From 954c0730961724dda04e63528eaafe64493f1e74 Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Sun, 10 Nov 2024 14:42:28 +0000 Subject: [PATCH 1/3] Fix bogus xml:base attribute in XML catalog. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit The `group` element in the XML catalog contains a `xml:base` attribute with an empty value (`xml:base=""`). It is unclear whether an empty value is legal (though the XML Base specification [1] does not seem to explicitly forbid it), but in any case it does not make any sense, and some XML Catalog parsers barf upon encountering such an attribute. So here we simply remove it. This has (as expected) no effect on the parsing of the catalog by both Protégé and ROBOT. [1] https://www.w3.org/TR/xmlbase/ --- src/ontology/catalog-v001.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml index c77f13fa3..9eae1c78d 100644 --- a/src/ontology/catalog-v001.xml +++ b/src/ontology/catalog-v001.xml @@ -1,6 +1,6 @@ - + From b66528b55e472b03b2d35af693339e3c45cc24d0 Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Sun, 10 Nov 2024 15:05:08 +0000 Subject: [PATCH 2/3] Check foreign mapping sets against the ontology. When importing an externally maintained SSSOM set (the FBbt mapping set and the Biomappings set), check them against Uberon to (1) remove any mapping to an Uberon entity that does not exist or is deprecated, and (2) add any missing label for Uberon entities. --- src/ontology/uberon.Makefile | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/src/ontology/uberon.Makefile b/src/ontology/uberon.Makefile index bde371d72..8383a740c 100644 --- a/src/ontology/uberon.Makefile +++ b/src/ontology/uberon.Makefile @@ -1257,7 +1257,8 @@ ifeq ($(strip $(IMP)),true) $(MAPPINGDIR)/fbbt.sssom.tsv: .FORCE wget "http://purl.obolibrary.org/obo/fbbt/fbbt.sssom.tsv" -O - | \ sssom-cli --prefix-map-from-input \ - --rule 'object==UBERON:* -> include()' \ + --include 'object==UBERON:*' \ + --update-from-ontology=$(SRC):object,label,existence \ --output $@ # CL mapping set. We simply fetch it as it is from CL. It already @@ -1276,7 +1277,8 @@ $(MAPPINGDIR)/biomappings.sssom.tsv: $(TMPDIR)/biomappings.sssom.tsv \ sssom-cli --input $< --prefix 'UBERON=http://purl.obolibrary.org/obo/UBERON_' \ --rule '!(subject==UBERON:* || object==UBERON:*) -> stop()' \ --rule 'object==UBERON:* -> invert()' \ - --include-all | \ + --include-all \ + --update-from-ontology=$(SRC):subject,label,existence | \ sssom-cli --mangle-iris obo --output $@ $(TMPDIR)/biomappings.sssom.tsv: From 310955acd6747738741dd404d0140824ef518eda Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Sun, 10 Nov 2024 15:09:01 +0000 Subject: [PATCH 3/3] Use ODK 1.5.3 in GitHub Actions workflows. Recent changes in the SSSOM pipelines require SSSOM-CLI's `--update-from-ontology` option which was added in SSSOM-Java 0.7.9, which itself was included in ODK 1.5.3. --- .github/workflows/diff.yml | 8 ++++---- .github/workflows/qc.yml | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/diff.yml b/.github/workflows/diff.yml index 0d87dc280..3db66357d 100644 --- a/.github/workflows/diff.yml +++ b/.github/workflows/diff.yml @@ -61,7 +61,7 @@ jobs: needs: [branch_status] if: ${{ github.event.issue.pull_request }} runs-on: ubuntu-latest - container: obolibrary/odkfull:v1.5 + container: obolibrary/odkfull:v1.5.3 steps: - uses: khan/pull-request-comment-trigger@v1.1.0 id: check @@ -94,7 +94,7 @@ jobs: needs: [branch_status] if: ${{ github.event.issue.pull_request }} runs-on: ubuntu-latest - container: obolibrary/odkfull:v1.5 + container: obolibrary/odkfull:v1.5.3 steps: - uses: khan/pull-request-comment-trigger@v1.1.0 id: check @@ -122,7 +122,7 @@ jobs: needs: [branch_status] if: ${{ github.event.issue.pull_request }} runs-on: ubuntu-latest - container: obolibrary/odkfull:v1.5 + container: obolibrary/odkfull:v1.5.3 steps: - uses: khan/pull-request-comment-trigger@v1.1.0 id: check @@ -147,7 +147,7 @@ jobs: diff_classification: needs: [classify_branch, classify_main] runs-on: ubuntu-latest - container: obolibrary/odkfull:v1.5 + container: obolibrary/odkfull:v1.5.3 steps: - uses: khan/pull-request-comment-trigger@v1.1.0 id: check diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml index 48b4fc7ee..fdbf27bf8 100644 --- a/.github/workflows/qc.yml +++ b/.github/workflows/qc.yml @@ -23,7 +23,7 @@ jobs: ontology_qc: # The type of runner that the job will run on runs-on: ubuntu-latest - container: obolibrary/odkfull:v1.5.2 + container: obolibrary/odkfull:v1.5.3 # Steps represent a sequence of tasks that will be executed as part of the job steps: # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it