Merge branch 'release_21.09' into dev

client/src/components/Workflow/Editor/Node.vue

@@ -298,6 +298,7 @@ export default {
             this.$emit("onChange");
         },
         setData(data) {
+            this.content_id = data.content_id;
             this.tool_state = data.tool_state;
             this.errors = data.errors;
             this.tooltip = data.tooltip || "";
@@ -311,7 +312,6 @@ export default {
         },
         initData(data) {
             this.uuid = data.uuid;
-            this.content_id = data.config_form?.id || data.content_id;
             this.annotation = data.annotation;
             this.label = data.label;
             this.setData(data);

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

@@ -612,6 +612,7 @@ class WorkflowsAPIController(BaseGalaxyAPIController, UsesStoredWorkflowMixin, U
             'annotation': inputs.get('__annotation', ''),
             'name': module.get_name(),
             'tool_state': module.get_state(),
+            'content_id': module.get_content_id(),
             'inputs': module.get_all_inputs(connectable_only=True),
             'outputs': module.get_all_outputs(),
             'config_form': module.get_config_form(),

lib/galaxy_test/api/test_history_contents.py

@@ -251,6 +251,32 @@ class HistoryContentsApiTestCase(ApiTestCase):
         assert objects[0]["deleted"] is False
         assert objects[0]["visible"] is True
 
+    def test_update_batch_collections(self):
+        hdca = self._create_pair_collection()
+        assert hdca["deleted"] is False
+        assert hdca["visible"] is True
+
+        # update deleted flag => true
+        payload = dict(items=[{"history_content_type": "dataset_collection", "id": hdca["id"]}], deleted=True)
+        update_response = self._update_batch(payload)
+        objects = update_response.json()
+        assert objects[0]["deleted"] is True
+        assert objects[0]["visible"] is True
+
+        # update visibility flag => false
+        payload = dict(items=[{"history_content_type": "dataset_collection", "id": hdca["id"]}], visible=False)
+        update_response = self._update_batch(payload)
+        objects = update_response.json()
+        assert objects[0]["deleted"] is True
+        assert objects[0]["visible"] is False
+
+        # update both flags
+        payload = dict(items=[{"history_content_type": "dataset_collection", "id": hdca["id"]}], deleted=False, visible=True)
+        update_response = self._update_batch(payload)
+        objects = update_response.json()
+        assert objects[0]["deleted"] is False
+        assert objects[0]["visible"] is True
+
     def test_update_type_failures(self):
         hda1 = self._wait_for_new_hda()
         update_response = self._update(hda1["id"], dict(deleted='not valid'))

lib/galaxy_test/selenium/framework.py

@@ -386,6 +386,14 @@ class TestWithSeleniumMixin(GalaxyTestSeleniumContext, UsesApiTestCaseMixin):
             self.assert_no_error_message()
         return GALAXY_TEST_SELENIUM_ADMIN_USER_EMAIL
 
+    @retry_assertion_during_transitions
+    def assert_workflow_has_changes_and_save(self):
+        save_button = self.components.workflow_editor.save_button
+        save_button.wait_for_visible()
+        assert not save_button.has_class("disabled")
+        save_button.wait_for_and_click()
+        self.sleep_for(self.wait_types.UX_RENDER)
+
     def workflow_upload_yaml_with_random_name(self, content, **kwds):
         workflow_populator = self.workflow_populator
         name = self._get_random_name()

lib/galaxy_test/selenium/test_workflow_editor.py

@@ -71,7 +71,7 @@ class WorkflowEditorTestCase(SeleniumTestCase):
 
         new_annotation = 'look new annotation'
         edit_annotation.wait_for_and_send_keys(new_annotation)
-        self.assert_has_changes_and_save()
+        self.assert_workflow_has_changes_and_save()
         self.workflow_index_open_with_name(name)
         self.assert_wf_annotation_is(new_annotation)
 
@@ -84,7 +84,7 @@ class WorkflowEditorTestCase(SeleniumTestCase):
         edit_name = self.components.workflow_editor.edit_name
         edit_name.wait_for_and_send_keys(new_name)
 
-        self.assert_has_changes_and_save()
+        self.assert_workflow_has_changes_and_save()
         self.workflow_index_open_with_name(new_name)
         self.assert_wf_name_is(name)
 
@@ -104,19 +104,19 @@ class WorkflowEditorTestCase(SeleniumTestCase):
         self.sleep_for(self.wait_types.UX_RENDER)
         self.components.tool_form.parameter_input(parameter='select_single').wait_for_and_send_keys('e')
         self.sleep_for(self.wait_types.UX_RENDER)
-        self.assert_has_changes_and_save()
+        self.assert_workflow_has_changes_and_save()
         workflow = self.workflow_populator.download_workflow(workflow_id)
         tool_state = json.loads(workflow['steps']['0']['tool_state'])
         assert tool_state['select_single'] == 'parameter value'
         # Disable optional button, resets value to null
         self.components.tool_form.parameter_checkbox(parameter='select_single').wait_for_and_click()
-        self.assert_has_changes_and_save()
+        self.assert_workflow_has_changes_and_save()
         workflow = self.workflow_populator.download_workflow(workflow_id)
         tool_state = json.loads(workflow['steps']['0']['tool_state'])
         assert tool_state['select_single'] is None
         # Enable button but don't provide a value
         self.components.tool_form.parameter_checkbox(parameter='select_single').wait_for_and_click()
-        self.assert_has_changes_and_save()
+        self.assert_workflow_has_changes_and_save()
         workflow = self.workflow_populator.download_workflow(workflow_id)
         tool_state = json.loads(workflow['steps']['0']['tool_state'])
         assert tool_state['select_single'] == ""
@@ -193,7 +193,7 @@ steps:
         self.sleep_for(self.wait_types.UX_RENDER)
         self.set_text_element(columns, '4\n5\n6\n')
         self.sleep_for(self.wait_types.UX_RENDER)
-        self.assert_has_changes_and_save()
+        self.assert_workflow_has_changes_and_save()
         self.driver.refresh()
         node.title.wait_for_and_click()
         textarea_columns = columns.wait_for_visible()
@@ -272,6 +272,32 @@ steps:
         self.workflow_editor_connect("input_int#output", "tool_exec#inttest", screenshot_partial="workflow_editor_parameter_connection_dragging")
         self.assert_connected("input_int#output", "tool_exec#inttest")
 
+    @selenium_test
+    def test_non_data_map_over_carried_through(self):
+        # Use auto_layout=false, which prevents placing any
+        # step outside of the scroll area
+        # xref: https://github.com/galaxyproject/galaxy/issues/13211
+        self.open_in_workflow_editor("""
+class: GalaxyWorkflow
+inputs:
+  input_collection:
+    type: collection
+    collection_type: "list"
+steps:
+  param_value_from_file:
+    tool_id: param_value_from_file
+    in:
+      input1: input_collection
+  text_input_step:
+    tool_id: param_text_option
+    in:
+      text_param: param_value_from_file/text_param
+  collection_input:
+    tool_id: identifier_collection
+""", auto_layout=False)
+        self.workflow_editor_connect("text_input_step#out_file1", "collection_input#input1")
+        self.assert_connected("text_input_step#out_file1", "collection_input#input1")
+
     @selenium_test
     def test_existing_connections(self):
         self.open_in_workflow_editor(WORKFLOW_SIMPLE_CAT_TWICE)
@@ -301,7 +327,7 @@ steps:
         self.workflow_editor_connect("input1#output", "first_cat#input1")
         self.assert_connected("input1#output", "first_cat#input1")
         self.sleep_for(self.wait_types.UX_RENDER)
-        self.assert_has_changes_and_save()
+        self.assert_workflow_has_changes_and_save()
         self.workflow_index_open_with_name(name)
         self.assert_connected("input1#output", "first_cat#input1")
 
@@ -423,7 +449,7 @@ steps:
         assert self.select_dropdown_item('Switch to 0.2'), 'Switch to tool version dropdown item not found'
         self.screenshot("workflow_editor_version_update")
         self.sleep_for(self.wait_types.UX_RENDER)
-        self.assert_has_changes_and_save()
+        self.assert_workflow_has_changes_and_save()
         workflow = self.workflow_populator.download_workflow(workflow_id)
         assert workflow['steps']['0']['tool_version'] == '0.2'
 
@@ -436,7 +462,7 @@ steps:
         self.assert_modal_has_text("Using version '0.2' instead of version '0.0.1'")
         self.screenshot("workflow_editor_tool_upgrade")
         self.components.workflow_editor.modal_button_continue.wait_for_and_click()
-        self.assert_has_changes_and_save()
+        self.assert_workflow_has_changes_and_save()
 
     @selenium_test
     def test_editor_subworkflow_tool_upgrade_message(self):
@@ -463,7 +489,7 @@ steps:
         self.assert_modal_has_text("parameter 'inttest': an integer or workflow parameter is required")
         self.screenshot("workflow_editor_subworkflow_tool_upgrade")
         self.components.workflow_editor.modal_button_continue.wait_for_and_click()
-        self.assert_has_changes_and_save()
+        self.assert_workflow_has_changes_and_save()
 
     @staticmethod
     def set_text_element(element, value):
@@ -484,9 +510,9 @@ steps:
         self.set_text_element(editor.label_input, 'source label')
         # Select node using new label, ensures labels are synced between side panel and node
         cat_node = editor.node._(label="source label")
-        self.assert_has_changes_and_save()
+        self.assert_workflow_has_changes_and_save()
         editor.annotation_input.wait_for_and_send_keys("source annotation")
-        self.assert_has_changes_and_save()
+        self.assert_workflow_has_changes_and_save()
         editor.configure_output(output='out_file1').wait_for_and_click()
         output_label = editor.label_output(output='out_file1')
         self.set_text_element(output_label, 'workflow output label')
@@ -501,7 +527,7 @@ steps:
         output_label = editor.label_output(output='out_file1')
         self.set_text_element(output_label, 'cloned output label')
         self.sleep_for(self.wait_types.UX_RENDER)
-        self.assert_has_changes_and_save()
+        self.assert_workflow_has_changes_and_save()
         edited_workflow = self.workflow_populator.download_workflow(workflow_id)
         source_step = next(iter(step for step in edited_workflow['steps'].values() if step['label'] == 'source label'))
         cloned_step = next(iter(step for step in edited_workflow['steps'].values() if step['label'] == 'cloned label'))
@@ -533,7 +559,7 @@ steps:
         editor.tool_menu_section_link(section_name="workflows").wait_for_and_click()
         editor.workflow_link(workflow_title=child_workflow_name).wait_for_and_click()
         self.sleep_for(self.wait_types.UX_RENDER)
-        self.assert_has_changes_and_save()
+        self.assert_workflow_has_changes_and_save()
         workflow = self.workflow_populator.download_workflow(parent_workflow_id)
         subworkflow_step = workflow['steps']['1']
         assert subworkflow_step['name'] == child_workflow_name
@@ -630,11 +656,12 @@ steps:
         source_id, sink_id = self.workflow_editor_source_sink_terminal_ids(source, sink)
         self.components.workflow_editor.connector_for(source_id=source_id, sink_id=sink_id).wait_for_absent()
 
-    def open_in_workflow_editor(self, yaml_content):
+    def open_in_workflow_editor(self, yaml_content, auto_layout=True):
         name = self.workflow_upload_yaml_with_random_name(yaml_content)
         self.workflow_index_open()
         self.workflow_index_open_with_name(name)
-        self.workflow_editor_click_option("Auto Layout")
+        if auto_layout:
+            self.workflow_editor_click_option("Auto Layout")
         return name
 
     def workflow_editor_source_sink_terminal_ids(self, source, sink):
@@ -704,14 +731,6 @@ steps:
         workflow_populator.upload_yaml_workflow(content, name=name)
         return name
 
-    @retry_assertion_during_transitions
-    def assert_has_changes_and_save(self):
-        save_button = self.components.workflow_editor.save_button
-        save_button.wait_for_visible()
-        assert not save_button.has_class("disabled")
-        save_button.wait_for_and_click()
-        self.sleep_for(self.wait_types.UX_RENDER)
-
     @retry_assertion_during_transitions
     def assert_wf_name_is(self, expected_name):
         edit_name_element = self.components.workflow_editor.edit_name.wait_for_visible()

packages/test_base/MANIFEST.in

@@ -1 +1 @@
-include *.rst *.txt LICENSE
+include *.rst *.txt LICENSE galaxy_test/base/tool_sheds_conf.xml

packages/test_base/setup.py

@@ -38,7 +38,9 @@ ENTRY_POINTS = '''
 '''
 PACKAGE_DATA = {
     # Be sure to update MANIFEST.in for source dist.
-    'galaxy': [
+    'galaxy': [],
+    'galaxy_test': [
+        'galaxy_test/base/tool_sheds_conf.xml',
     ],
 }
 PACKAGE_DIR = {

test/integration/test_data_manager.py

@@ -5,8 +5,8 @@ import pytest
 from nose.plugins.skip import SkipTest
 
 from galaxy_test.base.populators import DatasetPopulator, skip_if_toolshed_down
+from galaxy_test.base.uses_shed import CONDA_AUTO_INSTALL_JOB_TIMEOUT, UsesShed
 from galaxy_test.driver import integration_util
-from .uses_shed import CONDA_AUTO_INSTALL_JOB_TIMEOUT, UsesShed
 
 FETCH_TOOL_ID = 'toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/data_manager_fetch_genome_all_fasta_dbkey/0.0.3'
 FETCH_GENOME_DBKEYS_ALL_FASTA_INPUT = {

test/integration/test_data_manager_refgenie.py

@@ -5,8 +5,8 @@ import string
 from nose.plugins.skip import SkipTest
 
 from galaxy_test.base.populators import DatasetPopulator
+from galaxy_test.base.uses_shed import CONDA_AUTO_INSTALL_JOB_TIMEOUT, UsesShed
 from galaxy_test.driver import integration_util
-from .uses_shed import CONDA_AUTO_INSTALL_JOB_TIMEOUT, UsesShed
 
 FETCH_TOOL_ID = 'toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/data_manager_fetch_genome_all_fasta_dbkey/0.0.3'
 FETCH_GENOME_DBKEYS_ALL_FASTA_INPUT = {

test/integration/test_repository_operations.py

@@ -2,9 +2,9 @@ import os
 from collections import namedtuple
 
 from galaxy_test.base.populators import DatasetPopulator
+from galaxy_test.base.uses_shed import UsesShed
 from galaxy_test.driver import integration_util
 from tool_shed.util import hg_util
-from .uses_shed import UsesShed
 
 REPO_TYPE = namedtuple('REPO_TYPE', 'name owner changeset')
 REPO = REPO_TYPE(

test/integration/test_shed_tool_tests.py

@@ -1,8 +1,8 @@
 import os
 
 from galaxy_test.base.populators import skip_if_toolshed_down
+from galaxy_test.base.uses_shed import UsesShed
 from galaxy_test.driver import integration_util
-from .uses_shed import UsesShed
 
 
 class ToolShedToolTestIntegrationTestCase(integration_util.IntegrationTestCase, UsesShed):

test/integration_selenium/test_workflow_repository_tool_update.py

@@ -0,0 +1,39 @@
+from galaxy_test.base.uses_shed import UsesShed
+from .framework import (
+    selenium_test,
+    SeleniumIntegrationTestCase
+)
+
+
+class WorkflowEditorToolUpgradeWithToolShedToolTestCase(SeleniumIntegrationTestCase, UsesShed):
+    requires_admin = True
+
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        cls.configure_shed(config)
+
+    @selenium_test
+    def test_tool_shed_tool_update_in_workflow_editor(self):
+        self.install_repository("iuc", "compose_text_param", "feb3acba1e0a")  # 0.1.0
+        self.install_repository("iuc", "compose_text_param", "e188c9826e0f")  # 0.1.1
+        self.login()
+        workflow_populator = self.workflow_populator
+        workflow_id = workflow_populator.upload_yaml_workflow("""class: GalaxyWorkflow
+inputs: []
+steps:
+  - tool_id: compose_text_param
+    tool_version: 0.1.0
+    label: compose_text_param
+        """, exact_tools=True)
+        self.workflow_index_open()
+        self.workflow_index_click_option("Edit")
+        editor = self.components.workflow_editor
+        editor.node._(label="compose_text_param").wait_for_and_click()
+        editor.tool_version_button.wait_for_and_click()
+        assert self.select_dropdown_item('Switch to 0.1.1'), 'Switch to tool version dropdown item not found'
+        self.screenshot("workflow_editor_version_update_tool_shed")
+        self.sleep_for(self.wait_types.UX_RENDER)
+        self.assert_workflow_has_changes_and_save()
+        workflow = self.workflow_populator.download_workflow(workflow_id)
+        assert workflow['steps']['0']['tool_version'] == '0.1.1'
+        assert workflow['steps']['0']['tool_id'] == 'toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1'