mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
285 lines
7.9 KiB
Python
285 lines
7.9 KiB
Python
from __future__ import print_function
|
|
|
|
import os
|
|
|
|
from .test_workflows import BaseWorkflowsApiTestCase
|
|
|
|
WORKFLOWS_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
|
|
|
|
|
|
class WorkflowsFromYamlApiTestCase( BaseWorkflowsApiTestCase ):
|
|
|
|
def setUp( self ):
|
|
super( WorkflowsFromYamlApiTestCase, self ).setUp()
|
|
|
|
def test_simple_upload(self):
|
|
workflow_id = self._upload_yaml_workflow("""
|
|
class: GalaxyWorkflow
|
|
steps:
|
|
- type: input
|
|
label: the_input
|
|
- tool_id: cat1
|
|
state:
|
|
input1:
|
|
$link: 0
|
|
- tool_id: cat1
|
|
state:
|
|
input1:
|
|
$link: 1#out_file1
|
|
- tool_id: random_lines1
|
|
label: random_line_label
|
|
state:
|
|
num_lines: 10
|
|
input:
|
|
$link: 2#out_file1
|
|
seed_source:
|
|
seed_source_selector: set_seed
|
|
seed: asdf
|
|
""")
|
|
workflow = self._get("workflows/%s/download" % workflow_id).json()
|
|
|
|
tool_count = {'random_lines1': 0, 'cat1': 0}
|
|
input_found = False
|
|
for step in workflow['steps'].values():
|
|
step_type = step['type']
|
|
if step_type == "data_input":
|
|
assert step['label'] == 'the_input'
|
|
input_found = True
|
|
else:
|
|
tool_id = step['tool_id']
|
|
tool_count[tool_id] += 1
|
|
if tool_id == "random_lines1":
|
|
assert step['label'] == "random_line_label"
|
|
|
|
assert input_found
|
|
assert tool_count['random_lines1'] == 1
|
|
assert tool_count['cat1'] == 2
|
|
|
|
# FIXME: This test fails on some machines due to (we're guessing) yaml.safe_loading
|
|
# order being not guaranteed and inconsistent across platforms. The workflow
|
|
# yaml.safe_loader probably needs to enforce order using something like the
|
|
# approach described here:
|
|
# https://stackoverflow.com/questions/13297744/pyyaml-control-ordering-of-items-called-by-yaml.safe_load
|
|
# def test_multiple_input( self ):
|
|
# history_id = self.dataset_populator.new_history()
|
|
# self._run_jobs("""
|
|
# steps:
|
|
# - type: input
|
|
# label: input1
|
|
# - type: input
|
|
# label: input2
|
|
# - tool_id: cat_list
|
|
# state:
|
|
# input1:
|
|
# - $link: input1
|
|
# - $link: input2
|
|
# test_data:
|
|
# input1: "hello world"
|
|
# input2: "123"
|
|
# """, history_id=history_id)
|
|
# contents1 = self.dataset_populator.get_history_dataset_content(history_id)
|
|
# assert contents1 == "hello world\n123\n"
|
|
|
|
def test_simple_output_actions( self ):
|
|
history_id = self.dataset_populator.new_history()
|
|
self._run_jobs("""
|
|
class: GalaxyWorkflow
|
|
steps:
|
|
- type: input
|
|
label: input1
|
|
- tool_id: cat1
|
|
label: first_cat
|
|
state:
|
|
input1:
|
|
$link: 0
|
|
outputs:
|
|
out_file1:
|
|
hide: true
|
|
rename: "the new value"
|
|
- tool_id: cat1
|
|
state:
|
|
input1:
|
|
$link: first_cat#out_file1
|
|
test_data:
|
|
input1: "hello world"
|
|
""", history_id=history_id)
|
|
|
|
details1 = self.dataset_populator.get_history_dataset_details(history_id, hid=2)
|
|
assert not details1["visible"]
|
|
assert details1["name"] == "the new value", details1
|
|
details2 = self.dataset_populator.get_history_dataset_details(history_id, hid=3)
|
|
assert details2["visible"]
|
|
|
|
def test_inputs_to_steps( self ):
|
|
history_id = self.dataset_populator.new_history()
|
|
self._run_jobs("""
|
|
class: GalaxyWorkflow
|
|
inputs:
|
|
- id: input1
|
|
steps:
|
|
- tool_id: cat1
|
|
label: first_cat
|
|
state:
|
|
input1:
|
|
$link: input1
|
|
queries:
|
|
- input2:
|
|
$link: input1
|
|
|
|
test_data:
|
|
input1: "hello world"
|
|
""", history_id=history_id)
|
|
contents1 = self.dataset_populator.get_history_dataset_content(history_id)
|
|
self.assertEquals(contents1.strip(), "hello world\nhello world")
|
|
|
|
def test_outputs( self ):
|
|
workflow_id = self._upload_yaml_workflow("""
|
|
class: GalaxyWorkflow
|
|
inputs:
|
|
- id: input1
|
|
outputs:
|
|
- id: wf_output_1
|
|
source: first_cat#out_file1
|
|
steps:
|
|
- tool_id: cat1
|
|
label: first_cat
|
|
state:
|
|
input1:
|
|
$link: input1
|
|
queries:
|
|
- input2:
|
|
$link: input1
|
|
|
|
test_data:
|
|
input1: "hello world"
|
|
""")
|
|
workflow = self._get("workflows/%s/download" % workflow_id).json()
|
|
self.assertEquals(workflow["steps"]["1"]["workflow_outputs"][0]["output_name"], "out_file1")
|
|
self.assertEquals(workflow["steps"]["1"]["workflow_outputs"][0]["label"], "wf_output_1")
|
|
|
|
def test_subworkflow_simple( self ):
|
|
workflow_id = self._upload_yaml_workflow("""
|
|
class: GalaxyWorkflow
|
|
inputs:
|
|
- id: outer_input
|
|
steps:
|
|
- tool_id: cat1
|
|
label: first_cat
|
|
state:
|
|
input1:
|
|
$link: outer_input
|
|
- run:
|
|
class: GalaxyWorkflow
|
|
inputs:
|
|
- id: inner_input
|
|
steps:
|
|
- tool_id: random_lines1
|
|
state:
|
|
num_lines: 1
|
|
input:
|
|
$link: inner_input
|
|
seed_source:
|
|
seed_source_selector: set_seed
|
|
seed: asdf
|
|
label: nested_workflow
|
|
connect:
|
|
inner_input: first_cat#out_file1
|
|
|
|
test_data:
|
|
outer_input:
|
|
value: 1.bed
|
|
type: File
|
|
""")
|
|
workflow = self._get("workflows/%s/download" % workflow_id).json()
|
|
by_label = self._steps_by_label(workflow)
|
|
if "nested_workflow" not in by_label:
|
|
template = "Workflow [%s] does not contain label 'nested_workflow'."
|
|
message = template % workflow
|
|
raise AssertionError(message)
|
|
|
|
subworkflow_step = by_label["nested_workflow"]
|
|
assert subworkflow_step["type"] == "subworkflow"
|
|
assert len(subworkflow_step["subworkflow"]["steps"]) == 2
|
|
|
|
subworkflow_connections = subworkflow_step["input_connections"]
|
|
assert len(subworkflow_connections) == 1
|
|
subworkflow_connection = subworkflow_connections["inner_input"]
|
|
assert subworkflow_connection["input_subworkflow_step_id"] == 0
|
|
|
|
workflow_reupload_id = self.import_workflow(workflow)["id"]
|
|
workflow_reupload = self._get("workflows/%s/download" % workflow_reupload_id).json()
|
|
by_label = self._steps_by_label(workflow_reupload)
|
|
subworkflow_step = by_label["nested_workflow"]
|
|
assert subworkflow_step["type"] == "subworkflow"
|
|
assert len(subworkflow_step["subworkflow"]["steps"]) == 2
|
|
|
|
subworkflow_connections = subworkflow_step["input_connections"]
|
|
assert len(subworkflow_connections) == 1
|
|
subworkflow_connection = subworkflow_connections["inner_input"]
|
|
assert subworkflow_connection["input_subworkflow_step_id"] == 0
|
|
|
|
# content = self.dataset_populator.get_history_dataset_content( history_id )
|
|
# self.assertEquals("chr5\t131424298\t131424460\tCCDS4149.1_cds_0_0_chr5_131424299_f\t0\t+\n", content)
|
|
|
|
def test_pause( self ):
|
|
workflow_id = self._upload_yaml_workflow("""
|
|
class: GalaxyWorkflow
|
|
steps:
|
|
- label: test_input
|
|
type: input
|
|
- label: first_cat
|
|
tool_id: cat1
|
|
state:
|
|
input1:
|
|
$link: test_input
|
|
- label: the_pause
|
|
type: pause
|
|
connect:
|
|
input:
|
|
- first_cat#out_file1
|
|
- label: second_cat
|
|
tool_id: cat1
|
|
state:
|
|
input1:
|
|
$link: the_pause
|
|
""")
|
|
print(self._get("workflows/%s/download" % workflow_id).json())
|
|
|
|
def test_implicit_connections( self ):
|
|
workflow_id = self._upload_yaml_workflow("""
|
|
class: GalaxyWorkflow
|
|
steps:
|
|
- label: test_input
|
|
type: input
|
|
- label: first_cat
|
|
tool_id: cat1
|
|
state:
|
|
input1:
|
|
$link: test_input
|
|
- label: the_pause
|
|
type: pause
|
|
connect:
|
|
input:
|
|
- first_cat#out_file1
|
|
- label: second_cat
|
|
tool_id: cat1
|
|
state:
|
|
input1:
|
|
$link: the_pause
|
|
- label: third_cat
|
|
tool_id: cat1
|
|
connect:
|
|
$step: second_cat
|
|
state:
|
|
input1:
|
|
$link: test_input
|
|
""")
|
|
workflow = self._get("workflows/%s/download" % workflow_id).json()
|
|
print(workflow)
|
|
|
|
def _steps_by_label(self, workflow_as_dict):
|
|
by_label = {}
|
|
for step in workflow_as_dict["steps"].values():
|
|
by_label[step['label']] = step
|
|
return by_label
|