Merge branch 'galaxyproject:dev' into type_annots

lib/galaxy/tools/__init__.py

@@ -3204,13 +3204,16 @@ class DatabaseOperationTool(Tool):
     require_terminal_states = True
     require_dataset_ok = True
     tool_type_local = True
+    require_terminal_or_paused_states = False
 
     @property
     def valid_input_states(self):
         if self.require_dataset_ok:
             return (model.Dataset.states.OK,)
         elif self.require_terminal_states:
             return model.Dataset.terminal_states
+        elif self.require_terminal_or_paused_states:
+            return model.Dataset.terminal_states or model.Dataset.states.PAUSED
         else:
             return model.Dataset.valid_input_states
 
@@ -3503,6 +3506,22 @@ def element_is_valid(element: model.DatasetCollectionElement):
         return element.element_object.is_ok
 
 
+class KeepSuccessDatasetsTool(FilterDatasetsTool):
+    tool_type = "keep_success_datasets_collection"
+    require_terminal_states = False
+    require_dataset_ok = False
+    require_terminal_or_paused_states = True
+
+    @staticmethod
+    def element_is_valid(element: model.DatasetCollectionElement):
+        if (
+            element.element_object.state != model.Dataset.states.PAUSED
+            and element.element_object.state in model.Dataset.non_ready_states
+        ):
+            raise ToolInputsNotReadyException("An input dataset is pending.")
+        return element.element_object.is_ok
+
+
 class FilterEmptyDatasetsTool(FilterDatasetsTool):
     tool_type = "filter_empty_datasets_collection"
     require_dataset_ok = False

lib/galaxy/tools/keep_success_collection.xml

@@ -0,0 +1,64 @@
+<tool id="__KEEP_SUCCESS_DATASETS__"
+      name="Keep success"
+      version="1.0.0"
+      tool_type="keep_success_datasets_collection">
+    <description></description>
+    <type class="KeepSuccessDatasetsTool" module="galaxy.tools" />
+    <action module="galaxy.tools.actions.model_operations"
+            class="ModelOperationToolAction"/>
+    <edam_operations>
+        <edam_operation>operation_3695</edam_operation>
+    </edam_operations>
+    <inputs>
+        <param type="data_collection" collection_type="list,list:paired" name="input" label="Input Collection" />
+    </inputs>
+    <outputs>
+        <collection name="output" format_source="input" type_source="input" label="${on_string} (only successed datasets)" >
+        </collection>
+    </outputs>
+    <tests>
+        <!-- Test framework has no way of creating a collection with
+             unsuccess elements, so best we can do is verify identity on
+             an okay collection.
+        -->
+        <test>
+            <param name="input">
+                <collection type="list">
+                    <element name="e1" value="simple_line.txt" />
+                </collection>
+            </param>
+            <output_collection name="output" type="list">
+                <element name="e1">
+                  <assert_contents>
+                      <has_text_matching expression="^This is a line of text.\n$" />
+                  </assert_contents>
+                </element>
+            </output_collection>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+========
+Synopsis
+========
+
+Keep datasets in success (green) from a collection.
+
+===========
+Description
+===========
+
+This tool takes a dataset collection and filters in (keep) datasets in the success (green) state. This is useful for continuing a multi-sample analysis when one of more of the samples fails or is in paused state.
+
+.. image:: ${static_path}/images/tools/collection_ops/keep_success.svg
+  :width: 500
+  :alt: Keep success datasets
+
+-----
+
+.. class:: infomark
+
+This tool will create new history datasets from your collection but your quota usage will not increase.
+
+      ]]></help>
+</tool>

lib/galaxy/webapps/base/webapp.py

@@ -665,7 +665,8 @@ def _ensure_valid_session(self, session_cookie: str, create: bool = True) -> Non
             galaxy_session = self.__create_new_session(prev_galaxy_session, user_for_new_session)
             galaxy_session_requires_flush = True
             self.galaxy_session = galaxy_session
-            self.get_or_create_default_history()
+            if self.webapp.name == "galaxy":
+                self.get_or_create_default_history()
             self.__update_session_cookie(name=session_cookie)
         else:
             self.galaxy_session = galaxy_session

lib/galaxy_test/api/test_workflows.py

@@ -3255,6 +3255,128 @@ def filter_jobs_by_tool(tool_id):
             # Follow proves one job was filtered out of the result of cat1
             assert len(filter_jobs_by_tool("cat1")) == 1, jobs
 
+    def test_keep_success_mapping_error(self):
+        with self.dataset_populator.test_history() as history_id:
+            summary = self._run_workflow(
+                """
+class: GalaxyWorkflow
+inputs:
+  input_c: collection
+
+steps:
+  mixed_collection:
+    tool_id: exit_code_from_file
+    in:
+       input: input_c
+
+  filtered_collection:
+    tool_id: "__KEEP_SUCCESS_DATASETS__"
+    in:
+      input: mixed_collection/out_file1
+
+  cat:
+    tool_id: cat1
+    in:
+      input1: filtered_collection/output
+""",
+                test_data="""
+input_c:
+  collection_type: list
+  elements:
+    - identifier: i1
+      content: "0"
+    - identifier: i2
+      content: "1"
+""",
+                history_id=history_id,
+                wait=True,
+                assert_ok=False,
+            )
+            jobs = summary.jobs
+
+            def filter_jobs_by_tool(tool_id):
+                return [j for j in summary.jobs if j["tool_id"] == tool_id]
+
+            assert len(filter_jobs_by_tool("exit_code_from_file")) == 2, jobs
+            assert len(filter_jobs_by_tool("__KEEP_SUCCESS_DATASETS__")) == 1, jobs
+            # Follow proves one job was filtered out of the exit_code_from_file
+            # And a single one has been sent to cat1
+            assert len(filter_jobs_by_tool("cat1")) == 1, jobs
+
+    def test_keep_success_mapping_paused(self):
+        with self.dataset_populator.test_history() as history_id:
+            summary = self._run_workflow(
+                """
+class: GalaxyWorkflow
+inputs:
+  input_c: collection
+
+steps:
+  mixed_collection:
+    tool_id: exit_code_from_file
+    in:
+       input: input_c
+
+  cat:
+    tool_id: cat1
+    in:
+      input1: mixed_collection/out_file1
+
+  filtered_collection:
+    tool_id: "__KEEP_SUCCESS_DATASETS__"
+    in:
+      input: cat/out_file1
+""",
+                test_data="""
+input_c:
+  collection_type: list
+  elements:
+    - identifier: i1
+      content: "0"
+    - identifier: i2
+      content: "1"
+    - identifier: i3
+      content: "0"
+""",
+                history_id=history_id,
+                wait=True,
+                assert_ok=False,
+            )
+            jobs = summary.jobs
+
+            def filter_jobs_by_tool(tool_id):
+                return [j for j in summary.jobs if j["tool_id"] == tool_id]
+
+            # Get invocation to access output collections
+            invocation = self.workflow_populator.get_invocation(summary.invocation_id, step_details=True)
+            # Check there are 3 exit_code_from_file
+            assert len(filter_jobs_by_tool("exit_code_from_file")) == 3, jobs
+            # Check output collection has 3 elements
+            output_mixed_collection_id = invocation["steps"][1]["output_collections"]["out_file1"]["id"]
+            mixed_collection = self.dataset_populator.get_history_collection_details(
+                history_id, content_id=output_mixed_collection_id, assert_ok=False
+            )
+            assert mixed_collection["element_count"] == 3, mixed_collection
+            # Check 3 jobs cat1 has been "scheduled":
+            assert len(filter_jobs_by_tool("cat1")) == 3, jobs
+            # Check 2 are 'ok' the other is 'paused'
+            output_cat_id = invocation["steps"][2]["output_collections"]["out_file1"]["id"]
+            cat_collection = self.dataset_populator.get_history_collection_details(
+                history_id, content_id=output_cat_id, assert_ok=False
+            )
+            assert cat_collection["element_count"] == 3, cat_collection
+            cat1_states = [e["object"]["state"] for e in cat_collection["elements"]]
+            assert "paused" in cat1_states, jobs
+            assert len([s for s in cat1_states if s == "ok"]) == 2, cat_collection
+            # Check the KEEP_SUCCESS_DATASETS have been run
+            assert len(filter_jobs_by_tool("__KEEP_SUCCESS_DATASETS__")) == 1, jobs
+            # Check the output has 2 elements
+            output_filtered_id = invocation["steps"][3]["output_collections"]["output"]["id"]
+            output_filtered = self.dataset_populator.get_history_collection_details(
+                history_id, content_id=output_filtered_id, assert_ok=False
+            )
+            assert output_filtered["element_count"] == 2, output_filtered
+
     def test_workflow_request(self):
         workflow = self.workflow_populator.load_workflow(name="test_for_queue")
         workflow_request, history_id, workflow_id = self._setup_workflow_run(workflow)

lib/tool_shed/webapp/buildapp.py

@@ -37,6 +37,10 @@ class ToolShedGalaxyWebTransaction(GalaxyWebTransaction):
     def repositories_hostname(self) -> str:
         return url_for("/", qualified=True).rstrip("/")
 
+    def get_or_create_default_history(self):
+        # tool shed has no concept of histories
+        raise NotImplementedError
+
 
 class CommunityWebApplication(galaxy.webapps.base.webapp.WebApplication):
     injection_aware: bool = True

test/functional/tools/sample_tool_conf.xml

@@ -292,6 +292,7 @@
   <tool file="${model_tools_path}/unzip_collection.xml" />
   <tool file="${model_tools_path}/zip_collection.xml" />
   <tool file="${model_tools_path}/filter_failed_collection.xml" />
+  <tool file="${model_tools_path}/keep_success_collection.xml" />
   <tool file="${model_tools_path}/filter_empty_collection.xml" />
   <tool file="${model_tools_path}/flatten_collection.xml" />
   <tool file="${model_tools_path}/sort_collection_list.xml" />