cerise.test package

Submodules

cerise.test.fixture_jobs module

class cerise.test.fixture_jobs.BrokenJob

Bases: object

A simple job with no inputs or outputs, and an invalid command. And an invalid scheme in the input description.

input_content = {}

local_input()

local_input_files = []

output_content = {}

output_files = []

remote_input()

remote_input_files = []

remote_output()

required_num_cores = 0

time_limit = 0

workflow = b'#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: CommandLineTool\nbaseCommand: this_comamnd_does_not_exist\ninputs: []\noutputs: []\n'

class cerise.test.fixture_jobs.FileArrayJob

Bases: object

A simple job with an array of input files.

input_content = {'hello_world.2nd': b'Hello, file arrays!', 'hello_world.txt': b'Hello, World!\n\nHere is a test file for the staging test.\n\n'}

local_input()

local_input_files = [<cerise.back_end.file.File object>, <cerise.back_end.file.File object>]

local_output = '{{ "counts": {{ "class": "File", "location": "output.txt" }} }}\n'

output_content = {'output.txt': b' 4 11 58 hello_world.txt'}

output_files = [<cerise.back_end.file.File object>]

remote_input()

remote_input_files = [('files', '01_hello_world.txt', b'Hello, World!\n\nHere is a test file for the staging test.\n\n'), ('files', '02_hello_world.2nd', b'Hello, file arrays!')]

remote_output()

required_num_cores = 0

time_limit = 60

workflow = b'#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: Workflow\ninputs:\n files:\n type: File[]\n\noutputs:\n counts:\n type: File\n outputSource: wc/output\n\nsteps:\n wc:\n run: test/file_array.cwl\n in:\n files: files\n out:\n [output]\n'

class cerise.test.fixture_jobs.HostnameJob

Bases: object

A simple job with no inputs and one output.

input_content = {}

local_input()

local_input_files = []

local_output = '{ "host": { "class": "File", "location": "output.txt" }}\n'

output_content = {'output.txt': b'hostname\n'}

output_files = [<cerise.back_end.file.File object>]

remote_input()

remote_input_files = []

remote_output()

required_num_cores = 2

time_limit = 101

workflow = b'#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: Workflow\ninputs: []\noutputs:\n host:\n type: File\n outputSource: hostname/output\n\nsteps:\n hostname:\n run: test/hostname.cwl\n out:\n [output]\nhints:\n TimeLimit: 101\n'

class cerise.test.fixture_jobs.InstallScriptTestJob

Bases: object

input_content = {}

local_input()

local_input_files = []

local_output = '{ "host": { "class": "File", "location": "output.txt" } }\n'

output_content = [('output.txt', b'Testing API installation\n')]

output_files = [<cerise.back_end.file.File object>]

remote_output()

required_num_cores = 0

time_limit = 0

workflow = b'#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: Workflow\nsteps:\n test_install:\n run: test/test_install_script.cwl\n out: [output]\n\ninputs: []\n\noutputs:\n output:\n type: File\n outputSource: test_install/output\n\n'

class cerise.test.fixture_jobs.LongRunningJob

Bases: object

local_input()

local_input_files = []

local_output = '{}\n'

output_content = {}

output_files = []

required_num_cores = 0

time_limit = 0

workflow = b'#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: Workflow\nsteps:\n sleep:\n run: test/sleep.cwl\n in:\n delay:\n default: 60\n\ninputs: []\n\noutputs: []\n'

class cerise.test.fixture_jobs.MissingInputJob

Bases: object

A broken job that references an input file that doesn’t exist.

input_content = {}

local_input()

local_input_files = [<cerise.back_end.file.File object>]

remote_input()

remote_input_files = []

required_num_cores = 0

time_limit = 60

workflow = b'#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: Workflow\ninputs:\n file:\n type: File\n\noutputs:\n counts:\n type: File\n outputSource: wc/output\n\nsteps:\n wc:\n run: test/wc.cwl\n in:\n file: file\n out:\n [output]\n'

class cerise.test.fixture_jobs.NoSuchStepJob

Bases: object

input_content = {}

local_input()

local_input_files = []

local_output = '{}\n'

output_content = {}

output_files = []

remote_input()

remote_input_files = []

remote_output()

required_num_cores = 0

time_limit = 0

workflow = b'#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: Workflow\nsteps:\n sleep:\n run: test/no_such_step.cwl\n in:\n delay:\n default: 120\n\ninputs: []\n\noutputs: []\n'

class cerise.test.fixture_jobs.NoWorkflowJob

Bases: object

A job without a workflow.

input_content = {}

local_input()

local_input_files = []

output_content = {}

output_files = []

remote_input()

remote_input_files = []

remote_output()

required_num_cores = 0

time_limit = 0

workflow = None

class cerise.test.fixture_jobs.PartiallyFailingJob

Bases: object

input_content = {}

local_input()

local_input_files = []

local_output = '{ "output": { "class": "File", "location": "output.txt" }, "missing_output": null }\n'

output_content = [('output.txt', b'Running on host: hostname\n')]

output_files = [<cerise.back_end.file.File object>]

remote_input()

remote_input_files = []

remote_output()

required_num_cores = 0

time_limit = 0

workflow = b'#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: Workflow\ninputs: []\noutputs:\n output:\n type: File\n outputSource: failing/output\n missing_output:\n type: File\n outputSource: failing/missing_output\n\nsteps:\n failing:\n run: test/partially_failing_step.cwl\n in: []\n out:\n [output, missing_output]\n'

class cerise.test.fixture_jobs.PassJob

Bases: object

A simple job with no inputs or outputs.

input_content = {}

local_input()

Argument is local input dir for this job.

That’s normally local_exchange / input / job_name.

local_input_files = []

local_output = '{}'

output_content = {}

output_files = []

remote_input()

remote_input_files = []

remote_output()

Argument is remote work dir for this job.

required_num_cores = 0

time_limit = 0

workflow = b'#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: CommandLineTool\nbaseCommand: echo\ninputs: []\noutputs: []\n'

class cerise.test.fixture_jobs.SecondaryFilesJob

Bases: object

A simple job with an input file with a secondary file.

input_content = {'hello_world.2nd': b'Hello, secondaryFiles!', 'hello_world.txt': b'Hello, World!\n\nHere is a test file for the staging test.\n\n'}

local_input()

local_input_files = [<cerise.back_end.file.File object>]

local_output = '{ "counts": { "class": "File", "location": "output.txt" } }\n'

output_content = {'output.txt': b' 4 11 58 hello_world.txt'}

output_files = [<cerise.back_end.file.File object>]

remote_input()

remote_input_files = [('file', '01_hello_world.txt', b'Hello, World!\n\nHere is a test file for the staging test.\n\n'), ('file', '02_hello_world.2nd', b'Hello, secondaryFiles!')]

remote_output()

required_num_cores = 0

time_limit = 0

workflow = b'#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: Workflow\ninputs:\n file:\n type: File\n\noutputs:\n counts:\n type: File\n outputSource: wc/output\n\nsteps:\n wc:\n run: test/secondary_files.cwl\n in:\n textfile: file\n out:\n [output]\n'

class cerise.test.fixture_jobs.SlowJob

Bases: object

input_content = {}

local_input()

local_input_files = []

local_output = '{}'

output_content = {}

output_files = []

remote_input()

remote_input_files = []

remote_output()

required_num_cores = 0

time_limit = 0

workflow = b'#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: Workflow\nsteps:\n sleep:\n run: test/sleep.cwl\n in:\n delay:\n default: 1\n\ninputs: []\n\noutputs: []\n'

class cerise.test.fixture_jobs.WcJob

Bases: object

A simple job with an input file and an output file.

input_content = {'hello_world.txt': b'Hello, World!\n\nHere is a test file for the staging test.\n\n'}

local_input()

local_input_files = [<cerise.back_end.file.File object>]

local_output = '{ "output": { "class": "File", "location": "output.txt" } }\n'

output_content = {'output.txt': b' 4 11 58 hello_world.txt'}

output_files = [<cerise.back_end.file.File object>]

remote_input()

remote_input_files = [('file', '01_hello_world.txt', b'Hello, World!\n\nHere is a test file for the staging test.\n\n')]

remote_output()

required_num_cores = 3

time_limit = 60

workflow = b'#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: Workflow\ninputs:\n file:\n type: File\n\noutputs:\n counts:\n type: File\n outputSource: wc/output\n\nsteps:\n wc:\n run: test/wc.cwl\n in:\n file: file\n out:\n [output]\n\nhints:\n ResourceRequirement:\n coresMin: 3\n'

cerise.test.test_config module

cerise.test.test_service module

Module contents