Update some tools.

Update the following tools to their latest available versions:

* Scala-CLI, from 1.5.4 to 1.8.0;
* Soufflé, from 2.4.1 to 2.5;
* Dicer, from 0.1.0 to 0.2.0;
* SSSOM-Java (ROBOT plugin and CLI tool), from 1.4.0 to 1.5.1.

The Dicer upgrade requires updating the Makefile template, as the
`dicer` tool now uses subcommands (call to `dicer` must be replaced by
`dicer policy`).

Author: gouttegd

Dockerfile

@@ -14,7 +14,7 @@ ENV ODK_VERSION=$ODK_VERSION
 ENV JENA_VERSION=4.9.0
 ENV KGCL_JAVA_VERSION=0.5.1
 ENV AMMONITE_VERSION=2.5.9
-ENV SCALA_CLI_VERSION=1.5.4
+ENV SCALA_CLI_VERSION=1.8.0
 ENV OWLTOOLS_VERSION=2020-04-06
 
 # Avoid repeated downloads of script dependencies by mounting the local coursier cache:

docker/builder/Dockerfile

@@ -8,7 +8,7 @@ WORKDIR /build
 
 # Software versions
 ENV RDFTAB_VERSION=0.1.1
-ENV SOUFFLE_VERSION=2.4.1
+ENV SOUFFLE_VERSION=2.5
 ENV FASTOBO_VALIDATOR_VERSION=0.4.6
 
 # Everything that we want to get into one of the final ODK images

docker/odklite/Dockerfile

@@ -4,9 +4,9 @@ LABEL maintainer="obo-tools@googlegroups.com"
 ENV ROBOT_VERSION=1.9.7
 ENV DOSDP_VERSION=0.19.3
 ENV RELATION_GRAPH=2.3.2
-ENV DICER_VERSION=0.1.0
+ENV DICER_VERSION=0.2.0
 ENV ODK_ROBOT_PLUGIN_VERSION=0.2.0
-ENV SSSOM_JAVA_VERSION=1.4.0
+ENV SSSOM_JAVA_VERSION=1.5.1
 
 WORKDIR /tools
 ENV JAVA_HOME="/usr"

template/src/ontology/Makefile.jinja2

@@ -1532,7 +1532,7 @@ normalize_src: $(SRC)
 
 .PHONY: validate_idranges
 validate_idranges:
-	if [ -f {{ project.id }}-idranges.owl ]; then dicer-cli {{ project.id }}-idranges.owl ; fi
+	if [ -f {{ project.id }}-idranges.owl ]; then dicer-cli policy {{ project.id }}-idranges.owl ; fi
 
 # Deprecated: Use 'sh run.sh odk.py update' without using the Makefile.
 .PHONY: update_repo