Merge pull request #5418 from jmchilton/collection_pja

[18.01] Implement more intuitive collection PJA

lib/galaxy/jobs/actions/post.py

@@ -86,7 +86,7 @@ class RenameDatasetAction(DefaultJobAction):
     verbose_name = "Rename Dataset"
 
     @classmethod
-    def execute_on_mapped_over(cls, app, sa_session, action, step_inputs, step_outputs, replacement_dict):
+    def execute_on_mapped_over(cls, trans, sa_session, action, step_inputs, step_outputs, replacement_dict):
         # Prevent renaming a dataset to the empty string.
         input_names = {}
         #  Lookp through inputs find one with "to_be_replaced" input
@@ -226,6 +226,16 @@ class HideDatasetAction(DefaultJobAction):
             if dataset_assoc.dataset.state != dataset_assoc.dataset.states.ERROR and (action.output_name == '' or dataset_assoc.name == action.output_name):
                 dataset_assoc.dataset.visible = False
 
+        for dataset_collection_assoc in job.output_dataset_collection_instances:
+            if action.output_name == '' or dataset_collection_assoc.name == action.output_name:
+                dataset_collection_assoc.dataset_collection_instance.visible = False
+
+    @classmethod
+    def execute_on_mapped_over(cls, trans, sa_session, action, step_inputs, step_outputs, replacement_dict):
+        for name, step_output in step_outputs.items():
+            if action.output_name == '' or name == action.output_name:
+                step_output.visible = False
+
     @classmethod
     def get_short_str(cls, pja):
         return "Hide output '%s'." % escape(pja.output_name)
@@ -242,6 +252,16 @@ class DeleteDatasetAction(DefaultJobAction):
             if action.output_name == '' or dataset_assoc.name == action.output_name:
                 dataset_assoc.dataset.deleted = True
 
+        for dataset_collection_assoc in job.output_dataset_collection_instances:
+            if action.output_name == '' or dataset_collection_assoc.name == action.output_name:
+                dataset_collection_assoc.dataset_collection_instance.deleted = True
+
+    @classmethod
+    def execute_on_mapped_over(cls, trans, sa_session, action, step_inputs, step_outputs, replacement_dict):
+        for name, step_output in step_outputs.items():
+            if action.output_name == '' or name == action.output_name:
+                step_output.deleted = True
+
     @classmethod
     def get_short_str(cls, pja):
         return "Delete this dataset after creation."
@@ -357,6 +377,15 @@ class TagDatasetAction(DefaultJobAction):
     action = "Add"
     direction = "to"
 
+    @classmethod
+    def execute_on_mapped_over(cls, trans, sa_session, action, step_inputs, step_outputs, replacement_dict):
+        if action.action_arguments:
+            tags = [t.replace('#', 'name:') if t.startswith('#') else t for t in [t.strip() for t in action.action_arguments.get('tags', '').split(',') if t.strip()]]
+            if tags:
+                for name, step_output in step_outputs.items():
+                    if action.output_name == '' or name == action.output_name:
+                        cls._execute(trans.app, trans.user, step_output, tags)
+
     @classmethod
     def execute(cls, app, sa_session, action, job, replacement_dict):
         if action.action_arguments:
@@ -365,11 +394,16 @@ class TagDatasetAction(DefaultJobAction):
                 for dataset_assoc in job.output_datasets:
                     if action.output_name == '' or dataset_assoc.name == action.output_name:
                         cls._execute(app, job.user, dataset_assoc.dataset, tags)
+
+                for dataset_collection_assoc in job.output_dataset_collection_instances:
+                    if action.output_name == '' or dataset_collection_assoc.name == action.output_name:
+                        cls._execute(app, job.user, dataset_collection_assoc.dataset_collection_instance, tags)
+
             sa_session.flush()
 
     @classmethod
-    def _execute(cls, app, user, dataset, tags):
-        app.tag_handler.add_tags_from_list(user, dataset, tags)
+    def _execute(cls, app, user, output, tags):
+        app.tag_handler.add_tags_from_list(user, output, tags)
 
     @classmethod
     def get_short_str(cls, pja):
@@ -389,8 +423,8 @@ class RemoveTagDatasetAction(TagDatasetAction):
     direction = "from"
 
     @classmethod
-    def _execute(cls, app, user, dataset, tags):
-        app.tag_handler.remove_tags_from_list(user, dataset, tags)
+    def _execute(cls, app, user, output, tags):
+        app.tag_handler.remove_tags_from_list(user, output, tags)
 
 
 class ActionBox(object):
@@ -413,7 +447,8 @@ class ActionBox(object):
                          'TagDatasetAction', 'RemoveTagDatasetAction']
     # Actions that will be applied to implicit mapped over collection outputs and not
     # just individual outputs when steps include mapped over tools and implicit collection outputs.
-    mapped_over_output_actions = ['RenameDatasetAction']
+    mapped_over_output_actions = ['RenameDatasetAction', 'HideDatasetAction',
+                                  'TagDatasetAction', 'RemoveTagDatasetAction']
 
     @classmethod
     def get_short_str(cls, action):
@@ -445,9 +480,9 @@ class ActionBox(object):
         return npd
 
     @classmethod
-    def execute_on_mapped_over(cls, app, sa_session, pja, step_inputs, step_outputs, replacement_dict=None):
+    def execute_on_mapped_over(cls, trans, sa_session, pja, step_inputs, step_outputs, replacement_dict=None):
         if pja.action_type in ActionBox.actions:
-            ActionBox.actions[pja.action_type].execute_on_mapped_over(app, sa_session, pja, step_inputs, step_outputs, replacement_dict)
+            ActionBox.actions[pja.action_type].execute_on_mapped_over(trans, sa_session, pja, step_inputs, step_outputs, replacement_dict)
 
     @classmethod
     def execute(cls, app, sa_session, pja, job, replacement_dict=None):

lib/galaxy/workflow/modules.py

@@ -986,7 +986,7 @@ class ToolModule(WorkflowModule):
         effective_post_job_actions = self._effective_post_job_actions(step)
         for pja in effective_post_job_actions:
             if pja.action_type in ActionBox.mapped_over_output_actions:
-                ActionBox.execute_on_mapped_over(self.trans.app, self.trans.sa_session, pja, step_inputs, step_outputs, replacement_dict)
+                ActionBox.execute_on_mapped_over(self.trans, self.trans.sa_session, pja, step_inputs, step_outputs, replacement_dict)
 
     def _handle_post_job_actions(self, step, job, replacement_dict):
         # Create new PJA associations with the created job, to be run on completion.

test/api/test_workflows.py

@@ -2000,7 +2000,7 @@ test_data: {}
             assert okay_dataset["state"] == "ok"
 
     @skip_without_tool("cat")
-    def test_run_rename_on_mapped_over_dataset(self):
+    def test_run_rename_on_mapped_over_collection(self):
         history_id = self.dataset_populator.new_history()
         self._run_jobs("""
 class: GalaxyWorkflow
@@ -2036,7 +2036,7 @@ test_data:
         assert name == "my new name", name
 
     @skip_without_tool("cat")
-    def test_run_rename_based_on_inputs_on_mapped_over_dataset(self):
+    def test_run_rename_based_on_inputs_on_mapped_over_collection(self):
         history_id = self.dataset_populator.new_history()
         self._run_jobs("""
 class: GalaxyWorkflow
@@ -2283,6 +2283,169 @@ test_data:
         name = content["name"]
         assert name == "the_dataset_pair suffix", name
 
+    @skip_without_tool("collection_creates_pair")
+    def test_run_hide_on_collection_output(self):
+        with self.dataset_populator.test_history() as history_id:
+            self._run_jobs("""
+class: GalaxyWorkflow
+inputs:
+  - id: input1
+steps:
+  - tool_id: collection_creates_pair
+    state:
+      input1:
+        $link: input1
+    outputs:
+      paired_output:
+        hide: true
+test_data:
+  input1:
+    value: 1.fasta
+    type: File
+    name: fasta1
+""", history_id=history_id)
+            details1 = self.dataset_populator.get_history_collection_details(history_id, hid=4, wait=True, assert_ok=True)
+
+            assert details1["history_content_type"] == "dataset_collection"
+            assert not details1["visible"], details1
+
+    @skip_without_tool("cat")
+    def test_run_hide_on_mapped_over_collection(self):
+        history_id = self.dataset_populator.new_history()
+        self._run_jobs("""
+class: GalaxyWorkflow
+inputs:
+  - id: input1
+    type: data_collection_input
+    collection_type: list
+steps:
+  - tool_id: cat
+    label: first_cat
+    state:
+      input1:
+        $link: input1
+    outputs:
+      out_file1:
+        hide: true
+test_data:
+  input1:
+    type: list
+    name: the_dataset_list
+    elements:
+      - identifier: el1
+        value: 1.fastq
+        type: File
+""", history_id=history_id)
+
+        content = self.dataset_populator.get_history_dataset_details(history_id, hid=4, wait=True, assert_ok=True)
+        assert content["history_content_type"] == "dataset"
+        assert content["visible"] is False
+
+        content = self.dataset_populator.get_history_collection_details(history_id, hid=3, wait=True, assert_ok=True)
+        assert content["history_content_type"] == "dataset_collection", content
+        assert content["visible"] is False
+
+    @skip_without_tool("collection_creates_pair")
+    def test_run_add_tag_on_collection_output(self):
+        with self.dataset_populator.test_history() as history_id:
+            self._run_jobs("""
+class: GalaxyWorkflow
+inputs:
+  - id: input1
+steps:
+  - tool_id: collection_creates_pair
+    state:
+      input1:
+        $link: input1
+    outputs:
+      paired_output:
+        add_tags:
+            - "name:foo"
+test_data:
+  input1:
+    value: 1.fasta
+    type: File
+    name: fasta1
+""", history_id=history_id)
+            details1 = self.dataset_populator.get_history_collection_details(history_id, hid=4, wait=True, assert_ok=True)
+
+            assert details1["history_content_type"] == "dataset_collection"
+            assert details1["tags"][0] == "name:foo", details1
+
+    @skip_without_tool("collection_creates_pair")
+    def test_run_add_tag_on_mapped_over_collection(self):
+        with self.dataset_populator.test_history() as history_id:
+            self._run_jobs("""
+class: GalaxyWorkflow
+inputs:
+  - id: input1
+    type: data_collection_input
+    collection_type: list
+steps:
+  - tool_id: cat
+    label: first_cat
+    state:
+      input1:
+        $link: input1
+    outputs:
+      out_file1:
+        add_tags:
+            - "name:foo"
+test_data:
+  input1:
+    type: list
+    name: the_dataset_list
+    elements:
+      - identifier: el1
+        value: 1.fastq
+        type: File
+""", history_id=history_id)
+            details1 = self.dataset_populator.get_history_collection_details(history_id, hid=3, wait=True, assert_ok=True)
+
+            assert details1["history_content_type"] == "dataset_collection"
+            assert details1["tags"][0] == "name:foo", details1
+
+    @skip_without_tool("collection_creates_pair")
+    @skip_without_tool("cat")
+    def test_run_remove_tag_on_collection_output(self):
+        with self.dataset_populator.test_history() as history_id:
+            self._run_jobs("""
+class: GalaxyWorkflow
+inputs:
+  - id: input1
+steps:
+  - tool_id: cat
+    label: first_cat
+    state:
+      input1:
+        $link: input1
+    outputs:
+      out_file1:
+        add_tags:
+          - "name:foo"
+  - tool_id: collection_creates_pair
+    state:
+      input1:
+        $link: first_cat#out_file1
+    outputs:
+      paired_output:
+        remove_tags:
+          - "name:foo"
+test_data:
+  input1:
+    value: 1.fasta
+    type: File
+    name: fasta1
+""", history_id=history_id)
+            details_dataset_with_tag = self.dataset_populator.get_history_dataset_details(history_id, hid=2, wait=True, assert_ok=True)
+
+            assert details_dataset_with_tag["history_content_type"] == "dataset", details_dataset_with_tag
+            assert details_dataset_with_tag["tags"][0] == "name:foo", details_dataset_with_tag
+
+            details_collection_without_tag = self.dataset_populator.get_history_collection_details(history_id, hid=5, wait=True, assert_ok=True)
+            assert details_collection_without_tag["history_content_type"] == "dataset_collection", details_collection_without_tag
+            assert len(details_collection_without_tag["tags"]) == 0, details_collection_without_tag
+
     @skip_without_tool("cat1")
     def test_run_with_runtime_pja(self):
         workflow = self.workflow_populator.load_workflow(name="test_for_pja_runtime")

test/base/workflows_format_2/converter.py

@@ -390,6 +390,28 @@ def transform_tool(context, step):
                 )
                 post_job_actions[action_name] = action
 
+            add_tags = output.get("add_tags", [])
+            if add_tags:
+                action_name = "TagDatasetAction%s" % name
+                arguments = dict(tags=",".join(add_tags))
+                action = _action(
+                    "TagDatasetAction",
+                    name,
+                    arguments
+                )
+                post_job_actions[action_name] = action
+
+            remove_tags = output.get("remove_tags", [])
+            if remove_tags:
+                action_name = "RemoveTagDatasetAction%s" % name
+                arguments = dict(tags=",".join(remove_tags))
+                action = _action(
+                    "RemoveTagDatasetAction",
+                    name,
+                    arguments
+                )
+                post_job_actions[action_name] = action
+
         del step["outputs"]