forked from pangaea-data-publisher/fuji
-
Notifications
You must be signed in to change notification settings - Fork 0
/
fair_object_controller.py
260 lines (249 loc) · 11.5 KB
/
fair_object_controller.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
# SPDX-FileCopyrightText: 2020 PANGAEA (https://www.pangaea.de/)
#
# SPDX-License-Identifier: MIT
import datetime
import connexion
from fuji_server.controllers.fair_check import FAIRCheck
from fuji_server.helper.identifier_helper import IdentifierHelper
from fuji_server.helper.preprocessor import Preprocessor
from fuji_server.helper.results_exporter import FAIRResultsMapper
from fuji_server.models.fair_results import FAIRResults
from fuji_server.models.harvest_results_metadata import HarvestResultsMetadata
async def assess_by_id(body):
"""assess_by_id
Evaluate FAIRness of a data object based on its identifier # noqa: E501
:param body:
:type body: dict | bytes
:rtype: FAIRResults
"""
allow_remote_logging = False
# Request POST BODY has to be JSON
if connexion.request.content_type == "application/json":
# The client has to send this HTTP header (Allow-Remote-Logging:True) explicitely to enable remote logging
# Useful for e.g. web clients..
allow_remote_logging = connexion.request.headers.get("Allow-Remote-Logging")
debug = True
results = []
# json_body = await connexion.request.json()
# body = Body.from_dict(json_body)
# clienturi = Body.from_dict(connexion.request
identifier = body.get("object_identifier")
debug = body.get("test_debug")
metadata_service_endpoint = body.get("metadata_service_endpoint")
oaipmh_endpoint = body.get("oaipmh_endpoint")
metadata_service_type = body.get("metadata_service_type")
usedatacite = body.get("use_datacite")
usegithub = body.get("use_github")
metric_version = body.get("metric_version")
print("BODY METRIC", metric_version)
auth_token = body.get("auth_token")
auth_token_type = body.get("auth_token_type")
logger = Preprocessor.logger
# updating re3data
Preprocessor.retrieve_datacite_re3repos()
logger.info("Assessment target: " + identifier)
print("Assessment target: ", identifier, flush=True)
starttimestmp = datetime.datetime.now().replace(microsecond=0).isoformat() + "Z"
ft = FAIRCheck(
uid=identifier,
test_debug=debug,
metadata_service_url=metadata_service_endpoint,
metadata_service_type=metadata_service_type,
use_datacite=usedatacite,
use_github=usegithub,
oaipmh_endpoint=oaipmh_endpoint,
metric_version=metric_version,
)
# dataset level authentication
if auth_token:
ft.set_auth_token(auth_token, auth_token_type)
# set target for remote logging
remote_log_host, remote_log_path = Preprocessor.remote_log_host, Preprocessor.remote_log_path
# print(remote_log_host, remote_log_path)
if remote_log_host and remote_log_path and allow_remote_logging:
print("Remote logging enabled...")
if ft.weblogger:
ft.logger.addHandler(ft.weblogger)
else:
print("Remote logging disabled...")
if ft.weblogger:
ft.logger.removeHandler(ft.weblogger)
print("starting harvesting ")
ft.harvest_all_metadata()
ft.set_harvested_metadata()
uid_result, pid_result = ft.check_unique_persistent_metadata_identifier()
if ft.repeat_pid_check:
ft.retrieve_metadata_external(ft.pid_url, repeat_mode=True)
ft.set_harvested_metadata()
ft.clean_metadata()
ft.harvest_re3_data()
ft.harvest_github()
core_metadata_result = ft.check_minimal_metatadata()
# print(ft.metadata_unmerged)
content_identifier_included_result = ft.check_data_identifier_included_in_metadata()
# print('F-UJI checks: access level')
access_level_result = ft.check_data_access_level()
# print('F-UJI checks: license')
license_result = ft.check_license()
license_file_result = ft.check_license_file()
# print('F-UJI checks: related')
related_resources_result = ft.check_relatedresources()
# print('F-UJI checks: searchable')
check_searchable_result = ft.check_searchable()
# print('F-UJI checks: data content')
ft.harvest_all_data()
uid_data_result = ft.check_unique_content_identifier()
pid_data_result = ft.check_persistent_data_identifier()
upid_software_result = ft.check_unique_persistent_software_identifier()
software_component_result = ft.check_software_component_identifier()
version_identifier_result = ft.check_version_identifier()
development_metadata_result = ft.check_development_metadata()
open_api_result = ft.check_open_api()
requirements_result = ft.check_requirements()
test_cases_result = ft.check_test_cases()
data_identifier_included_result = ft.check_data_content_metadata()
metadata_identifier_included_result = ft.check_metadata_identifier_included_in_metadata()
data_file_format_result = ft.check_data_file_format()
# print('F-UJI checks: data file format')
community_standards_result = ft.check_community_metadatastandards()
data_provenance_result = ft.check_data_provenance()
code_provenance_result = ft.check_code_provenance()
formal_metadata_result = ft.check_formal_metadata()
# print('F-UJI checks: semantic vocab')
semantic_vocab_result = ft.check_semantic_vocabulary()
metadata_preserved_result = ft.check_metadata_preservation()
standard_protocol_data_result = ft.check_standardised_protocol_data()
standard_protocol_metadata_result = ft.check_standardised_protocol_metadata()
if uid_result:
results.append(uid_result)
if pid_result:
results.append(pid_result)
if uid_data_result:
results.append(uid_data_result)
if pid_data_result:
results.append(pid_data_result)
if upid_software_result:
results.append(upid_software_result)
if software_component_result:
results.append(software_component_result)
if version_identifier_result:
results.append(version_identifier_result)
if development_metadata_result:
results.append(development_metadata_result)
if open_api_result:
results.append(open_api_result)
if requirements_result:
results.append(requirements_result)
if test_cases_result:
results.append(test_cases_result)
if core_metadata_result:
results.append(core_metadata_result)
if content_identifier_included_result:
results.append(content_identifier_included_result)
if check_searchable_result:
results.append(check_searchable_result)
if formal_metadata_result:
results.append(formal_metadata_result)
if semantic_vocab_result:
results.append(semantic_vocab_result)
if related_resources_result:
results.append(related_resources_result)
if data_identifier_included_result:
results.append(data_identifier_included_result)
if metadata_identifier_included_result:
results.append(metadata_identifier_included_result)
if license_result:
results.append(license_result)
if license_file_result:
results.append(license_file_result)
if access_level_result:
results.append(access_level_result)
if data_provenance_result:
results.append(data_provenance_result)
if code_provenance_result:
results.append(code_provenance_result)
if community_standards_result:
results.append(community_standards_result)
if data_file_format_result:
results.append(data_file_format_result)
if standard_protocol_data_result:
results.append(standard_protocol_data_result)
if standard_protocol_metadata_result:
results.append(standard_protocol_metadata_result)
if metadata_preserved_result:
results.append(metadata_preserved_result)
debug_messages = ft.get_log_messages_dict()
# ft.logger_message_stream.flush()
summary = ft.get_assessment_summary(results)
for res_k, res_v in enumerate(results):
if ft.isDebug:
debug_list = debug_messages.get(res_v["metric_identifier"])
# debug_list= ft.msg_filter.getMessage(res_v['metric_identifier'])
if debug_list is not None:
results[res_k]["test_debug"] = debug_messages.get(res_v["metric_identifier"])
else:
results[res_k]["test_debug"] = ["INFO: No debug messages received"]
else:
results[res_k]["test_debug"] = ["INFO: Debugging disabled"]
debug_messages = {}
if len(ft.logger.handlers) > 1:
ft.logger.handlers = [ft.logger.handlers[-1]]
# endtimestmp = datetime.datetime.now().replace(microsecond=0).isoformat()
endtimestmp = (
datetime.datetime.now().replace(microsecond=0).isoformat() + "Z"
) # use timestamp format from RFC 3339 as specified in openapi3
metric_spec = ft.metric_helper.metric_specification
resolved_url = ft.landing_url
if not resolved_url:
resolved_url = "not defined"
# metric_version = os.path.basename(Preprocessor.METRIC_YML_PATH)
totalmetrics = len(results)
request = body
if ft.pid_url:
idhelper = IdentifierHelper(ft.pid_url)
request["normalized_object_identifier"] = idhelper.get_normalized_id()
results.sort(key=lambda d: d["id"]) # sort results by metric ID
#### metadata summary
harvest_result = []
for metadata in ft.metadata_unmerged:
harvest_result.append(
HarvestResultsMetadata(
metadata.get("offering_method"),
metadata.get("url"),
metadata.get("format"),
metadata.get("schema"),
metadata.get("namespaces"),
metadata.get("metadata"),
)
)
###
final_response = FAIRResults(
request=request,
start_timestamp=starttimestmp,
end_timestamp=endtimestmp,
software_version=ft.FUJI_VERSION,
test_id=ft.test_id,
metric_version=metric_version,
metric_specification=metric_spec,
total_metrics=totalmetrics,
results=results,
summary=summary,
resolved_url=resolved_url,
harvested_metadata=harvest_result,
)
accept_header = connexion.request.headers.get("Accept")
print("ACCEPT HEADER ", accept_header)
# RDF
rdf_mimes = FAIRResultsMapper.allowed_serialisations
if connexion.request.headers.get("Accept") in rdf_mimes:
rdf_mapper = FAIRResultsMapper(final_response)
rdf = rdf_mapper.getQualityVocabularyRDF(connexion.request.headers.get("Accept"))
print("RDF")
return rdf, 200, {"content-type": connexion.request.headers.get("Accept")}
# Standard JSON
elif connexion.request.headers.get("Accept") in ["application/json", "*/*"]:
return final_response, 200, {"content-type": "application/json"}
else:
return "", 400, {"content-type": "application/json"}
else:
return "", 400, {"content-type": "application/json"}