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synced 2026-09-21 13:50:20 +08:00
Move zip collection workflow test into workflow framework tests
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@@ -2741,45 +2741,6 @@ outer_input:
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details = self.dataset_populator.get_history_dataset_details(history_id)
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assert details["name"] == "moocow suffix"
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def test_placements_from_text_inputs_nested(self):
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with self.dataset_populator.test_history() as history_id:
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run_def = """
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class: GalaxyWorkflow
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inputs:
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replacemeouter: text
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steps:
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nested_workflow:
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run:
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class: GalaxyWorkflow
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inputs:
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replacemeinner: text
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outputs:
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workflow_output_1:
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outputSource: create_2/out_file1
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workflow_output_2:
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outputSource: create_2/out_file2
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steps:
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create_2:
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tool_id: create_2
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state:
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sleep_time: 0
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outputs:
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out_file1:
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rename: "${replacemeinner} name"
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out_file2:
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rename: "${replacemeinner} name 2"
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in:
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replacemeinner: replacemeouter
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test_data:
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replacemeouter:
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value: moocow
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type: raw
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"""
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self._run_jobs(run_def, history_id=history_id)
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details = self.dataset_populator.get_history_dataset_details(history_id)
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assert details["name"] == "moocow name 2", details["name"]
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@skip_without_tool("random_lines1")
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def test_run_runtime_parameters_after_pause(self):
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with self.dataset_populator.test_history() as history_id:
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@@ -2839,44 +2800,6 @@ test_data:
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run_test(NESTED_WORKFLOW_AUTO_LABELS_MODERN_SYNTAX)
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@skip_without_tool("cat1")
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@skip_without_tool("collection_paired_test")
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def test_workflow_run_zip_collections(self):
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with self.dataset_populator.test_history() as history_id:
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workflow_id = self._upload_yaml_workflow(
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"""
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class: GalaxyWorkflow
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inputs:
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test_input_1: data
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test_input_2: data
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steps:
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first_cat:
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tool_id: cat1
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in:
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input1: test_input_1
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zip_it:
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tool_id: "__ZIP_COLLECTION__"
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in:
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input_forward: first_cat/out_file1
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input_reverse: test_input_2
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concat_pair:
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tool_id: collection_paired_test
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in:
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f1: zip_it/output
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"""
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)
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hda1 = self.dataset_populator.new_dataset(history_id, content="samp1\t10.0\nsamp2\t20.0\n")
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hda2 = self.dataset_populator.new_dataset(history_id, content="samp1\t20.0\nsamp2\t40.0\n")
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self.dataset_populator.wait_for_history(history_id, assert_ok=True)
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inputs = {
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"0": self._ds_entry(hda1),
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"1": self._ds_entry(hda2),
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}
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invocation_id = self.__invoke_workflow(workflow_id, inputs=inputs, history_id=history_id)
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self.workflow_populator.wait_for_invocation_and_jobs(history_id, workflow_id, invocation_id)
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content = self.dataset_populator.get_history_dataset_content(history_id)
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assert content.strip() == "samp1\t10.0\nsamp2\t20.0\nsamp1\t20.0\nsamp2\t40.0"
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@skip_without_tool("collection_paired_test")
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def test_workflow_flatten(self):
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with self.dataset_populator.test_history() as history_id:
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@@ -0,0 +1,10 @@
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- doc: |
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Test simple use of __ZIP_COLLECTION__ in a workflow.
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job:
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test_input_1: "samp1\t10.0\nsamp2\t20.0\n"
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test_input_2: "samp1\t20.0\nsamp2\t40.0\n"
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outputs:
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out:
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asserts:
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- that: has_text
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text: "samp1\t10.0\nsamp2\t20.0\nsamp1\t20.0\nsamp2\t40.0"
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@@ -0,0 +1,21 @@
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class: GalaxyWorkflow
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inputs:
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test_input_1: data
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test_input_2: data
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outputs:
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out:
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outputSource: concat_pair/out1
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steps:
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first_cat:
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tool_id: cat
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in:
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input1: test_input_1
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zip_it:
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tool_id: "__ZIP_COLLECTION__"
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in:
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input_forward: first_cat/out_file1
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input_reverse: test_input_2
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concat_pair:
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tool_id: collection_paired_test
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in:
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f1: zip_it/output
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