diff --git a/build.gradle b/build.gradle
index cba2a3457fa7d0d0c90a98145807d29ab5a8857e..8eecde42f116e13e4b7365c5ef0284ef3ab2cb96 100644
--- a/build.gradle
+++ b/build.gradle
@@ -385,9 +385,10 @@ dependencies {
compile "org.apache.httpcomponents:httpcore-nio:4.4.4"
compile "org.codehaus.groovy:groovy-all:${vGroovy}"
- compile "org.python:jython-standalone:${vJython}"
+ compile "org.python:jython:${vJython}"
compile "net.sourceforge.saxon:saxon:${vSaxon}"
+ compile "xalan:xalan:2.7.2"
compile "nl.bitwalker:UserAgentUtils:1.2.4"
compile "com.twmacinta:fast-md5:2.7.1"
@@ -423,7 +424,6 @@ dependencies {
runtime "net.imagej:ij:1.50e"
runtime "net.bull.javamelody:javamelody-core:1.58.0"
runtime "org.javassist:javassist:3.20.0-GA"
- runtime "xalan:xalan:2.7.2"
providedCompile "javax.servlet:javax.servlet-api:${vServletApi}"
diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
index 972604aef5c43767c8547fdca27ec9a5e8214015..740384b0ef641f50fa8d9cfe30b23130fa2ce6c6 100644
--- a/gradle/wrapper/gradle-wrapper.properties
+++ b/gradle/wrapper/gradle-wrapper.properties
@@ -1,6 +1,6 @@
-#Sat May 28 14:49:32 CDT 2016
+#Thu Jul 07 14:39:27 CDT 2016
distributionBase=GRADLE_USER_HOME
distributionPath=wrapper/dists
zipStoreBase=GRADLE_USER_HOME
zipStorePath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-2.13-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-2.13-all.zip
diff --git a/src/main/java/org/nrg/xapi/rest/dicomscp/DicomSCPApi.java b/src/main/java/org/nrg/xapi/rest/dicomscp/DicomSCPApi.java
index b4e5c40ec99efb64e71b018bc5f2bb7da022b0b0..e4e51c0d725ddb83255534cba3c57330dce5186d 100644
--- a/src/main/java/org/nrg/xapi/rest/dicomscp/DicomSCPApi.java
+++ b/src/main/java/org/nrg/xapi/rest/dicomscp/DicomSCPApi.java
@@ -6,7 +6,7 @@ import org.nrg.dcm.preferences.DicomSCPInstance;
import org.nrg.framework.annotations.XapiRestController;
import org.nrg.framework.exceptions.NrgServiceException;
import org.nrg.xapi.rest.NotFoundException;
-import org.nrg.xdat.rest.AbstractXnatRestApi;
+import org.nrg.xdat.rest.AbstractXapiRestController;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.http.HttpStatus;
@@ -20,7 +20,7 @@ import java.util.List;
@Api(description = "XNAT DICOM SCP management API")
@XapiRestController
@RequestMapping(value = "/dicomscp")
-public class DicomSCPApi extends AbstractXnatRestApi {
+public class DicomSCPApi extends AbstractXapiRestController {
private static final Logger _log = LoggerFactory.getLogger(DicomSCPApi.class);
@ApiOperation(value = "Get list of all configured DICOM SCP receiver definitions.", notes = "The primary DICOM SCP retrieval function returns a list of all DICOM SCP receivers defined for the current system.", response = DicomSCPInstance.class, responseContainer = "List")
diff --git a/src/main/java/org/nrg/xapi/rest/notifications/NotificationsApi.java b/src/main/java/org/nrg/xapi/rest/notifications/NotificationsApi.java
index db69a9e3566c4526dfe1228fc84acee976cc9d68..ebb5c42a9e22c2bbc2a7227fb4d4ed7f5ead0ecc 100644
--- a/src/main/java/org/nrg/xapi/rest/notifications/NotificationsApi.java
+++ b/src/main/java/org/nrg/xapi/rest/notifications/NotificationsApi.java
@@ -9,7 +9,7 @@ import org.nrg.notify.services.NotificationService;
import org.nrg.prefs.exceptions.InvalidPreferenceName;
import org.nrg.xapi.exceptions.InitializationException;
import org.nrg.xdat.preferences.NotificationsPreferences;
-import org.nrg.xdat.rest.AbstractXnatRestApi;
+import org.nrg.xdat.rest.AbstractXapiRestController;
import org.nrg.xnat.services.XnatAppInfo;
import org.nrg.xnat.utils.XnatHttpUtils;
import org.slf4j.Logger;
@@ -29,7 +29,7 @@ import java.util.*;
@Api(description = "XNAT Notifications management API")
@XapiRestController
@RequestMapping(value = "/notifications")
-public class NotificationsApi extends AbstractXnatRestApi {
+public class NotificationsApi extends AbstractXapiRestController {
public static final String POST_PROPERTIES_NOTES = "Sets the mail service host, port, username, password, and protocol. You can set "
+ "extra properties on the mail sender (e.g. for configuring SSL or TLS transport) by "
diff --git a/src/main/java/org/nrg/xapi/rest/settings/SiteConfigApi.java b/src/main/java/org/nrg/xapi/rest/settings/SiteConfigApi.java
index c9172788f223c1f510df6e36b16063924711c46f..8efe9d55314e6afe2027f7b5f5eb6778c5035a22 100644
--- a/src/main/java/org/nrg/xapi/rest/settings/SiteConfigApi.java
+++ b/src/main/java/org/nrg/xapi/rest/settings/SiteConfigApi.java
@@ -7,7 +7,7 @@ import org.nrg.framework.annotations.XapiRestController;
import org.nrg.prefs.exceptions.InvalidPreferenceName;
import org.nrg.xapi.exceptions.InitializationException;
import org.nrg.xdat.preferences.SiteConfigPreferences;
-import org.nrg.xdat.rest.AbstractXnatRestApi;
+import org.nrg.xdat.rest.AbstractXapiRestController;
import org.nrg.xnat.services.XnatAppInfo;
import org.nrg.xnat.turbine.utils.ArcSpecManager;
import org.nrg.xnat.utils.XnatHttpUtils;
@@ -32,7 +32,7 @@ import java.util.Properties;
@Api(description = "Site Configuration Management API")
@XapiRestController
@RequestMapping(value = "/siteConfig")
-public class SiteConfigApi extends AbstractXnatRestApi {
+public class SiteConfigApi extends AbstractXapiRestController {
@ApiOperation(value = "Returns a map of application build properties.", notes = "This includes the implementation version, Git commit hash, and build number and number.", response = Properties.class)
@ApiResponses({@ApiResponse(code = 200, message = "Application build properties successfully retrieved."), @ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."), @ApiResponse(code = 500, message = "Unexpected error")})
@RequestMapping(value = "buildInfo", produces = {MediaType.APPLICATION_JSON_VALUE}, method = {RequestMethod.GET})
diff --git a/src/main/java/org/nrg/xapi/rest/users/UsersApi.java b/src/main/java/org/nrg/xapi/rest/users/UsersApi.java
index e59a3e6513906fe184b960bc241dd0246a6c452e..dca118723dd34a2b6b3cadeaeccd3a6b51d6d261 100644
--- a/src/main/java/org/nrg/xapi/rest/users/UsersApi.java
+++ b/src/main/java/org/nrg/xapi/rest/users/UsersApi.java
@@ -7,7 +7,7 @@ import org.nrg.xapi.model.users.User;
import org.nrg.xapi.rest.NotFoundException;
import org.nrg.xdat.XDAT;
import org.nrg.xdat.preferences.SiteConfigPreferences;
-import org.nrg.xdat.rest.AbstractXnatRestApi;
+import org.nrg.xdat.rest.AbstractXapiRestController;
import org.nrg.xdat.security.UserGroupI;
import org.nrg.xdat.security.helpers.Groups;
import org.nrg.xdat.security.helpers.Users;
@@ -32,7 +32,7 @@ import java.util.*;
@Api(description = "User Management API")
@XapiRestController
@RequestMapping(value = "/users")
-public class UsersApi extends AbstractXnatRestApi {
+public class UsersApi extends AbstractXapiRestController {
private static final Logger _log = LoggerFactory.getLogger(UsersApi.class);
@ApiOperation(value = "Get list of users.", notes = "The primary users function returns a list of all users of the XNAT system.", response = User.class, responseContainer = "List")
diff --git a/src/main/java/org/nrg/xnat/restlet/resources/search/SavedSearchResource.java b/src/main/java/org/nrg/xnat/restlet/resources/search/SavedSearchResource.java
index 321ef8a28f2cd2d9b2aa2f4562c3046c2ac9a77a..ceb1700c66a2a3537bb1f281fb60d0c4608aef67 100644
--- a/src/main/java/org/nrg/xnat/restlet/resources/search/SavedSearchResource.java
+++ b/src/main/java/org/nrg/xnat/restlet/resources/search/SavedSearchResource.java
@@ -32,7 +32,6 @@ import org.nrg.xft.exception.ElementNotFoundException;
import org.nrg.xft.exception.XFTInitException;
import org.nrg.xft.schema.Wrappers.XMLWrapper.SAXReader;
import org.nrg.xft.search.ItemSearch;
-import org.nrg.xft.security.UserI;
import org.nrg.xft.utils.SaveItemHelper;
import org.nrg.xnat.restlet.presentation.RESTHTMLPresenter;
import org.nrg.xnat.restlet.representations.ItemXMLRepresentation;
@@ -50,385 +49,368 @@ import org.springframework.util.StringUtils;
import org.xml.sax.SAXException;
import java.io.File;
-import java.io.IOException;
import java.io.Reader;
import java.util.Hashtable;
import java.util.LinkedHashMap;
import java.util.Map;
public class SavedSearchResource extends ItemResource {
- XdatStoredSearch xss = null;
- String sID=null;
- boolean loadedFromFile=false;
-
- public SavedSearchResource(Context context, Request request,
- Response response) {
- super(context, request, response);
-
- sID= (String)getParameter(request,"SEARCH_ID");
- if(sID!=null){
- this.getVariants().add(new Variant(MediaType.TEXT_XML));
- }else{
- response.setStatus(Status.CLIENT_ERROR_GONE);
- }
- }
-
-
- /**
- * Returns a file containing search xmls which was stored on the file system. This provides a way to standardize search xmls outside of the database, for easy sharing across installations.
- * @return
- */
- private synchronized static File getFileSystemSearch(String name){
- if(name.indexOf("..")==-1){
- final File file=new File(new File(XFT.GetConfDir()).getParentFile().getParentFile(),"resources/searches/" + name);
- if(file.exists()){
- return file;
- }
- }
- return null;
- }
-
- @Override
- public Representation represent(Variant variant) {
- MediaType mt = overrideVariant(variant);
-
- if(xss==null && sID!=null){
- if(sID.startsWith("@")){
- try {
- String dv = this.getQueryVariable("dv");
- if(dv==null){
- dv="listing";
- }
- DisplaySearch ds = new DisplaySearch();
- ds.setUser(user);
- ds.setDisplay(dv);
- ds.setRootElement(sID.substring(1));
- xss=ds.convertToStoredSearch(sID);
- xss.setId(sID);
- } catch (XFTInitException e) {
- logger.error("",e);
- } catch (ElementNotFoundException e) {
- logger.error("",e);
- }
- }else{
- xss= XdatStoredSearch.getXdatStoredSearchsById(sID, user, true);
- }
- }
-
- if(xss != null) {
- if(!xss.hasAllowedUser(user.getLogin()) || !Permissions.canQuery(user, xss.getRootElementName())){
+ private XdatStoredSearch xss = null;
+ private String sID = null;
+ private boolean loadedFromFile = false;
+
+ public SavedSearchResource(Context context, Request request,
+ Response response) {
+ super(context, request, response);
+
+ sID = (String) getParameter(request, "SEARCH_ID");
+ if (sID != null) {
+ this.getVariants().add(new Variant(MediaType.TEXT_XML));
+ } else {
+ response.setStatus(Status.CLIENT_ERROR_GONE);
+ }
+ }
+
+ /**
+ * Returns a file containing search xmls which was stored on the file system. This provides a way to standardize search xmls outside of the database, for easy sharing across installations.
+ *
+ * @return The search XMLs stored on the file system.
+ */
+ private synchronized static File getFileSystemSearch(String name) {
+ if (!name.contains("..")) {
+ final File file = new File(new File(XFT.GetConfDir()).getParentFile().getParentFile(), "resources/searches/" + name);
+ if (file.exists()) {
+ return file;
+ }
+ }
+ return null;
+ }
+
+ @Override
+ public Representation represent(Variant variant) {
+ MediaType mt = overrideVariant(variant);
+
+ if (xss == null && sID != null) {
+ if (sID.startsWith("@")) {
+ try {
+ String dv = this.getQueryVariable("dv");
+ if (dv == null) {
+ dv = "listing";
+ }
+ DisplaySearch ds = new DisplaySearch();
+ ds.setUser(user);
+ ds.setDisplay(dv);
+ ds.setRootElement(sID.substring(1));
+ xss = ds.convertToStoredSearch(sID);
+ xss.setId(sID);
+ } catch (XFTInitException | ElementNotFoundException e) {
+ logger.error("", e);
+ }
+ } else {
+ xss = XdatStoredSearch.getXdatStoredSearchsById(sID, user, true);
+ }
+ }
+
+ if (xss != null) {
+ if (!xss.hasAllowedUser(user.getLogin()) && !Permissions.canQuery(user, xss.getRootElementName())) {
getResponse().setStatus(Status.CLIENT_ERROR_FORBIDDEN);
return null;
}
} else {
- //allow loading of saved searches from xml stored on hte file system
- File search_xml=getFileSystemSearch(sID);
-
- if(mt.equals(MediaType.TEXT_XML) && (filepath ==null || !filepath.startsWith("results")) && !this.hasQueryVariable("project")){
- return new FileRepresentation(search_xml, mt);
- }else{
- try {
- SAXReader reader = new SAXReader(user);
- XFTItem item = reader.parse(search_xml);
- xss = new XdatStoredSearch(item);
-
- loadedFromFile=true;
-
- if(this.getQueryVariable("project")!=null){
- final XdatCriteriaSet cs= new XdatCriteriaSet((UserI)user);
- cs.setMethod("OR");
-
- for(final String p: StringUtils.commaDelimitedListToSet(this.getQueryVariable("project"))){
- XdatCriteria c=new XdatCriteria((UserI)user);
- c.setSchemaField(xss.getRootElementName()+"/project");
- c.setComparisonType("=");
- c.setValue(p);
- cs.setCriteria(c);
-
- c=new XdatCriteria((UserI)user);
- c.setSchemaField(xss.getRootElementName()+"/sharing/share/project");
- c.setComparisonType("=");
- c.setValue(p);
- cs.setCriteria(c);
- }
-
- xss.setSearchWhere(cs);
- }
- } catch (Exception e) {
- logger.error("",e);
- getResponse().setStatus(Status.CLIENT_ERROR_NOT_FOUND);
- return null;
- }
- }
- }
-
- if(xss!=null){
- if(filepath !=null && filepath.startsWith("results")){
+ //allow loading of saved searches from xml stored on hte file system
+ final File searchXml = getFileSystemSearch(sID);
+
+ if (searchXml != null) {
+ if (mt.equals(MediaType.TEXT_XML) && (filepath == null || !filepath.startsWith("results")) && !this.hasQueryVariable("project")) {
+ return new FileRepresentation(searchXml, mt);
+ } else {
+ try {
+ SAXReader reader = new SAXReader(user);
+ XFTItem item = reader.parse(searchXml);
+ xss = new XdatStoredSearch(item);
+
+ loadedFromFile = true;
+
+ if (this.getQueryVariable("project") != null) {
+ final XdatCriteriaSet cs = new XdatCriteriaSet(user);
+ cs.setMethod("OR");
+
+ for (final String p : StringUtils.commaDelimitedListToSet(this.getQueryVariable("project"))) {
+ XdatCriteria c = new XdatCriteria(user);
+ c.setSchemaField(xss.getRootElementName() + "/project");
+ c.setComparisonType("=");
+ c.setValue(p);
+ cs.setCriteria(c);
+
+ c = new XdatCriteria(user);
+ c.setSchemaField(xss.getRootElementName() + "/sharing/share/project");
+ c.setComparisonType("=");
+ c.setValue(p);
+ cs.setCriteria(c);
+ }
+
+ xss.setSearchWhere(cs);
+ }
+ } catch (Exception e) {
+ logger.error("", e);
+ getResponse().setStatus(Status.CLIENT_ERROR_NOT_FOUND);
+ return null;
+ }
+ }
+ }
+ }
+
+ if (xss != null) {
+ if (filepath != null && filepath.startsWith("results")) {
if ((mt.equals(SecureResource.TEXT_CSV) || mt.equals(MediaType.APPLICATION_EXCEL)) &&
- !filepath.endsWith(".csv")){
+ !filepath.endsWith(".csv")) {
this.setContentDisposition(filepath + ".csv");
}
- try {
- DisplaySearch ds=xss.getDisplaySearch(user);
- String sortBy = this.getQueryVariable("sortBy");
- String sortOrder = this.getQueryVariable("sortOrder");
- if (sortBy != null){
- ds.setSortBy(sortBy);
- if(sortOrder != null)
- {
- ds.setSortOrder(sortOrder);
- }
- }
-
- MaterializedViewI mv=null;
-
- if(xss.getId()!=null && !xss.getId().equals("")){
- mv = MaterializedView.getViewBySearchID(xss.getId(), user,getQueryVariable(MaterializedView.CACHING_HANDLER,MaterializedView.DEFAULT_MATERIALIZED_VIEW_SERVICE_CODE));
- }
-
- if(mv!=null && (xss.getId().startsWith("@") || this.isQueryVariableTrue("refresh"))){
- mv.delete();
- mv=null;
- }
-
- LinkedHashMap<String,Map<String,String>> cp=SearchResource.setColumnProperties(ds,user,this);
-
- XFTTable table=null;
- if(mv!=null){
- if (mt.equals(SecureResource.APPLICATION_XLIST)){
- table=(XFTTable)ds.execute(new RESTHTMLPresenter(TurbineUtils.GetRelativePath(ServletCall.getRequest(this.getRequest())),this.getCurrentURI(),user,sortBy),user.getLogin());
- }else if(this.isQueryVariableTrue("guiStyle")){
- table=(XFTTable)ds.execute(new CSVPresenter(),user.getLogin());
- }else{
- table=mv.getData(null, null, null);
+ try {
+ DisplaySearch ds = xss.getDisplaySearch(user);
+ String sortBy = this.getQueryVariable("sortBy");
+ String sortOrder = this.getQueryVariable("sortOrder");
+ if (sortBy != null) {
+ ds.setSortBy(sortBy);
+ if (sortOrder != null) {
+ ds.setSortOrder(sortOrder);
}
- }else{
+ }
+
+ MaterializedViewI mv = null;
+
+ if (xss.getId() != null && !xss.getId().equals("")) {
+ mv = MaterializedView.getViewBySearchID(xss.getId(), user, getQueryVariable(MaterializedView.CACHING_HANDLER, MaterializedView.DEFAULT_MATERIALIZED_VIEW_SERVICE_CODE));
+ }
+
+ if (mv != null && (xss.getId().startsWith("@") || this.isQueryVariableTrue("refresh"))) {
+ mv.delete();
+ mv = null;
+ }
+
+ LinkedHashMap<String, Map<String, String>> cp = SearchResource.setColumnProperties(ds, user, this);
+
+ final XFTTable table;
+ if (mv != null) {
+ if (mt.equals(SecureResource.APPLICATION_XLIST)) {
+ table = (XFTTable) ds.execute(new RESTHTMLPresenter(TurbineUtils.GetRelativePath(ServletCall.getRequest(this.getRequest())), this.getCurrentURI(), user, sortBy), user.getLogin());
+ } else if (this.isQueryVariableTrue("guiStyle")) {
+ table = (XFTTable) ds.execute(new CSVPresenter(), user.getLogin());
+ } else {
+ table = mv.getData(null, null, null);
+ }
+ } else {
ds.setPagingOn(false);
- if (mt.equals(SecureResource.APPLICATION_XLIST)){
- table=(XFTTable)ds.execute(new RESTHTMLPresenter(TurbineUtils.GetRelativePath(ServletCall.getRequest(this.getRequest())),this.getCurrentURI(),user,sortBy),user.getLogin());
- }else if(this.isQueryVariableTrue("guiStyle")){
- table=(XFTTable)ds.execute(new CSVPresenter(),user.getLogin());
- }else{
- table=(XFTTable)ds.execute(null,user.getLogin());
+ if (mt.equals(SecureResource.APPLICATION_XLIST)) {
+ table = (XFTTable) ds.execute(new RESTHTMLPresenter(TurbineUtils.GetRelativePath(ServletCall.getRequest(this.getRequest())), this.getCurrentURI(), user, sortBy), user.getLogin());
+ } else if (this.isQueryVariableTrue("guiStyle")) {
+ table = (XFTTable) ds.execute(new CSVPresenter(), user.getLogin());
+ } else {
+ table = (XFTTable) ds.execute(null, user.getLogin());
}
}
- Hashtable<String,Object> tableParams=new Hashtable<String,Object>();
- tableParams.put("totalRecords", table.getNumRows());
-
- return this.representTable(table, mt, tableParams,cp);
- } catch (Exception e) {
- logger.error("",e);
- this.getResponse().setStatus(Status.SERVER_ERROR_INTERNAL);
- }
- }else{
- if (mt.equals(MediaType.TEXT_XML)){
- ItemXMLRepresentation rep= new ItemXMLRepresentation(xss.getItem(),MediaType.TEXT_XML);
- if(sID.startsWith("@") || loadedFromFile){
- rep.setAllowDBAccess(false);
- }
-
- return rep;
- }
- }
- }
-
- return null;
-
- }
-
- @Override
- public boolean allowDelete() {
- return true;
- }
-
- @Override
- public boolean allowPut() {
- return true;
- }
-
- @Override
- public void handlePut() {
- try {
- Reader sax=this.getRequest().getEntity().getReader();
-
- SAXReader reader = new SAXReader(user);
- XFTItem item = reader.parse(sax);
-
- if(!item.instanceOf("xdat:stored_search")){
- this.getResponse().setStatus(Status.CLIENT_ERROR_UNPROCESSABLE_ENTITY);
- return;
- }
- XdatStoredSearch search = new XdatStoredSearch(item);
-
- boolean isNew=false;
-
- if(search.getId()==null || !search.getId().equals(sID)){
- search.setId(sID);
- isNew=true;
- }else{
- XFTItem xss= search.getCurrentDBVersion(false);
- if(xss==null){
- isNew=true;
- }else if(this.isQueryVariableTrue("saveAs")){
- while(xss!=null){
- search.setId(search.getId()+"_1");
- xss= search.getCurrentDBVersion(false);
- }
- isNew=true;
- }
- }
- if (isNew && search.getTag() != null) {
- CriteriaCollection cc = new CriteriaCollection("AND");
- cc.addClause("xdat:stored_search/tag", search.getTag());
- cc.addClause("xdat:stored_search/brief-description", search.getBriefDescription());
- ItemCollection result = ItemSearch.GetItems(cc, user, false);
- if (result.size() > 0) {
- isNew = false;
- search.setId(result.getFirst().getStringProperty("ID"));
- }
- }
-
- if(!Permissions.canQuery(user, search.getRootElementName())){
- getResponse().setStatus(Status.CLIENT_ERROR_FORBIDDEN);
- return;
- }
-
- final boolean isPrimary = (search.getTag() != null && (search.getId().equals(search.getTag() + "_" + search.getRootElementName()))) ||
- (org.apache.commons.lang3.StringUtils.isNotBlank(search.getBriefDescription()) && search.getBriefDescription().equals(DisplayManager.GetInstance().getPluralDisplayNameForElement(search.getRootElementName())));
-
- if(isNew && isPrimary){
- if(!Permissions.can(user,"xnat:projectData/ID", search.getTag(), SecurityManager.DELETE)){
- isNew=false;
- }
- }
-
- if(this.isQueryVariableTrue("saveAs")){
- while(search.getAllowedGroups_groupid().size()>0){
- search.removeAllowedGroups_groupid(0);
- }
-
- while(search.getAllowedUser().size()>0){
- search.removeAllowedUser(0);
- }
- }
-
- boolean found=false;
- for(XdatStoredSearchAllowedUser au : search.getAllowedUser()){
- if(au.getLogin().equals(user.getLogin())){
- found=true;
- }
- }
-
- for(XdatStoredSearchGroupid ag : search.getAllowedGroups_groupid()){
- if(Groups.isMember(user,ag.getGroupid())){
- found=true;
- }
- }
-
- if(!found && !isNew){
- if(search.getTag()!=null && !search.getTag().equals("")){
- if(!Permissions.canEdit(user,"xnat:projectData/ID", search.getTag())){
- this.getResponse().setStatus(Status.CLIENT_ERROR_FORBIDDEN);
- return;
- }else{
- XdatStoredSearchAllowedUser au = new XdatStoredSearchAllowedUser((UserI)user);
- au.setLogin(user.getLogin());
- search.setAllowedUser(au);
- }
- }else{
- this.getResponse().setStatus(Status.CLIENT_ERROR_FORBIDDEN);
- return;
- }
- }
-
- if(isNew && !found){
- XdatStoredSearchAllowedUser au = new XdatStoredSearchAllowedUser((UserI)user);
- au.setLogin(user.getLogin());
- search.setAllowedUser(au);
- }
-
- try {
- SaveItemHelper.unauthorizedSave(search,user, false, true,this.newEventInstance(EventUtils.CATEGORY.SIDE_ADMIN, (isNew)?"Creating new stored search":"Modified existing stored search"));
- } catch (Exception e) {
- logger.error("",e);
- this.getResponse().setStatus(Status.SERVER_ERROR_INTERNAL);
- }
-
- } catch (IOException e) {
- logger.error("",e);
- this.getResponse().setStatus(Status.SERVER_ERROR_INTERNAL);
- } catch (SAXException e) {
- logger.error("",e);
- this.getResponse().setStatus(Status.CLIENT_ERROR_UNPROCESSABLE_ENTITY);
- } catch (ElementNotFoundException e) {
- logger.error("",e);
- this.getResponse().setStatus(Status.SERVER_ERROR_INTERNAL);
- } catch (Exception e) {
- logger.error("",e);
- this.getResponse().setStatus(Status.SERVER_ERROR_INTERNAL);
- }
- }
-
-
-
- @Override
- public void handleDelete() {
- if(sID!=null){
- try {
- XdatStoredSearch search = XdatStoredSearch.getXdatStoredSearchsById(sID, user, false);
-
- if(search!=null){
- XdatStoredSearchAllowedUser mine=null;
- XdatStoredSearchGroupid group=null;
-
- for(XdatStoredSearchAllowedUser au : search.getAllowedUser()){
- if(au.getLogin().equals(user.getLogin())){
- mine=au;
- break;
- }
- }
-
- for(XdatStoredSearchGroupid ag : search.getAllowedGroups_groupid()){
- if(Groups.isMember(user,ag.getGroupid())){
- group=ag;
- break;
- }
- }
-
- if(mine!=null){
- if(search.getAllowedUser().size()>1 || search.getAllowedGroups_groupid().size()>0){
- SaveItemHelper.authorizedDelete(mine.getItem(), user,this.newEventInstance(EventUtils.CATEGORY.SIDE_ADMIN,"Removed user from stored search"));
- }else{
- SaveItemHelper.authorizedDelete(search.getItem(), user,this.newEventInstance(EventUtils.CATEGORY.SIDE_ADMIN,"Removed stored search"));
- }
- }else if(group!=null){
- if(search.getAllowedUser().size()>0 || search.getAllowedGroups_groupid().size()>1){
- SaveItemHelper.authorizedDelete(group.getItem(), user,this.newEventInstance(EventUtils.CATEGORY.SIDE_ADMIN,"Removed group from stored search"));
- }else{
- SaveItemHelper.authorizedDelete(search.getItem(), user,this.newEventInstance(EventUtils.CATEGORY.SIDE_ADMIN,"Removed stored search"));
- }
- }else if(Roles.isSiteAdmin(user)){
- SaveItemHelper.authorizedDelete(search.getItem(), user,this.newEventInstance(EventUtils.CATEGORY.SIDE_ADMIN,"Removed stored search"));
- }else{
- this.getResponse().setStatus(Status.CLIENT_ERROR_FORBIDDEN);
- return;
- }
- }
- } catch (IOException e) {
- logger.error("",e);
- this.getResponse().setStatus(Status.SERVER_ERROR_INTERNAL);
- } catch (SAXException e) {
- logger.error("",e);
- this.getResponse().setStatus(Status.CLIENT_ERROR_UNPROCESSABLE_ENTITY);
- } catch (ElementNotFoundException e) {
- logger.error("",e);
- this.getResponse().setStatus(Status.SERVER_ERROR_INTERNAL);
- } catch (Exception e) {
- logger.error("",e);
- this.getResponse().setStatus(Status.SERVER_ERROR_INTERNAL);
- }
- }
- }
+ Hashtable<String, Object> tableParams = new Hashtable<>();
+ tableParams.put("totalRecords", table.getNumRows());
+
+ return this.representTable(table, mt, tableParams, cp);
+ } catch (Exception e) {
+ logger.error("", e);
+ this.getResponse().setStatus(Status.SERVER_ERROR_INTERNAL);
+ }
+ } else {
+ if (mt.equals(MediaType.TEXT_XML)) {
+ ItemXMLRepresentation rep = new ItemXMLRepresentation(xss.getItem(), MediaType.TEXT_XML);
+ if (sID.startsWith("@") || loadedFromFile) {
+ rep.setAllowDBAccess(false);
+ }
+
+ return rep;
+ }
+ }
+ }
+
+ return null;
+
+ }
+
+ @Override
+ public boolean allowDelete() {
+ return true;
+ }
+
+ @Override
+ public boolean allowPut() {
+ return true;
+ }
+
+ @Override
+ public void handlePut() {
+ try {
+ Reader sax = this.getRequest().getEntity().getReader();
+
+ SAXReader reader = new SAXReader(user);
+ XFTItem item = reader.parse(sax);
+
+ if (!item.instanceOf("xdat:stored_search")) {
+ this.getResponse().setStatus(Status.CLIENT_ERROR_UNPROCESSABLE_ENTITY);
+ return;
+ }
+ XdatStoredSearch search = new XdatStoredSearch(item);
+
+ boolean isNew = false;
+
+ if (search.getId() == null || !search.getId().equals(sID)) {
+ search.setId(sID);
+ isNew = true;
+ } else {
+ XFTItem xss = search.getCurrentDBVersion(false);
+ if (xss == null) {
+ isNew = true;
+ } else if (this.isQueryVariableTrue("saveAs")) {
+ while (xss != null) {
+ search.setId(search.getId() + "_1");
+ xss = search.getCurrentDBVersion(false);
+ }
+ isNew = true;
+ }
+ }
+ if (isNew && search.getTag() != null) {
+ CriteriaCollection cc = new CriteriaCollection("AND");
+ cc.addClause("xdat:stored_search/tag", search.getTag());
+ cc.addClause("xdat:stored_search/brief-description", search.getBriefDescription());
+ ItemCollection result = ItemSearch.GetItems(cc, user, false);
+ if (result.size() > 0) {
+ isNew = false;
+ search.setId(result.getFirst().getStringProperty("ID"));
+ }
+ }
+
+ if (!Permissions.canQuery(user, search.getRootElementName())) {
+ getResponse().setStatus(Status.CLIENT_ERROR_FORBIDDEN);
+ return;
+ }
+
+ final boolean isPrimary = (search.getTag() != null && (search.getId().equals(search.getTag() + "_" + search.getRootElementName()))) ||
+ (org.apache.commons.lang3.StringUtils.isNotBlank(search.getBriefDescription()) && search.getBriefDescription().equals(DisplayManager.GetInstance().getPluralDisplayNameForElement(search.getRootElementName())));
+
+ if (isNew && isPrimary) {
+ if (!Permissions.can(user, "xnat:projectData/ID", search.getTag(), SecurityManager.DELETE)) {
+ isNew = false;
+ }
+ }
+
+ if (this.isQueryVariableTrue("saveAs")) {
+ while (search.getAllowedGroups_groupid().size() > 0) {
+ search.removeAllowedGroups_groupid(0);
+ }
+
+ while (search.getAllowedUser().size() > 0) {
+ search.removeAllowedUser(0);
+ }
+ }
+
+ boolean found = false;
+ for (XdatStoredSearchAllowedUser au : search.getAllowedUser()) {
+ if (au.getLogin().equals(user.getLogin())) {
+ found = true;
+ }
+ }
+
+ for (XdatStoredSearchGroupid ag : search.getAllowedGroups_groupid()) {
+ if (Groups.isMember(user, ag.getGroupid())) {
+ found = true;
+ }
+ }
+
+ if (!found && !isNew) {
+ if (search.getTag() != null && !search.getTag().equals("")) {
+ if (!Permissions.canEdit(user, "xnat:projectData/ID", search.getTag())) {
+ this.getResponse().setStatus(Status.CLIENT_ERROR_FORBIDDEN);
+ return;
+ } else {
+ XdatStoredSearchAllowedUser au = new XdatStoredSearchAllowedUser(user);
+ au.setLogin(user.getLogin());
+ search.setAllowedUser(au);
+ }
+ } else {
+ this.getResponse().setStatus(Status.CLIENT_ERROR_FORBIDDEN);
+ return;
+ }
+ }
+
+ if (isNew && !found) {
+ XdatStoredSearchAllowedUser au = new XdatStoredSearchAllowedUser(user);
+ au.setLogin(user.getLogin());
+ search.setAllowedUser(au);
+ }
+
+ try {
+ SaveItemHelper.unauthorizedSave(search, user, false, true, this.newEventInstance(EventUtils.CATEGORY.SIDE_ADMIN, (isNew) ? "Creating new stored search" : "Modified existing stored search"));
+ } catch (Exception e) {
+ logger.error("", e);
+ this.getResponse().setStatus(Status.SERVER_ERROR_INTERNAL);
+ }
+
+ } catch (SAXException e) {
+ logger.error("", e);
+ this.getResponse().setStatus(Status.CLIENT_ERROR_UNPROCESSABLE_ENTITY);
+ } catch (Exception e) {
+ logger.error("", e);
+ this.getResponse().setStatus(Status.SERVER_ERROR_INTERNAL);
+ }
+ }
+
+ @Override
+ public void handleDelete() {
+ if (sID != null) {
+ try {
+ XdatStoredSearch search = XdatStoredSearch.getXdatStoredSearchsById(sID, user, false);
+
+ if (search != null) {
+ XdatStoredSearchAllowedUser mine = null;
+ XdatStoredSearchGroupid group = null;
+
+ for (XdatStoredSearchAllowedUser au : search.getAllowedUser()) {
+ if (au.getLogin().equals(user.getLogin())) {
+ mine = au;
+ break;
+ }
+ }
+
+ for (XdatStoredSearchGroupid ag : search.getAllowedGroups_groupid()) {
+ if (Groups.isMember(user, ag.getGroupid())) {
+ group = ag;
+ break;
+ }
+ }
+
+ if (mine != null) {
+ if (search.getAllowedUser().size() > 1 || search.getAllowedGroups_groupid().size() > 0) {
+ SaveItemHelper.authorizedDelete(mine.getItem(), user, this.newEventInstance(EventUtils.CATEGORY.SIDE_ADMIN, "Removed user from stored search"));
+ } else {
+ SaveItemHelper.authorizedDelete(search.getItem(), user, this.newEventInstance(EventUtils.CATEGORY.SIDE_ADMIN, "Removed stored search"));
+ }
+ } else if (group != null) {
+ if (search.getAllowedUser().size() > 0 || search.getAllowedGroups_groupid().size() > 1) {
+ SaveItemHelper.authorizedDelete(group.getItem(), user, this.newEventInstance(EventUtils.CATEGORY.SIDE_ADMIN, "Removed group from stored search"));
+ } else {
+ SaveItemHelper.authorizedDelete(search.getItem(), user, this.newEventInstance(EventUtils.CATEGORY.SIDE_ADMIN, "Removed stored search"));
+ }
+ } else if (Roles.isSiteAdmin(user)) {
+ SaveItemHelper.authorizedDelete(search.getItem(), user, this.newEventInstance(EventUtils.CATEGORY.SIDE_ADMIN, "Removed stored search"));
+ } else {
+ this.getResponse().setStatus(Status.CLIENT_ERROR_FORBIDDEN);
+ }
+ }
+ } catch (SAXException e) {
+ logger.error("", e);
+ this.getResponse().setStatus(Status.CLIENT_ERROR_UNPROCESSABLE_ENTITY);
+ } catch (Exception e) {
+ logger.error("", e);
+ this.getResponse().setStatus(Status.SERVER_ERROR_INTERNAL);
+ }
+ }
+ }
}
diff --git a/src/main/java/org/nrg/xnat/restlet/resources/search/SearchResource.java b/src/main/java/org/nrg/xnat/restlet/resources/search/SearchResource.java
index ec3d1116b0fdbb28be085d9666766c19b6ba7d08..722a41cc4a95d8ee308d6aa571dc837865db48b7 100644
--- a/src/main/java/org/nrg/xnat/restlet/resources/search/SearchResource.java
+++ b/src/main/java/org/nrg/xnat/restlet/resources/search/SearchResource.java
@@ -10,25 +10,15 @@
*/
package org.nrg.xnat.restlet.resources.search;
-import java.io.IOException;
-import java.io.Reader;
-import java.sql.SQLException;
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-
+import com.noelios.restlet.ext.servlet.ServletCall;
import org.apache.commons.fileupload.FileItem;
import org.apache.commons.fileupload.FileUploadException;
import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
import org.nrg.xdat.collections.DisplayFieldCollection.DisplayFieldNotFoundException;
import org.nrg.xdat.display.DisplayFieldReferenceI;
import org.nrg.xdat.display.HTMLLink;
import org.nrg.xdat.display.HTMLLinkProperty;
import org.nrg.xdat.display.SQLQueryField;
-import org.nrg.xdat.exceptions.IllegalAccessException;
import org.nrg.xdat.om.XdatCriteriaSet;
import org.nrg.xdat.search.DisplaySearch;
import org.nrg.xdat.security.XdatStoredSearch;
@@ -39,9 +29,7 @@ import org.nrg.xft.XFTItem;
import org.nrg.xft.XFTTable;
import org.nrg.xft.db.MaterializedView;
import org.nrg.xft.db.MaterializedViewI;
-import org.nrg.xft.exception.DBPoolException;
import org.nrg.xft.exception.ElementNotFoundException;
-import org.nrg.xft.exception.FieldNotFoundException;
import org.nrg.xft.exception.XFTInitException;
import org.nrg.xft.schema.Wrappers.XMLWrapper.SAXReader;
import org.nrg.xft.security.UserI;
@@ -55,450 +43,438 @@ import org.restlet.data.Response;
import org.restlet.data.Status;
import org.restlet.resource.Representation;
import org.restlet.resource.Variant;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.xml.sax.SAXException;
import org.xml.sax.SAXParseException;
-import com.noelios.restlet.ext.servlet.ServletCall;
+import java.io.Reader;
+import java.util.*;
public class SearchResource extends SecureResource {
- static org.apache.log4j.Logger logger = Logger.getLogger(SearchResource.class);
- XFTTable table= null;
- Long rows=null;
- String tableName=null;
-
- String rootElementName=null;
-
- Hashtable<String,Object> tableParams=new Hashtable<String,Object>();
- Map<String,Map<String,String>> cp=new LinkedHashMap<String,Map<String,String>>();
-
- public SearchResource(Context context, Request request, Response response) {
- super(context, request, response);
- this.getVariants().add(new Variant(MediaType.APPLICATION_JSON));
- this.getVariants().add(new Variant(MediaType.TEXT_HTML));
- this.getVariants().add(new Variant(MediaType.TEXT_XML));
- }
-
- @Override
- public boolean allowGet() {
- return false;
- }
-
- @Override
- public boolean allowPost() {
- return true;
- }
-
- @Override
- public void handlePost() {
- try {
- String cacheRequest = this.getQueryVariable("cache");
- boolean cache = false;
- if (cacheRequest!=null && cacheRequest.equalsIgnoreCase("true")){
- cache =true;
- }
-
- XFTItem item=null;
- Representation entity = this.getRequest().getEntity();
- if(entity!=null && entity.getMediaType()!=null && entity.getMediaType().getName().equals(MediaType.MULTIPART_FORM_DATA.getName())){
- try {
- org.apache.commons.fileupload.DefaultFileItemFactory factory = new org.apache.commons.fileupload.DefaultFileItemFactory();
- org.restlet.ext.fileupload.RestletFileUpload upload = new org.restlet.ext.fileupload.RestletFileUpload(factory);
-
- List<FileItem> items = upload.parseRequest(this.getRequest());
+ private static final Logger logger = LoggerFactory.getLogger(SearchResource.class);
+ private XFTTable table = null;
+ private Long rows = null;
+ private String tableName = null;
+
+ private String rootElementName = null;
+
+ private final Hashtable<String, Object> tableParams = new Hashtable<>();
+ private final Map<String, Map<String, String>> cp = new LinkedHashMap<>();
+
+ public SearchResource(Context context, Request request, Response response) {
+ super(context, request, response);
+ getVariants().add(new Variant(MediaType.APPLICATION_JSON));
+ getVariants().add(new Variant(MediaType.TEXT_HTML));
+ getVariants().add(new Variant(MediaType.TEXT_XML));
+ }
+
+ @Override
+ public boolean allowGet() {
+ return false;
+ }
+
+ @Override
+ public boolean allowPost() {
+ return true;
+ }
+
+ @Override
+ public void handlePost() {
+ try {
+ String cacheRequest = getQueryVariable("cache");
+ boolean cache = false;
+ if (cacheRequest != null && cacheRequest.equalsIgnoreCase("true")) {
+ cache = true;
+ }
+
+ XFTItem item = null;
+ Representation entity = getRequest().getEntity();
+ if (entity != null && entity.getMediaType() != null && entity.getMediaType().getName().equals(MediaType.MULTIPART_FORM_DATA.getName())) {
+ try {
+ @SuppressWarnings("deprecation") org.apache.commons.fileupload.DefaultFileItemFactory factory = new org.apache.commons.fileupload.DefaultFileItemFactory();
+ org.restlet.ext.fileupload.RestletFileUpload upload = new org.restlet.ext.fileupload.RestletFileUpload(factory);
+
+ List<FileItem> items = upload.parseRequest(getRequest());
for (final FileItem fi : items) {
- if(fi.getName().endsWith(".xml")){
- SAXReader reader = new SAXReader(user);
- try {
- item = reader.parse(fi.getInputStream());
-
- if(!reader.assertValid()){
- throw reader.getErrors().get(0);
- }
- if (XFT.VERBOSE)
- System.out.println("Loaded XML Item:" + item.getProperName());
-
- if(item!=null){
- completeDocument=true;
- }
- } catch (SAXParseException e) {
- logger.error("",e);
- this.getResponse().setStatus(Status.CLIENT_ERROR_UNPROCESSABLE_ENTITY,e.getMessage());
- throw e;
- } catch (IOException e) {
- logger.error("",e);
- this.getResponse().setStatus(Status.SERVER_ERROR_INTERNAL);
- } catch (Exception e) {
- logger.error("",e);
- this.getResponse().setStatus(Status.SERVER_ERROR_INTERNAL);
- }
- }
- }
- } catch (FileUploadException e) {
+ if (fi.getName().endsWith(".xml")) {
+ SAXReader reader = new SAXReader(user);
+ try {
+ item = reader.parse(fi.getInputStream());
+
+ if (!reader.assertValid()) {
+ throw reader.getErrors().get(0);
+ }
+ if (XFT.VERBOSE) {
+ System.out.println("Loaded XML Item:" + item.getProperName());
+ }
+
+ if (item != null) {
+ completeDocument = true;
+ }
+ } catch (SAXParseException e) {
+ logger.error("", e);
+ getResponse().setStatus(Status.CLIENT_ERROR_UNPROCESSABLE_ENTITY, e.getMessage());
+ throw e;
+ } catch (Exception e) {
+ logger.error("", e);
+ getResponse().setStatus(Status.SERVER_ERROR_INTERNAL);
+ }
+ }
+ }
+ } catch (FileUploadException e) {
logger.error("", e);
- this.getResponse().setStatus(Status.SERVER_ERROR_INTERNAL);
- }
- }else{
- if(entity!=null){
- Reader sax=entity.getReader();
- try {
-
- SAXReader reader = new SAXReader(user);
- item = reader.parse(sax);
-
- if(!reader.assertValid()){
- throw reader.getErrors().get(0);
- }
- if (XFT.VERBOSE)
- System.out.println("Loaded XML Item:" + item.getProperName());
-
- if(item!=null){
- completeDocument=true;
- }
-
- } catch (SAXParseException e) {
- logger.error("",e);
- this.getResponse().setStatus(Status.CLIENT_ERROR_UNPROCESSABLE_ENTITY,e.getMessage());
- throw e;
- } catch (IOException e) {
- logger.error("",e);
- this.getResponse().setStatus(Status.SERVER_ERROR_INTERNAL);
- } catch (Exception e) {
- logger.error("",e);
- this.getResponse().setStatus(Status.SERVER_ERROR_INTERNAL);
- }
- }
- }
-
- if(item == null || !item.instanceOf("xdat:stored_search")){
- this.getResponse().setStatus(Status.CLIENT_ERROR_UNPROCESSABLE_ENTITY);
- return;
- }
-
- XdatStoredSearch search = new XdatStoredSearch(item);
-
- // If a user has been manually added to a secret search, it is allowed (the criteria cannot be modified,
- // which is checked in the canQueryByAllowedUser() method)
- boolean allowed = canQueryByAllowedUser(search);
-
- // If the user is not explicitly allowed to perform a search...
- if(!allowed) {
- // See if the user can *implicitly* perform the search.
- if (!Permissions.canQuery(user,search.getRootElementName())) {
- getResponse().setStatus(Status.CLIENT_ERROR_FORBIDDEN);
- return;
+ getResponse().setStatus(Status.SERVER_ERROR_INTERNAL);
+ }
+ } else {
+ if (entity != null) {
+ Reader sax = entity.getReader();
+ try {
+
+ SAXReader reader = new SAXReader(user);
+ item = reader.parse(sax);
+
+ if (!reader.assertValid()) {
+ throw reader.getErrors().get(0);
+ }
+ if (XFT.VERBOSE) {
+ System.out.println("Loaded XML Item:" + item.getProperName());
+ }
+
+ if (item != null) {
+ completeDocument = true;
+ }
+
+ } catch (SAXParseException e) {
+ logger.error("", e);
+ getResponse().setStatus(Status.CLIENT_ERROR_UNPROCESSABLE_ENTITY, e.getMessage());
+ throw e;
+ } catch (Exception e) {
+ logger.error("", e);
+ getResponse().setStatus(Status.SERVER_ERROR_INTERNAL);
}
- }
-
- rootElementName=search.getRootElementName();
-
- DisplaySearch ds=search.getDisplaySearch(user);
-
- String sortBy = this.getQueryVariable("sortBy");
- String sortOrder = this.getQueryVariable("sortOrder");
- if (sortBy != null){
- ds.setSortBy(sortBy);
+ }
+ }
+
+ if (item == null || !item.instanceOf("xdat:stored_search")) {
+ getResponse().setStatus(Status.CLIENT_ERROR_UNPROCESSABLE_ENTITY);
+ return;
+ }
+
+ XdatStoredSearch search = new XdatStoredSearch(item);
+
+ // If a user has been manually added to a secret search, it is allowed (the criteria cannot be modified,
+ // which is checked in the canQueryByAllowedUser() method)
+ boolean allowed = canQueryByAllowedUser(search);
+
+ // If the user is not explicitly allowed to perform a search...
+ if (!allowed) {
+ // See if the user can *implicitly* perform the search.
+ if (!Permissions.canQuery(user, search.getRootElementName())) {
+ getResponse().setStatus(Status.CLIENT_ERROR_FORBIDDEN);
+ return;
+ }
+ }
+
+ rootElementName = search.getRootElementName();
+
+ DisplaySearch ds = search.getDisplaySearch(user);
+
+ String sortBy = getQueryVariable("sortBy");
+ String sortOrder = getQueryVariable("sortOrder");
+ if (sortBy != null) {
+ ds.setSortBy(sortBy);
if (sortOrder != null) {
- ds.setSortOrder(sortOrder);
- }
- }
-
- MaterializedViewI mv=null;
-
- if(search.getId()!=null && !search.getId().equals("")){
- mv = MaterializedView.getViewBySearchID(search.getId(), user,getQueryVariable(MaterializedView.CACHING_HANDLER,MaterializedView.DEFAULT_MATERIALIZED_VIEW_SERVICE_CODE));
- }
-
- if(mv!=null && (search.getId().startsWith("@") || this.isQueryVariableTrue("refresh"))){
- mv.delete();
- mv=null;
- }
-
- cp=setColumnProperties(ds,user,this);
-
- if (!cache){
- if(mv!=null){
- table=mv.getData(null, null, null);
- }else{
- ds.setPagingOn(false);
- MediaType mt = this.getRequestedMediaType();
- if (mt!=null && mt.equals(SecureResource.APPLICATION_XLIST)){
- table=(XFTTable)ds.execute(new RESTHTMLPresenter(TurbineUtils.GetRelativePath(ServletCall.getRequest(this.getRequest())),null,user,sortBy),user.getLogin());
- }else{
- table=(XFTTable)ds.execute(null,user.getLogin());
- }
- //table=(XFTTable)ds.execute(null,user.getLogin());
-
- }
- }else{
- if(mv!=null){
- if(search.getId()!=null && !search.getId().equals("") && mv.getLast_access()!=null)
- tableParams.put("last_access", mv.getLast_access());
- table=mv.getData(null, null, 0);
- tableName=mv.getTable_name();
- rows=mv.getSize();
- }else{
- ds.setPagingOn(false);
- ds.addKeyColumn(true);
-
- String query = ds.getSQLQuery(null);
- query = StringUtils.replace(query, "'", "*'*");
- query = StringUtils.replace(query,"*'*","''");
-
- String codeToUse = getQueryVariable(MaterializedView.CACHING_HANDLER,MaterializedView.DEFAULT_MATERIALIZED_VIEW_SERVICE_CODE);
- mv = MaterializedView.createView(user,codeToUse);
- if(search.getId()!=null && !search.getId().equals(""))
- mv.setSearch_id(search.getId());
- mv.setSearch_sql(query);
- mv.setSearch_xml(item.writeToFlatString(0));
-
- MaterializedView.save(mv,codeToUse);
-
- if(search.getId()!=null && !search.getId().equals("") && mv.getLast_access()!=null)
- tableParams.put("last_access", mv.getLast_access());
-
- tableName=mv.getTable_name();
-
- int limit=0;
- if(this.getQueryVariable("limit")!=null)
- limit=Integer.valueOf(this.getQueryVariable("limit"));
- table=mv.getData(null, null, limit);
- rows=mv.getSize();
- }
- }
-
- this.returnDefaultRepresentation();
- } catch (IOException e) {
- logger.error("Failed POST",e);
- this.getResponse().setStatus(Status.SERVER_ERROR_INTERNAL);
- } catch (SAXException e) {
- logger.error("Failed POST",e);
- this.getResponse().setStatus(Status.CLIENT_ERROR_UNPROCESSABLE_ENTITY);
- } catch (ElementNotFoundException e) {
- logger.error("Failed POST",e);
- this.getResponse().setStatus(Status.SERVER_ERROR_INTERNAL);
- } catch (XFTInitException e) {
- logger.error("Failed POST",e);
- this.getResponse().setStatus(Status.SERVER_ERROR_INTERNAL);
- } catch (FieldNotFoundException e) {
- logger.error("Failed POST",e);
- this.getResponse().setStatus(Status.SERVER_ERROR_INTERNAL);
- } catch (DBPoolException e) {
- logger.error("Failed POST",e);
- this.getResponse().setStatus(Status.SERVER_ERROR_INTERNAL);
- } catch (SQLException e) {
- logger.error("Failed POST",e);
- this.getResponse().setStatus(Status.SERVER_ERROR_INTERNAL);
- } catch (IllegalAccessException e) {
- logger.error("Failed POST",e);
- this.getResponse().setStatus(Status.SERVER_ERROR_INTERNAL);
- } catch (Exception e) {
- logger.error("Failed POST",e);
- this.getResponse().setStatus(Status.SERVER_ERROR_INTERNAL);
- }
- }
+ ds.setSortOrder(sortOrder);
+ }
+ }
+
+ MaterializedViewI mv = null;
+
+ if (search.getId() != null && !search.getId().equals("")) {
+ mv = MaterializedView.getViewBySearchID(search.getId(), user, getQueryVariable(MaterializedView.CACHING_HANDLER, MaterializedView.DEFAULT_MATERIALIZED_VIEW_SERVICE_CODE));
+ }
+
+ if (mv != null && (search.getId().startsWith("@") || isQueryVariableTrue("refresh"))) {
+ mv.delete();
+ mv = null;
+ }
+
+ cp.clear();
+ cp.putAll(setColumnProperties(ds, user, this));
+
+ if (!cache) {
+ if (mv != null) {
+ table = mv.getData(null, null, null);
+ } else {
+ ds.setPagingOn(false);
+ MediaType mt = getRequestedMediaType();
+ if (mt != null && mt.equals(SecureResource.APPLICATION_XLIST)) {
+ table = (XFTTable) ds.execute(new RESTHTMLPresenter(TurbineUtils.GetRelativePath(ServletCall.getRequest(getRequest())), null, user, sortBy), user.getLogin());
+ } else {
+ table = (XFTTable) ds.execute(null, user.getLogin());
+ }
+ //table=(XFTTable)ds.execute(null,user.getLogin());
+
+ }
+ } else {
+ if (mv != null) {
+ if (search.getId() != null && !search.getId().equals("") && mv.getLast_access() != null) {
+ tableParams.put("last_access", mv.getLast_access());
+ }
+ table = mv.getData(null, null, 0);
+ tableName = mv.getTable_name();
+ rows = mv.getSize();
+ } else {
+ ds.setPagingOn(false);
+ ds.addKeyColumn(true);
+
+ String query = ds.getSQLQuery(null);
+ query = StringUtils.replace(query, "'", "*'*");
+ query = StringUtils.replace(query, "*'*", "''");
+
+ String codeToUse = getQueryVariable(MaterializedView.CACHING_HANDLER, MaterializedView.DEFAULT_MATERIALIZED_VIEW_SERVICE_CODE);
+ mv = MaterializedView.createView(user, codeToUse);
+ if (search.getId() != null && !search.getId().equals("")) {
+ mv.setSearch_id(search.getId());
+ }
+ mv.setSearch_sql(query);
+ mv.setSearch_xml(item.writeToFlatString(0));
+
+ MaterializedView.save(mv, codeToUse);
+
+ if (search.getId() != null && !search.getId().equals("") && mv.getLast_access() != null) {
+ tableParams.put("last_access", mv.getLast_access());
+ }
+
+ tableName = mv.getTable_name();
+
+ int limit = 0;
+ if (getQueryVariable("limit") != null) {
+ limit = Integer.valueOf(getQueryVariable("limit"));
+ }
+ table = mv.getData(null, null, limit);
+ rows = mv.getSize();
+ }
+ }
+
+ returnDefaultRepresentation();
+ } catch (SAXException e) {
+ logger.error("Failed POST", e);
+ getResponse().setStatus(Status.CLIENT_ERROR_UNPROCESSABLE_ENTITY);
+ } catch (Exception e) {
+ logger.error("Failed POST", e);
+ getResponse().setStatus(Status.SERVER_ERROR_INTERNAL);
+ }
+ }
@Override
- public Representation represent(Variant variant) {
- if(tableName!=null){
- tableParams.put("ID", tableName);
- }
-
- if(rows!=null){
- tableParams.put("totalRecords", rows);
- }else{
- tableParams.put("totalRecords", table.getNumRows());
- }
-
- if(rootElementName!=null){
- tableParams.put("rootElementName", rootElementName);
- }
-
- MediaType mt = overrideVariant(variant);
-
- return this.representTable(table, mt, tableParams,cp);
- }
-
- public static LinkedHashMap<String,Map<String,String>> setColumnProperties(DisplaySearch search,UserI user, SecureResource sr){
- LinkedHashMap<String,Map<String,String>> cp=new LinkedHashMap<String,Map<String,String>>();
- try {
- List<DisplayFieldReferenceI> fields = search.getAllFields("");
-
- //int fieldCount = visibleFields.size() + search.getInClauses().size();
+ public Representation represent(Variant variant) {
+ if (tableName != null) {
+ tableParams.put("ID", tableName);
+ }
+
+ if (rows != null) {
+ tableParams.put("totalRecords", rows);
+ } else {
+ tableParams.put("totalRecords", table.getNumRows());
+ }
+
+ if (rootElementName != null) {
+ tableParams.put("rootElementName", rootElementName);
+ }
+
+ MediaType mt = overrideVariant(variant);
+
+ return representTable(table, mt, tableParams, cp);
+ }
+
+ @SuppressWarnings("ConstantConditions")
+ public static LinkedHashMap<String, Map<String, String>> setColumnProperties(DisplaySearch search, UserI user, SecureResource sr) {
+ LinkedHashMap<String, Map<String, String>> cp = new LinkedHashMap<>();
+ try {
+ List<DisplayFieldReferenceI> fields = search.getAllFields("");
+
+ //int fieldCount = visibleFields.size() + search.getInClauses().size();
if (search.getInClauses().size() > 0) {
for (int i = 0; i < search.getInClauses().size(); i++) {
- cp.put("search_field"+i,new Hashtable<String,String>());
- cp.get("search_field"+i).put("header", "");
- }
- }
+ cp.put("search_field" + i, new Hashtable<String, String>());
+ cp.get("search_field" + i).put("header", "");
+ }
+ }
- //POPULATE HEADERS
+ //POPULATE HEADERS
for (DisplayFieldReferenceI dfr : fields) {
- try {
+ try {
String id;
- if(dfr.getValue()!=null && !dfr.getValue().equals("")){
- if(dfr.getValue().equals("{XDAT_USER_ID}")){
- dfr.setValue(user.getID());
- }
- }
+ if (dfr.getValue() != null && !dfr.getValue().equals("")) {
+ if (dfr.getValue().equals("{XDAT_USER_ID}")) {
+ dfr.setValue(user.getID());
+ }
+ }
if (dfr.getElementName().equalsIgnoreCase(search.getRootElement().getFullXMLName())) {
- id = dfr.getRowID().toLowerCase();
- }else{
- id = dfr.getElementSQLName().toLowerCase() + "_" + dfr.getRowID().toLowerCase();
- }
- cp.put(id,new Hashtable<String,String>());
- cp.get(id).put("element_name", dfr.getElementName());
- try {
- String temp_id=dfr.getDisplayField().getId();
- if(dfr.getValue()!=null)
- temp_id+="="+dfr.getValue();
- cp.get(id).put("id", temp_id);
- } catch (DisplayFieldNotFoundException e2) {
- logger.error("",e2);
- }
- cp.get(id).put("xPATH", dfr.getElementName() + "." + dfr.getSortBy());
-
+ id = dfr.getRowID().toLowerCase();
+ } else {
+ id = dfr.getElementSQLName().toLowerCase() + "_" + dfr.getRowID().toLowerCase();
+ }
+ cp.put(id, new Hashtable<String, String>());
+ cp.get(id).put("element_name", dfr.getElementName());
+ try {
+ String temp_id = dfr.getDisplayField().getId();
+ if (dfr.getValue() != null) {
+ temp_id += "=" + dfr.getValue();
+ }
+ cp.get(id).put("id", temp_id);
+ } catch (DisplayFieldNotFoundException e2) {
+ logger.error("", e2);
+ }
+ cp.get(id).put("xPATH", dfr.getElementName() + "." + dfr.getSortBy());
+
if (dfr.getHeader().equalsIgnoreCase("")) {
- cp.get(id).put("header", " ");
- }else{
- cp.get(id).put("header", dfr.getHeader());
- }
-
- String t=dfr.getType();
- if(t==null){
- try {
- if(dfr.getDisplayField()!=null){
- t=dfr.getDisplayField().getDataType();
- }
- } catch (DisplayFieldNotFoundException e) {
- logger.error("",e);
- }
- }
- if(t!=null){
- cp.get(id).put("type", t);
- }
-
- try {
- if(!dfr.isVisible()){
- cp.get(id).put("visible","false");
- }
- } catch (DisplayFieldNotFoundException e1) {
- logger.error("",e1);
- }
+ cp.get(id).put("header", " ");
+ } else {
+ cp.get(id).put("header", dfr.getHeader());
+ }
+
+ String t = dfr.getType();
+ if (t == null) {
+ try {
+ if (dfr.getDisplayField() != null) {
+ t = dfr.getDisplayField().getDataType();
+ }
+ } catch (DisplayFieldNotFoundException e) {
+ logger.error("", e);
+ }
+ }
+ if (t != null) {
+ cp.get(id).put("type", t);
+ }
+
+ try {
+ if (!dfr.isVisible()) {
+ cp.get(id).put("visible", "false");
+ }
+ } catch (DisplayFieldNotFoundException e1) {
+ logger.error("", e1);
+ }
if (dfr.getHTMLLink() != null && sr.getQueryVariable("format") != null && sr.getQueryVariable("format").equalsIgnoreCase("json")) {
- cp.get(id).put("clickable", "true");
- HTMLLink link = dfr.getHTMLLink();
-
+ cp.get(id).put("clickable", "true");
+ HTMLLink link = dfr.getHTMLLink();
+
StringBuilder linkProps = new StringBuilder("[");
- int propCounter=0;
- for(HTMLLinkProperty prop: link.getProperties()){
- if(propCounter++>0)linkProps.append(",");
- linkProps.append("{");
- linkProps.append("\"name\":\"");
- linkProps.append(prop.getName()).append("\"");
- linkProps.append(",\"value\":\"");
- String v =prop.getValue();
- v = StringUtils.replace(v,"@WEBAPP",TurbineUtils.GetRelativePath(ServletCall.getRequest(sr.getRequest())) + "/");
-
- linkProps.append(v).append("\"");
+ int propCounter = 0;
+ for (HTMLLinkProperty prop : link.getProperties()) {
+ if (propCounter++ > 0) {
+ linkProps.append(",");
+ }
+ linkProps.append("{");
+ linkProps.append("\"name\":\"");
+ linkProps.append(prop.getName()).append("\"");
+ linkProps.append(",\"value\":\"");
+ String v = prop.getValue();
+ v = StringUtils.replace(v, "@WEBAPP", TurbineUtils.GetRelativePath(ServletCall.getRequest(sr.getRequest())) + "/");
+
+ linkProps.append(v).append("\"");
if (prop.getInsertedValues().size() > 0) {
- linkProps.append(",\"inserts\":[");
- int valueCounter=0;
+ linkProps.append(",\"inserts\":[");
+ int valueCounter = 0;
for (Map.Entry<String, String> entry : prop.getInsertedValues().entrySet()) {
- if(valueCounter++>0)linkProps.append(",");
- linkProps.append("{\"name\":\"");
- linkProps.append(entry.getKey()).append("\"");
- linkProps.append(",\"value\":\"");
-
- String insert_value = entry.getValue();
- if (insert_value.startsWith("@WHERE")){
+ if (valueCounter++ > 0) {
+ linkProps.append(",");
+ }
+ linkProps.append("{\"name\":\"");
+ linkProps.append(entry.getKey()).append("\"");
+ linkProps.append(",\"value\":\"");
+
+ String insert_value = entry.getValue();
+ if (insert_value.startsWith("@WHERE")) {
try {
- if (dfr.getDisplayField() instanceof SQLQueryField){
- Object insertValue = dfr.getValue();
+ if (dfr.getDisplayField() instanceof SQLQueryField) {
+ Object insertValue = dfr.getValue();
if (insertValue == null) {
- insertValue = "NULL";
- }else{
+ insertValue = "NULL";
+ } else {
if (insertValue.toString().contains(",")) {
- insert_value = insert_value.substring(6);
- try {
- Integer i = Integer.parseInt(insert_value);
- ArrayList<String> al = XftStringUtils.CommaDelimitedStringToArrayList(insertValue.toString());
- insertValue =al.get(i);
- } catch (Throwable e) {
- logger.error("",e);
- }
- }
- }
+ insert_value = insert_value.substring(6);
+ //noinspection Duplicates
+ try {
+ Integer i = Integer.parseInt(insert_value);
+ ArrayList<String> al = XftStringUtils.CommaDelimitedStringToArrayList(insertValue.toString());
+ insertValue = al.get(i);
+ } catch (Throwable e) {
+ logger.error("", e);
+ }
+ }
+ }
linkProps.append("@").append(insertValue);
- }
- } catch (DisplayFieldNotFoundException e) {
- logger.error("",e);
- }
- }else{
+ }
+ } catch (DisplayFieldNotFoundException e) {
+ logger.error("", e);
+ }
+ } else {
if (!dfr.getElementName().equalsIgnoreCase(search.getRootElement().getFullXMLName())) {
- insert_value = dfr.getElementSQLName().toLowerCase() + "_" + insert_value.toLowerCase();
- }else{
- insert_value=insert_value.toLowerCase();
- }
- if(cp.get(insert_value)==null){
- cp.put(insert_value,new Hashtable<String,String>());
-
+ insert_value = dfr.getElementSQLName().toLowerCase() + "_" + insert_value.toLowerCase();
+ } else {
+ insert_value = insert_value.toLowerCase();
+ }
+ if (cp.get(insert_value) == null) {
+ cp.put(insert_value, new Hashtable<String, String>());
+
if (!dfr.getElementName().equalsIgnoreCase(search.getRootElement().getFullXMLName())) {
- cp.get(insert_value).put("xPATH", dfr.getElementName() + "." + insert_value);
- }else{
- cp.get(insert_value).put("xPATH", insert_value);
+ cp.get(insert_value).put("xPATH", dfr.getElementName() + "." + insert_value);
+ } else {
+ cp.get(insert_value).put("xPATH", insert_value);
}
- }
-
- linkProps.append(insert_value);
+ }
+
+ linkProps.append(insert_value);
}
- linkProps.append("\"}");
- }
- linkProps.append("]");
- }
- linkProps.append("}");
- }
- linkProps.append("]");
-
- cp.get(id).put("linkProps", linkProps.toString());
- }
-
+ linkProps.append("\"}");
+ }
+ linkProps.append("]");
+ }
+ linkProps.append("}");
+ }
+ linkProps.append("]");
+
+ cp.get(id).put("linkProps", linkProps.toString());
+ }
+
if (dfr.isImage()) {
- cp.get(id).put("imgRoot", TurbineUtils.GetRelativePath(ServletCall.getRequest(sr.getRequest())) + "/");
- }
- } catch (XFTInitException | ElementNotFoundException e) {
- logger.error("",e);
- }
+ cp.get(id).put("imgRoot", TurbineUtils.GetRelativePath(ServletCall.getRequest(sr.getRequest())) + "/");
+ }
+ } catch (XFTInitException | ElementNotFoundException e) {
+ logger.error("", e);
+ }
+ }
- }
-
- cp.put("quarantine_status",new Hashtable<String,String>());
- } catch (ElementNotFoundException | XFTInitException e) {
- logger.error("",e);
- }
+ cp.put("quarantine_status", new Hashtable<String, String>());
+ } catch (ElementNotFoundException | XFTInitException e) {
+ logger.error("", e);
+ }
- return cp;
- }
+ return cp;
+ }
private boolean canQueryByAllowedUser(final XdatStoredSearch search) {
- boolean allowed=false;
- if(StringUtils.isNotBlank(search.getId()))
- {
+ boolean allowed = false;
+ if (StringUtils.isNotBlank(search.getId())) {
//need to check against unmodified stored search
final org.nrg.xdat.om.XdatStoredSearch stored = XdatStoredSearch.getXdatStoredSearchsById(search.getId(), user, true);
//if the user was added to the search
- if(stored != null && stored.hasAllowedUser(user.getUsername())){
+ if (stored != null && stored.hasAllowedUser(user.getUsername())) {
//confirm it has a WHERE clause and hasn't been modified
- if(XdatCriteriaSet.compareCriteriaSets(stored.getSearchWhere(), search.getSearchWhere())){
- allowed=true;
+ if (XdatCriteriaSet.compareCriteriaSets(stored.getSearchWhere(), search.getSearchWhere())) {
+ allowed = true;
}
}
}