/*
* 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;
import com.eaglegenomics.simlims.core.User;
import com.eaglegenomics.simlims.core.Group;
import com.eaglegenomics.simlims.core.Activity;
import com.eaglegenomics.simlims.core.Protocol;
import com.eaglegenomics.simlims.core.SecurityProfile;
import com.eaglegenomics.simlims.core.manager.ProtocolManager;
import com.eaglegenomics.simlims.core.manager.SecurityManager;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.propertyeditors.*;
import org.springframework.util.NumberUtils;
import org.springframework.web.bind.WebDataBinder;
import org.springframework.web.bind.support.WebBindingInitializer;
import org.springframework.web.context.request.WebRequest;
import uk.ac.bbsrc.tgac.miso.core.data.*;
import uk.ac.bbsrc.tgac.miso.core.data.Project;
import uk.ac.bbsrc.tgac.miso.core.data.impl.*;
import uk.ac.bbsrc.tgac.miso.core.data.impl.illumina.IlluminaPool;
import uk.ac.bbsrc.tgac.miso.core.data.impl.kit.KitDescriptor;
import uk.ac.bbsrc.tgac.miso.core.data.impl.ls454.LS454Pool;
import uk.ac.bbsrc.tgac.miso.core.data.impl.solid.SolidPool;
import uk.ac.bbsrc.tgac.miso.core.data.type.*;
import uk.ac.bbsrc.tgac.miso.core.manager.RequestManager;
import java.beans.PropertyEditorSupport;
import java.io.IOException;
import java.net.InetAddress;
import java.net.UnknownHostException;
import java.text.SimpleDateFormat;
import java.util.*;
/**
* Class that binds all the MISO model datatypes to the Spring form path types
*/
public class LimsBindingInitializer extends org.springframework.web.bind.support.ConfigurableWebBindingInitializer implements WebBindingInitializer {
protected static final Logger log = LoggerFactory.getLogger(LimsBindingInitializer.class);
@Autowired
private ProtocolManager protocolManager;
@Autowired
private RequestManager requestManager;
@Autowired
private SecurityManager securityManager;
/**
* Sets the requestManager of this LimsBindingInitializer object.
*
* @param requestManager requestManager.
*/
public void setRequestManager(RequestManager requestManager) {
assert (requestManager != null);
this.requestManager = requestManager;
}
/**
* Sets the protocolManager of this LimsBindingInitializer object.
*
* @param protocolManager protocolManager.
*/
public void setProtocolManager(ProtocolManager protocolManager) {
assert (protocolManager != null);
this.protocolManager = protocolManager;
}
/**
* Sets the securityManager of this LimsBindingInitializer object.
*
* @param securityManager securityManager.
*/
public void setSecurityManager(SecurityManager securityManager) {
assert (securityManager != null);
this.securityManager = securityManager;
}
/**
* Init this binder, registering all the custom editors to class types
*
* @param binder of type WebDataBinder
* @param req of type WebRequest
*/
public void initBinder(WebDataBinder binder, WebRequest req) {
binder.registerCustomEditor(Long.class, new CustomNumberEditor(Long.class, false));
binder.registerCustomEditor(Boolean.class, new CustomBooleanEditor(CustomBooleanEditor.VALUE_TRUE, CustomBooleanEditor.VALUE_FALSE, true));
binder.registerCustomEditor(Date.class, new CustomDateEditor(
new SimpleDateFormat("dd/MM/yyyy"), true));
binder.registerCustomEditor(InetAddress.class, new PropertyEditorSupport() {
@Override
public void setAsText(String element) throws IllegalArgumentException {
setValue(resolveInetAddress(element));
}
});
binder.registerCustomEditor(Activity.class, new PropertyEditorSupport() {
@Override
public void setAsText(String element) throws IllegalArgumentException {
setValue(resolveActivity(element));
}
});
/*
binder.registerCustomEditor(Request.class, new PropertyEditorSupport() {
@Override
public void setAsText(String element) throws IllegalArgumentException {
setValue(resolveRequest(element));
}
});
*/
binder.registerCustomEditor(Protocol.class, new PropertyEditorSupport() {
@Override
public void setAsText(String element) throws IllegalArgumentException {
setValue(resolveProtocol(element));
}
});
binder.registerCustomEditor(Group.class, new PropertyEditorSupport() {
@Override
public void setAsText(String element) throws IllegalArgumentException {
setValue(resolveGroup(element));
}
});
binder.registerCustomEditor(Set.class, "users", new CustomCollectionEditor(Set.class) {
@Override
protected Object convertElement(Object element) {
return resolveUser(element);
}
});
binder.registerCustomEditor(Set.class, "groups", new CustomCollectionEditor(Set.class) {
@Override
protected Object convertElement(Object element) {
return resolveGroup(element);
}
});
//TGAC Classes
binder.registerCustomEditor(com.eaglegenomics.simlims.core.User.class, new PropertyEditorSupport() {
@Override
public void setAsText(String element) throws IllegalArgumentException {
setValue(resolveUser(element));
}
});
binder.registerCustomEditor(Project.class, new PropertyEditorSupport() {
@Override
public void setAsText(String element) throws IllegalArgumentException {
setValue(resolveProject(element));
}
});
/*
binder.registerCustomEditor(ProjectOverview.class, new PropertyEditorSupport() {
@Override
public void setAsText(String element) throws IllegalArgumentException {
log.info("Overviews set found... resolving...");
setValue(resolveProjectOverview(element));
}
});
binder.registerCustomEditor(Set.class, "overviews", new CustomCollectionEditor(Set.class) {
@Override
public void setAsText(String element) throws IllegalArgumentException {
setValue(resolveProjectOverview(element));
}
});
*/
binder.registerCustomEditor(Set.class, "studies", new CustomCollectionEditor(Set.class) {
@Override
protected Object convertElement(Object element) {
return resolveStudy(element);
}
});
binder.registerCustomEditor(Study.class, "study", new PropertyEditorSupport() {
@Override
public void setAsText(String element) throws IllegalArgumentException {
setValue(resolveStudy(element));
}
});
binder.registerCustomEditor(Set.class, "experiments", new CustomCollectionEditor(Set.class) {
@Override
protected Object convertElement(Object element) {
return resolveExperiment(element);
}
});
binder.registerCustomEditor(Experiment.class, new PropertyEditorSupport() {
@Override
public void setAsText(String element) throws IllegalArgumentException {
setValue(resolveExperiment(element));
}
});
binder.registerCustomEditor(Pool.class, "sequencerPartitionContainers.partitions.pool", new PropertyEditorSupport() {
@Override
public void setAsText(String element) throws IllegalArgumentException {
setValue(resolvePool(element));
}
});
/*
binder.registerCustomEditor(Pool.class, "flowcells.lanes.pool", new PropertyEditorSupport() {
@Override
public void setAsText(String element) throws IllegalArgumentException {
setValue(resolvePool(element));
}
});
*/
binder.registerCustomEditor(Set.class, "samples", new CustomCollectionEditor(Set.class) {
@Override
protected Object convertElement(Object element) {
return resolveSample(element);
}
});
binder.registerCustomEditor(Sample.class, "sample", new PropertyEditorSupport() {
@Override
public void setAsText(String element) throws IllegalArgumentException {
setValue(resolveSample(element));
}
});
binder.registerCustomEditor(Set.class, "runs", new CustomCollectionEditor(Set.class) {
@Override
protected Object convertElement(Object element) {
return resolveRun(element);
}
});
binder.registerCustomEditor(Run.class, new PropertyEditorSupport() {
@Override
public void setAsText(String element) throws IllegalArgumentException {
setValue(resolveRun(element));
}
});
binder.registerCustomEditor(Pool.class, new PropertyEditorSupport() {
@Override
public void setAsText(String element) throws IllegalArgumentException {
setValue(resolvePool(element));
}
});
binder.registerCustomEditor(PlatformType.class, new PropertyEditorSupport() {
@Override
public void setAsText(String element) throws IllegalArgumentException {
setValue(resolvePlatformType(element));
}
});
binder.registerCustomEditor(Set.class, "platformTypes", new CustomCollectionEditor(Set.class) {
@Override
protected Object convertElement(Object element) {
return resolvePlatformType(element);
}
});
binder.registerCustomEditor(List.class, "partitions", new CustomCollectionEditor(List.class) {
@Override
protected Object convertElement(Object element) {
return resolvePartition(element);
}
});
binder.registerCustomEditor(SequencerPartitionContainer.class, new PropertyEditorSupport() {
@Override
public void setAsText(String element) throws IllegalArgumentException {
setValue(resolveSequencerPartitionContainer(element));
}
});
binder.registerCustomEditor(List.class, "sequencerPartitionContainers", new CustomCollectionEditor(List.class) {
@Override
protected Object convertElement(Object element) {
return resolveSequencerPartitionContainer(element);
}
});
binder.registerCustomEditor(Library.class, new PropertyEditorSupport() {
@Override
public void setAsText(String element) throws IllegalArgumentException {
setValue(resolveLibrary(element));
}
});
binder.registerCustomEditor(Set.class, "libraries", new CustomCollectionEditor(Set.class) {
@Override
protected Object convertElement(Object element) {
return resolveLibrary(element);
}
});
binder.registerCustomEditor(Dilution.class, new PropertyEditorSupport() {
@Override
public void setAsText(String element) throws IllegalArgumentException {
log.info("Binding dilution " + element);
setValue(resolveDilution(element));
}
});
binder.registerCustomEditor(Set.class, "dilutions", new CustomCollectionEditor(Set.class) {
@Override
protected Object convertElement(Object element) {
log.info("Binding dilution set " + element.toString());
return resolveDilution(element);
}
});
binder.registerCustomEditor(LibraryDilution.class, new PropertyEditorSupport() {
@Override
public void setAsText(String element) throws IllegalArgumentException {
log.info("Binding library dilution " + element);
setValue(resolveLibraryDilution(element));
}
});
binder.registerCustomEditor(Set.class, "libraryDilutions", new CustomCollectionEditor(Set.class) {
@Override
protected Object convertElement(Object element) {
log.info("Binding library dilution set " + element.toString());
return resolveLibraryDilution(element);
}
});
binder.registerCustomEditor(LibraryType.class, new PropertyEditorSupport() {
@Override
public void setAsText(String element) throws IllegalArgumentException {
setValue(resolveLibraryType(element));
}
});
binder.registerCustomEditor(Set.class, "libraryTypes", new CustomCollectionEditor(Set.class) {
@Override
protected Object convertElement(Object element) {
return resolveLibraryType(element);
}
});
binder.registerCustomEditor(LibrarySelectionType.class, new PropertyEditorSupport() {
@Override
public void setAsText(String element) throws IllegalArgumentException {
setValue(resolveLibrarySelectionType(element));
}
});
binder.registerCustomEditor(Set.class, "librarySelectionTypes", new CustomCollectionEditor(Set.class) {
@Override
protected Object convertElement(Object element) {
return resolveLibrarySelectionType(element);
}
});
binder.registerCustomEditor(LibraryStrategyType.class, new PropertyEditorSupport() {
@Override
public void setAsText(String element) throws IllegalArgumentException {
setValue(resolveLibraryStrategyType(element));
}
});
binder.registerCustomEditor(Set.class, "libraryStrategyTypes", new CustomCollectionEditor(Set.class) {
@Override
protected Object convertElement(Object element) {
return resolveLibraryStrategyType(element);
}
});
binder.registerCustomEditor(TagBarcode.class, new PropertyEditorSupport() {
@Override
public void setAsText(String element) throws IllegalArgumentException {
setValue(resolveTagBarcode(element));
}
});
binder.registerCustomEditor(HashMap.class, "tagBarcodes", new CustomMapEditor(HashMap.class) {
@Override
protected Object convertValue(Object element) {
return resolveTagBarcode(element);
}
});
binder.registerCustomEditor(emPCRDilution.class, new PropertyEditorSupport() {
@Override
public void setAsText(String element) throws IllegalArgumentException {
setValue(resolveEmPcrDilution(element));
}
});
binder.registerCustomEditor(Set.class, "pcrDilutions", new CustomCollectionEditor(Set.class) {
@Override
protected Object convertElement(Object element) {
return resolveEmPcrDilution(element);
}
});
binder.registerCustomEditor(Platform.class, new PropertyEditorSupport() {
@Override
public void setAsText(String element) throws IllegalArgumentException {
setValue(resolvePlatform(element));
}
});
binder.registerCustomEditor(SequencerReference.class, new PropertyEditorSupport() {
@Override
public void setAsText(String element) throws IllegalArgumentException {
setValue(resolveSequencerReference(element));
}
});
binder.registerCustomEditor(Status.class, new PropertyEditorSupport() {
@Override
public void setAsText(String element) throws IllegalArgumentException {
setValue(resolveStatus(element));
}
});
binder.registerCustomEditor(SecurityProfile.class, new PropertyEditorSupport() {
@Override
public void setAsText(String element) throws IllegalArgumentException {
setValue(resolveSecurityProfile(element));
}
});
binder.registerCustomEditor(Submittable.class, "submissionElement", new PropertyEditorSupport() {
@Override
public void setAsText(String element) throws IllegalArgumentException {
setValue(resolveSubmittable(element));
}
});
binder.registerCustomEditor(Set.class, "submissionElements", new CustomCollectionEditor(Set.class) {
@Override
protected Object convertElement(Object element) {
return resolveSubmittable(element);
}
});
binder.registerCustomEditor(Kit.class, new PropertyEditorSupport() {
@Override
public void setAsText(String element) throws IllegalArgumentException {
setValue(resolveKit(element));
}
});
binder.registerCustomEditor(Set.class, "kits", new CustomCollectionEditor(Set.class) {
@Override
protected Object convertElement(Object element) {
return resolveKit(element);
}
});
binder.registerCustomEditor(KitDescriptor.class, new PropertyEditorSupport() {
@Override
public void setAsText(String element) throws IllegalArgumentException {
setValue(resolveKitDescriptor(element));
}
});
binder.registerCustomEditor(Set.class, "kitDescriptors", new CustomCollectionEditor(Set.class) {
@Override
protected Object convertElement(Object element) {
return resolveKitDescriptor(element);
}
});
binder.registerCustomEditor(Set.class, "poolableElements", new CustomCollectionEditor(Set.class) {
@Override
protected Object convertElement(Object element) {
return resolvePoolable(element);
}
});
}
/**
* Resolve an InetAddress object from a String
*
* @param element of type Object
* @return InetAddress
* @throws IllegalArgumentException when
*/
private InetAddress resolveInetAddress(Object element) throws IllegalArgumentException {
InetAddress i = null;
try {
if (element instanceof String) i = InetAddress.getByName((String)element);
return i;
}
catch (UnknownHostException e) {
if (log.isDebugEnabled()) {
log.debug("Failed to resolve InetAddress " + element, e);
}
throw new IllegalArgumentException(e);
}
}
/**
* Resolve a Group object from an ID String
*
* @param element of type Object
* @return Group
* @throws IllegalArgumentException when
*/
private Group resolveGroup(Object element) throws IllegalArgumentException {
Long id = null;
if (element instanceof String)
id = NumberUtils.parseNumber((String) element, Long.class).longValue();
try {
return id != null ? securityManager.getGroupById(id) : null;
}
catch (IOException e) {
if (log.isDebugEnabled()) {
log.debug("Failed to resolve group " + element, e);
}
throw new IllegalArgumentException(e);
}
}
/**
* Resolve a User object from an ID String
*
* @param element of type Object
* @return User
* @throws IllegalArgumentException when
*/
private User resolveUser(Object element) throws IllegalArgumentException {
Long id = null;
if (element instanceof String && !"".equals(element))
id = NumberUtils.parseNumber((String) element, Long.class).longValue();
try {
return id != null ? securityManager.getUserById(id) : null;
}
catch (IOException e) {
if (log.isDebugEnabled()) {
log.debug("Failed to resolve user " + element, e);
}
throw new IllegalArgumentException(e);
}
}
/**
* Resolve a SecurityProfile object from an ID String
*
* @param element of type Object
* @return SecurityProfile
* @throws IllegalArgumentException when
*/
private SecurityProfile resolveSecurityProfile(Object element) throws IllegalArgumentException {
Long id = null;
if (element instanceof String)
id = NumberUtils.parseNumber((String) element, Long.class).longValue();
try {
return id != null ? securityManager.getSecurityProfileById(id) : null;
}
catch (IOException e) {
if (log.isDebugEnabled()) {
log.debug("Failed to resolve SecurityProfile " + element, e);
}
throw new IllegalArgumentException(e);
}
}
/*
private Request resolveRequest(Object element) throws IllegalArgumentException {
Long id = null;
if (element instanceof String)
id = NumberUtils.parseNumber((String) element, Long.class).longValue();
try {
return id != null ? requestManager.getRequestById(id) : null;
}
catch (IOException e) {
if (log.isDebugEnabled()) {
log.debug("Failed to resolve request " + element, e);
}
throw new IllegalArgumentException(e);
}
}
*/
/**
* Resolve a Project object from an ID or {@link uk.ac.bbsrc.tgac.miso.core.data.Project.PREFIX} String
*
* @param element of type Object
* @return Project
* @throws IllegalArgumentException when
*/
private Project resolveProject(Object element) throws IllegalArgumentException {
Long id = null;
if (element instanceof String) {
if (((String)element).startsWith(Project.PREFIX)) {
String ident = ((String)element).substring(Project.PREFIX.length());
id = NumberUtils.parseNumber(ident, Long.class).longValue();
}
else {
id = NumberUtils.parseNumber((String) element, Long.class).longValue();
}
}
try {
return id != null ? requestManager.getProjectById(id) : null;
}
catch (IOException e) {
if (log.isDebugEnabled()) {
log.debug("Failed to resolve project " + element, e);
}
throw new IllegalArgumentException(e);
}
}
private ProjectOverview resolveProjectOverview(Object element) throws IllegalArgumentException {
Long id = null;
if (element instanceof String)
id = NumberUtils.parseNumber((String) element, Long.class).longValue();
try {
log.info("Resolved project overview");
return id != null ? requestManager.getProjectOverviewById(id) : null;
}
catch (IOException e) {
if (log.isDebugEnabled()) {
log.debug("Failed to resolve project overview" + element, e);
}
throw new IllegalArgumentException(e);
}
}
/**
* Resolve an Activity object from an ID String
*
* @param element of type Object
* @return Activity
* @throws IllegalArgumentException when
*/
private Activity resolveActivity(Object element) throws IllegalArgumentException {
String id = null;
if (element instanceof String)
id = element.toString();
try {
return id != null ? protocolManager.getActivity(id) : null;
}
catch (IOException e) {
if (log.isDebugEnabled()) {
log.debug("Failed to resolve activity " + element, e);
}
throw new IllegalArgumentException(e);
}
}
/**
* Resolve a Protocol object from an ID String
*
* @param element of type Object
* @return Protocol
* @throws IllegalArgumentException when
*/
private Protocol resolveProtocol(Object element) throws IllegalArgumentException {
String id = null;
if (element instanceof String)
id = element.toString();
try {
return id != null ? protocolManager.getProtocol(id) : null;
}
catch (IOException e) {
if (log.isDebugEnabled()) {
log.debug("Failed to resolve protocol " + element, e);
}
throw new IllegalArgumentException(e);
}
}
/**
* Resolve a Study object from an ID or {@link uk.ac.bbsrc.tgac.miso.core.data.Study.PREFIX} String
*
* @param element of type Object
* @return Study
* @throws IllegalArgumentException when
*/
private Study resolveStudy(Object element) throws IllegalArgumentException {
Long id = null;
if (element instanceof String) {
if (((String)element).startsWith(Study.PREFIX)) {
String ident = ((String)element).substring(Study.PREFIX.length());
id = NumberUtils.parseNumber(ident, Long.class).longValue();
}
else {
id = NumberUtils.parseNumber((String) element, Long.class).longValue();
}
}
try {
return id != null ? requestManager.getStudyById(id) : null;
}
catch (IOException e) {
if (log.isDebugEnabled()) {
log.debug("Failed to resolve study " + element, e);
}
throw new IllegalArgumentException(e);
}
}
/**
* Resolve an Experiment object from an ID String
*
* @param element of type Object
* @return Experiment
* @throws IllegalArgumentException when
*/
private Experiment resolveExperiment(Object element) throws IllegalArgumentException {
Long id = null;
log.info("Resolving experiment: " + element.toString());
if (element instanceof String) {
// if (((String)element).startsWith(Experiment.PREFIX)) {
// String ident = ((String)element).substring(Experiment.PREFIX.length());
// id = NumberUtils.parseNumber(ident, Long.class).longValue();
// }
// else {
id = NumberUtils.parseNumber((String) element, Long.class).longValue();
// }
}
try {
return id != null ? requestManager.getExperimentById(id) : null;
}
catch (IOException e) {
if (log.isDebugEnabled()) {
log.debug("Failed to resolve experiment " + element, e);
}
throw new IllegalArgumentException(e);
}
}
/**
* Resolve a Sample object from an ID or {@link uk.ac.bbsrc.tgac.miso.core.data.Sample.PREFIX} String
*
* @param element of type Object
* @return Sample
* @throws IllegalArgumentException when
*/
private Sample resolveSample(Object element) throws IllegalArgumentException {
Long id = null;
if (element instanceof String) {
if (((String)element).startsWith(Sample.PREFIX)) {
String ident = ((String)element).substring(Sample.PREFIX.length());
id = NumberUtils.parseNumber(ident, Long.class).longValue();
}
else {
id = NumberUtils.parseNumber((String) element, Long.class).longValue();
}
}
try {
return id != null ? requestManager.getSampleById(id) : null;
}
catch (IOException e) {
if (log.isDebugEnabled()) {
log.debug("Failed to resolve sample " + element, e);
}
throw new IllegalArgumentException(e);
}
}
/**
* Resolve a Run object from an ID String
*
* @param element of type Object
* @return Run
* @throws IllegalArgumentException when
*/
private Run resolveRun(Object element) throws IllegalArgumentException {
Long id = null;
if (element instanceof String)
id = NumberUtils.parseNumber((String) element, Long.class).longValue();
try {
return id != null ? requestManager.getRunById(id) : null;
}
catch (IOException e) {
if (log.isDebugEnabled()) {
log.debug("Failed to resolve run " + element, e);
}
throw new IllegalArgumentException(e);
}
}
/**
* Resolve a PlatformType enum from a given key String
*
* @param element of type Object
* @return PlatformType
* @throws IllegalArgumentException when
*/
private PlatformType resolvePlatformType(Object element) throws IllegalArgumentException {
if (element instanceof String) {
return PlatformType.get((String)element);
}
else {
if (log.isDebugEnabled()) {
log.debug("Failed to resolve PlatformType " + element);
}
throw new IllegalArgumentException("Cannot resolve PlatformType from key: " + element + ". Accepted keys are: [" + PlatformType.getKeys() + "]");
}
}
/**
* Resolve a Pool object from an ID or {@link uk.ac.bbsrc.tgac.miso.core.data.Pool} PREFIX String
*
* @param element of type Object
* @return Pool
* @throws IllegalArgumentException when
*/
private Pool resolvePool(Object element) throws IllegalArgumentException {
Long id = null;
if (element instanceof String)
id = NumberUtils.parseNumber((String) element, Long.class).longValue();
try {
return id != null ? requestManager.getPoolById(id) : null;
}
catch (IOException e) {
if (log.isDebugEnabled()) {
log.debug("Failed to resolve pool " + element, e);
}
throw new IllegalArgumentException(e);
}
}
/**
* Resolve a Partition object from an ID String
*
* @param element of type Object
* @return Partition
* @throws IllegalArgumentException when
*/
private SequencerPoolPartition resolvePartition(Object element) throws IllegalArgumentException {
Long id = null;
if (element instanceof String) {
String s = (String)element;
if (!"".equals(s)) {
id = NumberUtils.parseNumber((String) element, Long.class).longValue();
}
}
try {
return id != null ? requestManager.getSequencerPoolPartitionById(id) : null;
}
catch (IOException e) {
if (log.isDebugEnabled()) {
log.debug("Failed to resolve Partition " + element, e);
}
throw new IllegalArgumentException(e);
}
}
/**
* Resolve a SequencerPartitionContainer object from an ID String
*
* @param element of type Object
* @return SequencerPartitionContainer
* @throws IllegalArgumentException when
*/
private SequencerPartitionContainer resolveSequencerPartitionContainer(Object element) throws IllegalArgumentException {
Long id = null;
if (element instanceof String) {
String s = (String)element;
if (!"".equals(s)) {
id = NumberUtils.parseNumber((String) element, Long.class).longValue();
}
}
try {
return id != null ? requestManager.getSequencerPartitionContainerById(id) : null;
}
catch (IOException e) {
if (log.isDebugEnabled()) {
log.debug("Failed to resolve SequencerPartitionContainer " + element, e);
}
throw new IllegalArgumentException(e);
}
}
/**
* Resolve a Library object from an ID String
*
* @param element of type Object
* @return Library
* @throws IllegalArgumentException when
*/
private Library resolveLibrary(Object element) throws IllegalArgumentException {
Long id = null;
if (element instanceof String)
id = NumberUtils.parseNumber((String) element, Long.class).longValue();
try {
return id != null ? requestManager.getLibraryById(id) : null;
}
catch (IOException e) {
if (log.isDebugEnabled()) {
log.debug("Failed to resolve library " + element, e);
}
throw new IllegalArgumentException(e);
}
}
/**
* Resolve a Dilution object from an ID String
*
* @param element of type Object
* @return Dilution
* @throws IllegalArgumentException when
*/
private Dilution resolveDilution(Object element) throws IllegalArgumentException {
Long id = null;
if (element instanceof String) {
String prefix = ((String)element).substring(0, 3);
String ident = ((String)element).substring(3);
id = NumberUtils.parseNumber(ident, Long.class).longValue();
try {
if ("LDI".equals(prefix)) {
log.debug(prefix + ":" + ident + " -> Dilution");
return id != null ? requestManager.getLibraryDilutionById(id) : null;
}
else if ("EDI".equals(prefix)) {
log.debug(prefix + ":" + ident + " -> Dilution");
return id != null ? requestManager.getEmPcrDilutionById(id) : null;
}
else {
log.debug("Failed to resolve dilution with identifier: " + prefix+ident);
}
}
catch (IOException e) {
if (log.isDebugEnabled()) {
log.debug("Failed to resolve dilution " + element, e);
}
throw new IllegalArgumentException(e);
}
}
return null;
}
/**
* Resolve a LibraryDilution object from an ID String
*
* @param element of type Object
* @return LibraryDilution
* @throws IllegalArgumentException when
*/
private LibraryDilution resolveLibraryDilution(Object element) throws IllegalArgumentException {
Long id = null;
if (element instanceof String)
id = NumberUtils.parseNumber((String) element, Long.class).longValue();
try {
return id != null ? requestManager.getLibraryDilutionById(id) : null;
}
catch (IOException e) {
if (log.isDebugEnabled()) {
log.debug("Failed to resolve dilution " + element, e);
}
throw new IllegalArgumentException(e);
}
}
/**
* Resolve an emPCRDilution object from an ID String
*
* @param element of type Object
* @return emPCRDilution
* @throws IllegalArgumentException when
*/
private emPCRDilution resolveEmPcrDilution(Object element) throws IllegalArgumentException {
Long id = null;
if (element instanceof String)
id = NumberUtils.parseNumber((String) element, Long.class).longValue();
try {
return id != null ? requestManager.getEmPcrDilutionById(id) : null;
}
catch (IOException e) {
if (log.isDebugEnabled()) {
log.debug("Failed to resolve dilution " + element, e);
}
throw new IllegalArgumentException(e);
}
}
/**
* Resolve a Platform object from an ID String
*
* @param element of type Object
* @return Platform
* @throws IllegalArgumentException when
*/
private Platform resolvePlatform(Object element) throws IllegalArgumentException {
Long id = null;
if (element instanceof String)
id = NumberUtils.parseNumber((String) element, Long.class).longValue();
try {
return id != null ? requestManager.getPlatformById(id) : null;
}
catch (IOException e) {
if (log.isDebugEnabled()) {
log.debug("Failed to resolve platform " + element, e);
}
throw new IllegalArgumentException(e);
}
}
/**
* Resolve a SequencerReference object from an ID String
*
* @param element of type Object
* @return SequencerReference
* @throws IllegalArgumentException when
*/
private SequencerReference resolveSequencerReference(Object element) throws IllegalArgumentException {
Long id = null;
if (element instanceof String)
id = NumberUtils.parseNumber((String) element, Long.class).longValue();
try {
return id != null ? requestManager.getSequencerReferenceById(id) : null;
}
catch (IOException e) {
if (log.isDebugEnabled()) {
log.debug("Failed to resolve SequencerReference " + element, e);
}
throw new IllegalArgumentException(e);
}
}
/**
* Resolve a Status object from an ID String
*
* @param element of type Object
* @return Status
* @throws IllegalArgumentException when
*/
private Status resolveStatus(Object element) throws IllegalArgumentException {
Long id = null;
if (element instanceof String)
id = NumberUtils.parseNumber((String) element, Long.class).longValue();
try {
return id != null ? requestManager.getStatusById(id) : null;
}
catch (IOException e) {
if (log.isDebugEnabled()) {
log.debug("Failed to resolve status " + element, e);
}
throw new IllegalArgumentException(e);
}
}
/**
* Resolve a Submittable object from a PREFIX
*
* @param element of type Object
* @return Submittable
* @throws IllegalArgumentException when
*/
private Submittable resolveSubmittable(Object element) throws IllegalArgumentException {
Long id = null;
if (element instanceof String) {
String prefix = ((String)element).substring(0, 3);
String ident = ((String)element).substring(3);
id = NumberUtils.parseNumber(ident, Long.class).longValue();
try {
if (Study.PREFIX.equals(prefix)) {
log.info(prefix + ":" + ident + " -> Study");
return id != null ? requestManager.getStudyById(id) : null;
}
else if (Sample.PREFIX.equals(prefix)) {
log.info(prefix + ":" + ident + " -> Sample");
return id != null ? requestManager.getSampleById(id) : null;
}
else if (Experiment.PREFIX.equals(prefix)) {
log.info(prefix + ":" + ident + " -> Experiment");
return id != null ? requestManager.getExperimentById(id) : null;
}
else if ("PAR".equals(prefix)) {
log.info(prefix + ":" + ident + " -> Partition");
return id != null ? requestManager.getSequencerPoolPartitionById(id) : null;
}
else {
log.debug("Failed to resolve submittable element with identifier: " + prefix+ident);
}
}
catch (IOException e) {
if (log.isDebugEnabled()) {
log.debug("Failed to resolve submittable element " + element, e);
}
throw new IllegalArgumentException(e);
}
}
return null;
}
/**
* Resolve a Kit object from an ID String
*
* @param element of type Object
* @return Kit
* @throws IllegalArgumentException when
*/
private Kit resolveKit(Object element) throws IllegalArgumentException {
Long id = null;
if (element instanceof String && !"".equals(element))
id = NumberUtils.parseNumber((String) element, Long.class).longValue();
try {
return id != null ? requestManager.getKitById(id) : null;
}
catch (IOException e) {
if (log.isDebugEnabled()) {
log.debug("Failed to resolve kit " + element, e);
}
throw new IllegalArgumentException(e);
}
}
/**
* Resolve a KitDescriptor object from an ID String
*
* @param element of type Object
* @return KitDescriptor
* @throws IllegalArgumentException when
*/
private KitDescriptor resolveKitDescriptor(Object element) throws IllegalArgumentException {
Long id = null;
if (element instanceof String)
id = NumberUtils.parseNumber((String) element, Long.class).longValue();
try {
return id != null ? requestManager.getKitDescriptorById(id) : null;
}
catch (IOException e) {
if (log.isDebugEnabled()) {
log.debug("Failed to resolve kit descriptor " + element, e);
}
throw new IllegalArgumentException(e);
}
}
/**
* Resolve a LibraryType object from an ID String
*
* @param element of type Object
* @return LibraryType
* @throws IllegalArgumentException when
*/
private LibraryType resolveLibraryType(Object element) throws IllegalArgumentException {
Long id = null;
if (element instanceof String)
id = NumberUtils.parseNumber((String) element, Long.class).longValue();
try {
return id != null ? requestManager.getLibraryTypeById(id) : null;
}
catch (IOException e) {
if (log.isDebugEnabled()) {
log.debug("Failed to resolve LibraryType " + element, e);
}
throw new IllegalArgumentException(e);
}
}
/**
* Resolve a LibrarySelectionType object from an ID String
*
* @param element of type Object
* @return LibrarySelectionType
* @throws IllegalArgumentException when
*/
private LibrarySelectionType resolveLibrarySelectionType(Object element) throws IllegalArgumentException {
Long id = null;
if (element instanceof String)
id = NumberUtils.parseNumber((String) element, Long.class).longValue();
try {
return id != null ? requestManager.getLibrarySelectionTypeById(id) : null;
}
catch (IOException e) {
if (log.isDebugEnabled()) {
log.debug("Failed to resolve LibrarySelectionType " + element, e);
}
throw new IllegalArgumentException(e);
}
}
/**
* Resolve a LibraryStrategyType object from an ID String
*
* @param element of type Object
* @return LibraryStrategyType
* @throws IllegalArgumentException when
*/
private LibraryStrategyType resolveLibraryStrategyType(Object element) throws IllegalArgumentException {
Long id = null;
if (element instanceof String)
id = NumberUtils.parseNumber((String) element, Long.class).longValue();
try {
return id != null ? requestManager.getLibraryStrategyTypeById(id) : null;
}
catch (IOException e) {
if (log.isDebugEnabled()) {
log.debug("Failed to resolve LibrarySelectionType " + element, e);
}
throw new IllegalArgumentException(e);
}
}
/**
* Resolve a TagBarcode object from an ID String
*
* @param element of type Object
* @return TagBarcode
* @throws IllegalArgumentException when
*/
private TagBarcode resolveTagBarcode(Object element) throws IllegalArgumentException {
Long id = null;
if (element instanceof String && !"".equals(element))
id = NumberUtils.parseNumber((String) element, Long.class).longValue();
try {
return id != null ? requestManager.getTagBarcodeById(id) : null;
}
catch (IOException e) {
if (log.isDebugEnabled()) {
log.debug("Failed to resolve TagBarcode " + element, e);
}
throw new IllegalArgumentException(e);
}
}
/**
* Resolve a Poolable object from a PREFIX
*
* @param element of type Object
* @return Poolable
* @throws IllegalArgumentException when
*/
private Poolable resolvePoolable(Object element) throws IllegalArgumentException {
Long id = null;
if (element instanceof String) {
String prefix = ((String)element).substring(0, 3);
String ident = ((String)element).substring(3);
id = NumberUtils.parseNumber(ident, Long.class).longValue();
try {
if ("LDI".equals(prefix)) {
log.info(prefix + ":" + ident + " -> LibraryDilution");
return id != null ? requestManager.getLibraryDilutionById(id) : null;
}
else if ("EDI".equals(prefix)) {
log.info(prefix + ":" + ident + " -> EmPCRDilution");
return id != null ? requestManager.getEmPcrDilutionById(id) : null;
}
else if ("PLA".equals(prefix)) {
log.info(prefix + ":" + ident + " -> Plate");
return id != null ? requestManager.getPlateById(id) : null;
}
else {
log.debug("Failed to resolve poolable element with identifier: " + prefix+ident);
}
}
catch (IOException e) {
if (log.isDebugEnabled()) {
log.debug("Failed to resolve poolable element " + element, e);
}
throw new IllegalArgumentException(e);
}
}
return null;
}
}