"""Test module for different kind of links under PyTables.""" import re import tempfile from pathlib import Path import tables as tb from tables.tests import common # Test for hard links class HardLinkTestCase(common.TempFileMixin, common.PyTablesTestCase): def setUp(self): super().setUp() self._createFile() def _createFile(self): self.h5file.create_array("/", "arr1", [1, 2]) group1 = self.h5file.create_group("/", "group1") arr2 = self.h5file.create_array(group1, "arr2", [1, 2, 3]) lgroup1 = self.h5file.create_hard_link("/", "lgroup1", "/group1") self.assertIsNotNone(lgroup1) larr1 = self.h5file.create_hard_link(group1, "larr1", "/arr1") self.assertIsNotNone(larr1) larr2 = self.h5file.create_hard_link("/", "larr2", arr2) self.assertIsNotNone(larr2) def test00_create(self): """Creating hard links.""" self._checkEqualityGroup( self.h5file.root.group1, self.h5file.root.lgroup1, hardlink=True ) self._checkEqualityLeaf( self.h5file.root.arr1, self.h5file.root.group1.larr1, hardlink=True ) self._checkEqualityLeaf( self.h5file.root.lgroup1.arr2, self.h5file.root.larr2, hardlink=True, ) def test01_open(self): """Opening a file with hard links.""" self._reopen() self._checkEqualityGroup( self.h5file.root.group1, self.h5file.root.lgroup1, hardlink=True ) self._checkEqualityLeaf( self.h5file.root.arr1, self.h5file.root.group1.larr1, hardlink=True ) self._checkEqualityLeaf( self.h5file.root.lgroup1.arr2, self.h5file.root.larr2, hardlink=True, ) def test02_removeLeaf(self): """Removing a hard link to a Leaf.""" # First delete the initial link self.h5file.root.arr1.remove() self.assertNotIn("/arr1", self.h5file) # The second link should still be there if common.verbose: print("Remaining link:", self.h5file.root.group1.larr1) self.assertIn("/group1/larr1", self.h5file) # Remove the second link self.h5file.root.group1.larr1.remove() self.assertNotIn("/group1/larr1", self.h5file) def test03_removeGroup(self): """Removing a hard link to a Group.""" if common.verbose: print("Original object tree:", self.h5file) # First delete the initial link self.h5file.root.group1._f_remove(force=True) self.assertNotIn("/group1", self.h5file) # The second link should still be there if common.verbose: print("Remaining link:", self.h5file.root.lgroup1) print("Object tree:", self.h5file) self.assertIn("/lgroup1", self.h5file) # Remove the second link self.h5file.root.lgroup1._g_remove(recursive=True) self.assertNotIn("/lgroup1", self.h5file) if common.verbose: print("Final object tree:", self.h5file) # Test for soft links class SoftLinkTestCase(common.TempFileMixin, common.PyTablesTestCase): def setUp(self): super().setUp() self._createFile() def _createFile(self): self.h5file.create_array("/", "arr1", [1, 2]) group1 = self.h5file.create_group("/", "group1") arr2 = self.h5file.create_array(group1, "arr2", [1, 2, 3]) lgroup1 = self.h5file.create_soft_link("/", "lgroup1", "/group1") self.assertIsNotNone(lgroup1) larr1 = self.h5file.create_soft_link(group1, "larr1", "/arr1") self.assertIsNotNone(larr1) larr2 = self.h5file.create_soft_link("/", "larr2", arr2) self.assertIsNotNone(larr2) def test00_create(self): """Creating soft links.""" self._checkEqualityGroup( self.h5file.root.group1, self.h5file.root.lgroup1() ) self._checkEqualityLeaf( self.h5file.root.arr1, self.h5file.root.group1.larr1() ) self._checkEqualityLeaf( self.h5file.root.lgroup1().arr2, self.h5file.root.larr2() ) def test01_open(self): """Opening a file with soft links.""" self._reopen() self._checkEqualityGroup( self.h5file.root.group1, self.h5file.root.lgroup1() ) self._checkEqualityLeaf( self.h5file.root.arr1, self.h5file.root.group1.larr1() ) self._checkEqualityLeaf( self.h5file.root.lgroup1().arr2, self.h5file.root.larr2() ) def test02_remove(self): """Removing a soft link.""" # First delete the referred link self.h5file.root.arr1.remove() self.assertNotIn("/arr1", self.h5file) # The soft link should still be there (but dangling) if common.verbose: print("Dangling link:", self.h5file.root.group1.larr1) self.assertIn("/group1/larr1", self.h5file) # Remove the soft link itself self.h5file.root.group1.larr1.remove() self.assertNotIn("/group1/larr1", self.h5file) def test03_copy(self): """Copying a soft link.""" # Copy the link into another location root = self.h5file.root lgroup1 = root.lgroup1 lgroup2 = lgroup1.copy("/", "lgroup2") self.assertIn("/lgroup1", self.h5file) self.assertIn("/lgroup2", self.h5file) self.assertIn("lgroup2", root._v_children) self.assertIn("lgroup2", root._v_links) if common.verbose: print("Copied link:", lgroup2) # Remove the first link lgroup1.remove() self._checkEqualityGroup( self.h5file.root.group1, self.h5file.root.lgroup2() ) def test03_overwrite(self): """Overwrite a soft link.""" # Copy the link into another location root = self.h5file.root lgroup1 = root.lgroup1 lgroup2 = lgroup1.copy("/", "lgroup2") lgroup2 = lgroup1.copy("/", "lgroup2", overwrite=True) self.assertIn("/lgroup1", self.h5file) self.assertIn("/lgroup2", self.h5file) self.assertIn("lgroup2", root._v_children) self.assertIn("lgroup2", root._v_links) if common.verbose: print("Copied link:", lgroup2) # Remove the first link lgroup1.remove() self._checkEqualityGroup( self.h5file.root.group1, self.h5file.root.lgroup2() ) def test04_move(self): """Moving a soft link.""" # Move the link into another location lgroup1 = self.h5file.root.lgroup1 group2 = self.h5file.create_group("/", "group2") lgroup1.move(group2, "lgroup2") lgroup2 = self.h5file.root.group2.lgroup2 if common.verbose: print("Moved link:", lgroup2) self.assertNotIn("/lgroup1", self.h5file) self.assertIn("/group2/lgroup2", self.h5file) self._checkEqualityGroup( self.h5file.root.group1, self.h5file.root.group2.lgroup2() ) def test05_rename(self): """Renaming a soft link.""" # Rename the link lgroup1 = self.h5file.root.lgroup1 lgroup1.rename("lgroup2") lgroup2 = self.h5file.root.lgroup2 if common.verbose: print("Moved link:", lgroup2) self.assertNotIn("/lgroup1", self.h5file) self.assertIn("/lgroup2", self.h5file) self._checkEqualityGroup( self.h5file.root.group1, self.h5file.root.lgroup2() ) def test06a_relative_path(self): """Using soft links with relative paths.""" # Create new group self.h5file.create_group("/group1", "group3") # ... and relative link lgroup3 = self.h5file.create_soft_link("/group1", "lgroup3", "group3") if common.verbose: print("Relative path link:", lgroup3) self.assertIn("/group1/lgroup3", self.h5file) self._checkEqualityGroup( self.h5file.root.group1.group3, self.h5file.root.group1.lgroup3() ) def test06b_relative_path(self): """Using soft links with relative paths (./ version)""" # Create new group self.h5file.create_group("/group1", "group3") # ... and relative link lgroup3 = self.h5file.create_soft_link( "/group1", "lgroup3", "./group3" ) if common.verbose: print("Relative path link:", lgroup3) self.assertIn("/group1/lgroup3", self.h5file) self._checkEqualityGroup( self.h5file.root.group1.group3, self.h5file.root.group1.lgroup3() ) def test07_walkNodes(self): """Checking `walk_nodes` with `classname` option.""" links = [ node._v_pathname for node in self.h5file.walk_nodes("/", classname="Link") ] if common.verbose: print("detected links (classname='Link'):", links) self.assertEqual(links, ["/larr2", "/lgroup1", "/group1/larr1"]) links = [ node._v_pathname for node in self.h5file.walk_nodes("/", classname="SoftLink") ] if common.verbose: print("detected links (classname='SoftLink'):", links) self.assertEqual(links, ["/larr2", "/lgroup1", "/group1/larr1"]) def test08__v_links(self): """Checking `Group._v_links`.""" links = [node for node in self.h5file.root._v_links] if common.verbose: print("detected links (under root):", links) self.assertEqual(len(links), 2) links = [node for node in self.h5file.root.group1._v_links] if common.verbose: print("detected links (under /group1):", links) self.assertEqual(links, ["larr1"]) def test09_link_to_link(self): """Checking linked links.""" # Create a link to another existing link lgroup2 = self.h5file.create_soft_link("/", "lgroup2", "/lgroup1") # Dereference it once: self.assertIs(lgroup2(), self.h5file.get_node("/lgroup1")) if common.verbose: print("First dereference is correct:", lgroup2()) # Dereference it twice: self.assertIs(lgroup2()(), self.h5file.get_node("/group1")) if common.verbose: print("Second dereference is correct:", lgroup2()()) def test10_copy_link_to_file(self): """Checking copying a link to another file.""" fname = tempfile.mktemp(".h5") h5f = tb.open_file(fname, "a") h5f.create_array("/", "arr1", [1, 2]) h5f.create_group("/", "group1") lgroup1 = self.h5file.root.lgroup1 lgroup1_ = lgroup1.copy(h5f.root, "lgroup1") self.assertIn("/lgroup1", self.h5file) self.assertIn("/lgroup1", h5f) self.assertIn(lgroup1_, h5f) if common.verbose: print("Copied link:", lgroup1_, "in:", lgroup1_._v_file.filename) h5f.close() Path(fname).unlink() def test11_direct_attribute_access(self): """Check direct get/set attributes via link-->target.attribute""" larr1 = self.h5file.get_node("/lgroup1/larr1") arr1 = self.h5file.get_node("/arr1") # get self.assertEqual(larr1.shape, (2,)) self.assertEqual(larr1[:], [1, 2]) # set larr1[0] = -1 self.assertEqual(arr1[:], [-1, 2]) def test12_access_child_node_attributes(self): """Check get/set attributes via link-->target.child.attribute""" lgroup1 = self.h5file.get_node("/lgroup1") arr2 = self.h5file.get_node("/group1/arr2") # get child attribute self.assertEqual(lgroup1.arr2[:], [1, 2, 3]) # set child attribute lgroup1.arr2[0] = -1 self.assertEqual(arr2[:], [-1, 2, 3]) def test13_direct_attribute_access_via_chained_softlinks(self): """Check get/set access via link2-->link1-->target.child.attribute""" self.h5file.get_node("/lgroup1") arr2 = self.h5file.get_node("/group1/arr2") # multiple chained links l_lgroup1 = self.h5file.create_soft_link("/", "l_lgroup1", "/lgroup1") # get child attribute self.assertEqual(l_lgroup1.arr2[:], [1, 2, 3]) # set child attribute l_lgroup1.arr2[0] = -1 self.assertEqual(arr2[:], [-1, 2, 3]) def test14_child_of_softlink_to_group(self): """Create an array whose parent is a softlink to another group""" self.h5file.get_node("/group1") lgroup1 = self.h5file.get_node("/lgroup1") self.h5file.create_array(lgroup1, "new_arr", obj=[1, 2, 3]) new_arr2 = self.h5file.get_node("/group1/new_arr") self.assertEqual(new_arr2[:], [1, 2, 3]) def test_str(self): s = str(self.h5file) self.assertEqual(len(re.findall(r"\(SoftLink\)", s)), 3) self.assertEqual(len(re.findall(r"\(dangling\)", s)), 0) def test_str_with_dangling_link(self): self.h5file.root.group1.arr2.remove() s = str(self.h5file) self.assertEqual(len(re.findall(r"\(SoftLink\)", s)), 3) self.assertEqual(len(re.findall(r"\(dangling\)", s)), 1) # Test for external links @common.unittest.skipIf( tb.file._FILE_OPEN_POLICY == "strict", 'FILE_OPEN_POLICY = "strict"' ) class ExternalLinkTestCase(common.TempFileMixin, common.PyTablesTestCase): def setUp(self): super().setUp() self.extfname = tempfile.mktemp(".h5") self.exth5file = tb.open_file(self.extfname, "w") self._createFile() def tearDown(self): """Remove ``extfname``.""" extfname = self.extfname self.exth5file.close() super().tearDown() # open_files = tables.file._open_files # if self.extfname in open_files: # #assert False # for handler in open_files.get_handlers_by_name(self.extfname): # handler.close() Path(extfname).unlink() # comment this for debugging purposes only def _createFile(self): self.h5file.create_array("/", "arr1", [1, 2]) group1 = self.h5file.create_group("/", "group1") self.h5file.create_array(group1, "arr2", [1, 2, 3]) # The external file extarr1 = self.exth5file.create_array("/", "arr1", [1, 2]) self.assertIsNotNone(extarr1) extgroup1 = self.exth5file.create_group("/", "group1") extarr2 = self.exth5file.create_array(extgroup1, "arr2", [1, 2, 3]) # Create external links lgroup1 = self.h5file.create_external_link( "/", "lgroup1", "%s:/group1" % self.extfname ) self.assertIsNotNone(lgroup1) larr1 = self.h5file.create_external_link( group1, "larr1", "%s:/arr1" % self.extfname ) self.assertIsNotNone(larr1) larr2 = self.h5file.create_external_link("/", "larr2", extarr2) self.assertIsNotNone(larr2) # Re-open the external file in 'r'ead-only mode self.exth5file.close() self.exth5file = tb.open_file(self.extfname, "r") def test00_create(self): """Creating soft links.""" self._checkEqualityGroup( self.exth5file.root.group1, self.h5file.root.lgroup1() ) self._checkEqualityLeaf( self.exth5file.root.arr1, self.h5file.root.group1.larr1() ) self._checkEqualityLeaf( self.h5file.root.lgroup1().arr2, self.h5file.root.larr2() ) def test01_open(self): """Opening a file with soft links.""" self._reopen() self._checkEqualityGroup( self.exth5file.root.group1, self.h5file.root.lgroup1() ) self._checkEqualityLeaf( self.exth5file.root.arr1, self.h5file.root.group1.larr1() ) self._checkEqualityLeaf( self.h5file.root.lgroup1().arr2, self.h5file.root.larr2() ) def test02_remove(self): """Removing an external link.""" # Re-open the external file in 'a'ppend mode self.exth5file.close() self.exth5file = tb.open_file(self.extfname, "a") # First delete the referred link self.exth5file.root.arr1.remove() self.assertNotIn("/arr1", self.exth5file) # The external link should still be there (but dangling) if common.verbose: print("Dangling link:", self.h5file.root.group1.larr1) self.assertIn("/group1/larr1", self.h5file) # Remove the external link itself self.h5file.root.group1.larr1.remove() self.assertNotIn("/group1/larr1", self.h5file) def test03_copy(self): """Copying an external link.""" # Copy the link into another location root = self.h5file.root lgroup1 = root.lgroup1 lgroup2 = lgroup1.copy("/", "lgroup2") self.assertIn("/lgroup1", self.h5file) self.assertIn("/lgroup2", self.h5file) self.assertIn("lgroup2", root._v_children) self.assertIn("lgroup2", root._v_links) if common.verbose: print("Copied link:", lgroup2) # Remove the first link lgroup1.remove() self._checkEqualityGroup( self.exth5file.root.group1, self.h5file.root.lgroup2() ) def test03_overwrite(self): """Overwrite an external link.""" # Copy the link into another location root = self.h5file.root lgroup1 = root.lgroup1 lgroup2 = lgroup1.copy("/", "lgroup2") lgroup2 = lgroup1.copy("/", "lgroup2", overwrite=True) self.assertIn("/lgroup1", self.h5file) self.assertIn("/lgroup2", self.h5file) self.assertIn("lgroup2", root._v_children) self.assertIn("lgroup2", root._v_links) if common.verbose: print("Copied link:", lgroup2) # Remove the first link lgroup1.remove() self._checkEqualityGroup( self.exth5file.root.group1, self.h5file.root.lgroup2() ) def test04_move(self): """Moving an external link.""" # Move the link into another location lgroup1 = self.h5file.root.lgroup1 group2 = self.h5file.create_group("/", "group2") lgroup1.move(group2, "lgroup2") lgroup2 = self.h5file.root.group2.lgroup2 if common.verbose: print("Moved link:", lgroup2) self.assertNotIn("/lgroup1", self.h5file) self.assertIn("/group2/lgroup2", self.h5file) self._checkEqualityGroup( self.exth5file.root.group1, self.h5file.root.group2.lgroup2() ) def test05_rename(self): """Renaming an external link.""" # Rename the link lgroup1 = self.h5file.root.lgroup1 lgroup1.rename("lgroup2") lgroup2 = self.h5file.root.lgroup2 if common.verbose: print("Moved link:", lgroup2) self.assertNotIn("/lgroup1", self.h5file) self.assertIn("/lgroup2", self.h5file) self._checkEqualityGroup( self.exth5file.root.group1, self.h5file.root.lgroup2() ) def test07_walkNodes(self): """Checking `walk_nodes` with `classname` option.""" # Create a new soft link self.h5file.create_soft_link("/group1", "lgroup3", "./group3") links = [ node._v_pathname for node in self.h5file.walk_nodes("/", classname="Link") ] if common.verbose: print("detected links (classname='Link'):", links) self.assertEqual( links, ["/larr2", "/lgroup1", "/group1/larr1", "/group1/lgroup3"] ) links = [ node._v_pathname for node in self.h5file.walk_nodes("/", classname="ExternalLink") ] if common.verbose: print("detected links (classname='ExternalLink'):", links) self.assertEqual(links, ["/larr2", "/lgroup1", "/group1/larr1"]) def test08__v_links(self): """Checking `Group._v_links`.""" links = [node for node in self.h5file.root._v_links] if common.verbose: print("detected links (under root):", links) self.assertEqual(len(links), 2) links = [node for node in self.h5file.root.group1._v_links] if common.verbose: print("detected links (under /group1):", links) self.assertEqual(links, ["larr1"]) def test09_umount(self): """Checking `umount()` method.""" link = self.h5file.root.lgroup1 self.assertIsNone(link.extfile) # Dereference an external node (and hence, 'mount' a file) enode = link() self.assertIsNotNone(enode) self.assertIsNotNone(link.extfile) # Umount the link link.umount() self.assertIsNone(link.extfile) def test10_copy_link_to_file(self): """Checking copying a link to another file.""" h5fname2 = tempfile.mktemp(".h5") try: with tb.open_file(h5fname2, "a") as h5file2: h5file2.create_array("/", "arr1", [1, 2]) h5file2.create_group("/", "group1") lgroup1 = self.h5file.root.lgroup1 lgroup1_ = lgroup1.copy(h5file2.root, "lgroup1") self.assertIn("/lgroup1", self.h5file) self.assertIn("/lgroup1", h5file2) self.assertIn(lgroup1_, h5file2) if common.verbose: print( "Copied link:", lgroup1_, "in:", lgroup1_._v_file.filename, ) finally: if Path(h5fname2).is_file(): Path(h5fname2).unlink() def test11_copy_entire_file_with_hardlink_option(self): """Checking copying the entire file (that contains external links) in a similar way ptrepack does (with hardlink kwargs activated)""" h5fname2 = tempfile.mktemp(".h5") try: with tb.open_file(h5fname2, "a") as h5file2: self.h5file.root._f_copy_children( h5file2.root, recursive=True, use_hardlinks=True ) self.assertIn("/lgroup1", h5file2) finally: if Path(h5fname2).is_file(): Path(h5fname2).unlink() def suite(): """Return a test suite consisting of all the test cases in the module.""" theSuite = common.unittest.TestSuite() niter = 1 # common.heavy = 1 # uncomment this only for testing purposes for i in range(niter): theSuite.addTest(common.make_suite(HardLinkTestCase)) theSuite.addTest(common.make_suite(SoftLinkTestCase)) theSuite.addTest(common.make_suite(ExternalLinkTestCase)) return theSuite if __name__ == "__main__": import sys common.parse_argv(sys.argv) common.print_versions() common.unittest.main(defaultTest="suite")