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Maint: ebrains datasets, private some properties and methods #444

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merged 2 commits into from
Sep 8, 2023
Merged

Maint: ebrains datasets, private some properties and methods #444

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6bdca8e
Maint: ebrains datasets, detail property should be private
AhmetNSimsek Aug 30, 2023
0823292
Merge branch 'v0.5_dev' into maint_ebrainsdatasets
AhmetNSimsek Sep 8, 2023
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2 changes: 1 addition & 1 deletion siibra/features/dataset/ebrains.py
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Original file line number Diff line number Diff line change
Expand Up @@ -71,7 +71,7 @@ def version_identifier(self):

@property
def version_history(self):
return self._dataset.version_changes
return self._dataset.version_changelog

@property
def url(self):
Expand Down
48 changes: 24 additions & 24 deletions siibra/retrieval/datasets.py
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Original file line number Diff line number Diff line change
Expand Up @@ -127,7 +127,7 @@ def id(self) -> str:
return self._id

@property
def detail(self):
def _detail(self):
if not self._cached_data:
match = re.search(r"([a-f0-9-]+)$", self.id)
instance_id = match.group(1)
Expand All @@ -144,7 +144,7 @@ def detail(self):
@property
def name(self) -> str:
if self._name is None:
self._name = self.detail.get("name")
self._name = self._detail.get("name")
return self._name

@property
Expand All @@ -153,29 +153,29 @@ def urls(self) -> List[EbrainsDatasetUrl]:
{
"url": f if f.startswith("http") else f"https://doi.org/{f}",
}
for f in self.detail.get("kgReference", [])
for f in self._detail.get("kgReference", [])
]

@property
def description(self) -> str:
return self.detail.get("description")
return self._detail.get("description")

@property
def contributors(self) -> List[EbrainsDatasetPerson]:
return self.detail.get("contributors")
return self._detail.get("contributors")

@property
def ebrains_page(self):
return f"https://search.kg.ebrains.eu/instances/{self.id}"

@property
def custodians(self) -> EbrainsDatasetPerson:
return self.detail.get("custodians")
return self._detail.get("custodians")


class EbrainsV3DatasetVersion(EbrainsBaseDataset):
@staticmethod
def parse_person(d: dict) -> EbrainsDatasetPerson:
def _parse_person(d: dict) -> EbrainsDatasetPerson:
assert "https://openminds.ebrains.eu/core/Person" in d.get("type"), "Cannot convert a non person to a person dict!"
_id = d.get("id")
name = f"{d.get('givenName')} {d.get('familyName')}"
Expand All @@ -194,7 +194,7 @@ def __init__(self, id, *, cached_data=None) -> None:
self._cached_data = cached_data

@property
def detail(self):
def _detail(self):
if not self._cached_data:
match = re.search(r"([a-f0-9-]+)$", self._id)
instance_id = match.group(1)
Expand All @@ -214,30 +214,30 @@ def id(self) -> str:

@property
def name(self) -> str:
fullname = self.detail.get("fullName")
fullname = self._detail.get("fullName")
if not fullname:
for dataset in self.is_version_of:
if fullname:
break
fullname = dataset.name
version_id = self.detail.get("versionIdentifier")
version_id = self._detail.get("versionIdentifier")
return f"{fullname} ({version_id})"

@property
def is_version_of(self):
if not hasattr(self, "_is_version_of"):
self._is_version_of = [EbrainsV3Dataset(id=id.get("id")) for id in self.detail.get("isVersionOf", [])]
self._is_version_of = [EbrainsV3Dataset(id=id.get("id")) for id in self._detail.get("isVersionOf", [])]
return self._is_version_of

@property
def urls(self) -> List[EbrainsDatasetUrl]:
return [{
"url": doi.get("identifier", None)
} for doi in self.detail.get("doi", [])]
} for doi in self._detail.get("doi", [])]

@property
def description(self) -> str:
description = self.detail.get("description")
description = self._detail.get("description")
for ds in self.is_version_of:
if description:
break
Expand All @@ -246,7 +246,7 @@ def description(self) -> str:

@property
def contributors(self) -> List[EbrainsDatasetPerson]:
return [EbrainsV3DatasetVersion.parse_person(d) for d in self.detail.get("author", [])]
return [EbrainsV3DatasetVersion._parse_person(d) for d in self._detail.get("author", [])]

@property
def ebrains_page(self) -> str:
Expand All @@ -256,15 +256,15 @@ def ebrains_page(self) -> str:

@property
def custodians(self) -> EbrainsDatasetPerson:
return [EbrainsV3DatasetVersion.parse_person(d) for d in self.detail.get("custodian", [])]
return [EbrainsV3DatasetVersion._parse_person(d) for d in self._detail.get("custodian", [])]

@property
def version_changes(self):
return self.detail.get("versionInnovation", "")
def version_changelog(self):
return self._detail.get("versionInnovation", "")

@property
def version_identifier(self):
return self.detail.get("versionIdentifier", "")
return self._detail.get("versionIdentifier", "")


class EbrainsV3Dataset(EbrainsBaseDataset):
Expand All @@ -281,16 +281,16 @@ def id(self) -> str:

@property
def name(self) -> str:
return self.detail.get("fullName")
return self._detail.get("fullName")

@property
def urls(self) -> List[EbrainsDatasetUrl]:
return [{
"url": doi.get("identifier", None)
} for doi in self.detail.get("doi", [])]
} for doi in self._detail.get("doi", [])]

@property
def detail(self):
def _detail(self):
if not self._cached_data:
match = re.search(r"([a-f0-9-]+)$", self._id)
instance_id = match.group(1)
Expand All @@ -306,7 +306,7 @@ def detail(self):

@property
def description(self) -> str:
return self.detail.get("description", "")
return self._detail.get("description", "")

@property
def contributors(self):
Expand All @@ -327,8 +327,8 @@ def ebrains_page(self) -> str:

@property
def custodians(self) -> EbrainsDatasetPerson:
return [EbrainsV3DatasetVersion.parse_person(d) for d in self.detail.get("custodian", [])]
return [EbrainsV3DatasetVersion._parse_person(d) for d in self._detail.get("custodian", [])]

@property
def version_ids(self) -> List['str']:
return [version.get("id") for version in self.detail.get("versions", [])]
return [version.get("id") for version in self._detail.get("versions", [])]