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Merge pull request #15 from German-BioImaging/issue13-namespace
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Namespace handling
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@CFGrote
CFGrote authored Dec 19, 2024
2 parents 3161d4c + 9b3c2e7 commit e547b4c
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3 changes: 2 additions & 1 deletion README.md
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Expand Up @@ -24,8 +24,9 @@ cd ..
```

### Add ontop database user
This step must be redone every time after resetting the test infrastructure.
```console
psql -U postgres -W -h localhost -p 15432 -d postgres < sql/ontop_user.sql
utils/setup_ontop_dbuser.short
```

### Get omero-py
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143 changes: 102 additions & 41 deletions ontop/omemap.obda
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Expand Up @@ -15,52 +15,113 @@ ome_marshal: http://www.openmicroscopy.org/Schemas/OME/2015-01/
ome_instance: https://example.org/site/

[MappingDeclaration] @collection [[
mappingId MAPID-project
target ome_instance:Project/{project_id} a ome_core:Project ; rdfs:label {project_name} ; rdfs:comment {project_description} ; ome_core:dataset ome_instance:Dataset/{dataset_id} ; <{map_key}> {map_value} .
mappingId MAPID-project(1)
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,
projectannotationlink.child as annotation_id,
projectdatasetlink.child as dataset_id,
project.name as project_name,
project.description as project_description,
concat(annotation.ns, annotation_mapvalue.name) as map_key,
annotation_mapvalue.value as map_value
from project
join projectannotationlink on projectannotationlink.parent = project.id
join annotation on projectannotationlink.child = annotation.id
join annotation_mapvalue on annotation.id = annotation_mapvalue.annotation_id
join projectdatasetlink on project.id = projectdatasetlink.parent;
_project.id as project_id,
_project.name as project_name,
_project.description as project_description
from project as _project

mappingId MAPID-dataset
target ome_instance:Dataset/{dataset_id} a ome_core:Dataset ; rdfs:label {dataset_name} ; rdfs:comment {dataset_description} ; ome_core:image ome_instance:Image/{image_id} ; <{map_key}> {map_value} .
mappingId MAPID-project(2)
target ome_instance:Project/{project_id} a ome_core:Project ; ome_core:dataset ome_instance:Dataset/{dataset_id} .
source select
dataset.id as dataset_id,
datasetannotationlink.child as annotation_id,
datasetimagelink.child as image_id,
dataset.name as dataset_name,
dataset.description as dataset_description,
concat(annotation.ns, annotation_mapvalue.name) as map_key,
annotation_mapvalue.value as map_value,
annotation.textvalue as tag_text
from dataset
join datasetannotationlink on datasetannotationlink.parent = dataset.id
join annotation on datasetannotationlink.child = annotation.id
join annotation_mapvalue on annotation.id = annotation_mapvalue.annotation_id join datasetimagelink on dataset.id = datasetimagelink.parent;
_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-Image
target ome_instance:Image/{image_id} a ome_core:Image ; rdfs:label {image_name} ; rdfs:comment {image_description} ; <{map_key}> {map_value} ; ome_core:acquisitionDate {image_acquisitiondate}^^xsd:dateTime ; dc:identifier {image_id}^^xsd:string .
mappingId MAPID-project(3)
target ome_instance:Project/{project_id} a ome_core:Project ; <{map_key}> {map_value} .
source select
image.id as image_id,
image.acquisitiondate as image_acquisitiondate,
imageannotationlink.child as annotation_id,
image.name as image_name,
image.description as image_description,
concat(annotation.ns, annotation_mapvalue.name) as map_key,
annotation_mapvalue.value as map_value
from image
join imageannotationlink on imageannotationlink.parent = image.id
join annotation on imageannotationlink.child = annotation.id
join annotation_mapvalue on annotation.id = annotation_mapvalue.annotation_id;
_project.id as project_id,
concat( regexp_replace(
regexp_replace(
case
when _annotation.ns is null then 'www.openmicroscopy.org/ns/default'
else _annotation.ns
end,
'^([^h])',
'http://\1'),
'([^\/,#])$',
'\1/'
),
_annotation_mapvalue.name) 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}.
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}.
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

mappingId MAPID-dataset-2
target ome_instance:Dataset/{dataset_id} <{map_key}> {map_value} .
source select
_dataset.id as dataset_id,
_datasetannotationlink.child as annotation_id,
concat( regexp_replace(
regexp_replace(
case
when _annotation.ns is null then 'www.openmicroscopy.org/ns/default'
else _annotation.ns
end,
'^([^h])',
'http://\1'),
'([^\/,#])$',
'\1/'
),
_annotation_mapvalue.name) 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 .
source select
_image.id as image_id,
_image.acquisitiondate as image_acquisitiondate,
_image.name as image_name,
_image.description as image_description
from image as _image

mappingId MAPID-Image-1
target ome_instance:Image/{image_id} a ome_core:Image; <{map_key}> {map_value} .
source select
_image.id as image_id,
concat( regexp_replace(
regexp_replace(
case
when _annotation.ns is null then 'www.openmicroscopy.org/ns/default'
else _annotation.ns
end,
'^([^h])',
'http://\1'),
'([^\/,#])$',
'\1/'
),
_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

mappingId MAPID-experimentergroup
target ome_instance:ExperimenterGroup/{experimentergroup_id} a ome_core:ExperimenterGroup .
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6 changes: 3 additions & 3 deletions ontop/omemap.ttl
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Expand Up @@ -62,12 +62,12 @@ ome_core:tagAnnotationValue rdf:type owl:DatatypeProperty .

### http://www.openmicroscopy.org/Schemas/OME/2015-01/Dataset
ome_marshal:Dataset rdf:type owl:Class ;
owl:equivalentClass ome_core:Dataset .
owl:equivalentClass ome_core:Dataset .


### http://www.openmicroscopy.org/rdf/2016-06/ome_core/Dataset
ome_core:Dataset owl:disjointWith ome_core:Image ;
rdfs:isDefinedBy ome_marshal:Dataset .
rdfs:isDefinedBy ome_marshal:Dataset .


### http://www.openmicroscopy.org/rdf/2016-06/ome_core/Folder
Expand All @@ -82,4 +82,4 @@ ome_core:Image owl:disjointWith ome_core:Project .
ome_core:StructuredAnnotation rdfs:subClassOf ome_core:Annotation .


### Generated by the OWL API (version 4.5.29.2024-05-13T12:11:03Z) https://github.com/owlcs/owlapi
### Generated by the OWL API (version 4.5.25.2023-02-15T19:15:49Z) https://github.com/owlcs/owlapi
4 changes: 2 additions & 2 deletions ontop/test_infra.properties
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@@ -1,5 +1,5 @@
#Fri Dec 06 14:46:57 CET 2024
#Wed Dec 18 20:28:06 CET 2024
jdbc.password=\!ontop$
jdbc.user=ontop
jdbc.password=!ontop$
jdbc.url=jdbc\:postgresql\://localhost\:15432/postgres
jdbc.driver=org.postgresql.Driver
30 changes: 28 additions & 2 deletions queries/sparql/queries.org
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Expand Up @@ -494,9 +494,8 @@ Find all datasets tagged "TestTag".
:PROPERTIES:
:ID: b11378ed-b938-4bb9-ad4b-b9cd0df59f75
:END:
#+header: :url http://localhost:8080/sparql

#+begin_src sparql
#+begin_src sparql :url http://localhost:8080/sparql

PREFIX ome_core: <http://www.openmicroscopy.org/rdf/2016-06/ome_core/>

Expand All @@ -507,3 +506,30 @@ Find all datasets tagged "TestTag".
group by ?ds
#+end_src

#+RESULTS:
| ds | number_of_images |
|------------------------------------+------------------|
| https://example.org/site/Dataset/3 | 3 |
| https://example.org/site/Dataset/2 | 7 |
| https://example.org/site/Dataset/1 | 2 |

* Namespace fixed
:PROPERTIES:
:ID: f538ab93-67f7-4a3e-aa6e-9b6d82e2f99c
:END:

#+begin_src sparql :url http://localhost:8080/sparql
PREFIX ome_core: <http://www.openmicroscopy.org/rdf/2016-06/ome_core/>
PREFIX image: <https://example.org/site/Image/>
PREFIX ome_ns: <http://www.openmicroscopy.org/ns/default/>

SELECT DISTINCT * WHERE {
image:11 ome_ns:sampletype ?val.
}
#+end_src

#+RESULTS:
| val |
|--------|
| screen |

2 changes: 1 addition & 1 deletion queries/sql/admin.org
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Expand Up @@ -31,7 +31,7 @@ create user ontop with password '!ontop$';
:ID: a9a1f234-6f10-44b1-819e-70a642c1d1bb
:END:
#+begin_src sql :engine postgres :dbhost micropop046 :dbport 15432 :dbuser postgres :dbpassword postgres :database postgres
select usename from pg_catalog.pg_user;
select usename from pg_catalog.pg_user
#+end_src

#+RESULTS:
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