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add coverage tests to missing code paths
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@fmigneault
fmigneault committed Nov 20, 2024
1 parent 3bd7fbe commit 90af73c
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Showing 2 changed files with 93 additions and 63 deletions.
154 changes: 92 additions & 62 deletions tests/processes/test_wps_package.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@
"""
import contextlib
import copy
import inspect
import io
import itertools
import json
Expand All @@ -16,7 +17,7 @@
import sys
import tempfile
import warnings
from typing import TYPE_CHECKING
from typing import TYPE_CHECKING, cast

import cwltool.process
import mock
Expand All @@ -33,6 +34,9 @@
from weaver.exceptions import PackageExecutionError, PackageTypeError
from weaver.formats import ContentType
from weaver.processes.constants import (
CWL_NAMESPACE_SCHEMA_DEFINITION,
CWL_NAMESPACE_SCHEMA_ID,
CWL_NAMESPACE_SCHEMA_URL,
CWL_REQUIREMENT_APP_DOCKER,
CWL_REQUIREMENT_APP_DOCKER_GPU,
CWL_REQUIREMENT_CUDA,
Expand All @@ -57,10 +61,10 @@
from weaver.wps_restapi import swagger_definitions as sd

if TYPE_CHECKING:
from typing import Any, Dict, TypeVar
from typing import Any, Callable, Dict, TypeVar, Union
from typing_extensions import Literal

from weaver.typedefs import CWL
from weaver.typedefs import CWL, CWL_AnyRequirements, ProcessOfferingMapping

KT = TypeVar("KT")
VT_co = TypeVar("VT_co", covariant=True)
Expand Down Expand Up @@ -302,8 +306,8 @@ def _add_requirement(reqs1, reqs2):
if field not in reqs2:
continue
reqs1.setdefault(field, {})
defs1 = reqs1[field]
defs2 = reqs2[field]
defs1 = cast("CWL_AnyRequirements", reqs1[field]) # type: CWL_AnyRequirements
defs2 = cast("CWL_AnyRequirements", reqs2[field]) # type: CWL_AnyRequirements
if isinstance(defs1, list):
if isinstance(defs2, dict):
defs2 = [_combine({"class": req}, val) for req, val in defs2.items()]
Expand Down Expand Up @@ -847,18 +851,16 @@ def test_format_extension_validator_basic(data_input, mode, expect):


@pytest.mark.parametrize(
["cwl_package_original", "cwl_package_expected"],
["cwl_package_package", "wps_package_metadata", "cwl_package_expected"],
[
(
# Test author metadata with empty wps_package
{
"cwl_package_package": {
"s:author": [
{"class": "s:Person", "s:name": "John Doe", "s:affiliation": "Example Inc."}
],
},
"wps_package_metadata": {}
"s:author": [
{"class": "s:Person", "s:name": "John Doe", "s:affiliation": "Example Inc."}
],
},
{},
{
"abstract": "",
"title": "",
Expand All @@ -877,11 +879,9 @@ def test_format_extension_validator_basic(data_input, mode, expect):
(
# Test codeRepository
{
"cwl_package_package": {
"s:codeRepository": "https://gitlab.com/",
},
"wps_package_metadata": {}
"s:codeRepository": "https://gitlab.com/",
},
{},
{
"abstract": "",
"title": "",
Expand All @@ -897,18 +897,16 @@ def test_format_extension_validator_basic(data_input, mode, expect):
(
# Test Version with existing metadata
{
"cwl_package_package": {
"s:version": "1.0"
},
"wps_package_metadata": {
"metadata": [
{
"type": "text/html",
"rel": "codeRepository",
"href": "https://gitlab.com/"
}
]
}
"s:version": "1.0"
},
{
"metadata": [
{
"type": "text/html",
"rel": "codeRepository",
"href": "https://gitlab.com/"
}
]
},
{
"abstract": "",
Expand All @@ -926,11 +924,9 @@ def test_format_extension_validator_basic(data_input, mode, expect):
(
# Test softwareVersion
{
"cwl_package_package": {
"s:softwareVersion": "1.0.0"
},
"wps_package_metadata": {}
"s:softwareVersion": "1.0.0"
},
{},
{
"abstract": "",
"title": "",
Expand All @@ -940,14 +936,12 @@ def test_format_extension_validator_basic(data_input, mode, expect):
(
# Test contributor
{
"cwl_package_package": {
"s:contributor": [
{"class": "s:Person", "s:name": "John Doe", "s:affiliation": "Example Inc."},
{"class": "s:Person", "s:name": "Other Guy", "s:affiliation": "Elsewhere"},
],
},
"wps_package_metadata": {}
"s:contributor": [
{"class": "s:Person", "s:name": "John Doe", "s:affiliation": "Example Inc."},
{"class": "s:Person", "s:name": "Other Guy", "s:affiliation": "Elsewhere"},
],
},
{},
{
"abstract": "",
"title": "",
Expand All @@ -974,11 +968,9 @@ def test_format_extension_validator_basic(data_input, mode, expect):
(
# Test citation
{
"cwl_package_package": {
"s:citation": "https://dx.doi.org/10.6084/m9.figshare.3115156.v2"
},
"wps_package_metadata": {}
"s:citation": "https://dx.doi.org/10.6084/m9.figshare.3115156.v2"
},
{},
{
"abstract": "",
"title": "",
Expand All @@ -994,20 +986,18 @@ def test_format_extension_validator_basic(data_input, mode, expect):
(
# Test dateCreated with existing metadata
{
"cwl_package_package": {
"s:dateCreated": "2016-12-13",
},
"wps_package_metadata": {
"abstract": "",
"title": "",
"metadata": [
{
"type": "text/plain",
"rel": "citation",
"href": "https://dx.doi.org/10.6084/m9.figshare.3115156.v2"
},
],
}
"s:dateCreated": "2016-12-13",
},
{
"abstract": "",
"title": "",
"metadata": [
{
"type": "text/plain",
"rel": "citation",
"href": "https://dx.doi.org/10.6084/m9.figshare.3115156.v2"
},
],
},
{
"abstract": "",
Expand All @@ -1025,13 +1015,53 @@ def test_format_extension_validator_basic(data_input, mode, expect):
]
}
),
(
# test CWL '$schemas' and '$namespace' mapping to alternate metadata references
{
"$schemas": [CWL_NAMESPACE_SCHEMA_URL],
"$namespaces": dict(CWL_NAMESPACE_SCHEMA_DEFINITION),
},
{
"metadata": [
{
"role": "test",
"value": "test",
}
]
},
{
"abstract": "",
"title": "",
"metadata": [
{
"role": "test",
"value": "test",
},
{
"title": CWL_NAMESPACE_SCHEMA_ID,
"href": CWL_NAMESPACE_SCHEMA_URL,
}
]
}
),
(
# test CWL 's:keywords' vs WPS 'keywords'
{
"s:keywords": ["a", "b", "c"],
},
{
"keywords": ["a", "x", "y", "d", "e", "f"],
},
lambda src: set(src["keywords"]) == {"a", "b", "c", "x", "y", "d", "e", "f"},
),
]
)
def test_process_metadata(cwl_package_original, cwl_package_expected):
# type: (CWL, CWL) -> None
cwl_package_package = cwl_package_original["cwl_package_package"]
wps_package_metadata = cwl_package_original["wps_package_metadata"]
def test_process_metadata(cwl_package_package, wps_package_metadata, cwl_package_expected):
# type: (CWL, ProcessOfferingMapping, Union[CWL, Callable[[CWL], bool]]) -> None
cwl_package_validated = sd.CWLMetadata().deserialize(cwl_package_package) # must not raise
assert cwl_package_validated == cwl_package_package # should be unchanged
_update_package_metadata(wps_package_metadata, cwl_package_package)
assert wps_package_metadata == cwl_package_expected
if inspect.isfunction(cwl_package_expected):
assert cwl_package_expected(wps_package_metadata)
else:
assert wps_package_metadata == cwl_package_expected
2 changes: 1 addition & 1 deletion weaver/processes/wps_package.py
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Original file line number Diff line number Diff line change
Expand Up @@ -784,7 +784,7 @@ def _update_package_metadata(wps_package_metadata, cwl_package_package):
and isinstance(cwl_package_package["$namespaces"], dict)
):
metadata = wps_package_metadata.get("metadata", [])
namespaces_inv = {v: k for k, v in cwl_package_package["$namespaces"]}
namespaces_inv = {v: k for k, v in cwl_package_package["$namespaces"].items()}
for schema in cwl_package_package["$schemas"]:
for namespace_url in namespaces_inv:
if schema.startswith(namespace_url):
Expand Down

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