Merge pull request #1 from Wishartlab-openscience/javaloadable-api

Javaloadable api

README.md

@@ -1,2 +1,14 @@
 # biotransformer-apis
 A library that provides APIs to facilitate the integration of various libraries into BioTransformer.
+This repository contains the Predictor Model Interface which every Java Loadable prediction application should implement.
+
+<br>
+
+To add this to your project -
+1. Build the project.
+2. Create a lib/ folder outside of src/ in your application.
+3. Put the biotransformer-api.jar in the the lib/ folder.
+4. Run Maven Goal -
+   mvn org.apache.maven.plugins:maven-install-plugin:3.0.0-M1:install-file -Dfile=lib/biotransformer-api.jar -DgroupId=biotransformer -DartifactId=biotransformer-api -Dversion=1.0.0 -Dpackaging=jar
+5. This would install the jar in your local .m2 directory.
+6. Implement the interface now. 

pom.xml

@@ -0,0 +1,91 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+
+    <groupId>biotransformer</groupId>
+    <artifactId>biotransformer-apis</artifactId>
+    <version>1.0.0</version>
+
+    <properties>
+        <jdk.version>8</jdk.version>
+        <maven.compiler.source>${jdk.version}</maven.compiler.source>
+        <maven.compiler.target>${jdk.version}</maven.compiler.target>
+        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+        <start-class>Main.java</start-class>
+    </properties>
+    <dependencies>
+        <dependency>
+            <groupId>org.kie.modules</groupId>
+            <artifactId>org-apache-commons-lang3</artifactId>
+            <version>6.5.0.Final</version>
+            <type>pom</type>
+        </dependency>
+    </dependencies>
+    <build>
+        <finalName>biotransformer-apis</finalName>
+        <resources>
+            <!--
+                <resource>
+                    <directory>src/main/resources/database</directory>
+                </resource>
+                <resource>
+                    <directory>src/main/resources/supportfiles</directory>
+                </resource>
+                -->
+        </resources>
+
+        <plugins>
+
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-surefire-plugin</artifactId>
+                <version>2.12.4</version>
+                <configuration>
+                    <skipTests>true</skipTests>
+                </configuration>
+            </plugin>
+
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-assembly-plugin</artifactId>
+                <version>3.1.1</version>
+                <configuration>
+                    <!-- get all project dependencies -->
+                    <appendAssemblyId>false</appendAssemblyId>
+                    <descriptorRefs>
+                        <descriptorRef>jar-with-dependencies</descriptorRef>
+                    </descriptorRefs>
+                    <!-- MainClass in mainfest make a executable jar -->
+                    <archive>
+                        <manifest>
+                            <mainClass>executable.BiotransformerExecutable</mainClass>
+                        </manifest>
+                    </archive>
+                </configuration>
+                <executions>
+                    <execution>
+                        <id>make-assembly</id>
+                        <phase>package</phase> <!-- bind to the packaging phase -->
+                        <goals>
+                            <goal>single</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-site-plugin</artifactId>
+                <version>3.7.1</version>
+            </plugin>
+
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-project-info-reports-plugin</artifactId>
+                <version>3.0.0</version>
+            </plugin>
+        </plugins>
+
+    </build>
+</project>

src/main/java/Main.java

@@ -0,0 +1,6 @@
+
+public class Main {
+    public static void main(String[] args) {
+
+    }
+}

src/main/java/biotransformerapis/predictors/BioTransformerAPIs.java

@@ -0,0 +1,8 @@
+package biotransformerapis.predictors;
+
+import java.util.LinkedHashMap;
+
+public interface BioTransformerAPIs {
+
+    public Object predict (LinkedHashMap<String, Object> inputParameters) throws Exception;
+}

src/main/java/utils/Validator.java

@@ -0,0 +1,67 @@
+package utils;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.LinkedHashMap;
+import org.apache.commons.lang3.StringUtils;
+
+public class Validator {
+
+    public enum ioFormats{
+        SDFILE, IATOMCONTAINERSET
+    }
+    LinkedHashMap<String, ArrayList<String>> validParams = new LinkedHashMap<String, ArrayList<String>>();
+
+    public Validator() {
+        ArrayList<String> required = new ArrayList<String>();
+        ArrayList<String> optional = new ArrayList<String>();
+        required.add("input");
+        required.add("inputFormat");
+        required.add("outputFormat");
+        optional.add("output");
+        this.validParams.put("required", required);
+        this.validParams.put("optional", required);
+    }
+
+    public Boolean validateParameters(LinkedHashMap<String, Object> parameters) throws Exception {
+        Boolean isValid = true;
+
+        for(String requiredParam : validParams.get("required")) {
+            if(!parameters.containsKey(requiredParam)) {
+                throw new IOException("The required parameter \'" + requiredParam + "\' is missing. Please provide an adequate value.");
+            }
+        }
+
+
+        ioFormats inputFormat           = ioFormats.valueOf( StringUtils.upperCase( (String) parameters.get("inputFormat") ))  ;
+        ioFormats outputFormat              = ioFormats.valueOf( StringUtils.upperCase( (String) parameters.get("outputFormat") ))  ;
+
+
+        if(!Arrays.asList(ioFormats.values()).contains(inputFormat)) {
+            isValid = false;
+            throw new IOException("The provided input \'" + inputFormat + "\' format is not support by PhaseIIFilter");
+        }
+        if(!Arrays.asList(ioFormats.values()).contains(outputFormat)) {
+            isValid = false;
+            throw new IOException("The provided output \'" + inputFormat + "\' format is not support by PhaseIIFilter");
+        }
+
+        if(inputFormat == ioFormats.SDFILE) {
+            File inputFile = new File((String) parameters.get("input"));
+            if((!inputFile.exists()) || inputFile.isDirectory()) {
+                isValid = false;
+                throw new IOException("A pathname to the input file is missing. Please provide a pathname to the input file");
+
+            }
+        }
+
+        if(outputFormat == ioFormats.SDFILE && !parameters.containsKey("output")) {
+            isValid = false;
+            throw new IOException("A pathname to the output file is missing. Please provide a pathname to the output file");
+        }
+
+        return  isValid;
+    }
+}