From 9553296a6900cf218d0b477114865755358ee882 Mon Sep 17 00:00:00 2001
From: janezd <janez.demsar@fri.uni-lj.si>
Date: Wed, 7 Jun 2023 20:11:30 +0200
Subject: [PATCH] Pajek reader: Allow giving labels instead of weights

---
 orangecontrib/network/network/readwrite.py    | 32 ++++++++++++-------
 .../network/network/tests/test_readwrite.py   | 21 ++++++++++--
 orangecontrib/network/network/tests/towns.net | 12 +++++++
 3 files changed, 51 insertions(+), 14 deletions(-)
 create mode 100644 orangecontrib/network/network/tests/towns.net

diff --git a/orangecontrib/network/network/readwrite.py b/orangecontrib/network/network/readwrite.py
index 1f13bbad..8305b049 100644
--- a/orangecontrib/network/network/readwrite.py
+++ b/orangecontrib/network/network/readwrite.py
@@ -51,17 +51,27 @@ def read_vertices(lines):
 
 
 def read_edges(id_idx, lines, nvertices):
-    lines = [(id_idx[v1], id_idx[v2], abs(float(value)))
-             for v1, v2, value, *_ in (line.split()[:3] + [1]
-                                       for line in lines)]
-    v1s, v2s, values = zip(*lines)
-    values = np.array(values)
-    if values.size and np.all(values == values[0]):
-        values = np.lib.stride_tricks.as_strided(
-            values[0], (len(values), ), (0, ))
+    def fake_data(x, n):
+        values = np.lib.stride_tricks.as_strided(x, (n, ), (0,))
         values.flags.writeable = False
-    return sp.coo_matrix((values, (np.array(v1s), np.array(v2s))),
-                         shape=(nvertices, nvertices))
+        return values
+
+
+    lines = [(id_idx[v1], id_idx[v2], value)
+             for v1, v2, value, *_ in (
+             (line.split(maxsplit=2) + [None])[:3] for line in lines)]
+    v1s, v2s, values = zip(*lines)
+    try:
+        values = np.array(values, dtype=float)
+        if values.size and np.all(values == values[0]):
+            values = fake_data(values[0], len(values))
+        edge_data = None
+    except ValueError:
+        edge_data = np.array(values)
+        values = fake_data(np.array(1.), len(v1s))
+    return (sp.coo_matrix((values, (np.array(v1s), np.array(v2s))),
+                          shape=(nvertices, nvertices)),
+            edge_data)
 
 
 def read_edges_list(id_idx, lines, nvertices):
@@ -121,7 +131,7 @@ def check_has_vertices():
             check_has_vertices()
             edges.append(
                 EdgeType[part_type=="*arcs"](
-                    read_edges(id_idx, line_part, len(labels)),
+                    *read_edges(id_idx, line_part, len(labels)),
                     name=part_args.strip() or part_type[1:]))
         elif part_type in ("*edgeslist", "*arcslist"):
             check_has_vertices()
diff --git a/orangecontrib/network/network/tests/test_readwrite.py b/orangecontrib/network/network/tests/test_readwrite.py
index 4cf7d9a1..ec00febc 100644
--- a/orangecontrib/network/network/tests/test_readwrite.py
+++ b/orangecontrib/network/network/tests/test_readwrite.py
@@ -1,5 +1,6 @@
 import os
 import unittest
+from pkg_resources import resource_filename
 from tempfile import NamedTemporaryFile
 
 import numpy as np
@@ -8,12 +9,15 @@
 
 
 def _fullpath(name):
-    return os.path.join(os.path.split(__file__)[0], name)
+    return os.path.join(resource_filename("orangecontrib.network", "networks"), name)
+
+def _fullpathtest(name):
+    return os.path.join(resource_filename(__name__, ""), name)
 
 
 class TestReadPajek(unittest.TestCase):
     def test_two_mode(self):
-        davis = readwrite.read_pajek(_fullpath("../networks/davis.net"))
+        davis = readwrite.read_pajek(_fullpath("davis.net"))
         self.assertEqual(davis.number_of_nodes(), 32)
         self.assertEqual(
             list(davis.nodes),
@@ -25,6 +29,17 @@ def test_two_mode(self):
             )
         self.assertEqual(davis.in_first_mode, 18)
 
+    def test_edge_labels(self):
+        net = readwrite.read_pajek(_fullpathtest("towns.net"))
+        self.assertEqual(net.number_of_nodes(), 4)
+        self.assertEqual(
+            list(net.nodes),
+            ["Ljubljana", "Kranj", "Maribor", "Novo mesto"]
+            )
+        self.assertEqual(
+            list(net.edges[0].edge_data),
+            ['near', 'far', 'not near, not far', 'huh?'])
+
     def test_write_pajek(self):
         net = readwrite.read_pajek(_fullpath("../networks/leu_by_genesets.net"))
         with NamedTemporaryFile("wt", suffix=".net", delete=False) as f:
@@ -62,7 +77,7 @@ def test_write_pajek_multiple_edge_types(self):
             self.assertRaises(TypeError, readwrite.write_pajek, f, net)
 
     def test_edge_list(self):
-        net = readwrite.read_pajek(_fullpath("test-arcslist.net"))
+        net = readwrite.read_pajek(_fullpathtest("test-arcslist.net"))
         neighs = [(1, (2, 3, 6)),
                   (2, (1, 4, 5, 6)),
                   (5, (1, 2)),
diff --git a/orangecontrib/network/network/tests/towns.net b/orangecontrib/network/network/tests/towns.net
new file mode 100644
index 00000000..0c65e456
--- /dev/null
+++ b/orangecontrib/network/network/tests/towns.net
@@ -0,0 +1,12 @@
+*Network "Test"
+*Description "Slovenian towns"
+*Vertices
+1 "Ljubljana"
+2 "Kranj"
+3 "Maribor"
+4 "Novo mesto"
+*Edges
+1	2	near
+1	3	far
+1	4	not near, not far
+3	4	huh?