From a7d122afd9a12612d5b57fe64a6f11851cf84af0 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Tue, 5 May 2026 20:44:35 +0100 Subject: [PATCH] Update test workflows to respect gxformat2 0.26.0 syntax --- .../api/test_workflow_extraction.py | 19 +++-- lib/galaxy_test/api/test_workflows.py | 81 ++++++++----------- .../api/test_workflows_from_yaml.py | 4 +- lib/galaxy_test/base/workflow_fixtures.py | 15 ++-- .../selenium/test_workflow_extraction.py | 4 +- .../test_workflow_handler_configuration.py | 4 +- .../test_workflow_scheduling_options.py | 19 +---- 7 files changed, 59 insertions(+), 87 deletions(-) diff --git a/lib/galaxy_test/api/test_workflow_extraction.py b/lib/galaxy_test/api/test_workflow_extraction.py index 483534613f7..87769646f30 100644 --- a/lib/galaxy_test/api/test_workflow_extraction.py +++ b/lib/galaxy_test/api/test_workflow_extraction.py @@ -191,9 +191,9 @@ class TestWorkflowExtractionApi(BaseWorkflowsApiTestCase, WorkflowStructureAsser jobs_summary = self._run_workflow( """ class: GalaxyWorkflow +inputs: + text_input1: collection steps: - - label: text_input1 - type: input_collection - tool_id: collection_paired_test state: f1: @@ -269,9 +269,9 @@ test_data: jobs_summary = self._run_workflow( """ class: GalaxyWorkflow +inputs: + text_input1: collection steps: - - label: text_input1 - type: input_collection - label: noop tool_id: cat1 state: @@ -340,11 +340,10 @@ steps: jobs_summary = self._run_workflow( """ class: GalaxyWorkflow +inputs: + text_input1: data + text_input2: data steps: - - label: text_input1 - type: input - - label: text_input2 - type: input - label: cat_inputs tool_id: cat1 state: @@ -391,9 +390,9 @@ test_data: jobs_summary = self._run_workflow( """ class: GalaxyWorkflow +inputs: + text_input1: collection steps: - - label: text_input1 - type: input_collection - label: cat_inputs tool_id: cat1 state: diff --git a/lib/galaxy_test/api/test_workflows.py b/lib/galaxy_test/api/test_workflows.py index 1398d98e4ff..4f8469aced6 100644 --- a/lib/galaxy_test/api/test_workflows.py +++ b/lib/galaxy_test/api/test_workflows.py @@ -283,7 +283,7 @@ steps: tool_id: cat in: input1: input1 - outputs: + out: out_file1: change_datatype: bed set_columns: @@ -1024,7 +1024,7 @@ steps: subworkflow: in: dataset: dataset - outputs: + out: output: outputSource: cat1/out_file1 run: @@ -3016,7 +3016,7 @@ steps: steps: empty_output: tool_id: empty_output - outputs: + out: out_file1: change_datatype: tabular column_param: @@ -3039,7 +3039,7 @@ steps: steps: empty_output: tool_id: empty_output - outputs: + out: out_file1: change_datatype: tabular column_param_list: @@ -3064,7 +3064,7 @@ steps: steps: empty_output: tool_id: empty_output - outputs: + out: out_file1: change_datatype: tabular column_param_list: @@ -3783,7 +3783,7 @@ steps: in: some_collection: some_collection should_run: should_run - outputs: + out: inner_out: a_tool_step/out_file1 when: $(inputs.should_run) outputs: @@ -3843,7 +3843,7 @@ steps: in: some_file: some_file should_run: should_run - outputs: + out: inner_out: a_tool_step/out_file1 when: $(inputs.should_run) outputs: @@ -5818,7 +5818,7 @@ steps: tool_id: random_lines1 in: input: text_input1 - outputs: + out: out_file1: change_datatype: csv """, @@ -5848,7 +5848,7 @@ steps: tool_id: collection_split_on_column in: input1: input - outputs: + out: split_output: change_datatype: csv outputs: @@ -6166,11 +6166,6 @@ steps: tool_id: create_2 state: sleep_time: 0 - outputs: - out_file1: - rename: "my new name" - out_file2: - rename: "my other new name" first_cat1: tool_id: cat in: @@ -6198,11 +6193,6 @@ steps: tool_id: create_2 state: sleep_time: 0 - outputs: - out_file1: - rename: "my new name" - out_file2: - rename: "my other new name" outputs: main_out: outputSource: create_2/does_not_exist @@ -7574,7 +7564,7 @@ steps: cat1: in: input1: apply/output - outputs: + out: out_file1: rename: "#{inner_text_input} suffix" """, @@ -7639,7 +7629,7 @@ steps: tool_id: cat1 in: input1: input1 - outputs: + out: out_file1: hide: true """, @@ -7985,7 +7975,7 @@ steps: tool_id: cat in: input1: input1 - outputs: + out: out_file1: rename: "my new name" """, @@ -8026,7 +8016,7 @@ steps: tool_id: cat in: input1: input1 - outputs: + out: out_file1: rename: "#{input1} suffix" """, @@ -8060,7 +8050,7 @@ steps: - tool_id: collection_creates_pair in: input1: input1 - outputs: + out: paired_output: rename: "my new name" """, @@ -8095,7 +8085,7 @@ steps: datasets: - id_cond: id_select: id - outputs: + out: output: hide: true """, @@ -8130,7 +8120,7 @@ steps: datasets: - id_cond: id_select: id - outputs: + out: output: delete_intermediate_datasets: true """, @@ -8168,7 +8158,7 @@ steps: datasets: - id_cond: id_select: idx - outputs: + out: output: change_datatype: txt - tool_id: __BUILD_LIST__ @@ -8218,7 +8208,7 @@ steps: tool_id: __EXTRACT_DATASET__ in: input: build_list/output - outputs: + out: output: change_datatype: vcf_bgzip """, @@ -8249,7 +8239,7 @@ steps: datasets: - id_cond: id_select: idx - outputs: + out: output: rename: "my new name" """, @@ -8280,7 +8270,7 @@ steps: tool_id: create_2 state: sleep_time: 0 - outputs: + out: out_file1: rename: "my new name" out_file2: @@ -8319,14 +8309,11 @@ steps: failbool: true input1: $link: input1 - outputs: - out_file1: - rename: "cat1 out" cat: tool_id: cat in: input1: first_fail/out_file1 - outputs: + out: out_file1: rename: "#{input1} suffix" """, @@ -8374,7 +8361,7 @@ steps: tool_id: cat in: input1: input1 - outputs: + out: out_file1: rename: "#{input1} #{input1 | upper} suffix" """, @@ -8408,7 +8395,7 @@ steps: queries: - input2: $link: input2 - outputs: + out: out_file1: rename: "#{queries_0.input2| basename} suffix" """, @@ -8447,7 +8434,7 @@ steps: $link: fastq_input reference: $link: fasta_input - outputs: + out: out_file1: rename: "#{fastq_input.fastq_input1 | basename} suffix" """, @@ -8488,7 +8475,7 @@ steps: $link: fastq_input reference: $link: fasta_input - outputs: + out: out_file1: # The fully prefixed variant test in "test_run_rename_based_on_input_conditional" should be preferred, # but we don't want to break old workflow renaming actions @@ -8526,7 +8513,7 @@ steps: state: input1: $link: input1 - outputs: + out: paired_output: hide: true """, @@ -8560,7 +8547,7 @@ steps: tool_id: cat in: input1: input1 - outputs: + out: out_file1: hide: true """, @@ -8599,7 +8586,7 @@ steps: tool_id: cat in: input1: input1 - outputs: + out: out_file1: add_tags: - "name:treated1fb" @@ -8647,7 +8634,7 @@ steps: tool_id: collection_creates_pair in: input1: input1 - outputs: + out: paired_output: add_tags: - "name:foo" @@ -8683,7 +8670,7 @@ steps: tool_id: cat in: input1: input1 - outputs: + out: out_file1: add_tags: - "name:foo" @@ -8721,7 +8708,7 @@ steps: tool_id: cat in: input1: input1 - outputs: + out: out_file1: add_tags: - "name:foo" @@ -8729,7 +8716,7 @@ steps: tool_id: collection_creates_pair in: input1: first_cat/out_file1 - outputs: + out: paired_output: remove_tags: - "name:foo" @@ -8772,7 +8759,7 @@ steps: tool_id: __EXTRACT_DATASET__ in: input: input1 - outputs: + out: output: add_tags: - "name:foo" @@ -8903,7 +8890,7 @@ steps: tool_id: cat1 in: input1: second_cat/out_file1 - outputs: + out: out_file1: delete_intermediate_datasets: true """, diff --git a/lib/galaxy_test/api/test_workflows_from_yaml.py b/lib/galaxy_test/api/test_workflows_from_yaml.py index 28ddb33f455..6f9e5d24f95 100644 --- a/lib/galaxy_test/api/test_workflows_from_yaml.py +++ b/lib/galaxy_test/api/test_workflows_from_yaml.py @@ -210,9 +210,9 @@ $graph: def test_pause(self): workflow_id = self._upload_yaml_workflow(""" class: GalaxyWorkflow +inputs: + test_input: data steps: - test_input: - type: input first_cat: tool_id: cat1 state: diff --git a/lib/galaxy_test/base/workflow_fixtures.py b/lib/galaxy_test/base/workflow_fixtures.py index 9a86ad6be98..7cda45dfe28 100644 --- a/lib/galaxy_test/base/workflow_fixtures.py +++ b/lib/galaxy_test/base/workflow_fixtures.py @@ -239,12 +239,13 @@ steps: WORKFLOW_WITH_OUTPUT_COLLECTION_MAPPING = """ class: GalaxyWorkflow +inputs: + input_collection: collection steps: - - type: input_collection - tool_id: collection_creates_pair state: input1: - $link: 0 + $link: "0" - tool_id: collection_paired_test state: f1: @@ -547,7 +548,7 @@ inputs: steps: first_cat: tool_id: cat1 - outputs: + out: out_file1: hide: true rename: "the new value" @@ -733,7 +734,7 @@ steps: input: required state: lineNum: - $link: expression/out1 + $link: expression/out1 count_multi_file: tool_id: count_multi_file in: @@ -798,7 +799,7 @@ steps: state: input1: $link: input1 - outputs: + out: out_file1: rename: "#{input1 | basename} suffix" test_data: @@ -817,7 +818,7 @@ steps: tool_id: cat in: input1: input1 - outputs: + out: out_file1: rename: "${replaceme} suffix" """ @@ -843,7 +844,7 @@ steps: label: first_cat in: input1: inner_input - outputs: + out: out_file1: rename: "${replaceme} suffix" in: diff --git a/lib/galaxy_test/selenium/test_workflow_extraction.py b/lib/galaxy_test/selenium/test_workflow_extraction.py index eb4222c6b9f..60ac3fffc2f 100644 --- a/lib/galaxy_test/selenium/test_workflow_extraction.py +++ b/lib/galaxy_test/selenium/test_workflow_extraction.py @@ -130,9 +130,9 @@ class TestWorkflowExtractionSelenium(SeleniumTestCase, WorkflowStructureAssertio self.workflow_populator.run_workflow( """ class: GalaxyWorkflow +inputs: + text_input1: collection steps: - - label: text_input1 - type: input_collection - label: noop tool_id: cat1 state: diff --git a/test/integration/test_workflow_handler_configuration.py b/test/integration/test_workflow_handler_configuration.py index 11e3db488d7..80ea28cffc5 100644 --- a/test/integration/test_workflow_handler_configuration.py +++ b/test/integration/test_workflow_handler_configuration.py @@ -70,9 +70,9 @@ WORKFLOW_SCHEDULER_HANDLER_PATTERN = re.compile(r"work\d") PAUSE_WORKFLOW = """ class: GalaxyWorkflow +inputs: + test_input: data steps: -- label: test_input - type: input - label: the_pause type: pause connect: diff --git a/test/integration/test_workflow_scheduling_options.py b/test/integration/test_workflow_scheduling_options.py index b769dba1dcf..97e6e41660b 100644 --- a/test/integration/test_workflow_scheduling_options.py +++ b/test/integration/test_workflow_scheduling_options.py @@ -8,6 +8,7 @@ from galaxy_test.base.populators import ( DatasetPopulator, WorkflowPopulator, ) +from galaxy_test.base.workflow_fixtures import WORKFLOW_WITH_OUTPUT_COLLECTION_MAPPING from galaxy_test.driver import integration_util @@ -62,23 +63,7 @@ class TestMaximumWorkflowJobsPerSchedulingIteration(integration_util.Integration config["maximum_workflow_jobs_per_scheduling_iteration"] = 1 def test_collection_explicit_and_implicit(self): - workflow_id = self.workflow_populator.upload_yaml_workflow(""" -class: GalaxyWorkflow -steps: - - type: input_collection - - tool_id: collection_creates_pair - state: - input1: - $link: 0 - - tool_id: collection_paired_test - state: - f1: - $link: 1/paired_output - - tool_id: cat_list - state: - input1: - $link: 2/out1 -""") + workflow_id = self.workflow_populator.upload_yaml_workflow(WORKFLOW_WITH_OUTPUT_COLLECTION_MAPPING) with self.dataset_populator.test_history() as history_id: fetch_response = self.dataset_collection_populator.create_list_in_history( history_id, contents=["a\nb\nc\nd\n", "e\nf\ng\nh\n"]