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wdltest

Wdltest is python3 package to test wdl workflows.

Requirements

  • Java (version at least 8)
  • Python3 (>= 3.7)

How to install

pip3 install --upgrade wdltest==1.15.0

How to run

wdltest -t test.json

How to configure

It is possible to use environment variables in scripts using ${var_name} notation

wdltest configuration parameters

  • wdl - path to wdl file
  • threads - number of threads to utilize
  • tests - array of test configurations

test configuration parameters

  • name - name of test
  • bcoCheck - flag (true/false) informing whether to check if bco.json is generated
  • tsdoutCheck - flag (true/false) informing whether to check if stdout is generated
  • expecterror - flag (true/false) informing if the test should end with fail (conditions can be set as emptyy array then)
  • inputs - inputs for wdl execution
  • conditions - array of conditions to be met for test to be passed

condition parameters

  • file - name of output
  • index - optional index if output is array. Default: 0
  • name - name of unit test to be printes
  • error_message - error message in case of test failure
  • command - test command. Status 0 gives succeed status.

Example test configuration

{
    "wdl":"${ROOTDIR}/src/main/wdl/modules/panel-hpo/panel-hpo.wdl",
    "threads": 1,
    "tests": [
        {
            "name":"Primary test",
            "bcoCheck": true,
            "stdoutCheck": true,
            "inputs": {
              "panel_hpo.hpo_terms": "HP:0001679, HP:0007018. HP:0000722, HP:0000256",
              "panel_hpo.genes": "HTT",
              "panel_hpo.diseases": "Osteogenesis imperfecta, Ehlers-Danlos",
              "panel_hpo.sample_id": "test",
              "panel_hpo.panel_names": ["ACMG_Incidental_Findings", "COVID-19_research", "Cancer_Germline", "Cardiovascular_disorders"],
              "panel_hpo.phenotypes_description": "Increased height, disproportionately long limbs and digits, anterior chest deformity, mild to moderate joint laxity, vertebral column deformity (scoliosis and thoracic lordosis), and a narrow, highly arched palate with crowding of the teeth are frequent skeletal features"
            },
            "conditions": [
            ]
        },
        {
            "name":"Error test",
            "expecterror": true
            "inputs": {
              "panel_hpo.hpo_terms": "HP:0001679, HP:0007018. HP:0000722, HP:0000256",
              "panel_hpo.genes": "HTT",
              "panel_hpo.diseases": "Osteogenesis imperfecta, Ehlers-Danlos",
              "panel_hpo.sample_id": "test",
              "panel_hpo.panel_names": ["ACMG_Incidental_Findings", "COVID-19'_research", "Cancer_Germline", "Cardiovascular_disorders"],
              "panel_hpo.phenotypes_description": "Increased height, disproportionately long limbs and digits, anterior chest deformity, mild to moderate joint laxity, vertebral column deformity (scoliosis and thoracic lordosis), and a narrow, highly arched palate with crowding of the teeth are frequent skeletal features"
            },
            "conditions": [
            ]
        },
        {
            "name":"Primary test",
            "inputs": {
              "panel_hpo.hpo_terms": "HP:0001679, HP:0007018. HP:0000722, HP:0000256",
              "panel_hpo.genes": "HTT",
              "panel_hpo.diseases": "Osteogenesis imperfecta, Ehlers-Danlos",
              "panel_hpo.sample_id": "test",
              "panel_hpo.panel_names": ["ACMG_Incidental_Findings", "COVID-19_research", "Cancer_Germline", "Cardiovascular_disorders"],
              "panel_hpo.phenotypes_description": "Increased height, disproportionately long limbs and digits, anterior chest deformity, mild to moderate joint laxity, vertebral column deformity (scoliosis and thoracic lordosis), and a narrow, highly arched palate with crowding of the teeth are frequent skeletal features"
            },
            "conditions": [
                {
                    "file":"bco",
                    "name":"Bco exists",
                    "error_message":"Bco does not exist",
                    "command":"echo $file"
                },
                {
                    "file":"bco",
                    "name":"Provenance domain exists and is not empty",
                    "error_message":"Provenance domain not found in bco or is empty",
                    "command":"grep -q -m1 provenance_domain $file && jq -e 'if (.provenance_domain | length) == 0 then false else true end' $file"
                },
                {
                    "file":"bco",
                    "name":"Execution domain exists and is not empty",
                    "error_message":"Execution domain not found in bco or is empty",
                    "command":"grep -q -m1 execution_domain $file && jq -e 'if (.execution_domain | length) == 0 then false else true end' $file"
                },
                {
                    "file":"bco",
                    "name":"Parametric domain exists and is not empty",
                    "error_message":"Parametric domain not found in bco or is empty",
                    "command":"grep -q -m1 parametric_domain $file && jq -e 'if (.parametric_domain | length) == 0 then false else true end' $file"
                },
                {
                    "file":"bco",
                    "name":"Description domain exists and is not empty",
                    "warning":"true",
                    "command":"grep -q -m1 descripcion_domain $file && jq -e 'if (.description_domain | length) == 0 then false else true end' $file"
                },
                {
                    "file":"stdout_log",
                    "name":"Stdout exits",
                    "command":"test -f $file"
                },
                {
                    "file":"stdout_log",
                    "name":"Stdout exits",
                    "command":"test -f r$file"
                }

            ]
        }

    ]
}

development

test

ROOTDIR=$(pwd) python3 setup.py nosetests -s

build

python3 setup.py sdist bdist_wheel

upload

twine upload --repository testpypi dist/wdltest-1.0.0*
twine upload --repository pypi dist/wdltest-1.0.0*

install

pip3 install --upgrade --no-deps wdltest==1.0.6

kill cromwells

ps aux | grep Dweb | cut -d " " -f 2 | xargs kill -9
ps aux | grep Dweb

Versions

1.14.0

Resolved bug with Array outputs