fix bioexcel test has no timeout

jamesmkrieger · Apr 17, 2024 · 8d64deb · 8d64deb
1 parent 6eb9946
commit 8d64deb
Showing 1 changed file with 19 additions and 9 deletions.
diff --git a/prody/tests/database/test_bioexcel.py b/prody/tests/database/test_bioexcel.py
@@ -20,6 +20,8 @@
     N_FRAMES_1 = 10
     N_FRAMES_2 = 6
 
+    TIMEOUT = 120
+
     class TestFetchParseBioexcelPDB(unittest.TestCase):
 
         @classmethod
@@ -417,7 +419,8 @@ def testFetchFrames1(self):
 
             try:
                 a = fetchBioexcelTrajectory(self.query, folder=self.workdir, 
-                                            frames=self.frames1)
+                                            frames=self.frames1,
+                                            timeout=TIMEOUT)
             except OSError:
                 pass
             else:
@@ -448,7 +451,8 @@ def testFetchSelectionFrames2(self):
 
             try:
                 a = fetchBioexcelTrajectory(self.query, folder=self.workdir,
-                                            selection='_C', frames=self.frames2)
+                                            selection='_C', frames=self.frames2,
+                                            timeout=TIMEOUT)
             except OSError:
                 pass
             else:
@@ -466,7 +470,8 @@ def testFetchConvertFalse(self):
 
             try:
                 a = fetchBioexcelTrajectory(self.query, folder=self.workdir, 
-                                            convert=False, frames=self.frames1)
+                                            convert=False, frames=self.frames1,
+                                            timeout=TIMEOUT)
             except OSError:
                 pass
             else:
@@ -488,7 +493,8 @@ def testParseFrames1(self):
 
             try:
                 ens = parseBioexcelTrajectory(self.query, folder=self.workdir,
-                                            frames=self.frames1)
+                                            frames=self.frames1,
+                                            timeout=TIMEOUT)
             except OSError:
                 pass
             else:
@@ -504,7 +510,8 @@ def testParseSelectionFrames2(self):
             using selection='_C'."""
             try:
                 ens = parseBioexcelTrajectory(self.query, folder=self.workdir,
-                                            selection='_C', frames=self.frames2)
+                                            selection='_C', frames=self.frames2,
+                                            timeout=TIMEOUT)
             except OSError:
                 pass
             else:
@@ -519,7 +526,8 @@ def testFetchAndParse(self):
             """Test the outcome of a simple fetch and parse scenario"""
             try:
                 a = fetchBioexcelTrajectory(self.query, folder=self.workdir,
-                                            frames=self.frames1)
+                                            frames=self.frames1,
+                                            timeout=TIMEOUT)
             except OSError:
                 pass
             else:
@@ -536,7 +544,8 @@ def testFetchNoConvParse(self):
             """Test the outcome of a simple fetch, then internally convert and parse scenario."""
             try:
                 a = fetchBioexcelTrajectory(self.query, folder=self.workdir, 
-                                            convert=False, frames=self.frames1)
+                                            convert=False, frames=self.frames1,
+                                            timeout=TIMEOUT)
             except OSError:
                 pass
             else:
@@ -553,7 +562,8 @@ def testFetchConvParse(self):
             """Test the outcome of a simple fetch, externally convert and then parse scenario."""
             try:
                 a = fetchBioexcelTrajectory(self.query, folder=self.workdir, 
-                                            convert=False, frames=self.frames1)
+                                            convert=False, frames=self.frames1,
+                                            timeout=TIMEOUT)
             except OSError:
                 pass
             else:
@@ -570,7 +580,7 @@ def testFetchConvParse(self):
         def testConvertWrongType(self):
             with self.assertRaises(TypeError):
                 fetchBioexcelTrajectory(self.query, folder=self.workdir, convert='False',
-                                        timeout=self.timeout)
+                                        timeout=TIMEOUT)
 
         @classmethod
         def tearDownClass(cls):