From 05c28c1e471ae12d26552e1ba439cb51fe4e316c Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Fri, 26 May 2023 00:48:46 +0100 Subject: [PATCH 1/5] Update ROBOT to version 1.9.4. --- docker/odklite/Dockerfile | 2 +- docker/robot/Dockerfile | 2 +- docker/robot/Makefile | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/docker/odklite/Dockerfile b/docker/odklite/Dockerfile index 8cb7c045..91ff26ed 100644 --- a/docker/odklite/Dockerfile +++ b/docker/odklite/Dockerfile @@ -1,7 +1,7 @@ FROM ubuntu:22.04 LABEL maintainer="obo-tools@googlegroups.com" -ENV ROBOT_VERSION=1.9.3 +ENV ROBOT_VERSION=1.9.4 ENV DOSDP_VERSION=0.19.3 ENV OWLTOOLS_VERSION=2020-04-06 ENV AMMONITE_VERSION=2.0.3 diff --git a/docker/robot/Dockerfile b/docker/robot/Dockerfile index 5b36f87b..afa12a50 100644 --- a/docker/robot/Dockerfile +++ b/docker/robot/Dockerfile @@ -3,7 +3,7 @@ LABEL maintainer="obo-tools@googlegroups.com" WORKDIR /tools -ENV ROBOT v1.9.1 +ENV ROBOT v1.9.4 ARG ROBOT_JAR=https://github.com/ontodev/robot/releases/download/$ROBOT/robot.jar ENV ROBOT_JAR ${ROBOT_JAR} diff --git a/docker/robot/Makefile b/docker/robot/Makefile index 0cba484d..289771e7 100644 --- a/docker/robot/Makefile +++ b/docker/robot/Makefile @@ -1,6 +1,6 @@ # Building docker image -VERSION = "v1.8.1" +VERSION = "v1.9.4" IM=obolibrary/robot CACHE= From 641bef2480b3ab2c7e7ab499d7645fae0a02c13c Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Fri, 26 May 2023 00:49:03 +0100 Subject: [PATCH 2/5] Update Python packages. --- constraints.txt | 263 +++++++++++++++++++++++------------------------- 1 file changed, 128 insertions(+), 135 deletions(-) diff --git a/constraints.txt b/constraints.txt index 23b0ceaf..3bb7fab8 100644 --- a/constraints.txt +++ b/constraints.txt @@ -1,5 +1,3 @@ -aiohttp==3.8.4 -aiosignal==1.3.1 airium==0.2.5 alabaster==0.7.13 antlr4-python3-runtime==4.9.3 @@ -9,82 +7,80 @@ argon2-cffi==21.3.0 argon2-cffi-bindings==21.2.0 arrow==1.2.3 asttokens==2.2.1 -async-timeout==4.0.2 -attrs==22.2.0 -Babel==2.11.0 +attrs==23.1.0 +Babel==2.12.1 backcall==0.2.0 bcp47==0.0.4 -beautifulsoup4==4.11.2 +beautifulsoup4==4.12.2 bidict==0.22.1 -bioregistry==0.5.143 -black==21.12b0 +bioregistry==0.9.15 bleach==6.0.0 -bmt==1.0.2 +bmt==1.0.13 cachetools==5.3.0 -certifi==2022.12.7 +cattrs==22.2.0 +certifi==2023.5.7 cffi==1.15.1 CFGraph==0.2.1 chardet==5.1.0 -charset-normalizer==3.0.1 -class-resolver==0.3.10 +charset-normalizer==3.1.0 +class-resolver==0.4.2 click==8.1.3 colorama==0.4.6 -comm==0.1.2 +comm==0.1.3 commonmark==0.9.1 contourpy==1.0.7 -cryptography==39.0.1 -curies==0.4.2 +cryptography==40.0.2 +curies==0.5.5 cycler==0.11.0 -dacite==1.8.0 +dacite==1.8.1 daff==1.3.46 dataclasses==0.6 dataclasses-json==0.5.7 dataclasses-jsonschema==2.16.0 -debugpy==1.6.6 +debugpy==1.6.7 decorator==5.1.1 defusedxml==0.7.1 Deprecated==1.2.13 deprecation==2.1.0 -diskcache==5.4.0 +diskcache==5.6.1 distlib==0.3.6 docker==5.0.3 -docutils==0.16 +docutils==0.18.1 dosdp==0.1.10.dev1 +EditorConfig==0.12.3 et-xmlfile==1.1.0 -exceptiongroup==1.1.0 +eutils==0.6.0 +exceptiongroup==1.1.1 executing==1.2.0 -fastjsonschema==2.16.2 +fastjsonschema==2.16.3 fastobo==0.12.2 -filelock==3.9.0 -flake8==6.0.0 -fonttools==4.38.0 +filelock==3.12.0 +fonttools==4.39.4 fqdn==1.5.1 -frozenlist==1.3.3 -fsspec==2023.1.0 funowl==0.1.13 ghp-import==2.1.0 google==3.0.0 google-api-core==2.11.0 -google-api-python-client==2.77.0 -google-auth==2.16.0 +google-api-python-client==2.86.0 +google-auth==2.18.0 google-auth-httplib2==0.1.0 google-auth-oauthlib==1.0.0 -googleapis-common-protos==1.58.0 +googleapis-common-protos==1.59.0 graphviz==0.20.1 -greenlet==2.0.2 -gspread==5.7.2 +greenlet==2.0.1 +gspread==5.9.0 gspread-formatting==1.1.2 hbreader==0.9.1 -httplib2==0.21.0 +httplib2==0.22.0 idna==3.4 ijson==3.2.0.post0 imagesize==1.4.1 -importlib-metadata==4.13.0 +importlib-metadata==6.6.0 iniconfig==2.0.0 -ipykernel==6.21.1 -ipython==8.10.0 +ipykernel==6.23.1 +ipython==8.13.2 ipython-genutils==0.2.0 -ipywidgets==8.0.4 +ipywidgets==8.0.6 isodate==0.6.1 isoduration==20.11.0 j2cli==0.3.10 @@ -92,6 +88,7 @@ jaraco.classes==3.2.3 jedi==0.18.2 jeepney==0.8.0 Jinja2==3.1.2 +jsbeautifier==1.14.7 jsobject==0.10.2 json-flattener==0.1.9 jsonasobj==1.3.1 @@ -106,204 +103,200 @@ jsonschema==4.17.3 jsonschema2md==0.4.0 jsonstreams==0.6.0 jupyter==1.0.0 -jupyter-console==6.5.0 +jupyter-console==6.6.3 jupyter-events==0.6.3 -jupyter_client==8.0.2 -jupyter_core==5.2.0 -jupyter_server==2.2.1 +jupyter_client==8.2.0 +jupyter_core==5.3.0 +jupyter_server==2.5.0 jupyter_server_terminals==0.4.4 jupyterlab-pygments==0.2.2 -jupyterlab-widgets==3.0.5 +jupyterlab-widgets==3.0.7 keyring==23.13.1 -kgcl-rdflib==0.3.0 -kgcl-schema==0.3.1 -kgx==1.7.2 +kgcl-rdflib==0.5.0 +kgcl-schema==0.5.0 +kgx==2.0.2 kiwisolver==1.4.4 lark==1.1.5 lightrdf==0.3.1 -linkml==1.4.4 +linkml==1.5.2 linkml-dataops==0.1.0 linkml-renderer==0.1.2 -linkml-runtime==1.4.5 +linkml-runtime==1.5.3 +lxml==4.9.2 Markdown==3.3.7 -markdown-it-py==2.1.0 +markdown-it-py==2.2.0 MarkupSafe==2.1.2 marshmallow==3.19.0 marshmallow-enum==1.5.1 -matplotlib==3.6.3 +matplotlib==3.7.1 matplotlib-inline==0.1.6 -matplotlib-venn==0.11.7 -mccabe==0.7.0 -mdit-py-plugins==0.3.3 +matplotlib-venn==0.11.9 +mdit-py-plugins==0.3.5 mdurl==0.1.2 mergedeep==1.3.4 mistune==2.0.5 -mkdocs==1.4.2 -mkdocs-material==9.0.12 +mkdocs==1.4.3 +mkdocs-material==9.1.12 mkdocs-material-extensions==1.1.1 +mkdocs-mermaid2-plugin==0.6.0 +mkdocs-table-reader-plugin==2.0 more-click==0.1.2 -more-itertools==9.0.0 -multidict==6.0.4 -mypy==1.0.0 +more-itertools==9.1.0 +mypy==1.3.0 mypy-extensions==1.0.0 -myst-parser==0.18.1 -nbclassic==0.5.1 -nbclient==0.7.2 -nbconvert==7.2.9 -nbformat==5.7.3 -neo4j==4.3.0 +myst-parser==1.0.0 +nbclassic==1.0.0 +nbclient==0.7.4 +nbconvert==7.4.0 +nbformat==5.8.0 +ndex2==3.5.1 +neo4j==4.4.11 nest-asyncio==1.5.6 -networkx==2.8.8 -notebook==6.5.2 -notebook_shim==0.2.2 -numpy==1.24.2 -nxontology==0.4.1 -oaklib==0.1.71 +networkx==3.1 +notebook==6.5.4 +notebook_shim==0.2.3 +numpy==1.24.3 +oaklib==0.5.6 oauthlib==3.2.2 -ols-client==0.1.2 -ontobio==2.8.3 +ols-client==0.1.4 +ontobio==2.8.6 ontodev-cogs==0.3.3 ontodev-gizmos==0.3.2 -ontoportal-client==0.0.3 -openpyxl==3.1.0 +ontoportal-client==0.0.4 +openpyxl==3.1.2 ordered-set==4.1.0 -packaging==23.0 +packaging==23.1 pandas==1.5.3 -pandasql==0.7.3 pandocfilters==1.5.0 +pansql==0.0.1 parse==1.19.0 parso==0.8.3 -pathspec==0.11.0 pexpect==4.8.0 pickleshare==0.7.5 -Pillow==9.4.0 +Pillow==9.5.0 pkginfo==1.9.6 -platformdirs==3.0.0 -plotly==5.13.0 +platformdirs==3.5.1 +plotly==5.14.1 pluggy==1.0.0 ply==3.11 -pockets==0.9.1 prefixcommons==0.1.12 -prefixmaps==0.1.4 +prefixmaps==0.1.5 prologterms==0.0.6 prometheus-client==0.16.0 -prompt-toolkit==3.0.36 -pronto==2.5.3 -protobuf==4.21.12 -psutil==5.9.4 +prompt-toolkit==3.0.38 +pronto==2.5.4 +protobuf==4.23.0 +psutil==5.9.5 ptyprocess==0.7.0 pure-eval==0.2.2 py==1.11.0 -pyasn1==0.4.8 -pyasn1-modules==0.2.8 -pycodestyle==2.10.0 +pyasn1==0.5.0 +pyasn1-modules==0.3.0 pycparser==2.21 -pydantic==1.10.4 +pydantic==1.10.7 pydotplus==2.0.2 -pyflakes==3.0.1 -PyGithub==1.57 -Pygments==2.14.0 +PyGithub==1.58.2 +Pygments==2.15.1 PyJSG==0.11.10 -PyJWT==2.6.0 -pymdown-extensions==9.9.2 +PyJWT==2.7.0 +pymdown-extensions==9.11 PyNaCl==1.5.0 pyparsing==2.4.7 pyrsistent==0.19.3 PyShEx==0.8.1 PyShExC==0.9.1 pysolr==3.9.0 -pyspellchecker==0.7.1 -pystow==0.4.9 -pytest==7.2.1 +pyspellchecker==0.7.2 +pystow==0.5.0 +pytest==7.3.1 pytest-logging==2015.11.4 python-dateutil==2.8.2 -python-json-logger==2.0.5 +python-json-logger==2.0.7 PyTrie==0.4.0 -pytz==2022.7.1 +pytz==2023.3 PyYAML==6.0 pyyaml_env_tag==0.1 -pyzmq==25.0.0 -qtconsole==5.4.0 -QtPy==2.3.0 +pyzmq==25.0.2 +qtconsole==5.4.3 +QtPy==2.3.1 ratelimit==2.2.1 rdflib==6.2.0 rdflib-jsonld==0.6.1 rdflib-shim==1.0.3 readme-renderer==37.3 recommonmark==0.7.1 -regex==2022.10.31 -requests==2.28.2 +regex==2023.5.5 +requests==2.30.0 +requests-cache==1.0.1 requests-oauthlib==1.3.1 -requests-toolbelt==0.10.1 +requests-toolbelt==1.0.0 rfc3339-validator==0.1.4 rfc3986==2.0.0 rfc3986-validator==0.1.1 rfc3987==1.3.8 -rich==13.3.1 +rich==13.3.5 rsa==4.9 -ruamel.yaml==0.17.21 +ruamel.yaml==0.17.26 ruamel.yaml.clib==0.2.7 -scipy==1.10.0 +scipy==1.10.1 seaborn==0.12.2 SecretStorage==3.3.3 -semsql==0.2.5 -Send2Trash==1.8.0 +semsimian==0.1.13 +semsql==0.3.2 +Send2Trash==1.8.2 ShExJSG==0.8.2 six==1.16.0 sniffio==1.3.0 snowballstemmer==2.2.0 sortedcontainers==2.4.0 -soupsieve==2.3.2.post1 +soupsieve==2.4.1 sparqlslurper==0.5.1 -SPARQLWrapper==2.0.0 -Sphinx==5.3.0 +SPARQLWrapper==1.8.5 +Sphinx==6.2.1 sphinx-click==4.4.0 sphinx-rtd-theme==1.2.0 -sphinx_autodoc_typehints==1.22 sphinxcontrib-applehelp==1.0.4 sphinxcontrib-devhelp==1.0.2 sphinxcontrib-htmlhelp==2.0.1 -sphinxcontrib-jquery==2.0.0 +sphinxcontrib-jquery==4.1 sphinxcontrib-jsmath==1.0.1 -sphinxcontrib-napoleon==0.7 sphinxcontrib-qthelp==1.0.3 sphinxcontrib-serializinghtml==1.1.5 -SQLAlchemy==1.4.46 +SQLAlchemy==2.0.13 SQLAlchemy-Utils==0.38.3 -sssom==0.3.22 -sssom-schema==0.9.4 +sssom==0.3.30 +sssom-schema==0.11.0 stack-data==0.6.2 stringcase==1.2.0 tabulate==0.9.0 -tenacity==8.2.1 -termcolor==2.2.0 +tenacity==8.2.2 +termcolor==2.3.0 terminado==0.17.1 terminaltables==3.1.10 tinycss2==1.2.1 -toml==0.10.2 -tomli==1.2.3 -tornado==6.2 -tox==3.25.1 -tox-docker==3.1.0 -tqdm==4.64.1 +tomli==2.0.1 +tornado==6.3.2 +tox==3.28.0 +tox-docker==4.1.0 +tqdm==4.65.0 traitlets==5.9.0 tsvalid==0.0.3 twine==4.0.2 typing-inspect==0.8.0 -typing_extensions==4.4.0 +typing_extensions==4.5.0 UpSetPlot==0.8.0 uri-template==1.2.0 uritemplate==4.1.1 -urllib3==1.26.14 +url-normalize==1.4.3 +urllib3==1.26.15 validators==0.20.0 -virtualenv==20.19.0 -watchdog==2.2.1 +virtualenv==20.23.0 +watchdog==3.0.0 wcwidth==0.2.6 -webcolors==1.12 +webcolors==1.13 webencodings==0.5.1 websocket-client==1.5.1 -widgetsnbextension==4.0.5 -wrapt==1.14.1 +widgetsnbextension==4.0.7 +wrapt==1.15.0 yamldown==0.1.8 -yarl==1.8.2 -zipp==3.13.0 +zipp==3.15.0 From 5547c7219d3b0d968b3128eb1acba959a0fcebde Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Fri, 26 May 2023 00:51:33 +0100 Subject: [PATCH 3/5] Prepare 1.4.1 release. Bump version number and update changelog. --- CHANGELOG.md | 8 ++++++++ Makefile | 2 +- docker/odklite/Makefile | 2 +- 3 files changed, 10 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8ca238e2..27a3bdc5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,11 @@ +# v1.4.1 + +- New [ROBOT version 1.9.4](https://github.com/ontodev/robot/releases/tag/v1.9.4) +- Newer versions of several Python packages, including: + - oaklib 1.5.6 + - bioregistry 0.9.15 + - linkml 1.5.2 + # v1.4 A full record of all changes can be seen [here](https://github.com/INCATools/ontology-development-kit/milestone/6?closed=1). diff --git a/Makefile b/Makefile index 4754342a..455d2f54 100644 --- a/Makefile +++ b/Makefile @@ -61,7 +61,7 @@ docs: @ODK_IMAGE=odklite ./odk.sh python ./odk/schema_documentation.py # Building docker image -VERSION = "v1.4" +VERSION = "v1.4.1" IM=obolibrary/odkfull IMLITE=obolibrary/odklite ROB=obolibrary/robot diff --git a/docker/odklite/Makefile b/docker/odklite/Makefile index e21dbd31..7076cfc4 100644 --- a/docker/odklite/Makefile +++ b/docker/odklite/Makefile @@ -1,6 +1,6 @@ # Building docker image -VERSION = "v1.2.30" +VERSION = "v1.4.1" IM=obolibrary/odklite TAGS_OPTION=-t $(IM):$(VERSION) -t $(IM):latest From b6336f8056a143489a242c6fde657aa79381387e Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Sat, 25 Feb 2023 18:27:31 +0000 Subject: [PATCH 4/5] Do not set UID/GID in seed-via-docker.sh. PR #771 partially reverted a temporarily introduced change in the run.sh script (the use of docker's -u option), but it did not revert a similar change in seed-via-docker.sh. As a result, the test suite was still run under the identity of a non-root user, which caused at least one test to fail (the sssom test, because the sssom tool uses the bioregistry module, which caches some data in the home directory). --- seed-via-docker.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/seed-via-docker.sh b/seed-via-docker.sh index a21a96db..783eea03 100755 --- a/seed-via-docker.sh +++ b/seed-via-docker.sh @@ -9,4 +9,4 @@ ODK_TAG=${ODK_TAG:-latest} ODK_GITNAME=${ODK_GITNAME:-$(git config --get user.name)} ODK_GITEMAIL=${ODK_GITEMAIL:-$(git config --get user.email)} -docker run -u $(id -u):$(id -g) -v $PWD:/work -w /work --rm obolibrary/$ODK_IMAGE:$ODK_TAG /tools/odk.py seed --gitname "$ODK_GITNAME" --gitemail "$ODK_GITEMAIL" "$@" +docker run -v $PWD:/work -w /work --rm obolibrary/$ODK_IMAGE:$ODK_TAG /tools/odk.py seed --gitname "$ODK_GITNAME" --gitemail "$ODK_GITEMAIL" "$@" From 6be42413faad5f3f352c0ebe36a704ad0991a350 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Tue, 7 Mar 2023 16:07:10 +0200 Subject: [PATCH 5/5] Fix test ontologies in ODK --- tests/test-base.yaml | 4 +++- tests/test-components-make-base.yaml | 4 +++- tests/test-components.yaml | 3 +++ tests/test-dosdp-matches.yaml | 2 ++ tests/test-edit-obo.yaml | 3 ++- tests/test-github-release.yaml | 3 +++ tests/test-import-minimal.yaml | 5 +++-- tests/test-module-custom.yaml | 1 + tests/test-module-minimal-large.yaml | 2 +- tests/test-module-minimal.yaml | 2 ++ tests/test-module-mireot.yaml | 2 ++ tests/test-module-mirror.yaml | 5 +++-- tests/test-module-star.yaml | 2 ++ tests/test-non-import-release.yaml | 4 +++- tests/test-patterns.yaml | 2 ++ tests/test-release-format-patterns.yaml | 2 ++ tests/test-release-format.yaml | 5 ++++- tests/test-release-imports-not-edit.yaml | 1 + tests/test-release.yaml | 5 ++++- tests/test-robot-report-baseiri.yaml | 2 ++ tests/test-robot-report.yaml | 4 +++- tests/test-robot-validate-profile.yaml | 1 + tests/test-sparql-report.yaml | 1 + tests/test-sssom.yaml | 1 + tests/test-templates.yaml | 1 + tests/test-uribase-suffix.yaml | 3 +-- tests/test-uribase.yaml | 3 +-- 27 files changed, 57 insertions(+), 16 deletions(-) diff --git a/tests/test-base.yaml b/tests/test-base.yaml index d8f04589..9d017b9d 100644 --- a/tests/test-base.yaml +++ b/tests/test-base.yaml @@ -11,8 +11,10 @@ import_group: mirror_max_time_download: 400 products: - id: ro + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl - id: pato use_base: TRUE + # This test cannot be easily replaced, because use_base and custom URL dont mix - id: pr make_base: TRUE - mirror_from: https://raw.githubusercontent.com/obophenotype/pro_obo_slim/master/pr_slim.owl + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/pr_slim.owl diff --git a/tests/test-components-make-base.yaml b/tests/test-components-make-base.yaml index 7020a501..6bd6afd6 100644 --- a/tests/test-components-make-base.yaml +++ b/tests/test-components-make-base.yaml @@ -12,11 +12,13 @@ export_formats: import_group: products: - id: ro + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl - id: bfo + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/bfo.owl components: products: - filename: pato.owl - source: http://purl.obolibrary.org/obo/pato.owl + source: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/pato.owl base_iris: - http://purl.obolibrary.org/obo/PATO_ - http://purl.obolibrary.org/obo/pato# diff --git a/tests/test-components.yaml b/tests/test-components.yaml index 1d7fb39f..e837f405 100644 --- a/tests/test-components.yaml +++ b/tests/test-components.yaml @@ -17,8 +17,11 @@ export_formats: import_group: products: - id: pato + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/pato.owl - id: ro + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl - id: bfo + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/bfo.owl components: products: - filename: wbphenotype-equivalent-axioms-subq.owl diff --git a/tests/test-dosdp-matches.yaml b/tests/test-dosdp-matches.yaml index 2fe9fdcb..53af817e 100644 --- a/tests/test-dosdp-matches.yaml +++ b/tests/test-dosdp-matches.yaml @@ -11,7 +11,9 @@ export_formats: import_group: products: - id: ro + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl - id: pato + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/pato.owl pattern_pipelines_group: products: - id: manual diff --git a/tests/test-edit-obo.yaml b/tests/test-edit-obo.yaml index 10b5525c..648b87af 100644 --- a/tests/test-edit-obo.yaml +++ b/tests/test-edit-obo.yaml @@ -6,4 +6,5 @@ report_fail_on: ERROR edit_format: obo import_group: products: - - id: ro \ No newline at end of file + - id: ro + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl \ No newline at end of file diff --git a/tests/test-github-release.yaml b/tests/test-github-release.yaml index fadfb4be..1bacf166 100644 --- a/tests/test-github-release.yaml +++ b/tests/test-github-release.yaml @@ -13,8 +13,11 @@ primary_release: simple import_group: products: - id: ro + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl - id: pato + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/pato.owl - id: mpath + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/mpath.owl public_release: github_curl public_release_assets: - rtgh.owl diff --git a/tests/test-import-minimal.yaml b/tests/test-import-minimal.yaml index 8bfe6861..bab11c64 100644 --- a/tests/test-import-minimal.yaml +++ b/tests/test-import-minimal.yaml @@ -15,8 +15,9 @@ primary_release: full import_group: products: - id: ro - - id: iao - - id: pco + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl + - id: omo + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/omo.owl components: products: - filename: pato_ext.owl diff --git a/tests/test-module-custom.yaml b/tests/test-module-custom.yaml index 2d69dfbd..bc069034 100644 --- a/tests/test-module-custom.yaml +++ b/tests/test-module-custom.yaml @@ -11,6 +11,7 @@ import_group: products: - id: ro mirror_type: base + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl - id: wikidata mirror_type: no_mirror module_type: custom diff --git a/tests/test-module-minimal-large.yaml b/tests/test-module-minimal-large.yaml index de81ae47..b0fa64a4 100644 --- a/tests/test-module-minimal-large.yaml +++ b/tests/test-module-minimal-large.yaml @@ -10,7 +10,7 @@ export_formats: import_group: products: - id: ro - use_base: TRUE + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl - id: pato is_large: TRUE module_type: minimal diff --git a/tests/test-module-minimal.yaml b/tests/test-module-minimal.yaml index 64a6b078..bb0fb21f 100644 --- a/tests/test-module-minimal.yaml +++ b/tests/test-module-minimal.yaml @@ -10,6 +10,8 @@ export_formats: import_group: products: - id: ro + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl - id: pato + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/pato.owl module_type: minimal diff --git a/tests/test-module-mireot.yaml b/tests/test-module-mireot.yaml index 84881046..0bbbd53a 100644 --- a/tests/test-module-mireot.yaml +++ b/tests/test-module-mireot.yaml @@ -10,6 +10,8 @@ export_formats: import_group: products: - id: ro + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl - id: pato + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/pato.owl module_type: mireot diff --git a/tests/test-module-mirror.yaml b/tests/test-module-mirror.yaml index 98e9fd77..45cd213e 100644 --- a/tests/test-module-mirror.yaml +++ b/tests/test-module-mirror.yaml @@ -1,5 +1,5 @@ id: modmir -title: "Test ROBOT extract minimal with base and large option" +title: "Test ROBOT extract with module type mirror" github_org: INCATools repo: ontology-development-kit edit_format: obo @@ -8,7 +8,8 @@ export_formats: - obo import_group: products: - - id: envo + - id: pato + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/pato.owl module_type: mirror allow_equivalents: all diff --git a/tests/test-module-star.yaml b/tests/test-module-star.yaml index 3ccacf77..3934332c 100644 --- a/tests/test-module-star.yaml +++ b/tests/test-module-star.yaml @@ -10,7 +10,9 @@ export_formats: import_group: products: - id: ro + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl - id: pato + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/pato.owl module_type: slme module_type_slme: STAR slme_individuals: exclude diff --git a/tests/test-non-import-release.yaml b/tests/test-non-import-release.yaml index cacf28ab..5f5dd5e7 100644 --- a/tests/test-non-import-release.yaml +++ b/tests/test-non-import-release.yaml @@ -14,4 +14,6 @@ import_group: release_imports: TRUE products: - id: ro - - id: pato \ No newline at end of file + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl + - id: pato + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/pato.owl \ No newline at end of file diff --git a/tests/test-patterns.yaml b/tests/test-patterns.yaml index dbbb4c9e..20306f97 100644 --- a/tests/test-patterns.yaml +++ b/tests/test-patterns.yaml @@ -11,7 +11,9 @@ export_formats: import_group: products: - id: ro + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl - id: pato + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/pato.owl pattern_pipelines_group: products: - id: manual diff --git a/tests/test-release-format-patterns.yaml b/tests/test-release-format-patterns.yaml index fb22cc9a..68a1db2e 100644 --- a/tests/test-release-format-patterns.yaml +++ b/tests/test-release-format-patterns.yaml @@ -22,7 +22,9 @@ export_formats: import_group: products: - id: ro + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl - id: pato + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/pato.owl pattern_pipelines_group: products: - id: manual diff --git a/tests/test-release-format.yaml b/tests/test-release-format.yaml index 137b51d1..fbeac6d1 100644 --- a/tests/test-release-format.yaml +++ b/tests/test-release-format.yaml @@ -22,5 +22,8 @@ export_formats: import_group: products: - id: ro + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl - id: pato - - id: mpath \ No newline at end of file + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/pato.owl + - id: mpath + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/mpath.owl \ No newline at end of file diff --git a/tests/test-release-imports-not-edit.yaml b/tests/test-release-imports-not-edit.yaml index f2187f77..27306afa 100644 --- a/tests/test-release-imports-not-edit.yaml +++ b/tests/test-release-imports-not-edit.yaml @@ -19,3 +19,4 @@ import_group: release_imports: TRUE products: - id: ro + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl diff --git a/tests/test-release.yaml b/tests/test-release.yaml index c55dca13..45bdfba6 100644 --- a/tests/test-release.yaml +++ b/tests/test-release.yaml @@ -21,5 +21,8 @@ import_group: release_imports: TRUE products: - id: ro + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl - id: pato - - id: mpath \ No newline at end of file + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/pato.owl + - id: mpath + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/mpath.owl \ No newline at end of file diff --git a/tests/test-robot-report-baseiri.yaml b/tests/test-robot-report-baseiri.yaml index 1acbfb9b..472adfa4 100644 --- a/tests/test-robot-report-baseiri.yaml +++ b/tests/test-robot-report-baseiri.yaml @@ -8,7 +8,9 @@ namespaces: import_group: products: - id: ro + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl - id: omo + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/omo.owl robot_report: use_base_iris: True release_reports: True diff --git a/tests/test-robot-report.yaml b/tests/test-robot-report.yaml index cdbc384c..e04edf47 100644 --- a/tests/test-robot-report.yaml +++ b/tests/test-robot-report.yaml @@ -14,7 +14,9 @@ release_artefacts: import_group: products: - id: ro - - id: iao + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl + - id: omo + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/omo.owl robot_report: release_reports: True fail_on : ERROR diff --git a/tests/test-robot-validate-profile.yaml b/tests/test-robot-validate-profile.yaml index d7b4486d..a8d0e874 100644 --- a/tests/test-robot-validate-profile.yaml +++ b/tests/test-robot-validate-profile.yaml @@ -8,6 +8,7 @@ export_formats: import_group: products: - id: ro + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl robot_report: release_reports: True fail_on : ERROR diff --git a/tests/test-sparql-report.yaml b/tests/test-sparql-report.yaml index a9154721..2e0834b2 100644 --- a/tests/test-sparql-report.yaml +++ b/tests/test-sparql-report.yaml @@ -11,6 +11,7 @@ release_artefacts: import_group: products: - id: ro + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl robot_report: release_reports: True fail_on : ERROR diff --git a/tests/test-sssom.yaml b/tests/test-sssom.yaml index f59d7aab..ee7c8be3 100644 --- a/tests/test-sssom.yaml +++ b/tests/test-sssom.yaml @@ -8,6 +8,7 @@ export_formats: import_group: products: - id: ro + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl sssom_mappingset_group: products: - id: modmini-onta diff --git a/tests/test-templates.yaml b/tests/test-templates.yaml index 7c49654a..7a5b4ca7 100644 --- a/tests/test-templates.yaml +++ b/tests/test-templates.yaml @@ -8,6 +8,7 @@ export_formats: import_group: products: - id: ro + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl components: products: - filename: test-with-context.owl diff --git a/tests/test-uribase-suffix.yaml b/tests/test-uribase-suffix.yaml index e9b6f979..71196c05 100644 --- a/tests/test-uribase-suffix.yaml +++ b/tests/test-uribase-suffix.yaml @@ -7,5 +7,4 @@ uribase_suffix: ontology import_group: products: - id: ro - - id: pato - use_base: TRUE \ No newline at end of file + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl diff --git a/tests/test-uribase.yaml b/tests/test-uribase.yaml index 7be79685..9961e049 100644 --- a/tests/test-uribase.yaml +++ b/tests/test-uribase.yaml @@ -6,5 +6,4 @@ uribase: https://w3id.org/odk import_group: products: - id: ro - - id: pato - use_base: TRUE \ No newline at end of file + mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl