Merge pull request #111 from biocodellc/develop

Merging develop into master to sync with release 3.0.12

.gitignore

@@ -4,3 +4,6 @@ resources/geome_secrets.json
 .idea/
 build/
 out/
+*.iml
+*.ipr
+*.iws

JBD_readme.md

@@ -0,0 +1,18 @@
+# JBD Readme
+
+Random notes about working in the LIMS development environmeent
+
+# if we ever get class conflicts of the same class name, some steps to rectify:
+NOTE: I believe this happens when i switch versions of geneious... doesn't seem to happen
+if i stay on a single geneious version or with a single genious API.
+there is probably a more elegant way to proceed here but this is what i've found helpful
+  * clean the Data directory or provide an entirely new one
+  * rm -fr /Library/Application\ Support/Geneious/plugins/com.biomatters.plugins.biocode.BiocodePlugin/
+  * rm -fr ~/.gradle/caches
+  * may have to clean gradle like ./gradlew clean
+
+# Quickly create a plugin, without running time-consuming Tests... Only for development
+# only run from the command line
+```
+./gradlew quickCreatePlugin
+```

PluginVersions.xml

@@ -1,9 +1,10 @@
 <PluginVersions>
-    <LatestVersion>3.0.9</LatestVersion>
-    <LatestVersionURL>https://github.com/biocodellc/biocode-lims/releases/download/3.0.9/BiocodePlugin_3_0_9.gplugin</LatestVersionURL>
-    <ReleaseNotes>==Biocode Plugin 3.0.9 - 6 March 2019==
-        * Fix Project search bug
-        * Add Genbank Metadata data properties to results list for Geome
+    <LatestVersion>3.0.12</LatestVersion>
+    <LatestVersionURL>https://github.com/biocodellc/biocode-lims/releases/download/3.0.12/BiocodePlugin_3_0_12.gplugin</LatestVersionURL>
+    <ReleaseNotes>==Biocode Plugin 3.0.12 - 14 May 2019==
+       * Fixes bug in fetching tissues for plates
+       * Fixes "Already connected" exception occuring in Geneious v9
+       * Changed behaviour when creating new extractions that use existing extractions ID's
     </ReleaseNotes>
     <ExtraInformation/>
 </PluginVersions>

build.gradle

@@ -11,24 +11,22 @@ plugins {
     id 'net.saliman.properties' version '1.4.5'
 }
 
-println "Gradle " + GradleVersion.current().getVersion() + ' - ' + GradleVersion.current().getBuildTime() + ' - ' + GradleVersion.current().getRevision() + (GradleVersion.current().isSnapshot() ? " SNAPSHOT" : "")
+//println "Gradle " + GradleVersion.current().getVersion() + ' - ' + GradleVersion.current().getBuildTime() + ' - ' + GradleVersion.current().getRevision() + (GradleVersion.current().isSnapshot() ? " SNAPSHOT" : "")
 
 
 apply plugin: "java"
 apply plugin: "idea"
 
-version = '3.0.9'
+version = '3.0.12'
 
 defaultTasks 'createPlugin';
 
-task wrapper(type: Wrapper) {
-    gradleVersion = "3.5"
-}
-
 ext {
     shortName = "BiocodePlugin"
     pluginName = "com.biomatters.plugins.biocode." + shortName
-    geneiousPublicAPIVersion = "10.0.5"
+    geneiousPublicAPIVersion = "11.1.5"
+    //geneiousPublicAPIVersion = "2019.1.1"
+    //geneiousPublicAPIVersion = "9.0.5"
     pluginDistFilename = "${shortName}_" + version.replaceAll("\\.", "_") + ".gplugin"
     geneiousFilesName = "GeneiousFiles"
     geneiousFilesPath = "$buildDir/$geneiousFilesName"
@@ -46,9 +44,11 @@ repositories {
 }
 
 dependencies {
+
     compile group: "com.biomatters", name: "geneious.publicapi", version: "$geneiousPublicAPIVersion", configuration: "api", changing: true
     compile group: "com.google.guava", name: "guava", version:"15.0"
 
+    compile group: 'javax.xml.bind', name: 'jaxb-api', version: '2.3.1'
     compile group: "org.hsqldb", name:"hsqldb", version:"2.3.0"
     compile group: "org.jcommon", name:"jcommon", version:"1.0"
     compile group: "org.jfree", name:"jfreechart", version:"1.0.15"
@@ -71,7 +71,10 @@ dependencies {
     compile group: "commons-beanutils", name:"commons-beanutils", version:"1.9.2"
     compile group: "mysql", name:"mysql-connector-java", version:"5.1.6"
 
-
+    compile group: 'org.apache.httpcomponents', name: 'httpclient', version: '4.5.8'
+    compile group: 'commons-httpclient', name: 'commons-httpclient', version: '3.1'
+    compile group: 'org.jsslutils', name: 'jsslutils', version: '1.0.8'
+
     testCompile "junit:junit:4.+"
     testRuntime group: "com.biomatters", name: "geneious.publicapi", version: "$geneiousPublicAPIVersion", configuration: "runtime"
 
@@ -165,6 +168,21 @@ sourceSets {
         runtimeClasspath += fileTree("$geneiousFiles/lib")
     }
 }
+task quickCreatePlugin ( dependsOn: assemble, type: Zip) {
+    description "Creates the gplugin to install into Geneious"
+
+    from {
+        configurations.compile.filter {
+            !it.getName().startsWith("GeneiousPublicAPI-") && !it.getName().startsWith("jdom-") && !it.getName().startsWith("jebl-")
+        }
+    }
+    from(libsDir)
+    from(sourceSets.main.resources)
+    into "$pluginName"
+
+    archiveName pluginDistFilename
+}
+
 task createPlugin(dependsOn: build, type: Zip) {
     description "Creates the gplugin to install into Geneious"
 
@@ -181,6 +199,8 @@ task createPlugin(dependsOn: build, type: Zip) {
 }
 
 task runGeneious(dependsOn: [extractGeneiousRuntimeFiles, assemble], type: JavaExec) {
+    // NOTE, the expectation is that we java java 11 linked here
+    //executable '/usr/bin/java'
     main 'com.biomatters.iseek.application.ISeekMain'
     classpath sourceSets.main.runtimeClasspath
     args 'extraPlugins=' + pluginName

development.md

@@ -0,0 +1,67 @@
+## Developers Section
+This section is intended for developers interested in contributing to the Biocode LIMS development.
+
+## Requirements
+* Java Development Kit 1.6+
+* Gradle
+
+### Geneious Plugin
+Run the following command from the root directory to create the gplugin file:
+
+    ./gradlew  createPlugin
+
+Drag and drop the gplugin file from the build/distributoin directory into Geneious to install the plugin.
+
+### LIMS Server (Under Development)
+The LIMS Server is packaged as a distributable WAR file that can be deployed on most Java Web Servers.  (eg) Jetty 
+or Apache Tomcat.
+
+Run the following command from the **biocode-server** directory to create the war file:
+
+    ./gradelw create-war
+
+The war file will be created in the biocode-server directory.
+
+## Development
+The development of this project follows the [Gitflow branching strategy](https://www.atlassian.com/git/tutorials/comparing-workflows/gitflow-workflow).  
+All development is done in the develop branch and merged to master when complete.  Thus master only contains released code.
+
+When switching branches it is always a good idea to run a build with
+
+    ./gradlew  build-plugin
+
+This will ensure any dependency changes for the new branch are applied and everything compiles.
+
+### Modules
+The project currently contains two modules:
+
+* biocode-lims - The Geneious plugin
+* biocode-server - The unreleased server
+
+In most cases you will only need to make changes to the biocode-lims source code.
+
+
+### Dependency Management
+The plugin uses Apache Ivy for depenedency management and the repository includes everything that is required for its use.
+
+
+### Use of an IDE
+Many modern IDEs come with Apache Ivy integration.  If you are using such a feature, please note that the biocode-server 
+depends on some Geneious core classes and this is not reflected in the Ivy configuration.  The main reason for this is
+  that the required libraries are not provided standalone in any repositories.
+
+In the gradle build, the complete Geneious runtime is downloaded and the required libraries are extracted from it.
+
+## Contributing
+Please contact [email protected]
+
+## Biocode LIMS Server 
+The Biocode LIMS server is an extension to the original LIMS that adds security, user management, access control and 
+the ability to offload tasks from the Geneious client.  
+
+The server needs to be deployed in a compatible Java Web Application server and acts as a middle man between the 
+client and the LIMS database.  The client communicates with the server using a REST interface.  By providing this
+interface rather than a proprietary one, there is the possibility of other future clients outside of the Geneious 
+software package.
+
+It is currently in active development and has not been released yet.