13837341397

Committed 13 Mar 2025 02:40PM UTC coverage: 78.893% (-12.9%) from 91.745%

Build # 13837341397

Build Type

push

github

Committed by

aaxelb

Commit Message

update github actions workflow

- bump actions/setup-python to v5
- bump actions/checkout to v4
- update postgres version(s)
- remove pin on coverallsapp/github-action, update to latest v2
- work around coveralls error; build and specify xml explicitly
- omit `tests/` from coverage calculation

Run Details

12305 of 15597 relevant lines covered (78.89%)

1.58 hits per line

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98.04

/api/normalizeddata/views.py

import logging
import json

from django.urls import reverse
from rest_framework import status
from rest_framework import generics
from rest_framework.exceptions import ValidationError
from rest_framework.response import Response
import sentry_sdk

from share import models as share_db
from share.util.graph import MutableGraph
from share.util.osf import guess_osf_guid
from api.base.views import ShareViewSet
from api.normalizeddata.serializers import BasicNormalizedDataSerializer
from api.normalizeddata.serializers import FullNormalizedDataSerializer
from api.pagination import CursorPagination
from api.permissions import ReadOnlyOrTokenHasScopeOrIsAuthenticated
from trove import digestive_tract


logger = logging.getLogger(__name__)


class NormalizedDataViewSet(ShareViewSet, generics.ListCreateAPIView, generics.RetrieveAPIView):
    """View showing all normalized data in the SHARE Dataset.

    ## Submitting changes to the SHARE dataset
    Changes, whether they are additions or modifications, are submitted as a subset of [JSON-LD graphs](https://www.w3.org/TR/json-ld/#named-graphs).
    Each [node](https://www.w3.org/TR/json-ld/#dfn-node) of the graph MUST contain both an `@id` and `@type` key.

        Method:        POST
        Body (JSON):   {
                        'data': {
                            'type': 'NormalizedData'
                            'attributes': {
                                'data': {
                                    '@graph': [{
                                        '@type': <type of document, exp: person>,
                                        '@id': <_:random>,
                                        <attribute_name>: <value>,
                                        <relationship_name>: {
                                            '@type': <type>,
                                            '@id': <id>
                                        }
                                    }]
                                }
                            }
                        }
                       }
        Success:       200 OK
    """
    ordering = ('-id', )
    pagination_class = CursorPagination
    permission_classes = (ReadOnlyOrTokenHasScopeOrIsAuthenticated, )
    required_scopes = ('upload_normalized_manuscript', )
    resource_name = 'NormalizedData'

    def get_serializer_class(self):
        if not self.request.user.is_authenticated:
            return BasicNormalizedDataSerializer
        elif self.request.user.is_robot:
            return FullNormalizedDataSerializer
        return BasicNormalizedDataSerializer

    def get_queryset(self):
        return share_db.NormalizedData.objects.all()

    def create(self, request, *args, **kwargs):
        if share_db.FeatureFlag.objects.flag_is_up(share_db.FeatureFlag.IGNORE_SHAREV2_INGEST):
            return Response({
                'errors': [
                    {'detail': (
                        'this route was deprecated and has been removed'
                        f' (use {reverse("trove:ingest-rdf")} instead)'
                    )},
                ],
            }, status=status.HTTP_410_GONE)
        try:
            return self._do_create(request, *args, **kwargs)
        except Exception:
            sentry_sdk.capture_exception()  # get some insight into common validation errors
            raise

    def _do_create(self, request, *args, **kwargs):
        serializer = self.get_serializer_class()(data=request.data, context={'request': request})
        serializer.is_valid(raise_exception=True)

        data = serializer.validated_data['data']
        suid = serializer.validated_data.get('suid', None)
        if not suid:
            # HACK: try for an osf guid -- may still be None tho
            suid = guess_osf_guid(MutableGraph.from_jsonld(data))
            if not suid:
                raise ValidationError("'suid' is a required attribute")
        _task_id = digestive_tract.swallow__sharev2_legacy(
            from_user=request.user,
            record=json.dumps(data, sort_keys=True),
            record_identifier=suid,
            transformer_key='v2_push',
            urgent=True,
        )
        return Response({
            'type': 'NormalizedData',
            'attributes': {
                'task': _task_id,
            },
        }, status=status.HTTP_202_ACCEPTED)

1	import logging	2✔
2	import json	2✔
3
4	from django.urls import reverse	2✔
5	from rest_framework import status	2✔
6	from rest_framework import generics	2✔
7	from rest_framework.exceptions import ValidationError	2✔
8	from rest_framework.response import Response	2✔
9	import sentry_sdk	2✔
10
11	from share import models as share_db	2✔
12	from share.util.graph import MutableGraph	2✔
13	from share.util.osf import guess_osf_guid	2✔
14	from api.base.views import ShareViewSet	2✔
15	from api.normalizeddata.serializers import BasicNormalizedDataSerializer	2✔
16	from api.normalizeddata.serializers import FullNormalizedDataSerializer	2✔
17	from api.pagination import CursorPagination	2✔
18	from api.permissions import ReadOnlyOrTokenHasScopeOrIsAuthenticated	2✔
19	from trove import digestive_tract	2✔
20
21
22	logger = logging.getLogger(__name__)	2✔
23
24
25	class NormalizedDataViewSet(ShareViewSet, generics.ListCreateAPIView, generics.RetrieveAPIView):	2✔
26	"""View showing all normalized data in the SHARE Dataset.
27
28	## Submitting changes to the SHARE dataset
29	Changes, whether they are additions or modifications, are submitted as a subset of [JSON-LD graphs](https://www.w3.org/TR/json-ld/#named-graphs).
30	Each [node](https://www.w3.org/TR/json-ld/#dfn-node) of the graph MUST contain both an `@id` and `@type` key.
31
32	Method: POST
33	Body (JSON): {
34	'data': {
35	'type': 'NormalizedData'
36	'attributes': {
37	'data': {
38	'@graph': [{
39	'@type': <type of document, exp: person>,
40	'@id': <_:random>,
41	<attribute_name>: <value>,
42	<relationship_name>: {
43	'@type': <type>,
44	'@id': <id>
45	}
46	}]
47	}
48	}
49	}
50	}
51	Success: 200 OK
52	"""
53	ordering = ('-id', )	2✔
54	pagination_class = CursorPagination	2✔
55	permission_classes = (ReadOnlyOrTokenHasScopeOrIsAuthenticated, )	2✔
56	required_scopes = ('upload_normalized_manuscript', )	2✔
57	resource_name = 'NormalizedData'	2✔
58
59	def get_serializer_class(self):	2✔
60	if not self.request.user.is_authenticated:	2✔
61	return BasicNormalizedDataSerializer	2✔
62	elif self.request.user.is_robot:	2✔
63	return FullNormalizedDataSerializer	2✔
64	return BasicNormalizedDataSerializer	2✔
65
66	def get_queryset(self):	2✔
67	return share_db.NormalizedData.objects.all()	2✔
68
69	def create(self, request, args, *kwargs):	2✔
70	if share_db.FeatureFlag.objects.flag_is_up(share_db.FeatureFlag.IGNORE_SHAREV2_INGEST):	2✔
71	return Response({	×
72	'errors': [
73	{'detail': (
74	'this route was deprecated and has been removed'
75	f' (use {reverse("trove:ingest-rdf")} instead)'
76	)},
77	],
78	}, status=status.HTTP_410_GONE)
79	try:	2✔
80	return self._do_create(request, args, *kwargs)	2✔
81	except Exception:	2✔
82	sentry_sdk.capture_exception() # get some insight into common validation errors	2✔
83	raise	2✔
84
85	def _do_create(self, request, args, *kwargs):	2✔
86	serializer = self.get_serializer_class()(data=request.data, context={'request': request})	2✔
87	serializer.is_valid(raise_exception=True)	2✔
88
89	data = serializer.validated_data['data']	2✔
90	suid = serializer.validated_data.get('suid', None)	2✔
91	if not suid:	2✔
92	# HACK: try for an osf guid -- may still be None tho
93	suid = guess_osf_guid(MutableGraph.from_jsonld(data))	2✔
94	if not suid:	2✔
95	raise ValidationError("'suid' is a required attribute")	2✔
96	_task_id = digestive_tract.swallow__sharev2_legacy(	2✔
97	from_user=request.user,
98	record=json.dumps(data, sort_keys=True),
99	record_identifier=suid,
100	transformer_key='v2_push',
101	urgent=True,
102	)
103	return Response({	2✔
104	'type': 'NormalizedData',
105	'attributes': {
106	'task': _task_id,
107	},
108	}, status=status.HTTP_202_ACCEPTED)

CenterForOpenScience / SHARE / 13837341397

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