/*
* 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.spring.ajax;
import com.eaglegenomics.simlims.core.User;
import com.eaglegenomics.simlims.core.manager.SecurityManager;
import net.sf.json.JSONObject;
import net.sourceforge.fluxion.ajax.Ajaxified;
import net.sourceforge.fluxion.ajax.util.JSONUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.security.core.context.SecurityContextHolder;
import uk.ac.bbsrc.tgac.miso.core.data.Platform;
import uk.ac.bbsrc.tgac.miso.core.data.SequencerReference;
import uk.ac.bbsrc.tgac.miso.core.data.impl.SequencerReferenceImpl;
import uk.ac.bbsrc.tgac.miso.core.manager.RequestManager;
import javax.servlet.http.HttpSession;
import java.io.IOException;
import java.net.InetAddress;
import java.util.Collection;
/**
* uk.ac.bbsrc.tgac.miso.spring.ajax
* <p/>
* Info
*
* @author Rob Davey
* @since 0.0.2
*/
@Ajaxified
public class SequencerReferenceControllerHelperService {
protected static final Logger log = LoggerFactory.getLogger(SubmissionControllerHelperService.class);
@Autowired
private com.eaglegenomics.simlims.core.manager.SecurityManager securityManager;
@Autowired
private RequestManager requestManager;
public JSONObject listPlatforms(HttpSession session, JSONObject json) {
try {
Collection<Platform> ps = requestManager.listAllPlatforms();
StringBuilder sb = new StringBuilder();
for (Platform p : ps) {
sb.append("<option value="+p.getPlatformId()+">"+p.getNameAndModel()+"</option>");
}
return JSONUtils.JSONObjectResponse("platforms", sb.toString());
}
catch (IOException e) {
e.printStackTrace();
}
return JSONUtils.SimpleJSONError("Cannot list available platforms");
}
public JSONObject listSequencers(HttpSession session, JSONObject json) {
try {
Collection<SequencerReference> sr = requestManager.listAllSequencerReferences();
StringBuilder sb = new StringBuilder();
for (SequencerReference s : sr) {
sb.append("<option value="+s.getId()+">"+s.getPlatform().getNameAndModel()+" - "+s.getName()+"</option>");
}
return JSONUtils.JSONObjectResponse("sequencers", sb.toString());
}
catch (IOException e) {
e.printStackTrace();
}
return JSONUtils.SimpleJSONError("Cannot list available sequencers");
}
public JSONObject checkServerAvailability(HttpSession session, JSONObject json) {
try {
if (json.has("server") && !json.get("server").equals("")) {
InetAddress i = InetAddress.getByName(json.getString("server"));
if (i.isReachable(2000)) {
return JSONUtils.JSONObjectResponse("html", "OK");
}
else {
return JSONUtils.JSONObjectResponse("html", "FAIL");
}
}
}
catch (Exception e) {
log.debug("Failed to check server availability: ", e);
return JSONUtils.JSONObjectResponse("html", "FAIL");
}
return JSONUtils.SimpleJSONError("Cannot check server availability");
}
public JSONObject addSequencerReference(HttpSession session, JSONObject json) {
try {
if (json.has("server") && !json.get("server").equals("")) {
InetAddress i = InetAddress.getByName(json.getString("server"));
String name = json.getString("name");
Platform p = requestManager.getPlatformById(json.getInt("platform"));
SequencerReference sr = new SequencerReferenceImpl(name, i, p);
sr.setAvailable(i.isReachable(2000));
log.info(sr.toString());
requestManager.saveSequencerReference(sr);
return JSONUtils.SimpleJSONResponse("Saved successfully");
}
}
catch (Exception e) {
log.debug("Failed to add server: ", e);
return JSONUtils.SimpleJSONError("Failed to add server");
}
return JSONUtils.SimpleJSONError("Failed to add server");
}
public JSONObject deleteSequencerReference(HttpSession session, JSONObject json) {
User user;
try {
user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
}
catch (IOException e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError("Error getting currently logged in user.");
}
if (user != null && user.isAdmin()) {
if (json.has("refId")) {
Long refId = json.getLong("refId");
try {
requestManager.deleteSequencerReference(requestManager.getSequencerReferenceById(refId));
return JSONUtils.SimpleJSONResponse("Sequencer Reference deleted");
}
catch (IOException e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError("Cannot delete sequencer reference: " + e.getMessage());
}
}
else {
return JSONUtils.SimpleJSONError("No Sequencer Reference specified to delete.");
}
}
else {
return JSONUtils.SimpleJSONError("Only admins can delete objects.");
}
}
public void setRequestManager(RequestManager requestManager) {
this.requestManager = requestManager;
}
public void setSecurityManager(SecurityManager securityManager) {
this.securityManager = securityManager;
}
}