From b34c9dcfb9230bc4008d0e8d37162673851c6bec Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Mon, 19 Apr 2021 14:16:22 -0400 Subject: [PATCH 1/6] Clarify README: the webserver does not serve content at `/`. --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index c21dfd9..bbff90d 100644 --- a/README.md +++ b/README.md @@ -19,6 +19,8 @@ can be used to resolve [phyloreferences](http://phyloref.org): - You can also use the `/version` endpoint to test whether the software is working. It will report on the version of JPhyloRef, OWLAPI and reasoner being used. + - Note that no content is served at `/`; you will need to use `/version` to + test that the server is running. - `java -jar jphyloref.jar test input.owl`: Test all the phyloreferences in `input.owl` by comparing their resolution with the expected resolution recorded in the file. From 683e3f288d5b93598494150223fe5c1a554a1ace Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Mon, 19 Apr 2021 14:25:20 -0400 Subject: [PATCH 2/6] Added a separate note on running just the test suite. Might be useful if the reader doesn't know much about the Maven system. --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index bbff90d..b174395 100644 --- a/README.md +++ b/README.md @@ -33,6 +33,8 @@ Development of JPhyloRef takes place in [our GitHub repository]. This includes [ # Build and execution instructions +Once you have downloaded the source code to your computer, you can compile and test the code by running `mvn test`. + JPhyloRef can be built from source by running `mvn package` from the root directory of this repository. This will create a JAR file in the `target/` directory, which can be executed by running, for example: From 783dbc27e604c87441c12b40d94dff8ced37e42b Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Thu, 17 Jun 2021 15:07:07 -0400 Subject: [PATCH 3/6] Added some Java installation instructions. Includes note about JAVA_HOME environment variable as per #81. --- README.md | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/README.md b/README.md index b174395..8cb8f87 100644 --- a/README.md +++ b/README.md @@ -33,6 +33,11 @@ Development of JPhyloRef takes place in [our GitHub repository]. This includes [ # Build and execution instructions +You will need [Java] and [Apache Maven] to build the software from source. We recommend installing these +tools using a package manager, such as [Homebrew] on macOS. You can use [jEnv] instead if you want to install +multiple Java versions on the same computer. Installation should set up the `JAVA_HOME` environment +variable; if not, you will need to set it to point at the directory containing your Java installation. + Once you have downloaded the source code to your computer, you can compile and test the code by running `mvn test`. JPhyloRef can be built from source by running `mvn package` from the root directory of this repository. This will create a JAR file in the `target/` directory, which can be executed by running, @@ -88,6 +93,10 @@ Once you're set up, you can run `mvn clean deploy` to publish the package to the OSSRH. If your version number ends in `-SNAPSHOT`, this will be published to the OSSRH Snapshots repository. + [Java]: https://www.java.com/en/ + [Apache Maven]: https://maven.apache.org/ + [Homebrew]: https://brew.sh/ + [jEnv]: https://www.jenv.be/ [Sonatype OSSRH]: https://central.sonatype.org/pages/ossrh-guide.html [the Sonatype website]: https://central.sonatype.org/pages/apache-maven.html [Maven settings.xml file]: https://central.sonatype.org/pages/apache-maven.html From 1525a2eed19df8a36c1d33a405193a4393cd5aee Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Thu, 17 Jun 2021 16:43:37 -0400 Subject: [PATCH 4/6] Removed unused JSONLD package. --- pom.xml | 7 ------- 1 file changed, 7 deletions(-) diff --git a/pom.xml b/pom.xml index 4ea359c..03ae192 100644 --- a/pom.xml +++ b/pom.xml @@ -97,13 +97,6 @@ 2.3.2 - - - com.github.jsonld-java - jsonld-java - 0.12.0 - - From 47c6df860b1b88fe3f473be6b519191003a6cf66 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Thu, 17 Jun 2021 16:45:50 -0400 Subject: [PATCH 5/6] Replaced owlapi-distribution with owlapi-apibinding. The latter package seems to be more specific, and appears to cover everything we need. --- pom.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pom.xml b/pom.xml index 03ae192..e8c2493 100644 --- a/pom.xml +++ b/pom.xml @@ -108,10 +108,10 @@ - + net.sourceforge.owlapi - owlapi-distribution + owlapi-apibinding 4.5.19 From bbf672c911a3bb1a051bb09eca03272725010847 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Thu, 17 Jun 2021 16:50:46 -0400 Subject: [PATCH 6/6] Recreate JAR file on each run. This prevents overlapping class warnings from shaded JARs (https://stackoverflow.com/a/11015175/27310). --- pom.xml | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/pom.xml b/pom.xml index e8c2493..200d29a 100644 --- a/pom.xml +++ b/pom.xml @@ -242,6 +242,16 @@ + + + org.apache.maven.plugins + maven-jar-plugin + 3.2.0 + + true + + + org.apache.maven.plugins maven-shade-plugin