Adding omero-test-infra CI

.github/workflows/omero_test_infra.yaml

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+# Install and test and OMERO plugin e.g. a Web app, a CLI plugin or a library
+#
+# This workflow will install omero-test-infra, start an OMERO environment
+# including database, server and web deployment, configure the OMERO plugin
+# and run integration tests.
+#
+# 1. Set up the stage variable depending on the plugin. Supported stages
+# are: app, cli, scripts, lib, srv
+#
+# 2. Adjust the cron schedule as necessary
+
+name: OMERO
+on:
+  push:
+  pull_request:
+  schedule:
+    - cron: '0 0 * * 0'
+
+jobs:
+  test:
+    name: Run integration tests against OMERO
+    runs-on: ubuntu-latest
+    env:
+      STAGE: app
+    steps:
+      - uses: actions/checkout@v4
+      - name: Checkout omero-test-infra
+        uses: actions/checkout@master
+        with:
+          repository: ome/omero-test-infra
+          path: .omero
+          ref: ${{ secrets.OMERO_TEST_INFRA_REF }}
+      - name: Build and run OMERO tests
+        run: .omero/docker $STAGE

.gitignore

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+*.properties

README.md

@@ -7,3 +7,110 @@ This repository contains the ONTOP module for the Image Data Resource (IDR) that
 This project was developed with support from the Biohackathon 2024.
 
 <img src="https://2024.biohackathon.org/images/bh24-logo.png" alt="Biohackathon 2024" width="200">
+
+## Howto Ontop
+### Software
+- Protege: https://protege.stanford.edu/software.php#desktop-protege
+- Unpack on your system into a writable directory
+- Download ontop command line client (ontop-cli-x.y.z.zip) and ontop plugin for Protege (it.unibz.inf.ontop.protege-x.y.z.jar) from https://github.com/ontop/ontop/releases/latest
+- Unpack ontop-cli zip 
+- Save ontop plugin into your Protege's plugin directory.
+- Download postgresql jdbc driver for your system's java version: https://jdbc.postgresql.org/download/
+- Save the jdbc driver into the jdbc/ subdirectory of the unpacked ontop-cli archive.
+
+### Configure omero postgres db
+If you run ontop on a different host than your omero instance, you have to allow remote tcp/ip access to the latter via port 5432. By default, this is disabled and only connections from localhost are permitted.
+To this end, edit these two files (paths may vary according to host OS, on debian/ubuntu servers it will likely be */etc/postgresql/VERSION/main/*). 
+- *postgres.conf*
+either allow all connections
+```
+listen_addresses = '*'          # what IP address(es) to listen on;
+```
+or specify clients as comma separated values:
+```
+listen_addresses = '192.168.1.10,172.5.16.4,localhost'          # what IP address(es) to listen on;
+```
+
+- *pg_hba.conf*
+Adding these two lines worked for me but may be too permissive in your situation (in particular if your omero is not behind a firewall):
+```
+host    all             all             0.0.0.0/0               md5
+host    all             all             ::/0                    md5
+```
+
+- restart your postgres service, i.e.
+```
+sudo service postgresql restart
+```
+
+### Test the connection
+- Launch Protege
+- If not present, add ontop Tabs (Menu -> Window -> Tabs -> Ontop Mappings)
+- Configure postgres jdbc driver:
+  - Select Menu -> File -> Preferences -> JDBC Drivers
+  - Click Add
+  - Select "org.postgresql.Driver" from Class name dropdown menu
+  - Select postgres jdbc driver jar file downloaded earlier from the ontop-cli jdbc directory
+- Setup connection:
+  - In the Ontop Mappings Tab, select "Connection parameters" subtab
+    - Enter connection URL: "jdbc:postgresql://your.omero.url:5432/omero"
+    - Enter a db username with at least read access to all tables in the omero db.
+    - Enter db user's password
+    - Select "org.postgresql.Driver" as JDBC driver class.
+- Click test connection
+  - On error: Check postgres config on omero host and connection details.
+  - On success: Hurray!
+
+### Crunch time: Your first mapping
+#### Add entity and property to active ontology
+Add one class (e.g. `:Dataset`) and one data property (e.g. `:name`) to the ontology. 
+
+More general, tables are mapped to classes, table index columns are mapped to
+class instances (triple subjects), table columns headers are mapped to
+properties (table predicates), table column values are mapped to property values
+(table subjects).
+
+#### Define mapping
+- Select "Mapping manager" tab
+- Click "New"
+- Enter 
+```ttl
+:dataset/{id} a :Dataset;
+              :name {name} .
+```
+into the field "Target" and
+```sql
+select id, name from dataset;
+```
+into the "Source" field.
+
+You may want to test your query by clicking the "Execute the sql query" which will populate the "SQL Query results" field.
+
+### SPARQL query
+Select the "Ontop SPARQL" tab. Click "Prefixes" and select the base prefix and further prefixes as needed.
+In the query editor enter
+```sparql
+select * where {
+    ?subj a :Dataset;
+          :name ?name .
+}
+```
+And click "Execute". Find your omero dataset ids and names in the SPARQL results field and observe the generated SQL query in the "SQL tranlation" tab.
+
+### Save mapping, ontology, and properties
+Select Menu -> Save (or Save as). Select "Turtle syntax" for the file format and
+select a file name. This filename will serve as the basis for three files:
+*<filename>.properties* (db connection settings), *<filename>.ttl* (ontology),
+and *<filename>.obda* (mapping definition in ontop format).
+
+### Launch ontop SPARQL endpoint
+In a terminal, navigate to the directory where you just saved your mapping definition files to.
+In that directory, run
+
+```console
+path/to/ontop-cli/ontop endpoint -m <filename>.obda -t <filename>.ttl -p <filename>.properties
+```
+
+**replace** *<filename>* with the actual filename from above.
+
+Open your webbrowser at http://localhost:8080 where a beautiful SPARQL frontend awaits your queries. Sparqly happy queries!

mpi_sandbox/omemap.obda

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+[PrefixDeclaration]
+:		https://www.openmicroscopy.org/omemap/
+owl:		http://www.w3.org/2002/07/owl#
+rdf:		http://www.w3.org/1999/02/22-rdf-syntax-ns#
+xml:		http://www.w3.org/XML/1998/namespace
+xsd:		http://www.w3.org/2001/XMLSchema#
+obda:		https://w3id.org/obda/vocabulary#
+rdfs:		http://www.w3.org/2000/01/rdf-schema#
+omemap:		https://www.openmicroscopy.org/omemap#
+ome_core:	http://www.openmicroscopy.org/rdf/2016-06/ome_core/
+
+[MappingDeclaration] @collection [[
+mappingId	MAPID-ad72dafe19404fc2a460e734b0a2a0ee
+target		ome_core:Dataset/{id} a ome_core:Dataset ; rdfs:label {name}^^xsd:string ; rdfs:comment {description}^^xsd:string ; ome_core:annotation ome_core:Annotation/{child} . 
+source		select dataset.id, datasetannotationlink.child, dataset.name, dataset.description from datasetannotationlink join dataset on datasetannotationlink.parent = dataset.id;
+
+mappingId	MAPID-a4cb3fa530c84c5b90ddb5e81cbbcb72
+target		ome_core:Annotation/{id} a ome_core:Annotation ; rdfs:comment {textvalue}^^xsd:string . 
+source		select id, textvalue from annotation;
+
+mappingId	MAPID-a5fcd77a0a164d7fb12ac427c70e93a0
+target		ome_core:TagAnnotation/{id} a ome_core:TagAnnotation ; rdfs:comment {textvalue}^^xsd:string . 
+source		select * from annotation where discriminator='/basic/text/tag/' order by id
+
+mappingId	MAPID-e7112763f8224ae6b61c7ce5665fe204
+target		ome_core:Image/{id} a ome_core:Image ; rdfs:label {name}^^xsd:string ; rdfs:comment {description}^^xsd:string ; ome_core:annotation ome_core:Annotation/{child} . 
+source		select image.id, image.name, image.description, imageannotationlink.child from image join imageannotationlink on image.id=imageannotationlink.parent;
+
+mappingId	MAPID-3d5abba8f4834197b0edbd8d667802b3
+target		ome_core:Project/{id} a ome_core:Project ; rdfs:label {name}^^xsd:string ; rdfs:comment {description}^^xsd:string ; ome_core:dataset ome_core:Dataset/{child} . 
+source		select project.id, project.name, project.description, projectdatasetlink.child from project join projectdatasetlink on project.id = projectdatasetlink.parent;
+]]
+

mpi_sandbox/omemap.ttl

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+@prefix : <https://www.openmicroscopy.org/omemap/> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix xml: <http://www.w3.org/XML/1998/namespace> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+@prefix obda: <https://w3id.org/obda/vocabulary#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix omemap: <https://www.openmicroscopy.org/omemap#> .
+@prefix ome_core: <http://www.openmicroscopy.org/rdf/2016-06/ome_core/> .
+@base <https://www.openmicroscopy.org/omemap/> .
+
+<https://www.openmicroscopy.org/omemap> rdf:type owl:Ontology ;
+    owl:imports <https://gitlab.com/openmicroscopy/incubator/ome-owl/-/raw/master/ontology/owl/ome_core/ome_core.owl.ttl> .
+
+
+#################################################################
+#    Data properties
+#################################################################
+
+###  https://www.openmicroscopy.org/omemap#annotation_type
+omemap:annotation_type rdf:type owl:DatatypeProperty ;
+                       rdfs:domain ome_core:Annotation .
+
+
+###  Generated by the OWL API (version 4.5.29.2024-05-13T12:11:03Z) https://github.com/owlcs/owlapi

mpi_sandbox/queries.org

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+#+begin_src sparql :url http://localhost:8080/sparql
+  PREFIX : <https://www.openmicroscopy.org/omemap/>
+  PREFIX owl: <http://www.w3.org/2002/07/owl#>
+  PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+  PREFIX xml: <http://www.w3.org/XML/1998/namespace>
+  PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
+  PREFIX obda: <https://w3id.org/obda/vocabulary#>
+  PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+  PREFIX omemap: <https://www.openmicroscopy.org/omemap#>
+  PREFIX ome_core: <http://www.openmicroscopy.org/rdf/2016-06/ome_core/>
+
+  select * where {
+  ?ant a ome_core:Annotation ;
+          rdfs:comment ?cmnt .
+  ?ds a ome_core:Dataset ;
+         ome_core:annotation ?ant .
+  }
+  limit 10
+#+end_src
+
+#+RESULTS:
+| ant                                                                | cmnt                    | ds                                                             |
+|--------------------------------------------------------------------+-------------------------+----------------------------------------------------------------|
+| http://www.openmicroscopy.org/rdf/2016-06/ome_core/Annotation/3222 | pseudomonas fluorescens | http://www.openmicroscopy.org/rdf/2016-06/ome_core/Dataset/602 |
+| http://www.openmicroscopy.org/rdf/2016-06/ome_core/Annotation/3219 | mat formation           | http://www.openmicroscopy.org/rdf/2016-06/ome_core/Dataset/712 |
+| http://www.openmicroscopy.org/rdf/2016-06/ome_core/Annotation/3221 | mirror                  | http://www.openmicroscopy.org/rdf/2016-06/ome_core/Dataset/709 |
+| http://www.openmicroscopy.org/rdf/2016-06/ome_core/Annotation/3217 | AxioZoom                | http://www.openmicroscopy.org/rdf/2016-06/ome_core/Dataset/602 |
+| http://www.openmicroscopy.org/rdf/2016-06/ome_core/Annotation/3218 | darkfield               | http://www.openmicroscopy.org/rdf/2016-06/ome_core/Dataset/703 |
+| http://www.openmicroscopy.org/rdf/2016-06/ome_core/Annotation/3221 | mirror                  | http://www.openmicroscopy.org/rdf/2016-06/ome_core/Dataset/603 |
+| http://www.openmicroscopy.org/rdf/2016-06/ome_core/Annotation/3224 | upright                 | http://www.openmicroscopy.org/rdf/2016-06/ome_core/Dataset/752 |
+| http://www.openmicroscopy.org/rdf/2016-06/ome_core/Annotation/3220 | microscopy              | http://www.openmicroscopy.org/rdf/2016-06/ome_core/Dataset/707 |
+| http://www.openmicroscopy.org/rdf/2016-06/ome_core/Annotation/2106 | Lateral                 | http://www.openmicroscopy.org/rdf/2016-06/ome_core/Dataset/606 |
+| http://www.openmicroscopy.org/rdf/2016-06/ome_core/Annotation/2105 | Top                     | http://www.openmicroscopy.org/rdf/2016-06/ome_core/Dataset/603 |
+
+#+begin_src sparql :url http://localhost:8080/sparql
+  PREFIX : <https://www.openmicroscopy.org/omemap/>
+  PREFIX owl: <http://www.w3.org/2002/07/owl#>
+  PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+  PREFIX xml: <http://www.w3.org/XML/1998/namespace>
+  PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
+  PREFIX obda: <https://w3id.org/obda/vocabulary#>
+  PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+  PREFIX omemap: <https://www.openmicroscopy.org/omemap#>
+  PREFIX ome_core: <http://www.openmicroscopy.org/rdf/2016-06/ome_core/>
+
+  select * where {
+  ?proj a ome_core:Project ;
+           rdfs:label ?lbl .
+  ?ds a ome_core:Dataset .
+  ?proj ome_core:dataset ?ds .
+  }
+limit 20
+#+end_src
+
+#+RESULTS:
+| proj                                                            | lbl                             | ds                                                              |
+|-----------------------------------------------------------------+---------------------------------+-----------------------------------------------------------------|
+| http://www.openmicroscopy.org/rdf/2016-06/ome_core/Project/865  | MouseCT                         | http://www.openmicroscopy.org/rdf/2016-06/ome_core/Dataset/3654 |
+| http://www.openmicroscopy.org/rdf/2016-06/ome_core/Project/1303 | Elio shading test               | http://www.openmicroscopy.org/rdf/2016-06/ome_core/Dataset/4544 |
+| http://www.openmicroscopy.org/rdf/2016-06/ome_core/Project/904  | Imaging for Elisa Brambilla     | http://www.openmicroscopy.org/rdf/2016-06/ome_core/Dataset/2962 |
+| http://www.openmicroscopy.org/rdf/2016-06/ome_core/Project/655  | MouseCT_backup                  | http://www.openmicroscopy.org/rdf/2016-06/ome_core/Dataset/1442 |
+| http://www.openmicroscopy.org/rdf/2016-06/ome_core/Project/865  | MouseCT                         | http://www.openmicroscopy.org/rdf/2016-06/ome_core/Dataset/2870 |
+| http://www.openmicroscopy.org/rdf/2016-06/ome_core/Project/865  | MouseCT                         | http://www.openmicroscopy.org/rdf/2016-06/ome_core/Dataset/2571 |
+| http://www.openmicroscopy.org/rdf/2016-06/ome_core/Project/1308 | 3D Cell Atlas                   | http://www.openmicroscopy.org/rdf/2016-06/ome_core/Dataset/4612 |
+| http://www.openmicroscopy.org/rdf/2016-06/ome_core/Project/1002 | Mat_imaging                     | http://www.openmicroscopy.org/rdf/2016-06/ome_core/Dataset/3759 |
+| http://www.openmicroscopy.org/rdf/2016-06/ome_core/Project/865  | MouseCT                         | http://www.openmicroscopy.org/rdf/2016-06/ome_core/Dataset/3193 |
+| http://www.openmicroscopy.org/rdf/2016-06/ome_core/Project/151  | 2016                            | http://www.openmicroscopy.org/rdf/2016-06/ome_core/Dataset/331  |
+| http://www.openmicroscopy.org/rdf/2016-06/ome_core/Project/865  | MouseCT                         | http://www.openmicroscopy.org/rdf/2016-06/ome_core/Dataset/3383 |
+| http://www.openmicroscopy.org/rdf/2016-06/ome_core/Project/655  | MouseCT_backup                  | http://www.openmicroscopy.org/rdf/2016-06/ome_core/Dataset/1834 |
+| http://www.openmicroscopy.org/rdf/2016-06/ome_core/Project/804  | 2020_2021_VPL_microscopy        | http://www.openmicroscopy.org/rdf/2016-06/ome_core/Dataset/2200 |
+| http://www.openmicroscopy.org/rdf/2016-06/ome_core/Project/865  | MouseCT                         | http://www.openmicroscopy.org/rdf/2016-06/ome_core/Dataset/2890 |
+| http://www.openmicroscopy.org/rdf/2016-06/ome_core/Project/1256 | Omnipose_Training_2D            | http://www.openmicroscopy.org/rdf/2016-06/ome_core/Dataset/4448 |
+| http://www.openmicroscopy.org/rdf/2016-06/ome_core/Project/1223 | Alejandro Microscopy            | http://www.openmicroscopy.org/rdf/2016-06/ome_core/Dataset/4073 |
+| http://www.openmicroscopy.org/rdf/2016-06/ome_core/Project/1223 | Alejandro Microscopy            | http://www.openmicroscopy.org/rdf/2016-06/ome_core/Dataset/4427 |
+| http://www.openmicroscopy.org/rdf/2016-06/ome_core/Project/655  | MouseCT_backup                  | http://www.openmicroscopy.org/rdf/2016-06/ome_core/Dataset/2024 |
+| http://www.openmicroscopy.org/rdf/2016-06/ome_core/Project/1007 | Microscopy_2024                 | http://www.openmicroscopy.org/rdf/2016-06/ome_core/Dataset/4556 |
+| http://www.openmicroscopy.org/rdf/2016-06/ome_core/Project/1052 | minD oscillation in DrodA cells | http://www.openmicroscopy.org/rdf/2016-06/ome_core/Dataset/4537 |
+
+

pyproject.toml

@@ -0,0 +1,9 @@
+[build-system]
+requires = ["setuptools", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "omero-ontop-mappings"
+version = "0.1"
+description = "Placeholder pyproject.toml for omero-ontop-mappings"
+

test/test_mock.py

@@ -0,0 +1,4 @@
+def test_mock():
+    a = True
+    if a:
+        return True