From 045a2f0d471f7b4186aff625f3cea9abfa549fa2 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 27 Nov 2016 18:39:13 +0100
Subject: [PATCH] Add `force_rebuild` param to build_dependency_cache

This will remove a pre-existing cached dependency directory.
---
 lib/galaxy/tools/__init__.py           |  5 +++--
 lib/galaxy/tools/deps/__init__.py      |  7 +++++++
 lib/galaxy/webapps/galaxy/api/tools.py | 11 +++++++++--
 3 files changed, 19 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 34a34b37f31..ba8ee6ce1a2 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1306,7 +1306,7 @@ class Tool( object, Dictifiable ):
         visit_input_values( self.inputs, values, validate_inputs )
         return messages
 
-    def build_dependency_cache(self):
+    def build_dependency_cache(self, **kwds):
         if isinstance(self.app.toolbox.dependency_manager, CachedDependencyManager):
             self.app.toolbox.dependency_manager.build_cache(
                 requirements=self.requirements,
@@ -1314,7 +1314,8 @@ class Tool( object, Dictifiable ):
                 tool_dir=self.tool_dir,
                 job_directory=None,
                 metadata=False,
-                tool_instance=self
+                tool_instance=self,
+                **kwds
             )
 
     def build_dependency_shell_commands( self, job_directory=None, metadata=False ):
diff --git a/lib/galaxy/tools/deps/__init__.py b/lib/galaxy/tools/deps/__init__.py
index 4f0a6d2a7d4..640726f73d9 100644
--- a/lib/galaxy/tools/deps/__init__.py
+++ b/lib/galaxy/tools/deps/__init__.py
@@ -5,6 +5,7 @@ Dependency management for tools.
 import json
 import logging
 import os.path
+import shutil
 
 from collections import OrderedDict
 
@@ -175,6 +176,12 @@ class CachedDependencyManager(DependencyManager):
         resolved_dependencies = self.requirements_to_dependencies(requirements, **kwds)
         cacheable_dependencies = [dep for req, dep in resolved_dependencies.items() if dep.cacheable]
         hashed_requirements_dir = self.get_hashed_requirements_path(cacheable_dependencies)
+        if kwds.get('force_rebuild', False) and os.path.exists(hashed_requirements_dir):
+            try:
+                shutil.rmtree(hashed_requirements_dir)
+            except Exception:
+                log.warning("Could not delete cached requirements directory '%s'" % hashed_requirements_dir)
+                pass
         [dep.build_cache(hashed_requirements_dir) for dep in cacheable_dependencies]
 
     def dependency_shell_commands( self, requirements, **kwds ):
diff --git a/lib/galaxy/webapps/galaxy/api/tools.py b/lib/galaxy/webapps/galaxy/api/tools.py
index f91081d6b82..b76dd9a3f40 100644
--- a/lib/galaxy/webapps/galaxy/api/tools.py
+++ b/lib/galaxy/webapps/galaxy/api/tools.py
@@ -135,11 +135,15 @@ class ToolsController( BaseAPIController, UsesVisualizationMixin ):
         """
         POST /api/tools/{tool_id}/install_dependencies
         Attempts to install requirements via the dependency resolver
+
+        parameters:
+            build_dependency_cache:  If true, attempts to cache dependencies for this tool
+            force_rebuild:           If true and chache dir exists, attempts to delete cache dir
         """
         tool = self._get_tool(id)
         [tool._view.install_dependency(id=None, **req.to_dict()) for req in tool.requirements]
         if kwds.get('build_dependency_cache'):
-            tool.build_dependency_cache()
+            tool.build_dependency_cache(**kwds)
         # TODO: rework resolver install system to log and report what has been done.
         # _view.install_dependency should return a dict with stdout, stderr and success status
         return tool.tool_requirements_status
@@ -150,9 +154,12 @@ class ToolsController( BaseAPIController, UsesVisualizationMixin ):
         """
         POST /api/tools/{tool_id}/build_dependency_cache
         Attempts to cache installed dependencies.
+
+        parameters:
+            force_rebuild:           If true and chache dir exists, attempts to delete cache dir
         """
         tool = self._get_tool(id)
-        tool.build_dependency_cache()
+        tool.build_dependency_cache(**kwds)
         # TODO: Should also have a more meaningful return.
         return tool.tool_requirements_status