restructure build

draeger-lab · Sep 6, 2024 · 9f35b28 · 9f35b28
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diff --git a/.gitignore b/.gitignore
@@ -9,8 +9,6 @@
 /.vscode/
 /bin
 /build/
-/gradle
-/lib
 /minimalSysBio.xml
 /model_polisher.log
 /out

diff --git a/README.md b/README.md
@@ -61,14 +61,14 @@ ModelPolisher can also be run locally.
 If you want to process a large number of models, or you don't feel comfortable using the Python API client package, this is the recommendend usage.
 
 ### Parameters
-Parameters can be passed via a [json file](examples/config.json) or as command line arguments.
+Parameters can be passed via a [json file](app/examples/config.json) or as command line arguments.
 
 See [the Wiki](https://github.com/draeger-lab/ModelPolisher/wiki/Parameters) for more information.
 
 ### Using Docker
 ModelPolisher is provided as a Docker image.
 
-This repository contains a [`docker-compose.yml`](./docker-compose.yml) which also sets up BiGG DB and AnnotateDB as Docker containers, to support the [annotation functionality](https://github.com/draeger-lab/ModelPolisher/wiki/Annotation).
+This repository contains a [`docker-compose.yml`](app/docker-compose.yml) which also sets up BiGG DB and AnnotateDB as Docker containers, to support the [annotation functionality](https://github.com/draeger-lab/ModelPolisher/wiki/Annotation).
 
 For a single model file, you can use
 ``` shell

diff --git a/Dockerfile → app/Dockerfile b/Dockerfile → app/Dockerfile
@@ -4,7 +4,7 @@ FROM openjdk:17-slim
 LABEL maintainer="[email protected]"
 
 # Copy the ModelPolisher jar file into the root directory of the image
-COPY target/ModelPolisher-2.1-pre-release-STANDALONE.jar /
+COPY ../target/ModelPolisher-2.1-pre-release-STANDALONE.jar /
 
 # Set the container to run the ModelPolisher jar file as the default executable
 ENTRYPOINT ["java", "-jar", "/ModelPolisher-2.1-pre-release-STANDALONE.jar"]

diff --git a/app/build.gradle b/app/build.gradle
@@ -0,0 +1,126 @@
+import com.github.jk1.license.filter.ExcludeTransitiveDependenciesFilter
+import com.github.jk1.license.filter.LicenseBundleNormalizer
+
+plugins {
+    id 'com.github.jk1.dependency-license-report' version '2.0'
+    id "java"
+    id "application"
+    id "maven-publish"
+}
+
+group = "de.uni-halle.informatik.biodata"
+version = "2.1"
+
+
+application {
+    mainClass.set('de.uni_halle.informatik.biodata.mp.ModelPolisherCLILauncher')
+}
+
+
+sourceSets {
+    main {
+        java {
+            srcDirs = ["src/main/java"]
+        }
+        resources {
+            srcDirs = ["src/main/resources"]
+        }
+    }
+}
+
+dependencies {
+    implementation(libs.sysbio)
+    implementation(libs.jsbml) {
+        exclude group: "org.apache.logging.log4j", module: "log4j-core"
+        exclude group: "org.apache.logging.log4j", module: "log4j-slf4j-impl"
+        exclude group: "org.apache.commons", module: "logging"
+    }
+
+    implementation(libs.biojavaOntology) {
+        exclude group: "org.apache.logging.log4j", module: "log4j-core"
+        exclude group: "org.apache.logging.log4j", module: "log4j-slf4j-impl"
+    }
+
+    implementation(libs.jacksonDatabinding)
+
+    implementation(libs.commonsIO)
+    implementation(libs.commonsLang)
+
+    implementation(libs.slf4j)
+    implementation(libs.julToSlf4j)
+    implementation(libs.jclOverSlf4j)
+    implementation(libs.log4jOverSlf4j)
+    implementation(libs.osgiOverSlf4j)
+
+    implementation(libs.logback)
+
+    implementation project(':lib')
+}
+
+// config for all jar tasks
+tasks.withType(Jar).configureEach {
+    duplicatesStrategy = DuplicatesStrategy.EXCLUDE
+    destinationDirectory = file("$rootDir/target")
+    manifest {
+        attributes("Version": project.version,
+                "Implementation-Title": "ModelPolisher",
+                "Implementation-Version": project.version,
+                "Specification-Vendor": "Martin-Luther-Universität Halle-Wittenberg, BioDatA Arbeitsgruppe",
+                "Specification-Title": "ModelPolisher",
+                "Implementation-Vendor-Id": "de.uni-halle.informatik.biodata",
+                "Implementation-Vendor": "Martin-Luther-Universität Halle-Wittenberg, BioDatA Arbeitsgruppe",
+                "Main-Class": "de.uni_halle.informatik.biodata.mp.ModelPolisherCLILauncher")
+    }
+
+    into("META-INF/maven/${project.group}/${rootProject.name}") {
+        from { generatePomFileForModelPolisherStandalonePublication }
+        rename { it.replace('pom-default.xml', 'pom.xml') }
+    }
+
+    archiveFileName = "${rootProject.name}-${project.version}-STANDALONE.jar"
+
+    from sourceSets.main.output
+
+    dependsOn configurations.runtimeClasspath
+    from {
+        configurations.runtimeClasspath.findAll { it.name.endsWith('jar') }.collect { zipTree(it) }
+    }
+}
+
+
+publishing {
+    publications {
+        modelPolisherStandalone(MavenPublication) {
+            from components.java
+
+            artifactId = 'ModelPolisher'
+            version = "2.1-STANDALONE   "
+        }
+    }
+    // https://reposilite.com/guide/gradle
+    repositories {
+        maven {
+            name = "reposilite"
+            url = "https://biodata.informatik.uni-halle.de/maven/releases"
+            credentials(PasswordCredentials)
+            authentication {
+                basic(BasicAuthentication)
+            }
+        }
+    }
+}
+
+
+licenseReport {
+    filters = [new LicenseBundleNormalizer(),
+               new ExcludeTransitiveDependenciesFilter()]
+}
+
+tasks.withType(Javadoc).configureEach {
+    enabled = false
+}
+
+clean.doFirst {
+    file(".gradle").deleteDir()
+    file("target").deleteDir()
+}
diff --git a/app/build/publications/modelPolisherStandalone/module.json b/app/build/publications/modelPolisherStandalone/module.json
@@ -0,0 +1,177 @@
+{
+  "formatVersion": "1.1",
+  "component": {
+    "group": "de.uni-halle.informatik.biodata",
+    "module": "ModelPolisher",
+    "version": "2.1-STANDALONE",
+    "attributes": {
+      "org.gradle.status": "release"
+    }
+  },
+  "createdBy": {
+    "gradle": {
+      "version": "8.10"
+    }
+  },
+  "variants": [
+    {
+      "name": "apiElements",
+      "attributes": {
+        "org.gradle.category": "library",
+        "org.gradle.dependency.bundling": "external",
+        "org.gradle.jvm.version": 17,
+        "org.gradle.libraryelements": "jar",
+        "org.gradle.usage": "java-api"
+      },
+      "files": [
+        {
+          "name": "ModelPolisher-2.1-STANDALONE.jar",
+          "url": "ModelPolisher-2.1-STANDALONE.jar",
+          "size": 15506284,
+          "sha512": "4642cc0b0339d805b6b4954b76a95815cabede6addfdf78e0d23285415a6a9c9be1e3a6e5ddf0b7b591b9d65ca0de53c83eb91ed7506cf9622bc69981d35f0e0",
+          "sha256": "00fc618c0faa6bb331f58e2fd528023ff3fa0ed5da6a04785d5ded55e20380d9",
+          "sha1": "11b53446e069b42955fb16cefa98feb4eccf79a7",
+          "md5": "168891d7aceb03fa357715f103030948"
+        }
+      ]
+    },
+    {
+      "name": "runtimeElements",
+      "attributes": {
+        "org.gradle.category": "library",
+        "org.gradle.dependency.bundling": "external",
+        "org.gradle.jvm.version": 17,
+        "org.gradle.libraryelements": "jar",
+        "org.gradle.usage": "java-runtime"
+      },
+      "dependencies": [
+        {
+          "group": "de.zbit.SysBio",
+          "module": "SysBio",
+          "version": {
+            "requires": "1390"
+          }
+        },
+        {
+          "group": "org.sbml.jsbml",
+          "module": "jsbml",
+          "version": {
+            "requires": "1.6.1"
+          },
+          "excludes": [
+            {
+              "group": "org.apache.logging.log4j",
+              "module": "log4j-slf4j-impl"
+            },
+            {
+              "group": "org.apache.logging.log4j",
+              "module": "log4j-core"
+            },
+            {
+              "group": "org.apache.commons",
+              "module": "logging"
+            }
+          ]
+        },
+        {
+          "group": "org.biojava",
+          "module": "biojava-ontology",
+          "version": {
+            "requires": "7.1.1"
+          },
+          "excludes": [
+            {
+              "group": "org.apache.logging.log4j",
+              "module": "log4j-slf4j-impl"
+            },
+            {
+              "group": "org.apache.logging.log4j",
+              "module": "log4j-core"
+            }
+          ]
+        },
+        {
+          "group": "com.fasterxml.jackson.core",
+          "module": "jackson-databind",
+          "version": {
+            "requires": "2.17.1"
+          }
+        },
+        {
+          "group": "commons-io",
+          "module": "commons-io",
+          "version": {
+            "requires": "2.16.1"
+          }
+        },
+        {
+          "group": "org.apache.commons",
+          "module": "commons-lang3",
+          "version": {
+            "requires": "3.15.0"
+          }
+        },
+        {
+          "group": "org.slf4j",
+          "module": "slf4j-api",
+          "version": {
+            "requires": "2.0.16"
+          }
+        },
+        {
+          "group": "org.slf4j",
+          "module": "jul-to-slf4j",
+          "version": {
+            "requires": "2.0.16"
+          }
+        },
+        {
+          "group": "org.slf4j",
+          "module": "jcl-over-slf4j",
+          "version": {
+            "requires": "2.0.16"
+          }
+        },
+        {
+          "group": "org.slf4j",
+          "module": "log4j-over-slf4j",
+          "version": {
+            "requires": "2.0.16"
+          }
+        },
+        {
+          "group": "org.slf4j",
+          "module": "osgi-over-slf4j",
+          "version": {
+            "requires": "2.0.16"
+          }
+        },
+        {
+          "group": "ch.qos.logback",
+          "module": "logback-classic",
+          "version": {
+            "requires": "1.5.7"
+          }
+        },
+        {
+          "group": "de.uni-halle.informatik.biodata",
+          "module": "ModelPolisher",
+          "version": {
+            "requires": "2.1"
+          }
+        }
+      ],
+      "files": [
+        {
+          "name": "ModelPolisher-2.1-STANDALONE.jar",
+          "url": "ModelPolisher-2.1-STANDALONE.jar",
+          "size": 15506284,
+          "sha512": "4642cc0b0339d805b6b4954b76a95815cabede6addfdf78e0d23285415a6a9c9be1e3a6e5ddf0b7b591b9d65ca0de53c83eb91ed7506cf9622bc69981d35f0e0",
+          "sha256": "00fc618c0faa6bb331f58e2fd528023ff3fa0ed5da6a04785d5ded55e20380d9",
+          "sha1": "11b53446e069b42955fb16cefa98feb4eccf79a7",
+          "md5": "168891d7aceb03fa357715f103030948"
+        }
+      ]
+    }
+  ]
+}
-Original file line number
+Diff line change
@@ Expand Up / @@ -9,8 +9,6 @@ @@
     /.vscode/
     /bin
     /build/
-    /gradle
-    /lib
     /minimalSysBio.xml
     /model_polisher.log
     /out
@@ Expand Down @@