Mercurial > repos > shellac > guppy_basecaller
diff env/lib/python3.7/site-packages/prov/tests/examples.py @ 5:9b1c78e6ba9c draft default tip
"planemo upload commit 6c0a8142489327ece472c84e558c47da711a9142"
| author | shellac |
|---|---|
| date | Mon, 01 Jun 2020 08:59:25 -0400 |
| parents | 79f47841a781 |
| children |
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--- a/env/lib/python3.7/site-packages/prov/tests/examples.py Thu May 14 16:47:39 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,503 +0,0 @@ -# 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), -]