talipot-python: Add a new Trvial Graph Format import plugin

See https://en.wikipedia.org/wiki/Trivial_Graph_Format.

library/talipot-python/plugins/import/TrivialGraphFormatImport.py

@@ -0,0 +1,80 @@
+# Copyright (C) 2023  The Talipot developers
+#
+# Talipot is a fork of Tulip, created by David Auber
+# and the Tulip development Team from LaBRI, University of Bordeaux
+#
+# See the AUTHORS file at the top-level directory of this distribution
+# License: GNU General Public License version 3, or any later version
+# See top-level LICENSE file for more information
+
+# That plugin imports a graph from a file in the Trivial Graph Format (TGF)
+# (see https://en.wikipedia.org/wiki/Trivial_Graph_Format)
+
+import talipotplugins
+
+from talipot import tlp
+
+
+class TrivialGraphFormatImport(tlp.ImportModule):
+    def __init__(self, context):
+        tlp.ImportModule.__init__(self, context)
+        self.addFileParameter("filename", True, "The TGF file to import")
+
+    def fileExtensions(self):
+        return ["tgf"]
+
+    def parseTGF(self, tgfFile):
+        parsingEdges = False
+        nodesMap = {}
+        for line in tgfFile:
+            line = line.rstrip()
+            if not line:
+                continue
+            if line.startswith("#"):
+                parsingEdges = True
+                continue
+            if not parsingEdges:
+                split = line.split(" ", maxsplit=1)
+                n = self.graph.addNode()
+                nodesMap[split[0]] = n
+                self.graph["viewLabel"][n] = split[1] if len(split) > 1 else split[0]
+
+            else:
+                split = line.split(" ", maxsplit=2)
+                if len(split) < 2:
+                    raise ValueError(f"Invalid edge definition: {line}")
+                for i in range(2):
+                    if split[i] not in nodesMap:
+                        raise ValueError(
+                            f"Invalid node identifier found when parsing edges: {split[i]}"
+                        )
+                e = self.graph.addEdge(nodesMap[split[0]], nodesMap[split[1]])
+                if len(split) > 2:
+                    self.graph["viewLabel"][e] = split[2]
+
+    def importGraph(self):
+        # parse the TGF file
+        with open(self.dataSet["filename"], "r") as tgfFile:
+            self.parseTGF(tgfFile)
+
+        return True
+
+
+pluginDoc = """
+<p>Supported extension: tgf</p><p>Imports a graph from a file in the
+Trivial Graph Format (hhttps://en.wikipedia.org/wiki/Trivial_Graph_Format).
+The format consists of a list of node definitions, which map node IDs to labels,
+followed by a list of edges, which specify node pairs and an optional edge label.</p>
+"""
+
+# The line below does the magic to register the plugin to the plugin database
+# and updates the GUI to make it accessible through the menus.
+talipotplugins.registerPluginOfGroup(
+    "TrivialGraphFormatImport",
+    "Trivial Graph Format (TGF)",
+    "Antoine Lambert",
+    "16/11/2023",
+    pluginDoc,
+    "1.0",
+    "File",
+)

tests/python/CMakeLists.txt

@@ -2,3 +2,4 @@ UNIT_TEST(PythonGraphStructureTest test_graph_structure)
 UNIT_TEST(PythonGraphPropertiesTest test_graph_properties)
 UNIT_TEST(PythonPluginParametersTest test_plugin_registration_and_parameters)
 UNIT_TEST(PythonTalipotPluginsTest test_talipot_plugins)
+UNIT_TEST(PythonTGFImportTest test_tgf_import)

tests/python/test_tgf_import.py

@@ -0,0 +1,128 @@
+# Copyright (C) 2023  The Talipot developers
+#
+# Talipot is a fork of Tulip, created by David Auber
+# and the Tulip development Team from LaBRI, University of Bordeaux
+#
+# See the AUTHORS file at the top-level directory of this distribution
+# License: GNU General Public License version 3, or any later version
+# See top-level LICENSE file for more information
+
+import os
+import tempfile
+import textwrap
+import unittest
+
+from talipot import tlp
+
+
+class TestTalipotPlugins(unittest.TestCase):
+    @classmethod
+    def setUpClass(cls):
+        cls.tgfPluginName = "Trivial Graph Format (TGF)"
+        if "TALIPOT_BUILD_DIR" in os.environ:
+            talipot_build_dir = os.environ["TALIPOT_BUILD_DIR"]
+            if talipot_build_dir:
+                tlp.loadPluginsFromDir(
+                    os.path.join(talipot_build_dir, "library/talipot-python")
+                )
+
+    def test_tgf_plugin_loaded(self):
+        self.assertTrue("Trivial Graph Format (TGF)" in tlp.getImportPluginsList())
+
+    def test_load_tgf_graph_no_labels(self):
+        with tempfile.NamedTemporaryFile() as tgfFile:
+            with open(tgfFile.name, "w") as tgfFileWriter:
+                tgfFileWriter.write(
+                    textwrap.dedent(
+                        """
+                        0
+                        1
+                        2
+                        3
+                        #
+                        0 1
+                        0 2
+                        1 2
+                        1 3
+                        3 0
+                        """
+                    )
+                )
+            graph = tlp.importGraph(self.tgfPluginName, {"filename": tgfFile.name})
+            self.assertTrue(graph is not None)
+            self.assertEqual(graph.numberOfNodes(), 4)
+            self.assertEqual(graph.numberOfEdges(), 5)
+            nodes = graph.nodes()
+            self.assertTrue(graph.existEdge(nodes[0], nodes[1]))
+            self.assertTrue(graph.existEdge(nodes[0], nodes[2]))
+            self.assertTrue(graph.existEdge(nodes[1], nodes[2]))
+            self.assertTrue(graph.existEdge(nodes[1], nodes[3]))
+            self.assertTrue(graph.existEdge(nodes[3], nodes[0]))
+            self.assertEqual(
+                [graph["viewLabel"][n] for n in graph.nodes()], ["0", "1", "2", "3"]
+            )
+
+    def test_load_tgf_graph_with_labels(self):
+        with tempfile.NamedTemporaryFile() as tgfFile:
+            with open(tgfFile.name, "w") as tgfFileWriter:
+                tgfFileWriter.write(
+                    textwrap.dedent(
+                        """
+                        0 Node 0
+                        1 Node 1
+                        2 Node 2
+                        3 Node 3
+                        #
+                        0 1 Edge 0
+                        0 2 Edge 1
+                        1 2 Edge 2
+                        1 3 Edge 3
+                        3 0 Edge 4
+                        """
+                    )
+                )
+            graph = tlp.importGraph(self.tgfPluginName, {"filename": tgfFile.name})
+            self.assertEqual(
+                [graph["viewLabel"][n] for n in graph.nodes()],
+                [f"Node {i}" for i in range(4)],
+            )
+            self.assertEqual(
+                [graph["viewLabel"][e] for e in graph.edges()],
+                [f"Edge {i}" for i in range(5)],
+            )
+
+    def test_load_tgf_graph_invalid_edge(self):
+        with tempfile.NamedTemporaryFile() as tgfFile:
+            with open(tgfFile.name, "w") as tgfFileWriter:
+                tgfFileWriter.write(
+                    textwrap.dedent(
+                        """
+                        0
+                        1
+                        2
+                        3
+                        #
+                        4
+                        """
+                    )
+                )
+            graph = tlp.importGraph(self.tgfPluginName, {"filename": tgfFile.name})
+            self.assertTrue(graph is None)
+
+    def test_load_tgf_graph_invalid_node_id(self):
+        with tempfile.NamedTemporaryFile() as tgfFile:
+            with open(tgfFile.name, "w") as tgfFileWriter:
+                tgfFileWriter.write(
+                    textwrap.dedent(
+                        """
+                        0
+                        1
+                        2
+                        3
+                        #
+                        4 5
+                        """
+                    )
+                )
+            graph = tlp.importGraph(self.tgfPluginName, {"filename": tgfFile.name})
+            self.assertTrue(graph is None)