Add basic tests for vis modules.

Author: Oliver Scott

tests/vis/__init__.py

@@ -0,0 +1,5 @@
+"""
+scaffoldgraph tests.vis
+"""
+
+from ..test_network import long_test_network

tests/vis/test_notebook.py

@@ -0,0 +1,16 @@
+"""
+scaffoldgraph tests.vis.test_notebook
+"""
+
+from pytest import mark
+
+
+@mark.filterwarnings('ignore::UserWarning')
+def test_resources():
+    # Import inside function to supress user warning.
+    from scaffoldgraph.vis.notebook import cytoscape
+    check = cytoscape.DEFAULT_STYLE
+    assert check.parent.exists()  # resource directory
+    assert check.exists()  # cytoscape.json
+    style = cytoscape.read_style_file(str(check))
+    assert style is not None

tests/vis/test_vis_utils.py

@@ -0,0 +1,125 @@
+"""
+scaffoldgraph tests.vis.test_vis_utils
+"""
+
+import scaffoldgraph.vis.utils as vis_utils
+import matplotlib.pyplot as plt
+import random
+import pytest
+import re
+
+from rdkit.Chem.Draw import rdMolDraw2D
+from rdkit import Chem
+
+from scaffoldgraph.utils import suppress_rdlogger
+from . import long_test_network
+
+
+SVG_PATTERN = r'(?:<\?xml\b[^>]*>[^<]*)?(?:<!--.*?-->[^<]*)*(?:<svg|<!DOCTYPE svg)\b'
+SVG_REGEX = re.compile(SVG_PATTERN, re.DOTALL)
+
+SVG_DIM_PATTERN = r"width='(\d+px)'\s+height='(\d+px)"
+SVG_DIM_REGEX = re.compile(SVG_DIM_PATTERN)
+
+HEX_PATTERN = r'^#([A-Fa-f0-9]{6}|[A-Fa-f0-9]{3})$'
+HEX_REGEX = re.compile(HEX_PATTERN)
+
+
+def naive_svg_check(svg_string):
+    """Validate SVG format (naive)."""
+    return SVG_REGEX.match(svg_string) is not None
+
+
+def svg_dimensions(svg_string):
+    """Return dimensions of an (rdkit) SVG string."""
+    matches = SVG_DIM_REGEX.findall(svg_string)
+    if not matches:
+        return (None, None)
+    dims = map(lambda x: int(x.replace('px', '')), matches[0])
+    return tuple(dims)
+
+
+def insert_random_node_attribute(graph, key, high=1, low=0):
+    """Add a random attribute to nodes in a graph."""
+    for _, data in graph.nodes(data=True):
+        value = random.uniform(low, high)
+        data[key] = value
+
+
+def is_valid_hex(hex):
+    """Validate hexadecimal color code."""
+    if hex is None:
+        return False
+    if HEX_REGEX.search(hex):
+        return True
+    return False
+
+
+def test_smiles_to_svg():
+    smi = 'Cc1ccc(NC(=O)c2ccc(CN3CCN(C)CC3)cc2)cc1Nc1nccc(-c2cccnc2)n1'
+    img = vis_utils.smiles_to_svg(smi)  # smiles to SVG
+    assert img is not None
+    assert naive_svg_check(img) is True
+    # Check size updates.
+    dims = (450, 400)
+    img = vis_utils.smiles_to_svg(smi, size=dims)
+    assert svg_dimensions(img) == dims
+    # Check drawing options (clear background).
+    drawOpts = rdMolDraw2D.MolDrawOptions()
+    drawOpts.clearBackground = True
+    img = vis_utils.smiles_to_svg(smi, draw_options=drawOpts)
+    assert '</rect>' in img  # <rect> exists with background
+    drawOpts.clearBackground = False
+    img = vis_utils.smiles_to_svg(smi, draw_options=drawOpts)
+    assert '</rect>' not in img
+
+
+@suppress_rdlogger()
+def test_smiles_to_image():
+    # These aren't paticularly great tests for this function...
+    smi = 'Cc1ccc(NC(=O)c2ccc(CN3CCN(C)CC3)cc2)cc1Nc1nccc(-c2cccnc2)n1'
+    img = vis_utils.smiles_to_image(smi)  # smiles to SVG
+    assert img is not None
+    assert img != 'data:image/svg+xml;charset=utf-8,'
+    null_smi = 'xxx'
+    img = vis_utils.smiles_to_image(null_smi)
+    assert img == 'data:image/svg+xml;charset=utf-8,'
+
+
+def test_embed_node_mol_images(network):
+    # Embed images into node attributes.
+    vis_utils.embed_node_mol_images(network)
+    for _, data in network.nodes(data=True):
+        img = data.get('img', None)
+        assert img is not None
+    # Remove images from node attributes.
+    vis_utils.remove_node_mol_images(network)
+    for _, data in network.nodes(data=True):
+        img = data.get('img', None)
+        assert img is None
+
+
+def test_color_nodes_by_attribute(network):
+    key = 'attr'
+    insert_random_node_attribute(network, key)
+    # Color scaffold nodes.
+    vis_utils.color_scaffold_nodes_by_attribute(network, key, 'BuPu')
+    for _, data in network.get_scaffold_nodes(data=True):
+        c = data.get('color', None)
+        assert c is not None
+        assert is_valid_hex(c)
+    # Color molecule nodes.
+    cmap = plt.get_cmap('hot')
+    vis_utils.color_molecule_nodes_by_attribute(network, key, cmap, 'col')
+    for _, data in network.get_molecule_nodes(data=True):
+        c = data.get('col', None)
+        assert c is not None
+        assert is_valid_hex(c)
+
+
+def test_root_node(network):
+    vis_utils.add_root_node(network)
+    assert network.has_node('root') is True
+    assert network.in_degree('root') == 0
+    vis_utils.remove_root_node(network)
+    assert network.has_node('root') is False