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Cleaned up html in queryname and workplace
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mem61 committed Jun 12, 2024
1 parent b6727a2 commit 1c8a9cd
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Showing 4 changed files with 190 additions and 343 deletions.
1 change: 1 addition & 0 deletions edu.harvard.i2b2.crc/src/server/edu/harvard/i2b2/crc/ejb/QueryManagerBean.java
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Original file line number Diff line number Diff line change
Expand Up @@ -437,6 +437,7 @@ private String saveQuery(SetFinderDAOFactory sfDAOFactory,
String userId = userType.getLogin();
String groupId = userType.getGroup();
QueryDefinitionType queryDefType = getQueryDefinition(i2b2RequestMsgType);
queryDefType.setQueryName(queryDefType.getQueryName().replaceAll("\\<[^>]*>",""));
edu.harvard.i2b2.crc.datavo.setfinder.query.ObjectFactory of = new edu.harvard.i2b2.crc.datavo.setfinder.query.ObjectFactory();

QueryProcessorUtil qpUtil = QueryProcessorUtil.getInstance();
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157 changes: 0 additions & 157 deletions edu.harvard.i2b2.crc/src/server/edu/harvard/i2b2/crc/loader/ws/RestfulService.java
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188 changes: 95 additions & 93 deletions edu.harvard.i2b2.workplace/src/edu/harvard/i2b2/workplace/delegate/AnnotateChildHandler.java
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@@ -1,93 +1,95 @@
/*******************************************************************************
* Copyright (c) 2006-2018 Massachusetts General Hospital
* All rights reserved. This program and the accompanying materials
* are made available under the terms of the Mozilla Public License,
* v. 2.0. If a copy of the MPL was not distributed with this file, You can
* obtain one at http://mozilla.org/MPL/2.0/. I2b2 is also distributed under
* the terms of the Healthcare Disclaimer.
******************************************************************************/
/*
*
* Contributors:
* Lori Phillips
*/
package edu.harvard.i2b2.workplace.delegate;

import edu.harvard.i2b2.common.exception.I2B2DAOException;
import edu.harvard.i2b2.common.exception.I2B2Exception;
import edu.harvard.i2b2.workplace.datavo.i2b2message.MessageHeaderType;
import edu.harvard.i2b2.workplace.datavo.i2b2message.ResponseMessageType;
import edu.harvard.i2b2.workplace.datavo.wdo.AnnotateChildType;
import edu.harvard.i2b2.workplace.datavo.pm.ProjectType;
import edu.harvard.i2b2.workplace.dao.FolderDao;
import edu.harvard.i2b2.workplace.ws.AnnotateChildDataMessage;
import edu.harvard.i2b2.workplace.ws.MessageFactory;


public class AnnotateChildHandler extends RequestHandler {
private AnnotateChildDataMessage annotateChildMsg = null;
private AnnotateChildType annotateChildType = null;
private ProjectType projectInfo = null;

public AnnotateChildHandler(AnnotateChildDataMessage requestMsg) throws I2B2Exception {
annotateChildMsg = requestMsg;
annotateChildType = requestMsg.getAnnotateChildType();

// test bad username -- good 2/1/08
// annotateChildMsg.getMessageHeaderType().getSecurity().setUsername("bad");
projectInfo = getRoleInfo(requestMsg.getMessageHeaderType());
setDbInfo(requestMsg.getMessageHeaderType());
}

@Override
public String execute() throws I2B2Exception {
// call ejb and pass input object
FolderDao annotateChildDao = new FolderDao();
ResponseMessageType responseMessageType = null;
int numAnnotated = -1;

// check to see if we have projectInfo (if not indicates PM service problem)
if(projectInfo == null) {
String response = null;
responseMessageType = MessageFactory.doBuildErrorResponse(annotateChildMsg.getMessageHeaderType(), "User was not validated");
response = MessageFactory.convertToXMLString(responseMessageType);
log.debug("USER_INVALID or PM_SERVICE_PROBLEM");
return response;
}

else {
try {
numAnnotated = annotateChildDao.annotateNode(annotateChildType, projectInfo, this.getDbInfo());
} catch (I2B2DAOException e) {
log.error("AnnotateChildHandler received I2B2DAO exception from DAO");
responseMessageType = MessageFactory.doBuildErrorResponse(annotateChildMsg.getMessageHeaderType(), "Database error");
} catch (I2B2Exception e) {
log.error("AnnotateChildHandler received I2B2 exception from DAO");
responseMessageType = MessageFactory.doBuildErrorResponse(annotateChildMsg.getMessageHeaderType(), "Database error");
}
}

// no errors found
if(responseMessageType == null) {
// no db error but response is empty
if (numAnnotated == 0) {
log.error("annotate object not found");
responseMessageType = MessageFactory.doBuildErrorResponse(annotateChildMsg.getMessageHeaderType(), "Node not found");
}
else if (numAnnotated == -1) {
log.error("database error");
responseMessageType = MessageFactory.doBuildErrorResponse(annotateChildMsg.getMessageHeaderType(), "Database error");
}
else {
MessageHeaderType messageHeader = MessageFactory.createResponseMessageHeader(annotateChildMsg.getMessageHeaderType());
// responseMessageType = MessageFactory.createBuildResponse(messageHeader, null);
responseMessageType = MessageFactory.createBuildResponse(messageHeader);
}
}
String responseWdo = null;
responseWdo = MessageFactory.convertToXMLString(responseMessageType);
return responseWdo;
}

}
/*******************************************************************************
* Copyright (c) 2006-2018 Massachusetts General Hospital
* All rights reserved. This program and the accompanying materials
* are made available under the terms of the Mozilla Public License,
* v. 2.0. If a copy of the MPL was not distributed with this file, You can
* obtain one at http://mozilla.org/MPL/2.0/. I2b2 is also distributed under
* the terms of the Healthcare Disclaimer.
******************************************************************************/
/*
*
* Contributors:
* Lori Phillips
*/
package edu.harvard.i2b2.workplace.delegate;

import edu.harvard.i2b2.common.exception.I2B2DAOException;
import edu.harvard.i2b2.common.exception.I2B2Exception;
import edu.harvard.i2b2.workplace.datavo.i2b2message.MessageHeaderType;
import edu.harvard.i2b2.workplace.datavo.i2b2message.ResponseMessageType;
import edu.harvard.i2b2.workplace.datavo.wdo.AnnotateChildType;
import edu.harvard.i2b2.workplace.datavo.pm.ProjectType;
import edu.harvard.i2b2.workplace.dao.FolderDao;
import edu.harvard.i2b2.workplace.ws.AnnotateChildDataMessage;
import edu.harvard.i2b2.workplace.ws.MessageFactory;


public class AnnotateChildHandler extends RequestHandler {
private AnnotateChildDataMessage annotateChildMsg = null;
private AnnotateChildType annotateChildType = null;
private ProjectType projectInfo = null;

public AnnotateChildHandler(AnnotateChildDataMessage requestMsg) throws I2B2Exception {
annotateChildMsg = requestMsg;
annotateChildType = requestMsg.getAnnotateChildType();
annotateChildType.setNode(annotateChildType.getNode().replaceAll("\\<[^>]*>",""));
annotateChildType.setTooltip(annotateChildType.getTooltip().replaceAll("\\<[^>]*>",""));

// test bad username -- good 2/1/08
// annotateChildMsg.getMessageHeaderType().getSecurity().setUsername("bad");
projectInfo = getRoleInfo(requestMsg.getMessageHeaderType());
setDbInfo(requestMsg.getMessageHeaderType());
}

@Override
public String execute() throws I2B2Exception {
// call ejb and pass input object
FolderDao annotateChildDao = new FolderDao();
ResponseMessageType responseMessageType = null;
int numAnnotated = -1;

// check to see if we have projectInfo (if not indicates PM service problem)
if(projectInfo == null) {
String response = null;
responseMessageType = MessageFactory.doBuildErrorResponse(annotateChildMsg.getMessageHeaderType(), "User was not validated");
response = MessageFactory.convertToXMLString(responseMessageType);
log.debug("USER_INVALID or PM_SERVICE_PROBLEM");
return response;
}

else {
try {
numAnnotated = annotateChildDao.annotateNode(annotateChildType, projectInfo, this.getDbInfo());
} catch (I2B2DAOException e) {
log.error("AnnotateChildHandler received I2B2DAO exception from DAO");
responseMessageType = MessageFactory.doBuildErrorResponse(annotateChildMsg.getMessageHeaderType(), "Database error");
} catch (I2B2Exception e) {
log.error("AnnotateChildHandler received I2B2 exception from DAO");
responseMessageType = MessageFactory.doBuildErrorResponse(annotateChildMsg.getMessageHeaderType(), "Database error");
}
}

// no errors found
if(responseMessageType == null) {
// no db error but response is empty
if (numAnnotated == 0) {
log.error("annotate object not found");
responseMessageType = MessageFactory.doBuildErrorResponse(annotateChildMsg.getMessageHeaderType(), "Node not found");
}
else if (numAnnotated == -1) {
log.error("database error");
responseMessageType = MessageFactory.doBuildErrorResponse(annotateChildMsg.getMessageHeaderType(), "Database error");
}
else {
MessageHeaderType messageHeader = MessageFactory.createResponseMessageHeader(annotateChildMsg.getMessageHeaderType());
// responseMessageType = MessageFactory.createBuildResponse(messageHeader, null);
responseMessageType = MessageFactory.createBuildResponse(messageHeader);
}
}
String responseWdo = null;
responseWdo = MessageFactory.convertToXMLString(responseMessageType);
return responseWdo;
}

}
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