install_tree: symlink handling and add 'ignore' option (#9019)

Fixes #9001

#8289 added support for install_tree and copy_tree to merge into an existing
directory structure. However, it did not properly handle relative symlinks and
also removed support for the 'ignore' keyword. Additionally, some of the tests
were overly-strict when checking the permissions on the copied files.

This updates the install_tree/copy_tree methods and their tests:

* copy_tree/install_tree now preserve relative link targets (if the symlink in the
  source directory structure is relative, the symlink created in the destination
  will be relative)
* Added support for 'ignore' argument back to copy_tree/install_tree (removed
  in #8289). It is no longer the object output by shutil.ignore_patterns: you pass a
  function that accepts a path relative to the source and returns whether that
  path should be copied.
* The openfoam packages (currently the only ones making use of the 'ignore'
  argument) are updated for the new API
* When a symlink target is absolute, copy_tree and install_tree now rewrite the
  source prefix to be the destination prefix
* copy_tree tests no longer check permissions: copy_tree doesn't enforce
  anything about permissions so its tests don't check for that
* install_tree tests no longer check for exact permission matching since it can add
  file permissions

2 files changed, 86 insertions, 19 deletions

diff --git a/lib/spack/llnl/util/filesystem.py b/lib/spack/llnl/util/filesystem.py
index 40eb6a7aa8..7dacb9804f 100644
--- a/lib/spack/llnl/util/filesystem.py
+++ b/lib/spack/llnl/util/filesystem.py
@@ -306,7 +306,21 @@ def install(src, dest):
     copy(src, dest, _permissions=True)
 
 
-def copy_tree(src, dest, symlinks=True, _permissions=False):
+def resolve_link_target_relative_to_the_link(l):
+    """
+    os.path.isdir uses os.path.exists, which for links will check
+    the existence of the link target. If the link target is relative to
+    the link, we need to construct a pathname that is valid from
+    our cwd (which may not be the same as the link's directory)
+    """
+    target = os.readlink(l)
+    if os.path.isabs(target):
+        return target
+    link_dir = os.path.dirname(os.path.abspath(l))
+    return os.path.join(link_dir, target)
+
+
+def copy_tree(src, dest, symlinks=True, ignore=None, _permissions=False):
     """Recursively copy an entire directory tree rooted at *src*.
 
     If the destination directory *dest* does not already exist, it will
@@ -317,10 +331,14 @@ def copy_tree(src, dest, symlinks=True, _permissions=False):
     will be copied as far as the platform allows; if false, the contents and
     metadata of the linked files are copied to the new tree.
 
+    If *ignore* is set, then each path relative to *src* will be passed to
+    this function; the function returns whether that path should be skipped.
+
     Parameters:
         src (str): the directory to copy
         dest (str): the destination directory
         symlinks (bool): whether or not to preserve symlinks
+        ignore (function): function indicating which files to ignore
         _permissions (bool): for internal use only
     """
     if _permissions:
@@ -330,23 +348,41 @@ def copy_tree(src, dest, symlinks=True, _permissions=False):
 
     mkdirp(dest)
 
-    for s, d in traverse_tree(src, dest, order='pre', follow_nonexisting=True):
-        if symlinks and os.path.islink(s):
-            # Note that this won't rewrite absolute links into the old
-            # root to point at the new root. Should we handle that case?
-            target = os.readlink(s)
-            os.symlink(os.path.abspath(target), d)
-        elif os.path.isdir(s):
-            mkdirp(d)
+    src = os.path.abspath(src)
+    dest = os.path.abspath(dest)
+
+    for s, d in traverse_tree(src, dest, order='pre',
+                              follow_symlinks=not symlinks,
+                              ignore=ignore,
+                              follow_nonexisting=True):
+        if os.path.islink(s):
+            link_target = resolve_link_target_relative_to_the_link(s)
+            if symlinks:
+                target = os.readlink(s)
+                if os.path.isabs(target):
+                    new_target = re.sub(src, dest, target)
+                    if new_target != target:
+                        tty.debug("Redirecting link {0} to {1}"
+                                  .format(target, new_target))
+                        target = new_target
+
+                os.symlink(target, d)
+            elif os.path.isdir(link_target):
+                mkdirp(d)
+            else:
+                shutil.copyfile(s, d)
         else:
-            shutil.copyfile(s, d)
+            if os.path.isdir(s):
+                mkdirp(d)
+            else:
+                shutil.copyfile(s, d)
 
         if _permissions:
             set_install_permissions(d)
             copy_mode(s, d)
 
 
-def install_tree(src, dest, symlinks=True):
+def install_tree(src, dest, symlinks=True, ignore=None):
     """Recursively install an entire directory tree rooted at *src*.
 
     Same as :py:func:`copy_tree` with the addition of setting proper
@@ -356,8 +392,9 @@ def install_tree(src, dest, symlinks=True):
         src (str): the directory to install
         dest (str): the destination directory
         symlinks (bool): whether or not to preserve symlinks
+        ignore (function): function indicating which files to ignore
     """
-    copy_tree(src, dest, symlinks, _permissions=True)
+    copy_tree(src, dest, symlinks=symlinks, ignore=ignore, _permissions=True)
 
 
 def is_exe(path):
@@ -564,7 +601,7 @@ def traverse_tree(source_root, dest_root, rel_path='', **kwargs):
     Keyword Arguments:
         order (str): Whether to do pre- or post-order traversal. Accepted
             values are 'pre' and 'post'
-        ignore (str): Predicate indicating which files to ignore
+        ignore (function): function indicating which files to ignore
         follow_nonexisting (bool): Whether to descend into directories in
             ``src`` that do not exit in ``dest``. Default is True
         follow_links (bool): Whether to descend into symlinks in ``src``
@@ -578,7 +615,7 @@ def traverse_tree(source_root, dest_root, rel_path='', **kwargs):
         raise ValueError("Order must be 'pre' or 'post'.")
 
     # List of relative paths to ignore under the src root.
-    ignore = kwargs.get('ignore', lambda filename: False)
+    ignore = kwargs.get('ignore', None) or (lambda filename: False)
 
     # Don't descend into ignored directories
     if ignore(rel_path):
@@ -597,6 +634,9 @@ def traverse_tree(source_root, dest_root, rel_path='', **kwargs):
         rel_child = os.path.join(rel_path, f)
 
         # Treat as a directory
+        # TODO: for symlinks, os.path.isdir looks for the link target. If the
+        # target is relative to the link, then that may not resolve properly
+        # relative to our cwd - see resolve_link_target_relative_to_the_link
         if os.path.isdir(source_child) and (
                 follow_links or not os.path.islink(source_child)):
 
diff --git a/lib/spack/spack/test/llnl/util/filesystem.py b/lib/spack/spack/test/llnl/util/filesystem.py
index 7701185dbe..24ab02a613 100644
--- a/lib/spack/spack/test/llnl/util/filesystem.py
+++ b/lib/spack/spack/test/llnl/util/filesystem.py
@@ -26,6 +26,7 @@
 
 import llnl.util.filesystem as fs
 import os
+import stat
 import pytest
 
 
@@ -45,8 +46,10 @@ def stage(tmpdir_factory):
         fs.touchp('source/c/d/6')
         fs.touchp('source/c/d/e/7')
 
-        # Create symlink
+        # Create symlinks
         os.symlink(os.path.abspath('source/1'), 'source/2')
+        os.symlink('b/2', 'source/a/b2')
+        os.symlink('a/b', 'source/f')
 
         # Create destination directory
         fs.mkdirp('dest')
@@ -64,7 +67,6 @@ class TestCopy:
             fs.copy('source/1', 'dest/1')
 
             assert os.path.exists('dest/1')
-            assert os.stat('source/1').st_mode == os.stat('dest/1').st_mode
 
     def test_dir_dest(self, stage):
         """Test using a directory as the destination."""
@@ -73,7 +75,14 @@ class TestCopy:
             fs.copy('source/1', 'dest')
 
             assert os.path.exists('dest/1')
-            assert os.stat('source/1').st_mode == os.stat('dest/1').st_mode
+
+
+def check_added_exe_permissions(src, dst):
+    src_mode = os.stat(src).st_mode
+    dst_mode = os.stat(dst).st_mode
+    for perm in [stat.S_IXUSR, stat.S_IXGRP, stat.S_IXOTH]:
+        if src_mode & perm:
+            assert dst_mode & perm
 
 
 class TestInstall:
@@ -86,7 +95,7 @@ class TestInstall:
             fs.install('source/1', 'dest/1')
 
             assert os.path.exists('dest/1')
-            assert os.stat('source/1').st_mode == os.stat('dest/1').st_mode
+            check_added_exe_permissions('source/1', 'dest/1')
 
     def test_dir_dest(self, stage):
         """Test using a directory as the destination."""
@@ -95,7 +104,7 @@ class TestInstall:
             fs.install('source/1', 'dest')
 
             assert os.path.exists('dest/1')
-            assert os.stat('source/1').st_mode == os.stat('dest/1').st_mode
+            check_added_exe_permissions('source/1', 'dest/1')
 
 
 class TestCopyTree:
@@ -126,6 +135,24 @@ class TestCopyTree:
             assert os.path.exists('dest/2')
             assert os.path.islink('dest/2')
 
+            assert os.path.exists('dest/a/b2')
+            with fs.working_dir('dest/a'):
+                assert os.path.exists(os.readlink('b2'))
+
+            assert (os.path.realpath('dest/f/2') ==
+                    os.path.abspath('dest/a/b/2'))
+            assert os.path.realpath('dest/2') == os.path.abspath('dest/1')
+
+    def test_symlinks_true_ignore(self, stage):
+        """Test copying when specifying relative paths that should be ignored
+        """
+        with fs.working_dir(str(stage)):
+            ignore = lambda p: p in ['c/d/e', 'a']
+            fs.copy_tree('source', 'dest', symlinks=True, ignore=ignore)
+            assert not os.path.exists('dest/a')
+            assert os.path.exists('dest/c/d')
+            assert not os.path.exists('dest/c/d/e')
+
     def test_symlinks_false(self, stage):
         """Test copying without symlink preservation."""