com.novartis.opensource.yada.plugin.ScriptPreprocessor.java Source code

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Here is the source code for com.novartis.opensource.yada.plugin.ScriptPreprocessor.java

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/**
 * Copyright 2016 Novartis Institutes for BioMedical Research Inc.
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 * http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
package com.novartis.opensource.yada.plugin;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.util.ArrayList;
import java.util.List;

import org.apache.log4j.Logger;
import org.json.JSONArray;
import org.json.JSONException;
import org.json.JSONObject;

import com.novartis.opensource.yada.Finder;
import com.novartis.opensource.yada.YADARequest;
import com.novartis.opensource.yada.YADARequestException;
import com.novartis.opensource.yada.YADAResourceException;

/**
 * A java API enabling execution of pre-existing scripts, in pre-defined locations on the YADA server, as Preprocess plugins.
 * For more information see <a href="../../../../../../../plugins.html">Plugin Guide</a>
 * @author David Varon
 *
 */
public class ScriptPreprocessor extends AbstractPreprocessor {
    /**
     * Local logger handle
     */
    private static Logger l = Logger.getLogger(ScriptPreprocessor.class);

    /**
     * Enables the execution of a script stored in the {@code YADA_BIN} directory.
     * To execute a script preprocessor plugin, pass {@code preArgs}, or just {@code args}
     * the first argument being the name of the script executable, and the rest of the arguments
     * those, in order, to pass to it. If {@link YADARequest#getPreArgs()} is not null
     * and {@link YADARequest#getPlugin()} is null, then the plugin will be set to 
     * {@link YADARequest#SCRIPT_PREPROCESSOR} automatically.  
     * <p>
     * The script must return a JSON object with name/value pairs corresponding
     * to {@link YADARequest} parameters. These name/value pairs are then marshaled into
     * {@code yadaReq}, which is subsequently returned by the method.
     * </p>
     * @see com.novartis.opensource.yada.plugin.Bypass#engage(com.novartis.opensource.yada.YADARequest)
     */
    @Override
    public YADARequest engage(YADARequest yadaReq) throws YADAPluginException {
        List<String> cmds = new ArrayList<>();
        // get args
        List<String> args = yadaReq.getPreArgs().size() == 0 ? yadaReq.getArgs() : yadaReq.getPreArgs();
        // add plugin
        try {
            cmds.add(Finder.getEnv("yada_bin") + args.remove(0));
        } catch (YADAResourceException e) {
            String msg = "There was a problem locating the resource or variable identified by the supplied JNDI path (yada_bin) in the initial context.";
            throw new YADAPluginException(msg, e);
        }
        // add args
        cmds.addAll(args);
        for (String arg : args) {
            cmds.add(arg);
        }
        // add yadaReq json
        cmds.add(yadaReq.toString());
        l.debug("Executing script plugin: " + cmds);
        String scriptResult = "";
        String s = null;
        try {
            ProcessBuilder builder = new ProcessBuilder(cmds);
            builder.redirectErrorStream(true);
            Process process = builder.start();
            try (BufferedReader si = new BufferedReader(new InputStreamReader(process.getInputStream()))) {
                while ((s = si.readLine()) != null) {
                    l.debug("  LINE: " + s);
                    scriptResult += s;
                }
            }
            process.waitFor();
            JSONObject params = new JSONObject(scriptResult);
            for (String param : JSONObject.getNames(params)) {
                JSONArray ja = (JSONArray) params.get(param);
                l.debug("JSON array " + ja.toString());
                // remove square brackets and leading/trailing quotes
                String values = ja.toString().substring(2, ja.toString().length() - 2);
                // remove "," between values and stuff in array
                String[] value = values.split("\",\"");
                l.debug("Value has " + value.length + " elements");
                yadaReq.invokeSetter(param, value);
            }
        } catch (IOException e) {
            String msg = "Failed to get input from InputStream.";
            throw new YADAPluginException(msg, e);
        } catch (InterruptedException e) {
            String msg = "The external process executing the script was interrupted.";
            throw new YADAPluginException(msg, e);
        } catch (JSONException e) {
            String msg = "Parameter configuration failed. The script return value should conform to the syntax:\n";
            msg += "  {\"key\":[\"value\"...],...}.\n";
            msg += "  The array syntax for values complies to the return value of HTTPServletResponse.getParameterMap().toString()";
            throw new YADAPluginException(msg, e);
        } catch (YADARequestException e) {
            String msg = "Unable to set parameters.";
            throw new YADAPluginException(msg, e);
        }

        return yadaReq;
    }
}