Interpret `rdfs:Class` as classes on SimPhoNy v3, include dcmitype and dcterms namespaces by domgz · Pull Request #760 · simphony/simphony-osp

domgz · 2022-02-24T07:48:48Z

No description provided.

…ble type to namespace and namespace_registry

domgz · 2022-02-24T07:49:58Z

@MBueschelberger just made the PR myself from your branch. As said, I will look into merging this.

MBueschelberger · 2022-02-24T08:40:49Z

Hi @kysrpex, thanks for regarding my commits!

I will have a meeting on Friday this week in order to discuss the inluded yml-specs. If there are no further suggestions on the implementation, I would consider this PR to be ready from my side.

… enh/add-dcat-and-datamodel

…d RDFS properties.

domgz · 2022-03-17T17:57:33Z

@MBueschelberger I think with the latest changes most things are OK. I am still unsure about the requirements declared on the new yml files (they look OK at first sight though) and whether defining the relationships you chose as active makes sense or not. I might ask tomorrow for some assistance from somebody else that has used these ontologies.

domgz · 2022-03-17T18:10:13Z

@pablo-de-andres @yoavnash Please read this comment and judge whether this should be documented or not. It is essentially incomplete support for RDFS vocabularies (only classes). Also if you consider yourself experienced enough with the ontologies that @MBueschelberger has introduced, please consider reviewing these aspects.

@MBueschelberger please consider also making a PR on the docs and documenting it yourself if @pablo-de-andres or @yoavnash require documentation, because within the coming days I have not much flexibility to do this + look at the requirements and active relationships issue and your PR can be delayed even further.

domgz · 2022-03-17T18:11:16Z

@yoavnash @pablo-de-andres I am aware that tests are failing for Python 3.6, but there are a lot of things that can be reviewed already.

pablo-de-andres · 2022-03-18T07:22:39Z

Maybe a point could be added to this section with the predicates that are used to define classes?

…gical relationships.

…repo.

domgz · 2022-03-18T10:58:35Z

Maybe a point could be added to this section with the predicates that are used to define classes?

Done (see docs PR)

domgz · 2022-03-18T11:05:49Z

@yoavnash @pablo-de-andres I am aware that tests are failing for Python 3.6, but there are a lot of things that can be reviewed already.

This has been solved now, the PR is fully ready to review together with docs.

domgz · 2022-03-24T16:57:40Z

Added quick and dirty dependency resolution as @yoavnash requested here, together with a lot of technical debt. Thank god it is on SimPhoNy v3.

Examples:

$ pico install dcat2
INFO 2022-03-24 17:52:19,681 [osp.core.ontology.installation]: Additional ontology packages were queued for installation because some of the packages to be installed depend on them: dcmitype was queued because dcterms depends on it; dcterms was queued because dcat2 depends on it; foaf was queued because dcat2 depends on it; prov was queued because dcat2 depends on it.
INFO 2022-03-24 17:52:19,681 [osp.core.ontology.installation]: Will install the following namespaces: ['prov', 'foaf', 'dcmitype', 'dcterms', 'dcat2']
INFO 2022-03-24 17:52:19,682 [osp.core.ontology.namespace_registry]: Loading namespaces prov, http://www.w3.org/ns/prov#.
INFO 2022-03-24 17:52:19,682 [osp.core.ontology.parser.owl.parser]: Downloading http://www.w3.org/ns/prov-o.
INFO 2022-03-24 17:52:25,624 [osp.core.ontology.namespace_registry]: Loading namespaces foaf, http://xmlns.com/foaf/0.1/.
INFO 2022-03-24 17:52:25,624 [osp.core.ontology.parser.owl.parser]: Downloading http://xmlns.com/foaf/spec/index.rdf.
INFO 2022-03-24 17:52:26,382 [osp.core.ontology.namespace_registry]: Loading namespaces dcmitype, http://purl.org/dc/dcmitype/.
INFO 2022-03-24 17:52:26,382 [osp.core.ontology.parser.owl.parser]: Downloading https://www.dublincore.org/specifications/dublin-core/dcmi-terms/dublin_core_type.ttl.
INFO 2022-03-24 17:52:26,547 [osp.core.ontology.namespace_registry]: Loading namespaces dcterms, http://purl.org/dc/terms/.
INFO 2022-03-24 17:52:26,547 [osp.core.ontology.parser.owl.parser]: Downloading https://www.dublincore.org/specifications/dublin-core/dcmi-terms/dublin_core_terms.ttl.
WARNING 2022-03-24 17:52:26,746 [osp.core.ontology.parser.owl.parser]: The ontology package dcterms contains the following RDF properties: http://purl.org/dc/terms/accessRights, http://purl.org/dc/terms/accrualPolicy, http://purl.org/dc/terms/accrualPeriodicity, http://purl.org/dc/terms/abstract, http://purl.org/dc/terms/accrualMethod and 50 more. 
As RDF properties are not supported by OSP-core, the aforementioned properties will be ignored.
INFO 2022-03-24 17:52:26,792 [osp.core.ontology.namespace_registry]: Loading namespaces dcat2, http://www.w3.org/ns/dcat#.
INFO 2022-03-24 17:52:26,792 [osp.core.ontology.parser.owl.parser]: Downloading https://www.w3.org/ns/dcat2.rdf.
INFO 2022-03-24 17:52:28,170 [osp.core.ontology.installation]: Installation successful

$ pico uninstall dcmitype
ERROR 2022-03-24 17:53:03,996 [osp.core.pico]: An Exception occurred during installation.
Traceback (most recent call last):
  File "/home/jose/.local/lib/python3.10/site-packages/osp/core/pico.py", line 114, in terminal
    uninstall(*args.packages)
  File "/home/jose/.local/lib/python3.10/site-packages/osp/core/pico.py", line 42, in uninstall
    ontology_installer.uninstall(*package_names)
  File "/home/jose/.local/lib/python3.10/site-packages/osp/core/ontology/installation.py", line 71, in uninstall
    self._install(files_or_namespaces, self._get_remaining_packages, True)
  File "/home/jose/.local/lib/python3.10/site-packages/osp/core/ontology/installation.py", line 278, in _install
    files = self._sort_for_installation(filter_func(files),
  File "/home/jose/.local/lib/python3.10/site-packages/osp/core/ontology/installation.py", line 176, in _get_remaining_packages
    raise RuntimeError(message)
RuntimeError: Cannot remove package dcmitype, because other installed packages depend on it: package dcat2 depends on dcterms; package dcterms depends on dcmitype. Please remove the packages dcterms, dcat2 and dcmitype all together.
ERROR 2022-03-24 17:53:03,997 [osp.core.pico]: Consider running 'pico --log-level debug uninstall ...'

$ pico uninstall prov
ERROR 2022-03-24 17:53:32,505 [osp.core.pico]: An Exception occurred during installation.
Traceback (most recent call last):
  File "/home/jose/.local/lib/python3.10/site-packages/osp/core/pico.py", line 114, in terminal
    uninstall(*args.packages)
  File "/home/jose/.local/lib/python3.10/site-packages/osp/core/pico.py", line 42, in uninstall
    ontology_installer.uninstall(*package_names)
  File "/home/jose/.local/lib/python3.10/site-packages/osp/core/ontology/installation.py", line 71, in uninstall
    self._install(files_or_namespaces, self._get_remaining_packages, True)
  File "/home/jose/.local/lib/python3.10/site-packages/osp/core/ontology/installation.py", line 278, in _install
    files = self._sort_for_installation(filter_func(files),
  File "/home/jose/.local/lib/python3.10/site-packages/osp/core/ontology/installation.py", line 176, in _get_remaining_packages
    raise RuntimeError(message)
RuntimeError: Cannot remove package prov, because other installed packages depend on it: dcat2. Please remove the packages prov and dcat2 all together.
ERROR 2022-03-24 17:53:32,505 [osp.core.pico]: Consider running 'pico --log-level debug uninstall ...'

$ pico uninstall foaf
ERROR 2022-03-24 17:54:20,238 [osp.core.pico]: An Exception occurred during installation.
Traceback (most recent call last):
  File "/home/jose/.local/lib/python3.10/site-packages/osp/core/pico.py", line 114, in terminal
    uninstall(*args.packages)
  File "/home/jose/.local/lib/python3.10/site-packages/osp/core/pico.py", line 42, in uninstall
    ontology_installer.uninstall(*package_names)
  File "/home/jose/.local/lib/python3.10/site-packages/osp/core/ontology/installation.py", line 71, in uninstall
    self._install(files_or_namespaces, self._get_remaining_packages, True)
  File "/home/jose/.local/lib/python3.10/site-packages/osp/core/ontology/installation.py", line 278, in _install
    files = self._sort_for_installation(filter_func(files),
  File "/home/jose/.local/lib/python3.10/site-packages/osp/core/ontology/installation.py", line 176, in _get_remaining_packages
    raise RuntimeError(message)
RuntimeError: Cannot remove package foaf, because other installed packages depend on it: dcat2. Please remove the packages dcat2 and foaf all together.
ERROR 2022-03-24 17:54:20,238 [osp.core.pico]: Consider running 'pico --log-level debug uninstall ...'

$ pico uninstall foaf prov dcmitype foaf dcat2 dcterms
INFO 2022-03-24 17:55:09,448 [osp.core.ontology.installation]: Will install the following namespaces: []
INFO 2022-03-24 17:55:09,451 [osp.core.ontology.installation]: Uninstallation successful

@yoavnash If this is not enough, I would say to drop the idea of automatic dependency resolution for SimPhoNy v3. It would be much more worthwile to invest the time in a long-term solution for SimPhoNy v4. This is already consuming a lot of time that is not being invested in SimPhoNy v4.

…ecause it is not on the URL).

domgz · 2022-03-25T10:42:34Z

For reference: the last commit implements additional changes requested on the docs PR.

…d dcterms namespaces (#201) Documentation for [PR #760](simphony/simphony-osp#760) with the same title from the OSP-core repository.

MBueschelberger added 3 commits February 14, 2022 16:23

add yml-specs for datamode, dcterms, prov, dcmitype. Update for dcat2

43613e8

update dcat2, dcmitype and dcterms ontology. Add RDFS.Class as availa…

519f1ff

…ble type to namespace and namespace_registry

update yml-spec for datamodel

5fd1528

domgz added 🌱 new feature Solving the issue involves the incorporation of a new feature. 📜 ontology labels Feb 24, 2022

domgz self-assigned this Feb 24, 2022

MBueschelberger and others added 11 commits March 1, 2022 15:04

Merge branch 'dev' into enh/add-dcat-and-datamodel

b51037e

Fix ontology2dot.

7604d37

Merge remote-tracking branch 'origin/enh/add-dcat-and-datamodel' into…

9361a66

… enh/add-dcat-and-datamodel

Validate ontology files before installation and warn about unsupporte…

69159d2

…d RDFS properties.

Fix flake8.

224a7e9

Merge branch 'dev' into enh/add-dcat-and-datamodel

a4766a4

Fix tests.

bc52700

Rename EMMO datamodel package and namespace.

8d69627

Reorganize names of ontology packages again.

e342915

Fix problems with warnings.

6e0c153

Fix flake8.

58980e9

domgz marked this pull request as ready for review March 17, 2022 18:10

domgz requested review from pablo-de-andres and yoavnash as code owners March 17, 2022 18:10

domgz linked an issue Mar 17, 2022 that may be closed by this pull request

Make dcat ontology and datamodel-ontology as built-in pico-installable #757

Closed

domgz added 3 commits March 18, 2022 08:57

Review active relationships for dcat2.yml.

6b25fe0

Review active relationships for emmo-datamodel.yml. Keep only mereolo…

db49c43

…gical relationships.

Review prov.yml.

fe8aa78

MBueschelberger reviewed Mar 18, 2022

View reviewed changes

Comment thread osp/core/ontology/docs/dcat2.yml

domgz added a commit to simphony/docs that referenced this pull request Mar 18, 2022

Documentation for [PR #760](simphony/simphony-osp#760) from OSP-core …

ae782d0

…repo.

domgz mentioned this pull request Mar 18, 2022

Interpret rdfs:Class as classes on SimPhoNy v3, include dcmitype and dcterms namespaces simphony/docs#201

Merged

Fix problems with Python 3.6.

5cbb21b

Add automatic resolution of dependencies.

895912a

domgz added 6 commits March 24, 2022 18:16

Show installation logs when pico is used as a module.

8ae35e7

Fix tests.

cead7af

Fix flake8.

dff2b73

Try to fix tests again for Python 3.6.

ca826ce

Fix bug with prov on Python 3.6 (format not guessed by RDFLib 5.0.0 b…

43e64b8

…ecause it is not on the URL).

Code review changes.

9e4949d

Fix bug that ignored custom files for dependencies provided by the user.

f5b2612

yoavnash approved these changes Mar 30, 2022

View reviewed changes

domgz merged commit db42213 into dev Mar 30, 2022

domgz deleted the enh/add-dcat-and-datamodel branch March 30, 2022 13:56

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Interpret `rdfs:Class` as classes on SimPhoNy v3, include dcmitype and dcterms namespaces#760

Interpret `rdfs:Class` as classes on SimPhoNy v3, include dcmitype and dcterms namespaces#760
domgz merged 26 commits into
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