Mercurial > repos > shellac > guppy_basecaller
view env/lib/python3.7/site-packages/prov/dot.py @ 3:758bc20232e8 draft
"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author | shellac |
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date | Thu, 14 May 2020 16:20:52 -0400 |
parents | 26e78fe6e8c4 |
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"""Graphical visualisation support for prov.model. This module produces graphical visualisation for provenanve graphs. Requires pydot module and Graphviz. References: * pydot homepage: https://github.com/erocarrera/pydot * Graphviz: http://www.graphviz.org/ * DOT Language: http://www.graphviz.org/doc/info/lang.html .. moduleauthor:: Trung Dong Huynh <trungdong@donggiang.com> """ from __future__ import (absolute_import, division, print_function, unicode_literals) try: from html import escape except ImportError: from cgi import escape from datetime import datetime import pydot import six from prov.model import ( PROV_ACTIVITY, PROV_AGENT, PROV_ALTERNATE, PROV_ASSOCIATION, PROV_ATTRIBUTION, PROV_BUNDLE, PROV_COMMUNICATION, PROV_DERIVATION, PROV_DELEGATION, PROV_ENTITY, PROV_GENERATION, PROV_INFLUENCE, PROV_INVALIDATION, PROV_END, PROV_MEMBERSHIP, PROV_MENTION, PROV_SPECIALIZATION, PROV_START, PROV_USAGE, Identifier, PROV_ATTRIBUTE_QNAMES, sorted_attributes, ProvException ) __author__ = 'Trung Dong Huynh' __email__ = 'trungdong@donggiang.com' # Visual styles for various elements (nodes) and relations (edges) # see http://graphviz.org/content/attrs DOT_PROV_STYLE = { # Generic node 0: { 'shape': 'oval', 'style': 'filled', 'fillcolor': 'lightgray', 'color': 'dimgray' }, # Elements PROV_ENTITY: { 'shape': 'oval', 'style': 'filled', 'fillcolor': '#FFFC87', 'color': '#808080' }, PROV_ACTIVITY: { 'shape': 'box', 'style': 'filled', 'fillcolor': '#9FB1FC', 'color': '#0000FF' }, PROV_AGENT: { 'shape': 'house', 'style': 'filled', 'fillcolor': '#FED37F' }, PROV_BUNDLE: { 'shape': 'folder', 'style': 'filled', 'fillcolor': 'aliceblue' }, # Relations PROV_GENERATION: { 'label': 'wasGeneratedBy', 'fontsize': '10.0', 'color': 'darkgreen', 'fontcolor': 'darkgreen' }, PROV_USAGE: { 'label': 'used', 'fontsize': '10.0', 'color': 'red4', 'fontcolor': 'red' }, PROV_COMMUNICATION: { 'label': 'wasInformedBy', 'fontsize': '10.0' }, PROV_START: { 'label': 'wasStartedBy', 'fontsize': '10.0' }, PROV_END: { 'label': 'wasEndedBy', 'fontsize': '10.0' }, PROV_INVALIDATION: { 'label': 'wasInvalidatedBy', 'fontsize': '10.0' }, PROV_DERIVATION: { 'label': 'wasDerivedFrom', 'fontsize': '10.0' }, PROV_ATTRIBUTION: { 'label': 'wasAttributedTo', 'fontsize': '10.0', 'color': '#FED37F' }, PROV_ASSOCIATION: { 'label': 'wasAssociatedWith', 'fontsize': '10.0', 'color': '#FED37F' }, PROV_DELEGATION: { 'label': 'actedOnBehalfOf', 'fontsize': '10.0', 'color': '#FED37F' }, PROV_INFLUENCE: { 'label': 'wasInfluencedBy', 'fontsize': '10.0', 'color': 'grey' }, PROV_ALTERNATE: { 'label': 'alternateOf', 'fontsize': '10.0' }, PROV_SPECIALIZATION: { 'label': 'specializationOf', 'fontsize': '10.0' }, PROV_MENTION: { 'label': 'mentionOf', 'fontsize': '10.0' }, PROV_MEMBERSHIP: { 'label': 'hadMember', 'fontsize': '10.0' }, } ANNOTATION_STYLE = { 'shape': 'note', 'color': 'gray', 'fontcolor': 'black', 'fontsize': '10' } ANNOTATION_LINK_STYLE = { 'arrowhead': 'none', 'style': 'dashed', 'color': 'gray' } ANNOTATION_START_ROW = '<<TABLE cellpadding=\"0\" border=\"0\">' ANNOTATION_ROW_TEMPLATE = """ <TR> <TD align=\"left\" href=\"%s\">%s</TD> <TD align=\"left\"%s>%s</TD> </TR>""" ANNOTATION_END_ROW = ' </TABLE>>' def htlm_link_if_uri(value): try: uri = value.uri return '<a href="%s">%s</a>' % (uri, six.text_type(value)) except AttributeError: return six.text_type(value) def prov_to_dot(bundle, show_nary=True, use_labels=False, direction='BT', show_element_attributes=True, show_relation_attributes=True): """ Convert a provenance bundle/document into a DOT graphical representation. :param bundle: The provenance bundle/document to be converted. :type bundle: :class:`ProvBundle` :param show_nary: shows all elements in n-ary relations. :type show_nary: bool :param use_labels: uses the prov:label property of an element as its name (instead of its identifier). :type use_labels: bool :param direction: specifies the direction of the graph. Valid values are "BT" (default), "TB", "LR", "RL". :param show_element_attributes: shows attributes of elements. :type show_element_attributes: bool :param show_relation_attributes: shows attributes of relations. :type show_relation_attributes: bool :returns: :class:`pydot.Dot` -- the Dot object. """ if direction not in {'BT', 'TB', 'LR', 'RL'}: # Invalid direction is provided direction = 'BT' # reset it to the default value maindot = pydot.Dot(graph_type='digraph', rankdir=direction, charset='utf-8') node_map = {} count = [0, 0, 0, 0] # counters for node ids def _bundle_to_dot(dot, bundle): def _attach_attribute_annotation(node, record): # Adding a node to show all attributes attributes = list( (attr_name, value) for attr_name, value in record.attributes if attr_name not in PROV_ATTRIBUTE_QNAMES ) if not attributes: return # No attribute to display # Sort the attributes. attributes = sorted_attributes(record.get_type(), attributes) ann_rows = [ANNOTATION_START_ROW] ann_rows.extend( ANNOTATION_ROW_TEMPLATE % ( attr.uri, escape(six.text_type(attr)), ' href=\"%s\"' % value.uri if isinstance(value, Identifier) else '', escape(six.text_type(value) if not isinstance(value, datetime) else six.text_type(value.isoformat()))) for attr, value in attributes ) ann_rows.append(ANNOTATION_END_ROW) count[3] += 1 annotations = pydot.Node( 'ann%d' % count[3], label='\n'.join(ann_rows), **ANNOTATION_STYLE ) dot.add_node(annotations) dot.add_edge(pydot.Edge(annotations, node, **ANNOTATION_LINK_STYLE)) def _add_bundle(bundle): count[2] += 1 subdot = pydot.Cluster( graph_name='c%d' % count[2], URL='"%s"' % bundle.identifier.uri ) if use_labels: if bundle.label == bundle.identifier: bundle_label = '"%s"' % six.text_type(bundle.label) else: # Fancier label if both are different. The label will be # the main node text, whereas the identifier will be a # kind of subtitle. bundle_label = ('<%s<br />' '<font color="#333333" point-size="10">' '%s</font>>') bundle_label = bundle_label % ( six.text_type(bundle.label), six.text_type(bundle.identifier) ) subdot.set_label('"%s"' % six.text_type(bundle_label)) else: subdot.set_label('"%s"' % six.text_type(bundle.identifier)) _bundle_to_dot(subdot, bundle) dot.add_subgraph(subdot) return subdot def _add_node(record): count[0] += 1 node_id = 'n%d' % count[0] if use_labels: if record.label == record.identifier: node_label = '"%s"' % six.text_type(record.label) else: # Fancier label if both are different. The label will be # the main node text, whereas the identifier will be a # kind of subtitle. node_label = ('<%s<br />' '<font color="#333333" point-size="10">' '%s</font>>') node_label = node_label % (six.text_type(record.label), six.text_type(record.identifier)) else: node_label = '"%s"' % six.text_type(record.identifier) uri = record.identifier.uri style = DOT_PROV_STYLE[record.get_type()] node = pydot.Node( node_id, label=node_label, URL='"%s"' % uri, **style ) node_map[uri] = node dot.add_node(node) if show_element_attributes: _attach_attribute_annotation(node, rec) return node def _add_generic_node(qname): count[0] += 1 node_id = 'n%d' % count[0] node_label = '"%s"' % six.text_type(qname) uri = qname.uri style = DOT_PROV_STYLE[0] node = pydot.Node( node_id, label=node_label, URL='"%s"' % uri, **style ) node_map[uri] = node dot.add_node(node) return node def _get_bnode(): count[1] += 1 bnode_id = 'b%d' % count[1] bnode = pydot.Node( bnode_id, label='""', shape='point', color='gray' ) dot.add_node(bnode) return bnode def _get_node(qname): if qname is None: return _get_bnode() uri = qname.uri if uri not in node_map: _add_generic_node(qname) return node_map[uri] records = bundle.get_records() relations = [] for rec in records: if rec.is_element(): _add_node(rec) else: # Saving the relations for later processing relations.append(rec) if not bundle.is_bundle(): for bundle in bundle.bundles: _add_bundle(bundle) for rec in relations: args = rec.args # skipping empty records if not args: continue # picking element nodes nodes = [ value for attr_name, value in rec.formal_attributes if attr_name in PROV_ATTRIBUTE_QNAMES ] other_attributes = [ (attr_name, value) for attr_name, value in rec.attributes if attr_name not in PROV_ATTRIBUTE_QNAMES ] add_attribute_annotation = ( show_relation_attributes and other_attributes ) add_nary_elements = len(nodes) > 2 and show_nary style = DOT_PROV_STYLE[rec.get_type()] if len(nodes) < 2: # too few elements for a relation? continue # cannot draw this if add_nary_elements or add_attribute_annotation: # a blank node for n-ary relations or the attribute annotation bnode = _get_bnode() # the first segment dot.add_edge( pydot.Edge( _get_node(nodes[0]), bnode, arrowhead='none', **style ) ) style = dict(style) # copy the style del style['label'] # not showing label in the second segment # the second segment dot.add_edge(pydot.Edge(bnode, _get_node(nodes[1]), **style)) if add_nary_elements: style['color'] = 'gray' # all remaining segment to be gray for node in nodes[2:]: if node is not None: dot.add_edge( pydot.Edge(bnode, _get_node(node), **style) ) if add_attribute_annotation: _attach_attribute_annotation(bnode, rec) else: # show a simple binary relations with no annotation dot.add_edge( pydot.Edge( _get_node(nodes[0]), _get_node(nodes[1]), **style ) ) try: unified = bundle.unified() except ProvException: # Could not unify this bundle # try the original document anyway unified = bundle _bundle_to_dot(maindot, unified) return maindot