Merge pull request #119 from biocodellc/develop

merge develop to master

PluginVersions.xml

@@ -1,6 +1,6 @@
 <PluginVersions>
-    <LatestVersion>3.0.12</LatestVersion>
-    <LatestVersionURL>https://github.com/biocodellc/biocode-lims/releases/download/3.0.12/BiocodePlugin_3_0_12.gplugin</LatestVersionURL>
+    <LatestVersion>3.0.13</LatestVersion>
+    <LatestVersionURL>https://github.com/biocodellc/biocode-lims/releases/download/3.0.13/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

build.gradle

@@ -9,6 +9,8 @@ buildscript {
 
 plugins {
     id 'net.saliman.properties' version '1.4.5'
+    //id 'org.openjfx.javafxplugin' version '0.0.8'
+
 }
 
 //println "Gradle " + GradleVersion.current().getVersion() + ' - ' + GradleVersion.current().getBuildTime() + ' - ' + GradleVersion.current().getRevision() + (GradleVersion.current().isSnapshot() ? " SNAPSHOT" : "")
@@ -17,13 +19,14 @@ plugins {
 apply plugin: "java"
 apply plugin: "idea"
 
-version = '3.0.12'
+version = '3.0.13'
 
 defaultTasks 'createPlugin';
 
 ext {
     shortName = "BiocodePlugin"
     pluginName = "com.biomatters.plugins.biocode." + shortName
+    //pluginName = shortName + version
     geneiousPublicAPIVersion = "11.1.5"
     //geneiousPublicAPIVersion = "2019.1.1"
     //geneiousPublicAPIVersion = "9.0.5"
@@ -74,7 +77,12 @@ dependencies {
     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'
-
+    //compile group: 'org.openjfx', name: 'javafx-swing', version: '11.0.2'
+    // this one results in Could not get resource 'http://assets.geneious.com/developer/geneious/ivy/javafx/javafx.controls/ivys/ivy-11.0.0.xml'.
+    //compile 'javafx:javafx.controls:11.0.0'
+
+
+
     testCompile "junit:junit:4.+"
     testRuntime group: "com.biomatters", name: "geneious.publicapi", version: "$geneiousPublicAPIVersion", configuration: "runtime"
 
@@ -87,6 +95,11 @@ dependencies {
     }
 }
 
+//javafx {
+//    version = "11.0.2"
+//    modules = [ 'javafx.controls', 'javafx.fxml' ]
+//}
+
 configurations.all {
     resolutionStrategy {
         //BioJava uses old versions of log4j that have vulnerabilities - forcing gradle to bundle in the oldest version that fixes the issues

development.md

@@ -2,7 +2,7 @@
 This section is intended for developers interested in contributing to the Biocode LIMS development.
 
 ## Requirements
-* Java Development Kit 1.6+
+* Java Development Kit 1.8+
 * Gradle
 
 ### Geneious Plugin

readme.md

@@ -10,4 +10,8 @@ including the user guide.
 * Information for developers on contributing to the Biocode LIMS plugin is on our [development page](https://github.com/biocodellc/biocode-lims/blob/develop/development.md)
 
 
-
+## Developer Information
+The Biocode LIMS plugin is built and developed using IntelliJ and gradle.  Currently, we develop against the geneiousPublicAPIVersion = 11.1.5 and use Java 8.
+There are a couple of issues preventing compiling using Java 11 and hence being able to develop against GeneiousPrime:
+ * openJFK libraries were removed in Java 11.  See issue: https://github.com/biocodellc/biocode-lims/issues/116
+ * ClassLoader issues cropped up in Java 9 See issue: https://community.oracle.com/thread/4011800

src/com/biomatters/plugins/biocode/BiocodePlugin.java

@@ -47,7 +47,7 @@ public class BiocodePlugin extends GeneiousPlugin {
     }
 
     private static GeneiousActionOptions superBiocodeAction;
-    public static final String PLUGIN_VERSION = "3.0.12";
+    public static final String PLUGIN_VERSION = "3.0.13";
     public static final String SUPPORT_EMAIL = "[email protected]";
 
     public static GeneiousActionOptions getSuperBiocodeAction() {

src/com/biomatters/plugins/biocode/assembler/annotate/AnnotateFimsDataOperation.java

@@ -128,6 +128,7 @@ private static FimsSample getFimsSample(List<FimsSample> fimsSamples, String pla
 
     private static FimsSample getFimsSample(List<FimsSample> fimsSamples, DocumentField searchField, AnnotatedPluginDocument document, AnnotateFimsDataOptions options) {
         String searchValue = getFieldValue(document, options);
+        System.out.println("searching for " + searchValue);
         if(searchValue == null) {
             return null;
         }
@@ -207,7 +208,10 @@ private static String getPlateId(AnnotatedPluginDocument document, AnnotateFimsD
 
     private static String getFieldValue(AnnotatedPluginDocument document, AnnotateFimsDataOptions options) {
         if(options.matchField()) {
-            return BiocodeUtilities.getStringFromFileName(document.getName(), options.getNameSeaparator(), options.getNamePart());
+            String docName = document.getName();
+            String nameSeparator = options.getNameSeaparator();
+            int namePart = options.getNamePart();
+            return BiocodeUtilities.getStringFromFileName(docName, nameSeparator, namePart);
         }
         return null;
     }
@@ -252,10 +256,13 @@ private static List<String> getFieldValues(AnnotatedPluginDocument[] documents,
         for(AnnotatedPluginDocument document : documents) {
             Object value = document.getFieldValue(field);
             if(value != null) {
+                // i'm not sure why getFieldValues needs to parse separator and part for cases
+                // we're looking up annotated plate/well combinations
                 String finalValue = BiocodeUtilities.getStringFromFileName(value.toString(), separator, part);
                 if(finalValue != null) {
                     fieldValues.add(finalValue);
                 }
+
             }
         }
         return fieldValues;

src/com/biomatters/plugins/biocode/labbench/fims/MySQLFimsConnection.java

@@ -143,7 +143,7 @@ public void _disconnect() {
     @Override
     public List<String> getTissueIdsMatchingQuery(Query query, List<FimsProject> projectsToMatch) throws ConnectionException {
         StringBuilder queryBuilder = new StringBuilder();
-        queryBuilder.append("SELECT '").append(getTissueCol()).append("' FROM ").append(tableName);
+        queryBuilder.append("SELECT `").append(getTissueCol()).append("` FROM ").append(tableName);
 
         List<Object> parameters = new ArrayList<Object>();
         String sqlString = SqlUtilities.getQuerySQLString(query, getSearchAttributes(), FIELD_PREFIX, false);
@@ -207,7 +207,7 @@ protected String getTissueCol() {
 
     @Override
     public List<FimsSample> _retrieveSamplesForTissueIds(List<String> tissueIds, RetrieveCallback callback) throws ConnectionException {
-        StringBuilder query = new StringBuilder("SELECT * FROM " + tableName + " WHERE '" + getTissueCol() + "' IN ");
+        StringBuilder query = new StringBuilder("SELECT * FROM " + tableName + " WHERE `" + getTissueCol() + "` IN ");
         SqlUtilities.appendSetOfQuestionMarks(query, tissueIds.size());
 
         String queryString = query.toString();