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apdavisonapdavison
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update openminds module from most recent schemas
1 parent 7e91a70 commit 1504377

25 files changed

Lines changed: 204 additions & 5 deletions

‎builder/update_openminds.py‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -729,8 +729,8 @@ def get_type(prop):
729729
else:
730730
forward_link_name = sorted(forward_link_names)[0]
731731
print(f"Multiple forward link names found: {forward_link_names}, using {forward_link_name}")
732-
# if "FileRepository" in self._schema_payload["_type"]:
733-
# breakpoint()
732+
# todo: we should fix this at some point, using just the first forward_link_name causes things to break
733+
# making this a dictionary keyed by class names should work?
734734
_forward_link_name_python = generate_python_name(forward_link_name)
735735
iri = f"^vocab:{forward_iri}"
736736
doc = f"reverse of '{_forward_link_name_python}'"

‎fairgraph/openminds/computation/validation_test_version.py‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -159,6 +159,7 @@ class ValidationTestVersion(KGObject):
159159
"openminds.controlled_terms.Language",
160160
"openminds.controlled_terms.Laterality",
161161
"openminds.controlled_terms.LearningResourceType",
162+
"openminds.controlled_terms.MRAcquisitionType",
162163
"openminds.controlled_terms.MRIPulseSequence",
163164
"openminds.controlled_terms.MRIWeighting",
164165
"openminds.controlled_terms.MeasuredQuantity",

‎fairgraph/openminds/computation/workflow_recipe_version.py‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -158,6 +158,7 @@ class WorkflowRecipeVersion(KGObject):
158158
"openminds.controlled_terms.Language",
159159
"openminds.controlled_terms.Laterality",
160160
"openminds.controlled_terms.LearningResourceType",
161+
"openminds.controlled_terms.MRAcquisitionType",
161162
"openminds.controlled_terms.MRIPulseSequence",
162163
"openminds.controlled_terms.MRIWeighting",
163164
"openminds.controlled_terms.MeasuredQuantity",

‎fairgraph/openminds/controlled_terms/__init__.py‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -49,6 +49,7 @@
4949
from .model_abstraction_level import ModelAbstractionLevel
5050
from .model_scope import ModelScope
5151
from .molecular_entity import MolecularEntity
52+
from .mr_acquisition_type import MRAcquisitionType
5253
from .mri_pulse_sequence import MRIPulseSequence
5354
from .mri_weighting import MRIWeighting
5455
from .olfactory_stimulus_type import OlfactoryStimulusType

‎fairgraph/openminds/controlled_terms/mr_acquisition_type.py‎

Lines changed: 122 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,122 @@
1+
"""
2+
<description not available>
3+
"""
4+
5+
# this file was auto-generated
6+
7+
from fairgraph import KGObject, IRI
8+
from fairgraph.properties import Property
9+
10+
11+
from fairgraph.base import IRI
12+
13+
14+
class MRAcquisitionType(KGObject):
15+
"""
16+
<description not available>
17+
"""
18+
19+
default_space = "controlled"
20+
type_ = "https://openminds.ebrains.eu/controlledTerms/MRAcquisitionType"
21+
properties = [
22+
Property(
23+
"definition",
24+
str,
25+
"vocab:definition",
26+
doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.",
27+
),
28+
Property(
29+
"description",
30+
str,
31+
"vocab:description",
32+
doc="Longer statement or account giving the characteristics of the m r acquisition type.",
33+
),
34+
Property(
35+
"interlex_identifier",
36+
IRI,
37+
"vocab:interlexIdentifier",
38+
doc="Persistent identifier for a term registered in the InterLex project.",
39+
),
40+
Property(
41+
"knowledge_space_link",
42+
IRI,
43+
"vocab:knowledgeSpaceLink",
44+
doc="Persistent link to an encyclopedia entry in the Knowledge Space project.",
45+
),
46+
Property(
47+
"name",
48+
str,
49+
"vocab:name",
50+
required=True,
51+
doc="Word or phrase that constitutes the distinctive designation of the m r acquisition type.",
52+
),
53+
Property(
54+
"preferred_ontology_identifier",
55+
IRI,
56+
"vocab:preferredOntologyIdentifier",
57+
doc="Persistent identifier of a preferred ontological term.",
58+
),
59+
Property(
60+
"synonyms",
61+
str,
62+
"vocab:synonym",
63+
multiple=True,
64+
doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.",
65+
),
66+
]
67+
reverse_properties = [
68+
Property(
69+
"describes",
70+
[
71+
"openminds.computation.ValidationTestVersion",
72+
"openminds.computation.WorkflowRecipeVersion",
73+
"openminds.core.DatasetVersion",
74+
"openminds.core.MetaDataModelVersion",
75+
"openminds.core.ModelVersion",
76+
"openminds.core.SoftwareVersion",
77+
"openminds.core.WebServiceVersion",
78+
"openminds.publications.Book",
79+
"openminds.publications.Chapter",
80+
"openminds.publications.LearningResource",
81+
"openminds.publications.LivePaperVersion",
82+
"openminds.publications.ScholarlyArticle",
83+
"openminds.sands.BrainAtlasVersion",
84+
"openminds.sands.CommonCoordinateSpaceVersion",
85+
],
86+
"^vocab:keyword",
87+
reverse="keywords",
88+
multiple=True,
89+
doc="reverse of 'keywords'",
90+
),
91+
]
92+
existence_query_properties = ("name",)
93+
94+
def __init__(
95+
self,
96+
name=None,
97+
definition=None,
98+
describes=None,
99+
description=None,
100+
interlex_identifier=None,
101+
knowledge_space_link=None,
102+
preferred_ontology_identifier=None,
103+
synonyms=None,
104+
id=None,
105+
data=None,
106+
space=None,
107+
scope=None,
108+
):
109+
return super().__init__(
110+
id=id,
111+
space=space,
112+
scope=scope,
113+
data=data,
114+
name=name,
115+
definition=definition,
116+
describes=describes,
117+
description=description,
118+
interlex_identifier=interlex_identifier,
119+
knowledge_space_link=knowledge_space_link,
120+
preferred_ontology_identifier=preferred_ontology_identifier,
121+
synonyms=synonyms,
122+
)

‎fairgraph/openminds/controlled_terms/service.py‎

Lines changed: 10 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -88,6 +88,14 @@ class Service(KGObject):
8888
multiple=True,
8989
doc="reverse of 'keywords'",
9090
),
91+
Property(
92+
"hosts",
93+
"openminds.publications.LivePaperResourceItem",
94+
"^vocab:hostedBy",
95+
reverse="hosted_by",
96+
multiple=True,
97+
doc="reverse of 'hosted_by'",
98+
),
9199
Property(
92100
"linked_from",
93101
"openminds.core.ServiceLink",
@@ -105,6 +113,7 @@ def __init__(
105113
definition=None,
106114
describes=None,
107115
description=None,
116+
hosts=None,
108117
interlex_identifier=None,
109118
knowledge_space_link=None,
110119
linked_from=None,
@@ -124,6 +133,7 @@ def __init__(
124133
definition=definition,
125134
describes=describes,
126135
description=description,
136+
hosts=hosts,
127137
interlex_identifier=interlex_identifier,
128138
knowledge_space_link=knowledge_space_link,
129139
linked_from=linked_from,

‎fairgraph/openminds/core/data/file.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -307,7 +307,7 @@ def from_local_file(cls, relative_path):
307307
value=float(os.stat(relative_path).st_size), unit=UnitOfMeasurement(name="bytes")
308308
),
309309
hashes=Hash(algorithm="SHA1", digest=sha1sum(relative_path)),
310-
format=ContentType(name=mimetypes.guess_type(relative_path)[0])
310+
format=ContentType(name=mimetypes.guess_type(relative_path)[0]),
311311
# todo: query ContentTypes since that contains additional, EBRAINS-specific content types
312312
)
313313
return obj

‎fairgraph/openminds/core/products/dataset_version.py‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -186,6 +186,7 @@ class DatasetVersion(KGObject):
186186
"openminds.controlled_terms.Language",
187187
"openminds.controlled_terms.Laterality",
188188
"openminds.controlled_terms.LearningResourceType",
189+
"openminds.controlled_terms.MRAcquisitionType",
189190
"openminds.controlled_terms.MRIPulseSequence",
190191
"openminds.controlled_terms.MRIWeighting",
191192
"openminds.controlled_terms.MeasuredQuantity",

‎fairgraph/openminds/core/products/meta_data_model_version.py‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -139,6 +139,7 @@ class MetaDataModelVersion(KGObject):
139139
"openminds.controlled_terms.Language",
140140
"openminds.controlled_terms.Laterality",
141141
"openminds.controlled_terms.LearningResourceType",
142+
"openminds.controlled_terms.MRAcquisitionType",
142143
"openminds.controlled_terms.MRIPulseSequence",
143144
"openminds.controlled_terms.MRIWeighting",
144145
"openminds.controlled_terms.MeasuredQuantity",

‎fairgraph/openminds/core/products/model_version.py‎

Lines changed: 14 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -28,6 +28,17 @@ class ModelVersion(KGObject):
2828
required=True,
2929
doc="Level to which something is accessible to the model version.",
3030
),
31+
Property(
32+
"configuration",
33+
[
34+
"openminds.core.Configuration",
35+
"openminds.core.File",
36+
"openminds.core.PropertyValueList",
37+
"openminds.core.WebResource",
38+
],
39+
"vocab:configuration",
40+
doc="no description available",
41+
),
3142
Property(
3243
"copyright",
3344
"openminds.core.Copyright",
@@ -154,6 +165,7 @@ class ModelVersion(KGObject):
154165
"openminds.controlled_terms.Language",
155166
"openminds.controlled_terms.Laterality",
156167
"openminds.controlled_terms.LearningResourceType",
168+
"openminds.controlled_terms.MRAcquisitionType",
157169
"openminds.controlled_terms.MRIPulseSequence",
158170
"openminds.controlled_terms.MRIWeighting",
159171
"openminds.controlled_terms.MeasuredQuantity",
@@ -365,6 +377,7 @@ def __init__(
365377
alias=None,
366378
accessibility=None,
367379
comments=None,
380+
configuration=None,
368381
copyright=None,
369382
custodians=None,
370383
description=None,
@@ -413,6 +426,7 @@ def __init__(
413426
alias=alias,
414427
accessibility=accessibility,
415428
comments=comments,
429+
configuration=configuration,
416430
copyright=copyright,
417431
custodians=custodians,
418432
description=description,

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