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Add a --include-indirect option to materialize

6

From slack: Hi all, I have a question about the use of the materialize command. Let's consider the following axioms: ``` car SubclassOf has part some wheel convertible SubclassOf car...

cmungall

Resolves #1213 - [ ] `docs/` have been added/updated - [ ] tests have been added/updated - [ ] `mvn verify` says all tests pass - [ ] `mvn site`...

souzadevinicius

Given ```yaml [Term] id: CHEBI:0 name: c0 is_a: CHEBI:1 [Term] id: CHEBI:1 name: c1 is_obsolete: true replaced_by: CHEBI:2 is_a: CHEBI:3 [Term] id: CHEBI:2 name: c2 [Term] id: CHEBI:3 name: c3...

cmungall

When ROBOT expects to see a class label or CURIE in a template cell, and it sees a raw IRI instead, interpret it as an OWLClass. - [X] tests have...

jamesaoverton

Bumps [com.fasterxml.jackson.core:jackson-core](https://github.com/FasterXML/jackson-core) from 2.12.2 to 2.15.0. Changelog Sourced from com.fasterxml.jackson.core:jackson-core's changelog. #release configuration #Sun Apr 23 14:19:10 PDT 2023 scm.commentPrefix=[maven-release-plugin] exec.pomFileName=pom.xml pushChanges=false releaseStrategyId=default project.dev.com.fasterxml.jackson.core:jackson-core=2.15.1-SNAPSHOT project.scm.com.fasterxml.jackson.core:jackson-core.connection=scm:git:[email protected]:FasterXML/jackson-core.git scm.tag=jackson-core-2.15.0 remoteTagging=true project.scm.com.fasterxml.jackson.core:jackson-core.developerConnection=scm:git:[email protected]:FasterXML/jackson-core.git exec.additionalArguments=-Prelease scm.branchCommitComment=@{prefix}...

dependabot[bot]

Consider making the --output argument more universal (particularly robot export & query)

5

Would it be possible to add `--output` / `-o` as an argument to robot export as an alias for the `--export` argument. Most of the other robot commands (report, extract,...

allenbaron

This took me a while to figure out. In a chain of commands like this: ``` robot --catalog catalog-v001.xml \ merge --collapse-import-closure false -i go-edit-filtered-xrefs.ofn -i imports/go_taxon_constraints.owl -i imports/reactome_xrefs_import.owl -i...

balhoff

Merging axiom annotations cause unexpected loss of information in OBO output

4

Now that the `repair --merge-axiom-annotations` command has been fixed (#1240), I noticed that this feature has an unexpected effect when writing to OBO. Consider the following minimal example: ``` Prefix(fbbt:=)...

gouttegd

Removing annotation properties can lead to duplicated axioms

2

The `remove` command sometimes leads to duplicated axioms when producing OFN output. This is best illustrated by an example. Let us consider the following minimal ontology: ``` Prefix(EX:=) Prefix(oboInOwl:=) Prefix(rdfs:=)...

gouttegd

`robot diff` always shows all axioms have changed for blank nodes

4

I'd like to use `robot diff` to get a summary of the changes in a GitHub pull request, or during development. For the PR, (in essence) the script run `robot`...

paulmillar