-
import logging
import mock
import unittest
runner = mock.MagicMock()
runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
runner.ignore_docker_for_reuse = False
- document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("draft-3")
+ runner.num_retries = 0
+ document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
tool = {
"inputs": [],
runner = mock.MagicMock()
runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
runner.ignore_docker_for_reuse = False
- document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("draft-3")
+ runner.num_retries = 0
+ arvados_cwl.add_arv_hints()
+
+ document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
+
tool = {
"inputs": [],
"coresMin": 3,
"ramMin": 3000,
"tmpdirMin": 4000
+ }, {
+ "class": "http://arvados.org/cwl#RuntimeConstraints",
+ "keep_cache": 512,
+ "outputDirType": "keep_output_dir"
+ }, {
+ "class": "http://arvados.org/cwl#APIRequirement",
}],
"baseCommand": "ls"
}
'script_parameters': {
'tasks': [{
'task.env': {'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'},
+ 'task.keepTmpOutput': True,
'command': ['ls']
}]
},
'docker_image': 'arvados/jobs',
'min_cores_per_node': 3,
'min_ram_mb_per_node': 3000,
- 'min_scratch_mb_per_node': 5024 # tmpdirSize + outdirSize
+ 'min_scratch_mb_per_node': 5024, # tmpdirSize + outdirSize
+ 'keep_cache_mb_per_task': 512
}
},
find_or_create=True,
['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'],
['docker_image_locator', 'in docker', 'arvados/jobs']])
- @mock.patch("arvados.collection.Collection")
- def test_done(self, col):
+ @mock.patch("arvados.collection.CollectionReader")
+ def test_done(self, reader):
api = mock.MagicMock()
runner = mock.MagicMock()
runner.num_retries = 0
runner.ignore_docker_for_reuse = False
- col().open.return_value = []
+ reader().open.return_value = []
api.collections().list().execute.side_effect = ({"items": []},
{"items": [{"manifest_text": "XYZ"}]})
'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
'name': 'Output 9999999 of testjob'})
- @mock.patch("arvados.collection.Collection")
- def test_done_use_existing_collection(self, col):
+ @mock.patch("arvados.collection.CollectionReader")
+ def test_done_use_existing_collection(self, reader):
api = mock.MagicMock()
runner = mock.MagicMock()
runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
runner.num_retries = 0
- col().open.return_value = []
+ reader().open.return_value = []
api.collections().list().execute.side_effect = ({"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2"}]},)
arvjob = arvados_cwl.ArvadosJob(runner)
class TestWorkflow(unittest.TestCase):
# The test passes no builder.resources
# Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
- def test_run(self):
- arvados_cwl.add_arv_hints()
+ @mock.patch("arvados.collection.Collection")
+ def test_run(self, mockcollection):
+ try:
+ arvados_cwl.add_arv_hints()
- runner = arvados_cwl.ArvCwlRunner(mock.MagicMock())
- runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
- runner.ignore_docker_for_reuse = False
- document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
+ runner = arvados_cwl.ArvCwlRunner(mock.MagicMock())
+ runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
+ runner.ignore_docker_for_reuse = False
+ runner.num_retries = 0
+ document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
- tool, metadata = document_loader.resolve_ref("tests/wf/scatter2.cwl")
- metadata["cwlVersion"] = tool["cwlVersion"]
+ tool, metadata = document_loader.resolve_ref("tests/wf/scatter2.cwl")
+ metadata["cwlVersion"] = tool["cwlVersion"]
- make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
- arvtool = arvados_cwl.ArvadosWorkflow(runner, tool, work_api="jobs", avsc_names=avsc_names,
- basedir="", make_fs_access=make_fs_access, loader=document_loader,
- makeTool=runner.arv_make_tool, metadata=metadata)
- arvtool.formatgraph = None
- it = arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access)
- it.next().run()
- it.next().run()
+ mockcollection().portable_data_hash.return_value = "99999999999999999999999999999999+118"
- runner.api.jobs().create.assert_called_with(
- body={
- 'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
- 'repository': 'arvados',
- 'script_version': 'master',
- 'script': 'crunchrunner',
- 'script_parameters': {
- 'tasks': [{'task.env': {
- 'HOME': '$(task.outdir)',
- 'TMPDIR': '$(task.tmpdir)'},
- 'task.vwd': {
- 'workflow.json': '$(task.keep)/f101400a398097d4398cdb3eb5d1a7ca+118/workflow.json',
- 'cwl.input.json': '$(task.keep)/f101400a398097d4398cdb3eb5d1a7ca+118/cwl.input.json'
- },
- 'command': [u'cwltool', u'--no-container', u'--move-outputs', u'workflow.json', u'cwl.input.json'],
- 'task.stdout': 'cwl.output.json'}]},
- 'runtime_constraints': {
- 'min_scratch_mb_per_node': 2048,
- 'min_cores_per_node': 1,
- 'docker_image': 'arvados/jobs',
- 'min_ram_mb_per_node': 1024
- },
- 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'},
- filters=[['repository', '=', 'arvados'],
- ['script', '=', 'crunchrunner'],
- ['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'],
- ['docker_image_locator', 'in docker', 'arvados/jobs']],
- find_or_create=True)
+ make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
+ arvtool = arvados_cwl.ArvadosWorkflow(runner, tool, work_api="jobs", avsc_names=avsc_names,
+ basedir="", make_fs_access=make_fs_access, loader=document_loader,
+ makeTool=runner.arv_make_tool, metadata=metadata)
+ arvtool.formatgraph = None
+ it = arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access)
+ it.next().run()
+ it.next().run()
+
+ with open("tests/wf/scatter2_subwf.cwl") as f:
+ subwf = f.read()
+
+ mockcollection().open().__enter__().write.assert_has_calls([mock.call(subwf)])
+ mockcollection().open().__enter__().write.assert_has_calls([mock.call('{sleeptime: 5}')])
+
+ runner.api.jobs().create.assert_called_with(
+ body={
+ 'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
+ 'repository': 'arvados',
+ 'script_version': 'master',
+ 'script': 'crunchrunner',
+ 'script_parameters': {
+ 'tasks': [{'task.env': {
+ 'HOME': '$(task.outdir)',
+ 'TMPDIR': '$(task.tmpdir)'},
+ 'task.vwd': {
+ 'workflow.cwl': '$(task.keep)/99999999999999999999999999999999+118/workflow.cwl',
+ 'cwl.input.yml': '$(task.keep)/99999999999999999999999999999999+118/cwl.input.yml'
+ },
+ 'command': [u'cwltool', u'--no-container', u'--move-outputs', u'--preserve-entire-environment', u'workflow.cwl#main', u'cwl.input.yml'],
+ 'task.stdout': 'cwl.output.json'}]},
+ 'runtime_constraints': {
+ 'min_scratch_mb_per_node': 2048,
+ 'min_cores_per_node': 1,
+ 'docker_image': 'arvados/jobs',
+ 'min_ram_mb_per_node': 1024
+ },
+ 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'},
+ filters=[['repository', '=', 'arvados'],
+ ['script', '=', 'crunchrunner'],
+ ['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'],
+ ['docker_image_locator', 'in docker', 'arvados/jobs']],
+ find_or_create=True)
+ except:
+ logging.exception("")
projects / arvados.git / blobdiff