diff --git a/test/api/test_workflows.py b/test/api/test_workflows.py index de5128f5739e..a89e21dc2f4a 100644 --- a/test/api/test_workflows.py +++ b/test/api/test_workflows.py @@ -33,7 +33,7 @@ NESTED_WORKFLOW_AUTO_LABELS = """ class: GalaxyWorkflow inputs: - - id: outer_input + outer_input: data outputs: outer_output: outputSource: second_cat/out_file1 @@ -1016,11 +1016,10 @@ def test_workflow_run_zip_collections(self): with self.dataset_populator.test_history() as history_id: workflow_id = self._upload_yaml_workflow(""" class: GalaxyWorkflow +inputs: + test_input_1: data + test_input_2: data steps: - - label: test_input_1 - type: input - - label: test_input_2 - type: input - label: first_cat tool_id: cat1 state: @@ -1088,8 +1087,8 @@ def test_filter_failed_mapping(self): summary = self._run_jobs(""" class: GalaxyWorkflow inputs: - - type: collection - label: input_c + input_c: collection + steps: - label: mixed_collection tool_id: exit_code_from_file @@ -1144,7 +1143,7 @@ def test_workflow_output_dataset(self): summary = self._run_jobs(""" class: GalaxyWorkflow inputs: - - id: input1 + input1: data outputs: wf_output_1: outputSource: first_cat/out_file1 @@ -1171,7 +1170,7 @@ def test_workflow_output_dataset_collection(self): summary = self._run_jobs(""" class: GalaxyWorkflow inputs: - - id: input1 + input1: type: data_collection_input collection_type: list outputs: @@ -1213,7 +1212,7 @@ def test_workflow_input_mapping(self): summary = self._run_jobs(""" class: GalaxyWorkflow inputs: - - id: input1 + input1: data outputs: wf_output_1: outputSource: first_cat/out_file1 @@ -1255,7 +1254,7 @@ def test_workflow_run_input_mapping_with_output_collections(self): summary = self._run_jobs(""" class: GalaxyWorkflow inputs: - - id: text_input + text_input: data outputs: wf_output_1: outputSource: split_up/paired_output @@ -1337,7 +1336,7 @@ def test_subworkflow_recover_mapping_1(self): self._run_jobs(""" class: GalaxyWorkflow inputs: - - id: outer_input + outer_input: data outputs: outer_output: outputSource: second_cat/out_file1 @@ -1349,7 +1348,7 @@ def test_subworkflow_recover_mapping_1(self): - run: class: GalaxyWorkflow inputs: - - id: inner_input + inner_input: data outputs: workflow_output: outputSource: random_lines/out_file1 @@ -1395,7 +1394,7 @@ def test_subworkflow_recover_mapping_2(self): self._run_jobs(""" class: GalaxyWorkflow inputs: - - id: outer_input + outer_input: data outputs: outer_output: outputSource: second_cat/out_file1 @@ -1407,7 +1406,7 @@ def test_subworkflow_recover_mapping_2(self): - run: class: GalaxyWorkflow inputs: - - id: inner_input + inner_input: data outputs: workflow_output: outputSource: inner_cat/out_file1 @@ -1452,7 +1451,7 @@ def test_recover_mapping_in_subworkflow(self): self._run_jobs(""" class: GalaxyWorkflow inputs: - - id: outer_input + outer_input: data outputs: outer_output: outputSource: second_cat/out_file1 @@ -1464,7 +1463,7 @@ def test_recover_mapping_in_subworkflow(self): - run: class: GalaxyWorkflow inputs: - - id: inner_input + inner_input: data outputs: workflow_output: outputSource: split/output @@ -1504,7 +1503,7 @@ def test_empty_list_mapping(self): self._run_jobs(""" class: GalaxyWorkflow inputs: - - id: input1 + input1: data outputs: count_list: outputSource: count_list/out_file1 @@ -1538,9 +1537,9 @@ def test_mapping_and_subcollection_mapping(self): with self.dataset_populator.test_history() as history_id: jobs_summary = self._run_jobs(""" class: GalaxyWorkflow +inputs: + text_input1: collection steps: - - label: text_input1 - type: input_collection - tool_id: collection_type_source_map_over in: input_collect: text_input1 @@ -1560,7 +1559,7 @@ def test_empty_list_reduction(self): self._run_jobs(""" class: GalaxyWorkflow inputs: - - id: input1 + input1: data outputs: count_multi_file: outputSource: count_multi_file/out_file1 @@ -1735,8 +1734,8 @@ def test_pause_outputs_with_deleted_inputs(self): workflow_id = self._upload_yaml_workflow(""" class: GalaxyWorkflow inputs: - - id: input1 - type: data_collection_input + input1: + type: collection collection_type: list steps: - tool_id: cat @@ -1775,9 +1774,9 @@ def test_run_with_implicit_connection(self): with self.dataset_populator.test_history() as history_id: run_summary = self._run_jobs(""" class: GalaxyWorkflow +inputs: + test_input: data steps: -- label: test_input - type: input - label: first_cat tool_id: cat1 in: @@ -1823,8 +1822,7 @@ def test_run_with_validated_parameter_connection_valid(self): run_summary = self._run_jobs(""" class: GalaxyWorkflow inputs: - - label: text_input - type: text + text_input: text steps: - tool_id: validation_repeat state: @@ -1846,8 +1844,7 @@ def test_run_with_validated_parameter_connection_invalid(self): self._run_jobs(""" class: GalaxyWorkflow inputs: - - label: text_input - type: text + text_input: text steps: - tool_id: validation_repeat state: @@ -1865,10 +1862,8 @@ def test_run_with_text_connection(self): self._run_jobs(""" class: GalaxyWorkflow inputs: - - label: data_input - type: data - - label: text_input - type: text + data_input: data + text_input: text steps: - label: randomlines tool_id: random_lines1 @@ -2071,8 +2066,8 @@ def test_run_rename_on_mapped_over_collection(self): self._run_jobs(""" class: GalaxyWorkflow inputs: - - id: input1 - type: data_collection_input + input1: + type: collection collection_type: list steps: - tool_id: cat @@ -2106,8 +2101,8 @@ def test_run_rename_based_on_inputs_on_mapped_over_collection(self): self._run_jobs(""" class: GalaxyWorkflow inputs: - - id: input1 - type: data_collection_input + input1: + type: collection collection_type: list steps: - tool_id: cat @@ -2137,7 +2132,7 @@ def test_run_rename_collection_output(self): self._run_jobs(""" class: GalaxyWorkflow inputs: - - id: input1 + input1: data steps: - tool_id: collection_creates_pair in: @@ -2193,7 +2188,7 @@ def test_run_rename_when_resuming_jobs(self): self._run_jobs(""" class: GalaxyWorkflow inputs: - - id: input1 + input1: data steps: - tool_id: fail_identifier label: first_fail @@ -2240,7 +2235,7 @@ def test_run_rename_based_on_input_recursive(self): self._run_jobs(""" class: GalaxyWorkflow inputs: - - id: input1 + input1: data steps: - tool_id: cat label: first_cat @@ -2265,8 +2260,8 @@ def test_run_rename_based_on_input_repeat(self): self._run_jobs(""" class: GalaxyWorkflow inputs: - - id: input1 - - id: input2 + input1: data + input2: data steps: - tool_id: cat label: first_cat @@ -2299,8 +2294,8 @@ def test_run_rename_based_on_input_conditional(self): self._run_jobs(""" class: GalaxyWorkflow inputs: - - id: fasta_input - - id: fastq_input + fasta_input: data + fastq_input: data steps: - tool_id: mapper2 state: @@ -2337,8 +2332,8 @@ def test_run_rename_based_on_input_collection(self): self._run_jobs(""" class: GalaxyWorkflow inputs: - - id: fasta_input - - id: fastq_inputs + fasta_input: data + fastq_inputs: data steps: - tool_id: mapper2 state: @@ -2380,7 +2375,7 @@ def test_run_hide_on_collection_output(self): self._run_jobs(""" class: GalaxyWorkflow inputs: - - id: input1 + input1: data steps: - tool_id: collection_creates_pair state: @@ -2412,9 +2407,8 @@ def test_run_hide_on_mapped_over_collection(self): steps: - tool_id: cat label: first_cat - state: - input1: - $link: input1 + in: + input1: input1 outputs: out_file1: hide: true @@ -2442,7 +2436,7 @@ def test_tag_auto_propagation(self): self._run_jobs(""" class: GalaxyWorkflow inputs: - - id: input1 + input1: data steps: - label: first_cat tool_id: cat @@ -2485,7 +2479,7 @@ def test_run_add_tag_on_collection_output(self): self._run_jobs(""" class: GalaxyWorkflow inputs: - - id: input1 + input1: data steps: - tool_id: collection_creates_pair in: @@ -2511,8 +2505,8 @@ def test_run_add_tag_on_mapped_over_collection(self): self._run_jobs(""" class: GalaxyWorkflow inputs: - - id: input1 - type: data_collection_input + input1: + type: collection collection_type: list steps: - tool_id: cat @@ -2544,7 +2538,7 @@ def test_run_remove_tag_on_collection_output(self): self._run_jobs(""" class: GalaxyWorkflow inputs: - - id: input1 + input1: data steps: - tool_id: cat label: first_cat @@ -2614,7 +2608,7 @@ def test_run_with_delayed_runtime_pja(self): workflow_id = self._upload_yaml_workflow(""" class: GalaxyWorkflow inputs: - - id: test_input + test_input: data steps: - label: first_cat tool_id: cat1 @@ -2667,7 +2661,7 @@ def test_delete_intermediate_datasets_pja_1(self): self._run_jobs(""" class: GalaxyWorkflow inputs: - - id: input1 + input1: data outputs: wf_output_1: outputSource: third_cat/out_file1 @@ -2969,8 +2963,7 @@ def _run_mapping_workflow(self): summary = self._run_jobs(""" class: GalaxyWorkflow inputs: - - type: collection - label: input_c + input_c: collection steps: - label: cat1 tool_id: cat1 diff --git a/test/api/test_workflows_from_yaml.py b/test/api/test_workflows_from_yaml.py index 121c60b6239c..76b9d56eac85 100644 --- a/test/api/test_workflows_from_yaml.py +++ b/test/api/test_workflows_from_yaml.py @@ -114,7 +114,7 @@ def test_subworkflow_simple(self): workflow_id = self._upload_yaml_workflow(""" class: GalaxyWorkflow inputs: - - id: outer_input + outer_input: data steps: - tool_id: cat1 label: first_cat @@ -123,7 +123,7 @@ def test_subworkflow_simple(self): - run: class: GalaxyWorkflow inputs: - - id: inner_input + inner_input: data steps: - tool_id: random_lines1 state: diff --git a/test/base/workflow_fixtures.py b/test/base/workflow_fixtures.py index 23aa3c343382..34bdaedb16d9 100644 --- a/test/base/workflow_fixtures.py +++ b/test/base/workflow_fixtures.py @@ -26,7 +26,7 @@ WORKFLOW_SIMPLE_CAT_TWICE = """ class: GalaxyWorkflow inputs: - - id: input1 + input1: data steps: - tool_id: cat label: first_cat @@ -39,7 +39,7 @@ WORKFLOW_WITH_OLD_TOOL_VERSION = """ class: GalaxyWorkflow inputs: - - id: input1 + input1: data steps: - tool_id: multiple_versions tool_version: "0.0.1" @@ -51,7 +51,7 @@ WORKFLOW_WITH_INVALID_STATE = """ class: GalaxyWorkflow inputs: - - id: input1 + input1: data steps: - tool_id: multiple_versions tool_version: "0.0.1" @@ -62,9 +62,9 @@ WORKFLOW_WITH_OUTPUT_COLLECTION = """ class: GalaxyWorkflow +inputs: + text_input: data steps: - - label: text_input - type: input - label: split_up tool_id: collection_creates_pair in: @@ -150,8 +150,7 @@ WORKFLOW_WITH_RULES_1 = """ class: GalaxyWorkflow inputs: - - type: collection - label: input_c + input_c: collection steps: - label: apply tool_id: __APPLY_RULES__ @@ -190,8 +189,7 @@ WORKFLOW_WITH_RULES_2 = """ class: GalaxyWorkflow inputs: - - type: collection - label: input_c + input_c: collection steps: - label: apply tool_id: __APPLY_RULES__ @@ -225,7 +223,7 @@ WORKFLOW_NESTED_SIMPLE = """ class: GalaxyWorkflow inputs: - - id: outer_input + outer_input: data outputs: outer_output: outputSource: second_cat/out_file1 @@ -237,7 +235,7 @@ - run: class: GalaxyWorkflow inputs: - - id: inner_input + inner_input: data outputs: workflow_output: outputSource: random_lines/out_file1 @@ -268,7 +266,7 @@ WORKFLOW_NESTED_RUNTIME_PARAMETER = """ class: GalaxyWorkflow inputs: - - id: outer_input + outer_input: data outputs: outer_output: outputSource: nested_workflow/workflow_output @@ -276,7 +274,7 @@ - run: class: GalaxyWorkflow inputs: - - id: inner_input + inner_input: data outputs: workflow_output: outputSource: random_lines#out_file1 @@ -300,7 +298,7 @@ WORKFLOW_WITH_OUTPUT_ACTIONS = """ class: GalaxyWorkflow inputs: - - id: input1 + input1: data steps: - tool_id: cat1 label: first_cat @@ -319,7 +317,7 @@ WORKFLOW_RUNTIME_PARAMETER_SIMPLE = """ class: GalaxyWorkflow inputs: - - id: input1 + input1: data steps: - tool_id: random_lines1 runtime_inputs: @@ -336,7 +334,7 @@ WORKFLOW_RUNTIME_PARAMETER_AFTER_PAUSE = """ class: GalaxyWorkflow inputs: - - id: input1 + input1: data steps: - label: the_pause type: pause @@ -356,7 +354,7 @@ WORKFLOW_RENAME_ON_INPUT = """ class: GalaxyWorkflow inputs: - - id: input1 + input1: data steps: - tool_id: cat label: first_cat @@ -376,7 +374,7 @@ WORKFLOW_RENAME_ON_REPLACEMENT_PARAM = """ class: GalaxyWorkflow inputs: - - id: input1 + input1: data steps: - tool_id: cat label: first_cat @@ -391,7 +389,7 @@ WORKFLOW_NESTED_REPLACEMENT_PARAMETER = """ class: GalaxyWorkflow inputs: - - id: outer_input + outer_input: data outputs: outer_output: outputSource: nested_workflow/workflow_output @@ -399,7 +397,7 @@ - run: class: GalaxyWorkflow inputs: - - id: inner_input + inner_input: data outputs: workflow_output: outputSource: first_cat/out_file1 @@ -419,7 +417,7 @@ WORKFLOW_WITH_OUTPUTS = """ class: GalaxyWorkflow inputs: - - id: input1 + input1: data outputs: wf_output_1: outputSource: first_cat/out_file1