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Fix namespace + map_name URL construction.
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Carsten committed Jan 14, 2025
1 parent 6ac943f commit e61a14b
Showing 1 changed file with 57 additions and 56 deletions.
113 changes: 57 additions & 56 deletions ontop/omemap.obda
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Original file line number Diff line number Diff line change
Expand Up @@ -16,85 +16,86 @@ ome_instance: https://example.org/site/

[MappingDeclaration] @collection [[
mappingId MAPID-project(1)
target ome_instance:Project/{project_id} a ome_core:Project ; rdfs:label {project_name} ; rdfs:comment {project_description} .
target ome_instance:Project/{project_id} a ome_core:Project ; rdfs:label {project_name} ; rdfs:comment {project_description} .
source select
_project.id as project_id,
_project.name as project_name,
_project.description as project_description
from project as _project

mappingId MAPID-project(2)
target ome_instance:Project/{project_id} a ome_core:Project ; ome_core:dataset ome_instance:Dataset/{dataset_id} .
target ome_instance:Project/{project_id} a ome_core:Project ; ome_core:dataset ome_instance:Dataset/{dataset_id} .
source select
_project.id as project_id,
_projectdatasetlink.child as dataset_id
from project as _project
left join projectdatasetlink as _projectdatasetlink on _project.id = _projectdatasetlink.parent

mappingId MAPID-project(3)
target ome_instance:Project/{project_id} a ome_core:Project ; <{map_key}> {map_value}^^xsd:string .
source select
_project.id as project_id,
concat(regexp_replace(regexp_replace(
case
when _annotation.ns is null then 'http://www.openmicroscopy.org/ns/default/'
else
case
when _annotation.ns ~ '^http[s]{0,1}:\/\/' then _annotation.ns
else 'http://www.openmicroscopy.org/ns/default/'
end
end,
'([^\/,#])$',
'\1/'
), '\s', '_'),
_annotation_mapvalue.name) as map_key,
target ome_instance:Project/{project_id} a ome_core:Project ; <{map_key}> {map_value}^^xsd:string .
source select
_project.id as project_id,
regexp_replace(regexp_replace(
concat(
case
when _annotation.ns is null then 'http://www.openmicroscopy.org/ns/default/'
else
case
when _annotation.ns ~ '^http[s]{0,1}:\/\/' then _annotation.ns
else 'http://www.openmicroscopy.org/ns/default/'
end
end, _annotation_mapvalue.name),
'([^\/,#])$',
'\1/'
), '[\s,\[,\],\{,\},\<,\>]', '_') as map_key,
_annotation_mapvalue.value as map_value
from project as _project
join projectannotationlink as _projectannotationlink on _projectannotationlink.parent = _project.id
join annotation as _annotation on _projectannotationlink.child = _annotation.id
join annotation_mapvalue as _annotation_mapvalue on _annotation.id = _annotation_mapvalue.annotation_id

mappingId MAPID-dataset-0
target ome_instance:Dataset/{dataset_id} a ome_core:Dataset ; rdfs:label {dataset_name} ; rdfs:comment {dataset_description}.
target ome_instance:Dataset/{dataset_id} a ome_core:Dataset ; rdfs:label {dataset_name} ; rdfs:comment {dataset_description} .
source select
_dataset.id as dataset_id,
_dataset.name as dataset_name,
_dataset.description as dataset_description
from dataset as _dataset

mappingId MAPID-dataset-1
target ome_instance:Dataset/{dataset_id} ome_core:image ome_instance:Image/{image_id}.
target ome_instance:Dataset/{dataset_id} ome_core:image ome_instance:Image/{image_id} .
source select
_dataset.id as dataset_id,
_datasetimagelink.child as image_id
from dataset as _dataset
left join datasetimagelink as _datasetimagelink on _dataset.id = _datasetimagelink.parent
left join datasetimagelink as _datasetimagelink on _dataset.id = _datasetimagelink.parent

mappingId MAPID-dataset-2
target ome_instance:Dataset/{dataset_id} <{map_key}> {map_value}^^xsd:string .
target ome_instance:Dataset/{dataset_id} <{map_key}> {map_value}^^xsd:string .
source select
_dataset.id as dataset_id,
_datasetannotationlink.child as annotation_id,
concat(regexp_replace(regexp_replace(
case
when _annotation.ns is null then 'http://www.openmicroscopy.org/ns/default/'
else
case
when _annotation.ns ~ '^http[s]{0,1}:\/\/' then _annotation.ns
else 'http://www.openmicroscopy.org/ns/default/'
end
end,
'([^\/,#])$',
'\1/'
), '\s', '_'), _annotation_mapvalue.name) as map_key,
regexp_replace(regexp_replace(
concat(
case
when _annotation.ns is null then 'http://www.openmicroscopy.org/ns/default/'
else
case
when _annotation.ns ~ '^http[s]{0,1}:\/\/' then _annotation.ns
else 'http://www.openmicroscopy.org/ns/default/'
end
end, _annotation_mapvalue.name),
'([^\/,#])$',
'\1/'),
'[\s,\[,\],\{,\},\<,\>]', '_') as map_key,
_annotation_mapvalue.value as map_value
from dataset as _dataset
join datasetannotationlink as _datasetannotationlink on _datasetannotationlink.parent = _dataset.id
join annotation as _annotation on _datasetannotationlink.child = _annotation.id
join annotation_mapvalue as _annotation_mapvalue on _annotation.id = _annotation_mapvalue.annotation_id

mappingId MAPID-Image-0
target ome_instance:Image/{image_id} a ome_core:Image ; rdfs:label {image_name} ; rdfs:comment {image_description} ; ome_core:acquisitionDate {image_acquisitiondate}^^xsd:dateTime ; dc:identifier {image_id}^^xsd:string .
target ome_instance:Image/{image_id} a ome_core:Image ; rdfs:label {image_name} ; rdfs:comment {image_description} ; ome_core:acquisitionDate {image_acquisitiondate}^^xsd:dateTime ; dc:identifier {image_id}^^xsd:string .
source select
_image.id as image_id,
_image.acquisitiondate as image_acquisitiondate,
Expand All @@ -103,27 +104,27 @@ source select
from image as _image

mappingId MAPID-Image-1
target ome_instance:Image/{image_id} a ome_core:Image; <{map_key}> {map_value}^^xsd:string .
source select
_image.id as image_id,
concat(regexp_replace(regexp_replace(
case
when _annotation.ns is null then 'http://www.openmicroscopy.org/ns/default/'
else
case
when _annotation.ns ~ '^http[s]{0,1}:\/\/' then _annotation.ns
else 'http://www.openmicroscopy.org/ns/default/'
end
end,
'([^\/,#])$',
'\1/'
), '\s', '_'),
_annotation_mapvalue.name) as map_key,
_annotation_mapvalue.value as map_value
from image as _image
join imageannotationlink as _imageannotationlink on _imageannotationlink.parent = _image.id
join annotation as _annotation on _imageannotationlink.child = _annotation.id
join annotation_mapvalue as _annotation_mapvalue on _annotation.id = _annotation_mapvalue.annotation_id
target ome_instance:Image/{image_id} a ome_core:Image ; <{map_key}> {map_value}^^xsd:string .
source select
_image.id as image_id,
regexp_replace(regexp_replace(
concat(
case
when _annotation.ns is null then 'http://www.openmicroscopy.org/ns/default/'
else
case
when _annotation.ns ~ '^http[s]{0,1}:\/\/' then _annotation.ns
else 'http://www.openmicroscopy.org/ns/default/'
end
end, _annotation_mapvalue.name),
'([^\/,#])$',
'\1/'),
'[\s,\[,\],\{,\},\<,\>]', '_') as map_key,
_annotation_mapvalue.value as map_value
from image as _image
join imageannotationlink as _imageannotationlink on _imageannotationlink.parent = _image.id
join annotation as _annotation on _imageannotationlink.child = _annotation.id
join annotation_mapvalue as _annotation_mapvalue on _annotation.id = _annotation_mapvalue.annotation_id

mappingId MAPID-experimentergroup
target ome_instance:ExperimenterGroup/{experimentergroup_id} a ome_core:ExperimenterGroup .
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