Mapping tutorial, Ontop CI #3

CFGrote · 2024-10-10T15:32:44Z

This PR

adds instructions for adding ontop mappings based on the ome_core owl ontology.
additions to CI
- java installation
- ontop-cli installation
- omero-py installation (through miniconda)
- mapping omero ports to host on same port numbers (patching the docker files in .omero/)
- launching docker in dev mode (.omero/docker dev start_up)
- a script to insert data into the spun up omero
- a properties file to run ontop against the test infra omero

Currently, the script to insert data fails with

source ci_utils/insert_data.sh
InternalException: Failed to connect: Ice.ConnectionLostException:
recv() returned zero
Error: Process completed with exit code 44.

This does not happen if run live on a PC. @joshmoore, do you have any clue what may be the cause?

- mapping and ontology based on ome_core.owl.tt from https://gitlab.com/openmicroscopy/incubator/ome-owl/

WIP: MapAnnotations and KV pairs.

- add section on mapping ome_core ontology. - add screenshots

- mapping based on ome_core.owl - screenshots - construct for key-value annotations

- add link to norio's paper - use org 'cause it rules ;)

…nfra

…maging#6

- Add two tags - Tag one dataset and all images with tag 1 and tag 2, respectively.

- Add tests to check querying of tagged dataset and images.

- Add new property ome_core:tagAnnotationValue because ontop complained about simultanous definition of tagAnnotation as ObjectProperty and DataProperty. Use new property in mappings for tagged objects.

- add mappings for tagged images, datasets, and projects.

- resolves issue German-BioImaging#6

- Add more examples for tagged objects and aggregations.

- small fixes in tutorial - add instructions to spin up the development environment to readme.

- add Experimenter mapping.

- Adding utility functions to run query and return results as dataframe. - Add test for Image properties.

- add id as Image property.

- add disjoint properties for image, dataset, project.

- remove experimenterGroup property as it caused multiple type relations.

- Add roi class mapping - add query for roi on images. - test new mapping. Note: Have to add ROIs to images 5,6 manually, see issue German-BioImaging#7.

- added two images with ROI - adjust insert_data.sh: Adds these images to Dataset:2 - adjust test_queries.py: Test that two images (11, 12) have a ROI

…a branch.

joshmoore · 2024-11-15T09:39:03Z

🎉

Mariana Meireles and others added 17 commits September 20, 2024 15:07

Adding omero-test-infra CI

05ced6e

Add workflows dir

cd81f19

Add mock project toml

afd7d7b

Add __init__

34d21bd

Add a mock test

d38ac53

Adding howto for omero-ontop.

f975868

Adding new files

4629cea

- mapping and ontology based on ome_core.owl.tt from https://gitlab.com/openmicroscopy/incubator/ome-owl/

Adding a query for projects and contained datasets.

7448568

Add annotations to image mapping.

dd24a84

Ignoring properties and emacs porn.

f8437ff

Add query.

3aef36c

Update.

1c5a49f

Adding more queries.

f6b0d59

Update mappings.

9aedf06

WIP: MapAnnotations and KV pairs.

Renamed directory.

23a39f4

Adding ome-owl repo as submodule.

eca744e

Update ontology and mappings.

8204fec

CFGrote marked this pull request as draft October 10, 2024 20:06

CFGrote marked this pull request as ready for review October 10, 2024 20:30

CFGrote and others added 11 commits October 10, 2024 22:38

Ignoring properties and emacs backups.

c744d42

Update.

6bdeee8

Adding more queries.

572ecec

Update mappings.

88ed5f6

WIP: MapAnnotations and KV pairs.

Renamed directory.

e2219e6

Adding ome-owl repo as submodule.

5278374

Update ontology and mappings.

22bc000

Update readme

859f807

- add section on mapping ome_core ontology. - add screenshots

Update readme

9a7f1c5

- mapping based on ome_core.owl - screenshots - construct for key-value annotations

Update readme

920456d

- add link to norio's paper - use org 'cause it rules ;)

Fixing link

8766c20

CFGrote and others added 27 commits October 18, 2024 16:08

Merge branch 'dataset_type_relations-German-BioImaging#5' into test-i…

658426d

…nfra

Update sparql and sql queries while prototyping for issue German-BioI…

8cc2c68

…maging#6

Update utils script insert_data.sh

7e11931

- Add two tags - Tag one dataset and all images with tag 1 and tag 2, respectively.

Update test_queries.pytest

78709cc

- Add tests to check querying of tagged dataset and images.

Update ontology

7389494

- Add new property ome_core:tagAnnotationValue because ontop complained about simultanous definition of tagAnnotation as ObjectProperty and DataProperty. Use new property in mappings for tagged objects.

Update mappings

5722a3f

- add mappings for tagged images, datasets, and projects.

Merge branch 'tags-German-BioImaging#6' into test-infra

01e7602

- resolves issue German-BioImaging#6

Update queries.org

6c66983

- Add more examples for tagged objects and aggregations.

Update tutorial and readme

14cd67c

- small fixes in tutorial - add instructions to spin up the development environment to readme.

Update sql queries and mappings.

1882f97

- add Experimenter mapping.

Added experimentergroup and owner relation to image.

d888a14

Adding query to list all column headers.

2791811

Update tests.

cecfb27

- Adding utility functions to run query and return results as dataframe. - Add test for Image properties.

Update mappings.

66ca30b

- add id as Image property.

Add module init.

90f4372

Clean up repo.

20ec95a

Delete empty directory.

dbf71b7

Adding ome-owl as submodule.'

03f4e65

Update ontology

a64b698

- add disjoint properties for image, dataset, project.

Update mappings.

6e2c7d6

- remove experimenterGroup property as it caused multiple type relations.

Resurrect ome-owl import paths.

1400a13

Clean up tests and util scripts.

3613385

Update mappings, prototype queries and tests.

ed904d2

- Add roi class mapping - add query for roi on images. - test new mapping. Note: Have to add ROIs to images 5,6 manually, see issue German-BioImaging#7.

Add ome-tiff files with ROIs

a8243e8

- added two images with ROI - adjust insert_data.sh: Adds these images to Dataset:2 - adjust test_queries.py: Test that two images (11, 12) have a ROI

Fix tests. Some failing ones remain but have to fix them in test_infr…

3d6f1f7

…a branch.

Merge branch 'issue#7-rois_for_testing' into test-infra

bfe6ade

Merge branch 'test-infra'

d3d06e1

CFGrote marked this pull request as ready for review November 15, 2024 09:20

CFGrote merged commit ebc2913 into German-BioImaging:main Nov 15, 2024

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Mapping tutorial, Ontop CI #3

Mapping tutorial, Ontop CI #3

CFGrote commented Oct 10, 2024 •

edited

Loading

joshmoore commented Nov 15, 2024

Mapping tutorial, Ontop CI #3

Mapping tutorial, Ontop CI #3

Conversation

CFGrote commented Oct 10, 2024 • edited Loading

joshmoore commented Nov 15, 2024

CFGrote commented Oct 10, 2024 •

edited

Loading