Python ProvDocument.wasAttributedTo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 wasAttributedTo [as 别名]
    def deriveDependency(self, aDO, aRO, derivedList):

        d1 = ProvDocument()  # d1 is now an empty provenance document
        d1.add_namespace("dt", "http://cs.ncl.ac.uk/dtsim/")
        e1 = d1.entity(DTns + aRO.id)  # deriving
        ag1 = d1.agent(DTns + str(aDO.id))
        for der in derivedList:
            # create provlet
            e2 = d1.entity(DTns + der.id)  # derived
            d1.wasAttributedTo(e2, ag1)
            d1.wasDerivedFrom(e2, e1)

            # update upstream pointer
            der.upstream = [(aRO, None)]  # aRO is upstream from aRO with no activity

            # update downstream
            aRO.downstream.append((der, None))  # aR1 is downstream from aR1 with no activity

        # update global graph
        e1 = pGlobal.entity(DTns + aRO.id)  # deriving
        ag1 = pGlobal.agent(DTns + str(aDO.id))
        pGlobal.wasAttributedTo(e2, ag1)
        for der in derivedList:
            e2 = pGlobal.entity(DTns + der.id)  # derived
            pGlobal.wasDerivedFrom(e2, e1)

        # trigger credit recomputation
        for der in derivedList:
            # aRO needs its credit updated with aRO1.credit
            aCreditManager.addDerivationCredit(aRO, der.currentTotalCredit)

        # 		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 wasAttributedTo [as 别名]
def bundles2():
    # https://github.com/lucmoreau/ProvToolbox/blob/master/prov-n/src/test/resources/prov/bundles2.provn
    #===========================================================================
    # document
    g = ProvDocument()

    #   prefix ex  <http://example.org/example/>
    g.add_namespace("ex", "http://www.example.com/")

    #   prefix alice  <http://example.org/alice/>
    #   prefix bob  <http://example.org/bob/>
    g.add_namespace('alice', 'http://example.org/alice/')
    g.add_namespace('bob', 'http://example.org/bob/')

    #   entity(bob:bundle4, [prov:type='prov:Bundle'])
    #   wasGeneratedBy(bob:bundle4, -, 2012-05-24T10:30:00)
    #   agent(ex:Bob)
    #   wasAttributedTo(bob:bundle4, ex:Bob)
    g.entity('bob:bundle4', {'prov:type': PROV['Bundle']})
    g.wasGeneratedBy('bob:bundle4', time='2012-05-24T10:30:00')
    g.agent('ex:Bob')
    g.wasAttributedTo('bob:bundle4', 'ex:Bob')

    #   entity(alice:bundle5, [ prov:type='prov:Bundle' ])
    #   wasGeneratedBy(alice:bundle5, -, 2012-05-25T11:15:00)
    #   agent(ex:Alice)
    #   wasAttributedTo(alice:bundle5, ex:Alice)
    g.entity('alice:bundle5', {'prov:type': PROV['Bundle']})
    g.wasGeneratedBy('alice:bundle5', time='2012-05-25T11:15:00')
    g.agent('ex:Alice')
    g.wasAttributedTo('alice:bundle5', 'ex:Alice')

    #   bundle bob:bundle4
    #     entity(ex:report1, [ prov:type="report", ex:version=1 ])
    #     wasGeneratedBy(ex:report1, -, 2012-05-24T10:00:01)
    #   endBundle
    b4 = g.bundle('bob:bundle4')
    b4.entity('ex:report1', {'prov:type': "report", 'ex:version': 1})
    b4.wasGeneratedBy('ex:report1', time='2012-05-24T10:00:01')

    #   bundle alice:bundle5
    #     entity(ex:report1bis)
    #     mentionOf(ex:report1bis, ex:report1, bob:bundle4)
    #     entity(ex:report2, [ prov:type="report", ex:version=2 ])
    #     wasGeneratedBy(ex:report2, -, 2012-05-25T11:00:01)
    #     wasDerivedFrom(ex:report2, ex:report1bis)
    #   endBundle
    b5 = g.bundle('alice:bundle5')
    b5.entity('ex:report1bis')
    b5.mentionOf('ex:report1bis', 'ex:report1', 'bob:bundle4')
    b5.entity('ex:report2', [('prov:type', "report"), ('ex:version', 2)])
    b5.wasGeneratedBy('ex:report2', time='2012-05-25T11:00:01')
    b5.wasDerivedFrom('ex:report2', 'ex:report1bis')

    # endDocument
    return g

# 需要导入模块: from prov.model import ProvDocument [as 别名]
# 或者: from prov.model.ProvDocument import wasAttributedTo [as 别名]
def bundles1():
    # https://github.com/lucmoreau/ProvToolbox/blob/master/prov-n/src/test/resources/prov/bundles1.provn
    #===============================================================================
    # document
    g = ProvDocument()

    #   prefix ex  <http://example.org/example/>
    EX = Namespace("ex", "http://www.example.com/")
    g.add_namespace(EX)

    #   prefix alice  <http://example.org/alice/>
    #   prefix bob  <http://example.org/bob/>
    g.add_namespace('alice', 'http://example.org/alice/')
    g.add_namespace('bob', 'http://example.org/bob/')

    #   entity(bob:bundle1, [prov:type='prov:Bundle'])
    g.entity('bob:bundle1', {'prov:type': PROV['Bundle']})
    #   wasGeneratedBy(bob:bundle1, -, 2012-05-24T10:30:00)
    g.wasGeneratedBy('bob:bundle1', time='2012-05-24T10:30:00')
    #   agent(ex:Bob)
    g.agent('ex:Bob')
    #   wasAttributedTo(bob:bundle1, ex:Bob)
    g.wasAttributedTo('bob:bundle1', 'ex:Bob')

    #   entity(alice:bundle2, [ prov:type='prov:Bundle' ])
    g.entity('alice:bundle2', {'prov:type': PROV['Bundle']})
    #   wasGeneratedBy(alice:bundle2, -, 2012-05-25T11:15:00)
    g.wasGeneratedBy('alice:bundle2', time='2012-05-25T11:15:00')
    #   agent(ex:Alice)
    g.agent('ex:Alice')
    #   wasAttributedTo(alice:bundle2, ex:Alice)
    g.wasAttributedTo('alice:bundle2', 'ex:Alice')

    #   bundle bob:bundle1
    b1 = g.bundle('bob:bundle1')
    #     entity(ex:report1, [ prov:type="report", ex:version=1 ])
    b1.entity('ex:report1', {'prov:type': "report", 'ex:version': 1})
    #     wasGeneratedBy(ex:report1, -, 2012-05-24T10:00:01)
    b1.wasGeneratedBy('ex:report1', time='2012-05-24T10:00:01')
    #   endBundle

    #   bundle alice:bundle2
    b2 = g.bundle('alice:bundle2')
    #     entity(ex:report1)
    b2.entity('ex:report1')
    #     entity(ex:report2, [ prov:type="report", ex:version=2 ])
    b2.entity('ex:report2', {'prov:type': "report", 'ex:version': 2})
    #     wasGeneratedBy(ex:report2, -, 2012-05-25T11:00:01)
    b2.wasGeneratedBy('ex:report2', time='2012-05-25T11:00:01')
    #     wasDerivedFrom(ex:report2, ex:report1)
    b2.wasDerivedFrom('ex:report2', 'ex:report1')
    #   endBundle

    # endDocument
    return g

# 需要导入模块: from prov.model import ProvDocument [as 别名]
# 或者: from prov.model.ProvDocument import wasAttributedTo [as 别名]
    def generateProvlet(self, aDO, aRO):
        # create provlet
        d1 = ProvDocument()  # d1 is now an empty provenance document
        d1.add_namespace("dt", "http://cs.ncl.ac.uk/dtsim/")

        e1 = d1.entity(DTns + aRO.id)
        ag1 = d1.agent(DTns + str(aDO.id))
        d1.wasAttributedTo(e1, ag1)

        # update global graph
        e1 = pGlobal.entity(DTns + aRO.id)
        ag1 = pGlobal.agent(DTns + str(aDO.id))
        pGlobal.wasAttributedTo(e1, ag1)

        # 		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 wasAttributedTo [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 wasAttributedTo [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 wasAttributedTo [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.........