How to visualize provenance

Note

This tutorial can be downloaded and run as a Jupyter Notebook: visualising_graphs.ipynb

The provenance graph of a database can be visually inspected, via graphviz, using both the python API and command-line interface.

See also

verdi graph generate -h

We first load the database and required modules:

from aiida import load_profile
profile = load_profile()

from aiida.common import LinkType
from aiida.orm.utils.links import LinkPair
from aiida.tools.visualization import Graph, pstate_node_styles
from tests.utils.archives import get_archive_file

The example provenance graph, used in this tutorial, can be downloaded from this link

It can then be imported into the database:

!verdi archive import -n graph1.aiida

dict1_uuid = '0ea79a16-501f-408a-8c84-a2704a778e4b'
calc1_uuid = 'b23e692e-4e01-48dd-b515-4c63877d73a4'

The Graph class is used to store visual representations of the nodes and edges, which can be added separately or cumulatively by one of the graph traversal methods. The graphviz attribute returns a graphviz.Digraph instance, which will auto-magically render the graph in the notebook, or can be used to save the graph to file.

graph = Graph()
graph.add_node(dict1_uuid)
graph.add_node(calc1_uuid)
graph.graphviz

graph.add_edge(
    dict1_uuid, calc1_uuid,
    link_pair=LinkPair(LinkType.INPUT_CALC, "input1"))
graph.graphviz

graph.add_incoming(calc1_uuid)
graph.add_outgoing(calc1_uuid)
graph.graphviz

The Graph can also be initialized with global style attributes, as outlined in the graphviz attributes table.

graph = Graph(node_id_type="uuid",
              global_node_style={"penwidth": 1},
              global_edge_style={"color": "blue"},
              graph_attr={"size": "6,6!", "rankdir": "LR"})
graph.add_incoming(calc1_uuid)
graph.add_outgoing(calc1_uuid)
graph.graphviz

Additionally functions can be parsed to the Graph initializer, to specify exactly how each node will be represented. For example, the pstate_node_styles() function colors process nodes by their process state.

def link_style(link_pair, **kwargs):
    return {"color": "blue"}

graph = Graph(node_style_fn=pstate_node_styles,
              link_style_fn=link_style,
              graph_attr={"size": "6,6!", "rankdir": "LR"})
graph.add_incoming(calc1_uuid)
graph.add_outgoing(calc1_uuid)
graph.graphviz

Edges can be annotated by one or both of their edge label and link type.

graph = Graph(graph_attr={"size": "6,6!", "rankdir": "LR"})
graph.add_incoming(calc1_uuid,
                   annotate_links="both")
graph.add_outgoing(calc1_uuid,
                   annotate_links="both")
graph.graphviz

The recurse_descendants() and recurse_ancestors() methods can be used to construct a full provenance graph.

graph = Graph(graph_attr={"size": "8,8!", "rankdir": "LR"})
graph.recurse_descendants(
    dict1_uuid,
    origin_style=None,
    include_process_inputs=True,
    annotate_links="both"
)
graph.graphviz

The link types can also be filtered, to view only the ‘data’ or ‘logical’ provenance.

graph = Graph(graph_attr={"size": "8,8!", "rankdir": "LR"})
graph.recurse_descendants(
    dict1_uuid,
    origin_style=None,
    include_process_inputs=True,
    annotate_links="both",
    link_types=("input_calc", "create")
)
graph.graphviz

graph = Graph(graph_attr={"size": "8,8!", "rankdir": "LR"})
graph.recurse_descendants(
    dict1_uuid,
    origin_style=None,
    include_process_inputs=True,
    annotate_links="both",
    link_types=("input_work", "return")
)
graph.graphviz

If you wish to highlight specific node classes, then the highlight_classes option can be used to only color specified nodes:

graph = Graph(graph_attr={"size": "20,20", "rankdir": "LR"})
graph.recurse_descendants(
    dict1_uuid,
    highlight_classes=['Dict']
)
graph.graphviz

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