Mercurial > repos > shellac > sam_consensus_v3
diff env/lib/python3.9/site-packages/prov/tests/examples.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
| author | shellac |
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| date | Mon, 22 Mar 2021 18:12:50 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/env/lib/python3.9/site-packages/prov/tests/examples.py Mon Mar 22 18:12:50 2021 +0000 @@ -0,0 +1,503 @@ +# 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:derek@example.org>"]) + g.agent('ex:derek', { + 'prov:type': PROV["Person"], 'foaf:givenName': "Derek", 'foaf:mbox': "<mailto:derek@example.org>" + }) + # 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:derek@example.org>" + }) + 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), +]