    #    activity(ex:compile)
    g.activity('ex:compile')  # since ex is registered, it can be used like this
    #    activity(ex:compile2)
    g.activity('ex:compile2')
    #    activity(ex:compose)
    g.activity('ex:compose')
    #    activity(ex:correct, 2012-03-31T09:21:00, 2012-04-01T15:21:00)
    g.activity('ex:correct', '2012-03-31T09:21:00', '2012-04-01T15:21:00')  # date time can be provided as strings
    #    activity(ex:illustrate)
    g.activity('ex:illustrate')

    #    used(ex:compose, ex:dataSet1, -,   [ prov:role = "ex:dataToCompose"])
    g.used('ex:compose', 'ex:dataSet1', other_attributes={'prov:role': "ex:dataToCompose"})
    #    used(ex:compose, ex:regionList, -, [ prov:role = "ex:regionsToAggregateBy"])
    g.used('ex:compose', 'ex:regionList', other_attributes={'prov:role': "ex:regionsToAggregateBy"})
    #    wasGeneratedBy(ex:composition, ex:compose, -)
    g.wasGeneratedBy('ex:composition', 'ex:compose')

    #    used(ex:illustrate, ex:composition, -)
    g.used('ex:illustrate', 'ex:composition')
    #    wasGeneratedBy(ex:chart1, ex:illustrate, -)
    g.wasGeneratedBy('ex:chart1', 'ex:illustrate')

    #    wasGeneratedBy(ex:chart1, ex:compile,  2012-03-02T10:30:00)
    g.wasGeneratedBy('ex:chart1', 'ex:compile', '2012-03-02T10:30:00')
    #    wasGeneratedBy(ex:chart2, ex:compile2, 2012-04-01T15:21:00)
    #
    #
    #    agent(ex:derek, [ prov:type="prov:Person", foaf:givenName = "Derek",
    #           foaf:mbox= "<mailto:[email protected]>"])
    g.agent('ex:derek', {
        'prov:type': PROV["Person"], 'foaf:givenName': "Derek", 'foaf:mbox': "<mailto:[email protected]>"
    })
    #    wasAssociatedWith(ex:compose, ex:derek, -)
    g.wasAssociatedWith('ex:compose', 'ex:derek')
    #    wasAssociatedWith(ex:illustrate, ex:derek, -)
    g.wasAssociatedWith('ex:illustrate', 'ex:derek')
    #
    #    agent(ex:chartgen, [ prov:type="prov:Organization",
    #           foaf:name = "Chart Generators Inc"])
    g.agent('ex:chartgen', {'prov:type': PROV["Organization"], 'foaf:name': "Chart Generators Inc"})
    #    actedOnBehalfOf(ex:derek, ex:chartgen, ex:compose)
    g.actedOnBehalfOf('ex:derek', 'ex:chartgen', 'ex:compose')
    #    wasAttributedTo(ex:chart1, ex:derek)
    g.wasAttributedTo('ex:chart1', 'ex:derek')

    #    wasGeneratedBy(ex:dataSet2, ex:correct, -)
    g.wasGeneratedBy('ex:dataSet2', 'ex:correct')
    #    used(ex:correct, ex:dataSet1, -)
    g.used('ex:correct', 'ex:dataSet1')
    #    wasDerivedFrom(ex:dataSet2, ex:dataSet1, [prov:type='prov:Revision'])
    g.wasDerivedFrom('ex:dataSet2', 'ex:dataSet1', other_attributes={'prov:type': PROV['Revision']})
    #    wasDerivedFrom(ex:chart2, ex:dataSet2)
    g.wasDerivedFrom('ex:chart2', 'ex:dataSet2')

    #    wasDerivedFrom(ex:blogEntry, ex:article, [prov:type='prov:Quotation'])
    g.wasDerivedFrom('ex:blogEntry', 'ex:article', other_attributes={'prov:type': PROV['Quotation']})
    #    specializationOf(ex:articleV1, ex:article)
    g.specializationOf('ex:articleV1', 'ex:article')
    #    wasDerivedFrom(ex:articleV1, ex:dataSet1)
    g.wasDerivedFrom('ex:articleV1', 'ex:dataSet1')

    #    specializationOf(ex:articleV2, ex:article)
    g.specializationOf('ex:articleV2', 'ex:article')
    #    wasDerivedFrom(ex:articleV2, ex:dataSet2)
#.........这里部分代码省略.........

# 需要导入模块: from prov.model import ProvDocument [as 别名]
# 或者: from prov.model.ProvDocument import used [as 别名]
def w3c_publication_2():
    # https://github.com/lucmoreau/ProvToolbox/blob/master/asn/src/test/resources/prov/w3c-publication2.prov-asn
    #===========================================================================
    # bundle
    #
    # prefix ex <http://example.org/>
    # prefix rec <http://example.org/record>
    #
    # prefix w3 <http://www.w3.org/TR/2011/>
    # prefix hg <http://dvcs.w3.org/hg/prov/raw-file/9628aaff6e20/model/releases/WD-prov-dm-20111215/>
    #
    #
    # entity(hg:Overview.html, [ prov:type="file in hg" ])
    # entity(w3:WD-prov-dm-20111215, [ prov:type="html4" ])
    #
    #
    # activity(ex:rcp,-,-,[prov:type="copy directory"])
    #
    # wasGeneratedBy(rec:g; w3:WD-prov-dm-20111215, ex:rcp, -)
    #
    # entity(ex:req3, [ prov:type="http://www.w3.org/2005/08/01-transitions.html#pubreq" %% xsd:anyURI ])
    #
    # used(rec:u; ex:rcp,hg:Overview.html,-)
    # used(ex:rcp, ex:req3, -)
    #
    #
    # wasDerivedFrom(w3:WD-prov-dm-20111215, hg:Overview.html, ex:rcp, rec:g, rec:u)
    #
    # agent(ex:webmaster, [ prov:type='prov:Person' ])
    #
    # wasAssociatedWith(ex:rcp, ex:webmaster, -)
    #
    # endBundle
    #===========================================================================

    ex = Namespace('ex', 'http://example.org/')
    rec = Namespace('rec', 'http://example.org/record')
    w3 = Namespace('w3', 'http://www.w3.org/TR/2011/')
    hg = Namespace('hg', 'http://dvcs.w3.org/hg/prov/raw-file/9628aaff6e20/model/releases/WD-prov-dm-20111215/')

    g = ProvDocument()

    g.entity(hg['Overview.html'], {'prov:type': "file in hg"})
    g.entity(w3['WD-prov-dm-20111215'], {'prov:type': "html4"})

    g.activity(ex['rcp'], None, None, {'prov:type': "copy directory"})

    g.wasGeneratedBy('w3:WD-prov-dm-20111215', 'ex:rcp', identifier=rec['g'])

    g.entity('ex:req3', {'prov:type': Identifier("http://www.w3.org/2005/08/01-transitions.html#pubreq")})

    g.used('ex:rcp', 'hg:Overview.html', identifier='rec:u')
    g.used('ex:rcp', 'ex:req3')

    g.wasDerivedFrom('w3:WD-prov-dm-20111215', 'hg:Overview.html', 'ex:rcp', 'rec:g', 'rec:u')

    g.agent('ex:webmaster', {'prov:type': "Person"})

    g.wasAssociatedWith('ex:rcp', 'ex:webmaster')

    return g

# 需要导入模块: from prov.model import ProvDocument [as 别名]
# 或者: from prov.model.ProvDocument import used [as 别名]
def w3c_publication_1():
    # https://github.com/lucmoreau/ProvToolbox/blob/master/asn/src/test/resources/prov/w3c-publication1.prov-asn
    #===========================================================================
    # bundle
    #
    # prefix ex  <http://example.org/>
    #
    # prefix w3      <http://www.w3.org/>
    # prefix tr      <http://www.w3.org/TR/2011/>
    # prefix process <http://www.w3.org/2005/10/Process-20051014/tr.html#>
    # prefix email   <https://lists.w3.org/Archives/Member/w3c-archive/>
    # prefix chairs  <https://lists.w3.org/Archives/Member/chairs/>
    # prefix trans   <http://www.w3.org/2005/08/01-transitions.html#>
    # prefix rec54   <http://www.w3.org/2001/02pd/rec54#>
    #
    #
    #  entity(tr:WD-prov-dm-20111018, [ prov:type='rec54:WD' ])
    #  entity(tr:WD-prov-dm-20111215, [ prov:type='rec54:WD' ])
    #  entity(process:rec-advance,    [ prov:type='prov:Plan' ])
    #
    #
    #  entity(chairs:2011OctDec/0004, [ prov:type='trans:transreq' ])
    #  entity(email:2011Oct/0141,     [ prov:type='trans:pubreq' ])
    #  entity(email:2011Dec/0111,     [ prov:type='trans:pubreq' ])
    #
    #
    #  wasDerivedFrom(tr:WD-prov-dm-20111215, tr:WD-prov-dm-20111018)
    #
    #
    #  activity(ex:act1,-,-,[prov:type="publish"])
    #  activity(ex:act2,-,-,[prov:type="publish"])
    #
    #  wasGeneratedBy(tr:WD-prov-dm-20111018, ex:act1, -)
    #  wasGeneratedBy(tr:WD-prov-dm-20111215, ex:act2, -)
    #
    #  used(ex:act1, chairs:2011OctDec/0004, -)
    #  used(ex:act1, email:2011Oct/0141, -)
    #  used(ex:act2, email:2011Dec/0111, -)
    #
    #  agent(w3:Consortium, [ prov:type='prov:Organization' ])
    #
    #  wasAssociatedWith(ex:act1, w3:Consortium, process:rec-advance)
    #  wasAssociatedWith(ex:act2, w3:Consortium, process:rec-advance)
    #
    # endBundle
    #===========================================================================

    g = ProvDocument()
    g.add_namespace('ex', 'http://example.org/')
    g.add_namespace('w3', 'http://www.w3.org/')
    g.add_namespace('tr', 'http://www.w3.org/TR/2011/')
    g.add_namespace('process', 'http://www.w3.org/2005/10/Process-20051014/tr.html#')
    g.add_namespace('email', 'https://lists.w3.org/Archives/Member/w3c-archive/')
    g.add_namespace('chairs', 'https://lists.w3.org/Archives/Member/chairs/')
    g.add_namespace('trans', 'http://www.w3.org/2005/08/01-transitions.html#')
    g.add_namespace('rec54', 'http://www.w3.org/2001/02pd/rec54#')

    g.entity('tr:WD-prov-dm-20111018', {'prov:type': 'rec54:WD'})
    g.entity('tr:WD-prov-dm-20111215', {'prov:type': 'rec54:WD'})
    g.entity('process:rec-advance', {'prov:type': 'prov:Plan'})

    g.entity('chairs:2011OctDec/0004', {'prov:type': 'trans:transreq'})
    g.entity('email:2011Oct/0141', {'prov:type': 'trans:pubreq'})
    g.entity('email:2011Dec/0111', {'prov:type': 'trans:pubreq'})

    g.wasDerivedFrom('tr:WD-prov-dm-20111215', 'tr:WD-prov-dm-20111018')

    g.activity('ex:act1', other_attributes={'prov:type': "publish"})
    g.activity('ex:act2', other_attributes={'prov:type': "publish"})

    g.wasGeneratedBy('tr:WD-prov-dm-20111018', 'ex:act1')
    g.wasGeneratedBy('tr:WD-prov-dm-20111215', 'ex:act2')

    g.used('ex:act1', 'chairs:2011OctDec/0004')
    g.used('ex:act1', 'email:2011Oct/0141')
    g.used('ex:act2', 'email:2011Dec/0111')

    g.agent('w3:Consortium', other_attributes={'prov:type': "Organization"})

    g.wasAssociatedWith('ex:act1', 'w3:Consortium', 'process:rec-advance')
    g.wasAssociatedWith('ex:act2', 'w3:Consortium', 'process:rec-advance')

    return g

# 需要导入模块: from prov.model import ProvDocument [as 别名]
# 或者: from prov.model.ProvDocument import used [as 别名]
def ctfToProv():
    d1 = ProvDocument()
    dummy = ProvDocument()
    ex = Namespace('ex', 'http://example/')  # namespaces do not need to be explicitly added to a document
    #data = event_field(os.path.join(trace_path,'../config.yaml'))
    counter = 0
    #counter_1 = 0
    relationships = []
    entityActivityList = []
    # activities = []
    can_events = defaultdict(list)
    for event in trace_collection.events:
        dataset = {'ex:'+k:event[k] for k in event.field_list_with_scope(
            babeltrace.CTFScope.EVENT_FIELDS)}
        #dataset.update({'ex:'+'timestamp':(event['timestamp']/1000000000)})
        dataset.update({'ex:'+'name':event.name})

        # #calculates PGN

        # pf = str(bin(int(dataset['node_id'], 16)))[5:13]

        # if int(pf) > 240:
        #     pgn = int(str(bin(int(dataset['node_id'], 16)))[3:21], 2)
        # else:
        #     pgn = int(str(bin(int(dataset['node_id'], 16)))[3:13], 2)



        # #Gets source address.
        # sa = str(bin(int(dataset['node_id'], 16)))[-8:]  #gets last byte.

        sa = event['producer_id']

        activity = event['activity']


        e1 = d1.entity(ex['event'+str(counter)],dataset)

        #create class object to store entity and activity data field.

        entity_activity = entityActivity()

        entity_activity.addEntityActivity(e1, activity)
        #entityActivityList.append(e1)
        #can_events.setdefault(str(sa),[]).append(e1)

        can_events[sa].append(entity_activity)
        #node_id = d1.agent('ex:'+event['node_id'])
        controller_agent = d1.agent('ex:'+event['controller_id'])


        # activity = d1.activity('ex:'+event['activity']+str(counter))
        # activities.append(activity)




        #d1.wasGeneratedBy(e1, activity)
        # strings used to detect if the relationship already exists in the d1 document
        # association_relationship = str(dummy.wasAssociatedWith(activity, sa))


        # used_relationship = str(dummy.used(network_id, sa))

        #add activity to sensor agent
       # d1.wasAssociatedWith(activity,sensor_agent)
        #check if the association already esists
        # if association_relationship not in relationships:
        #     d1.wasAssociatedWith(activity,sensor_agent)
        #     relationships.append(association_relationship)
        # if used_relationship not in relationships:
        #     d1.used(network_id, sa)
        #     relationships.append(used_relationship)
        #counter+=1
        #counter_1 +=1
    # for index in range(len(entityActivityList)-1):
    #     d1.wasAssociatedWith(entityActivityList[index], entityActivityList[index + 1])

    # for index in range(len(entityActivityList)):
    #     d1.wasGeneratedBy(entityActivityList[index], activities[index])
    #     d1.wasAssociatedWith(activities[index],sa)



    for key in can_events.keys():

        producer_agent = d1.agent('ex:'+str(key))
        used_relationship = str(dummy.used(controller_agent, producer_agent))
        #association_relationship = str(dummy.wasAssociatedWith(activity, sa))

        if used_relationship not in relationships:
            d1.used(controller_agent, producer_agent)
            relationships.append(used_relationship)

        entityActivityList = can_events[key]

        for index in range(len(entityActivityList)-1):
            d1.wasAssociatedWith(entityActivityList[index].getEntity(), entityActivityList[index + 1].getEntity())
            d1.wasGeneratedBy(entityActivityList[index], entityActivityList[index].getActivity())
            d1.wasAssociatedWith(entityActivityList[index].getActivity(), producer_agent)
#.........这里部分代码省略.........

# 需要导入模块: from prov.model import ProvDocument [as 别名]
# 或者: from prov.model.ProvDocument import used [as 别名]
    def useGenDependency(self, aDO, usedList, genList, throughActivity):

        aID = throughActivity.id

        # create provlet
        d1 = ProvDocument()  # d1 is now an empty provenance document
        d1.add_namespace("dt", "http://cs.ncl.ac.uk/dtsim/")

        usedEntities = []
        for aRO in usedList:
            usedEntities.append(d1.entity(DTns + aRO.id))

        genEntities = []
        for aRO1 in genList:
            genEntities.append(d1.entity(DTns + aRO1.id))

        a = d1.activity(DTns + aID)
        ag1 = d1.agent(DTns + str(aDO.id))

        d1.wasAssociatedWith(a, ag1)
        for ue in usedEntities:
            d1.used(a, ue)

        for gene in genEntities:
            d1.wasAttributedTo(gene, ag1)
            d1.wasGeneratedBy(gene, a)

        # associate this provlet to each generated RO
        for aRO1 in genList:
            aRO1.provlet = d1

        print "event {n}: DO {do}: {ro1} <- wgby <- {act} <- used {ro}".format(
            n=currentReuseCount, do=aDO.id, ro1=aRO1.id, act=aID, ro=aRO.id
        )

        for genRO in genList:
            for uRO in usedList:
                # update upstream pointer
                genRO.upstream.append(
                    (uRO, throughActivity)
                )  # dep on aRO through activity aID   FIXME URGENTLY!!!  not designed for M-M

        for uRO in usedList:
            for genRO in genList:
                # update downstream
                uRO.downstream.append((genRO, throughActivity))  # aR1 is downstream from aR1 through activity aID

        # update global graph
        globalUsedEntities = []
        for aRO in usedList:
            globalUsedEntities.append(pGlobal.entity(DTns + aRO.id))

        globalGenEntities = []
        for aR1 in genList:
            globalGenEntities.append(pGlobal.entity(DTns + aR1.id))

        a = pGlobal.activity(DTns + aID)
        ag1 = pGlobal.agent(DTns + str(aDO.id))

        pGlobal.wasAssociatedWith(a, ag1)
        for ue in globalUsedEntities:
            pGlobal.used(a, ue)

        for gene in globalGenEntities:
            pGlobal.wasAttributedTo(gene, ag1)
            pGlobal.wasGeneratedBy(gene, a)

        # trigger credit recomputation
        # each used RO needs its credit updated with aRO1.credit for each generated aRO1 through activity aID
        aCreditManager.addGenerationCredit(usedList, genList, throughActivity)

        # 		self.notify(d1)
        return d1

# 需要导入模块: from prov.model import ProvDocument [as 别名]
# 或者: from prov.model.ProvDocument import used [as 别名]
def example():

    g = ProvDocument()
    # Local namespace
    # Doesnt exist yet so we are creating it
    ap = Namespace('aip', 'https://araport.org/provenance/')
    # Dublin Core
    g.add_namespace("dcterms", "http://purl.org/dc/terms/")
    # FOAF
    g.add_namespace("foaf", "http://xmlns.com/foaf/0.1/")

    # Add sponsors and contributors as Agents
    # ap['matthew_vaughn']
    # aip:matthew_vaughn
    # https://araport.org/provenance/:matthew_vaughn
    # Learn this from a call to profiles service? Adds a dependency on Agave so I am open to figuring out another way
    me = g.agent(ap['matthew_vaughn'], {
        'prov:type': PROV["Person"], 'foaf:givenName': "Matthew Vaughn", 'foaf:mbox': "<mailto:[email protected]>"
    })
    # Hard coded for now
    walter = g.agent(ap['walter_moreira'], {
        'prov:type': PROV["Person"], 'foaf:givenName': "Walter Moreira", 'foaf:mbox': "<mailto:[email protected]>"
    })
    utexas = g.agent(ap['university_of_texas'], {
        'prov:type': PROV["Organization"], 'foaf:givenName': "University of Texas at Austin"
    })

    # Set delegation to our host University
    # We may have trouble doing this for other users since we don't always capture their host instituion
    g.actedOnBehalfOf(walter, utexas)
    g.actedOnBehalfOf(me, utexas)

    # Include the ADAMA platform as an Agent and set attribution
    # dcterms:title and dcterms:description are hardcoded
    # dcterms:language is hard-coded
    # dcterms:source is the URI of the public git source repository for ADAMA
    # "dcterms:updated": "2015-04-17T09:44:56" - this would actually be the date ADAMA was updated
    adama_platform = g.agent(ap['adama_platform'], {'dcterms:title': "ADAMA", 'dcterms:description': "Araport Data and Microservices API", 'dcterms:language':"en-US", 'dcterms:identifier':"https://api.araport.org/community/v0.3/", 'dcterms:updated': "2015-04-17T09:44:56" })
    g.wasGeneratedBy(adama_platform, walter)

    # Include the ADAMA microservice as an Agent and set attribution+delegation
    # dcterms:title and dcterms:description are inherited from the service's metadata
    # dcterms:language is hard-coded
    # dcterms:identifier is the deployment URI for the service
    # dcterms:source is the URI of the public git source repository. The URL in this example is just a dummy
    #
    # The name for each microservice should be unique. We've decided to
    # use the combination of namespace, service name, and version
    microservice_name = 'mwvaughn/bar_annotation_v1.0.0'
    adama_microservice = g.agent(ap[microservice_name], {'dcterms:title': "BAR Annotation Service", 'dcterms:description': "Returns annotation from locus ID", 'dcterms:language':"en-US", 'dcterms:identifier':"https://api.araport.org/community/v0.3/mwvaughn/bar_annotation_v1.0.0", 'dcterms:source':"https://github.com/Arabidopsis-Information-Portal/prov-enabled-api-sample" })

    # the microservice was generated by me on date X (don't use now, use when the service was updated)
    g.wasGeneratedBy(adama_microservice, me, datetime.datetime.now())
    # The microservice used the platform now
    g.used(adama_microservice, adama_platform, datetime.datetime.now())

    # Sources
    #
    # Define BAR
    # Agents
    nick = g.agent(ap['nicholas_provart'], {
        'prov:type': PROV["Person"], 'foaf:givenName': "Nicholas Provart", 'foaf:mbox': "[email protected]"
    })
    utoronto = g.agent(ap['university_of_toronto'], {
        'prov:type': PROV["Organization"], 'foaf:givenName': "University of Toronto", 'dcterms:identifier':"http://www.utoronto.ca/"
    })
    g.actedOnBehalfOf(nick, utoronto)

    # Entity
    # All fields derived from Sources.yml
    # dcterms:title and dcterms:description come straight from the YAML
    # dcterms:identifier - URI pointing to the source's canonical URI representation
    # optional - dcterms:language: Recommended best practice is to use a controlled vocabulary such as RFC 4646
    # optional - dcterms:updated: date the source was published or last updated
    # optional - dcterms:license: Simple string or URI to license. Validate URI if provided?
    datasource1 = g.entity(ap['datasource1'], {'dcterms:title': "BAR Arabidopsis AGI -> Annotation", 'dcterms:description': "Most recent annotation for given AGI", 'dcterms:language':"en-US", 'dcterms:identifier':"http://bar.utoronto.ca/webservices/agiToAnnot.php", 'dcterms:updated':"2015-04-17T09:44:56", 'dcterms:license':"Creative Commons 3.0" })
    # Set up attribution to Nick
    g.wasAttributedTo(datasource1, nick)

    # Define TAIR
    # Agents
    # dcterms:language: Recommended best practice is to use a controlled vocabulary such as RFC 4646
    eva = g.agent(ap['eva_huala'], {
        'prov:type': PROV["Person"], 'foaf:givenName': "Eva Huala"
    })
    phoenix = g.agent(ap['phoenix_bioinformatics'], {
        'prov:type': PROV["Organization"], 'foaf:givenName': "Phoenix Bioinformatics"
    })
    g.actedOnBehalfOf(eva, phoenix)

    # Entity
    # All fields derived from Sources.yml
    # optional - dcterms:citation: Plain text bibliographic citation. If only provided as doi, should we try to validate it?
    datasource2 = g.entity(ap['datasource2'], {'dcterms:title': "TAIR", 'dcterms:description': "The Arabidopsis Information Resource", 'dcterms:language':"en-US", 'dcterms:identifier':"https://www.arabidopsis.org/", 'dcterms:citation':"The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Research 2011 doi: 10.1093/nar/gkr1090"})
    g.wasAttributedTo(datasource2, eva)

    # In Sources.yml, these two sources are nested. Define that relationship here
    # There are other types of relationships but we will just use derived from for simplicity in this prototype
    g.wasDerivedFrom(ap['datasource1'], ap['datasource2'])

#.........这里部分代码省略.........