/*
* Copyright (c) 2012. The Genome Analysis Centre, Norwich, UK
* MISO project contacts: Robert Davey, Mario Caccamo @ TGAC
* *********************************************************************
*
* This file is part of MISO.
*
* MISO is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* MISO is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with MISO. If not, see <http://www.gnu.org/licenses/>.
*
* *********************************************************************
*/
package uk.ac.bbsrc.tgac.miso.notification.manager;
//import com.fasterxml.jackson.core.JsonGenerationException;
//import com.fasterxml.jackson.databind.JsonMappingException;
//import com.fasterxml.jackson.databind.ObjectMapper;
import net.sf.json.JSONArray;
import net.sf.json.JSONObject;
import net.sf.json.util.JSONUtils;
import org.codehaus.jackson.JsonGenerationException;
import org.codehaus.jackson.map.JsonMappingException;
import org.codehaus.jackson.map.ObjectMapper;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.ApplicationContext;
import org.springframework.context.support.ClassPathXmlApplicationContext;
import uk.ac.bbsrc.tgac.miso.notification.service.IlluminaTransformer;
import uk.ac.bbsrc.tgac.miso.notification.util.NotificationUtils;
import uk.ac.bbsrc.tgac.miso.tools.run.MultiFileQueueMessageSource;
import uk.ac.bbsrc.tgac.miso.tools.run.RunFolderScanner;
import uk.ac.bbsrc.tgac.miso.tools.run.util.FileSetTransformer;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import java.util.HashSet;
import java.util.Map;
import java.util.Properties;
import java.util.Set;
/**
* uk.ac.bbsrc.tgac.miso.notification.manager
* <p/>
* Info
*
* @author Rob Davey
* @date 15/04/13
* @since 0.2.0
*/
public class NotificationRequestManager {
protected static final Logger log = LoggerFactory.getLogger(NotificationRequestManager.class);
private ObjectMapper mapper = new ObjectMapper();
private ClassPathXmlApplicationContext context;
private Map<String, Set<File>> dataPaths;
public NotificationRequestManager() {
}
public NotificationRequestManager(ClassPathXmlApplicationContext context, Map<String, Set<File>> dataPaths) {
this.context = context;
this.dataPaths = dataPaths;
}
public void setApplicationContext(ClassPathXmlApplicationContext context) {
this.context = context;
}
public void setDataPaths(Map<String, Set<File>> dataPaths) {
this.dataPaths = dataPaths;
}
public String queryRunProgress(JSONObject request) throws IllegalStateException, IllegalArgumentException {
File folder = lookupRunAliasPath(request);
if (folder != null) {
String platformType = request.getString("platform").toLowerCase();
Map<String, String> status = parseRunFolder(platformType, folder);
if (status.isEmpty()) {
return "{'response':'No runs found with alias "+request.getString("run")+"'}";
}
for (String s : status.keySet()) {
if (!"".equals(status.get(s))) {
JSONArray runs = JSONArray.fromObject(status.get(s));
if (!runs.isEmpty()) {
return "{'progress':'"+s+"'}";
}
}
else {
return "{'response':'No runs found with status "+s+" with alias "+request.getString("run")+"'}";
}
}
}
return "";
}
public String queryRunStatus(JSONObject request) throws IllegalStateException, IllegalArgumentException {
File folder = lookupRunAliasPath(request);
if (folder != null) {
String platformType = request.getString("platform").toLowerCase();
Map<String, String> status = parseRunFolder(platformType, folder);
for (String s : status.keySet()) {
if (!"".equals(status.get(s))) {
log.debug("queryRunStatus: " + status.get(s));
JSONArray runs = JSONArray.fromObject(status.get(s));
if (!runs.isEmpty()) {
JSONObject run = runs.getJSONObject(0);
if (run.has("status")) {
return run.getString("status");
}
}
}
}
}
return "";
}
public String queryRunInfo(JSONObject request) throws IllegalStateException, IllegalArgumentException {
File folder = lookupRunAliasPath(request);
if (folder != null) {
String platformType = request.getString("platform").toLowerCase();
Map<String, String> status = parseRunFolder(platformType, folder);
for (String s : status.keySet()) {
if (!"".equals(status.get(s))) {
log.debug("queryRunInfo: " + status.get(s));
JSONArray runs = JSONArray.fromObject(status.get(s));
if (!runs.isEmpty()) {
JSONObject run = runs.getJSONObject(0);
if (run.has("runinfo")) {
return run.getString("runinfo");
}
}
}
}
}
return "";
}
public String queryRunParameters(JSONObject request) throws IllegalStateException, IllegalArgumentException {
File folder = lookupRunAliasPath(request);
if (folder != null) {
String platformType = request.getString("platform").toLowerCase();
Map<String, String> status = parseRunFolder(platformType, folder);
for (String s : status.keySet()) {
if (!"".equals(status.get(s))) {
log.debug("queryRunParameters: " + status.get(s));
JSONArray runs = JSONArray.fromObject(status.get(s));
if (!runs.isEmpty()) {
JSONObject run = runs.getJSONObject(0);
if (run.has("runparams")) {
return run.getString("runparams");
}
}
}
}
}
return "";
}
public String queryInterOpMetrics(JSONObject request) throws IllegalStateException, IllegalArgumentException {
File folder = lookupRunAliasPath(request);
if (folder != null) {
JSONArray runs = parseIlluminaInterOpFolder(folder);
if (!runs.isEmpty()) {
JSONObject run = runs.getJSONObject(0);
if (run.has("error")) {
return run.getString("error");
}
if (run.has("metrix")) {
return run.getString("metrix");
}
}
}
else {
return "{\"error\":\"Cannot find run folder "+request.getString("run").replaceAll("('|\")", "\\\\$1")+"\"}";
}
return "";
}
private File lookupRunAliasPath(JSONObject request) {
if (context != null && dataPaths != null) {
String platformType = request.getString("platform").toLowerCase();
if (!"".equals(platformType) && platformType != null) {
String runAlias = request.getString("run");
if (!"".equals(runAlias) && runAlias != null) {
RunFolderScanner rfs = (RunFolderScanner) context.getBean(platformType + "StatusRecursiveScanner");
if (rfs != null) {
for (File dataPath : dataPaths.get(platformType)) {
for (File runFolder : rfs.listFiles(dataPath)) {
if (runAlias.equals(runFolder.getName())) {
return runFolder;
}
}
}
}
}
}
return null;
}
else {
throw new IllegalStateException("ApplicationContext and/or datapaths not set. Cannot action requests on notification system.");
}
}
private Map<String, String> parseRunFolder(String platformType, File path) throws IllegalStateException, IllegalArgumentException {
if (context != null && dataPaths != null) {
if (!"".equals(platformType) && platformType != null) {
FileSetTransformer<String, String, File> fst = (FileSetTransformer<String, String, File>)context.getBean(platformType+"Transformer");
Set<File> fs = new HashSet<>();
fs.add(path);
return fst.transform(fs);
}
else {
throw new IllegalArgumentException("No platformType set. Cannot parse run folder.");
}
}
else {
throw new IllegalStateException("ApplicationContext and/or datapaths not set. Cannot action requests on notification system.");
}
}
private JSONArray parseIlluminaInterOpFolder(File path) throws IllegalStateException {
if (context != null && dataPaths != null) {
IlluminaTransformer fst = (IlluminaTransformer)context.getBean("illuminaTransformer");
if (fst != null) {
Set<File> fs = new HashSet<>();
fs.add(path);
return fst.transformInterOpOnly(fs);
}
else {
throw new IllegalStateException("No IlluminaTransformer available");
}
}
else {
throw new IllegalStateException("ApplicationContext and/or datapaths not set. Cannot action requests on notification system.");
}
}
}