from .matcher import JsonDiffMatcher, StripYAMLComments
from .mock_discovery import get_rootDesc
-import ruamel.yaml as yaml
+import ruamel.yaml
_rootDesc = None
stubs.api.collections().create.side_effect = functools.partial(collection_createstub, created_collections)
stubs.api.collections().get.side_effect = functools.partial(collection_getstub, created_collections)
- stubs.expect_job_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
- stubs.api.jobs().create().execute.return_value = {
- "uuid": stubs.expect_job_uuid,
- "state": "Queued",
- }
-
stubs.expect_container_request_uuid = "zzzzz-xvhdp-zzzzzzzzzzzzzzz"
stubs.api.container_requests().create().execute.return_value = {
"uuid": stubs.expect_container_request_uuid,
"state": "Queued"
}
- stubs.expect_pipeline_template_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz"
- stubs.api.pipeline_templates().create().execute.return_value = {
- "uuid": stubs.expect_pipeline_template_uuid,
- }
- stubs.expect_job_spec = {
- 'runtime_constraints': {
- 'docker_image': '999999999999999999999999999999d3+99',
- 'min_ram_mb_per_node': 1024
- },
- 'script_parameters': {
- 'x': {
- 'basename': 'blorp.txt',
- 'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
- 'class': 'File'
- },
- 'y': {
- 'basename': '99999999999999999999999999999998+99',
- 'location': 'keep:99999999999999999999999999999998+99',
- 'class': 'Directory'
- },
- 'z': {
- 'basename': 'anonymous',
- "listing": [{
- "basename": "renamed.txt",
- "class": "File",
- "location": "keep:99999999999999999999999999999998+99/file1.txt",
- "size": 0
- }],
- 'class': 'Directory'
- },
- 'cwl:tool': '57ad063d64c60dbddc027791f0649211+60/workflow.cwl#main'
- },
- 'repository': 'arvados',
- 'script_version': 'master',
- 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
- 'script': 'cwl-runner'
- }
- stubs.pipeline_component = stubs.expect_job_spec.copy()
- stubs.expect_pipeline_instance = {
- 'name': 'submit_wf.cwl',
- 'state': 'RunningOnServer',
- 'owner_uuid': None,
- "components": {
- "cwl-runner": {
- 'runtime_constraints': {'docker_image': '999999999999999999999999999999d3+99', 'min_ram_mb_per_node': 1024},
- 'script_parameters': {
- 'y': {"value": {'basename': '99999999999999999999999999999998+99', 'location': 'keep:99999999999999999999999999999998+99', 'class': 'Directory'}},
- 'x': {"value": {
- 'basename': 'blorp.txt',
- 'class': 'File',
- 'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
- "size": 16
- }},
- 'z': {"value": {'basename': 'anonymous', 'class': 'Directory',
- 'listing': [
- {
- 'basename': 'renamed.txt',
- 'class': 'File', 'location':
- 'keep:99999999999999999999999999999998+99/file1.txt',
- 'size': 0
- }
- ]}},
- 'cwl:tool': '57ad063d64c60dbddc027791f0649211+60/workflow.cwl#main',
- 'arv:debug': True,
- 'arv:enable_reuse': True,
- 'arv:on_error': 'continue'
- },
- 'repository': 'arvados',
- 'script_version': 'master',
- 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
- 'script': 'cwl-runner',
- 'job': {'state': 'Queued', 'uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'}
- }
- }
- }
- stubs.pipeline_create = copy.deepcopy(stubs.expect_pipeline_instance)
- stubs.expect_pipeline_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz"
- stubs.pipeline_create["uuid"] = stubs.expect_pipeline_uuid
- stubs.pipeline_with_job = copy.deepcopy(stubs.pipeline_create)
- stubs.pipeline_with_job["components"]["cwl-runner"]["job"] = {
- "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz",
- "state": "Queued"
- }
- stubs.api.pipeline_instances().create().execute.return_value = stubs.pipeline_create
- stubs.api.pipeline_instances().get().execute.return_value = stubs.pipeline_with_job
-
cwd = os.getcwd()
- filepath = os.path.join(cwd, "tests/wf/submit_wf_packed.cwl")
+ filepath = os.path.join(cwd, "tests/wf/submit_wf_wrapper.cwl")
with open(filepath) as f:
- expect_packed_workflow = yaml.round_trip_load(f)
+ yaml = ruamel.yaml.YAML(typ='rt', pure=True)
+ expect_packed_workflow = yaml.load(f)
if wfpath is None:
wfpath = wfname
mocktool = mock.NonCallableMock(tool=gitinfo_workflow["$graph"][0], metadata=gitinfo_workflow)
stubs.git_info = arvados_cwl.executor.ArvCwlExecutor.get_git_info(mocktool)
- expect_packed_workflow.update(stubs.git_info)
+ #expect_packed_workflow.update(stubs.git_info)
stubs.git_props = {"arv:"+k.split("#", 1)[1]: v for k,v in stubs.git_info.items()}
- if wfname == wfpath:
- container_name = "%s (%s)" % (wfpath, stubs.git_props["arv:gitDescribe"])
- else:
- container_name = wfname
+ #if wfname == wfpath:
+ # container_name = "%s (%s)" % (wfpath, stubs.git_props["arv:gitDescribe"])
+ #else:
+ container_name = wfname
stubs.expect_container_spec = {
'priority': 500,
'vcpus': 1,
'ram': (1024+256)*1024*1024
},
+ 'properties': {},
'use_existing': False,
- 'properties': stubs.git_props,
'secret_mounts': {}
}
+ #'properties': stubs.git_props,
stubs.expect_workflow_uuid = "zzzzz-7fd4e-zzzzzzzzzzzzzzz"
stubs.api.workflows().create().execute.return_value = {
def setUp(self):
cwltool.process._names = set()
- arvados_cwl.arvdocker.arv_docker_clear_cache()
+ #arvados_cwl.arvdocker.arv_docker_clear_cache()
def tearDown(self):
root_logger = logging.getLogger('')
@stubs()
def test_submit_container(self, stubs):
exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--api=containers", "--debug",
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--disable-git",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
'manifest_text':
'. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
'replication_desired': None,
- 'name': 'submit_wf.cwl ('+ stubs.git_props["arv:gitDescribe"] +') input (169f39d466a5438ac4a90e779bf750c7+53)',
+ 'name': 'submit_wf.cwl input (169f39d466a5438ac4a90e779bf750c7+53)',
}), ensure_unique_name=False),
mock.call(body=JsonDiffMatcher({
'manifest_text':
@mock.patch("cwltool.docker.DockerCommandLineJob.get_image")
@mock.patch("arvados.api")
def test_arvados_jobs_image(self, api, get_image, find_one_image_hash):
- arvados_cwl.arvdocker.arv_docker_clear_cache()
+ #arvados_cwl.arvdocker.arv_docker_clear_cache()
arvrunner = mock.MagicMock()
arvrunner.project_uuid = ""
def setUp(self):
cwltool.process._names = set()
- arvados_cwl.arvdocker.arv_docker_clear_cache()
+ #arvados_cwl.arvdocker.arv_docker_clear_cache()
def tearDown(self):
root_logger = logging.getLogger('')
projects / arvados.git / blobdiff