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Added IRIs as extra field properties in datamodels #434

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c05eb23
Added IRIs as extra field properties in datamodels
Feb 27, 2024
8fb9de3
reset DataCacheConfig signature
Feb 27, 2024
70c113b
Update oteapi/models/filterconfig.py
quaat Feb 29, 2024
c7d1974
Update oteapi/models/datacacheconfig.py
quaat Feb 29, 2024
f00b31e
Update oteapi/models/filterconfig.py
quaat Feb 29, 2024
37551c7
Update oteapi/models/filterconfig.py
quaat Feb 29, 2024
216d717
Update oteapi/models/filterconfig.py
quaat Feb 29, 2024
3f9b721
Update oteapi/models/transformationconfig.py
quaat Feb 29, 2024
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8 changes: 5 additions & 3 deletions oteapi/models/datacacheconfig.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,10 @@ class DataCacheConfig(AttrDict):
a configuration object.
"""

cacheDir: Path = Field(Path("oteapi"), description="Cache directory.")
cacheDir: Path = Field(
Path("oteapi"),
description="Cache directory.",
)
accessKey: Optional[str] = Field(
None,
description="Key with which the downloaded content can be accessed. "
Expand All @@ -36,6 +39,5 @@ class DataCacheConfig(AttrDict):
tag: Optional[str] = Field(
None,
description="Tag assigned to the downloaded content, typically "
"identifying a session. Used with the `evict()` method to clean up a "
"all cache entries with a given tag.",
"identifying a session. Used with the `evict()` method to clean up all cache entries with a given tag.",
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@jesper-friis jesper-friis Feb 28, 2024

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Please ahead to the PEP8 Python conventions. Max line length is 80 characters.

)
15 changes: 12 additions & 3 deletions oteapi/models/filterconfig.py
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@jesper-friis jesper-friis Feb 28, 2024 •
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The suggested properties for the query, condition and limit fields seems arbitrary chosen. Since there exists no properties in the DCAT and related W3C vocabularies that correspond to these fields, I think that it is better that we define our them in the OTE Interface Ontology (OTEIO).

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@quaat quaat Feb 29, 2024

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You are absolutely right about the IRIs being a bit random for certain properties, but I would much rather go to more generic concepts in established ontologies, than making up our own concepts in a custom ontology that nobody has adopted.

Original file line number Diff line number Diff line change
Expand Up @@ -11,13 +11,22 @@ class FilterConfig(GenericConfig):
"""Filter Strategy Data Configuration."""

filterType: str = Field(
..., description="Type of registered filter strategy. E.g., `filter/sql`."
...,
description="Type of registered filter strategy. E.g., `filter/sql`.",
json_schema_extra={"IRI": "http://purl.org/dc/terms/type"},
)
query: Optional[str] = Field(
None,
description="Define a query operation.",
json_schema_extra={"IRI": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Statement"},
)
query: Optional[str] = Field(None, description="Define a query operation.")
condition: Optional[str] = Field(
None,
description="Logical statement indicating when a filter should be applied.",
json_schema_extra={"IRI": "http://www.w3.org/2000/01/rdf-schema#comment"},
)
limit: Optional[int] = Field(
None, description="Number of items remaining after a filter expression."
None,
description="Number of items remaining after a filter expression.",
json_schema_extra={"IRI": "http://schema.org/Integer"},
)
3 changes: 3 additions & 0 deletions oteapi/models/mappingconfig.py
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Expand Up @@ -15,15 +15,18 @@ class MappingConfig(GenericConfig):
mappingType: str = Field(
...,
description="Type of registered mapping strategy.",
IRI="http://purl.org/dc/terms/type", # type: ignore
)
prefixes: Optional[Dict[str, str]] = Field(
None,
description=(
"Dictionary of shortnames that expands to an IRI given as local "
"value/IRI-expansion-pairs."
),
IRI="http://www.w3.org/2004/02/skos/core#notation", # type: ignore
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If using skos:notation for prefixes, then we need a to define a custom datatype, like oteio:prefixType, such that we can serialise a prefix as:

:mappingFilter skos:notation "rdfs: <http://www.w3.org/2000/01/rdf-schema#>"^^oteio:prefixType .

However, I think it would be simpler to define our own oteio:prefix, such that we can express the above as:

:mappingFilter oteio:prefix "rdfs: <http://www.w3.org/2000/01/rdf-schema#>" .

)
triples: Optional[Set[RDFTriple]] = Field(
None,
description="Set of RDF triples given as (subject, predicate, object).",
IRI="http://www.w3.org/1999/02/22-rdf-syntax-ns#Statement", # type: ignore
)
12 changes: 10 additions & 2 deletions oteapi/models/parserconfig.py
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Expand Up @@ -8,5 +8,13 @@
class ParserConfig(GenericConfig):
"""Parser Strategy Data Configuration."""

parserType: str = Field(..., description="Type of registered parser strategy.")
entity: AnyHttpUrl = Field(..., description="IRI to the entity or collection.")
parserType: str = Field(
...,
description="Type of registered parser strategy.",
IRI="http://purl.org/dc/terms/type",
) # type: ignore
entity: AnyHttpUrl = Field(
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Entity is a difficult name. It can mean anything. I am not found of freely mixing different vocabularies, but if we really want to identify this with schema:url, then I think the field should be named url.

...,
description="IRI to the metadata (entity) or collection of entities.",
IRI="http://schema.org/URL",
) # type: ignore
11 changes: 10 additions & 1 deletion oteapi/models/resourceconfig.py
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Expand Up @@ -21,7 +21,9 @@ class ResourceConfig(GenericConfig, SecretConfig):
"""

resourceType: Optional[str] = Field(
None, description="Type of registered resource strategy."
None,
description="Type of registered resource strategy.",
IRI="http://purl.org/dc/terms/type", # type: ignore
)

downloadUrl: Optional[HostlessAnyUrl] = Field(
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Please spell the field name as downloadURL to be consistent with DCAT.

Expand All @@ -32,6 +34,7 @@ class ResourceConfig(GenericConfig, SecretConfig):
" which this distribution is available directly, typically through a HTTPS"
" GET request or SFTP."
),
IRI="http://www.w3.org/ns/dcat#downloadURL", # type: ignore
)
mediaType: Optional[str] = Field(
None,
Expand All @@ -42,6 +45,7 @@ class ResourceConfig(GenericConfig, SecretConfig):
" type of the distribution is defined in IANA "
"[[IANA-MEDIA-TYPES](https://www.w3.org/TR/vocab-dcat-2/#bib-iana-media-types)]."
),
IRI="http://www.w3.org/ns/dcat#mediaType", # type: ignore
)
accessUrl: Optional[HostlessAnyUrl] = Field(
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Please spell the field name as accessURL to be consistent with DCAT.

None,
Expand All @@ -53,28 +57,33 @@ class ResourceConfig(GenericConfig, SecretConfig):
"query or API call.\n`downloadURL` is preferred for direct links to "
"downloadable resources."
),
IRI="http://www.w3.org/ns/dcat#accessURL", # type: ignore
)
accessService: Optional[str] = Field(
None,
description=(
"A data service that gives access to the distribution of the dataset."
),
IRI="http://www.w3.org/ns/dcat#accessService", # type: ignore
)
license: Optional[str] = Field(
None,
description=(
"A legal document under which the distribution is made available."
),
IRI="http://purl.org/dc/terms/license", # type: ignore
)
accessRights: Optional[str] = Field(
None,
description=(
"A rights statement that concerns how the distribution is accessed."
),
IRI="http://purl.org/dc/terms/accessRights", # type: ignore
)
publisher: Optional[str] = Field(
None,
description="The entity responsible for making the resource/item available.",
IRI="http://purl.org/dc/terms/publisher", # type: ignore
)

@model_validator(mode="after")
Expand Down
16 changes: 9 additions & 7 deletions oteapi/models/secretconfig.py
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Expand Up @@ -23,20 +23,22 @@ class SecretConfig(BaseModel):
"""Simple model for handling secret in other config-models."""

user: Optional[TogglableSecretStr] = Field(
None, description="User name for authentication."
None,
description="User name for authentication.",
)
password: Optional[TogglableSecretStr] = Field(
None, description="Password for authentication."
None,
description="Password for authentication.",
)
token: Optional[TogglableSecretStr] = Field(
None,
description=(
"An access token for providing access and meta data to an application."
),
description="An access token for providing access and meta data to an application.",
)
client_id: Optional[TogglableSecretStr] = Field(
None, description="Client ID for an OAUTH2 client."
None,
description="Client ID for an OAUTH2 client.",
)
client_secret: Optional[TogglableSecretStr] = Field(
None, description="Client secret for an OAUTH2 client."
None,
description="Client secret for an OAUTH2 client.",
)
30 changes: 24 additions & 6 deletions oteapi/models/transformationconfig.py
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Expand Up @@ -39,40 +39,58 @@ class TransformationConfig(GenericConfig, SecretConfig):
description=(
"Type of registered transformation strategy. E.g., `celery/remote`."
),
IRI="http://purl.org/dc/terms/type", # type: ignore
)
name: Optional[str] = Field(
None, description="Human-readable name of the transformation strategy."
None,
description="Human-readable name of the transformation strategy.",
IRI="http://purl.org/dc/terms/title", # type: ignore
)
due: Optional[datetime] = Field(
None,
description=(
"Optional field to indicate a due data/time for when a transformation "
"should finish."
),
IRI="http://purl.org/dc/terms/date", # type: ignore
)
priority: Optional[ProcessPriority] = Field(
ProcessPriority.MEDIUM,
description="Define the process priority of the transformation execution.",
IRI="http://www.w3.org/ns/adms#status", # type: ignore
)


class TransformationStatus(BaseModel):
"""Return from transformation status."""

id: str = Field(..., description="ID for the given transformation process.")
id: str = Field(
...,
description="ID for the given transformation process.",
IRI="http://purl.org/dc/terms/identifier", # type: ignore
)
status: Optional[str] = Field(
None, description="Status for the transformation process."
None,
description="Status for the transformation process.",
IRI="http://www.w3.org/ns/adms#status", # type: ignore
)
messages: Optional[List[str]] = Field(
None, description="Messages related to the transformation process."
None,
description="Messages related to the transformation process.",
IRI="http://purl.org/dc/terms/description", # type: ignore
)
created: Optional[datetime] = Field(
None,
description="Time of creation for the transformation process. Given in UTC.",
IRI="http://purl.org/dc/terms/created", # type: ignore
)
startTime: Optional[datetime] = Field(
None, description="Time when the transformation process started. Given in UTC."
None,
description="Time when the transformation process started. Given in UTC.",
IRI="http://purl.org/dc/terms/date", # type: ignore
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@jesper-friis jesper-friis Feb 29, 2024 •
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startTime and finishTime cannot have the same IRI. However, DCAT has dcat:startDate and dcat:endDate which are suitable here.

The only issue with dcat:startDate and dcat:endDate are that they have domain dcterms:PeriodOfTime. Since a TransformationStatus describes a time period, but isn't a time periode itself, the RDF serialisation cannot be straight forward, like

:transformation_status1 
  dcat:startTime "2024-02-29 08:45" ;
  dcat:endTime "2024-02-29 09:00" .

but has to has to be expressed as:

:transformation_status1 
  dcterms:temporal [
    a dcterms:PeriodOfTime ;
    dcat:startTime "2024-02-29 08:45" ;
    dcat:endTime "2024-02-29 09:00" ;
  ] .

)
finishTime: Optional[datetime] = Field(
None, description="Time when the tranformation process finished. Given in UTC."
None,
description="Time when the tranformation process finished. Given in UTC.",
IRI="http://purl.org/dc/terms/date", # type: ignore
)
1 change: 1 addition & 0 deletions oteapi/strategies/parse/application_json.py
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Expand Up @@ -45,6 +45,7 @@ class JSONParserConfig(ParserConfig):
"parser/json",
description=ParserConfig.model_fields["parserType"].description,
)

configuration: JSONConfig = Field(
..., description="JSON parse strategy-specific configuration."
)
Expand Down