Merge branch 'release_16.07' into dev

Conflicts:
	lib/galaxy/tools/deps/conda_util.py

config/galaxy.ini.sample

@@ -207,8 +207,6 @@ 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

doc/source/admin/interactive_environments.rst

@@ -122,6 +122,7 @@ As you can see most of these variables map directly to the command line
 arguments to the NodeJS script. There are a few extra parameters which will
 be needed if you run Galaxy behind an upstream proxy like nginx or
 Apache:
+
 .. code-block:: ini
 
     dynamic_proxy_external_proxy=True
@@ -182,7 +183,7 @@ Please note you will need to be using apache2.4 with ``mod_proxy_wstunnel``.
 
     # Project Jupyter / IPython specific. Other IEs may require their own routes.
     location ~ ^/galaxy/gie_proxy/jupyter/(?<nbtype>[^/]+)/api/kernels(?<rest>.*?)$ {
-        proxy_pass http://localhost:8800/galaxy/gie_proxy/$nbtype/api/kernels$rest;
+        proxy_pass http://localhost:8800/galaxy/gie_proxy/jupyter/$nbtype/api/kernels$rest;
         proxy_redirect off;
         proxy_http_version 1.1;
         proxy_set_header Upgrade $http_upgrade;

lib/galaxy/jobs/runners/cli.py

@@ -158,13 +158,16 @@ class ShellJobRunner( AsynchronousJobRunner ):
                         ajs.job_wrapper.change_state( state )
             else:
                 if state != old_state:
-                    log.debug("(%s/%s) state change: %s" % ( id_tag, external_job_id, state ) )
+                    log.debug("(%s/%s) state change: from %s to %s" % ( id_tag, external_job_id, old_state, state ) )
                     ajs.job_wrapper.change_state( state )
                 if state == model.Job.states.RUNNING and not ajs.running:
                     ajs.running = True
                     ajs.job_wrapper.change_state( model.Job.states.RUNNING )
             ajs.old_state = state
-            new_watched.append( ajs )
+            if state == model.Job.states.OK:
+                self.work_queue.put( ( self.finish_job, ajs ) )
+            else:
+                new_watched.append( ajs )
         # Replace the watch list with the updated version
         self.watched = new_watched
 

lib/galaxy/tools/deps/conda_util.py

@@ -423,33 +423,19 @@ def is_target_available(conda_target, conda_context=None, channels_override=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)
+                                  conda_context=conda_context)
     return list(filter(installed, conda_targets))
 
 

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

@@ -68,7 +68,6 @@ 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:
@@ -96,7 +95,6 @@ class CondaDependencyResolver(DependencyResolver, ListableDependencyResolver, In
         self.disabled = not galaxy.tools.deps.installable.ensure_installed(conda_context, install_conda, self.auto_init)
         self.auto_install = auto_install
         self.copy_dependencies = copy_dependencies
-        self.verbose_install_check = verbose_install_check
 
     def resolve(self, name, version, type, **kwds):
         # Check for conda just not being there, this way we can enable
@@ -113,7 +111,7 @@ 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)
@@ -178,7 +176,7 @@ 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:
@@ -190,7 +188,7 @@ 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))