Merge pull request #3127 from mvdbeek/remove_verbose_install_check_16.07

[16.07] Remove verbose_install_check option

config/galaxy.ini.sample

@@ -202,8 +202,6 @@ paste.app_factory = galaxy.web.buildapp:app_factory
 # Set to True to instruct Galaxy to look for and install missing tool
 # dependencies before each job runs.
 #conda_auto_install = False
-# Set to True to perform additional checking of installed Conda environment
-#conda_verbose_install_check=False
 # Set to True to instruct Galaxy to install Conda from the web automatically
 # if it cannot find a local copy and conda_exec is not configured.
 #conda_auto_init = False

lib/galaxy/tools/deps/conda_util.py

@@ -359,34 +359,20 @@ def is_target_available(conda_target, conda_context=None):
         return False
 
 
-def is_conda_target_installed(conda_target, conda_context=None, verbose_install_check=False):
+def is_conda_target_installed(conda_target, conda_context=None):
     conda_context = _ensure_conda_context(conda_context)
     # fail by default
-    success = False
     if conda_context.has_env(conda_target.install_environment):
-        if not verbose_install_check:
-            return True
-        # because export_list directs output to a file we
-        # need to make a temporary file, not use StringIO
-        f, package_list_file = tempfile.mkstemp(suffix='.env_packages')
-        os.close(f)
-        conda_context.export_list(conda_target.install_environment, package_list_file)
-        search_pattern = conda_target.package_specifier + '='
-        with open(package_list_file) as input_file:
-            for line in input_file:
-                if line.startswith(search_pattern):
-                    success = True
-                    break
-        os.remove(package_list_file)
-    return success
+        return True
+    else:
+        return False
 
 
-def filter_installed_targets(conda_targets, conda_context=None, verbose_install_check=False):
+def filter_installed_targets(conda_targets, conda_context=None):
     conda_context = _ensure_conda_context(conda_context)
     installed = functools.partial(is_conda_target_installed,
-                                  conda_context=conda_context,
-                                  verbose_install_check=verbose_install_check)
-    return filter(installed, conda_targets)
+                                  conda_context=conda_context)
+    return list(filter(installed, conda_targets))
 
 
 def build_isolated_environment(

lib/galaxy/tools/deps/resolvers/conda.py

@@ -71,7 +71,6 @@ class CondaDependencyResolver(DependencyResolver, ListableDependencyResolver, In
 
         conda_exec = get_option("exec")
         debug = _string_as_bool(get_option("debug"))
-        verbose_install_check = _string_as_bool(get_option("verbose_install_check"))
         ensure_channels = get_option("ensure_channels")
         use_path_exec = get_option("use_path_exec")
         if use_path_exec is None:
@@ -99,7 +98,6 @@ class CondaDependencyResolver(DependencyResolver, ListableDependencyResolver, In
         self.ensure_conda_installed()
         self.auto_install = auto_install
         self.copy_dependencies = copy_dependencies
-        self.verbose_install_check = verbose_install_check
 
     def ensure_conda_installed(self):
         """
@@ -149,7 +147,7 @@ class CondaDependencyResolver(DependencyResolver, ListableDependencyResolver, In
 
         conda_target = CondaTarget(name, version=version)
         is_installed = is_conda_target_installed(
-            conda_target, conda_context=self.conda_context, verbose_install_check=self.verbose_install_check
+            conda_target, conda_context=self.conda_context
         )
 
         job_directory = kwds.get("job_directory", None)
@@ -220,7 +218,7 @@ class CondaDependencyResolver(DependencyResolver, ListableDependencyResolver, In
         conda_target = CondaTarget(name, version=version)
 
         is_installed = is_conda_target_installed(
-            conda_target, conda_context=self.conda_context, verbose_install_check=self.verbose_install_check
+            conda_target, conda_context=self.conda_context
         )
 
         if is_installed:
@@ -232,7 +230,7 @@ class CondaDependencyResolver(DependencyResolver, ListableDependencyResolver, In
         else:
             # Recheck if installed
             is_installed = is_conda_target_installed(
-                conda_target, conda_context=self.conda_context, verbose_install_check=self.verbose_install_check
+                conda_target, conda_context=self.conda_context
             )
         if not is_installed:
             log.debug("Removing failed conda install of {}, version '{}'".format(name, version))