Merge pull request #13196 from mvdbeek/fix_tool_id_update

[21.09] Fix tool id update when updating tool shed tools in editor

client/src/components/Workflow/Editor/Forms/FormTool.vue

@@ -171,9 +171,16 @@ export default {
         },
         postChanges(newVersion) {
             const options = this.node.config_form;
+            let toolId = options.id;
+            let toolVersion = options.version;
+            if (newVersion) {
+                toolId = toolId.replace(toolVersion, newVersion);
+                toolVersion = newVersion;
+                console.debug("FormTool - Tool version changed.", toolId, toolVersion);
+            }
             this.$emit("onSetData", this.node.id, {
-                tool_id: options.id,
-                tool_version: newVersion || options.version,
+                tool_id: toolId,
+                tool_version: toolVersion,
                 type: "tool",
                 inputs: Object.assign({}, this.mainValues, this.sectionValues),
             });

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

@@ -314,6 +314,7 @@ export default {
         },
         setData(data) {
             this.config_form = data.config_form;
+            this.content_id = data.content_id;
             this.tool_state = data.tool_state;
             this.errors = data.errors;
             this.tooltip = data.tooltip || "";
@@ -326,7 +327,6 @@ 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

@@ -699,6 +699,7 @@ 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/selenium/framework.py

@@ -384,6 +384,14 @@ 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'] == ""
@@ -192,7 +192,7 @@ steps:
         assert textarea_column_names.get_attribute('value') == 'a\nb\nc\n'
         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()
@@ -300,7 +300,7 @@ 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")
 
@@ -422,7 +422,7 @@ 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'
 
@@ -435,7 +435,7 @@ 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):
@@ -462,7 +462,7 @@ 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):
@@ -483,9 +483,9 @@ 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')
@@ -499,7 +499,7 @@ steps:
         editor.label_input.wait_for_and_send_keys('cloned label')
         output_label = editor.label_output(output='out_file1')
         self.set_text_element(output_label, 'cloned output label')
-        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'))
@@ -531,7 +531,7 @@ 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
@@ -702,14 +702,6 @@ 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'