Merge remote-tracking branch 'upstream/release_18.09'

lib/galaxy/model/__init__.py

@@ -3928,6 +3928,13 @@ def get_internal_version(self, version):
             raise Exception("Version does not exist")
         return list(reversed(self.workflows))[version]
 
+    def show_in_tool_panel(self, user_id):
+        sa_session = object_session(self)
+        return bool(sa_session.query(StoredWorkflowMenuEntry).filter(
+            StoredWorkflowMenuEntry.stored_workflow_id == self.id,
+            StoredWorkflowMenuEntry.user_id == user_id,
+        ).count())
+
     def copy_tags_from(self, target_user, source_workflow):
         # Override to only copy owner tags.
         for src_swta in source_workflow.owner_tags:

lib/galaxy/tools/deps/container_resolvers/__init__.py

@@ -23,15 +23,12 @@ def __init__(self, app_info=None, **kwds):
         self.app_info = app_info
         self.resolver_kwds = kwds
 
-    def _get_config_option(self, key, default=None, config_prefix=None, **kwds):
+    def _get_config_option(self, key, default=None):
         """Look in resolver-specific settings for option and then fallback to
         global settings.
         """
-        global_key = "%s_%s" % (config_prefix, key)
-        if key in kwds:
-            return kwds.get(key)
-        elif self.app_info and hasattr(self.app_info, global_key):
-            return getattr(self.app_info, global_key)
+        if self.app_info and hasattr(self.app_info, key):
+            return getattr(self.app_info, key)
         else:
             return default
 

lib/galaxy/tools/deps/container_resolvers/mulled.py

@@ -351,11 +351,11 @@ def __init__(self, app_info=None, namespace="local", hash_func="v2", **kwds):
         self.hash_func = hash_func
         self._mulled_kwds = {
             'namespace': namespace,
-            'channels': self._get_config_option("channels", DEFAULT_CHANNELS, prefix="mulled"),
+            'channels': self._get_config_option("mulled_channels", DEFAULT_CHANNELS),
             'hash_func': self.hash_func,
             'command': 'build-and-test',
         }
-        self.auto_init = self._get_config_option("auto_init", DEFAULT_CHANNELS, prefix="involucro")
+        self.auto_init = self._get_config_option("involucro_auto_init", True)
 
     def resolve(self, enabled_container_types, tool_info):
         if tool_info.requires_galaxy_python_environment:
@@ -396,13 +396,13 @@ def __init__(self, app_info=None, hash_func="v2", **kwds):
         self.cache_directory = kwds.get("cache_directory", os.path.join(app_info.container_image_cache_path, "singularity", "mulled"))
         self.hash_func = hash_func
         self._mulled_kwds = {
-            'channels': self._get_config_option("channels", DEFAULT_CHANNELS, prefix="mulled"),
+            'channels': self._get_config_option("mulled_channels", DEFAULT_CHANNELS),
             'hash_func': self.hash_func,
             'command': 'build-and-test',
             'singularity': True,
             'singularity_image_dir': self.cache_directory,
         }
-        self.auto_init = self._get_config_option("auto_init", DEFAULT_CHANNELS, prefix="involucro")
+        self.auto_init = self._get_config_option("involucro_auto_init", True)
 
     def resolve(self, enabled_container_types, tool_info):
         if tool_info.requires_galaxy_python_environment:

lib/galaxy/tools/deps/mulled/mulled_build.py

@@ -39,7 +39,7 @@
 from ..conda_compat import MetaData
 
 DIRNAME = os.path.dirname(__file__)
-DEFAULT_CHANNELS = "conda-forge,bioconda"
+DEFAULT_CHANNELS = ["conda-forge", "bioconda"]
 DEFAULT_REPOSITORY_TEMPLATE = "quay.io/${namespace}/${image}"
 DEFAULT_BINDS = ["build/dist:/usr/local/"]
 DEFAULT_WORKING_DIR = '/source/'
@@ -322,7 +322,7 @@ def add_build_arguments(parser):
                         help='quay.io namespace.')
     parser.add_argument('-r', '--repository_template', dest='repository_template', default=DEFAULT_REPOSITORY_TEMPLATE,
                         help='Docker repository target for publication (only quay.io or compat. API is currently supported).')
-    parser.add_argument('-c', '--channels', dest='channels', default=DEFAULT_CHANNELS,
+    parser.add_argument('-c', '--channels', dest='channels', default=",".join(DEFAULT_CHANNELS),
                         help='Comma separated list of target conda channels.')
     parser.add_argument('--conda-version', dest="conda_version", default=None,
                         help="Change to specified version of Conda before installing packages.")

lib/galaxy/tools/wrappers.py

@@ -444,6 +444,10 @@ def keys(self):
     def is_collection(self):
         return True
 
+    @property
+    def element_identifier(self):
+        return self.name
+
     @property
     def is_input_supplied(self):
         return self.__input_supplied

lib/galaxy/webapps/galaxy/api/workflows.py

@@ -140,11 +140,7 @@ def get_workflows_list(self, trans, kwd):
             item['url'] = url_for('workflow', id=encoded_id)
             item['owner'] = wf.user.username
             item['number_of_steps'] = wf.latest_workflow.step_count
-            item['show_in_tool_panel'] = False
-            for x in user.stored_workflow_menu_entries:
-                if x.stored_workflow_id == wf.id:
-                    item['show_in_tool_panel'] = True
-                    break
+            item['show_in_tool_panel'] = wf.show_in_tool_panel(user_id=user.id)
             rval.append(item)
         for wf_sa in trans.sa_session.query(model.StoredWorkflowUserShareAssociation).join(
                 model.StoredWorkflowUserShareAssociation.stored_workflow).options(
@@ -159,11 +155,7 @@ def get_workflows_list(self, trans, kwd):
             item['slug'] = wf_sa.stored_workflow.slug
             item['owner'] = wf_sa.stored_workflow.user.username
             item['number_of_steps'] = wf_sa.stored_workflow.latest_workflow.step_count
-            item['show_in_tool_panel'] = False
-            for x in user.stored_workflow_menu_entries:
-                if x.stored_workflow_id == wf_sa.id:
-                    item['show_in_tool_panel'] = True
-                    break
+            item['show_in_tool_panel'] = wf_sa.stored_workflow.show_in_tool_panel(user_id=user.id)
             rval.append(item)
         if missing_tools:
             workflows_missing_tools = []

test/functional/tools/identifier_collection.xml

@@ -1,15 +1,33 @@
-<tool id="identifier_collection" name="identifier_collection">
+<tool id="identifier_collection" name="identifier_collection" version="0.1">
   <command>
     #for $input in $input1:
       echo '$input.element_identifier' >> 'output1';
     #end for
   </command>
   <inputs>
-    <param type="data_collection" collection_type="list" name="input1" label="Input 1" />
+    <param type="data_collection" collection_type="list,list:paired" name="input1" label="Input 1" />
   </inputs>
   <outputs>
     <data name="output1" format="tabular" from_work_dir="output1" />
   </outputs>
   <tests>
+    <!-- test getting identifier for list:pair collections -->
+    <test>
+      <param name="input1">
+        <collection type="list:paired">
+          <element name="i1">
+            <collection type="paired">
+              <element name="forward" value="simple_line.txt" />
+              <element name="reverse" value="simple_line_alternative.txt" />
+            </collection>
+          </element>
+        </collection>
+      </param>
+      <output name="output1">
+        <assert_contents>
+          <has_line line="i1" />
+        </assert_contents>
+      </output>
+    </test>
   </tests>
 </tool>