/*
* 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.webapp.controller.rest;
import com.eaglegenomics.simlims.core.User;
import org.codehaus.jackson.map.ObjectMapper;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Controller;
import org.springframework.web.bind.annotation.*;
import uk.ac.bbsrc.tgac.miso.core.data.*;
import uk.ac.bbsrc.tgac.miso.core.data.impl.LibraryDilution;
import uk.ac.bbsrc.tgac.miso.core.exception.MalformedDilutionException;
import uk.ac.bbsrc.tgac.miso.core.exception.MalformedLibraryException;
import uk.ac.bbsrc.tgac.miso.core.exception.MalformedLibraryQcException;
import uk.ac.bbsrc.tgac.miso.core.exception.MalformedSampleQcException;
import uk.ac.bbsrc.tgac.miso.core.manager.RequestManager;
import uk.ac.bbsrc.tgac.miso.core.util.jackson.LibraryRecursionAvoidanceMixin;
import uk.ac.bbsrc.tgac.miso.core.util.jackson.SampleProjectAvoidanceMixin;
import uk.ac.bbsrc.tgac.miso.core.util.jackson.UserInfoMixin;
import uk.ac.bbsrc.tgac.miso.webapp.util.RestUtils;
import java.io.IOException;
import java.util.Collection;
/**
* A controller to handle all REST requests for Projects
*
* @author Rob Davey
* @date 01-Sep-2011
* @since 0.1.0
*/
@Controller
@RequestMapping("/rest/project")
@SessionAttributes("project")
public class ProjectRestController {
protected static final Logger log = LoggerFactory.getLogger(ProjectRestController.class);
@Autowired
private RequestManager requestManager;
public void setRequestManager(RequestManager requestManager) {
this.requestManager = requestManager;
}
@RequestMapping(value = "/alias/{projectAlias}", method = RequestMethod.GET)
public @ResponseBody String getProjectByAlias(@PathVariable String projectAlias) throws IOException {
try {
Project project = requestManager.getProjectByAlias(projectAlias);
if (project != null) {
return getProjectById(project.getId());
}
return RestUtils.error("No such project with that alias.", "projectAlias", projectAlias).toString();
}
catch (IOException ioe) {
return RestUtils.error("Cannot retrieve project: " + ioe.getMessage(), "projectAlias", projectAlias).toString();
}
}
@RequestMapping(value = "{projectId}", method = RequestMethod.GET)
public @ResponseBody String getProjectById(@PathVariable Long projectId) throws IOException {
ObjectMapper mapper = new ObjectMapper();
try {
Project project = requestManager.getProjectById(projectId);
if (project != null) {
for (Sample s : project.getSamples()) {
if (s.getLibraries().isEmpty()) {
for (Library l : requestManager.listAllLibrariesBySampleId(s.getId())) {
try {
s.addLibrary(l);
}
catch (MalformedLibraryException e) {
e.printStackTrace();
}
}
}
if (s.getSampleQCs().isEmpty()) {
for (SampleQC qc : requestManager.listAllSampleQCsBySampleId(s.getId())) {
try {
s.addQc(qc);
}
catch (MalformedSampleQcException e) {
e.printStackTrace();
}
}
}
}
mapper.getSerializationConfig().addMixInAnnotations(Sample.class, SampleProjectAvoidanceMixin.class);
mapper.getSerializationConfig().addMixInAnnotations(Library.class, LibraryRecursionAvoidanceMixin.class);
mapper.getSerializationConfig().addMixInAnnotations(User.class, UserInfoMixin.class);
return mapper.writeValueAsString(project);
}
return mapper.writeValueAsString(RestUtils.error("No such project with that ID.", "projectId", projectId.toString()));
}
catch (IOException ioe) {
return mapper.writeValueAsString(RestUtils.error("Cannot retrieve project: " + ioe.getMessage(), "projectId", projectId.toString()));
}
}
@RequestMapping(value = "{projectId}/libraries", method = RequestMethod.GET)
public @ResponseBody String getProjectLibraries(@PathVariable Long projectId) throws IOException {
Collection<Library> lp = requestManager.listAllLibrariesByProjectId(projectId);
for (Library l : lp) {
for (LibraryDilution dil : requestManager.listAllLibraryDilutionsByLibraryId(l.getId())) {
try {
l.addDilution(dil);
}
catch (MalformedDilutionException e) {
e.printStackTrace();
}
}
for (LibraryQC qc : requestManager.listAllLibraryQCsByLibraryId(l.getId())) {
try {
l.addQc(qc);
}
catch (MalformedLibraryQcException e) {
e.printStackTrace();
}
}
}
ObjectMapper mapper = new ObjectMapper();
mapper.getSerializationConfig().addMixInAnnotations(Sample.class, SampleProjectAvoidanceMixin.class);
mapper.getSerializationConfig().addMixInAnnotations(Library.class, LibraryRecursionAvoidanceMixin.class);
mapper.getSerializationConfig().addMixInAnnotations(User.class, UserInfoMixin.class);
return mapper.writeValueAsString(lp);
}
@RequestMapping(method = RequestMethod.GET)
public @ResponseBody String listAllProjects() throws IOException {
Collection<Project> lp = requestManager.listAllProjects();
for (Project p : lp) {
p.setSamples(requestManager.listAllSamplesByProjectId(p.getProjectId()));
p.setStudies(requestManager.listAllStudiesByProjectId(p.getProjectId()));
}
ObjectMapper mapper = new ObjectMapper();
mapper.getSerializationConfig().addMixInAnnotations(Sample.class, SampleProjectAvoidanceMixin.class);
mapper.getSerializationConfig().addMixInAnnotations(Library.class, LibraryRecursionAvoidanceMixin.class);
mapper.getSerializationConfig().addMixInAnnotations(User.class, UserInfoMixin.class);
return mapper.writeValueAsString(lp);
}
}