From 19bc49d207a92288dc402900cfa0125b8da45111 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Tue, 22 Sep 2015 17:50:29 -0400 Subject: [PATCH 1/3] Binary sniffing; along with the registry forcing case insensitivity through lower() which was implemented a while back, the un/sniffable formats lists should as well. This resolves #753 --- lib/galaxy/datatypes/binary.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py index 62a72373b29..4a6bdf0756e 100644 --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -41,11 +41,11 @@ class Binary( data.Data ): @staticmethod def register_sniffable_binary_format(data_type, ext, type_class): - Binary.sniffable_binary_formats.append({"type": data_type, "ext": ext, "class": type_class}) + Binary.sniffable_binary_formats.append({"type": data_type, "ext": ext.lower(), "class": type_class}) @staticmethod def register_unsniffable_binary_ext(ext): - Binary.unsniffable_binary_formats.append(ext) + Binary.unsniffable_binary_formats.append(ext.lower()) @staticmethod def is_sniffable_binary( filename ): From 3f3c1b679bfef5dbd75d7c267d25fd2979f362d1 Mon Sep 17 00:00:00 2001 From: Eric Rasche Date: Wed, 23 Sep 2015 13:05:37 -0500 Subject: [PATCH 2/3] Pin IE versions --- .../interactive_environments/ipython/config/ipython.ini.sample | 2 +- .../interactive_environments/rstudio/config/rstudio.ini.sample | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/config/plugins/interactive_environments/ipython/config/ipython.ini.sample b/config/plugins/interactive_environments/ipython/config/ipython.ini.sample index ca488a1d594..01fbc73e8e1 100644 --- a/config/plugins/interactive_environments/ipython/config/ipython.ini.sample +++ b/config/plugins/interactive_environments/ipython/config/ipython.ini.sample @@ -12,7 +12,7 @@ command = docker # The docker image name that should be started. -image = bgruening/docker-ipython-notebook:dev +image = bgruening/docker-ipython-notebook:15.07 # Additional arguments that are passed to the `docker run` command. command_inject = --sig-proxy=true -e DEBUG=false diff --git a/config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample b/config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample index ed0b64ff7ce..e314254c385 100644 --- a/config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample +++ b/config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample @@ -7,7 +7,7 @@ ssl = False [docker] command = docker -image = erasche/docker-rstudio-notebook:dev +image = erasche/docker-rstudio-notebook:15.07 # Additional arguments that are passed to the `docker run` command. `-u` # settings are completely ignored. From bf60693ed001099b78189f28d46500b572be9df7 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 24 Sep 2015 15:35:17 +0100 Subject: [PATCH 3/3] Fix problem maintaining input maps when rescheduling workflows. Fixes #776. I suspect the problem has very little to do with dynamic output collections and in fact exhibits itself when workflow rescheduling occurs, it is just that workflow rescheduling is forced when using dynamic output collections. --- lib/galaxy/workflow/run.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/lib/galaxy/workflow/run.py b/lib/galaxy/workflow/run.py index b367ac0eb53..a019a3bfaed 100644 --- a/lib/galaxy/workflow/run.py +++ b/lib/galaxy/workflow/run.py @@ -285,7 +285,10 @@ class WorkflowProgress( object ): raise modules.DelayedWorkflowEvaluation() return replacement - def set_outputs_for_input( self, step, outputs={} ): + def set_outputs_for_input( self, step, outputs=None ): + if outputs is None: + outputs = {} + if self.inputs_by_step_id: outputs[ 'output' ] = self.inputs_by_step_id[ step.id ]