Merge branch 'release_16.04' into dev

Conflicts:
	test/unit/tools/test_select_parameters.py

lib/galaxy/jobs/runners/drmaa.py

@@ -22,6 +22,8 @@ log = logging.getLogger( __name__ )
 
 __all__ = [ 'DRMAAJobRunner' ]
 
+RETRY_EXCEPTIONS_LOWER = frozenset(['invalidjobexception', 'internalexception'])
+
 
 class DRMAAJobRunner( AsynchronousJobRunner ):
     """
@@ -34,12 +36,11 @@ class DRMAAJobRunner( AsynchronousJobRunner ):
         """Start the job runner"""
         global drmaa
 
-        runner_param_specs = dict(
-            drmaa_library_path=dict( map=str, default=os.environ.get( 'DRMAA_LIBRARY_PATH', None ) ),
-            invalidjobexception_state=dict( map=str, valid=lambda x: x in ( model.Job.states.OK, model.Job.states.ERROR ), default=model.Job.states.OK ),
-            invalidjobexception_retries=dict( map=int, valid=lambda x: int >= 0, default=0 ),
-            internalexception_state=dict( map=str, valid=lambda x: x in ( model.Job.states.OK, model.Job.states.ERROR ), default=model.Job.states.OK ),
-            internalexception_retries=dict( map=int, valid=lambda x: int >= 0, default=0 ) )
+        runner_param_specs = {
+            'drmaa_library_path': dict( map=str, default=os.environ.get( 'DRMAA_LIBRARY_PATH', None ) ) }
+        for retry_exception in RETRY_EXCEPTIONS_LOWER:
+            runner_param_specs[retry_exception + '_state'] = dict( map=str, valid=lambda x: x in ( model.Job.states.OK, model.Job.states.ERROR ), default=model.Job.states.OK )
+            runner_param_specs[retry_exception + '_retries'] = dict( map=int, valid=lambda x: int >= 0, default=0 )
 
         if 'runner_param_specs' not in kwargs:
             kwargs[ 'runner_param_specs' ] = dict()
@@ -248,12 +249,15 @@ class DRMAAJobRunner( AsynchronousJobRunner ):
             try:
                 assert external_job_id not in ( None, 'None' ), '(%s/%s) Invalid job id' % ( galaxy_id_tag, external_job_id )
                 state = self.ds.job_status( external_job_id )
+                # Reset exception retries
+                for retry_exception in RETRY_EXCEPTIONS_LOWER:
+                    setattr( ajs, retry_exception + '_retries', 0)
             except ( drmaa.InternalException, drmaa.InvalidJobException ) as e:
                 ecn = type(e).__name__
                 retry_param = ecn.lower() + '_retries'
                 state_param = ecn.lower() + '_state'
                 retries = getattr( ajs, retry_param, 0 )
-                log.warning("(%s/%s) unable to check job status because of %s exception for %d tries: %s", galaxy_id_tag, external_job_id, ecn, retries + 1, e)
+                log.warning("(%s/%s) unable to check job status because of %s exception for %d consecutive tries: %s", galaxy_id_tag, external_job_id, ecn, retries + 1, e)
                 if self.runner_params[ retry_param ] > 0:
                     if retries < self.runner_params[ retry_param ]:
                         # will retry check on next iteration

lib/galaxy/tools/deps/__init__.py

@@ -20,7 +20,7 @@ EXTRA_CONFIG_KWDS = {
     'conda_prefix': None,
     'conda_exec': None,
     'conda_debug': None,
-    'conda_ensure_channels': 'r,bioconda',
+    'conda_ensure_channels': 'r,bioconda,iuc',
     'conda_auto_install': False,
     'conda_auto_init': False,
 }

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

@@ -28,7 +28,7 @@ from ..conda_util import (
 
 DEFAULT_BASE_PATH_DIRECTORY = "_conda"
 DEFAULT_CONDARC_OVERRIDE = "_condarc"
-DEFAULT_ENSURE_CHANNELS = "r,bioconda"
+DEFAULT_ENSURE_CHANNELS = "r,bioconda,iuc"
 
 import logging
 log = logging.getLogger(__name__)

lib/galaxy/tools/parameters/basic.py

@@ -899,7 +899,12 @@ class SelectToolParameter( ToolParameter ):
 
     def from_json( self, value, trans, other_values={} ):
         legal_values = self.get_legal_values( trans, other_values )
-        if len(list(legal_values)) == 0 and trans.workflow_building_mode:
+        workflow_building_mode = trans.workflow_building_mode
+        for context_value in other_values.itervalues():
+            if isinstance( context_value, RuntimeValue ):
+                workflow_building_mode = True
+                break
+        if len( list( legal_values ) ) == 0 and workflow_building_mode:
             if self.multiple:
                 # While it is generally allowed that a select value can be '',
                 # we do not allow this to be the case in a dynamically

lib/galaxy/webapps/galaxy/controllers/workflow.py

@@ -516,8 +516,14 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
     @web.require_login( "use Galaxy workflows" )
     def gen_image( self, trans, id ):
         stored = self.get_stored_workflow( trans, id, check_ownership=True )
+        try:
+            svg = self._workflow_to_svg_canvas( trans, stored )
+        except Exception:
+            status = 'error'
+            message = 'Galaxy is unable to create the SVG image. Please check your workflow, there might be missing tools.'
+            return trans.fill_template( "/workflow/sharing.mako", use_panels=True, item=stored, status=status, message=message )
         trans.response.set_content_type("image/svg+xml")
-        return self._workflow_to_svg_canvas( trans, stored ).tostring()
+        return svg.tostring()
 
     @web.expose
     @web.require_login( "use Galaxy workflows" )

templates/webapps/galaxy/workflow/sharing.mako

@@ -238,11 +238,9 @@
     <hr/>
     <h3>Export</h3>
     <div class="sharing-section">
-    <button>
-        <a href="${h.url_for( controller=self.controller, action='display_by_username_and_slug', username=item.user.username, slug=item.slug, format='json-download' )}" style="text-decoration: none;">
+        <a class="action-button" href="${h.url_for( controller=self.controller, action='display_by_username_and_slug', username=item.user.username, slug=item.slug, format='json-download' )}">
         Download
         </a>
-    </button>
     ${get_class_display_name( item.__class__ ).lower()} as a file so that it can be saved or imported into another Galaxy server.
     </div>
 </%def>
@@ -278,11 +276,11 @@
                 method="POST">
             <div class="form-row">
                 <label>myExperiment username:</label>
-                <input type="text" name="myexp_username" value="" size="25" placeholder="username"/>
+                <input type="text" name="myexp_username" value="" size="25" placeholder="username" autocomplete="off"/>
             </div>
             <div class="form-row">
                 <label>myExperiment password:</label>
-                <input type="password" name="myexp_password" value="" size="25" placeholder="password"/>
+                <input type="password" name="myexp_password" value="" size="25" placeholder="password" autocomplete="off"/>
             </div>
             <div class="form-row">
                 <input type="submit" value="Export to myExperiment"/>
@@ -295,11 +293,9 @@
 <%def name="render_more(item)">
     ## Add link to render as SVG image.
     <div class="sharing-section">
-        <button>
-            <a href="${h.url_for(controller='workflow', action='gen_image', id=trans.security.encode_id( item.id ) )}" style="text-decoration: none;">
-                Create image
-            </a>
-        </button>
+        <a class="action-button" href="${h.url_for(controller='workflow', action='gen_image', id=trans.security.encode_id( item.id ) )}">
+            Create image
+        </a>
         of ${get_class_display_name( item.__class__ ).lower()} in SVG format
     </div>
     ## Add form to export to myExperiment.

test/unit/tools/test_select_parameters.py

@@ -33,7 +33,7 @@ class SelectToolParameterTestCase( BaseParameterTestCase ):
     def test_validated_datasets( self ):
         self.options_xml = '''<options><filter type="data_meta" ref="input_bam" key="dbkey"/></options>'''
         try:
-            self.param.from_json( model.HistoryDatasetAssociation(), self.trans, { "input_bam": basic.RuntimeValue() } )
+            self.param.from_json( model.HistoryDatasetAssociation(), self.trans, { "input_bam": None } )
         except ValueError as err:
             assert str(err) == "Parameter my_name requires a value, but has no legal values defined."
             return