diff --git a/build.gradle b/build.gradle
index 8b3159eb7d921506e4ee41cc22366ceab5e892f7..45afa1f18801119db8abb6c77098f7e2004984c2 100644
--- a/build.gradle
+++ b/build.gradle
@@ -126,11 +126,27 @@ cargo {
}
}
+task sourceJar(type: Jar, dependsOn: classes) {
+ from sourceSets.main.allSource
+}
+
+task javadocJar(type: Jar, dependsOn: javadoc) {
+ from javadoc.destinationDir
+}
+
publishing {
publications {
mavenJava(MavenPublication) {
from components.java
+ artifact sourceJar {
+ classifier "sources"
+ }
+
+ artifact javadocJar {
+ classifier "javadoc"
+ }
+
pom.withXml {
def root = asNode()
root.appendNode('name', 'XNAT Server')
diff --git a/src/main/java/org/nrg/dcm/preferences/DicomSCPInstance.java b/src/main/java/org/nrg/dcm/preferences/DicomSCPInstance.java
index 096f3d7f3d433b152e9c384ef70be27668f64f81..0d3a43d1bf1dce89d5f7e47d982375f09c4e53d3 100644
--- a/src/main/java/org/nrg/dcm/preferences/DicomSCPInstance.java
+++ b/src/main/java/org/nrg/dcm/preferences/DicomSCPInstance.java
@@ -1,11 +1,8 @@
package org.nrg.dcm.preferences;
import com.fasterxml.jackson.annotation.JsonInclude;
-import com.fasterxml.jackson.core.JsonParser;
-import com.fasterxml.jackson.databind.ObjectMapper;
-
-import java.io.IOException;
+@SuppressWarnings("WeakerAccess")
@JsonInclude(JsonInclude.Include.NON_DEFAULT)
public class DicomSCPInstance {
@SuppressWarnings("unused")
@@ -29,14 +26,6 @@ public class DicomSCPInstance {
setFileNamer(fileNamer);
}
- public static DicomSCPInstance deserialize(final String json) throws IOException {
- return _mapper.readValue(json, DicomSCPInstance.class);
- }
-
- public static String serialize(final DicomSCPInstance instance) throws IOException {
- return _mapper.writeValueAsString(instance);
- }
-
public String getScpId() {
return _scpId;
}
@@ -97,11 +86,6 @@ public class DicomSCPInstance {
'}';
}
- private static final ObjectMapper _mapper = new ObjectMapper();
- static {
- _mapper.configure(JsonParser.Feature.ALLOW_SINGLE_QUOTES, true);
- }
-
private String _scpId;
private int _port;
private String _aeTitle;
diff --git a/src/main/java/org/nrg/xnat/configuration/SerializerConfig.java b/src/main/java/org/nrg/xnat/configuration/SerializerConfig.java
new file mode 100644
index 0000000000000000000000000000000000000000..f4702c9e57e2c3e2f71ac2d2ffc3ab16919d54f8
--- /dev/null
+++ b/src/main/java/org/nrg/xnat/configuration/SerializerConfig.java
@@ -0,0 +1,47 @@
+package org.nrg.xnat.configuration;
+
+import com.fasterxml.jackson.core.JsonParser;
+import com.fasterxml.jackson.core.PrettyPrinter;
+import com.fasterxml.jackson.core.util.DefaultIndenter;
+import com.fasterxml.jackson.core.util.DefaultPrettyPrinter;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.dataformat.yaml.YAMLFactory;
+import org.jetbrains.annotations.NotNull;
+import org.nrg.xnat.utils.SerializerService;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+
+@Configuration
+public class SerializerConfig {
+
+ @Bean
+ @NotNull
+ public PrettyPrinter prettyPrinter() {
+ final DefaultIndenter indenter = new DefaultIndenter(" ", DefaultIndenter.SYS_LF);
+ final DefaultPrettyPrinter printer = new DefaultPrettyPrinter();
+ printer.indentObjectsWith(indenter);
+ printer.indentArraysWith(indenter);
+ return printer;
+ }
+
+ @Bean
+ public ObjectMapper jsonObjectMapper() {
+ final PrettyPrinter printer = prettyPrinter();
+ final ObjectMapper mapper = new ObjectMapper().setDefaultPrettyPrinter(printer);
+ mapper.configure(JsonParser.Feature.ALLOW_SINGLE_QUOTES, true);
+ return mapper;
+ }
+
+ @Bean
+ public ObjectMapper yamlObjectMapper() {
+ final PrettyPrinter printer = prettyPrinter();
+ final ObjectMapper mapper = new ObjectMapper(new YAMLFactory()).setDefaultPrettyPrinter(printer);
+ mapper.configure(JsonParser.Feature.ALLOW_SINGLE_QUOTES, true);
+ return mapper;
+ }
+
+ @Bean
+ public SerializerService serializerService() {
+ return new SerializerService();
+ }
+}
diff --git a/src/main/java/org/nrg/xnat/configuration/SpawnerConfig.java b/src/main/java/org/nrg/xnat/configuration/SpawnerConfig.java
new file mode 100644
index 0000000000000000000000000000000000000000..93f2d7afcef20a7354af68cf67573b9e31e5d66c
--- /dev/null
+++ b/src/main/java/org/nrg/xnat/configuration/SpawnerConfig.java
@@ -0,0 +1,30 @@
+package org.nrg.xnat.configuration;
+
+import org.nrg.framework.orm.hibernate.HibernateEntityPackageList;
+import org.nrg.xnat.spawner.services.SpawnerResourceLocator;
+import org.nrg.xnat.spawner.services.impl.SpawnerWorker;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.ComponentScan;
+import org.springframework.context.annotation.Configuration;
+
+import java.util.Collections;
+
+@Configuration
+@ComponentScan({"org.nrg.xnat.spawner.controllers", "org.nrg.xnat.spawner.services.impl.hibernate", "org.nrg.xnat.spawner.repositories"})
+public class SpawnerConfig {
+ @Bean
+ public SpawnerWorker spawnerWorker() {
+ return new SpawnerWorker();
+ }
+
+ @Bean
+ public HibernateEntityPackageList spawnerEntityPackages() {
+ return new HibernateEntityPackageList(Collections.singletonList("org.nrg.xnat.spawner.entities"));
+ }
+
+ @Bean
+ public SpawnerResourceLocator spawnerResourceLocator() {
+ // TODO: This uses the default spawner element pattern. It would be nice to set this as a site configuration property.
+ return new SpawnerResourceLocator();
+ }
+}
diff --git a/src/main/java/org/nrg/xnat/event/listeners/PipelineEmailHandlerAbst.java b/src/main/java/org/nrg/xnat/event/listeners/PipelineEmailHandlerAbst.java
index b9fc9febc1639b56d477bd5726fe434a89b53d03..f62842042a01eb3421d14f38cac51f6da980fc1f 100644
--- a/src/main/java/org/nrg/xnat/event/listeners/PipelineEmailHandlerAbst.java
+++ b/src/main/java/org/nrg/xnat/event/listeners/PipelineEmailHandlerAbst.java
@@ -1,15 +1,14 @@
package org.nrg.xnat.event.listeners;
import com.fasterxml.jackson.core.type.TypeReference;
-import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.collect.Lists;
import com.google.common.collect.Maps;
import org.apache.commons.lang.StringEscapeUtils;
import org.apache.commons.lang.StringUtils;
-import org.apache.log4j.Logger;
import org.apache.xmlbeans.XmlException;
import org.nrg.pipeline.xmlbeans.AllResolvedStepsDocument;
import org.nrg.pipeline.xmlbeans.ParameterData;
+import org.nrg.xdat.XDAT;
import org.nrg.xdat.model.WrkXnatexecutionenvironmentParameterI;
import org.nrg.xdat.om.WrkWorkflowdata;
import org.nrg.xdat.om.WrkXnatexecutionenvironment;
@@ -20,6 +19,9 @@ import org.nrg.xdat.turbine.utils.TurbineUtils;
import org.nrg.xft.db.PoolDBUtils;
import org.nrg.xft.event.WorkflowStatusEvent;
import org.nrg.xnat.notifications.NotifyProjectPipelineListeners;
+import org.nrg.xnat.utils.SerializerService;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import java.io.File;
import java.io.IOException;
@@ -27,26 +29,25 @@ import java.nio.charset.Charset;
import java.nio.file.Files;
import java.util.*;
-/**
- * Created by flavin on 2/27/15.
- */
+@SuppressWarnings("WeakerAccess")
public abstract class PipelineEmailHandlerAbst extends WorkflowStatusEventHandlerAbst {
- /** The logger. */
- static Logger logger = Logger.getLogger(PipelineEmailHandlerAbst.class);
-
/** The default template success. */
public final String DEFAULT_TEMPLATE_SUCCESS = "/screens/PipelineEmail_success.vm";
-
+
/** The default subject success. */
public final String DEFAULT_SUBJECT_SUCCESS = "processed without errors";
-
+
/** The default template failure. */
public final String DEFAULT_TEMPLATE_FAILURE = "/screens/PipelineEmail_failure.vm";
-
+
/** The default subject failure. */
public final String DEFAULT_SUBJECT_FAILURE = "";
+ protected PipelineEmailHandlerAbst() {
+ _serializer = XDAT.getContextService().getBean(SerializerService.class);
+ }
+
/**
* Send.
*
@@ -93,14 +94,14 @@ public abstract class PipelineEmailHandlerAbst extends WorkflowStatusEventHandle
}
if (completed(e) && Float.parseFloat(wrk.getPercentagecomplete()) < 100.0f) {
- logger.error("Workflow "+wrk.getWrkWorkflowdataId()+" is \"Complete\" but percentage is less than 100%. Not sending email.");
+ _log.error("Workflow " + wrk.getWrkWorkflowdataId() + " is \"Complete\" but percentage is less than 100%. Not sending email.");
return;
}
SchemaElement objXsiType;
try {
objXsiType = SchemaElement.GetElement(wrk.getDataType());
} catch (Throwable e1) {
- logger.error("", e1);//this shouldn't happen
+ _log.error("", e1);//this shouldn't happen
return;
}
@@ -131,24 +132,15 @@ public abstract class PipelineEmailHandlerAbst extends WorkflowStatusEventHandle
throw new Exception("Experiment " + wrk.getId() + " associated with workflow " + wrk.getWrkWorkflowdataId() + " is null");
}
-
-
if (wrk.getComments()!=null) {
String comments = StringEscapeUtils.unescapeXml(wrk.getComments());
if (StringUtils.isNotBlank(comments)) {
- ObjectMapper objectMapper = new ObjectMapper();
- HashMap<String, String> commentsMap = null;
try {
- commentsMap = objectMapper.readValue(comments, new TypeReference<HashMap<String, String>>(){});
+ params.putAll(getSerializer().deserializeJson(comments, new TypeReference<HashMap<String, String>>(){}));
} catch (Exception e1) {
// Do nothing. This isn't necessarily a problem.
- }
-
- if (commentsMap == null) {
params.put("comments",comments);
- } else {
- params.putAll(commentsMap);
}
}
}
@@ -156,7 +148,6 @@ public abstract class PipelineEmailHandlerAbst extends WorkflowStatusEventHandle
if(failed(e)) {
// Get a list of parameters. Using that information, find the pipeline execution logs.
WrkXnatexecutionenvironment wrkEE=null;
- List<WrkXnatexecutionenvironmentParameterI> pipelineCmdLineParameters = null;
HashMap<String,String> pipelineCmdLineParamsMap = Maps.newHashMap();
HashMap<String,String> pipelineParamsMap = Maps.newHashMap();
Map<String,File> attachments = Maps.newHashMap();
@@ -165,9 +156,9 @@ public abstract class PipelineEmailHandlerAbst extends WorkflowStatusEventHandle
try {
wrkEE = (WrkXnatexecutionenvironment) wrk.getExecutionenvironment();
} catch (ClassCastException e1){
- logger.error("Workflow Execution Environment is not an XNAT Execution Environment",e1);
+ _log.error("Workflow Execution Environment is not an XNAT Execution Environment", e1);
}
- pipelineCmdLineParameters = null==wrkEE ? new ArrayList<WrkXnatexecutionenvironmentParameterI>() : wrkEE.getParameters_parameter();
+ final List<WrkXnatexecutionenvironmentParameterI> pipelineCmdLineParameters = null == wrkEE ? new ArrayList<WrkXnatexecutionenvironmentParameterI>() : wrkEE.getParameters_parameter();
// Gather input params from command line
for (WrkXnatexecutionenvironmentParameterI pipelineParameter : pipelineCmdLineParameters) {
@@ -193,14 +184,14 @@ public abstract class PipelineEmailHandlerAbst extends WorkflowStatusEventHandle
stderr = logFileContents;
}
} catch (IOException e1) {
- logger.error("Could not read pipeline log file "+logFileObj.toPath(), e1);
+ _log.error("Could not read pipeline log file " + logFileObj.toPath(), e1);
}
} else if (logFileObj.getName().endsWith(".xml")) {
AllResolvedStepsDocument pipeParamsDoc = null;
try {
pipeParamsDoc = AllResolvedStepsDocument.Factory.parse(logFileObj);
} catch (XmlException | IOException e1) {
- logger.error("Encountered a problem parsing pipeline parameter XML for failure email.",e1);
+ _log.error("Encountered a problem parsing pipeline parameter XML for failure email.", e1);
}
if (null!=pipeParamsDoc) {
@@ -262,7 +253,7 @@ public abstract class PipelineEmailHandlerAbst extends WorkflowStatusEventHandle
}
} catch (Throwable e1) {
- logger.error("",e1);
+ _log.error("", e1);
}
}
@@ -283,5 +274,13 @@ public abstract class PipelineEmailHandlerAbst extends WorkflowStatusEventHandle
}
return retList;
}
+
+ protected SerializerService getSerializer() {
+ return _serializer;
+ }
+
+ private final static Logger _log = LoggerFactory.getLogger(PipelineEmailHandlerAbst.class);
+
+ private final SerializerService _serializer;
}
diff --git a/src/main/java/org/nrg/xnat/helpers/prearchive/PrearcDatabase.java b/src/main/java/org/nrg/xnat/helpers/prearchive/PrearcDatabase.java
index 0cbc305b2f96a0c5230b934c7966c1695ccc0559..29c48d481823db1c27a021daddde0bab95e19cc0 100644
--- a/src/main/java/org/nrg/xnat/helpers/prearchive/PrearcDatabase.java
+++ b/src/main/java/org/nrg/xnat/helpers/prearchive/PrearcDatabase.java
@@ -11,7 +11,6 @@
package org.nrg.xnat.helpers.prearchive;
import com.fasterxml.jackson.core.JsonFactory;
-import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.base.Strings;
import com.google.common.collect.Maps;
import org.apache.commons.collections.CollectionUtils;
@@ -42,6 +41,7 @@ import org.nrg.xnat.restlet.XNATApplication;
import org.nrg.xnat.restlet.actions.PrearcImporterA.PrearcSession;
import org.nrg.xnat.restlet.services.Archiver;
import org.nrg.xnat.turbine.utils.ArcSpecManager;
+import org.nrg.xnat.utils.SerializerService;
import org.nrg.xnat.utils.XnatUserProvider;
import org.restlet.data.Status;
import org.slf4j.Logger;
@@ -61,7 +61,6 @@ import java.util.*;
public final class PrearcDatabase {
private static final Logger logger = LoggerFactory.getLogger(PrearcTableBuilder.class);
- public static final ObjectMapper MAPPER = new ObjectMapper(new JsonFactory());
public static Connection conn;
final static String table = "prearchive";
final static String tableWithSchema = PoolDBUtils.search_schema_name + "." + PrearcDatabase.table;
@@ -73,6 +72,8 @@ public final class PrearcDatabase {
private static String prearcPath;
+ private static SerializerService _serializer;
+
public static final String SPLIT_PETMR_SESSION_ID = "SplitPetMrSessions";
public static final String DEFAULT_SPLIT_PETMR_SESSION_FILTER = "{\n" +
@@ -713,10 +714,17 @@ public final class PrearcDatabase {
} else {
content = script.getContent();
}
- final LinkedHashMap<String, String> keys = MAPPER.readValue(content, SeriesImportFilter.MAP_TYPE_REFERENCE);
+ final LinkedHashMap<String, String> keys = getSerializer().deserializeJson(content, SeriesImportFilter.MAP_TYPE_REFERENCE);
return DicomFilterService.buildSeriesImportFilter(keys);
}
+ private static SerializerService getSerializer() {
+ if (_serializer == null) {
+ _serializer = XDAT.getContextService().getBean(SerializerService.class);
+ }
+ return _serializer;
+ }
+
static String getUniqueSessionLabel(final String stem, final String target, final String replacement, final String projectId, final UserI user) {
String label;
if (stem.contains(target.toUpperCase())) {
diff --git a/src/main/java/org/nrg/xnat/initialization/XnatWebAppInitializer.java b/src/main/java/org/nrg/xnat/initialization/XnatWebAppInitializer.java
index 55ca5b3e349e21300aa2e6c15056b69d28ec8518..3c4f7fcdcff0763c666d222a2bcab18d6d9ebe31 100644
--- a/src/main/java/org/nrg/xnat/initialization/XnatWebAppInitializer.java
+++ b/src/main/java/org/nrg/xnat/initialization/XnatWebAppInitializer.java
@@ -7,6 +7,7 @@ import org.apache.commons.lang3.StringUtils;
import org.apache.turbine.Turbine;
import org.nrg.framework.exceptions.NrgServiceRuntimeException;
import org.nrg.framework.processors.XnatPluginBean;
+import org.nrg.framework.utilities.BasicXnatResourceLocator;
import org.nrg.xdat.servlet.XDATAjaxServlet;
import org.nrg.xdat.servlet.XDATServlet;
import org.nrg.xnat.restlet.servlet.XNATRestletServlet;
@@ -15,7 +16,6 @@ import org.nrg.xnat.security.XnatSessionEventPublisher;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.core.io.Resource;
-import org.springframework.core.io.support.PathMatchingResourcePatternResolver;
import org.springframework.core.io.support.PropertiesLoaderUtils;
import org.springframework.web.filter.DelegatingFilterProxy;
import org.springframework.web.servlet.support.AbstractAnnotationConfigDispatcherServletInitializer;
@@ -114,9 +114,7 @@ public class XnatWebAppInitializer extends AbstractAnnotationConfigDispatcherSer
private List<Class<?>> getPluginConfigs() {
final List<Class<?>> configs = new ArrayList<>();
try {
- final PathMatchingResourcePatternResolver resolver = new PathMatchingResourcePatternResolver();
- final Resource[] resources = resolver.getResources("classpath*:META-INF/xnat/**/*-plugin.properties");
- for (final Resource resource : resources) {
+ for (final Resource resource : BasicXnatResourceLocator.getResources("classpath*:META-INF/xnat/**/*-plugin.properties")) {
final Properties properties = PropertiesLoaderUtils.loadProperties(resource);
final XnatPluginBean plugin = new XnatPluginBean(properties);
final Class<?> config = plugin.getConfigClass();
diff --git a/src/main/java/org/nrg/xnat/restlet/extensions/DicomSCPRestlet.java b/src/main/java/org/nrg/xnat/restlet/extensions/DicomSCPRestlet.java
index 56617d3280cd269620881c0bc8bb3914b4f61906..03949ce06f1ad400bc72421110cb4507e8c6e79f 100644
--- a/src/main/java/org/nrg/xnat/restlet/extensions/DicomSCPRestlet.java
+++ b/src/main/java/org/nrg/xnat/restlet/extensions/DicomSCPRestlet.java
@@ -11,7 +11,6 @@
package org.nrg.xnat.restlet.extensions;
-import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.base.Joiner;
import org.apache.commons.lang3.StringUtils;
import org.nrg.dcm.DicomSCPManager;
@@ -42,10 +41,9 @@ public class DicomSCPRestlet extends SecureResource {
private static final List<String> ALLOWED_ACTIONS = new ArrayList<>(Arrays.asList("status", "start", "stop", "enable", "disable"));
private static final Logger _log = LoggerFactory.getLogger(DicomSCPRestlet.class);
- private static final ObjectMapper _mapper = new ObjectMapper();
- private final DicomSCPManager _dicomSCPManager;
- private final String _scpId;
- private final String _action;
+ private final DicomSCPManager _dicomSCPManager;
+ private final String _scpId;
+ private final String _action;
public DicomSCPRestlet(Context context, Request request, Response response) throws ResourceException {
super(context, request, response);
@@ -86,11 +84,11 @@ public class DicomSCPRestlet extends SecureResource {
try {
if (Method.DELETE.equals(getRequest().getMethod()) || (StringUtils.isNotBlank(_action) && _action.equalsIgnoreCase("status"))) {
- return new StringRepresentation(_mapper.writeValueAsString(_dicomSCPManager.areDicomSCPsStarted()));
+ return new StringRepresentation(getSerializer().toJson(_dicomSCPManager.areDicomSCPsStarted()));
} else if (StringUtils.isBlank(_scpId)) {
- return new StringRepresentation(_mapper.writeValueAsString(_dicomSCPManager.getDicomSCPInstances()));
+ return new StringRepresentation(getSerializer().toJson(_dicomSCPManager.getDicomSCPInstances()));
} else {
- return new StringRepresentation(DicomSCPInstance.serialize(_dicomSCPManager.getDicomSCPInstance(_scpId)));
+ return new StringRepresentation(getSerializer().toJson(_dicomSCPManager.getDicomSCPInstance(_scpId)));
}
} catch (IOException e) {
throw new ResourceException(Status.SERVER_ERROR_INTERNAL, "An error occurred marshaling the DICOM SCP statuses", e);
@@ -110,8 +108,8 @@ public class DicomSCPRestlet extends SecureResource {
getResponse().setStatus(Status.CLIENT_ERROR_BAD_REQUEST, "You should only POST to this URL to create a new DICOM SCP instance. The DICOM SCP ID " + _scpId + " is invalid in this context.");
}
try {
- final String serialized = getRequest().getEntity().getText();
- final DicomSCPInstance instance = DicomSCPInstance.deserialize(serialized);
+ final String serialized = getRequest().getEntity().getText();
+ final DicomSCPInstance instance = getSerializer().deserializeJson(serialized, DicomSCPInstance.class);
_dicomSCPManager.create(instance);
} catch (IOException e) {
getResponse().setStatus(Status.SERVER_ERROR_INTERNAL, e, "An error occurred trying to retrieve the body text of the PUT request.");
diff --git a/src/main/java/org/nrg/xnat/restlet/extensions/PipelineDetailsRestlet.java b/src/main/java/org/nrg/xnat/restlet/extensions/PipelineDetailsRestlet.java
index 30118abd40e2820e295d66db9f1bec63167c4098..117eb76a178e0ad5db3717ecae704b808e157dc7 100644
--- a/src/main/java/org/nrg/xnat/restlet/extensions/PipelineDetailsRestlet.java
+++ b/src/main/java/org/nrg/xnat/restlet/extensions/PipelineDetailsRestlet.java
@@ -10,7 +10,6 @@
*/
package org.nrg.xnat.restlet.extensions;
-import com.fasterxml.jackson.databind.ObjectMapper;
import org.apache.commons.lang.StringUtils;
import org.nrg.pipeline.PipelineRepositoryManager;
import org.nrg.pipeline.utils.PipelineFileUtils;
@@ -43,15 +42,13 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
-
-
@XnatRestlet({"/projects/{PROJECT_ID}/pipelines/{PIPELINE_NAME}", "/projects/{PROJECT_ID}/pipelines/{PIPELINE_NAME}/details"})
public class PipelineDetailsRestlet extends SecureResource {
public static final String PARAM_PROJECT_ID = "PROJECT_ID";
public static final String PARAM_PIPELINE_NAME = "PIPELINE_NAME";
- private final String _projectId;
- private final String _pipelineName;
+ private final String _projectId;
+ private final String _pipelineName;
private static final Logger _log = LoggerFactory.getLogger(PipelineDetailsRestlet.class);
@@ -79,8 +76,7 @@ public class PipelineDetailsRestlet extends SecureResource {
Map<String,Object> pipelineDetails = getPipelineDetailsMap();
// Make a json object from the pipelineDetails map
- ObjectMapper mapper = new ObjectMapper();
- String json = mapper.writeValueAsString(pipelineDetails);
+ String json = getSerializer().toJson(pipelineDetails);
return new StringRepresentation(json, MediaType.APPLICATION_JSON);
} catch (Exception exception) {
@@ -119,7 +115,7 @@ public class PipelineDetailsRestlet extends SecureResource {
}
// Build hash map
- Map<String,Object> pipelineDetails = new HashMap<String,Object>();
+ Map<String,Object> pipelineDetails = new HashMap<>();
// Basic info
pipelineDetails.put("path",pipelineDescriptorPath);
@@ -155,9 +151,9 @@ public class PipelineDetailsRestlet extends SecureResource {
pipelineDetails.put("publications",doc.getPublications().getPublicationArray());
}
if (doc.isSetAuthors()) {
- List<Map<String,String>> authorInfoList = new ArrayList<Map<String,String>>();
+ List<Map<String,String>> authorInfoList = new ArrayList<>();
for (Author aAuthor : doc.getAuthors().getAuthorArray()) {
- Map<String,String> authorInfo = new HashMap<String,String>();
+ Map<String,String> authorInfo = new HashMap<>();
if (StringUtils.isNotBlank(aAuthor.getFirstname())) {
authorInfo.put("firstname", aAuthor.getFirstname());
}
@@ -183,9 +179,9 @@ public class PipelineDetailsRestlet extends SecureResource {
}
// Step ids and descriptions
- List<Map<String,String>> stepInfoList = new ArrayList<Map<String,String>>();
+ List<Map<String,String>> stepInfoList = new ArrayList<>();
for (Step aStep : pipelineData.getSteps().getStepArray()) {
- Map<String,String> stepInfo = new HashMap<String,String>();
+ Map<String,String> stepInfo = new HashMap<>();
stepInfo.put("id",aStep.getId());
if (StringUtils.isNotBlank(aStep.getDescription())) {
@@ -196,11 +192,11 @@ public class PipelineDetailsRestlet extends SecureResource {
pipelineDetails.put("steps",stepInfoList);
// Project-level param defaults
- List<Map<String,Object>> paramInfoList = new ArrayList<Map<String,Object>>();
+ List<Map<String,Object>> paramInfoList = new ArrayList<>();
for (ArcPipelineparameterdataI aParamI : projectPipelineData.getParameters_parameter()) {
ArcPipelineparameterdata aParam = (ArcPipelineparameterdata) aParamI;
- Map<String,Object> paramInfo = new HashMap<String,Object>();
+ Map<String,Object> paramInfo = new HashMap<>();
paramInfo.put("name",aParam.getName());
if (StringUtils.isNotBlank(aParam.getDescription())) {
paramInfo.put("description", aParam.getDescription());
@@ -209,7 +205,7 @@ public class PipelineDetailsRestlet extends SecureResource {
String csv = aParam.getCsvvalues();
String schemaLink = aParam.getSchemalink();
if (StringUtils.isNotBlank(schemaLink) || StringUtils.isNotBlank(csv)) {
- Map<String,String> paramValues = new HashMap<String,String>();
+ Map<String,String> paramValues = new HashMap<>();
if (StringUtils.isNotBlank(schemaLink)) {
paramValues.put("schemaLink",schemaLink);
} else {
@@ -223,5 +219,4 @@ public class PipelineDetailsRestlet extends SecureResource {
return pipelineDetails;
}
-
}
diff --git a/src/main/java/org/nrg/xnat/restlet/extensions/UserSettingsRestlet.java b/src/main/java/org/nrg/xnat/restlet/extensions/UserSettingsRestlet.java
index 84f4b3bf53c99907be68953de22b708aca9716f0..c0e4474383c9b4cebea78fe556b7585afe51669d 100644
--- a/src/main/java/org/nrg/xnat/restlet/extensions/UserSettingsRestlet.java
+++ b/src/main/java/org/nrg/xnat/restlet/extensions/UserSettingsRestlet.java
@@ -12,7 +12,6 @@ package org.nrg.xnat.restlet.extensions;
import com.fasterxml.jackson.annotation.JsonIgnore;
import com.fasterxml.jackson.databind.JsonNode;
-import com.fasterxml.jackson.databind.ObjectMapper;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
@@ -49,8 +48,8 @@ import java.util.*;
@XnatRestlet({"/user", "/user/{USER_ID}", "/user/actions/{ACTION}", "/user/actions/{USER_ID}/{ACTION}"})
public class UserSettingsRestlet extends SecureResource {
- public static final String PARAM_USER_ID = "USER_ID";
- public static final String PARAM_ACTION = "ACTION";
+ private static final String PARAM_USER_ID = "USER_ID";
+ private static final String PARAM_ACTION = "ACTION";
public UserSettingsRestlet(Context context, Request request, Response response) throws ResourceException {
super(context, request, response);
@@ -114,7 +113,7 @@ public class UserSettingsRestlet extends SecureResource {
try {
if (StringUtils.isBlank(_userId)) {
Collection<String> logins = Users.getAllLogins();
- return new StringRepresentation(_isJsonRequested ? _serializer.writeValueAsString(logins) : createLoginListXml(logins));
+ return new StringRepresentation(_isJsonRequested ? getSerializer().toJson(logins) : createLoginListXml(logins));
}
UserI requestedUser = Users.getUser(_userId);
@@ -343,7 +342,7 @@ public class UserSettingsRestlet extends SecureResource {
private JsonNode getJsonNode() throws IOException {
if (_node == null) {
- _node = _serializer.readValue(_payload, JsonNode.class);
+ _node = getSerializer().deserializeJson(_payload);
}
return _node;
}
@@ -411,7 +410,7 @@ public class UserSettingsRestlet extends SecureResource {
return new StringRepresentation(output.toString());
}
- enum UserAction {
+ private enum UserAction {
Reset,
ResetEmailRequests;
@@ -437,7 +436,7 @@ public class UserSettingsRestlet extends SecureResource {
private static Map<String, UserAction> _actions = new TreeMap<>(String.CASE_INSENSITIVE_ORDER);
}
- enum UserProperty {
+ private enum UserProperty {
email,
enabled,
firstname,
@@ -458,11 +457,6 @@ public class UserSettingsRestlet extends SecureResource {
}
private static final Log _log = LogFactory.getLog(UserSettingsRestlet.class);
- private static final ObjectMapper _serializer = new ObjectMapper() {{
- // Migration: Get the mix-in annotations working for XDATUser.
- // getSerializationConfig().addMixInAnnotations(UserI.class, IgnoreSetValueMixIn.class);
- // getSerializationConfig().addMixInAnnotations(GenericWrapperField.class, IgnoreSetValueMixIn.class);
- }};
private static final Map<UserProperty, String> XPATH_EXPRESSIONS = new HashMap<UserProperty, String>() {{
put(UserProperty.userAuths, "//userAuths/userAuth");
put(UserProperty.authId, "authId");
diff --git a/src/main/java/org/nrg/xnat/restlet/resources/AutomationResource.java b/src/main/java/org/nrg/xnat/restlet/resources/AutomationResource.java
index 77d98174a1fcb1d5b7c52c04c55c8eccfad4c389..c0d62b297e404d0fc4dae92f524856a2d6cb75c1 100644
--- a/src/main/java/org/nrg/xnat/restlet/resources/AutomationResource.java
+++ b/src/main/java/org/nrg/xnat/restlet/resources/AutomationResource.java
@@ -1,7 +1,9 @@
package org.nrg.xnat.restlet.resources;
import org.apache.commons.lang.StringUtils;
-import com.fasterxml.jackson.databind.ObjectMapper;
+import org.apache.http.NameValuePair;
+import org.apache.http.client.utils.URLEncodedUtils;
+import org.nrg.action.ServerException;
import org.nrg.framework.constants.Scope;
import org.nrg.xdat.om.XnatProjectdata;
import org.nrg.xft.XFTTable;
@@ -11,19 +13,27 @@ import org.nrg.xft.event.persist.PersistentWorkflowI;
import org.nrg.xft.event.persist.PersistentWorkflowUtils;
import org.nrg.xnat.utils.WorkflowUtils;
import org.restlet.Context;
+import org.restlet.data.MediaType;
import org.restlet.data.Request;
import org.restlet.data.Response;
import org.restlet.data.Status;
+import org.restlet.resource.Representation;
import org.restlet.resource.ResourceException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
+import java.io.IOException;
+import java.nio.charset.Charset;
import java.util.HashMap;
+import java.util.List;
import java.util.Map;
+import java.util.Properties;
+@SuppressWarnings("WeakerAccess")
public abstract class AutomationResource extends SecureResource {
- public static final String SITE_SCOPE = Scope.encode(Scope.Site, "");
+ static final String SITE_SCOPE = Scope.encode(Scope.Site, "");
+ private static final Charset DEFAULT_CHARSET = Charset.forName("UTF-8");
public AutomationResource(final Context context, final Request request, final Response response) throws ResourceException {
super(context, request, response);
@@ -152,6 +162,29 @@ public abstract class AutomationResource extends SecureResource {
return buffer.toString();
}
+ protected Properties decodeProperties(final Representation entity, final MediaType mediaType) throws ServerException {
+ final Properties properties;
+ if (mediaType.equals(MediaType.APPLICATION_WWW_FORM)) {
+ try {
+ final List<NameValuePair> formMap = URLEncodedUtils.parse(entity.getText(), DEFAULT_CHARSET);
+ properties = new Properties();
+ for (final NameValuePair entry : formMap) {
+ properties.setProperty(entry.getName(), entry.getValue());
+ }
+ } catch (IOException e) {
+ throw new ServerException(Status.SERVER_ERROR_INTERNAL, "An error occurred trying to read the submitted form body.", e);
+ }
+ } else {
+ try {
+ final String text = entity.getText();
+ properties = getSerializer().deserializeJson(text, Properties.class);
+ } catch (IOException e) {
+ throw new ServerException(Status.SERVER_ERROR_INTERNAL, "An error occurred processing the script properties", e);
+ }
+ }
+ return properties;
+ }
+
private Map<String, String> validateEntityId(final String entityId) throws ResourceException {
if (getScope() == null) {
return null;
@@ -191,8 +224,6 @@ public abstract class AutomationResource extends SecureResource {
}
}
- protected static final ObjectMapper MAPPER = new ObjectMapper();
-
private static final Logger _log = LoggerFactory.getLogger(AutomationResource.class);
private static final String ENTITY_ID = "ENTITY_ID";
private static final String PROJECT_ID = "PROJECT_ID";
@@ -201,6 +232,7 @@ public abstract class AutomationResource extends SecureResource {
private static final String KEY_PROJECTID = "projectId";
private Scope _scope;
private boolean _hasProjectId;
+
private String _projectId;
private final String _path;
diff --git a/src/main/java/org/nrg/xnat/restlet/resources/EventResource.java b/src/main/java/org/nrg/xnat/restlet/resources/EventResource.java
index 14b078f347275d05ac8c8c49e0468882f04e484e..928689f8d727f946d1340afd128dcad2edb07657 100644
--- a/src/main/java/org/nrg/xnat/restlet/resources/EventResource.java
+++ b/src/main/java/org/nrg/xnat/restlet/resources/EventResource.java
@@ -35,8 +35,8 @@ import java.util.Properties;
public class EventResource extends AutomationResource {
- public static final String PROPERTY_EVENT_ID = "event_id";
- public static final String PROPERTY_EVENT_LABEL = "event_label";
+ private static final String PROPERTY_EVENT_ID = "event_id";
+ private static final String PROPERTY_EVENT_LABEL = "event_label";
public EventResource(Context context, Request request, Response response) throws ResourceException {
super(context, request, response);
@@ -142,7 +142,7 @@ public class EventResource extends AutomationResource {
final Map<String, String> event = new HashMap<>();
event.put(PROPERTY_EVENT_ID, getResourceId());
event.put(PROPERTY_EVENT_LABEL, label);
- return new StringRepresentation(MAPPER.writeValueAsString(event), mediaType);
+ return new StringRepresentation(getSerializer().toJson(event), mediaType);
}
} else {
// They're asking for list of existing script events, so give them that.
@@ -213,7 +213,7 @@ public class EventResource extends AutomationResource {
} else {
try {
final String text = entity.getText();
- _properties.putAll(MAPPER.readValue(text, Properties.class));
+ _properties.putAll(getSerializer().deserializeJson(text, Properties.class));
} catch (IOException e) {
throw new ResourceException(Status.SERVER_ERROR_INTERNAL, "An error occurred processing the script properties", e);
}
diff --git a/src/main/java/org/nrg/xnat/restlet/resources/ProjectPipelineListResource.java b/src/main/java/org/nrg/xnat/restlet/resources/ProjectPipelineListResource.java
index b81a49a931033297d58a757f4986fa6f6e83b689..d39440c5619a0955326a55f8cc2991b89697e070 100644
--- a/src/main/java/org/nrg/xnat/restlet/resources/ProjectPipelineListResource.java
+++ b/src/main/java/org/nrg/xnat/restlet/resources/ProjectPipelineListResource.java
@@ -87,7 +87,7 @@ public class ProjectPipelineListResource extends SecureResource {
}
}
//Send a 200 OK message back
- //getResponse().setStatus(Status.SUCCESS_OK,"Pipeline has been removed from project " + proj.getId());
+ //getResponse().setStatus(Status.SUCCESS_OK,"Pipeline has been removed from project " + _project.getId());
}
}catch(Exception e) {
e.printStackTrace();
diff --git a/src/main/java/org/nrg/xnat/restlet/resources/ProjectUserListResource.java b/src/main/java/org/nrg/xnat/restlet/resources/ProjectUserListResource.java
index a36eb43908a51030bfe1a4d21dbfc5f27184aa2f..12a5322df1983e49ea4e95d1d9b5279a0813a7ba 100644
--- a/src/main/java/org/nrg/xnat/restlet/resources/ProjectUserListResource.java
+++ b/src/main/java/org/nrg/xnat/restlet/resources/ProjectUserListResource.java
@@ -17,16 +17,15 @@ import org.nrg.xdat.XDAT;
import org.nrg.xdat.om.XnatProjectdata;
import org.nrg.xdat.security.helpers.Permissions;
import org.nrg.xdat.security.helpers.Roles;
-import org.nrg.xdat.security.helpers.UserHelper;
import org.nrg.xft.XFTTable;
import org.nrg.xft.exception.DBPoolException;
-import org.nrg.xft.exception.InvalidItemException;
import org.restlet.Context;
import org.restlet.data.MediaType;
import org.restlet.data.Request;
import org.restlet.data.Response;
import org.restlet.data.Status;
import org.restlet.resource.Representation;
+import org.restlet.resource.ResourceException;
import org.restlet.resource.Variant;
import java.io.IOException;
@@ -35,51 +34,50 @@ import java.util.Hashtable;
import java.util.List;
public class ProjectUserListResource extends SecureResource {
- XFTTable table = null;
- XnatProjectdata proj = null;
- boolean displayHiddenUsers = false;
+ private final XnatProjectdata _project;
+ private final boolean _displayHiddenUsers;
public ProjectUserListResource(Context context, Request request, Response response) throws Exception {
super(context, request, response);
+ setReadable(true);
+ setModifiable(false);
+
getVariants().add(new Variant(MediaType.APPLICATION_JSON));
getVariants().add(new Variant(MediaType.TEXT_HTML));
getVariants().add(new Variant(MediaType.TEXT_XML));
final String projectId = (String) getParameter(request, "PROJECT_ID");
- if (projectId != null) {
- proj = XnatProjectdata.getProjectByIDorAlias(projectId, user, false);
- }
- if (proj == null) {
+ _project = org.apache.commons.lang3.StringUtils.isNotBlank(projectId) ? XnatProjectdata.getProjectByIDorAlias(projectId, user, false) : null;
+ if (_project == null) {
+ _displayHiddenUsers = false;
getResponse().setStatus(Status.CLIENT_ERROR_NOT_FOUND, "The project ID " + projectId + " does not appear to be a valid project ID. Please verify your information.");
} else {
- if (!(Roles.isSiteAdmin(user) || Permissions.canEdit(user, proj) || isWhitelisted(projectId))) {
- logger.error("Unauthorized Access to project-level user resources. User: " + userName);
- getResponse().setStatus(Status.CLIENT_ERROR_FORBIDDEN, "Access Denied: Only project owners and site managers can access user resources.");
- }
- displayHiddenUsers = Boolean.parseBoolean((String) getParameter(request, "DISPLAY_HIDDEN_USERS"));
+ if (!(Roles.isSiteAdmin(user) || Permissions.canEdit(user, _project) || isWhitelisted(projectId))) {
+ logger.error("Unauthorized Access to project-level user resources. User: " + userName);
+ getResponse().setStatus(Status.CLIENT_ERROR_FORBIDDEN, "Access Denied: Only project owners and site managers can access user resources.");
}
+ _displayHiddenUsers = Boolean.parseBoolean((String) getParameter(request, "DISPLAY_HIDDEN_USERS"));
}
-
- @Override
- public boolean allowGet() {
- return true;
}
@Override
- public Representation represent(Variant variant) {
+ public Representation represent(Variant variant) throws ResourceException {
- if (proj != null) {
- final StringBuilder query = new StringBuilder("SELECT g.id AS \"GROUP_ID\", displayname,login,firstname,lastname,email FROM xdat_userGroup g RIGHT JOIN xdat_user_Groupid map ON g.id=map.groupid RIGHT JOIN xdat_user u ON map.groups_groupid_xdat_user_xdat_user_id=u.xdat_user_id WHERE tag='").append(proj.getId()).append("' ");
+ final XFTTable table;
+ if (_project != null) {
+ final StringBuilder query = new StringBuilder("SELECT g.id AS \"GROUP_ID\", displayname,login,firstname,lastname,email FROM xdat_userGroup g RIGHT JOIN xdat_user_Groupid map ON g.id=map.groupid RIGHT JOIN xdat_user u ON map.groups_groupid_xdat_user_xdat_user_id=u.xdat_user_id WHERE tag='").append(_project.getId()).append("' ");
try {
- if(!displayHiddenUsers){
+ if(!_displayHiddenUsers){
query.append(" and enabled = 1 ");
}
query.append(" ORDER BY g.id DESC;");
table = XFTTable.Execute(query.toString(), user.getDBName(), user.getLogin());
} catch (SQLException | DBPoolException e) {
- logger.warn("An error occurred trying to run the following query: " + query.toString(), e);
+ throw new ResourceException(Status.SERVER_ERROR_INTERNAL, "An error occurred trying to run the following query: " + query.toString(), e);
}
+ } else {
+ table = null;
}
Hashtable<String, Object> params = new Hashtable<>();
@@ -92,12 +90,12 @@ public class ProjectUserListResource extends SecureResource {
}
public boolean isWhitelisted() {
- final String projectId = (String) proj.getItem().getProps().get("id");
+ final String projectId = (String) _project.getItem().getProps().get("id");
final ConfigService configService = XDAT.getConfigService();
final String config = configService.getConfigContents("user-resource-whitelist", "whitelist.json", Scope.Project, projectId);
if (!StringUtils.isBlank(config)) {
try {
- List<String> projectUserResourceWhitelist = OBJECT_MAPPER.readValue(config, TYPE_REFERENCE_LIST_STRING);
+ List<String> projectUserResourceWhitelist = getSerializer().deserializeJson(config, TYPE_REFERENCE_LIST_STRING);
if (projectUserResourceWhitelist != null) {
return projectUserResourceWhitelist.contains(user.getUsername());
}
diff --git a/src/main/java/org/nrg/xnat/restlet/resources/ScriptResource.java b/src/main/java/org/nrg/xnat/restlet/resources/ScriptResource.java
index 6407ba30c303134227511a11a99ca53d64f109ab..92905f33715529813799ac44dc1fa818d0d313e7 100644
--- a/src/main/java/org/nrg/xnat/restlet/resources/ScriptResource.java
+++ b/src/main/java/org/nrg/xnat/restlet/resources/ScriptResource.java
@@ -1,8 +1,6 @@
package org.nrg.xnat.restlet.resources;
import org.apache.commons.lang.StringUtils;
-import org.apache.http.NameValuePair;
-import org.apache.http.client.utils.URLEncodedUtils;
import org.nrg.action.ClientException;
import org.nrg.action.ServerException;
import org.nrg.automation.entities.Script;
@@ -23,7 +21,6 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.IOException;
-import java.nio.charset.Charset;
import java.util.ArrayList;
import java.util.Hashtable;
import java.util.List;
@@ -95,7 +92,7 @@ public class ScriptResource extends AutomationResource {
try {
if (StringUtils.isNotBlank(_version)) {
//They're requesting a specific version of a specific script
- return new StringRepresentation(MAPPER.writeValueAsString(_scriptService.getVersion(_scriptId, _version)), mediaType);
+ return new StringRepresentation(toJson(_scriptService.getVersion(_scriptId, _version)), mediaType);
}
else {
// They're requesting a specific script, so return that to them.
@@ -110,7 +107,7 @@ public class ScriptResource extends AutomationResource {
// have to check if it's null, or else it will return a StringRepresentation containing the word null instead of a 404
if (script != null) {
- return new StringRepresentation(MAPPER.writeValueAsString(script), mediaType);
+ return new StringRepresentation(toJson(script), mediaType);
} else {
return null;
}
@@ -200,25 +197,7 @@ public class ScriptResource extends AutomationResource {
throw new ClientException(Status.CLIENT_ERROR_UNSUPPORTED_MEDIA_TYPE, "This function currently only supports " + MediaType.APPLICATION_WWW_FORM + " and " + MediaType.APPLICATION_JSON);
}
- final Properties properties;
- if (mediaType.equals(MediaType.APPLICATION_WWW_FORM)) {
- try {
- final List<NameValuePair> formMap = URLEncodedUtils.parse(entity.getText(), DEFAULT_CHARSET);
- properties = new Properties();
- for (final NameValuePair entry : formMap) {
- properties.setProperty(entry.getName(), entry.getValue());
- }
- } catch (IOException e) {
- throw new ServerException(Status.SERVER_ERROR_INTERNAL, "An error occurred trying to read the submitted form body.", e);
- }
- } else {
- try {
- final String text = entity.getText();
- properties = MAPPER.readValue(text, Properties.class);
- } catch (IOException e) {
- throw new ServerException(Status.SERVER_ERROR_INTERNAL, "An error occurred processing the script properties", e);
- }
- }
+ final Properties properties = decodeProperties(entity, mediaType);
if (properties.containsKey("scriptId")) {
properties.remove("scriptId");
@@ -253,7 +232,6 @@ public class ScriptResource extends AutomationResource {
private static final String SCRIPT_ID = "SCRIPT_ID";
private static final String VERSION = "VERSION";
- private static final Charset DEFAULT_CHARSET = Charset.forName("UTF-8");
private final ScriptService _scriptService;
private final ScriptRunnerService _runnerService;
diff --git a/src/main/java/org/nrg/xnat/restlet/resources/ScriptRunnerResource.java b/src/main/java/org/nrg/xnat/restlet/resources/ScriptRunnerResource.java
index 18258397708b816d0b82d8bce965d1b449746d94..31c458d3f9c1ab0c9ccea2fac9adc76cecaf1556 100644
--- a/src/main/java/org/nrg/xnat/restlet/resources/ScriptRunnerResource.java
+++ b/src/main/java/org/nrg/xnat/restlet/resources/ScriptRunnerResource.java
@@ -1,7 +1,5 @@
package org.nrg.xnat.restlet.resources;
-import com.fasterxml.jackson.core.JsonProcessingException;
-import com.fasterxml.jackson.databind.ObjectMapper;
import org.apache.commons.lang.StringUtils;
import org.nrg.automation.runners.ScriptRunner;
import org.nrg.automation.services.ScriptRunnerService;
@@ -58,13 +56,13 @@ public class ScriptRunnerResource extends AutomationResource {
if (!_runnerService.hasRunner(_language)) {
throw new ResourceException(Status.CLIENT_ERROR_NOT_FOUND, String.format("No script runner found for %s", _language));
}
- final String json = _serializer.writeValueAsString(_runnerService.getRunner(_language));
+ final String json = toJson(_runnerService.getRunner(_language));
return new StringRepresentation(json, mediaType);
} else {
final List<String> runners = _runnerService.getRunners();
- return new StringRepresentation(_serializer.writeValueAsString(runners), mediaType);
+ return new StringRepresentation(toJson(runners), mediaType);
}
- } catch (JsonProcessingException e) {
+ } catch (java.io.IOException e) {
throw new ResourceException(Status.SERVER_ERROR_INTERNAL, "There was an error processing the script runners to JSON", e);
}
}
@@ -73,7 +71,6 @@ public class ScriptRunnerResource extends AutomationResource {
private static final String LANGUAGE = "LANGUAGE";
- private static final ObjectMapper _serializer = new ObjectMapper();
private final ScriptRunnerService _runnerService;
private final String _language;
}
diff --git a/src/main/java/org/nrg/xnat/restlet/resources/ScriptTriggerResource.java b/src/main/java/org/nrg/xnat/restlet/resources/ScriptTriggerResource.java
index 1509ea080b85ebd8dc578ab7b2f54911a8e84254..4564240f0462576250900051802ada2ec4df64a4 100644
--- a/src/main/java/org/nrg/xnat/restlet/resources/ScriptTriggerResource.java
+++ b/src/main/java/org/nrg/xnat/restlet/resources/ScriptTriggerResource.java
@@ -1,8 +1,6 @@
package org.nrg.xnat.restlet.resources;
import org.apache.commons.lang.StringUtils;
-import org.apache.http.NameValuePair;
-import org.apache.http.client.utils.URLEncodedUtils;
import org.nrg.action.ClientException;
import org.nrg.action.ServerException;
import org.nrg.automation.entities.ScriptTrigger;
@@ -22,7 +20,6 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.IOException;
-import java.nio.charset.Charset;
import java.util.*;
public class ScriptTriggerResource extends AutomationResource {
@@ -124,7 +121,7 @@ public class ScriptTriggerResource extends AutomationResource {
if (_trigger != null) {
try {
// They're requesting a specific trigger, so return that to them.
- return new StringRepresentation(MAPPER.writeValueAsString(mapTrigger(_trigger)), mediaType);
+ return new StringRepresentation(toJson(mapTrigger(_trigger)), mediaType);
} catch (IOException e) {
throw new ResourceException(Status.SERVER_ERROR_INTERNAL, "An error occurred marshalling the script trigger data to JSON", e);
}
@@ -245,25 +242,7 @@ public class ScriptTriggerResource extends AutomationResource {
throw new ClientException(Status.CLIENT_ERROR_UNSUPPORTED_MEDIA_TYPE, "This function currently only supports " + MediaType.APPLICATION_WWW_FORM + " and " + MediaType.APPLICATION_JSON);
}
- final Properties properties;
- if (mediaType.equals(MediaType.APPLICATION_WWW_FORM)) {
- try {
- final List<NameValuePair> formMap = URLEncodedUtils.parse(entity.getText(), DEFAULT_CHARSET);
- properties = new Properties();
- for (final NameValuePair entry : formMap) {
- properties.setProperty(entry.getName(), entry.getValue());
- }
- } catch (IOException e) {
- throw new ServerException(Status.SERVER_ERROR_INTERNAL, "An error occurred trying to read the submitted form body.", e);
- }
- } else {
- try {
- final String text = entity.getText();
- properties = MAPPER.readValue(text, Properties.class);
- } catch (IOException e) {
- throw new ServerException(Status.SERVER_ERROR_INTERNAL, "An error occurred processing the script properties", e);
- }
- }
+ final Properties properties = decodeProperties(entity, mediaType);
// TODO: These remove definitions of scope, entity ID, and script ID that may be passed in on the API call.
// TODO: We may consider throwing an exception if something in the body parameters contradicts the URI
@@ -364,7 +343,6 @@ public class ScriptTriggerResource extends AutomationResource {
private static final String EVENT_ID = "EVENT_ID";
private static final String TRIGGER_ID = "TRIGGER_ID";
- private static final Charset DEFAULT_CHARSET = Charset.forName("UTF-8");
private final EventService _eventService;
private final ScriptTriggerService _scriptTriggerService;
diff --git a/src/main/java/org/nrg/xnat/restlet/resources/ScriptTriggerTemplateResource.java b/src/main/java/org/nrg/xnat/restlet/resources/ScriptTriggerTemplateResource.java
index a4318cad192091527e8b94431a87d13b448e604b..4ebd8205034dd6b4f209daeebab30585696fb367 100644
--- a/src/main/java/org/nrg/xnat/restlet/resources/ScriptTriggerTemplateResource.java
+++ b/src/main/java/org/nrg/xnat/restlet/resources/ScriptTriggerTemplateResource.java
@@ -2,7 +2,6 @@ package org.nrg.xnat.restlet.resources;
import com.google.common.base.Joiner;
import org.apache.commons.lang.StringUtils;
-import com.fasterxml.jackson.databind.ObjectMapper;
import org.nrg.action.ClientException;
import org.nrg.automation.entities.ScriptTrigger;
import org.nrg.automation.entities.ScriptTriggerTemplate;
@@ -224,7 +223,7 @@ public class ScriptTriggerTemplateResource extends AutomationResource {
} else if (entity.getMediaType().equals(MediaType.APPLICATION_JSON)) {
try {
final String text = entity.getText();
- found = MAPPER.readValue(text, ScriptTriggerTemplate.class);
+ found = getSerializer().deserializeJson(text, ScriptTriggerTemplate.class);
} catch (IOException e) {
throw new ClientException(Status.SERVER_ERROR_INTERNAL, "An error occurred processing the script properties", e);
}
@@ -310,6 +309,4 @@ public class ScriptTriggerTemplateResource extends AutomationResource {
}
return persisted.size() > 0 ? persisted : null;
}
-
- private static final ObjectMapper MAPPER = new ObjectMapper();
}
diff --git a/src/main/java/org/nrg/xnat/restlet/resources/ScriptVersionsResource.java b/src/main/java/org/nrg/xnat/restlet/resources/ScriptVersionsResource.java
index 4d62c1824fc4e387817d95eae1e6bce9da1f23b0..b017b3a32cf3b26115a0f0a71550b293427a9080 100644
--- a/src/main/java/org/nrg/xnat/restlet/resources/ScriptVersionsResource.java
+++ b/src/main/java/org/nrg/xnat/restlet/resources/ScriptVersionsResource.java
@@ -21,7 +21,6 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.IOException;
-import java.nio.charset.Charset;
import java.util.ArrayList;
import java.util.Hashtable;
import java.util.List;
@@ -88,7 +87,7 @@ public class ScriptVersionsResource extends AutomationResource {
// have to check if it's null, or else it will return a StringRepresentation containing the word null instead of a 404
if (versions != null) {
- return new StringRepresentation(MAPPER.writeValueAsString(versions), mediaType);
+ return new StringRepresentation(toJson(versions), mediaType);
} else {
return null;
}
@@ -136,7 +135,6 @@ public class ScriptVersionsResource extends AutomationResource {
private static final Logger _log = LoggerFactory.getLogger(ScriptVersionsResource.class);
private static final String SCRIPT_ID = "SCRIPT_ID";
- private static final Charset DEFAULT_CHARSET = Charset.forName("UTF-8");
private final ScriptService _scriptService;
private final ScriptRunnerService _runnerService;
diff --git a/src/main/java/org/nrg/xnat/restlet/resources/SecureResource.java b/src/main/java/org/nrg/xnat/restlet/resources/SecureResource.java
index 5fc9baa17314e52919d7972b02245a4b34bb0df4..f2d88bc8b39c2d7980a3e2cf40724757ce9aa064 100644
--- a/src/main/java/org/nrg/xnat/restlet/resources/SecureResource.java
+++ b/src/main/java/org/nrg/xnat/restlet/resources/SecureResource.java
@@ -11,7 +11,6 @@
package org.nrg.xnat.restlet.resources;
import com.fasterxml.jackson.core.type.TypeReference;
-import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.collect.Maps;
import com.noelios.restlet.http.HttpConstants;
import org.apache.commons.beanutils.BeanUtils;
@@ -67,6 +66,7 @@ import org.nrg.xnat.restlet.representations.*;
import org.nrg.xnat.restlet.util.FileWriterWrapperI;
import org.nrg.xnat.restlet.util.RequestUtil;
import org.nrg.xnat.turbine.utils.ArchivableItem;
+import org.nrg.xnat.utils.SerializerService;
import org.nrg.xnat.utils.WorkflowUtils;
import org.restlet.Context;
import org.restlet.data.*;
@@ -137,9 +137,17 @@ public abstract class SecureResource extends Resource {
protected String csrfToken = null;
+ private final SerializerService _serializer;
+
public SecureResource(Context context, Request request, Response response) {
super(context, request, response);
+ _serializer = XDAT.getContextService().getBean(SerializerService.class);
+ if (null == _serializer) {
+ getResponse().setStatus(Status.CLIENT_ERROR_FAILED_DEPENDENCY, "Serializer service was not properly initialized.");
+ throw new NrgServiceRuntimeException("ERROR: Serializer service was not properly initialized.");
+ }
+
requested_format = getQueryVariable("format");
// expects that the user exists in the session (either via traditional
@@ -247,6 +255,9 @@ public abstract class SecureResource extends Resource {
return convertFormToMap(getQueryVariableForm());
}
+ protected SerializerService getSerializer() {
+ return _serializer;
+ }
private Form _body;
private MediaType _mediaType;
@@ -519,6 +530,10 @@ public abstract class SecureResource extends Resource {
}
}
+ protected <T> String toJson(final T instance) throws IOException {
+ return getSerializer().toJson(instance);
+ }
+
public interface ItemHandlerI {
String getHandlerString();
@@ -1522,7 +1537,7 @@ public abstract class SecureResource extends Resource {
}
try {
- List<String> userResourceWhitelist = OBJECT_MAPPER.readValue(config, TYPE_REFERENCE_LIST_STRING);
+ List<String> userResourceWhitelist = getSerializer().deserializeJson(config, TYPE_REFERENCE_LIST_STRING);
if (userResourceWhitelist != null) {
return userResourceWhitelist.contains(user.getUsername());
}
@@ -1534,9 +1549,7 @@ public abstract class SecureResource extends Resource {
return false;
}
- protected final static TypeReference<ArrayList<String>> TYPE_REFERENCE_LIST_STRING = new TypeReference<ArrayList<String>>() {
- };
- protected final static ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+ protected final static TypeReference<ArrayList<String>> TYPE_REFERENCE_LIST_STRING = new TypeReference<ArrayList<String>>() {};
private static Map<String, List<FilteredResourceHandlerI>> handlers = Maps.newConcurrentMap();
diff --git a/src/main/java/org/nrg/xnat/restlet/services/AliasTokenRestlet.java b/src/main/java/org/nrg/xnat/restlet/services/AliasTokenRestlet.java
index 042ce9e13f76650b78b650e4bd65dbbdb4e8d939..fd347ffa82d06f67cfbc5e2ccabc923182bf9d86 100644
--- a/src/main/java/org/nrg/xnat/restlet/services/AliasTokenRestlet.java
+++ b/src/main/java/org/nrg/xnat/restlet/services/AliasTokenRestlet.java
@@ -11,14 +11,13 @@
package org.nrg.xnat.restlet.services;
import com.google.common.collect.Maps;
-
import org.apache.commons.lang.StringUtils;
-import com.fasterxml.jackson.databind.ObjectMapper;
import org.nrg.xdat.XDAT;
import org.nrg.xdat.entities.AliasToken;
import org.nrg.xdat.security.helpers.Roles;
import org.nrg.xdat.services.AliasTokenService;
import org.nrg.xnat.restlet.resources.SecureResource;
+import org.nrg.xnat.utils.SerializerService;
import org.restlet.Context;
import org.restlet.data.MediaType;
import org.restlet.data.Request;
@@ -34,15 +33,15 @@ import java.util.HashMap;
import java.util.Map;
public class AliasTokenRestlet extends SecureResource {
- public static final String PARAM_OPERATION = "OPERATION";
- public static final String PARAM_USERNAME = "USERNAME";
- public static final String PARAM_TOKEN = "TOKEN";
- public static final String PARAM_SECRET = "SECRET";
- public static final String OP_ISSUE = "issue";
- public static final String OP_VALIDATE = "validate";
- public static final String OP_INVALIDATE = "invalidate";
+ private static final String PARAM_OPERATION = "OPERATION";
+ private static final String PARAM_USERNAME = "USERNAME";
+ private static final String PARAM_TOKEN = "TOKEN";
+ private static final String PARAM_SECRET = "SECRET";
+ private static final String OP_ISSUE = "issue";
+ private static final String OP_VALIDATE = "validate";
+ private static final String OP_INVALIDATE = "invalidate";
- public AliasTokenRestlet(Context context, Request request, Response response) {
+ public AliasTokenRestlet(Context context, Request request, Response response) throws ResourceException {
super(context, request, response);
getVariants().add(new Variant(MediaType.APPLICATION_JSON));
_operation = (String) getRequest().getAttributes().get(PARAM_OPERATION);
@@ -50,6 +49,12 @@ public class AliasTokenRestlet extends SecureResource {
_token = (String) getRequest().getAttributes().get(PARAM_TOKEN);
final String secret = (String) getRequest().getAttributes().get(PARAM_SECRET);
_secret = StringUtils.isBlank(secret) ? INVALID : Long.parseLong(secret);
+
+ _serializer = XDAT.getContextService().getBean(SerializerService.class);
+ if (null == _serializer) {
+ getResponse().setStatus(Status.CLIENT_ERROR_FAILED_DEPENDENCY, "Serializer service was not properly initialized.");
+ throw new ResourceException(Status.CLIENT_ERROR_FAILED_DEPENDENCY, "ERROR: Serializer service was not properly initialized.");
+ }
}
@Override
@@ -69,9 +74,9 @@ public class AliasTokenRestlet extends SecureResource {
throw new ResourceException(Status.CLIENT_ERROR_UNAUTHORIZED, "You must specify both token and secret to validate a token.");
}
try {
- final HashMap<String, String> results = new HashMap<String, String>();
+ final HashMap<String, String> results = new HashMap<>();
results.put("valid", getService().validateToken(_token, _secret));
- return new StringRepresentation(_serializer.writeValueAsString(results));
+ return new StringRepresentation(_serializer.toJson(results));
} catch (IOException exception) {
throw new ResourceException(Status.SERVER_ERROR_INTERNAL, exception.toString());
}
@@ -89,7 +94,7 @@ public class AliasTokenRestlet extends SecureResource {
map.put("secret", Long.toString(token.getSecret()));
String value = "";
try {
- value = _serializer.writeValueAsString(map);
+ value = _serializer.toJson(map);
} catch (IOException e) {
//
}
@@ -109,10 +114,10 @@ public class AliasTokenRestlet extends SecureResource {
}
private static final int INVALID = -1;
- private static final ObjectMapper _serializer = new ObjectMapper();
- private AliasTokenService _service;
- private String _operation;
- private final String _username;
- private final String _token;
- private final long _secret;
+ private final SerializerService _serializer;
+ private AliasTokenService _service;
+ private String _operation;
+ private final String _username;
+ private final String _token;
+ private final long _secret;
}
diff --git a/src/main/java/org/nrg/xnat/restlet/services/SettingsRestlet.java b/src/main/java/org/nrg/xnat/restlet/services/SettingsRestlet.java
index e1efa228c74e3f15b34358779f3a04025b9b7a7e..5625fdcfef13fe6c9bc871ca79efc491c07652b4 100644
--- a/src/main/java/org/nrg/xnat/restlet/services/SettingsRestlet.java
+++ b/src/main/java/org/nrg/xnat/restlet/services/SettingsRestlet.java
@@ -10,8 +10,6 @@
*/
package org.nrg.xnat.restlet.services;
-import com.fasterxml.jackson.core.JsonFactory;
-import com.fasterxml.jackson.databind.ObjectMapper;
import org.apache.commons.lang.StringUtils;
import org.hibernate.PropertyNotFoundException;
import org.nrg.config.entities.Configuration;
@@ -66,12 +64,17 @@ public class SettingsRestlet extends SecureResource {
public SettingsRestlet(Context context, Request request, Response response) throws IOException {
super(context, request, response);
+
setModifiable(true);
- this.getVariants().add(new Variant(MediaType.APPLICATION_JSON));
- this.getVariants().add(new Variant(MediaType.TEXT_XML));
+
+ getVariants().add(new Variant(MediaType.APPLICATION_JSON));
+ getVariants().add(new Variant(MediaType.TEXT_XML));
+
+ _filterService = XDAT.getContextService().getBean(DicomFilterService.class);
_arcSpec = ArcSpecManager.GetInstance();
_property = (String) getRequest().getAttributes().get("PROPERTY");
+
if (!StringUtils.isBlank(_property)) {
if (_property.equals("initialize")) {
if (_arcSpec != null && _arcSpec.isComplete()) {
@@ -103,7 +106,7 @@ public class SettingsRestlet extends SecureResource {
if (StringUtils.isBlank(_property)) {
return mediaType == MediaType.TEXT_XML ?
new ItemXMLRepresentation(_arcSpec.getItem(), mediaType) :
- new StringRepresentation("{\"ResultSet\":{\"Result\":" + new ObjectMapper().writeValueAsString(getArcSpecAsMap()) + ", \"title\": \"Settings\"}}");
+ new StringRepresentation("{\"ResultSet\":{\"Result\":" + toJson(getArcSpecAsMap()) + ", \"title\": \"Settings\"}}");
} else {
if (!getArcSpecAsMap().containsKey(_property)) {
throw new PropertyNotFoundException(String.format("Setting '%s' was not found in the system.", _property));
@@ -114,7 +117,7 @@ public class SettingsRestlet extends SecureResource {
String xml = "<" + _property + ">" + propertyValue.toString() + "</" + _property + ">";
return new StringRepresentation(xml, mediaType);
} else {
- return new StringRepresentation("{\"ResultSet\":{\"Result\":" + new ObjectMapper().writeValueAsString(propertyValue) + ", \"title\": \"" + _property + "\"}}");
+ return new StringRepresentation("{\"ResultSet\":{\"Result\":" + toJson(propertyValue) + ", \"title\": \"" + _property + "\"}}");
}
}
} catch (PropertyNotFoundException exception) {
@@ -180,11 +183,6 @@ public class SettingsRestlet extends SecureResource {
}
private DicomFilterService getDicomFilterService() {
- if (_filterService == null) {
- synchronized (_log) {
- _filterService = XDAT.getContextService().getBean(DicomFilterService.class);
- }
- }
return _filterService;
}
@@ -225,7 +223,7 @@ public class SettingsRestlet extends SecureResource {
map.put(atoms[0], atoms[1]);
}
- return MAPPER.writeValueAsString(map);
+ return toJson(map);
} catch (IOException ignored) {
// We're not reading from a file, so we shouldn't encounter this.
}
@@ -234,7 +232,7 @@ public class SettingsRestlet extends SecureResource {
}
// TODO: Gross.
- public static final String ADMIN_USERNAME_FOR_SUBSCRIPTION = "admin";
+ private static final String ADMIN_USERNAME_FOR_SUBSCRIPTION = "admin";
/**
* This returns the current subscriber or subscribers to a particular <i>site-wide</i> event. If the event doesn't
@@ -934,11 +932,9 @@ public class SettingsRestlet extends SecureResource {
return users.get(0).getLogin();
}
- private static final ObjectMapper MAPPER = new ObjectMapper(new JsonFactory());
-
private static final Logger _log = LoggerFactory.getLogger(SettingsRestlet.class);
- private DicomFilterService _filterService;
+ private final DicomFilterService _filterService;
private NotificationService _notificationService;
private ArcArchivespecification _arcSpec;
diff --git a/src/main/java/org/nrg/xnat/services/impl/ThemeServiceImpl.java b/src/main/java/org/nrg/xnat/services/impl/ThemeServiceImpl.java
index f72a2cfaab5dae947be92c2b6da130b98c30673c..8f2d1315f6879cf53f9ad0c6562d9c92f3401f8e 100644
--- a/src/main/java/org/nrg/xnat/services/impl/ThemeServiceImpl.java
+++ b/src/main/java/org/nrg/xnat/services/impl/ThemeServiceImpl.java
@@ -12,11 +12,11 @@
package org.nrg.xnat.services.impl;
import com.fasterxml.jackson.core.JsonProcessingException;
-import com.fasterxml.jackson.databind.ObjectMapper;
import org.apache.commons.lang.ArrayUtils;
import org.apache.commons.lang.StringUtils;
import org.nrg.xnat.configuration.ThemeConfig;
import org.nrg.xnat.services.ThemeService;
+import org.nrg.xnat.utils.SerializerService;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
@@ -34,9 +34,11 @@ public class ThemeServiceImpl implements ThemeService {
private static String themesPath;
private static ThemeConfig themeConfig = null;
private static File themeFile = null;
- protected final ObjectMapper mapper = new ObjectMapper();
private static final int FILE_BUFFER_SIZE = 4096;
+ @Autowired
+ private SerializerService _serializer;
+
@Autowired
private ServletContext servletContext;
@@ -75,7 +77,7 @@ System.out.println("Theme Path: "+themeFile);
}
reader.close();
String contents = sb.toString();
- themeConfig = mapper.readValue(contents, ThemeConfig.class);
+ themeConfig = _serializer.deserializeJson(contents, ThemeConfig.class);
} catch (IOException e) {
e.printStackTrace();
}
@@ -86,7 +88,7 @@ System.out.println("Theme Path: "+themeFile);
e.printStackTrace();
}
}
- if(role != null){
+ if (role != null) {
// TODO: implement search through the roles array in the ThemeConfig object for a matching ThemeConfig object for the specified role
}
return themeConfig;
@@ -130,6 +132,7 @@ System.out.println("Theme Path: "+themeFile);
private String checkThemeFileExists(ThemeConfig theme, String pageName) {
return checkThemeFileExists(theme, pageName, null);
}
+
private String checkThemeFileExists(ThemeConfig theme, String pageName, String type) {
String pagePath = null, typeSep = type + "s" + File.separator;
String[] extensions = new String[]{};
@@ -174,7 +177,7 @@ System.out.println("Theme Path: "+themeFile);
themeConfig = new ThemeConfig();
}
if(themeExists(themeConfig.getName())) {
- String themeJson = mapper.writeValueAsString(themeConfig);
+ String themeJson = _serializer.toJson(themeConfig);
if (!themeFile.exists()) {
themeFile.createNewFile();
}
@@ -276,7 +279,7 @@ System.out.println("Theme Path: "+themeFile);
* @throws IOException
*/
public List<String> extractTheme(InputStream inputStream) throws IOException {
- ArrayList rootDirs = new ArrayList();
+ final List<String> rootDirs = new ArrayList<>();
ZipInputStream zipIn = new ZipInputStream(inputStream);
ZipEntry entry = zipIn.getNextEntry();
while (entry != null) { // iterate over entries in the zip file
@@ -284,8 +287,7 @@ System.out.println("Theme Path: "+themeFile);
if (!entry.isDirectory()) { // if the entry is a file, extract it // TODO: Make sure we get a directory the first iteration through (fail otherwise) so that no files get dumped in the root themes directory
this.extractFile(zipIn, filePath);
} else { // if the entry is a directory, make the directory
- String rootDir = "";
- rootDir = entry.getName();
+ String rootDir = entry.getName();
int slashIndex = rootDir.indexOf('/');
if(slashIndex>1){
int nextSlashIndex = rootDir.indexOf('/', slashIndex+1);
diff --git a/src/main/java/org/nrg/xnat/spawner/controllers/ManageElementsController.java b/src/main/java/org/nrg/xnat/spawner/controllers/ManageElementsController.java
index 2b2ad5a8cd891c4c9c7028fb8eaabaf73c33a6e5..e806046f2010b4aecb9d9785dc8facdeb5896c34 100644
--- a/src/main/java/org/nrg/xnat/spawner/controllers/ManageElementsController.java
+++ b/src/main/java/org/nrg/xnat/spawner/controllers/ManageElementsController.java
@@ -12,20 +12,23 @@ import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.servlet.ModelAndView;
import javax.inject.Inject;
+import java.util.List;
+@SuppressWarnings("SpringMVCViewInspection")
@Controller
@RequestMapping(value = "/spawner/elements", produces = "application/json")
public class ManageElementsController {
@RequestMapping
public ModelAndView getAvailableElements() {
- return new ModelAndView("spawner/elements", "elements", _service.getAvailableSpawnerElementIds());
+ final List<SpawnerElement> elements = _service.getAll();
+ return new ModelAndView("spawner/elements", "elements", elements);
}
@RequestMapping(value = "{elementId}", method = RequestMethod.GET)
public ModelAndView getElement(@PathVariable final String elementId) {
final SpawnerElement element = _service.retrieve(elementId);
- return new ModelAndView("spawner/element", element == null ? "error" : "element", element == null ? "The ID element " + elementId + " was not found in the system." : element);
+ return new ModelAndView("spawner/element", element == null ? "error" : "elementId", element == null ? "The ID element " + elementId + " was not found in the system." : elementId);
}
@RequestMapping(value = "{elementId}", method = RequestMethod.PUT)
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/screens/LaunchUploadApplet.java b/src/main/java/org/nrg/xnat/turbine/modules/screens/LaunchUploadApplet.java
index 2e97b3d45b8a9cf975c0a0430d26c3368aeb11bf..739fb9436059b98b2fd1dea8f28ab38c1d01df2c 100644
--- a/src/main/java/org/nrg/xnat/turbine/modules/screens/LaunchUploadApplet.java
+++ b/src/main/java/org/nrg/xnat/turbine/modules/screens/LaunchUploadApplet.java
@@ -15,7 +15,6 @@ import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.turbine.util.RunData;
import org.apache.velocity.context.Context;
-import com.fasterxml.jackson.databind.ObjectMapper;
import org.nrg.framework.utilities.Reflection;
import org.nrg.xdat.om.XnatPvisitdata;
import org.nrg.xdat.turbine.utils.TurbineUtils;
@@ -28,24 +27,25 @@ import java.util.List;
* @author timo
*
*/
+@SuppressWarnings({"WeakerAccess", "unused"})
public class LaunchUploadApplet extends UploadAppletScreen {
private static final Log _log = LogFactory.getLog(LaunchUploadApplet.class);
-
-
- @Override
+ @Override
public void doBuildTemplate(RunData data, Context context) {
context.put("jsessionid", XnatHttpUtils.getJSESSIONID(data));
- if(StringUtils.trimToEmpty((String)org.nrg.xdat.turbine.utils.TurbineUtils.GetPassedParameter("search_field",data)).equals("xnat:subjectData.ID")) {
- context.put("subject", StringUtils.trimToEmpty((String)org.nrg.xdat.turbine.utils.TurbineUtils.GetPassedParameter("search_value",data)));
+ if(StringUtils.trimToEmpty((String)TurbineUtils.GetPassedParameter("search_field",data)).equals("xnat:subjectData.ID")) {
+ context.put("subject", StringUtils.trimToEmpty((String)TurbineUtils.GetPassedParameter("search_value",data)));
}
- if(StringUtils.isNotBlank((String) org.nrg.xdat.turbine.utils.TurbineUtils.GetPassedParameter("pvisit", data))) {
- XnatPvisitdata visit = XnatPvisitdata.getXnatPvisitdatasById((String) org.nrg.xdat.turbine.utils.TurbineUtils.GetPassedParameter("pvisit", data), TurbineUtils.getUser(data), false);
- context.put("subject", visit.getSubjectId());
- context.put("visit", visit.getId());
+ if(StringUtils.isNotBlank((String) TurbineUtils.GetPassedParameter("pvisit", data))) {
+ final XnatPvisitdata visit = XnatPvisitdata.getXnatPvisitdatasById(TurbineUtils.GetPassedParameter("pvisit", data), TurbineUtils.getUser(data), false);
+ if (visit != null) {
+ context.put("subject", visit.getSubjectId());
+ context.put("visit", visit.getId());
+ }
}
try {
@@ -62,8 +62,7 @@ public class LaunchUploadApplet extends UploadAppletScreen {
if (json != null) {
try {
//we have JSON, so, create applet parameters from it.
- ObjectMapper mapper = new ObjectMapper();
- AppletConfig jsonParams = mapper.readValue(json, AppletConfig.class);
+ AppletConfig jsonParams = getSerializer().deserializeJson(json, AppletConfig.class);
if(jsonParams.getLaunch() != null){
for(String key:jsonParams.getLaunch().keySet()){
@@ -79,8 +78,8 @@ public class LaunchUploadApplet extends UploadAppletScreen {
}
}
- public interface ContextAction {
- public void execute(RunData data, Context context);
+ private interface ContextAction {
+ void execute(RunData data, Context context);
}
private void dynamicContextExpansion(RunData data, Context context) throws Exception {
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/screens/UploadApplet.java b/src/main/java/org/nrg/xnat/turbine/modules/screens/UploadApplet.java
index b98bf84bcd5d372a7011f096a1c87b5bb851172a..c78e6e1952416dd77fbc30f17c6b9cecb113a17f 100644
--- a/src/main/java/org/nrg/xnat/turbine/modules/screens/UploadApplet.java
+++ b/src/main/java/org/nrg/xnat/turbine/modules/screens/UploadApplet.java
@@ -12,7 +12,6 @@ package org.nrg.xnat.turbine.modules.screens;
import org.apache.turbine.util.RunData;
import org.apache.velocity.context.Context;
-import com.fasterxml.jackson.databind.ObjectMapper;
import org.nrg.xdat.turbine.utils.TurbineUtils;
import org.nrg.xnat.turbine.utils.ArcSpecManager;
import org.nrg.xnat.utils.AppletConfig;
@@ -20,6 +19,7 @@ import org.nrg.xnat.utils.XnatHttpUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
+@SuppressWarnings("unused")
public class UploadApplet extends UploadAppletScreen {
private static final Logger logger = LoggerFactory.getLogger(UploadApplet.class);
@@ -41,19 +41,19 @@ public class UploadApplet extends UploadAppletScreen {
// HH:MM or if HH:MM == 00:00 the applet will only verify the scan is on the same day as mm/dd/yyyy. If it receives no
// session_date, it will prompt the user for one. With that said, we want to build up the mm/dd/yyyy string if we can.
// we'll do it here.
- String hhmm = " 00:00";
+ String time = " 00:00";
if (TurbineUtils.HasPassedParameter("session_time_h", data) && TurbineUtils.HasPassedParameter("session_time_m", data)) {
// parameters are set with drop-downs so no need to validate here.
String hr = (String)TurbineUtils.GetPassedParameter("session_time_h", data);
String mm =(String)TurbineUtils.GetPassedParameter("session_time_m", data);
try{
//poor man's validation
- hhmm = Integer.parseInt(hr) + ":" + Integer.parseInt(mm);
+ time = Integer.parseInt(hr) + ":" + Integer.parseInt(mm);
} catch (Exception e){
//if one or both aren't an integer, we'll get here, which is fine. it just means they didn't select a time.
}
}
- context.put("session_date", ((String)TurbineUtils.GetPassedParameter("session_date", data)).replace('.', '/') + " " + hhmm);
+ context.put("session_date", ((String)TurbineUtils.GetPassedParameter("session_date", data)).replace('.', '/') + " " + time);
} else if (TurbineUtils.HasPassedParameter("no_session_date", data)) {
context.put("session_date", "no_session_date");
}
@@ -67,8 +67,7 @@ public class UploadApplet extends UploadAppletScreen {
if (json != null) {
try {
//we have JSON, so, create applet parameters from it.
- ObjectMapper mapper = new ObjectMapper();
- AppletConfig jsonParams = mapper.readValue(json, AppletConfig.class);
+ AppletConfig jsonParams = getSerializer().deserializeJson(json, AppletConfig.class);
StringBuilder sb = new StringBuilder();
if(jsonParams.getParameters() != null) {
for(String key:jsonParams.getParameters().keySet()) {
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/screens/UploadAppletScreen.java b/src/main/java/org/nrg/xnat/turbine/modules/screens/UploadAppletScreen.java
index b6fdafdd84e09fbcfb55b1bf8919e46b867c46fd..46ad360a7cc91d8c106c383877badbb8ad1f263b 100644
--- a/src/main/java/org/nrg/xnat/turbine/modules/screens/UploadAppletScreen.java
+++ b/src/main/java/org/nrg/xnat/turbine/modules/screens/UploadAppletScreen.java
@@ -8,11 +8,17 @@ import org.nrg.xdat.security.helpers.Permissions;
import org.nrg.xdat.turbine.modules.screens.SecureScreen;
import org.nrg.xft.security.UserI;
import org.nrg.xnat.utils.AppletConfig;
+import org.nrg.xnat.utils.SerializerService;
/**
* Contains basic methods used by upload applet screen classes.
*/
public abstract class UploadAppletScreen extends SecureScreen {
+
+ protected UploadAppletScreen() {
+ _serializer = XDAT.getContextService().getBean(SerializerService.class);
+ }
+
protected org.nrg.config.entities.Configuration getAppletConfiguration(final UserI user, final String projectName) {
//grab the applet config. Project level if it exists, otherwise, do the site-wide
ConfigService configService = XDAT.getConfigService();
@@ -53,4 +59,10 @@ public abstract class UploadAppletScreen extends SecureScreen {
}
return config;
}
+
+ protected SerializerService getSerializer() {
+ return _serializer;
+ }
+
+ private final SerializerService _serializer;
}
diff --git a/src/main/java/org/nrg/xnat/utils/SerializerService.java b/src/main/java/org/nrg/xnat/utils/SerializerService.java
new file mode 100644
index 0000000000000000000000000000000000000000..529f10b6777439e32150894975a3fb9f594621f2
--- /dev/null
+++ b/src/main/java/org/nrg/xnat/utils/SerializerService.java
@@ -0,0 +1,53 @@
+package org.nrg.xnat.utils;
+
+import com.fasterxml.jackson.core.type.TypeReference;
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import org.springframework.stereotype.Service;
+
+import javax.inject.Inject;
+import javax.inject.Named;
+import java.io.IOException;
+
+@Service
+public class SerializerService {
+ public JsonNode deserializeJson(final String json) throws IOException {
+ return _jsonObjectMapper.readTree(json);
+ }
+
+ public <T> T deserializeJson(final String json, final Class<T> clazz) throws IOException {
+ return _jsonObjectMapper.readValue(json, clazz);
+ }
+
+ public <T> T deserializeJson(final String json, final TypeReference<T> typeRef) throws IOException {
+ return _jsonObjectMapper.readValue(json, typeRef);
+ }
+
+ public <T> String toJson(final T instance) throws IOException {
+ return _jsonObjectMapper.writeValueAsString(instance);
+ }
+
+ public JsonNode deserializeYaml(final String yaml) throws IOException {
+ return _yamlObjectMapper.readTree(yaml);
+ }
+
+ public <T> T deserializeYaml(final String yaml, Class<T> clazz) throws IOException {
+ return _yamlObjectMapper.readValue(yaml, clazz);
+ }
+
+ public <T> T deserializeYaml(final String yaml, final TypeReference<T> typeRef) throws IOException {
+ return _yamlObjectMapper.readValue(yaml, typeRef);
+ }
+
+ public <T> String toYaml(final T instance) throws IOException {
+ return _yamlObjectMapper.writeValueAsString(instance);
+ }
+
+ @Inject
+ @Named("jsonObjectMapper")
+ private ObjectMapper _jsonObjectMapper;
+
+ @Inject
+ @Named("yamlObjectMapper")
+ private ObjectMapper _yamlObjectMapper;
+}
diff --git a/src/main/resources/META-INF/xnat/spawner/site-admin-elements.yaml b/src/main/resources/META-INF/xnat/spawner/site-admin-elements.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..f6e1311c8fde5ce996662230e772a31353b1c24e
--- /dev/null
+++ b/src/main/resources/META-INF/xnat/spawner/site-admin-elements.yaml
@@ -0,0 +1,117 @@
+# Initial element declarations for the site admin user interface elements.
+siteId:
+ label: Site ID
+ type: text
+ id: site-id
+ description: Identifies your XNAT site.
+ placeholder: Enter your XNAT site ID...
+ url: /xapi/services/prefs/siteId/{siteId}
+ default: XNAT
+ validation:
+ required: true
+ type: xnat-id
+
+siteUrl:
+ label: Site Url
+ type: url
+ description: The root URL for the site. This is passed to external services.
+ placeholder: Enter the URL for your XNAT site...
+ value: https://cnda.wustl.edu
+ validation:
+ required: true
+
+siteDescriptionPage:
+ id: desc-page
+ label: Page
+ type: site.path
+ description: The page to display for the site description, e.g. /screens/site_description.vm.
+ value: /screens/site_description.vm
+ placeholder: Enter a page for your site description...
+ validation:
+ required: true
+
+siteDescriptionMarkdown:
+ id: desc-markdown
+ label: Text (Markdown)
+ type: markdown
+ tooltip: XNAT allows you to use GitHub-flavored Markdown to create and format your own site description. [>> View Tutorial](http://foobar)
+ description: Compose a site description without referencing a template or site page.
+ validation:
+ required: true
+
+siteDescription:
+ label: Site Description
+ type: composite
+ selection: radio
+ url: /data/services/prefs/{desc}
+ children:
+ ${siteDescriptionPage}
+ ${siteDescriptionMarkdown}
+
+landingPage:
+ label: Landing Page
+ type: site.path
+ description: The page to display when the user logs in.
+ value: /screens/QuickSearch.vm
+ placeholder: Enter the default landing page...
+ overrides:
+ target: homePage
+ type: checkbox
+ position: right
+ description: Use this as my home page.
+ hideTarget: false
+ validation:
+ required: true
+
+homePage:
+ label: Home Page
+ type: site.path
+ description: The page to display when the user clicks the home link.
+ value: /screens/AdminUsers.vm
+ placeholder: Enter the default home page...
+ validation:
+ required: true
+
+siteInfo:
+ label: Site Information
+ type: panel
+ controls:
+ ${siteId}
+ ${siteUrl}
+ ${siteDescription}
+ ${landingPage}
+ ${homePage}
+
+siteAdminEmail:
+ label: Site Admin Email
+ type: email
+ placeholder: Administrator email address...
+ url: /xapi/services/prefs/siteAdminEmail/{siteAdminEmail}
+ validation:
+ required: true
+
+adminInfo:
+ label: Admin Information
+ type: panel
+ controls:
+ ${siteAdminEmail}
+
+siteSetup:
+ label: Site Setup
+ type: tab
+ contents:
+ ${siteInfo}
+ ${adminInfo}
+
+xnatSetup:
+ label: XNAT Setup
+ type: tabGroup
+ tabs:
+ ${siteSetup}
+
+siteAdmin:
+ label: Administer XNAT
+ type: page
+ contains: tabs
+ contents:
+ ${xnatSetup}
diff --git a/src/main/webapp/META-INF/context.xml b/src/main/webapp/META-INF/context.xml
index 16bd2bec3ce56149a803754e2972b96d298abe37..b4c53f63c28668cc23be5f6c85c64b2487290da0 100644
--- a/src/main/webapp/META-INF/context.xml
+++ b/src/main/webapp/META-INF/context.xml
@@ -1,5 +1,5 @@
-<?xml version='1.0' encoding='utf-8'?>
-<Context antiResourceLocking="true">
+<?xml version="1.0" encoding="utf-8"?>
+<Context>
<Loader className="org.apache.catalina.loader.VirtualWebappLoader" searchVirtualFirst="true" virtualClasspath="${xnat.home}/plugins/*.jar"/>
<JarScanner scanAllDirectories="true" />
<Parameter name="xnatHome" value="${xnat.home}"/>
diff --git a/src/main/webapp/WEB-INF/tags/spawner/layout.tag b/src/main/webapp/WEB-INF/tags/spawner/layout.tag
index 5e28cd9a34e305364548dab4f76d9faa4c974e4b..b096d29672bf34e178c3f841b9d897b312a33cfb 100644
--- a/src/main/webapp/WEB-INF/tags/spawner/layout.tag
+++ b/src/main/webapp/WEB-INF/tags/spawner/layout.tag
@@ -723,7 +723,7 @@
<div id="layout_content">
<!--BEGIN SCREEN CONTENT -->
- <jsp:doBody scope="page"/>
+ <jsp:doBody/>
<!-- END SCREEN CONTENT -->
</div>
diff --git a/src/main/webapp/WEB-INF/views/spawner/element.jsp b/src/main/webapp/WEB-INF/views/spawner/element.jsp
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..3954d9e9459d1388d87086a69dd661a5667135ac 100644
--- a/src/main/webapp/WEB-INF/views/spawner/element.jsp
+++ b/src/main/webapp/WEB-INF/views/spawner/element.jsp
@@ -0,0 +1,30 @@
+<%@ page contentType="text/html" pageEncoding="UTF-8" %>
+<%@ taglib prefix="sp" tagdir="/WEB-INF/tags/spawner" %>
+<%@ taglib prefix="c" uri="http://java.sun.com/jsp/jstl/core" %>
+<jsp:useBean id="elementId" scope="request" type="java.lang.String"/>
+
+<c:set var="title" value="Spawner Element: ${elementId}"/>
+<sp:layout title="${title}">
+ <h3 style="margin:0 0 15px 0;">${title}</h3>
+
+ <div style="margin:15px 0;max-width:696px;min-width:400px;">
+ Make your desired changes to the spawner element and click <b>Save</b> when completed.
+ </div>
+
+<script type="text/javascript">
+ var spawnerElement = $.ajax({
+ type : "GET",
+ url:serverRoot+"/xapi/spawner/${elementId}?XNAT_CSRF=" + window.csrfToken,
+ cache: false,
+ async: true,
+ context: this,
+ dataType: "yaml"
+ });
+ spawnerElement.done( function( data, textStatus, jqXHR ) {
+ if (typeof data.ResultSet !== "undefined" && typeof data.ResultSet.Result !== "undefined") {
+ alert(data);
+ }
+ });
+
+</script>
+</sp:layout>
\ No newline at end of file
diff --git a/src/main/webapp/WEB-INF/views/spawner/elements.jsp b/src/main/webapp/WEB-INF/views/spawner/elements.jsp
index ed05c3b0a19202b2d98b978aaa9e5496e7d20aa3..bea671ed2573041d7d256d8de89739360fd3d41e 100644
--- a/src/main/webapp/WEB-INF/views/spawner/elements.jsp
+++ b/src/main/webapp/WEB-INF/views/spawner/elements.jsp
@@ -3,13 +3,12 @@
<%@ taglib prefix="sp" tagdir="/WEB-INF/tags/spawner" %>
<%@ taglib prefix="c" uri="http://java.sun.com/jsp/jstl/core" %>
<jsp:useBean id="elements" scope="request" type="java.util.List"/>
-<jsp:useBean id="element" scope="request" type="org.nrg.xnat.spawner.entities.SpawnerElement"/>
<sp:layout title="Spawner Elements">
<h3 style="margin:0 0 15px 0;">Spawner Elements</h3>
<div style="margin:15px 0;max-width:696px;min-width:400px;">
- The Spawner is XNAT's system for managing dynamically configurable user interface elements.
+ The Spawner is XNAT's system for creating and updating dynamically configurable user interface elements.
</div>
<div class="yui-skin-sam">
@@ -105,14 +104,13 @@
<c:forEach var="element" items="${elements}">
<tr class="highlight events-list">
<td class="site-event-id">
- ${element.label}
+ <a href="elements/${element.elementId}" class="edit-event" data-action="editEvent"
+ title="edit existing event">${element.label}</a>
</td>
<td class="site-event-label">
${element.description}
</td>
<td class="actions" style="text-align:center;white-space:nowrap;">
- <a href="#!" class="edit-event" data-action="editEvent"
- title="edit existing event">edit</a>
<a href="#!" class="delete-event" data-action="deleteEvent"
title="delete existing event">delete</a>
</td>
diff --git a/src/main/webapp/resources/ui/skins/default/skin.props b/src/main/webapp/resources/ui/skins/default/skin.props
new file mode 100755
index 0000000000000000000000000000000000000000..59eecbe213ab4d3931579d7b71d4cc5e9161da8a
--- /dev/null
+++ b/src/main/webapp/resources/ui/skins/default/skin.props
@@ -0,0 +1,29 @@
+# These are the default properties
+bgcolor = #ffffff
+sansSerifFonts = verdana,geneva,helvetica
+#formLabelColor = #b3cc99
+#formFieldColor = #b3bb99
+#labelColor = #b3cc99
+#dataColor = #b3bb99
+formLabelColor = #ffffff
+formFieldColor = #ffffff
+labelColor = #ffffff
+dataColor = #ffffff
+#vlink = #330066
+#alink = #663399
+vlink = #000000
+alink = #000000
+tableCellSpacing = 0
+tableCellPadding = 0
+menuColor = #000000
+buttonAlignment = left
+buttonColor = #DDDDDD
+# Images alertImage = alert1.gif
+logo = logo.jpg
+poweredByImage = powered_by_tambora.gif
+line = line.gif
+#darkColor = #000088
+#lightColor = #DDDDDD
+darkColor = #000066
+lightColor = #333399
+tableColor = #AAAAAA
\ No newline at end of file
diff --git a/src/main/webapp/resources/ui/skins/default/skin.txt b/src/main/webapp/resources/ui/skins/default/skin.txt
new file mode 100755
index 0000000000000000000000000000000000000000..081a8930bd907dee5d0de030c6eb6cc8d5746a34
Binary files /dev/null and b/src/main/webapp/resources/ui/skins/default/skin.txt differ