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

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

"""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 <[e-mail]>
"""
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__ = '[e-mail]'


# 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