improved test coverage, automation scripts

tests/render/test_cytoscape.py

@@ -0,0 +1,227 @@
+"""tests for Cytoscape API requests, needs running Cytoscape server;
+Tests assume that no Cytoscape instance is running.
+The validation of the correct behaviour can only be done with a running instance,
+especially for layout and formatting tasks. A static test suite is not helpful in
+this case.
+"""
+
+import py4cytoscape as p4c
+import pytest
+from py4cytoscape.exceptions import CyError
+from requests.exceptions import RequestException
+
+from lang_main.constants import CYTO_BASE_NETWORK_NAME, CYTO_SELECTION_PROPERTY
+from lang_main.errors import GraphRenderError
+from lang_main.render import cytoscape as cyto
+
+_cyto_available: bool = True
+try:
+    p4c.cytoscape_ping()
+except RequestException:
+    _cyto_available = False
+
+
+@pytest.fixture(scope='module')
+def avail() -> bool:
+    return _cyto_available
+
+
+@pytest.mark.cyto
+def test_verify_connection(avail):
+    if avail:
+        cyto.verify_connection()
+    else:
+        with pytest.raises(RequestException):
+            cyto.verify_connection()
+
+
+def test_verify_graph_render_size(data_tk_graph_built):
+    cyto.verify_graph_render_size(
+        data_tk_graph_built, max_node_count=None, max_edge_count=None
+    )
+
+    with pytest.raises(GraphRenderError):
+        cyto.verify_graph_render_size(
+            data_tk_graph_built, max_node_count=0, max_edge_count=None
+        )
+
+    with pytest.raises(GraphRenderError):
+        cyto.verify_graph_render_size(
+            data_tk_graph_built, max_node_count=None, max_edge_count=0
+        )
+
+
+@pytest.mark.cyto
+def test_change_default_layout(avail):
+    if avail:
+        cyto.change_default_layout()
+    else:
+        with pytest.raises(RequestException):
+            cyto.change_default_layout()
+
+
+@pytest.mark.cyto
+def test_import_to_cytoscape(avail, data_tk_graph_built):
+    if avail:
+        cyto.import_to_cytoscape(data_tk_graph_built)
+    else:
+        with pytest.raises(RequestException):
+            cyto.import_to_cytoscape(data_tk_graph_built)
+
+
+@pytest.mark.cyto
+def test_verify_table_property(avail, data_tk_graph_built):
+    if avail:
+        cyto.import_to_cytoscape(data_tk_graph_built)
+        contained = cyto.verify_table_property(property='TEST', table_type='node')
+        assert not contained
+        contained = cyto.verify_table_property(property='name', table_type='node')
+        assert contained
+        contained = cyto.verify_table_property(property='degree_weighted', table_type='node')
+        assert contained
+    else:
+        with pytest.raises(RequestException):
+            contained = cyto.verify_table_property(property='TEST', table_type='node')
+
+
+@pytest.mark.cyto
+def test_analyse_network(avail, data_tk_graph_built):
+    if avail:
+        cyto.import_to_cytoscape(data_tk_graph_built)
+        cyto.analyse_network()
+        contained = cyto.verify_table_property(property='name', table_type='node')
+        assert contained
+        contained = cyto.verify_table_property(
+            property=CYTO_SELECTION_PROPERTY, table_type='node'
+        )
+        assert contained
+    else:
+        with pytest.raises(RequestException):
+            cyto.analyse_network(data_tk_graph_built)
+
+
+@pytest.mark.cyto
+def test_reset_current_network_to_base(avail):
+    if avail:
+        cyto.reset_current_network_to_base()
+    else:
+        with pytest.raises(RequestException):
+            cyto.reset_current_network_to_base()
+
+
+@pytest.mark.cyto
+def test_fit_content(avail, data_tk_graph_built):
+    if avail:
+        cyto.import_to_cytoscape(data_tk_graph_built)
+        cyto.fit_content()
+    else:
+        with pytest.raises(RequestException):
+            cyto.fit_content()
+
+
+@pytest.mark.cyto
+def test_export_network_to_image(avail, tmp_path, data_tk_graph_built):
+    filename = 'test_export'
+    if avail:
+        cyto.import_to_cytoscape(data_tk_graph_built)
+        cyto.export_network_to_image(filename=filename, target_folder=tmp_path)
+        target_file = tmp_path / f'{filename}.svg'
+        assert target_file.exists()
+        assert target_file.name == f'{filename}.svg'
+    else:
+        with pytest.raises(RequestException):
+            cyto.export_network_to_image(filename=filename, target_folder=tmp_path)
+
+
+@pytest.mark.cyto
+def test_layout_network(avail, data_tk_graph_built):
+    if avail:
+        cyto.import_to_cytoscape(data_tk_graph_built)
+        cyto.layout_network()
+    else:
+        with pytest.raises(RequestException):
+            cyto.layout_network()
+
+
+@pytest.mark.cyto
+def test_apply_style_to_network(avail, data_tk_graph_built, tmp_path):
+    if avail:
+        layout_not_existing = 'testing'
+        pth_not_existing = tmp_path / 'test.xml'
+        with pytest.raises(FileNotFoundError):
+            cyto.apply_style_to_network(
+                style_name=layout_not_existing,
+                pth_to_stylesheet=pth_not_existing,
+            )
+
+        cyto.import_to_cytoscape(data_tk_graph_built)
+        # not existing: so transfer necessary,
+        # but fails nevertheless because style is imported
+        # using the name provided by this style configuration
+        with pytest.raises(CyError):
+            cyto.apply_style_to_network(style_name=layout_not_existing)
+        cyto.apply_style_to_network()
+    else:
+        with pytest.raises(RequestException):
+            cyto.apply_style_to_network()
+
+
+@pytest.mark.cyto
+def test_get_subgraph_node_selection(avail, data_tk_graph_built):
+    num_subgraphs = 2
+    if avail:
+        cyto.import_to_cytoscape(data_tk_graph_built)
+        cyto.analyse_network()
+        suids = cyto.get_subgraph_node_selection(num_subgraphs=num_subgraphs)
+        assert len(suids) > 0
+    else:
+        with pytest.raises(RequestException):
+            cyto.get_subgraph_node_selection(num_subgraphs=num_subgraphs)
+
+
+@pytest.mark.cyto
+def test_select_neighbours_of_node(avail, data_tk_graph_built):
+    num_subgraphs = 2
+    if avail:
+        cyto.import_to_cytoscape(data_tk_graph_built)
+        suids = cyto.get_subgraph_node_selection(num_subgraphs=num_subgraphs)
+        assert len(suids) > 0
+        cyto.select_neighbours_of_node(suids[0], neighbour_iter_depth=2)
+    else:
+        with pytest.raises(RequestException):
+            cyto.select_neighbours_of_node(123, neighbour_iter_depth=2)
+
+
+@pytest.mark.cyto
+def test_make_subnetwork(avail, data_tk_graph_built, tmp_path):
+    if avail:
+        cyto.import_to_cytoscape(data_tk_graph_built)
+        suids = cyto.get_subgraph_node_selection(num_subgraphs=2)
+        assert len(suids) > 0
+        cyto.select_neighbours_of_node(suids[0], neighbour_iter_depth=2)
+        cyto.make_subnetwork(0, target_folder=tmp_path, export_image=True)
+        subnetwork_name = CYTO_BASE_NETWORK_NAME + '_sub_1'
+        networks = p4c.get_network_list()
+        assert len(networks) > 1
+        file = (tmp_path / subnetwork_name).with_suffix('.svg')
+        assert file.exists()
+    else:
+        with pytest.raises(RequestException):
+            cyto.make_subnetwork(0, target_folder=tmp_path, export_image=True)
+
+
+@pytest.mark.cyto
+def test_build_subnetworks(avail, data_tk_graph_built, tmp_path):
+    if avail:
+        cyto.import_to_cytoscape(data_tk_graph_built)
+        suids = cyto.get_subgraph_node_selection(num_subgraphs=1)
+        assert len(suids) > 0
+        cyto.build_subnetworks(suids, export_image=True, target_folder=tmp_path)
+        subnetwork_name = CYTO_BASE_NETWORK_NAME + '_sub_1'
+        networks = p4c.get_network_list()
+        assert len(networks) > 1
+        file = (tmp_path / subnetwork_name).with_suffix('.svg')
+        assert file.exists()
+    else:
+        with pytest.raises(RequestException):
+            cyto.build_subnetworks([123], export_image=True, target_folder=tmp_path)