Define a single test¶

See the folder example:

In [1]:

EXAMPLES_FOLDER = "../examples"

… where you can find the following files:

In [2]:

import os, pprint
[f for f in os.listdir(EXAMPLES_FOLDER) if not f.startswith('.')]

Out[2]:

['change_case',
 'fluxomics_stationary',
 'multivariate',
 'sacurine',
 'workflow-test-suite-full.yml',
 'workflow-test-suite-min.yml',
 'workflow-test-suite.yml',
 'workflows.json']

Consider the definition file workflow-test-suite-min.yml (steps[3-4]), which contains the two workflow tests named change_case and multivariate respectively:

In [3]:

suite_conf_filename = os.path.join(EXAMPLES_FOLDER, "workflow-test-suite-min.yml")

In [4]:

import json, yaml
with open(suite_conf_filename, "r") as fp:
    data = yaml.load(fp)
    print(json.dumps(data, indent=4))

{
    "enable_logger": false,
    "workflows": {
        "change_case": {
            "expected": {
                "OutputText": "change_case/expected_output"
            },
            "inputs": {
                "InputText": "change_case/input"
            },
            "file": "change_case/workflow.ga"
        },
        "multivariate": {
            "expected": {
                "variableMetadata_out": "multivariate/variableMetadata_out",
                "sampleMetadata_out": "multivariate/sampleMetadata_out"
            },
            "inputs": {
                "DataMatrix": "multivariate/dataMatrix.tsv",
                "SampleMetadata": "multivariate/sampleMetadata.tsv",
                "VariableMetadata": "multivariate/variableMetadata.tsv"
            },
            "params": {
                "3": {
                    "predI": "1",
                    "respC": "gender",
                    "orthoI": "NA",
                    "testL": "FALSE"
                }
            },
            "file": "multivariate/workflow.ga"
        }
    }
}

… and focus on the first example change_case:

wf-changecase-workflow

Figure 1. Workflow “ChangeCase”

As Fig. 1 shows, the workflow has one input and one output. To test it, both the input and the output must be uniquely identified. Typically, Galaxy identifies them using Names and Labels, respectively. For our sample workflow, the identifiers are:

Name “InputText” for the input (Fig. 2);
Label “OutputText” for the output (Fig. 3).

wf-changecase-inputdataset

Figure 2. Workflow input: “Input Dataset”

wf-changecase-outputdataset

Figure 3. Workflow output: “output1”

You can programmatically inpect the Galaxy workflow definition by means of the Workflow class, which allows you to see which are the workflow inputs and outputs (steps[5-8]):

In [5]:

from wft4galaxy.wrapper import Workflow

In [6]:

wf = Workflow.load(os.path.join(EXAMPLES_FOLDER, "change_case/workflow.ga"))

In [7]:

wf.show_inputs()

-  InputText

In [8]:

 wf.show_outputs()

'1': OutputText

Steps 9-13 define a WorkflowTestCase instance programmatically:

In [9]:

from wft4galaxy.core import WorkflowTestCase

In [10]:

# prepare the workflow definition file name
base_path = os.path.join(EXAMPLES_FOLDER, "change_case")
workflow_filename = "workflow.ga"

In [11]:

# prepare test inputs
inputs = {"InputText": {"file": "input"}}

In [12]:

# prepare test outputs
expected_outputs = {"OutputText": {"file": "expected_output"}}

In [13]:

# create test case instance
test_case = WorkflowTestCase(base_path=base_path,
                             workflow_filename=workflow_filename,
                             inputs=inputs, expected_outputs=expected_outputs)

You can now run your test case and inspect the results of its execution (steps [14-16]), as described in “Run a single test”:

In [14]:

test_result = test_case.run(enable_logger=True)

2017-03-30 14:53:38,244 [wft4galaxy] [ INFO]  Create a history '_WorkflowTestHistory_e46ecb26-1547-11e7-8812-a45e60c4fc6b' (id: u'795b4cb2a2107ba7')
2017-03-30 14:53:40,120 [wft4galaxy] [ INFO]  Workflow '_WorkflowTest_Change Case (imported from API)' (id: 795b4cb2a2107ba7) running ...
2017-03-30 14:53:45,298 [wft4galaxy] [ INFO]  waiting for datasets
2017-03-30 14:53:45,690 [wft4galaxy] [ INFO]  44015a2f24f1f430: queued
2017-03-30 14:53:46,639 [wft4galaxy] [ INFO]  44015a2f24f1f430: queued
2017-03-30 14:53:47,330 [wft4galaxy] [ INFO]  44015a2f24f1f430: running
2017-03-30 14:53:48,075 [wft4galaxy] [ INFO]  44015a2f24f1f430: running
2017-03-30 14:53:49,025 [wft4galaxy] [ INFO]  44015a2f24f1f430: running
2017-03-30 14:53:49,660 [wft4galaxy] [ INFO]  44015a2f24f1f430: ok
2017-03-30 14:53:50,165 [wft4galaxy] [ INFO]  Workflow '_WorkflowTest_Change Case (imported from API)' (id: 795b4cb2a2107ba7) executed
2017-03-30 14:53:50,168 [wft4galaxy] [ INFO]  Checking test output: ...
2017-03-30 14:53:50,341 [wft4galaxy] [ INFO]  Checking test output: DONE

In [15]:

print("Test %s:\n\t - workflow: [%s] \n\t - results: %r" % \
      (test_result.test_id, test_result.workflow.name, test_result.results))

Test e46ecb26-1547-11e7-8812-a45e60c4fc6b:
         - workflow: [_WorkflowTest_Change Case (imported from API)]
         - results: {u'OutputText': True}

In [16]:

test_result.check_output("OutputText")

Out[16]:

True