From 329ca243b4c1d3d821cb1f7a3f55c86414cdc881 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Wed, 21 Dec 2016 11:34:14 -0500
Subject: [PATCH] Do not replace Galaxy's Python environment for select tools.

This has never happened in my testing, but there have been multiple reports of Conda crafting environments for the set metadata tool that include Python. When this happens Galaxy's Python environment is lost and the tool cannot function properly.

Fixes #3238.
Fixes #3224.
Fixes https://biostar.usegalaxy.org/p/20865/.
---
 lib/galaxy/tools/__init__.py             | 11 +++++++++++
 lib/galaxy/tools/deps/resolvers/conda.py | 23 ++++++++++++++++-------
 2 files changed, 27 insertions(+), 7 deletions(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 9410f15197a8..77597db63b9b 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -375,6 +375,16 @@ def output_is_dynamic(output):
     def valid_input_states( self ):
         return model.Dataset.valid_input_states
 
+    @property
+    def requires_galaxy_python_environment(self):
+        """Indicates this tool's runtime requires Galaxy's Python environment."""
+        # All special tool types (data source, history import/export, etc...)
+        # seem to require Galaxy's Python.
+        return self.tool_type != "default" or self.id in [
+            "__SET_METADATA__",
+            "upload1",
+        ]
+
     def __get_job_tool_configuration(self, job_params=None):
         """Generalized method for getting this tool's job configuration.
 
@@ -1288,6 +1298,7 @@ def build_dependency_shell_commands( self, job_directory=None, metadata=False ):
             installed_tool_dependencies=self.installed_tool_dependencies,
             tool_dir=self.tool_dir,
             job_directory=job_directory,
+            preserve_python_environment=self.requires_galaxy_python_environment,
             metadata=metadata,
         )
 
diff --git a/lib/galaxy/tools/deps/resolvers/conda.py b/lib/galaxy/tools/deps/resolvers/conda.py
index 13477f771008..a66a993b1cd4 100644
--- a/lib/galaxy/tools/deps/resolvers/conda.py
+++ b/lib/galaxy/tools/deps/resolvers/conda.py
@@ -164,6 +164,8 @@ def resolve(self, name, version, type, **kwds):
                 log.warning("Conda dependency resolver not sent job directory.")
                 return NullDependency(version=version, name=name)
 
+        preserve_python_environment = kwds.get("preserve_python_environment", False)
+
         if not is_installed and self.auto_install:
             is_installed = self.install_dependency(name=name, version=version, type=type)
 
@@ -190,7 +192,8 @@ def resolve(self, name, version, type, **kwds):
                 conda_environment,
                 exact,
                 name,
-                version
+                version,
+                preserve_python_environment,
             )
         else:
             if len(conda_environment) > 79:
@@ -247,12 +250,13 @@ class CondaDependency(Dependency):
     dict_collection_visible_keys = Dependency.dict_collection_visible_keys + ['environment_path', 'name', 'version']
     dependency_type = 'conda'
 
-    def __init__(self, activate, environment_path, exact, name=None, version=None):
+    def __init__(self, activate, environment_path, exact, name=None, version=None, preserve_python_environment=False):
         self.activate = activate
         self.environment_path = environment_path
         self._exact = exact
         self._name = name
         self._version = version
+        self._preserve_python_environment = preserve_python_environment
 
     @property
     def exact(self):
@@ -267,11 +271,16 @@ def version(self):
         return self._version
 
     def shell_commands(self, requirement):
-        return """[ "$CONDA_DEFAULT_ENV" = "%s" ] || . %s '%s' 2>&1 """ % (
-            self.environment_path,
-            self.activate,
-            self.environment_path
-        )
+        if self._preserve_python_environment:
+            return """export PATH=$PATH:'%s/bin' """ % (
+                self.environment_path,
+            )
+        else:
+            return """[ "$CONDA_DEFAULT_ENV" = "%s" ] || . %s '%s' 2>&1 """ % (
+                self.environment_path,
+                self.activate,
+                self.environment_path
+            )
 
 
 def _string_as_bool( value ):