Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/prov/graph.py @ 4:79f47841a781 draft

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"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:47:39 -0400
parents 26e78fe6e8c4
children
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1 from __future__ import (absolute_import, division, print_function,
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2 unicode_literals)
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3
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4 import networkx as nx
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5 from prov.model import (
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6 ProvDocument, ProvRecord, ProvElement, ProvEntity, ProvActivity, ProvAgent,
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7 ProvRelation, PROV_ATTR_ENTITY, PROV_ATTR_ACTIVITY, PROV_ATTR_AGENT,
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8 PROV_ATTR_TRIGGER, PROV_ATTR_GENERATED_ENTITY, PROV_ATTR_USED_ENTITY,
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9 PROV_ATTR_DELEGATE, PROV_ATTR_RESPONSIBLE, PROV_ATTR_SPECIFIC_ENTITY,
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10 PROV_ATTR_GENERAL_ENTITY, PROV_ATTR_ALTERNATE1, PROV_ATTR_ALTERNATE2,
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11 PROV_ATTR_COLLECTION, PROV_ATTR_INFORMED, PROV_ATTR_INFORMANT
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12 )
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13
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14 __author__ = 'Trung Dong Huynh'
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15 __email__ = 'trungdong@donggiang.com'
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16
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17
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18 INFERRED_ELEMENT_CLASS = {
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19 PROV_ATTR_ENTITY: ProvEntity,
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20 PROV_ATTR_ACTIVITY: ProvActivity,
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21 PROV_ATTR_AGENT: ProvAgent,
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22 PROV_ATTR_TRIGGER: ProvEntity,
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23 PROV_ATTR_GENERATED_ENTITY: ProvEntity,
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24 PROV_ATTR_USED_ENTITY: ProvEntity,
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25 PROV_ATTR_DELEGATE: ProvAgent,
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26 PROV_ATTR_RESPONSIBLE: ProvAgent,
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27 PROV_ATTR_SPECIFIC_ENTITY: ProvEntity,
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28 PROV_ATTR_GENERAL_ENTITY: ProvEntity,
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29 PROV_ATTR_ALTERNATE1: ProvEntity,
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30 PROV_ATTR_ALTERNATE2: ProvEntity,
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31 PROV_ATTR_COLLECTION: ProvEntity,
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32 PROV_ATTR_INFORMED: ProvActivity,
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33 PROV_ATTR_INFORMANT: ProvActivity
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34 }
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35
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36
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37 def prov_to_graph(prov_document):
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38 """
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39 Convert a :class:`~prov.model.ProvDocument` to a `MultiDiGraph
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40 <https://networkx.readthedocs.io/en/stable/reference/classes.multigraph.html>`_
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41 instance of the `NetworkX <https://networkx.github.io/>`_ library.
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42
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43 :param prov_document: The :class:`~prov.model.ProvDocument` instance to convert.
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44 """
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45 g = nx.MultiDiGraph()
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46 unified = prov_document.unified()
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47 node_map = dict()
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48 for element in unified.get_records(ProvElement):
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49 g.add_node(element)
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50 node_map[element.identifier] = element
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51
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52 for relation in unified.get_records(ProvRelation):
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53 # taking the first two elements of a relation
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54 attr_pair_1, attr_pair_2 = relation.formal_attributes[:2]
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55 # only need the QualifiedName (i.e. the value of the attribute)
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56 qn1, qn2 = attr_pair_1[1], attr_pair_2[1]
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57 if qn1 and qn2: # only proceed if both ends of the relation exist
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58 try:
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59 if qn1 not in node_map:
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60 node_map[qn1] = \
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61 INFERRED_ELEMENT_CLASS[attr_pair_1[0]](None, qn1)
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62 if qn2 not in node_map:
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63 node_map[qn2] = \
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64 INFERRED_ELEMENT_CLASS[attr_pair_2[0]](None, qn2)
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65 except KeyError:
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66 # Unsupported attribute; cannot infer the type of the element
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67 continue # skipping this relation
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68 g.add_edge(node_map[qn1], node_map[qn2], relation=relation)
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69 return g
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70
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71
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72 def graph_to_prov(g):
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73 """
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74 Convert a `MultiDiGraph
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75 <https://networkx.readthedocs.io/en/stable/reference/classes.multigraph.html>`_
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76 that was previously produced by :func:`prov_to_graph` back to a
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77 :class:`~prov.model.ProvDocument`.
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78
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79 :param g: The graph instance to convert.
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80 """
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81 prov_doc = ProvDocument()
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82 for n in g.nodes_iter():
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83 if isinstance(n, ProvRecord) and n.bundle is not None:
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84 prov_doc.add_record(n)
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85 for _, _, edge_data in g.edges_iter(data=True):
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86 try:
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87 relation = edge_data['relation']
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88 if isinstance(relation, ProvRecord):
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89 prov_doc.add_record(relation)
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90 except KeyError:
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91 pass
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92
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93 return prov_doc