From 5b12568c4f17fb9914be9e903eff3aad007049ef Mon Sep 17 00:00:00 2001
From: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Date: Wed, 28 Apr 2021 17:00:58 +0200
Subject: Make Spack able to apply gz compressed remote patches (#22823)

Modified ncbi-rmblastn to retrieve patches from remote
---
 lib/spack/spack/fetch_strategy.py   |  2 ++
 lib/spack/spack/util/compression.py | 19 +++++++++++++++++--
 2 files changed, 19 insertions(+), 2 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/spack/fetch_strategy.py b/lib/spack/spack/fetch_strategy.py
index ff41c759ea..b5ce8495e3 100644
--- a/lib/spack/spack/fetch_strategy.py
+++ b/lib/spack/spack/fetch_strategy.py
@@ -467,6 +467,8 @@ class URLFetchStrategy(FetchStrategy):
         tarball_container = os.path.join(self.stage.path,
                                          "spack-expanded-archive")
 
+        # Below we assume that the command to decompress expand the
+        # archive in the current working directory
         mkdirp(tarball_container)
         with working_dir(tarball_container):
             decompress(self.archive_file)
diff --git a/lib/spack/spack/util/compression.py b/lib/spack/spack/util/compression.py
index 2f190e94e1..a1a0e1d6f3 100644
--- a/lib/spack/spack/util/compression.py
+++ b/lib/spack/spack/util/compression.py
@@ -22,6 +22,22 @@ def allowed_archive(path):
     return any(path.endswith(t) for t in ALLOWED_ARCHIVE_TYPES)
 
 
+def _gunzip(archive_file):
+    """Like gunzip, but extracts in the current working directory
+    instead of in-place.
+
+    Args:
+        archive_file (str): absolute path of the file to be decompressed
+    """
+    import gzip
+    decompressed_file = os.path.basename(archive_file.strip('.gz'))
+    working_dir = os.getcwd()
+    destination_abspath = os.path.join(working_dir, decompressed_file)
+    with gzip.open(archive_file, "rb") as f_in:
+        with open(destination_abspath, "wb") as f_out:
+            f_out.write(f_in.read())
+
+
 def decompressor_for(path, extension=None):
     """Get the appropriate decompressor for a path."""
     if ((extension and re.match(r'\.?zip$', extension)) or
@@ -30,8 +46,7 @@ def decompressor_for(path, extension=None):
         unzip.add_default_arg('-q')
         return unzip
     if extension and re.match(r'gz', extension):
-        gunzip = which('gunzip', required=True)
-        return gunzip
+        return _gunzip
     if extension and re.match(r'bz2', extension):
         bunzip2 = which('bunzip2', required=True)
         return bunzip2
-- 
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