[ARVADOS] updated: b2ad7e34cf7c99768a06db2ef9f4c6ce62a49253
Git user
git at public.curoverse.com
Mon Apr 25 16:56:48 EDT 2016
Summary of changes:
sdk/cwl/arvados_cwl/__init__.py | 91 ++++++++++++++-------
sdk/cwl/tests/order/inputs_test_order.json | 8 +-
sdk/cwl/tests/test_submit.py | 126 ++++++++++++++---------------
sdk/cwl/tests/wf/inputs_test.cwl | 4 +
4 files changed, 130 insertions(+), 99 deletions(-)
discards 5771118026ed8906350f416ac1e482bf810978fa (commit)
discards 82f2fc3b04aaa31a254e6f97da7bb2befb5cad83 (commit)
via b2ad7e34cf7c99768a06db2ef9f4c6ce62a49253 (commit)
via 9f0c1ef69a99fd5f1497942e9fc73ee70bd91a91 (commit)
This update added new revisions after undoing existing revisions. That is
to say, the old revision is not a strict subset of the new revision. This
situation occurs when you --force push a change and generate a repository
containing something like this:
* -- * -- B -- O -- O -- O (5771118026ed8906350f416ac1e482bf810978fa)
\
N -- N -- N (b2ad7e34cf7c99768a06db2ef9f4c6ce62a49253)
When this happens we assume that you've already had alert emails for all
of the O revisions, and so we here report only the revisions in the N
branch from the common base, B.
Those revisions listed above that are new to this repository have
not appeared on any other notification email; so we list those
revisions in full, below.
commit b2ad7e34cf7c99768a06db2ef9f4c6ce62a49253
Author: Tom Clegg <tom at curoverse.com>
Date: Mon Apr 25 16:47:50 2016 -0400
8653: Translate pipeline parameter specs from CWL to Arvados.
diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index d714a69..3f210f5 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -4,26 +4,27 @@
import argparse
import arvados
-import arvados.events
+import arvados.collection
import arvados.commands.keepdocker
import arvados.commands.run
-import arvados.collection
+import arvados.events
import arvados.util
+import copy
+import cwltool.docker
import cwltool.draft2tool
-import cwltool.workflow
+from cwltool.errors import WorkflowException
import cwltool.main
from cwltool.process import shortname
-from cwltool.errors import WorkflowException
-import threading
-import cwltool.docker
+import cwltool.workflow
import fnmatch
-import logging
-import re
-import os
-import sys
import functools
import json
+import logging
+import os
import pkg_resources # part of setuptools
+import re
+import sys
+import threading
from cwltool.process import get_feature, adjustFiles, scandeps
from arvados.api import OrderedJsonModel
@@ -418,16 +419,81 @@ class RunnerJob(object):
class RunnerTemplate(object):
"""An Arvados pipeline template that invokes a CWL workflow."""
+ type_to_dataclass = {
+ 'boolean': 'boolean',
+ 'File': 'File',
+ 'float': 'number',
+ 'int': 'number',
+ 'string': 'text',
+ }
+
def __init__(self, runner, tool, job_order, enable_reuse):
self.runner = runner
+ self.tool = tool
self.job = RunnerJob(
runner=runner,
tool=tool,
job_order=job_order,
enable_reuse=enable_reuse)
+ def pipeline_component_spec(self):
+ """Return a component that Workbench and a-r-p-i will understand.
+
+ Specifically, translate CWL input specs to Arvados pipeline
+ format, like {"dataclass":"File","value":"xyz"}.
+ """
+ spec = self.job.arvados_job_spec()
+ job_params = spec['script_parameters']
+ spec['script_parameters'] = {}
+
+ for param in self.tool.tool["inputs"]:
+ param = copy.deepcopy(param)
+
+ # Data type and "required" flag...
+ types = param['type']
+ if not isinstance(types, list):
+ types = [types]
+ param['required'] = "null" not in types
+ non_null_types = set(types) - set(["null"])
+ if len(non_null_types) == 1:
+ the_type = [c for c in non_null_types][0]
+ dataclass = self.type_to_dataclass.get(the_type)
+ if dataclass:
+ param['dataclass'] = dataclass
+ # Note: If we didn't figure out a single appropriate
+ # dataclass, we just left that attribute out. We leave
+ # the "type" attribute there in any case, which might help
+ # downstream.
+
+ # Title and description...
+ descr = param.get('description', '').rstrip('\n')
+ if descr:
+ if '\n' in descr:
+ (param['title'],
+ param['description']) = descr.split('\n', 1)
+ else:
+ param['title'] = param['description']
+ del param['description']
+
+ # Fill in the value from the current job order, if any.
+ param_id = param['id']
+ if '#' in param_id:
+ param_id = param_id.split('#', 1)[1]
+ value = job_params.get(param_id)
+ if value is None:
+ pass
+ elif not isinstance(value, dict):
+ param['value'] = value
+ elif param.get('dataclass') == 'File' and value.get('path'):
+ param['value'] = value['path']
+
+ del param['id']
+ spec['script_parameters'][param_id] = param
+ spec['script_parameters']['cwl:tool'] = job_params['cwl:tool']
+ return spec
+
def save(self):
- job_spec = self.job.arvados_job_spec()
+ job_spec = self.pipeline_component_spec()
response = self.runner.api.pipeline_templates().create(body={
"components": {
self.job.name: job_spec,
diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py
index 3a5c38f..021394c 100644
--- a/sdk/cwl/tests/test_submit.py
+++ b/sdk/cwl/tests/test_submit.py
@@ -141,7 +141,13 @@ class TestCreateTemplate(unittest.TestCase):
stubs.api.pipeline_instances().create.refute_called()
stubs.api.jobs().create.refute_called()
- expect_component = stubs.expect_job_spec
+ expect_component = copy.deepcopy(stubs.expect_job_spec)
+ expect_component['script_parameters']['x'] = {
+ 'dataclass': 'File',
+ 'required': True,
+ 'type': 'File',
+ 'value': '99999999999999999999999999999992+99/blorp.txt',
+ }
expect_template = {
"components": {
"submit_wf.cwl": expect_component,
@@ -150,11 +156,57 @@ class TestCreateTemplate(unittest.TestCase):
"owner_uuid": project_uuid,
}
stubs.api.pipeline_templates().create.assert_called_with(
- body=expect_template)
+ body=JsonDiffMatcher(expect_template))
self.assertEqual(capture_stdout.getvalue(),
json.dumps(stubs.expect_pipeline_template_uuid))
+
+class TestTemplateInputs(unittest.TestCase):
+ expect_template = {
+ "components": {
+ "inputs_test.cwl": {
+ 'runtime_constraints': {
+ 'docker_image': 'arvados/jobs',
+ },
+ 'script_parameters': {
+ 'cwl:tool':
+ '99999999999999999999999999999991+99/'
+ 'wf/inputs_test.cwl',
+ 'optionalFloatInput': None,
+ 'fileInput': {
+ 'type': 'File',
+ 'dataclass': 'File',
+ 'required': True,
+ 'title': "It's a file; we expect to find some characters in it.",
+ 'description': 'If there were anything further to say, it would be said here,\nor here.'
+ },
+ 'floatInput': {
+ 'type': 'float',
+ 'dataclass': 'number',
+ 'required': True,
+ 'title': 'Floats like a duck',
+ },
+ 'optionalFloatInput': {
+ 'type': ['null', 'float'],
+ 'dataclass': 'number',
+ 'required': False,
+ },
+ 'boolInput': {
+ 'type': 'boolean',
+ 'dataclass': 'boolean',
+ 'required': True,
+ 'title': 'True or false?',
+ },
+ },
+ 'repository': 'arvados',
+ 'script_version': 'master',
+ 'script': 'cwl-runner',
+ },
+ },
+ "name": "inputs_test.cwl",
+ }
+
@stubs
def test_inputs_empty(self, stubs):
exited = arvados_cwl.main(
@@ -163,42 +215,9 @@ class TestCreateTemplate(unittest.TestCase):
cStringIO.StringIO(), sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
- expect_template = {
- "owner_uuid": stubs.fake_user_uuid,
- "components": {
- "inputs_test.cwl": {
- 'runtime_constraints': {
- 'docker_image': 'arvados/jobs',
- },
- 'script_parameters': {
- 'cwl:tool':
- '99999999999999999999999999999991+99/'
- 'wf/inputs_test.cwl',
- '#optionalFloatInput': None,
- '#fileInput': {
- 'dataclass': 'File',
- 'required': True,
- },
- '#floatInput': {
- 'dataclass': 'number',
- 'required': True,
- },
- '#optionalFloatInput': {
- 'dataclass': 'number',
- 'required': False,
- },
- '#boolInput': {
- 'dataclass': 'Boolean',
- 'required': True,
- },
- },
- 'repository': 'arvados',
- 'script_version': 'master',
- 'script': 'cwl-runner',
- },
- },
- "name": "inputs_test.cwl",
- }
+ expect_template = copy.deepcopy(self.expect_template)
+ expect_template["owner_uuid"] = stubs.fake_user_uuid
+
stubs.api.pipeline_templates().create.assert_called_with(
body=JsonDiffMatcher(expect_template))
@@ -210,32 +229,15 @@ class TestCreateTemplate(unittest.TestCase):
cStringIO.StringIO(), sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
- expect_template = {
- "owner_uuid": stubs.fake_user_uuid,
- "components": {
- "inputs_test.cwl": {
- 'runtime_constraints': {
- 'docker_image': 'arvados/jobs',
- },
- 'script_parameters': {
- 'cwl:tool':
- '99999999999999999999999999999991+99/'
- 'wf/inputs_test.cwl',
- '#optionalFloatInput': None,
- '#fileInput': {
- 'path':
- '99999999999999999999999999999992+99/blorp.txt',
- 'class': 'File',
- },
- '#floatInput': 1.234,
- '#boolInput': True,
- },
- 'repository': 'arvados',
- 'script_version': 'master',
- 'script': 'cwl-runner',
- },
- },
- "name": "inputs_test.cwl",
- }
+ self.expect_template["owner_uuid"] = stubs.fake_user_uuid
+
+ expect_template = copy.deepcopy(self.expect_template)
+ expect_template["owner_uuid"] = stubs.fake_user_uuid
+ params = expect_template[
+ "components"]["inputs_test.cwl"]["script_parameters"]
+ params["fileInput"]["value"] = '99999999999999999999999999999992+99/blorp.txt'
+ params["floatInput"]["value"] = 1.234
+ params["boolInput"]["value"] = True
+
stubs.api.pipeline_templates().create.assert_called_with(
body=JsonDiffMatcher(expect_template))
diff --git a/sdk/cwl/tests/wf/inputs_test.cwl b/sdk/cwl/tests/wf/inputs_test.cwl
index 03d924c..61cb1c4 100644
--- a/sdk/cwl/tests/wf/inputs_test.cwl
+++ b/sdk/cwl/tests/wf/inputs_test.cwl
@@ -7,10 +7,14 @@ inputs:
type: File
description: |
It's a file; we expect to find some characters in it.
+ If there were anything further to say, it would be said here,
+ or here.
- id: "#boolInput"
type: boolean
+ description: True or false?
- id: "#floatInput"
type: float
+ description: Floats like a duck
- id: "#optionalFloatInput"
type: ["null", float]
outputs: []
commit 9f0c1ef69a99fd5f1497942e9fc73ee70bd91a91
Author: Tom Clegg <tom at curoverse.com>
Date: Sun Apr 24 16:06:37 2016 -0400
8653: Add test cases for input types.
diff --git a/sdk/cwl/tests/matcher.py b/sdk/cwl/tests/matcher.py
new file mode 100644
index 0000000..d3c9316
--- /dev/null
+++ b/sdk/cwl/tests/matcher.py
@@ -0,0 +1,23 @@
+import difflib
+import json
+
+
+class JsonDiffMatcher(object):
+ """Raise AssertionError with a readable JSON diff when not __eq__().
+
+ Used with assert_called_with() so it's possible for a human to see
+ the differences between expected and actual call arguments that
+ include non-trivial data structures.
+ """
+ def __init__(self, expected):
+ self.expected = expected
+
+ def __eq__(self, actual):
+ expected_json = json.dumps(self.expected, sort_keys=True, indent=2)
+ actual_json = json.dumps(actual, sort_keys=True, indent=2)
+ if expected_json != actual_json:
+ raise AssertionError("".join(difflib.context_diff(
+ expected_json.splitlines(1),
+ actual_json.splitlines(1),
+ fromfile="Expected", tofile="Actual")))
+ return True
diff --git a/sdk/cwl/tests/order/empty_order.json b/sdk/cwl/tests/order/empty_order.json
new file mode 100644
index 0000000..0967ef4
--- /dev/null
+++ b/sdk/cwl/tests/order/empty_order.json
@@ -0,0 +1 @@
+{}
diff --git a/sdk/cwl/tests/order/inputs_test_order.json b/sdk/cwl/tests/order/inputs_test_order.json
new file mode 100644
index 0000000..8830523
--- /dev/null
+++ b/sdk/cwl/tests/order/inputs_test_order.json
@@ -0,0 +1,9 @@
+{
+ "fileInput": {
+ "class": "File",
+ "path": "../input/blorp.txt"
+ },
+ "boolInput": true,
+ "floatInput": 1.234,
+ "optionalFloatInput": null
+}
diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py
index 750eeae..3a5c38f 100644
--- a/sdk/cwl/tests/test_submit.py
+++ b/sdk/cwl/tests/test_submit.py
@@ -11,6 +11,8 @@ import mock
import sys
import unittest
+from .matcher import JsonDiffMatcher
+
def stubs(func):
@functools.wraps(func)
@@ -124,7 +126,7 @@ class TestSubmit(unittest.TestCase):
class TestCreateTemplate(unittest.TestCase):
@stubs
- def test_create_pipeline_template(self, stubs):
+ def test_create(self, stubs):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
capture_stdout = cStringIO.StringIO()
@@ -152,3 +154,88 @@ class TestCreateTemplate(unittest.TestCase):
self.assertEqual(capture_stdout.getvalue(),
json.dumps(stubs.expect_pipeline_template_uuid))
+
+ @stubs
+ def test_inputs_empty(self, stubs):
+ exited = arvados_cwl.main(
+ ["--create-template", "--no-wait",
+ "tests/wf/inputs_test.cwl", "tests/order/empty_order.json"],
+ cStringIO.StringIO(), sys.stderr, api_client=stubs.api)
+ self.assertEqual(exited, 0)
+
+ expect_template = {
+ "owner_uuid": stubs.fake_user_uuid,
+ "components": {
+ "inputs_test.cwl": {
+ 'runtime_constraints': {
+ 'docker_image': 'arvados/jobs',
+ },
+ 'script_parameters': {
+ 'cwl:tool':
+ '99999999999999999999999999999991+99/'
+ 'wf/inputs_test.cwl',
+ '#optionalFloatInput': None,
+ '#fileInput': {
+ 'dataclass': 'File',
+ 'required': True,
+ },
+ '#floatInput': {
+ 'dataclass': 'number',
+ 'required': True,
+ },
+ '#optionalFloatInput': {
+ 'dataclass': 'number',
+ 'required': False,
+ },
+ '#boolInput': {
+ 'dataclass': 'Boolean',
+ 'required': True,
+ },
+ },
+ 'repository': 'arvados',
+ 'script_version': 'master',
+ 'script': 'cwl-runner',
+ },
+ },
+ "name": "inputs_test.cwl",
+ }
+ stubs.api.pipeline_templates().create.assert_called_with(
+ body=JsonDiffMatcher(expect_template))
+
+ @stubs
+ def test_inputs(self, stubs):
+ exited = arvados_cwl.main(
+ ["--create-template", "--no-wait",
+ "tests/wf/inputs_test.cwl", "tests/order/inputs_test_order.json"],
+ cStringIO.StringIO(), sys.stderr, api_client=stubs.api)
+ self.assertEqual(exited, 0)
+
+ expect_template = {
+ "owner_uuid": stubs.fake_user_uuid,
+ "components": {
+ "inputs_test.cwl": {
+ 'runtime_constraints': {
+ 'docker_image': 'arvados/jobs',
+ },
+ 'script_parameters': {
+ 'cwl:tool':
+ '99999999999999999999999999999991+99/'
+ 'wf/inputs_test.cwl',
+ '#optionalFloatInput': None,
+ '#fileInput': {
+ 'path':
+ '99999999999999999999999999999992+99/blorp.txt',
+ 'class': 'File',
+ },
+ '#floatInput': 1.234,
+ '#boolInput': True,
+ },
+ 'repository': 'arvados',
+ 'script_version': 'master',
+ 'script': 'cwl-runner',
+ },
+ },
+ "name": "inputs_test.cwl",
+ }
+ stubs.api.pipeline_templates().create.assert_called_with(
+ body=JsonDiffMatcher(expect_template))
diff --git a/sdk/cwl/tests/wf/inputs_test.cwl b/sdk/cwl/tests/wf/inputs_test.cwl
new file mode 100644
index 0000000..03d924c
--- /dev/null
+++ b/sdk/cwl/tests/wf/inputs_test.cwl
@@ -0,0 +1,22 @@
+# Test case for arvados-cwl-runner. Used to test propagation of
+# various input types as script_parameters in pipeline templates.
+
+class: Workflow
+inputs:
+ - id: "#fileInput"
+ type: File
+ description: |
+ It's a file; we expect to find some characters in it.
+ - id: "#boolInput"
+ type: boolean
+ - id: "#floatInput"
+ type: float
+ - id: "#optionalFloatInput"
+ type: ["null", float]
+outputs: []
+steps:
+ - id: step1
+ inputs:
+ - { id: x, source: "#x" }
+ outputs: []
+ run: ../tool/submit_tool.cwl
-----------------------------------------------------------------------
hooks/post-receive
--
More information about the arvados-commits
mailing list