Merge pull request #5620 from jmchilton/conda_fixes_1801

[18.01] Conda fix for commands using stdout redirection.

lib/galaxy/tools/deps/conda_util.py

@@ -204,7 +204,7 @@ def can_install_conda(self):
                         self.conda_prefix, self.conda_exec)
             return False
 
-    def exec_command(self, operation, args):
+    def exec_command(self, operation, args, stdout_path=None):
         """
         Execute the requested command.
 
@@ -219,17 +219,24 @@ def exec_command(self, operation, args):
         if self.condarc_override:
             env["CONDARC"] = self.condarc_override
         cmd_string = ' '.join(map(shlex_quote, cmd))
-        log.debug("Executing command: %s", cmd_string)
-        conda_exec_home = env['HOME'] = tempfile.mkdtemp(prefix='conda_exec_home_')  # We don't want to pollute ~/.conda, which may not even be writable
+        kwds = dict()
         try:
-            return self.shell_exec(cmd, env=env)
+            if stdout_path:
+                kwds['stdout'] = open(stdout_path, 'w')
+                cmd_string += " > '%s'" % stdout_path
+            conda_exec_home = env['HOME'] = tempfile.mkdtemp(prefix='conda_exec_home_')  # We don't want to pollute ~/.conda, which may not even be writable
+            log.debug("Executing command: %s", cmd_string)
+            return self.shell_exec(cmd, env=env, **kwds)
         except Exception:
             log.exception("Failed to execute command: %s", cmd_string)
             return 1
         finally:
-            shutil.rmtree(conda_exec_home, ignore_errors=True)
+            if kwds.get('stdout'):
+                kwds['stdout'].close()
+            if conda_exec_home:
+                shutil.rmtree(conda_exec_home, ignore_errors=True)
 
-    def exec_create(self, args, allow_local=True):
+    def exec_create(self, args, allow_local=True, stdout_path=None):
         """
         Return the process exit code (i.e. 0 in case of success).
         """
@@ -240,7 +247,7 @@ def exec_create(self, args, allow_local=True):
             create_base_args.extend(["--use-local"])
         create_base_args.extend(self._override_channels_args)
         create_base_args.extend(args)
-        return self.exec_command("create", create_base_args)
+        return self.exec_command("create", create_base_args, stdout_path=stdout_path)
 
     def exec_remove(self, args):
         """
@@ -256,7 +263,7 @@ def exec_remove(self, args):
         remove_base_args.extend(args)
         return self.exec_command("env", remove_base_args)
 
-    def exec_install(self, args, allow_local=True):
+    def exec_install(self, args, allow_local=True, stdout_path=None):
         """
         Return the process exit code (i.e. 0 in case of success).
         """
@@ -267,7 +274,7 @@ def exec_install(self, args, allow_local=True):
             install_base_args.append("--use-local")
         install_base_args.extend(self._override_channels_args)
         install_base_args.extend(args)
-        return self.exec_command("install", install_base_args)
+        return self.exec_command("install", install_base_args, stdout_path=stdout_path)
 
     def exec_clean(self, args=[], quiet=False):
         """
@@ -280,18 +287,19 @@ def exec_clean(self, args=[], quiet=False):
             "-y"
         ]
         clean_args = clean_base_args + args
+        stdout_path = None
         if quiet:
-            clean_args.extend([">", "/dev/null"])
-        return self.exec_command("clean", clean_args)
+            stdout_path = "/dev/null"
+        return self.exec_command("clean", clean_args, stdout_path=stdout_path)
 
     def export_list(self, name, path):
         """
         Return the process exit code (i.e. 0 in case of success).
         """
         return self.exec_command("list", [
             "--name", name,
-            "--export", ">", path
-        ])
+            "--export"
+        ], stdout_path=path)
 
     def env_path(self, env_name):
         return os.path.join(self.envs_path, env_name)
@@ -545,6 +553,7 @@ def build_isolated_environment(
         conda_packages = [conda_packages]
 
     # Lots we could do in here, hashing, checking revisions, etc...
+    tempdir = None
     try:
         hash = hash_conda_packages(conda_packages)
         tempdir = tempfile.mkdtemp(prefix="jobdeps", suffix=hash)
@@ -579,21 +588,23 @@ def build_isolated_environment(
             create_args.append("--copy")
         for export_path in export_paths:
             create_args.extend([
-                "--file", export_path, ">", "/dev/null"
+                "--file", export_path
             ])
 
+        stdout_path = None
         if quiet:
-            create_args.extend([">", "/dev/null"])
+            stdout_path = "/dev/null"
 
         if path is not None and os.path.exists(path):
-            exit_code = conda_context.exec_install(create_args)
+            exit_code = conda_context.exec_install(create_args, stdout_path=stdout_path)
         else:
-            exit_code = conda_context.exec_create(create_args)
+            exit_code = conda_context.exec_create(create_args, stdout_path=stdout_path)
 
         return (path or tempdir_name, exit_code)
     finally:
         conda_context.exec_clean(quiet=quiet)
-        shutil.rmtree(tempdir)
+        if tempdir is not None:
+            shutil.rmtree(tempdir)
 
 
 def requirement_to_conda_targets(requirement):