annotate env/lib/python3.9/site-packages/prov/tests/examples.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

# coding: utf8
from __future__ import (absolute_import, division, print_function,
                        unicode_literals)

from prov.model import ProvDocument, Namespace, Literal, PROV, Identifier
import datetime


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:[e-mail]>"])
    g.agent('ex:derek', {
        'prov:type': PROV["Person"], 'foaf:givenName': "Derek", 'foaf:mbox': "<mailto:[e-mail]>"
    })
    #    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)
    g.wasDerivedFrom('ex:articleV2', 'ex:dataSet2')

    #    alternateOf(ex:articleV2, ex:articleV1)
    g.alternateOf('ex:articleV2', 'ex:articleV1')

    # endDocument
    return g


def primer_example_alternate():
    g = ProvDocument(namespaces={
        'ex': 'http://example/',
        'dcterms': 'http://purl.org/dc/terms/',
        'foaf': 'http://xmlns.com/foaf/0.1/'
    })

    article = g.entity('ex:article', {'dcterms:title': "Crime rises in cities"})
    articleV1 = g.entity('ex:articleV1')
    articleV2 = g.entity('ex:articleV2')
    dataSet1 = g.entity('ex:dataSet1')
    dataSet2 = g.entity('ex:dataSet2')
    regionList = g.entity('ex:regionList')
    composition = g.entity('ex:composition')
    chart1 = g.entity('ex:chart1')
    chart2 = g.entity('ex:chart2')
    blogEntry = g.entity('ex:blogEntry')

    compile = g.activity('ex:compile')
    compile2 = g.activity('ex:compile2')
    compose = g.activity('ex:compose')
    correct = g.activity('ex:correct', '2012-03-31T09:21:00', '2012-04-01T15:21:00')
    illustrate = g.activity('ex:illustrate')

    compose.used(dataSet1, attributes={'prov:role': "ex:dataToCompose"})
    compose.used(regionList, attributes={'prov:role': "ex:regionsToAggregateBy"})
    composition.wasGeneratedBy(compose)

    illustrate.used(composition)
    chart1.wasGeneratedBy(illustrate)

    chart1.wasGeneratedBy(compile, '2012-03-02T10:30:00')

    derek = g.agent('ex:derek', {
        'prov:type': PROV['Person'], 'foaf:givenName': "Derek", 'foaf:mbox': "<mailto:[e-mail]>"
    })
    compose.wasAssociatedWith(derek)
    illustrate.wasAssociatedWith(derek)

    chartgen = g.agent('ex:chartgen', {
        'prov:type': PROV["Organization"], 'foaf:name': "Chart Generators Inc"
    })
    derek.actedOnBehalfOf(chartgen, compose)
    chart1.wasAttributedTo(derek)

    dataSet2.wasGeneratedBy(correct)
    correct.used(dataSet1)
    dataSet2.wasDerivedFrom(dataSet1, attributes={'prov:type': PROV['Revision']})
    chart2.wasDerivedFrom(dataSet2)

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

    articleV2.specializationOf(article)
    articleV2.wasDerivedFrom(dataSet2)

    articleV2.alternateOf(articleV1)

    return g


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


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


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


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


def collections():
    g = ProvDocument()
    ex = Namespace('ex', 'http://example.org/')

    c1 = g.collection(ex['c1'])
    e1 = g.entity('ex:e1')
    g.hadMember(c1, e1)

    return g


def datatypes():
    g = ProvDocument()
    ex = Namespace('ex', 'http://example.org/')
    g.add_namespace(ex)

    attributes = {
        'ex:int': 100,
        'ex:float': 100.123456,
        'ex:long': 123456789000,
        'ex:bool': True,
        'ex:str': 'Some string',
        'ex:unicode': u'Some unicode string with accents: Huỳnh Trung Đông',
        'ex:timedate': datetime.datetime(2012, 12, 12, 14, 7, 48),
        'ex:intstr': Literal("PROV Internationalized string", PROV["InternationalizedString"], "en"),
    }
    multiline = """Line1
    Line2
Line3"""
    attributes['ex:multi-line'] = multiline
    g.entity('ex:e1', attributes)
    return g


def long_literals():
    g = ProvDocument()

    long_uri = "http://Lorem.ipsum/dolor/sit/amet/consectetur/adipiscing/elit/Quisque/vel/sollicitudin/felis/nec/" \
               "venenatis/massa/Aenean/lectus/arcu/sagittis/sit/amet/nisl/nec/varius/eleifend/sem/In/hac/habitasse/" \
               "platea/dictumst/Aliquam/eget/fermentum/enim/Curabitur/auctor/elit/non/ipsum/interdum/at/orci/aliquam/"
    ex = Namespace('ex', long_uri)
    g.add_namespace(ex)

    g.entity('ex:e1', {
        'prov:label': 'Lorem ipsum dolor sit amet, consectetur adipiscing elit. Donec pellentesque luctus nulla vel '
                      'ullamcorper. Donec sit amet ligula sit amet lorem pretium rhoncus vel vel lorem. Sed at '
                      'consequat metus, eget eleifend massa. Fusce a facilisis turpis. Lorem volutpat.'
    })

    return g

tests = [
    ('Bundle1', bundles1),
    ('Bundle2', bundles2),
    ('Primer', primer_example),
    ('W3C Publication 1', w3c_publication_1),
    ('W3C Publication 2', w3c_publication_2),
    ('collections', collections),
    ('datatypes', datatypes),
    ('Long literals', long_literals),
]