<commit_before>package org.mskcc.portal.servlet;

import java.io.IOException;

import java.io.PrintWriter;
import java.rmi.RemoteException;
import java.util.*;

import javax.servlet.RequestDispatcher;
import javax.servlet.ServletContext;
import javax.servlet.ServletException;
import javax.servlet.http.HttpServlet;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;

import org.apache.commons.lang.StringUtils;

import org.springframework.context.ApplicationContext;
import org.springframework.context.support.ClassPathXmlApplicationContext;

import org.mskcc.cgds.model.ClinicalData;
import org.mskcc.portal.model.*;
import org.mskcc.portal.oncoPrintSpecLanguage.OncoPrintLangException;
import org.mskcc.portal.oncoPrintSpecLanguage.ParserOutput;
import org.mskcc.portal.remote.*;
import org.mskcc.portal.util.*;
import org.mskcc.portal.r_bridge.SurvivalPlot;
import org.mskcc.portal.validator.gene.GeneValidator;
import org.mskcc.portal.validator.gene.GeneValidationException;
import org.mskcc.cgds.model.CancerStudy;
import org.mskcc.cgds.model.CaseList;
import org.mskcc.cgds.model.GeneticProfile;
import org.mskcc.cgds.model.GeneticAlterationType;
import org.mskcc.cgds.model.ExtendedMutation;
import org.mskcc.cgds.dao.DaoException;
import org.mskcc.cgds.web_api.GetProfileData;
import org.mskcc.cgds.web_api.ProtocolException;
import org.mskcc.cgds.util.AccessControl;
import org.owasp.validator.html.PolicyException;

/**
 * Central Servlet for building queries.
 */
public class QueryBuilder extends HttpServlet {
    public static final String CLIENT_TRANSPOSE_MATRIX = "transpose_matrix";
    public static final String CANCER_TYPES_INTERNAL = "cancer_types";
    public static final String PROFILE_LIST_INTERNAL = "profile_list";
    public static final String CASE_SETS_INTERNAL = "case_sets";
    public static final String CANCER_STUDY_ID = "cancer_study_id";
    public static final String CLINICAL_DATA_LIST = "clinical_data_list";
    public static final String GENETIC_PROFILE_IDS = "genetic_profile_ids";
    public static final String GENE_SET_CHOICE = "gene_set_choice";
    public static final String CASE_SET_ID = "case_set_id";
    public static final String CASE_IDS = "case_ids";
    public static final String GENE_LIST = "gene_list";
    public static final String ACTION_NAME = "Action";
    public static final String OUTPUT = "output";
    public static final String FORMAT = "format";
    public static final String PLOT_TYPE = "plot_type";
    public static final String OS_SURVIVAL_PLOT = "os_survival_plot";
    public static final String DFS_SURVIVAL_PLOT = "dfs_survival_plot";
    public static final String XDEBUG = "xdebug";
    public static final String ACTION_SUBMIT = "Submit";
    public static final String STEP1_ERROR_MSG = "step1_error_msg";
    public static final String STEP2_ERROR_MSG = "step2_error_msg";
    public static final String STEP3_ERROR_MSG = "step3_error_msg";
    public static final String STEP4_ERROR_MSG = "step4_error_msg";
    public static final String MERGED_PROFILE_DATA_INTERNAL = "merged_profile_data";
    public static final String PROFILE_DATA_SUMMARY = "profile_data_summary";
    public static final String WARNING_UNION = "warning_union";
    public static final String DOWNLOAD_LINKS = "download_links";
    public static final String NETWORK = "network";
    public static final String HTML_TITLE = "html_title";
    public static final String TAB_INDEX = "tab_index";
    public static final String TAB_DOWNLOAD = "tab_download";
    public static final String TAB_VISUALIZE = "tab_visualize";
    public static final String USER_ERROR_MESSAGE = "user_error_message";
    public static final String ATTRIBUTE_URL_BEFORE_FORWARDING = "ATTRIBUTE_URL_BEFORE_FORWARDING";
    public static final String Z_SCORE_THRESHOLD = "Z_SCORE_THRESHOLD";
    public static final String MRNA_PROFILES_SELECTED = "MRNA_PROFILES_SELECTED";
    public static final String COMPUTE_LOG_ODDS_RATIO = "COMPUTE_LOG_ODDS_RATIO";
    public static final int MUTATION_DETAIL_LIMIT = 10;
    public static final String MUTATION_DETAIL_LIMIT_REACHED = "MUTATION_DETAIL_LIMIT_REACHED";
    public static final String XDEBUG_OBJECT = "xdebug_object";
    public static final String ONCO_PRINT_HTML = "oncoprint_html";<commit_msg>increased the maximum number of genes allowed for mutation details from 10 to 20.<commit_after>package org.mskcc.portal.servlet;

import java.io.IOException;

import java.io.PrintWriter;
import java.rmi.RemoteException;
import java.util.*;

import javax.servlet.RequestDispatcher;
import javax.servlet.ServletContext;
import javax.servlet.ServletException;
import javax.servlet.http.HttpServlet;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;

import org.apache.commons.lang.StringUtils;

import org.springframework.context.ApplicationContext;
import org.springframework.context.support.ClassPathXmlApplicationContext;

import org.mskcc.cgds.model.ClinicalData;
import org.mskcc.portal.model.*;
import org.mskcc.portal.oncoPrintSpecLanguage.OncoPrintLangException;
import org.mskcc.portal.oncoPrintSpecLanguage.ParserOutput;
import org.mskcc.portal.remote.*;
import org.mskcc.portal.util.*;
import org.mskcc.portal.r_bridge.SurvivalPlot;
import org.mskcc.portal.validator.gene.GeneValidator;
import org.mskcc.portal.validator.gene.GeneValidationException;
import org.mskcc.cgds.model.CancerStudy;
import org.mskcc.cgds.model.CaseList;
import org.mskcc.cgds.model.GeneticProfile;
import org.mskcc.cgds.model.GeneticAlterationType;
import org.mskcc.cgds.model.ExtendedMutation;
import org.mskcc.cgds.dao.DaoException;
import org.mskcc.cgds.web_api.GetProfileData;
import org.mskcc.cgds.web_api.ProtocolException;
import org.mskcc.cgds.util.AccessControl;
import org.owasp.validator.html.PolicyException;

/**
 * Central Servlet for building queries.
 */
public class QueryBuilder extends HttpServlet {
    public static final String CLIENT_TRANSPOSE_MATRIX = "transpose_matrix";
    public static final String CANCER_TYPES_INTERNAL = "cancer_types";
    public static final String PROFILE_LIST_INTERNAL = "profile_list";
    public static final String CASE_SETS_INTERNAL = "case_sets";
    public static final String CANCER_STUDY_ID = "cancer_study_id";
    public static final String CLINICAL_DATA_LIST = "clinical_data_list";
    public static final String GENETIC_PROFILE_IDS = "genetic_profile_ids";
    public static final String GENE_SET_CHOICE = "gene_set_choice";
    public static final String CASE_SET_ID = "case_set_id";
    public static final String CASE_IDS = "case_ids";
    public static final String GENE_LIST = "gene_list";
    public static final String ACTION_NAME = "Action";
    public static final String OUTPUT = "output";
    public static final String FORMAT = "format";
    public static final String PLOT_TYPE = "plot_type";
    public static final String OS_SURVIVAL_PLOT = "os_survival_plot";
    public static final String DFS_SURVIVAL_PLOT = "dfs_survival_plot";
    public static final String XDEBUG = "xdebug";
    public static final String ACTION_SUBMIT = "Submit";
    public static final String STEP1_ERROR_MSG = "step1_error_msg";
    public static final String STEP2_ERROR_MSG = "step2_error_msg";
    public static final String STEP3_ERROR_MSG = "step3_error_msg";
    public static final String STEP4_ERROR_MSG = "step4_error_msg";
    public static final String MERGED_PROFILE_DATA_INTERNAL = "merged_profile_data";
    public static final String PROFILE_DATA_SUMMARY = "profile_data_summary";
    public static final String WARNING_UNION = "warning_union";
    public static final String DOWNLOAD_LINKS = "download_links";
    public static final String NETWORK = "network";
    public static final String HTML_TITLE = "html_title";
    public static final String TAB_INDEX = "tab_index";
    public static final String TAB_DOWNLOAD = "tab_download";
    public static final String TAB_VISUALIZE = "tab_visualize";
    public static final String USER_ERROR_MESSAGE = "user_error_message";
    public static final String ATTRIBUTE_URL_BEFORE_FORWARDING = "ATTRIBUTE_URL_BEFORE_FORWARDING";
    public static final String Z_SCORE_THRESHOLD = "Z_SCORE_THRESHOLD";
    public static final String MRNA_PROFILES_SELECTED = "MRNA_PROFILES_SELECTED";
    public static final String COMPUTE_LOG_ODDS_RATIO = "COMPUTE_LOG_ODDS_RATIO";
    public static final int MUTATION_DETAIL_LIMIT = 20;
    public static final String MUTATION_DETAIL_LIMIT_REACHED = "MUTATION_DETAIL_LIMIT_REACHED";
    public static final String XDEBUG_OBJECT = "xdebug_object";
    public static final String ONCO_PRINT_HTML = "oncoprint_html";
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