diff --git a/src/main/resources/webapp/jsp/civic/civic-qtip-template.html b/src/main/resources/webapp/jsp/civic/civic-qtip-template.html deleted file mode 100644 index 1f87389d9b7..00000000000 --- a/src/main/resources/webapp/jsp/civic/civic-qtip-template.html +++ /dev/null @@ -1,49 +0,0 @@ - - - - - diff --git a/src/main/resources/webapp/jsp/co_expression.jsp b/src/main/resources/webapp/jsp/co_expression.jsp deleted file mode 100644 index a4dc16c0837..00000000000 --- a/src/main/resources/webapp/jsp/co_expression.jsp +++ /dev/null @@ -1,57 +0,0 @@ -<%-- -- Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. -- -- This library is distributed in the hope that it will be useful, but WITHOUT -- ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS -- FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder -- is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no -- obligations to provide maintenance, support, updates, enhancements or -- modifications. In no event shall Memorial Sloan-Kettering Cancer Center be -- liable to any party for direct, indirect, special, incidental or -- consequential damages, including lost profits, arising out of the use of this -- software and its documentation, even if Memorial Sloan-Kettering Cancer -- Center has been advised of the possibility of such damage. ---%> - -<%-- -- This file is part of cBioPortal. -- -- cBioPortal is free software: you can redistribute it and/or modify -- it under the terms of the GNU Affero General Public License as -- published by the Free Software Foundation, either version 3 of the -- License. -- -- This program is distributed in the hope that it will be useful, -- but WITHOUT ANY WARRANTY; without even the implied warranty of -- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -- GNU Affero General Public License for more details. -- -- You should have received a copy of the GNU Affero General Public License -- along with this program. If not, see . ---%> -
- - \ No newline at end of file diff --git a/src/main/resources/webapp/jsp/cross_cancer_plots_tab.jsp b/src/main/resources/webapp/jsp/cross_cancer_plots_tab.jsp deleted file mode 100644 index a303a76a04f..00000000000 --- a/src/main/resources/webapp/jsp/cross_cancer_plots_tab.jsp +++ /dev/null @@ -1,71 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - - - - -
- -
- - - diff --git a/src/main/resources/webapp/jsp/data_download.jsp b/src/main/resources/webapp/jsp/data_download.jsp deleted file mode 100644 index ff0f3ac4556..00000000000 --- a/src/main/resources/webapp/jsp/data_download.jsp +++ /dev/null @@ -1,79 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - -<%@ page import="org.mskcc.cbio.portal.model.GeneWithScore" %> -<%@ page import="org.mskcc.cbio.portal.util.ValueParser" %> -<%@ page import="java.util.TreeSet" %> -<%@ page import="org.mskcc.cbio.portal.model.DownloadLink" %> -<%@ page import="java.util.ArrayList" %> -<%@ page import="org.mskcc.cbio.portal.servlet.QueryBuilder" %> - -
-
- - - - -<% - String debugStr = request.getParameter("xdebug"); - boolean debug = false; - if (debugStr != null && debugStr.equals("1")) { - debug = true; - } - String textOnly = request.getParameter("text_only"); -%> diff --git a/src/main/resources/webapp/jsp/enrichments_tab.jsp b/src/main/resources/webapp/jsp/enrichments_tab.jsp deleted file mode 100644 index 8a0304717ec..00000000000 --- a/src/main/resources/webapp/jsp/enrichments_tab.jsp +++ /dev/null @@ -1,29 +0,0 @@ -
- - \ No newline at end of file diff --git a/src/main/resources/webapp/jsp/error.jsp b/src/main/resources/webapp/jsp/error.jsp deleted file mode 100644 index d2cade6da30..00000000000 --- a/src/main/resources/webapp/jsp/error.jsp +++ /dev/null @@ -1,65 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - -<%@ page import="org.mskcc.cbio.portal.servlet.QueryBuilder" %> -<%@ page import="org.mskcc.cbio.portal.util.GlobalProperties" %> -<% - request.setAttribute(QueryBuilder.HTML_TITLE, "cBio Cancer Genomics Pathway Portal::Error"); - String userMessage = (String) request.getAttribute(QueryBuilder.USER_ERROR_MESSAGE); - String emailContact = (userMessage != null && userMessage.contains("not authorized")) ? - "cbioportal-access at cbio dot mskcc dot org" : GlobalProperties.getEmailContact(); -%> - - -
-

- <% if (userMessage != null) { %> - Oops! <%= userMessage %>

- <% } else {%> - Oops! An Error Has occurred while processing your request. - <% } %> -  Please try again or send email to <%= emailContact %> if this is any error in this portal. -
- - - - - - - - - - - - - - diff --git a/src/main/resources/webapp/jsp/global/css_include.jsp b/src/main/resources/webapp/jsp/global/css_include.jsp deleted file mode 100644 index 76a56f5b033..00000000000 --- a/src/main/resources/webapp/jsp/global/css_include.jsp +++ /dev/null @@ -1,76 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - -<%@ page import="org.mskcc.cbio.portal.util.GlobalProperties" %> -<%@ taglib prefix='c' uri='http://java.sun.com/jsp/jstl/core' %> - - - - - - - - - - - - - - - -" type="text/css" rel="stylesheet"/> - - - - - - -<% - String authenticationMethod = GlobalProperties.authenticationMethod(); - String global_style = GlobalProperties.getProperty("global_css"); - String special_style = GlobalProperties.getProperty("special_css"); - if (global_style == null) { - global_style = "css/global_portal.css?"+GlobalProperties.getAppVersion(); - } else { - global_style = "css/" + global_style+"?"+GlobalProperties.getAppVersion(); - } - if (special_style != null) { - special_style = "css/" + special_style+"?"+GlobalProperties.getAppVersion(); - } - String globalStyleCSSPath = (authenticationMethod.equals("saml") || authenticationMethod.equals("saml_plus_basic")) ? - "/" + global_style : global_style; - pageContext.setAttribute("globalStyleCSSPath", globalStyleCSSPath); -%> -" type="text/css" rel="stylesheet" /> -<% if (special_style != null) { %> - -<% } %> diff --git a/src/main/resources/webapp/jsp/global/css_include_standard.jsp b/src/main/resources/webapp/jsp/global/css_include_standard.jsp deleted file mode 100644 index b21cfe1f536..00000000000 --- a/src/main/resources/webapp/jsp/global/css_include_standard.jsp +++ /dev/null @@ -1,65 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - -<%@ page import="org.mskcc.cbio.portal.util.GlobalProperties" %> - - - - - - - - - - - - - - - - -<% - String global_style = GlobalProperties.getProperty("global_css"); - String special_style = GlobalProperties.getProperty("special_css"); - if (global_style == null) { - global_style = "css/global_portal.css?"+GlobalProperties.getAppVersion(); - } else { - global_style = "css/" + global_style+"?"+GlobalProperties.getAppVersion(); - } - if (special_style != null) { - special_style = "css/" + special_style+"?"+GlobalProperties.getAppVersion(); - } -%> - -<% if (special_style != null) { %> - -<% } %> diff --git a/src/main/resources/webapp/jsp/global/footer.jsp b/src/main/resources/webapp/jsp/global/footer.jsp deleted file mode 100644 index 0185da1a410..00000000000 --- a/src/main/resources/webapp/jsp/global/footer.jsp +++ /dev/null @@ -1,31 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> diff --git a/src/main/resources/webapp/jsp/global/frontend_config.jsp b/src/main/resources/webapp/jsp/global/frontend_config.jsp deleted file mode 100644 index 59e5a748c22..00000000000 --- a/src/main/resources/webapp/jsp/global/frontend_config.jsp +++ /dev/null @@ -1,123 +0,0 @@ -<%@ page import="java.util.List" %> -<%@ page import="org.mskcc.cbio.portal.servlet.CheckDarwinAccessServlet" %> -<%@ page import="org.mskcc.cbio.portal.util.GlobalProperties" %> - - diff --git a/src/main/resources/webapp/jsp/global/global_variables.jsp b/src/main/resources/webapp/jsp/global/global_variables.jsp deleted file mode 100644 index 70c0dcba21a..00000000000 --- a/src/main/resources/webapp/jsp/global/global_variables.jsp +++ /dev/null @@ -1,159 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - - - -<%@ include file="src/main/webapp/jsp/global/selected_study_variables.jsp" %> - -<%@ page import="org.mskcc.cbio.portal.servlet.QueryBuilder" %> -<%@ page import="java.util.ArrayList" %> -<%@ page import="java.util.HashSet" %> -<%@ page import="org.mskcc.cbio.portal.model.*" %> -<%@ page import="java.text.NumberFormat" %> -<%@ page import="java.text.DecimalFormat" %> -<%@ page import="java.util.Set" %> -<%@ page import="java.util.*" %> -<%@ page import="java.util.Iterator" %> -<%@ page import="org.mskcc.cbio.portal.servlet.ServletXssUtil" %> -<%@ page import="java.util.Enumeration" %> -<%@ page import="java.net.URLEncoder" %> -<%@ page import="org.mskcc.cbio.portal.oncoPrintSpecLanguage.CallOncoPrintSpecParser" %> -<%@ page import="org.mskcc.cbio.portal.oncoPrintSpecLanguage.ParserOutput" %> -<%@ page import="org.mskcc.cbio.portal.oncoPrintSpecLanguage.OncoPrintSpecification" %> -<%@ page import="org.mskcc.cbio.portal.oncoPrintSpecLanguage.Utilities" %> -<%@ page import="org.mskcc.cbio.portal.model.CancerStudy" %> -<%@ page import="org.mskcc.cbio.portal.model.SampleList" %> -<%@ page import="org.mskcc.cbio.portal.model.GeneticProfile" %> -<%@ page import="org.mskcc.cbio.portal.model.GeneticAlterationType" %> -<%@ page import="org.mskcc.cbio.portal.model.Patient" %> -<%@ page import="org.mskcc.cbio.portal.dao.DaoGeneticProfile" %> -<%@ page import="org.apache.commons.logging.LogFactory" %> -<%@ page import="org.apache.commons.logging.Log" %> -<%@ page import="org.apache.commons.text.StringEscapeUtils" %> -<%@ page import="java.lang.reflect.Array" %> -<%@ page import="org.mskcc.cbio.portal.util.*" %> -<%@ page import="org.mskcc.cbio.portal.dao.DaoMutation" %> - -<%@include file="src/main/webapp/jsp/global/server_vars.jsp"%> -<% - Boolean showIGVtab = (Boolean) request.getAttribute("showIGVtab"); - Boolean has_mrna = (Boolean) request.getAttribute("hasMrna"); - Boolean has_methylation = (Boolean) request.getAttribute("hasMethylation"); - Boolean has_copy_no = (Boolean) request.getAttribute("hasCopyNo"); - Boolean has_survival = (Boolean) request.getAttribute("hasSurvival"); - boolean includeNetworks = GlobalProperties.includeNetworks(); - boolean computeLogOddsRatio = true; - Boolean mutationDetailLimitReached = (Boolean)request.getAttribute(QueryBuilder.MUTATION_DETAIL_LIMIT_REACHED); - boolean showCoexpTab = false; - - //are we using session service for bookmarking? - boolean useSessionServiceBookmark = !StringUtils.isBlank(GlobalProperties.getSessionServiceUrl()); - - //General site info - String siteTitle = GlobalProperties.getTitle(); - - request.setAttribute(QueryBuilder.HTML_TITLE, siteTitle+"::Results"); - - //check if show co-expression tab - if(!isVirtualStudy){ - GeneticProfile final_gp = CoExpUtil.getPreferedGeneticProfile(StudiesMap.keySet().iterator().next()); - if (final_gp != null) { - showCoexpTab = true; - } - } -%> - - - - - - - - - - - -<%! - public int countProfiles (ArrayList profileList, GeneticAlterationType type) { - int counter = 0; - for (int i = 0; i < profileList.size(); i++) { - GeneticProfile profile = profileList.get(i); - if (profile.getGeneticAlterationType() == type) { - counter++; - } - } - return counter; - } -%> diff --git a/src/main/resources/webapp/jsp/global/header.jsp b/src/main/resources/webapp/jsp/global/header.jsp deleted file mode 100644 index 1d16ef2e06b..00000000000 --- a/src/main/resources/webapp/jsp/global/header.jsp +++ /dev/null @@ -1,79 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - -<%@ taglib prefix="c" uri="http://java.sun.com/jsp/jstl/core"%> -<%@ taglib prefix="sec" uri="http://www.springframework.org/security/tags" %> - -<%@ page import="org.mskcc.cbio.portal.servlet.QueryBuilder" %> -<%@ page import="org.mskcc.cbio.portal.util.GlobalProperties" %> - -<%if(request.getAttribute("standard-js-css")!=null){%> - - -<%} else {%> - - -<%}%> - - - - - <%= request.getAttribute(QueryBuilder.HTML_TITLE)%> - - -
-
-
- -
-
- - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/src/main/resources/webapp/jsp/patient_view/drugs.jsp b/src/main/resources/webapp/jsp/patient_view/drugs.jsp deleted file mode 100644 index e1efd3923aa..00000000000 --- a/src/main/resources/webapp/jsp/patient_view/drugs.jsp +++ /dev/null @@ -1,261 +0,0 @@ -<%-- - - Copyright (c) 2015 - 2016 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - -<%-- - ~ Copyright (c) 2012 Memorial Sloan-Kettering Cancer Center. - ~ This library is free software; you can redistribute it and/or modify it - ~ under the terms of the GNU Lesser General Public License as published - ~ by the Free Software Foundation; either version 2.1 of the License, or - ~ any later version. - ~ - ~ This library is distributed in the hope that it will be useful, but - ~ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF - ~ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and - ~ documentation provided hereunder is on an "as is" basis, and - ~ Memorial Sloan-Kettering Cancer Center - ~ has no obligations to provide maintenance, support, - ~ updates, enhancements or modifications. In no event shall - ~ Memorial Sloan-Kettering Cancer Center - ~ be liable to any party for direct, indirect, special, - ~ incidental or consequential damages, including lost profits, arising - ~ out of the use of this software and its documentation, even if - ~ Memorial Sloan-Kettering Cancer Center - ~ has been advised of the possibility of such damage. See - ~ the GNU Lesser General Public License for more details. - ~ - ~ You should have received a copy of the GNU Lesser General Public License - ~ along with this library; if not, write to the Free Software Foundation, - ~ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA. - --%> - - - - -
- -
-
diff --git a/src/main/resources/webapp/jsp/global/header_bar.jsp b/src/main/resources/webapp/jsp/global/header_bar.jsp deleted file mode 100644 index a6eaf1510d8..00000000000 --- a/src/main/resources/webapp/jsp/global/header_bar.jsp +++ /dev/null @@ -1,237 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - -<%@ page import="org.mskcc.cbio.portal.util.GlobalProperties" %> -<%@ taglib prefix='c' uri='http://java.sun.com/jsp/jstl/core' %> -<%@ taglib prefix="s" uri="http://www.springframework.org/tags" %> -<%@ taglib prefix="sec" uri="http://www.springframework.org/security/tags" %> -<% - String principal = ""; - String authenticationMethod = GlobalProperties.authenticationMethod(); - pageContext.setAttribute("authenticationMethod", authenticationMethod); - if (authenticationMethod.equals("openid") || authenticationMethod.equals("ldap")) { - principal = "principal.name"; - } - else if (authenticationMethod.equals("googleplus") || - authenticationMethod.equals("saml") || - authenticationMethod.equals("ad") || - authenticationMethod.contains("social_auth") || - authenticationMethod.equals("saml_plus_basic")) { - principal = "principal.username"; - } - pageContext.setAttribute("principal", principal); -%> -<%-- Calling static methods is not supported in all versions of EL without - explicitly defining a function in an external taglib XML file. Using - Spring's SpEL instead to keep it short for this one function call --%> - - - - - - - - - - - -
-
- - - -
- -
- <%-- Display Sign Out Button for Real (Non-Anonymous) User --%> - -
Logged in as  |  - - - Sign out - - - Sign out - - -
- - - <% if (authenticationMethod.contains("social_auth")) { %> - - -
-   - -    -
- - - <% } %> - - - - - " alt="Institute Logo" /> - -
- -
- - - diff --git a/src/main/resources/webapp/jsp/global/js_include.jsp b/src/main/resources/webapp/jsp/global/js_include.jsp deleted file mode 100644 index c99baa2bded..00000000000 --- a/src/main/resources/webapp/jsp/global/js_include.jsp +++ /dev/null @@ -1,107 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - -<%@ page import="org.mskcc.cbio.portal.util.GlobalProperties" %> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -<%----> - - -<%-- - - - ---%> - - - - - - - - - - - - - - - - - - - - - -<%--The 3 files make expression tab work--%> - - - \ No newline at end of file diff --git a/src/main/resources/webapp/jsp/global/js_include_analytics_and_email.jsp b/src/main/resources/webapp/jsp/global/js_include_analytics_and_email.jsp deleted file mode 100644 index 62d732b84ee..00000000000 --- a/src/main/resources/webapp/jsp/global/js_include_analytics_and_email.jsp +++ /dev/null @@ -1,61 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - -<%@ page import="org.mskcc.cbio.portal.util.GlobalProperties" %> - -<% -String googleAnalyticsProfileId = GlobalProperties.getGoogleAnalyticsProfileId(); -if (googleAnalyticsProfileId!=null && !googleAnalyticsProfileId.isEmpty()) { -%> - - - - -<% } %> - - - diff --git a/src/main/resources/webapp/jsp/global/js_include_standard.jsp b/src/main/resources/webapp/jsp/global/js_include_standard.jsp deleted file mode 100644 index a1fe536a1c7..00000000000 --- a/src/main/resources/webapp/jsp/global/js_include_standard.jsp +++ /dev/null @@ -1,64 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - -<%@ page import="org.mskcc.cbio.portal.util.GlobalProperties" %> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/src/main/resources/webapp/jsp/global/legacy_head.jsp b/src/main/resources/webapp/jsp/global/legacy_head.jsp deleted file mode 100644 index e5524d201d7..00000000000 --- a/src/main/resources/webapp/jsp/global/legacy_head.jsp +++ /dev/null @@ -1,5 +0,0 @@ - - - - - \ No newline at end of file diff --git a/src/main/resources/webapp/jsp/global/right_column.jsp b/src/main/resources/webapp/jsp/global/right_column.jsp deleted file mode 100644 index 353fb778826..00000000000 --- a/src/main/resources/webapp/jsp/global/right_column.jsp +++ /dev/null @@ -1,94 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - -<%@ page import="org.mskcc.cbio.portal.util.GlobalProperties" %> -<%@ page import="org.mskcc.cbio.portal.util.DataSetsUtil" %> -<%@ page import="org.mskcc.cbio.portal.model.CancerStudyStats" %> -<%@ page import="java.util.List" %> -<%@ page import="java.util.ArrayList" %> - - - -
- - - - - - <% if (GlobalProperties.showRightNavDataSets()) { %> -
-

Data Sets

-

-
- -
- <% } %> - -<% if (GlobalProperties.showRightNavExamples()) {%> -
-

Example Queries

- <%@ include file="/content/examples.html" %> -
-<% } %> - -<% if (GlobalProperties.showRightNavTestimonials()) {%> -
-
-

What People are Saying

- -
-
-<% } %> -
diff --git a/src/main/resources/webapp/jsp/global/selected_study_variables.jsp b/src/main/resources/webapp/jsp/global/selected_study_variables.jsp deleted file mode 100644 index 42edd65b300..00000000000 --- a/src/main/resources/webapp/jsp/global/selected_study_variables.jsp +++ /dev/null @@ -1,34 +0,0 @@ -<%@page import="java.util.stream.Collectors"%> -<%@page import="com.fasterxml.jackson.databind.ObjectMapper"%> -<%@page import="java.util.Set"%> -<%@page import="java.util.HashMap"%> -<%@page import="com.fasterxml.jackson.core.type.TypeReference"%> -<%@ page import="org.mskcc.cbio.portal.servlet.QueryBuilder" %> - -<% - String cancerStudyId = (String)request.getAttribute(QueryBuilder.CANCER_STUDY_ID); - String cancerStudyIdListStr = (String)request.getAttribute(QueryBuilder.CANCER_STUDY_LIST); - - TypeReference>> typeRef = new TypeReference>>() {}; - ObjectMapper mapper = new ObjectMapper(); - HashMap> StudiesMap = new HashMap>(); - if((String)request.getAttribute("STUDY_SAMPLE_MAP") != null) - StudiesMap = mapper.readValue((String)request.getAttribute("STUDY_SAMPLE_MAP"), typeRef); - - //consider virtual study with one real study as regular study and show all the tabs if caseSetId is -1 - String _sampleSetId = (String) request.getAttribute(QueryBuilder.CASE_SET_ID); - Boolean isVirtualStudy = StudiesMap.size() > 1; - if(StudiesMap.size() == 1 && cancerStudyIdListStr != null && cancerStudyIdListStr.split(",").length>1 && !_sampleSetId.equals("-1")){ - isVirtualStudy = true; - } - - String normalizedCancerStudyIdListStr = StudiesMap.keySet().stream().collect(Collectors.joining(",")); - pageContext.setAttribute("normalizedCancerStudyIdListStr", normalizedCancerStudyIdListStr); -%> - diff --git a/src/main/resources/webapp/jsp/global/server_vars.jsp b/src/main/resources/webapp/jsp/global/server_vars.jsp deleted file mode 100644 index c809a3fa9b5..00000000000 --- a/src/main/resources/webapp/jsp/global/server_vars.jsp +++ /dev/null @@ -1,103 +0,0 @@ -<%@ page import="org.mskcc.cbio.portal.servlet.ServletXssUtil" %> -<%@ page import="org.mskcc.cbio.portal.util.XssRequestWrapper" %> -<%@ page import="java.util.HashSet" %> -<%@ page import="org.mskcc.cbio.portal.servlet.QueryBuilder" %> -<%@ page import="org.apache.commons.lang3.StringUtils" %> -<% - //Security Instance - ServletXssUtil xssUtil = ServletXssUtil.getInstance(); - - //Info about Genetic Profiles - HashSet geneticProfileIdSet = (HashSet) request.getAttribute(QueryBuilder.GENETIC_PROFILE_IDS); - String geneticProfiles = StringUtils.join(geneticProfileIdSet.iterator(), " "); - geneticProfiles = xssUtil.getCleanerInput(geneticProfiles.trim()); - - //Info about threshold settings - String zScoreThreshold = String.valueOf(request.getAttribute(QueryBuilder.Z_SCORE_THRESHOLD)); - String rppaScoreThreshold = String.valueOf(request.getAttribute(QueryBuilder.RPPA_SCORE_THRESHOLD)); - - //Onco Query Language Parser Instance - String oql = request.getParameter(QueryBuilder.GENE_LIST); - if (request instanceof XssRequestWrapper) { - oql = ((XssRequestWrapper)request).getRawParameter(QueryBuilder.GENE_LIST); - } - oql = xssUtil.getCleanerInput(oql); - - // List of queried gene sets - String genesetIds = request.getParameter(QueryBuilder.GENESET_LIST); - - String studySampleMapJson = (String)request.getAttribute("STUDY_SAMPLE_MAP"); - String sampleSetId = (String) request.getAttribute(QueryBuilder.CASE_SET_ID); - String sampleSetName = request.getAttribute("case_set_name") != null ? (String) request.getAttribute("case_set_name") : "User-defined Patient List"; - String sampleSetDescription = request.getAttribute("case_set_description") != null ? (String) request.getAttribute("case_set_description") : "User-defined Patient List."; - String sampleIdsKey = request.getAttribute(QueryBuilder.CASE_IDS_KEY) != null ? (String) request.getAttribute(QueryBuilder.CASE_IDS_KEY) : ""; - - String caseIds = (String) request.getAttribute(QueryBuilder.CASE_IDS); - if (request.getAttribute(QueryBuilder.CASE_IDS) != null) { - caseIds = caseIds.replace("\n","+"); - } - - sampleSetName = sampleSetName.replaceAll("'", "\\'"); - sampleSetName = sampleSetName.replaceAll("\"", "\\\""); - - Integer dataPriority = (Integer) request.getAttribute(QueryBuilder.DATA_PRIORITY); -%> - - diff --git a/src/main/resources/webapp/jsp/global/small_onco_print_legend.jsp b/src/main/resources/webapp/jsp/global/small_onco_print_legend.jsp deleted file mode 100644 index f4b65058f1e..00000000000 --- a/src/main/resources/webapp/jsp/global/small_onco_print_legend.jsp +++ /dev/null @@ -1,41 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - -
-amplified-notShown-normal.png -Amplification -homoDeleted-notShown-normal.png -Deep Deletion -diploid-notShown-mutated.png -Mutation -
Copy number alterations are putative.
-
diff --git a/src/main/resources/webapp/jsp/global/xdebug.jsp b/src/main/resources/webapp/jsp/global/xdebug.jsp deleted file mode 100644 index 1baa0f74eda..00000000000 --- a/src/main/resources/webapp/jsp/global/xdebug.jsp +++ /dev/null @@ -1,160 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - -<%@ page import="org.mskcc.cbio.portal.util.XDebug" %> -<%@ page import="org.mskcc.cbio.portal.util.XDebugParameter" %> -<%@ page import="java.util.Enumeration" %> -<%@ page import="java.util.Date" %> -<%@ page import="java.util.ArrayList" %> -<%@ page import="org.mskcc.cbio.portal.util.XDebugMessage" %> -<% - XDebug xdebug = (XDebug) request.getAttribute("xdebug_object"); - if (xdebug != null) { - xdebug.stopTimer(); - Enumeration enum0 = request.getAttributeNames(); - while (enum0.hasMoreElements()) { - String name = (String) enum0.nextElement(); - Object value = request.getAttribute(name); - xdebug.addParameter(XDebugParameter.REQUEST_ATTRIBUTE_TYPE, name, - value.toString()); - } -%> -<% - String xdebugParameter = request.getParameter("xdebug"); - if (xdebugParameter != null) { -%> - - - - - - - - - - - - - - - <%-- - *********************************** - Output Log Messages - *********************************** - --%> - <% - ArrayList messages = xdebug.getDebugMessages(); - for (int msgIndex = 0; msgIndex < messages.size(); msgIndex++) { - XDebugMessage msg = (XDebugMessage) messages.get(msgIndex); - %> - - - - - <% } %> - <%-- - *********************************** - Output Parameter Values - *********************************** - --%> - - - - - - <% - ArrayList parameters = xdebug.getParameters(); - String bgcolor; - for (int paramIndex=0; paramIndex - - - - - - - <% } %> -
- Total Time to Generate Page - - <%= xdebug.getTimeElapsed() %> ms -
- Current Time - - <%= new Date() %> ms -
- Class Name - - Message -
- <%= wrapText(msg.getClassName()) %> - - - <%= wrapText(msg.getMessage()) %> - -
Parameter TypeNameValue
<%= wrapText(param.getTypeName()) %><%= wrapText(param.getName()) %><%= wrapText(param.getValue()) %>
-<% } %> -<% } %> - -<%! - -// This is a little hack to replace .'s with .'s followed by a zero-width spacer. -// Enables browsers to wrap long words within tables -private String wrapText (String text) { - if (text != null) { - text = text.replaceAll("\\.", "\\. "); - text = text.replaceAll("&", "&"); - return text; - } else { - return new String ("Not Available"); - } -} -%> diff --git a/src/main/resources/webapp/jsp/igv.jsp b/src/main/resources/webapp/jsp/igv.jsp deleted file mode 100644 index 95f3473cce1..00000000000 --- a/src/main/resources/webapp/jsp/igv.jsp +++ /dev/null @@ -1,58 +0,0 @@ -<%-- - - Copyright (c) 2015 - 2016 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - - -
\ No newline at end of file diff --git a/src/main/resources/webapp/jsp/linkoutRedirect.jsp b/src/main/resources/webapp/jsp/linkoutRedirect.jsp deleted file mode 100644 index c77ff39ad17..00000000000 --- a/src/main/resources/webapp/jsp/linkoutRedirect.jsp +++ /dev/null @@ -1,21 +0,0 @@ -<%-- - Created by IntelliJ IDEA. - User: suny1 - Date: 6/15/16 - Time: 5:50 PM - To change this template use File | Settings | File Templates. ---%> -<%@ page contentType="text/html;charset=UTF-8" language="java" %> - - - - <% - String redirectURL = (String)request.getAttribute("redirect_url"); - %> - - - - - diff --git a/src/main/resources/webapp/jsp/mutation/mutation-file-example.txt b/src/main/resources/webapp/jsp/mutation/mutation-file-example.txt deleted file mode 100644 index c1aa00f3e5a..00000000000 --- a/src/main/resources/webapp/jsp/mutation/mutation-file-example.txt +++ /dev/null @@ -1,39 +0,0 @@ -Hugo_Symbol Sample_ID Protein_Change Mutation_Type Chromosome Start_Position End_Position Reference_Allele Variant_Allele -AR TCGA-13-0760 L729I Missense_Mutation 23 66937331 66937331 T A -AR TCGA-BS-A0UF R832* Nonsense_Mutation 23 66942713 66942713 C T -AR TCGA-D1-A17M L185P Missense_Mutation 23 66765542 66765542 T C -AR TCGA-B5-A0JY K222N Missense_Mutation 23 66765654 66765654 G T -BRCA1 TCGA-24-2298 Q1395fs Frame_Shift_Ins 17 41242962 41242963 - GA -BRCA1 TCGA-09-1669 E1345fs Frame_Shift_Del 17 41243513 41243513 T - -BRCA1 TCGA-25-1625 E116* Nonsense_Mutation 17 41256234 41256234 C A -BRCA1 TCGA-13-0804 C47W Missense_Mutation 17 41258544 41258544 G C -BRCA1 TCGA-23-1027 E23fs Frame_Shift_Del 17 41276045 41276046 CT - -BRCA1 TCGA-23-1118 E23fs Frame_Shift_Del 17 41276045 41276046 CT - -BRCA1 TCGA-AP-A051 L49M Missense_Mutation 17 41258540 41258540 G T -BRCA1 TCGA-B5-A11E A942V Missense_Mutation 17 41244723 41244723 G A -BRCA1 TCGA-BS-A0UF D1778_splice Splice_Site 17 41201212 41201212 C A -BRCA2 TCGA-13-0793 T3085fs Frame_Shift_Del 13 32954281 32954282 AG - -BRCA2 TCGA-24-1103 K1638E Missense_Mutation 13 32913404 32913404 A G -BRCA2 TCGA-24-2024 Y1710fs Frame_Shift_Del 13 32913620 32913623 TATG - -BRCA2 TCGA-04-1367 E294* Nonsense_Mutation 13 32906495 32906495 G T -BRCA2 TCGA-23-1030 T1354M Missense_Mutation 13 32912553 32912553 C T -BRCA2 TCGA-13-0792 E1143D Missense_Mutation 13 32911921 32911921 A T -BRCA2 TCGA-24-1555 E2878_splice Splice_Site 13 32950806 32950806 G C -BRCA2 TCGA-B5-A11E R2842C Missense_Mutation 13 32945129 32945129 C T -BRCA2 TCGA-B5-A0JY R2842C Missense_Mutation 13 32945129 32945129 C T -BRCA2 TCGA-AP-A059 S3239Y Missense_Mutation 13 32972366 32972366 C A -BRCA2 TCGA-BS-A0UV E1441* Nonsense_Mutation 13 32912813 32912813 G T -BRCA2 TCGA-AX-A05Z E897* Nonsense_Mutation 13 32911181 32911181 G T -POLE TCGA-57-1582 N1869K Missense_Mutation 12 133214671 133214671 G C -POLE TCGA-24-1104 T2245N Missense_Mutation 12 133201504 133201504 G T -POLE TCGA-AX-A05Z S1930* Nonsense_Mutation 12 133212500 133212500 G T -POLE TCGA-AP-A059 L2112M Missense_Mutation 12 133202900 133202900 G T -POLE TCGA-AP-A059 A25T Missense_Mutation 12 133257855 133257855 C T -TP53 TCGA-FI-A2EX R248W Missense_Mutation 17 7577539 7577539 G A -TP53 TCGA-B5-A11N T256fs Frame_Shift_Ins 17 7577514 7577515 - T -TP53 TCGA-DI-A1NN Q144* Nonsense_Mutation 17 7578500 7578500 G A -TP53 TCGA-AX-A0IU P278fs Frame_Shift_Ins 17 7577105 7577106 - GA -TP53 TCGA-AP-A1DQ R175H Missense_Mutation 17 7578406 7578406 C T -TP53 TCGA-AJ-A23M 277_277C>CC In_Frame_Ins 17 7577107 7577108 - CAG -TP53 TCGA-EY-A212 V173L Missense_Mutation 17 7578413 7578413 C G -TP53 TCGA-D1-A16I I332_splice Splice_Site 17 7574034 7574034 C G diff --git a/src/main/resources/webapp/jsp/mutation/mutationMapperTemplates.html b/src/main/resources/webapp/jsp/mutation/mutationMapperTemplates.html deleted file mode 100644 index 726553c4c9d..00000000000 --- a/src/main/resources/webapp/jsp/mutation/mutationMapperTemplates.html +++ /dev/null @@ -1,731 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/src/main/resources/webapp/jsp/mutation/standalone_mutation_view.jsp b/src/main/resources/webapp/jsp/mutation/standalone_mutation_view.jsp deleted file mode 100644 index c3f9a98f60a..00000000000 --- a/src/main/resources/webapp/jsp/mutation/standalone_mutation_view.jsp +++ /dev/null @@ -1,123 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - -<%@ page import="org.mskcc.cbio.portal.util.GlobalProperties" %> - - - - - - - - - - diff --git a/src/main/resources/webapp/jsp/mutation_details.jsp b/src/main/resources/webapp/jsp/mutation_details.jsp deleted file mode 100644 index c5b3140bcdc..00000000000 --- a/src/main/resources/webapp/jsp/mutation_details.jsp +++ /dev/null @@ -1,93 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> -
- loading -
- - - - diff --git a/src/main/resources/webapp/jsp/mutation_views.jsp b/src/main/resources/webapp/jsp/mutation_views.jsp deleted file mode 100644 index 4c40c313c7b..00000000000 --- a/src/main/resources/webapp/jsp/mutation_views.jsp +++ /dev/null @@ -1,33 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - -<%@ include file="src/main/webapp/jsp/mutation/mutationMapperTemplates.html" %> diff --git a/src/main/resources/webapp/jsp/mutex_tab.jsp b/src/main/resources/webapp/jsp/mutex_tab.jsp deleted file mode 100644 index 9cefc71c6ea..00000000000 --- a/src/main/resources/webapp/jsp/mutex_tab.jsp +++ /dev/null @@ -1,74 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - -<%@ page import="org.mskcc.cbio.portal.stats.OddsRatio" %> -<%@ page import="org.mskcc.cbio.portal.model.GeneWithScore" %> -<%@ page import="java.text.DecimalFormat" %> -<%@ page import="java.util.HashMap" %> -<%@ page import="java.util.Set" %> -<%@ page import="java.util.HashSet" %> -<%@ page import="org.apache.commons.lang3.math.DoubleRange" %> -<%@ page import="java.io.PrintWriter" %> -<%@ page import="java.io.IOException" %> - -
-
-
- - \ No newline at end of file diff --git a/src/main/resources/webapp/jsp/network_div.jsp b/src/main/resources/webapp/jsp/network_div.jsp deleted file mode 100644 index 5f6f28abe42..00000000000 --- a/src/main/resources/webapp/jsp/network_div.jsp +++ /dev/null @@ -1,54 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - -
-
- - - - - - -
-
- -
-
-
- loading -
- 		-
- -
-
-
diff --git a/src/main/resources/webapp/jsp/network_help.jsp b/src/main/resources/webapp/jsp/network_help.jsp deleted file mode 100644 index 44df79bd004..00000000000 --- a/src/main/resources/webapp/jsp/network_help.jsp +++ /dev/null @@ -1,278 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - -

- About the Network View -

-

- The network view shows the genes you entered (referred to as seed nodes) in the context of biological interactions derived from public pathway databases. - Each gene in the network view is color-coded with multi-dimensional genomic data derived from the cancer study you have selected. -

- -

- Source of Pathway Data -

-

- Pathway and interaction data is from HPRD, - Reactome, - NCI-Nature Pathway Interaction Database, - and the MSKCC Cancer Call Map, - as derived from Pathway Commons. -

- -

- Source of Drug Data -

-

- Drug data is derived from PiHelper. -

- -

- Seed Nodes vs. Linker Nodes -

-

- A seed node represents a gene that you have entered. - A linker node represents a gene that connects to one or more of your seed genes. -

-

- Seed nodes are represented with a thick border:

- seed node -

-

- Linker nodes are represented with a thin border:

- linker node -

- -

- Visualization Summary of Genomic Data -

-

- The exact genomic data displayed on the network depends on the genomic profiles you have selected. - For example, you can chose to include mutation, copy number and mRNA expression profiles. -

-

- By default, each node is color coded along a white to red color gradient, - indicating the total frequency of alteration across the selected case set - (deeper red indicates higher frequency of alteration). -

-

- For example, EGFR is frequently altered in glibolastoma:

- altered node -

-

- By contrast, STAT3 is not altered at all in glioblastoma:

- not altered node -

- -

- If you mouse over a node, or select "View::Always Show Profile Data", - you will see additional details regarding the genomic alterations affecting the gene. - This breaks down into mutation, copy number and mRNA expression changes affecting the gene across all cases. -

-

- Click here to see the gene legend. -

- -

- Drug Information -

-

- Drugs targeting genes in the network are hidden by default. If you would like - to see them, select "Show All Drugs" or, "Show FDA Approved Drugs" or "Show Cancer Drugs" - from the drop-down box under the "Genes & Drugs" tab. -

-

- Number of Genes Targeted shown in the drug inspector refers to the total number of genes - (regardless of whether or not any such gene is in the current network of interest) targeted by this drug. -

-

- Click here to see the drug legend. -

- -

- Understanding Interaction and Edge Types -

-

- The interaction types are derived from the BioPAX to binary interaction mapping rules defined within Pathway Commons. - They are encoded by different edge colors and can be seleted on the "Interactions" tab to the right of the network. - In addition, if selected, drug-gene interactions are shown as edges in the network. The interaction types are: -

    -
  • - Controls-state-change-of: - First protein controls a reaction that changes the state of the second protein. -
    • -
  • - Controls-transport-of: - First protein controls a reaction that changes the cellular location of the second protein. -
    • -
  • - Controls-phosphorylation-of: - First protein controls a reaction that changes the phosphorylation status of the second protein. -
    • -
  • - Controls-expression-of: - First protein controls a conversion or a template reaction that changes expression of the second protein. -
    • -
  • - Catalysis-precedes: - First protein controls a reaction whose output molecule is input to another reaction controled by the second protein. -
    • -
  • - In-complex-with: - Proteins are members of the same complex. -
    • -
  • - Interacts-with: - Proteins are participants of the same MolecularInteraction. -
    • -
  • - Neighbor-of: - Proteins are participants or controlers of the same interaction. -
    • -
  • - Consumption-controled-by: - The small molecule is consumed by a reaction that is controled by a protein -
    • -
  • - Controls-production-of: - The protein controls a reaction of which the small molecule is an output. -
    • -
  • - Controls-transport-of-chemical: - The protein controls a reaction that changes cellular location of the small molecule. -
    • -
  • - Chemical-affects: - A small molecule has an effect on the protein state. -
    • -
  • - Reacts-with: - Small molecules are input to a biochemical reaction. -
    • -
  • - Used-to-produce: - A reaction consumes a small molecule to produce another small molecule. -
    • -
-

-

- Click here to see the color codes. -

-

- Complete details are available on the Pathway Commons web site. -

-

- By default, redundant interactions are merged are merged into a single edge. - To see all interactions, uncheck "Merge Interactions" in the "View" menu. -

- -

- Complexity Management -

-

- There are a number of options to better deal with complex networks: -

    -
  • - Hide Selected/Crop: - Selected nodes can be hidden using "Topology::Hide Selected". - Alternatively, you can select the set of nodes that you would like to view and hide the rest - of the network using "Topology::Show Only Selected". - Alternatively, buttons are available for these operations on the "Genes & Drugs" tab. -
    • -
  • - Filter by Interaction Type or Source: - If you are interested in only certain types of interactions or interactions from selected sources, - you may use the filtering mechanisms on the "Interactions" tab by checking the corresponding check boxes and clicking "Update". -
    • -
  • - Filter by Total Alteration: - Networks can be filtered based on alteration frequencies of individual nodes using a slider under the "Genes & Drugs" tab. - You can specify a threshold of total alteration frequency - nodes with alteration frequencies below the threshold will be filtered out, - but seed nodes are always kept in the network. -
    • -
  • - Filter Drugs by FDA Approval: - Networks can be filtered based on whether drugs associated with genes of this network are FDA approved or not. -
    • -
  • - Filter Cancer Drugs: - Networks can be filtered based on whether drugs associated with genes of this network are cancer drugs or not. - Notice that all cancer drugs are FDA approved. -
    • -
-

-

- All filtering can be undone by clicking "Unhide" in the "Topology" menu. -

-

- When the flag "Remove Disconnected Nodes on Hide" in the "Topology" menu is checked, - an automatic layout is performed upon all changes to the network topology. -

- -

- Performing Layout -

-

- A Force-Directed layout algorithm is used by default. - However, you may choose to re-perform the layout with different parameters (by selecting "Layout::Layout Properties ...") or - after the topology of the network changes with operations such as hiding or filtering. - If you would like the layout to be performed automatically upon such operations - simply check "Layout::Auto Layout on Changes". -

- -

- Exporting Networks -

-

- You can export a network to a PNG file. - To do so, select "File::Save as Image (PNG)". - We do not currently support export to PDF. -

- -

- Detailed Process Level (SBGN) View -

-

- When you are interested in process level details of an interaction, - you may either right-click on that interaction or click the "Detailed Process (SBGN)" button - in the Details tab while inspecting the interaction. - This will pop up a detailed process view in SBGN Process Description Language. - The shown network corresponds to all paths between source and target genes of that interaction as returned by Pathway Commons' web service. - SBGN view allows users to modify the process level view in many ways, including changing its layout and topology through complexity management techniques such as hiding or collapsing. - You may also store the current network as a static image or in SBGN-ML format. For further help, please refer to the Help menu of this view. -

-

- Technology -

-

- Network visualization is powered by Cytoscape.js and SBGNViz.js. -

diff --git a/src/main/resources/webapp/jsp/network_menu.jsp b/src/main/resources/webapp/jsp/network_menu.jsp deleted file mode 100644 index b4b48850d16..00000000000 --- a/src/main/resources/webapp/jsp/network_menu.jsp +++ /dev/null @@ -1,158 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - -<% -Boolean includeNetLegend = (Boolean)request.getAttribute("include_network_legend"); -if (includeNetLegend==null) { - includeNetLegend = Boolean.TRUE; -} -%> - - -
- -
diff --git a/src/main/resources/webapp/jsp/network_tabs.jsp b/src/main/resources/webapp/jsp/network_tabs.jsp deleted file mode 100644 index 38af7adf8d2..00000000000 --- a/src/main/resources/webapp/jsp/network_tabs.jsp +++ /dev/null @@ -1,217 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - -<% -Boolean includeHelpTab = (Boolean)request.getAttribute("include_network_help_tab"); -if (includeHelpTab==null) { - includeHelpTab = Boolean.TRUE; -} -%> - -
- -
-
-

-
- -
-

-
- -
- - - - - -
-
- -
- - - - - -
-
-
-
- - - - - - - - -
- - - - - - - - - -
- - - - - -
- - - -
-
-
-
-
-
-
-
- -
- -
-
- -
-
-
- Currently there is no selected node/edge. Please, select a node/edge to see details.
-
-
-
-
-
- <%if(includeHelpTab){%> -
- -
- <%}%> -
- -<% /* -
-
- - - - - - - - - - - - - - - - - - - - - - - - -
- Edge Types: -
-
In Same Component
- 		-
-
-
Reacts With
- 		-
-
-
State Change
- 		-
-
-
Other
- 		-
-
-
Merged (with different types)
- 		-
-
-
-
-*/ %> diff --git a/src/main/resources/webapp/jsp/network_views.jsp b/src/main/resources/webapp/jsp/network_views.jsp deleted file mode 100644 index bcff6499ab6..00000000000 --- a/src/main/resources/webapp/jsp/network_views.jsp +++ /dev/null @@ -1,780 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - - - - - - - - - diff --git a/src/main/resources/webapp/jsp/networks.jsp b/src/main/resources/webapp/jsp/networks.jsp deleted file mode 100644 index 81a1cc11a79..00000000000 --- a/src/main/resources/webapp/jsp/networks.jsp +++ /dev/null @@ -1,67 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - - - - - - \ No newline at end of file diff --git a/src/main/resources/webapp/jsp/oncokb/oncokb-card-template.html b/src/main/resources/webapp/jsp/oncokb/oncokb-card-template.html deleted file mode 100644 index f1b484a23d4..00000000000 --- a/src/main/resources/webapp/jsp/oncokb/oncokb-card-template.html +++ /dev/null @@ -1,122 +0,0 @@ - - - - - - - - - diff --git a/src/main/resources/webapp/jsp/oncoprint/cna-file-example.txt b/src/main/resources/webapp/jsp/oncoprint/cna-file-example.txt deleted file mode 100644 index 82b00b59822..00000000000 --- a/src/main/resources/webapp/jsp/oncoprint/cna-file-example.txt +++ /dev/null @@ -1,3 +0,0 @@ -Hugo_Symbol Entrez_Gene_Id TCGA-04-1348 TCGA-04-1357 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1514 TCGA-09-0366 TCGA-09-0369 TCGA-09-1662 TCGA-09-1666 TCGA-09-1669 TCGA-09-2044 TCGA-09-2045 TCGA-09-2051 TCGA-09-2056 TCGA-10-0928 TCGA-13-0730 TCGA-13-0800 TCGA-13-0890 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 TCGA-13-0924 TCGA-13-1403 TCGA-13-1405 TCGA-13-1410 TCGA-13-1481 TCGA-13-1497 TCGA-13-1498 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1512 TCGA-13-2060 TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 TCGA-23-2077 TCGA-23-2081 TCGA-24-0975 TCGA-24-1103 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1423 TCGA-24-1424 TCGA-24-1427 TCGA-24-1428 TCGA-24-1436 TCGA-24-1469 TCGA-24-1474 TCGA-24-1544 TCGA-24-1548 TCGA-24-1549 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1616 TCGA-24-2019 TCGA-24-2024 TCGA-24-2035 TCGA-24-2038 TCGA-24-2254 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2281 TCGA-24-2288 TCGA-24-2290 TCGA-24-2298 TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1321 TCGA-25-1322 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1627 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2399 TCGA-25-2400 TCGA-25-2404 TCGA-25-2409 TCGA-29-2427 TCGA-30-1862 TCGA-30-1891 TCGA-31-1953 TCGA-36-1568 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1993 TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 TCGA-59-2363 TCGA-61-1728 TCGA-61-1736 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2097 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 -BRCA1 672 -1 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 -1 -1 0 -1 -1 1 1 -1 -1 0 0 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 0 1 2 -1 -1 -1 0 0 -1 -1 0 -1 -1 -1 -1 -1 -1 0 -1 0 -1 -1 -1 -1 -1 -1 -1 0 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 0 -1 0 -1 0 -1 -1 1 -1 0 -1 -1 -1 -1 -1 1 -1 -1 0 0 -1 -1 -1 -1 -1 -1 0 -1 -1 1 -1 0 -1 -1 1 -1 -1 0 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 0 -1 -1 0 -1 -1 -1 -1 -1 0 -1 -1 -1 -1 -1 0 -1 0 -1 -1 -1 0 -1 -1 0 -1 -1 -1 -1 -1 -BRCA2 675 -1 0 0 2 -1 -1 -1 1 0 0 0 0 -1 0 -1 -1 -1 -1 0 -1 0 -1 2 0 -1 -1 0 0 -1 2 0 -1 1 0 0 -1 -1 0 -1 -1 -1 -1 -1 -1 -1 -1 -1 0 -1 1 -1 0 -1 0 -1 1 -1 -1 -1 -1 -1 -1 -1 0 -1 0 0 -1 -1 0 -1 -1 0 -1 -1 -1 -1 -1 0 0 -1 -1 -1 -1 0 0 -1 -1 0 -1 -1 0 1 -1 -1 -1 2 -1 0 0 1 0 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 0 -1 -1 0 0 -1 -1 -1 1 -1 0 1 0 -1 1 0 -1 -1 -1 1 0 0 1 -1 -1 0 0 2 1 -1 -1 -1 0 -1 -1 -1 -1 0 -1 -1 -1 0 diff --git a/src/main/resources/webapp/jsp/oncoprint/controls-templates.jsp b/src/main/resources/webapp/jsp/oncoprint/controls-templates.jsp deleted file mode 100644 index 2246cba8c68..00000000000 --- a/src/main/resources/webapp/jsp/oncoprint/controls-templates.jsp +++ /dev/null @@ -1,80 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - - - - - - \ No newline at end of file diff --git a/src/main/resources/webapp/jsp/oncoprint/example-clinic-events.txt b/src/main/resources/webapp/jsp/oncoprint/example-clinic-events.txt deleted file mode 100644 index 4ae9348a133..00000000000 --- a/src/main/resources/webapp/jsp/oncoprint/example-clinic-events.txt +++ /dev/null @@ -1,99 +0,0 @@ -SAMPLE_ID TUMOR_STAGE_2009 GRADE\n\ -sample string string\n\ -TCGA-61-1895 IIIB G3\n\ -TCGA-13-1510 IIIC G3\n\ -TCGA-23-1809 IIC G3\n\ -TCGA-20-1687 IV G3\n\ -TCGA-13-1404 IIIC G3\n\ -TCGA-13-1506 IIIC G3\n\ -TCGA-23-1116 IIIC G3\n\ -TCGA-20-1686 IIIC G3\n\ -TCGA-13-1505 IIIC G3\n\ -TCGA-24-1846 IIIC G3\n\ -TCGA-13-1412 IV G3\n\ -TCGA-23-1111 IIIC G3\n\ -TCGA-24-1843 IIIC G3\n\ -TCGA-24-1844 IIIC G3\n\ -TCGA-23-1120 IIIC G3\n\ -TCGA-13-1507 IIIC G3\n\ -TCGA-24-1845 IIIC G3\n\ -TCGA-24-1842 IIIC G3\n\ -TCGA-24-1847 IV G3\n\ -TCGA-13-1512 IIIC G3\n\ -TCGA-61-2088 IIIC G3\n\ -TCGA-13-1407 IIIC G3\n\ -TCGA-23-1121 IIIC G3\n\ -TCGA-13-1509 IV G3\n\ -TCGA-29-1781 IIIC G3\n\ -TCGA-13-0921 IIIC G3\n\ -TCGA-13-1410 IV NA\n\ -TCGA-24-1426 IIIC G3\n\ -TCGA-24-1416 IV G3\n\ -TCGA-24-1470 IIIB G3\n\ -TCGA-29-1784 IIIC G3\n\ -TCGA-24-1850 IIIC G3\n\ -TCGA-09-2044 IIB G3\n\ -TCGA-24-1425 IIIC G3\n\ -TCGA-24-1849 IIIC G3\n\ -TCGA-24-1423 IIIC G3\n\ -TCGA-13-0924 IV G3\n\ -TCGA-13-0923 IIIC G3\n\ -TCGA-24-1413 IIIC G3\n\ -TCGA-13-0802 IIIC G3\n\ -TCGA-29-1783 IIIC G3\n\ -TCGA-24-1424 IIIC G3\n\ -TCGA-13-1405 IV G3\n\ -TCGA-24-1417 IV G3\n\ -TCGA-24-1418 IIIC G3\n\ -TCGA-13-0799 IIIC G3\n\ -TCGA-13-1496 IIIC G3\n\ -TCGA-61-1899 IIIC G3\n\ -TCGA-61-1900 IIIB G3\n\ -TCGA-13-0801 IIIC G3\n\ -TCGA-13-0800 IIIC G3\n\ -TCGA-13-0768 IIIC G3\n\ -TCGA-61-1904 IIIC G3\n\ -TCGA-24-1419 IIIC G3\n\ -TCGA-13-2060 IV G3\n\ -TCGA-13-0797 IIIC G3\n\ -TCGA-24-1469 IIIC G3\n\ -TCGA-24-1920 IIIC G3\n\ -TCGA-23-1024 IV G3\n\ -TCGA-23-1029 IIIC G3\n\ -TCGA-13-1403 IIIC G3\n\ -TCGA-13-1504 IIIC G3\n\ -TCGA-09-2056 IIIC G3\n\ -TCGA-13-0919 IIIC G3\n\ -TCGA-29-1778 IIIC G3\n\ -TCGA-20-1685 IIIC G3\n\ -TCGA-20-1684 IIIC G3\n\ -TCGA-13-0916 IIIC G3\n\ -TCGA-29-1769 IIIC G3\n\ -TCGA-20-1682 IIIC NA\n\ -TCGA-13-0910 IIIC G3\n\ -TCGA-13-0762 IIIC G3\n\ -TCGA-29-1711 IIIC G2\n\ -TCGA-61-1910 IIC G3\n\ -TCGA-09-2053 IIIC G3\n\ -TCGA-61-1737 IV G3\n\ -TCGA-13-0906 IIIC G3\n\ -TCGA-29-2428 IIIC G3\n\ -TCGA-13-0905 IIIC G3\n\ -TCGA-25-2391 IIIC G3\n\ -TCGA-61-1913 IIIB G3\n\ -TCGA-61-2092 IIIC G3\n\ -TCGA-13-0900 IIIC G3\n\ -TCGA-61-2097 IIC G2\n\ -TCGA-13-0889 IV NA\n\ -TCGA-04-1347 IV G3\n\ -TCGA-13-0890 IIIC G3\n\ -TCGA-61-2098 IIIC G2\n\ -TCGA-13-0888 IIIC G3\n\ -TCGA-61-1915 IIC G3\n\ -TCGA-04-1367 IIIC G3\n\ -TCGA-13-1492 IIIC G3\n\ -TCGA-13-0886 IIIC G3\n\ -TCGA-61-2094 IIIC G3\n\ -TCGA-09-2050 IIA G2\n\ -TCGA-13-1481 IIIC G2\n\ -TCGA-23-1118 IIIC G3\n\ diff --git a/src/main/resources/webapp/jsp/oncoprint/example-genomic-events.txt b/src/main/resources/webapp/jsp/oncoprint/example-genomic-events.txt deleted file mode 100644 index 1c84dcae266..00000000000 --- a/src/main/resources/webapp/jsp/oncoprint/example-genomic-events.txt +++ /dev/null @@ -1,591 +0,0 @@ -Sample Gene Alteration Type\n\ -TCGA-25-2392-01 TP53 FUSION FUSION\n\ -TCGA-25-2393-01 TP53 FUSION FUSION\n\ -TCGA-04-1331-01 PTEN HOMDEL CNA\n\ -TCGA-04-1365-01 PTEN HOMDEL CNA\n\ -TCGA-04-1648-01 TP53 HOMDEL CNA\n\ -TCGA-09-1666-01 PTEN AMP CNA\n\ -TCGA-13-0720-01 PTEN HOMDEL CNA\n\ -TCGA-13-0801-01 BRCA1 HOMDEL CNA\n\ -TCGA-13-0801-01 PTEN HOMDEL CNA\n\ -TCGA-13-0905-01 PTEN HOMDEL CNA\n\ -TCGA-13-0924-01 PTEN HOMDEL CNA\n\ -TCGA-13-1405-01 PTEN HOMDEL CNA\n\ -TCGA-13-1408-01 TP53 HOMDEL CNA\n\ -TCGA-13-1488-01 PTEN HOMDEL CNA\n\ -TCGA-23-1023-01 PTEN HOMDEL CNA\n\ -TCGA-23-1032-01 PTEN HOMDEL CNA\n\ -TCGA-23-1107-01 PTEN HOMDEL CNA\n\ -TCGA-23-1114-01 BRCA2 HOMDEL CNA\n\ -TCGA-23-1118-01 PTEN AMP CNA\n\ -TCGA-23-1121-01 PTEN AMP CNA\n\ -TCGA-23-2084-01 TP53 HOMDEL CNA\n\ -TCGA-24-0968-01 PTEN HOMDEL CNA\n\ -TCGA-24-0970-01 BRCA2 AMP CNA\n\ -TCGA-24-1103-01 PTEN HOMDEL CNA\n\ -TCGA-24-1474-01 TP53 AMP CNA\n\ -TCGA-24-1567-01 PTEN HOMDEL CNA\n\ -TCGA-24-2030-01 PTEN HOMDEL CNA\n\ -TCGA-24-2036-01 PTEN HOMDEL CNA\n\ -TCGA-24-2262-01 PTEN HOMDEL CNA\n\ -TCGA-24-2297-01 PTEN HOMDEL CNA\n\ -TCGA-25-1322-01 BRCA2 AMP CNA\n\ -TCGA-25-2391-01 PTEN HOMDEL CNA\n\ -TCGA-25-2401-01 BRCA2 HOMDEL CNA\n\ -TCGA-29-1697-01 PTEN AMP CNA\n\ -TCGA-29-1702-01 TP53 AMP CNA\n\ -TCGA-29-1761-01 PTEN HOMDEL CNA\n\ -TCGA-30-1860-01 PTEN HOMDEL CNA\n\ -TCGA-31-1951-01 PTEN HOMDEL CNA\n\ -TCGA-31-1959-01 BRCA1 HOMDEL CNA\n\ -TCGA-31-1959-01 PTEN HOMDEL CNA\n\ -TCGA-36-1570-01 PTEN HOMDEL CNA\n\ -TCGA-57-1586-01 BRCA1 HOMDEL CNA\n\ -TCGA-61-1728-01 PTEN HOMDEL CNA\n\ -TCGA-61-1895-01 PTEN HOMDEL CNA\n\ -TCGA-61-1907-01 BRCA2 HOMDEL CNA\n\ -TCGA-61-2012-01 TP53 AMP CNA\n\ -TCGA-61-2094-01 PTEN HOMDEL CNA\n\ -TCGA-61-2097-01 BRCA2 HOMDEL CNA\n\ -TCGA-29-1702-01 TP53 UP EXP\n\ -TCGA-61-2012-01 TP53 UP EXP\n\ -TCGA-36-1570-01 PTEN DOWN EXP\n\ -TCGA-57-1586-01 BRCA1 DOWN EXP\n\ -TCGA-61-1728-01 PTEN DOWN EXP\n\ -TCGA-61-1895-01 PTEN DOWN EXP\n\ -TCGA-61-1907-01 BRCA2 DOWN EXP\n\ -TCGA-25-1625-01 BRCA1 E116* TRUNC\n\ -TCGA-04-1357-01 BRCA1 Q1538A MISSENSE\n\ -TCGA-13-0893-01 BRCA1 K503fs TRUNC\n\ -TCGA-61-2109-01 BRCA1 K654fs TRUNC\n\ -TCGA-13-0761-01 BRCA1 R1495_splice TRUNC\n\ -TCGA-23-1118-01 BRCA1 E23fs TRUNC\n\ -TCGA-29-2427-01 BRCA1 L431* TRUNC\n\ -TCGA-23-1122-01 BRCA1 Q1756fs TRUNC\n\ -TCGA-25-2392-01 BRCA1 E1345fs TRUNC\n\ -TCGA-23-1027-01 BRCA1 E23fs TRUNC\n\ -TCGA-25-1632-01 BRCA1 L1216fs TRUNC\n\ -TCGA-23-1026-01 BRCA1 G813fs TRUNC\n\ -TCGA-13-0804-01 BRCA1 C47W MISSENSE\n\ -TCGA-24-2298-01 BRCA1 Q1395fs TRUNC\n\ -TCGA-61-2008-01 BRCA1 W1815* TRUNC\n\ -TCGA-09-2045-01 BRCA1 Q1779fs TRUNC\n\ -TCGA-04-1356-01 BRCA1 V722fs TRUNC\n\ -TCGA-25-1630-01 BRCA1 K519fs TRUNC\n\ -TCGA-24-1470-01 BRCA1 L1676fs TRUNC\n\ -TCGA-13-0730-01 BRCA1 R1835* TRUNC\n\ -TCGA-13-0883-01 BRCA1 Q1756fs TRUNC\n\ -TCGA-25-2401-01 BRCA1 Q1756fs TRUNC\n\ -TCGA-13-0903-01 BRCA1 R504fs TRUNC\n\ -TCGA-13-0887-01 BRCA1 E23fs TRUNC\n\ -TCGA-13-1494-01 BRCA1 K45_splice TRUNC\n\ -TCGA-09-2051-01 BRCA1 Q1756fs TRUNC\n\ -TCGA-23-2078-01 BRCA1 E23fs TRUNC\n\ -TCGA-23-2079-01 BRCA1 E23fs TRUNC\n\ -TCGA-10-0931-01 BRCA1 E23fs TRUNC\n\ -TCGA-59-2348-01 BRCA1 E797* TRUNC\n\ -TCGA-23-2077-01 BRCA1 Q1756fs TRUNC\n\ -TCGA-09-1669-01 BRCA1 E1345fs TRUNC\n\ -TCGA-23-2081-01 BRCA1 Q1756fs TRUNC\n\ -TCGA-13-1408-01 BRCA1 E23fs TRUNC\n\ -TCGA-13-1489-01 BRCA1 N1265fs TRUNC\n\ -TCGA-25-1318-01 BRCA2 L1491fs TRUNC\n\ -TCGA-13-0793-01 BRCA2 T3085fs TRUNC\n\ -TCGA-24-1463-01 BRCA2 G602fs TRUNC\n\ -TCGA-13-0913-01 BRCA2 E1857fs TRUNC\n\ -TCGA-04-1367-01 BRCA2 E294* TRUNC\n\ -TCGA-24-1562-01 BRCA2 K3326* TRUNC\n\ -TCGA-04-1331-01 BRCA2 C711* TRUNC\n\ -TCGA-24-1103-01 BRCA2 K1638E MISSENSE\n\ -TCGA-13-0885-01 BRCA2 K1406fs TRUNC\n\ -TCGA-13-0890-01 BRCA2 V1229fs TRUNC\n\ -TCGA-13-1512-01 BRCA2 K3326* TRUNC\n\ -TCGA-23-1030-01 BRCA2 T1354M MISSENSE\n\ -TCGA-23-1026-01 BRCA2 K3326* TRUNC\n\ -TCGA-25-1634-01 BRCA2 E2878_splice TRUNC\n\ -TCGA-24-1555-01 BRCA2 T2607fs TRUNC\n\ -TCGA-13-0886-01 BRCA2 S1982fs TRUNC\n\ -TCGA-13-0792-01 BRCA2 E1143D MISSENSE\n\ -TCGA-24-2293-01 BRCA2 R2520* TRUNC\n\ -TCGA-23-1120-01 BRCA2 L3277fs TRUNC\n\ -TCGA-57-1584-01 BRCA2 Q1782fs TRUNC\n\ -TCGA-13-0900-01 BRCA2 T256fs TRUNC\n\ -TCGA-24-2280-01 BRCA2 S1982fs TRUNC\n\ -TCGA-24-0975-01 BRCA2 V211_splice TRUNC\n\ -TCGA-24-2288-01 BRCA2 T219fs TRUNC\n\ -TCGA-24-1417-01 BRCA2 R1704fs TRUNC\n\ -TCGA-13-1498-01 BRCA2 S1982fs TRUNC\n\ -TCGA-13-1499-01 BRCA2 S1982fs TRUNC\n\ -TCGA-13-0726-01 BRCA2 R2394* TRUNC\n\ -TCGA-25-2404-01 BRCA2 E342fs TRUNC\n\ -TCGA-13-1481-01 BRCA2 L2696fs TRUNC\n\ -TCGA-10-0930-01 PTEN V175L MISSENSE\n\ -TCGA-13-1492-01 PTEN R233fs TRUNC\n\ -TCGA-24-0968-01 TP53 H193R MISSENSE\n\ -TCGA-13-1505-01 TP53 P75fs TRUNC\n\ -TCGA-04-1336-01 TP53 R248W MISSENSE\n\ -TCGA-24-2261-01 TP53 Y163C MISSENSE\n\ -TCGA-13-0912-01 TP53 S261_splice TRUNC\n\ -TCGA-36-1580-01 TP53 R273C MISSENSE\n\ -TCGA-59-2352-01 TP53 G266V MISSENSE\n\ -TCGA-25-2409-01 TP53 R248W MISSENSE\n\ -TCGA-61-1919-01 TP53 I195T MISSENSE\n\ -TCGA-13-0919-01 TP53 V157F MISSENSE\n\ -TCGA-09-2051-01 TP53 P222fs TRUNC\n\ -TCGA-09-2050-01 TP53 L257Q MISSENSE\n\ -TCGA-25-1626-01 TP53 G245V MISSENSE\n\ -TCGA-09-2049-01 TP53 G245S MISSENSE\n\ -TCGA-24-1417-01 TP53 R248W MISSENSE\n\ -TCGA-24-1422-01 TP53 R248W MISSENSE\n\ -TCGA-13-0924-01 TP53 F270L MISSENSE\n\ -TCGA-61-2109-01 TP53 R306fs TRUNC\n\ -TCGA-24-1416-01 TP53 R282W MISSENSE\n\ -TCGA-24-1564-01 TP53 G187_splice TRUNC\n\ -TCGA-61-2088-01 TP53 MCN237del INFRAME\n\ -TCGA-10-0934-01 TP53 R248Q MISSENSE\n\ -TCGA-61-2003-01 TP53 R175H MISSENSE\n\ -TCGA-10-0934-01 TP53 R273H MISSENSE\n\ -TCGA-09-1666-01 TP53 Y126_splice TRUNC\n\ -TCGA-13-0714-01 TP53 S127F MISSENSE\n\ -TCGA-13-1510-01 TP53 R213* TRUNC\n\ -TCGA-36-1576-01 TP53 R337fs TRUNC\n\ -TCGA-25-1329-01 TP53 P47fs TRUNC\n\ -TCGA-13-1481-01 TP53 P177R MISSENSE\n\ -TCGA-04-1337-01 TP53 C135R MISSENSE\n\ -TCGA-24-1428-01 TP53 I195N MISSENSE\n\ -TCGA-24-1567-01 TP53 R282W MISSENSE\n\ -TCGA-04-1332-01 TP53 R181P MISSENSE\n\ -TCGA-04-1349-01 TP53 S241F MISSENSE\n\ -TCGA-61-2008-01 TP53 G117fs TRUNC\n\ -TCGA-13-0791-01 TP53 R273L MISSENSE\n\ -TCGA-09-1669-01 TP53 Q331_splice TRUNC\n\ -TCGA-24-2019-01 TP53 I232N MISSENSE\n\ -TCGA-24-1425-01 TP53 Y234C MISSENSE\n\ -TCGA-24-1423-01 TP53 P191del INFRAME\n\ -TCGA-10-0926-01 TP53 Y163C MISSENSE\n\ -TCGA-13-0760-01 TP53 L265P MISSENSE\n\ -TCGA-24-1556-01 TP53 A307_splice TRUNC\n\ -TCGA-24-1558-01 TP53 R273H MISSENSE\n\ -TCGA-25-2404-01 TP53 H214R MISSENSE\n\ -TCGA-24-1616-01 TP53 Y236C MISSENSE\n\ -TCGA-13-0720-01 TP53 A159V MISSENSE\n\ -TCGA-24-2280-01 TP53 Q192* TRUNC\n\ -TCGA-13-0793-01 TP53 C124fs TRUNC\n\ -TCGA-24-1604-01 TP53 A307_splice TRUNC\n\ -TCGA-09-1659-01 TP53 E294* TRUNC\n\ -TCGA-24-1413-01 TP53 E198* TRUNC\n\ -TCGA-09-1662-01 TP53 C176Y MISSENSE\n\ -TCGA-13-0724-01 TP53 V157F MISSENSE\n\ -TCGA-24-2030-01 TP53 G187_splice TRUNC\n\ -TCGA-13-1484-01 TP53 Y234N MISSENSE\n\ -TCGA-24-2254-01 TP53 S241F MISSENSE\n\ -TCGA-61-2101-01 TP53 P85fs TRUNC\n\ -TCGA-09-0366-01 TP53 K132N MISSENSE\n\ -TCGA-04-1365-01 TP53 Y126_splice TRUNC\n\ -TCGA-09-2053-01 TP53 Y163H MISSENSE\n\ -TCGA-24-2024-01 TP53 V272M MISSENSE\n\ -TCGA-23-1120-01 TP53 R110L MISSENSE\n\ -TCGA-24-0970-01 TP53 G187_splice TRUNC\n\ -TCGA-13-1489-01 TP53 R342* TRUNC\n\ -TCGA-24-1103-01 TP53 A307_splice TRUNC\n\ -TCGA-57-1993-01 TP53 R248Q MISSENSE\n\ -TCGA-25-1322-01 TP53 Y205C MISSENSE\n\ -TCGA-13-0751-01 TP53 L348fs TRUNC\n\ -TCGA-04-1356-01 TP53 Y220C MISSENSE\n\ -TCGA-10-0928-01 TP53 G105S MISSENSE\n\ -TCGA-23-2077-01 TP53 R175H MISSENSE\n\ -TCGA-13-0890-01 TP53 Y126_splice TRUNC\n\ -TCGA-04-1525-01 TP53 R282fs TRUNC\n\ -TCGA-23-1022-01 TP53 K164E MISSENSE\n\ -TCGA-13-0905-01 TP53 R273P MISSENSE\n\ -TCGA-30-1862-01 TP53 E224_splice TRUNC\n\ -TCGA-13-0765-01 TP53 AMP64_264L>LSSGNL INFRAME\n\ -TCGA-31-1953-01 TP53 V97fs TRUNC\n\ -TCGA-04-1514-01 TP53 Y126_splice TRUNC\n\ -TCGA-13-1509-01 TP53 L330fs TRUNC\n\ -TCGA-24-1419-01 TP53 R248Q MISSENSE\n\ -TCGA-25-1321-01 TP53 R273C MISSENSE\n\ -TCGA-20-0987-01 TP53 G105R MISSENSE\n\ -TCGA-23-1024-01 TP53 G108fs TRUNC\n\ -TCGA-24-2290-01 TP53 V274G MISSENSE\n\ -TCGA-23-1124-01 TP53 R156P MISSENSE\n\ -TCGA-61-2094-01 TP53 L130V MISSENSE\n\ -TCGA-25-1625-01 TP53 V216M MISSENSE\n\ -TCGA-61-1736-01 TP53 G245R MISSENSE\n\ -TCGA-13-0800-01 TP53 K132M MISSENSE\n\ -TCGA-24-1555-01 TP53 H179Q MISSENSE\n\ -TCGA-25-2391-01 TP53 E51fs TRUNC\n\ -TCGA-24-1434-01 TP53 L344fs TRUNC\n\ -TCGA-04-1517-01 TP53 R65* TRUNC\n\ -TCGA-09-1661-01 TP53 G187_splice TRUNC\n\ -TCGA-61-1995-01 TP53 C238Y MISSENSE\n\ -TCGA-31-1959-01 TP53 C238F MISSENSE\n\ -TCGA-24-1614-01 TP53 V157F MISSENSE\n\ -TCGA-36-1569-01 TP53 W53* TRUNC\n\ -TCGA-24-2271-01 TP53 K321* TRUNC\n\ -TCGA-23-1123-01 TP53 C176Y MISSENSE\n\ -TCGA-13-1507-01 TP53 T140fs TRUNC\n\ -TCGA-13-0913-01 TP53 P278R MISSENSE\n\ -TCGA-13-0899-01 TP53 Q317* TRUNC\n\ -TCGA-23-1110-01 TP53 C176Y MISSENSE\n\ -TCGA-25-1319-01 TP53 Y220C MISSENSE\n\ -TCGA-24-1548-01 TP53 Y220C MISSENSE\n\ -TCGA-13-0910-01 TP53 C275Y MISSENSE\n\ -TCGA-04-1346-01 TP53 H179R MISSENSE\n\ -TCGA-04-1350-01 TP53 H179R MISSENSE\n\ -TCGA-25-1326-01 TP53 E286K MISSENSE\n\ -TCGA-24-1549-01 TP53 V225_splice TRUNC\n\ -TCGA-13-0891-01 TP53 Y220C MISSENSE\n\ -TCGA-10-0931-01 TP53 Q136* TRUNC\n\ -TCGA-13-1411-01 TP53 C277F MISSENSE\n\ -TCGA-13-1498-01 TP53 I332_splice TRUNC\n\ -TCGA-24-2260-01 TP53 R248Q MISSENSE\n\ -TCGA-23-1030-01 TP53 R175H MISSENSE\n\ -TCGA-04-1342-01 TP53 N288fs TRUNC\n\ -TCGA-13-0723-01 TP53 T150fs TRUNC\n\ -TCGA-24-2289-01 TP53 R196* TRUNC\n\ -TCGA-61-1728-01 TP53 Y220C MISSENSE\n\ -TCGA-13-0883-01 TP53 C238fs TRUNC\n\ -TCGA-23-1026-01 TP53 K132R MISSENSE\n\ -TCGA-61-2097-01 TP53 R342* TRUNC\n\ -TCGA-59-2354-01 TP53 Y220C MISSENSE\n\ -TCGA-59-2350-01 TP53 Y220C MISSENSE\n\ -TCGA-59-2363-01 TP53 Y220C MISSENSE\n\ -TCGA-23-1122-01 TP53 R175H MISSENSE\n\ -TCGA-13-0887-01 TP53 R213* TRUNC\n\ -TCGA-13-0762-01 TP53 H193R MISSENSE\n\ -TCGA-59-2351-01 TP53 T140fs TRUNC\n\ -TCGA-25-2398-01 TP53 154_154G>GTDSTPPPG INFRAME\n\ -TCGA-25-1315-01 TP53 R273H MISSENSE\n\ -TCGA-24-2298-01 TP53 V225_splice TRUNC\n\ -TCGA-13-1497-01 TP53 R333fs TRUNC\n\ -TCGA-13-0792-01 TP53 C238fs TRUNC\n\ -TCGA-13-0903-01 TP53 Y205C MISSENSE\n\ -TCGA-30-1853-01 TP53 G245D MISSENSE\n\ -TCGA-57-1582-01 TP53 Y236C MISSENSE\n\ -TCGA-24-0966-01 TP53 G245V MISSENSE\n\ -TCGA-24-1557-01 TP53 Y126_splice TRUNC\n\ -TCGA-59-2355-01 TP53 Q331_splice TRUNC\n\ -TCGA-23-1023-01 TP53 D281G MISSENSE\n\ -TCGA-10-0927-01 TP53 P36fs TRUNC\n\ -TCGA-09-2044-01 TP53 G187_splice TRUNC\n\ -TCGA-13-0906-01 TP53 F134V MISSENSE\n\ -TCGA-25-1627-01 TP53 Y220C MISSENSE\n\ -TCGA-13-1482-01 TP53 R280I MISSENSE\n\ -TCGA-24-2281-01 TP53 R175H MISSENSE\n\ -TCGA-13-0889-01 TP53 R273C MISSENSE\n\ -TCGA-24-1562-01 TP53 S33_splice TRUNC\n\ -TCGA-13-1488-01 TP53 R306* TRUNC\n\ -TCGA-61-2016-01 TP53 E204* TRUNC\n\ -TCGA-04-1362-01 TP53 V225_splice TRUNC\n\ -TCGA-13-0717-01 TP53 AMP44_246GGM>V INFRAME\n\ -TCGA-61-2104-01 TP53 Y163N MISSENSE\n\ -TCGA-13-0885-01 TP53 W146* TRUNC\n\ -TCGA-24-2288-01 TP53 P250L MISSENSE\n\ -TCGA-13-0726-01 TP53 R282W MISSENSE\n\ -TCGA-10-0938-01 TP53 Q331_splice TRUNC\n\ -TCGA-24-2035-01 TP53 S315fs TRUNC\n\ -TCGA-13-1492-01 TP53 G187_splice TRUNC\n\ -TCGA-24-1105-01 TP53 V157F MISSENSE\n\ -TCGA-13-1494-01 TP53 G105C MISSENSE\n\ -TCGA-24-0979-01 TP53 R248Q MISSENSE\n\ -TCGA-04-1361-01 TP53 Y234C MISSENSE\n\ -TCGA-25-1628-01 TP53 E51* TRUNC\n\ -TCGA-13-1491-01 TP53 C275Y MISSENSE\n\ -TCGA-25-1635-01 TP53 D259Y MISSENSE\n\ -TCGA-13-1506-01 TP53 M66fs TRUNC\n\ -TCGA-24-1560-01 TP53 G244C MISSENSE\n\ -TCGA-13-1410-01 TP53 L130fs TRUNC\n\ -TCGA-13-0804-01 TP53 R273H MISSENSE\n\ -TCGA-24-1464-01 TP53 N239S MISSENSE\n\ -TCGA-10-0935-01 TP53 G187_splice TRUNC\n\ -TCGA-23-1032-01 TP53 R248Q MISSENSE\n\ -TCGA-25-1630-01 TP53 V173L MISSENSE\n\ -TCGA-61-2012-01 TP53 Y220C MISSENSE\n\ -TCGA-36-1568-01 TP53 G245S MISSENSE\n\ -TCGA-23-2072-01 TP53 Q331_splice TRUNC\n\ -TCGA-13-1487-01 TP53 M237K MISSENSE\n\ -TCGA-24-1426-01 TP53 R273C MISSENSE\n\ -TCGA-24-1470-01 TP53 S260fs TRUNC\n\ -TCGA-13-0920-01 TP53 Q100* TRUNC\n\ -TCGA-13-0761-01 TP53 R273H MISSENSE\n\ -TCGA-25-1320-01 TP53 C124fs TRUNC\n\ -TCGA-23-1021-01 TP53 A159V MISSENSE\n\ -TCGA-04-1348-01 TP53 G266R MISSENSE\n\ -TCGA-23-1027-01 TP53 E198* TRUNC\n\ -TCGA-04-1338-01 TP53 G245S MISSENSE\n\ -TCGA-23-1117-01 TP53 Q144fs TRUNC\n\ -TCGA-36-1578-01 TP53 R273H MISSENSE\n\ -TCGA-36-1575-01 TP53 R273H MISSENSE\n\ -TCGA-36-1574-01 TP53 R273H MISSENSE\n\ -TCGA-25-2399-01 TP53 R175H MISSENSE\n\ -TCGA-25-1634-01 TP53 A70fs TRUNC\n\ -TCGA-30-1891-01 TP53 L194R MISSENSE\n\ -TCGA-36-1577-01 TP53 E224_splice TRUNC\n\ -TCGA-13-0900-01 TP53 R273H MISSENSE\n\ -TCGA-24-1466-01 TP53 R249G MISSENSE\n\ -TCGA-61-2092-01 TP53 D208V MISSENSE\n\ -TCGA-04-1347-01 TP53 S215R MISSENSE\n\ -TCGA-20-0990-01 TP53 Q144* TRUNC\n\ -TCGA-13-1499-01 TP53 R273C MISSENSE\n\ -TCGA-24-1104-01 TP53 I195T MISSENSE\n\ -TCGA-24-1418-01 TP53 S227fs TRUNC\n\ -TCGA-57-1583-01 TP53 C229fs TRUNC\n\ -TCGA-29-2427-01 TP53 G244D MISSENSE\n\ -TCGA-13-1499-01 TP53 R248Q MISSENSE\n\ -TCGA-13-0795-01 TP53 C135Y MISSENSE\n\ -TCGA-13-1496-01 TP53 R248Q MISSENSE\n\ -TCGA-09-2045-01 TP53 H179R MISSENSE\n\ -TCGA-23-2081-01 TP53 G262V MISSENSE\n\ -TCGA-24-1474-01 TP53 Q192* TRUNC\n\ -TCGA-25-1623-01 TP53 R282W MISSENSE\n\ -TCGA-24-1551-01 TP53 R248W MISSENSE\n\ -TCGA-24-1431-01 TP53 Q192* TRUNC\n\ -TCGA-13-2060-01 TP53 H179R MISSENSE\n\ -TCGA-25-1631-01 TP53 T125_splice TRUNC\n\ -TCGA-13-0893-01 TP53 G245D MISSENSE\n\ -TCGA-13-1495-01 TP53 I195F MISSENSE\n\ -TCGA-24-1603-01 TP53 S315fs TRUNC\n\ -TCGA-04-1530-01 TP53 R273H MISSENSE\n\ -TCGA-04-1542-01 TP53 R273H MISSENSE\n\ -TCGA-24-1471-01 TP53 E271* TRUNC\n\ -TCGA-61-2102-01 TP53 G266R MISSENSE\n\ -TCGA-24-1469-01 TP53 I195T MISSENSE\n\ -TCGA-57-1584-01 TP53 C176Y MISSENSE\n\ -TCGA-13-1407-01 TP53 F109C MISSENSE\n\ -TCGA-13-1512-01 TP53 R273L MISSENSE\n\ -TCGA-23-1028-01 TP53 P250L MISSENSE\n\ -TCGA-13-0894-01 TP53 H193Y MISSENSE\n\ -TCGA-13-1409-01 TP53 S261_splice TRUNC\n\ -TCGA-24-0982-01 TP53 R248W MISSENSE\n\ -TCGA-36-1570-01 TP53 R248fs TRUNC\n\ -TCGA-13-0730-01 TP53 H178fs TRUNC\n\ -TCGA-61-2000-01 TP53 K132E MISSENSE\n\ -TCGA-61-2110-01 TP53 S127Y MISSENSE\n\ -TCGA-31-1950-01 TP53 I195T MISSENSE\n\ -TCGA-24-1424-01 TP53 I195T MISSENSE\n\ -TCGA-25-1632-01 TP53 R248G MISSENSE\n\ -TCGA-24-1427-01 TP53 V272fs TRUNC\n\ -TCGA-61-1998-01 TP53 S215R MISSENSE\n\ -TCGA-13-0904-01 TP53 G279E MISSENSE\n\ -TCGA-13-0923-01 TP53 G187_splice TRUNC\n\ -TCGA-24-1563-01 TP53 I195T MISSENSE\n\ -TCGA-13-1504-01 TP53 I251S MISSENSE\n\ -TCGA-25-1324-01 TP53 Y126_splice TRUNC\n\ -TCGA-13-0897-01 TP53 R283fs TRUNC\n\ -TCGA-04-1331-01 TP53 R306* TRUNC\n\ -TCGA-10-0937-01 TP53 R282W MISSENSE\n\ -TCGA-13-1405-01 TP53 R196* TRUNC\n\ -TCGA-04-1364-01 TP53 R248Q MISSENSE\n\ -TCGA-20-0991-01 TP53 S241F MISSENSE\n\ -TCGA-24-2267-01 TP53 T284fs TRUNC\n\ -TCGA-13-1404-01 TP53 C176Y MISSENSE\n\ -TCGA-13-0911-01 TP53 L43fs TRUNC\n\ -TCGA-25-1313-01 TP53 L145R MISSENSE\n\ -TCGA-36-1571-01 TP53 R337C MISSENSE\n\ -TCGA-13-0884-01 TP53 R342* TRUNC\n\ -TCGA-23-2078-01 TP53 T256del INFRAME\n\ -TCGA-13-1412-01 TP53 M237I MISSENSE\n\ -TCGA-24-1545-01 TP53 S241Y MISSENSE\n\ -TCGA-25-2401-01 TP53 L194R MISSENSE\n\ -TCGA-24-1436-01 TP53 Q331_splice TRUNC\n\ -TCGA-25-2400-01 TP53 E224_splice TRUNC\n\ -TCGA-04-1357-01 TP53 P223fs TRUNC\n\ -TCGA-13-1403-01 TP53 T125_splice TRUNC\n\ -TCGA-13-0886-01 TP53 V272M MISSENSE\n\ -TCGA-25-1318-01 TP53 R175H MISSENSE\n\ -TCGA-23-1116-01 TP53 S261_splice TRUNC\n\ -TCGA-10-0925-01\n\ -TCGA-10-0926-01\n\ -TCGA-10-0927-01\n\ -TCGA-10-0928-01\n\ -TCGA-10-0930-01\n\ -TCGA-10-0931-01\n\ -TCGA-10-0933-01\n\ -TCGA-10-0934-01\n\ -TCGA-20-1684-01\n\ -TCGA-20-1685-01\n\ -TCGA-20-1686-01\n\ -TCGA-20-1687-01\n\ -TCGA-23-1021-01\n\ -TCGA-23-1022-01\n\ -TCGA-23-1023-01\n\ -TCGA-23-1024-01\n\ -TCGA-23-1026-01\n\ -TCGA-23-1027-01\n\ -TCGA-23-1028-01\n\ -TCGA-23-1029-01\n\ -TCGA-23-1030-01\n\ -TCGA-23-1031-01\n\ -TCGA-23-1032-01\n\ -TCGA-23-1107-01\n\ -TCGA-23-1109-01\n\ -TCGA-23-1110-01\n\ -TCGA-23-1111-01\n\ -TCGA-23-1113-01\n\ -TCGA-23-1114-01\n\ -TCGA-23-1116-01\n\ -TCGA-23-1117-01\n\ -TCGA-23-1118-01\n\ -TCGA-23-1119-01\n\ -TCGA-23-1120-01\n\ -TCGA-23-1121-01\n\ -TCGA-23-1122-01\n\ -TCGA-23-1123-01\n\ -TCGA-23-1124-01\n\ -TCGA-23-1809-01\n\ -TCGA-23-2072-01\n\ -TCGA-23-2077-01\n\ -TCGA-23-2078-01\n\ -TCGA-23-2079-01\n\ -TCGA-23-2081-01\n\ -TCGA-23-2084-01\n\ -TCGA-23-2641-01\n\ -TCGA-23-2643-01\n\ -TCGA-23-2645-01\n\ -TCGA-23-2647-01\n\ -TCGA-23-2649-01\n\ -TCGA-24-0966-01\n\ -TCGA-24-0968-01\n\ -TCGA-24-0970-01\n\ -TCGA-24-0975-01\n\ -TCGA-24-0979-01\n\ -TCGA-24-0980-01\n\ -TCGA-24-0981-01\n\ -TCGA-24-0982-01\n\ -TCGA-24-1103-01\n\ -TCGA-24-1104-01\n\ -TCGA-24-1105-01\n\ -TCGA-24-1413-01\n\ -TCGA-24-1416-01\n\ -TCGA-24-1417-01\n\ -TCGA-24-1418-01\n\ -TCGA-24-1419-01\n\ -TCGA-24-1422-01\n\ -TCGA-24-1423-01\n\ -TCGA-24-1424-01\n\ -TCGA-24-1425-01\n\ -TCGA-24-1426-01\n\ -TCGA-24-1427-01\n\ -TCGA-24-1428-01\n\ -TCGA-24-1430-01\n\ -TCGA-24-1431-01\n\ -TCGA-24-1434-01\n\ -TCGA-24-1435-01\n\ -TCGA-24-1436-01\n\ -TCGA-24-1463-01\n\ -TCGA-24-1464-01\n\ -TCGA-24-1466-01\n\ -TCGA-24-1467-01\n\ -TCGA-24-1469-01\n\ -TCGA-24-1470-01\n\ -TCGA-24-1471-01\n\ -TCGA-24-1474-01\n\ -TCGA-24-1544-01\n\ -TCGA-24-1545-01\n\ -TCGA-24-1546-01\n\ -TCGA-24-1548-01\n\ -TCGA-24-1549-01\n\ -TCGA-24-1550-01\n\ -TCGA-24-1551-01\n\ -TCGA-24-1552-01\n\ -TCGA-24-1553-01\n\ -TCGA-24-1555-01\n\ -TCGA-24-1556-01\n\ -TCGA-24-1557-01\n\ -TCGA-24-1558-01\n\ -TCGA-24-1560-01\n\ -TCGA-24-1562-01\n\ -TCGA-24-1563-01\n\ -TCGA-24-1564-01\n\ -TCGA-24-1565-01\n\ -TCGA-24-1567-01\n\ -TCGA-24-1603-01\n\ -TCGA-24-1604-01\n\ -TCGA-24-1614-01\n\ -TCGA-24-1616-01\n\ -TCGA-24-1842-01\n\ -TCGA-24-1843-01\n\ -TCGA-24-1844-01\n\ -TCGA-24-1845-01\n\ -TCGA-24-1846-01\n\ -TCGA-24-1847-01\n\ -TCGA-24-1849-01\n\ -TCGA-24-1850-01\n\ -TCGA-24-1852-01\n\ -TCGA-24-1920-01\n\ -TCGA-24-1923-01\n\ -TCGA-24-1924-01\n\ -TCGA-24-1927-01\n\ -TCGA-24-1928-01\n\ -TCGA-24-1930-01\n\ -TCGA-24-2019-01\n\ -TCGA-24-2020-01\n\ -TCGA-24-2023-01\n\ -TCGA-24-2024-01\n\ -TCGA-24-2026-01\n\ -TCGA-24-2027-01\n\ -TCGA-24-2029-01\n\ -TCGA-24-2030-01\n\ -TCGA-24-2033-01\n\ -TCGA-24-2035-01\n\ -TCGA-24-2036-01\n\ -TCGA-24-2038-01\n\ -TCGA-24-2254-01\n\ -TCGA-24-2260-01\n\ -TCGA-24-2261-01\n\ -TCGA-24-2262-01\n\ -TCGA-24-2267-01\n\ -TCGA-24-2271-01\n\ -TCGA-24-2280-01\n\ -TCGA-24-2281-01\n\ -TCGA-24-2288-01\n\ -TCGA-24-2289-01\n\ -TCGA-24-2290-01\n\ -TCGA-24-2293-01\n\ -TCGA-24-2295-01\n\ -TCGA-24-2297-01\n\ -TCGA-24-2298-01\n\ -TCGA-25-1312-01\n\ -TCGA-25-1313-01\n\ -TCGA-25-1314-01\n\ -TCGA-25-1315-01\n\ -TCGA-25-1316-01\n\ -TCGA-25-1317-01\n\ -TCGA-25-1318-01\n\ -TCGA-25-1319-01\n\ -TCGA-25-1320-01\n\ -TCGA-25-1321-01\n\ -TCGA-25-1322-01\n\ -TCGA-25-1323-01\n\ -TCGA-25-1324-01\n\ -TCGA-25-1325-01\n\ -TCGA-25-1326-01\n\ -TCGA-25-1328-01\n\ -TCGA-25-1329-01\n\ -TCGA-25-1623-01\n\ -TCGA-25-1625-01\n\ -TCGA-25-1626-01\n\ -TCGA-25-1627-01\n\ -TCGA-25-1628-01\n\ -TCGA-25-1630-01\n\ -TCGA-25-1631-01\n\ -TCGA-25-1632-01\n\ -TCGA-25-1633-01\n\ -TCGA-25-1634-01\n\ -TCGA-25-1635-01\n\ -TCGA-25-1870-01\n\ -TCGA-25-1871-01\n\ -TCGA-25-1877-01\n\ -TCGA-25-1878-01\n\ -TCGA-25-2042-01\n\ -TCGA-25-2390-01\n\ -TCGA-25-2391-01\n\ -TCGA-25-2396-01\n\ -TCGA-25-2397-01\n\ -TCGA-25-2398-01\n\ -TCGA-25-2399-01\n\ -TCGA-25-2400-01\n\ -TCGA-25-2401-01\n\ -TCGA-25-2392-01\n\ -TCGA-25-2393-01\n\ diff --git a/src/main/resources/webapp/jsp/oncoprint/legend-template.jsp b/src/main/resources/webapp/jsp/oncoprint/legend-template.jsp deleted file mode 100644 index 3d84159f5f2..00000000000 --- a/src/main/resources/webapp/jsp/oncoprint/legend-template.jsp +++ /dev/null @@ -1,47 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - - diff --git a/src/main/resources/webapp/jsp/oncoprint/main.jsp b/src/main/resources/webapp/jsp/oncoprint/main.jsp deleted file mode 100644 index f48c36a4c25..00000000000 --- a/src/main/resources/webapp/jsp/oncoprint/main.jsp +++ /dev/null @@ -1,77 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. ---%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - -<%@ page import="org.mskcc.cbio.portal.util.GlobalProperties" %> -<%@ page import="org.mskcc.cbio.portal.dao.DaoMutation" %> -<%@ page import="org.mskcc.cbio.portal.servlet.QueryBuilder" %> -<%@ page import="java.util.List" %> -<%@ taglib prefix="c" uri="http://java.sun.com/jsp/jstl/core" %> -<%@ taglib prefix="fn" uri="http://java.sun.com/jsp/jstl/functions" %> - - - - -
-
\ No newline at end of file diff --git a/src/main/resources/webapp/jsp/oncoprint/mutation-file-example.txt b/src/main/resources/webapp/jsp/oncoprint/mutation-file-example.txt deleted file mode 100644 index 7441b607f99..00000000000 --- a/src/main/resources/webapp/jsp/oncoprint/mutation-file-example.txt +++ /dev/null @@ -1,15 +0,0 @@ -Hugo_Symbol Entrez_Gene_Id sample_id Protein_Change -BRCA1 672 TCGA-04-1357 Q1538* -BRCA1 672 TCGA-13-0730 R1835* -BRCA1 672 TCGA-23-1026 G813fs -BRCA1 672 TCGA-24-2035 G1710fs -BRCA1 672 TCGA-25-1625 E116* -BRCA1 672 TCGA-25-1630 K519fs -BRCA1 672 TCGA-25-1632 L1216fs -BRCA1 672 TCGA-29-2427 L431* -BRCA2 675 TCGA-13-0890 V1229fs -BRCA2 675 TCGA-13-1481 L2696fs -BRCA2 675 TCGA-23-1120 L3277fs -BRCA2 675 TCGA-24-1103 K1638E -BRCA2 675 TCGA-24-1555 T2607fs -BRCA2 675 TCGA-24-1562 K3326* diff --git a/src/main/resources/webapp/jsp/pancancer_study_summary.jsp b/src/main/resources/webapp/jsp/pancancer_study_summary.jsp deleted file mode 100644 index e291b791f14..00000000000 --- a/src/main/resources/webapp/jsp/pancancer_study_summary.jsp +++ /dev/null @@ -1,92 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - -<%-- - - This is the main page for loading the pan-cancer study view, - - where "pan-cancer study" = a study comprising more than 1 cancer type. - --%> - - -<%@ page import="org.mskcc.cbio.portal.util.GlobalProperties" %> - - - -<%@ include file="src/main/webapp/jsp/pancancer_study_summary/pancancer_study_summary_templates.html" %> - - - - - -
- -
- - - - diff --git a/src/main/resources/webapp/jsp/pancancer_study_summary/pancancer_study_summary_templates.html b/src/main/resources/webapp/jsp/pancancer_study_summary/pancancer_study_summary_templates.html deleted file mode 100644 index 8248a292e14..00000000000 --- a/src/main/resources/webapp/jsp/pancancer_study_summary/pancancer_study_summary_templates.html +++ /dev/null @@ -1,148 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/src/main/resources/webapp/jsp/patient_view/clinical_timeline.jsp b/src/main/resources/webapp/jsp/patient_view/clinical_timeline.jsp deleted file mode 100644 index af5b32af765..00000000000 --- a/src/main/resources/webapp/jsp/patient_view/clinical_timeline.jsp +++ /dev/null @@ -1,248 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - - -<%@ page import="org.mskcc.cbio.portal.util.GlobalProperties" %> - - - - - - - -
- Clinical Events -
-
- -
-
-
diff --git a/src/main/resources/webapp/jsp/patient_view/cna.jsp b/src/main/resources/webapp/jsp/patient_view/cna.jsp deleted file mode 100644 index 9e30f255ed4..00000000000 --- a/src/main/resources/webapp/jsp/patient_view/cna.jsp +++ /dev/null @@ -1,596 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - -<%@ page import="org.mskcc.cbio.portal.servlet.PatientView" %> -<%@ page import="org.mskcc.cbio.portal.servlet.CnaJSON" %> - - - -
loading
-
The following table contains filtered copy number alterations (CNAs). -
- - - - - -
- - <%@ include file="src/main/webapp/jsp/patient_view/cna_table_template.jsp"%> -
-
diff --git a/src/main/resources/webapp/jsp/patient_view/cna_table_template.jsp b/src/main/resources/webapp/jsp/patient_view/cna_table_template.jsp deleted file mode 100644 index c28bbb31a15..00000000000 --- a/src/main/resources/webapp/jsp/patient_view/cna_table_template.jsp +++ /dev/null @@ -1,46 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - - -
CNA Event IDTumorsGeneCNAAnnotationCytobandmRNA Expr.CohortDrugs
- - - - - - - - - -
Drug NameDrug Target(s)DescriptionFDA approved?Data Sources
-
loading
diff --git a/src/main/resources/webapp/jsp/patient_view/mdacc_patient_heatmap_viewer.jsp b/src/main/resources/webapp/jsp/patient_view/mdacc_patient_heatmap_viewer.jsp deleted file mode 100644 index 9c714a072c2..00000000000 --- a/src/main/resources/webapp/jsp/patient_view/mdacc_patient_heatmap_viewer.jsp +++ /dev/null @@ -1,104 +0,0 @@ -<%-- - - Copyright (c) 2016 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - - -<%-- For the PATIENT view --%> - -<%@ page import="org.mskcc.cbio.portal.util.GlobalProperties" %> - - - - -
\ No newline at end of file diff --git a/src/main/resources/webapp/jsp/patient_view/mutations.jsp b/src/main/resources/webapp/jsp/patient_view/mutations.jsp deleted file mode 100644 index 4b25b3421f6..00000000000 --- a/src/main/resources/webapp/jsp/patient_view/mutations.jsp +++ /dev/null @@ -1,1321 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - -<%@ page import="org.mskcc.cbio.portal.dao.DaoMutSig" %> -<%@ page import="org.mskcc.cbio.portal.servlet.MutationsJSON" %> -<%@ page import="org.mskcc.cbio.portal.servlet.PatientView" %> - - - - - - - -
loading
-
The following table contains filtered mutations. -
-
- - - - - diff --git a/src/main/resources/webapp/jsp/patient_view/mutations_table_template.jsp b/src/main/resources/webapp/jsp/patient_view/mutations_table_template.jsp deleted file mode 100644 index cb6c2e22ad7..00000000000 --- a/src/main/resources/webapp/jsp/patient_view/mutations_table_template.jsp +++ /dev/null @@ -1,63 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - - - - - Mutation Event ID - Tumors - Gene - Protein
Change - Annotation - Chr - Start - End - Ref - Var - Validation - Type - Allele
Freq - Variant
Reads - Ref
Reads - Allele
Freq (N) - Variant
Reads (N) - Ref
Reads (N) - BAM - Copy # - mRNA Expr. - Cohort - cBioPortal - COSMIC - Mutation
Assessor - Drugs - - diff --git a/src/main/resources/webapp/jsp/patient_view/path_report.jsp b/src/main/resources/webapp/jsp/patient_view/path_report.jsp deleted file mode 100644 index c591d4b3fb5..00000000000 --- a/src/main/resources/webapp/jsp/patient_view/path_report.jsp +++ /dev/null @@ -1,53 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - - - - -

It appears you don't have a PDF plugin for this browser.

-

You can click here to - download the pathology report PDF file.

- - - - diff --git a/src/main/resources/webapp/jsp/patient_view/pathways.jsp b/src/main/resources/webapp/jsp/patient_view/pathways.jsp deleted file mode 100644 index 1bd3c6c58a6..00000000000 --- a/src/main/resources/webapp/jsp/patient_view/pathways.jsp +++ /dev/null @@ -1,76 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - -<% -request.setAttribute("include_network_help_tab", Boolean.FALSE); -request.setAttribute("include_network_legend", Boolean.FALSE); -%> - - - - - - - - - - - diff --git a/src/main/resources/webapp/jsp/patient_view/patient_view.jsp b/src/main/resources/webapp/jsp/patient_view/patient_view.jsp deleted file mode 100644 index 3e3dcbdb99c..00000000000 --- a/src/main/resources/webapp/jsp/patient_view/patient_view.jsp +++ /dev/null @@ -1,69 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - -<%@ page import="org.mskcc.cbio.portal.servlet.QueryBuilder" %> -<%@ page import="org.mskcc.cbio.portal.servlet.PatientView" %> -<%@ page import="org.mskcc.cbio.portal.servlet.DrugsJSON" %> -<%@ page import="org.mskcc.cbio.portal.servlet.ServletXssUtil" %> -<%@ page import="org.mskcc.cbio.portal.servlet.CheckDarwinAccessServlet" %> -<%@ page import="org.mskcc.cbio.portal.model.CancerStudy" %> -<%@ page import="org.mskcc.cbio.portal.model.GeneticProfile" %> -<%@ page import="org.mskcc.cbio.portal.util.GlobalProperties" %> -<%@ page import="java.util.HashMap" %> -<%@ page import="java.util.Map" %> -<%@ page import="java.util.Set" %> -<%@ page import= "java.net.URL" %> -<%@ page import="org.apache.commons.lang3.StringUtils" %> -<%@ page import="com.fasterxml.jackson.databind.ObjectMapper" %> -<%@ page import="org.mskcc.cbio.portal.util.GlobalProperties" %> -<%@ page import="org.mskcc.cbio.portal.util.IGVLinking" %> -<%@ taglib prefix="c" uri="http://java.sun.com/jsp/jstl/core"%> -<%@ taglib prefix="sec" uri="http://www.springframework.org/security/tags" %> - - - - <%@taglib prefix="t" tagdir="/WEB-INF/tags" %> - - - - - - - - -
- - - diff --git a/src/main/resources/webapp/jsp/patient_view/samples_table.jsp b/src/main/resources/webapp/jsp/patient_view/samples_table.jsp deleted file mode 100644 index c0963d21bdc..00000000000 --- a/src/main/resources/webapp/jsp/patient_view/samples_table.jsp +++ /dev/null @@ -1,68 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - -<%-- - ~ Copyright (c) 2012 Memorial Sloan-Kettering Cancer Center. - ~ This library is free software; you can redistribute it and/or modify it - ~ under the terms of the GNU Lesser General Public License as published - ~ by the Free Software Foundation; either version 2.1 of the License, or - ~ any later version. - ~ - ~ This library is distributed in the hope that it will be useful, but - ~ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF - ~ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and - ~ documentation provided hereunder is on an "as is" basis, and - ~ Memorial Sloan-Kettering Cancer Center - ~ has no obligations to provide maintenance, support, - ~ updates, enhancements or modifications. In no event shall - ~ Memorial Sloan-Kettering Cancer Center - ~ be liable to any party for direct, indirect, special, - ~ incidental or consequential damages, including lost profits, arising - ~ out of the use of this software and its documentation, even if - ~ Memorial Sloan-Kettering Cancer Center - ~ has been advised of the possibility of such damage. See - ~ the GNU Lesser General Public License for more details. - ~ - ~ You should have received a copy of the GNU Lesser General Public License - ~ along with this library; if not, write to the Free Software Foundation, - ~ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA. - --%> - -<%@ page import="org.mskcc.cbio.portal.dao.DaoTypeOfCancer" %> -<%@ page import="org.mskcc.cbio.portal.model.TypeOfCancer" %> -<%@ page import="org.mskcc.cbio.portal.dao.DaoException" %><% - String cancerTypeId = cancerStudy.getTypeOfCancerId().trim(); - TypeOfCancer typeOfCancerById = DaoTypeOfCancer.getTypeOfCancerById(cancerTypeId); -%> - - -
diff --git a/src/main/resources/webapp/jsp/patient_view/similar_patients.jsp b/src/main/resources/webapp/jsp/patient_view/similar_patients.jsp deleted file mode 100644 index c615afec423..00000000000 --- a/src/main/resources/webapp/jsp/patient_view/similar_patients.jsp +++ /dev/null @@ -1,187 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - -<%@ page import="org.mskcc.cbio.portal.servlet.SimilarPatientsJSON" %> - -<%if(showPlaceHoder){%> -A genomic overview with events aligned across patients goes here... -<%}%> - - - -
loading
- - - - - -
- - - - - - - - -
PatientCancer StudyShared Events of Interest
-
\ No newline at end of file diff --git a/src/main/resources/webapp/jsp/patient_view/summary.jsp b/src/main/resources/webapp/jsp/patient_view/summary.jsp deleted file mode 100644 index d1dc8ff3905..00000000000 --- a/src/main/resources/webapp/jsp/patient_view/summary.jsp +++ /dev/null @@ -1,295 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - -<%@ page import="org.mskcc.cbio.portal.servlet.CnaJSON" %> -<%@ page import="org.mskcc.cbio.portal.dao.DaoSample" %> -<%@ page import="org.mskcc.cbio.portal.model.Sample" %> -<%@ page import="java.util.ArrayList" %> -<%@ page import="java.util.List" %> -<%@ page import="org.mskcc.cbio.portal.util.GlobalProperties" %> - - - - - - - - - - - - -<%if(showTimeline){%> - -
-<%}%> - -<%if(showGenomicOverview){%> -
-Genomic Overview - - - - <%if(hasAlleleFrequencyData && caseIds.size() > 1) {%> - - <%} else {%> - - <%}%> - -
 - - - -
- -
- 		- -
- - -
-
-<%}%> -<%if(hasAlleleFrequencyData && caseIds.size() >= 1) {%> - - -<%}%> - - - -<%if(showMutations){%> - - - -<%}if(showCNA){%> - - - -<%}%> -
-
loading Loading mutations ...
- - - - - -
-
-
loading Loading copy number alterations ...
- - - - -
- - <%@ include file="src/main/webapp/jsp/patient_view/cna_table_template.jsp"%> -
-
-
diff --git a/src/main/resources/webapp/jsp/patient_view/tissue_images.jsp b/src/main/resources/webapp/jsp/patient_view/tissue_images.jsp deleted file mode 100644 index 88ec048af04..00000000000 --- a/src/main/resources/webapp/jsp/patient_view/tissue_images.jsp +++ /dev/null @@ -1,47 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - - - - -
loading
\ No newline at end of file diff --git a/src/main/resources/webapp/jsp/plots_tab.jsp b/src/main/resources/webapp/jsp/plots_tab.jsp deleted file mode 100644 index 3b4579cb758..00000000000 --- a/src/main/resources/webapp/jsp/plots_tab.jsp +++ /dev/null @@ -1,193 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - -<%@ page import="org.mskcc.cbio.portal.model.GeneWithScore" %> -<%@ page import="org.mskcc.cbio.portal.servlet.QueryBuilder" %> -<%@ page import="java.util.ArrayList" %> -<%@ page import="java.io.PrintWriter" %> -<%@ page import="java.io.IOException" %> -<%@ page import="org.mskcc.cbio.portal.model.GeneticProfile" %> -<%@ page import="org.mskcc.cbio.portal.model.GeneticAlterationType" %> - - - - - - - - - - - - - - - - - - - - - -
-
-
- - - - diff --git a/src/main/resources/webapp/jsp/preview.jsp b/src/main/resources/webapp/jsp/preview.jsp deleted file mode 100644 index f8be9dc89f1..00000000000 --- a/src/main/resources/webapp/jsp/preview.jsp +++ /dev/null @@ -1,198 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - - - -
-
    -
  • - Cross cancer query of CDKN2A -
    • -
  • - Patient-specific view for a TCGA endometrial cancer case -
    • -
  • - Network of genomic alterations in Serous Ovarian Cancer -
    • -
  • - EGFR Amplifications in Gliobastoma -
    • -
  • - Survival Analysis of BRCA Mutated v. Non-BRCA Mutated in Serous Ovarian Cancer -
    • -
  • - Epigenetic Silencing of BRCA1 in Serous Ovarian Cancer -
    • -
  • - Structural view of a PIK3R1 mutation in Glioblastoma -
    • -
  • - TP53 mutations in ovarian cancer -
    • -
-
- - \ No newline at end of file diff --git a/src/main/resources/webapp/jsp/preview_su2c.jsp b/src/main/resources/webapp/jsp/preview_su2c.jsp deleted file mode 100644 index 641d2201c49..00000000000 --- a/src/main/resources/webapp/jsp/preview_su2c.jsp +++ /dev/null @@ -1,113 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - - - -
-
    -
  • - Survival Analysis of BRCA Mutated v. Non-BRCA Mutated in Serous Ovarian Cancer -
    • -
  • - Epigenetic Silencing of BRCA1 in Serous Ovarian Cancer -
    • -
  • - TP53 mutations in ovarian cancer -
    • -
-
- - \ No newline at end of file diff --git a/src/main/resources/webapp/jsp/query_form.jsp b/src/main/resources/webapp/jsp/query_form.jsp deleted file mode 100644 index de1a36df7fc..00000000000 --- a/src/main/resources/webapp/jsp/query_form.jsp +++ /dev/null @@ -1,226 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - -<%@ page import="org.mskcc.cbio.portal.servlet.*" %> -<%@ page import="org.mskcc.cbio.portal.util.XssRequestWrapper" %> -<%@ page import="java.util.HashSet" %> -<%@ page import="java.io.IOException" %> -<%@ page import="java.net.URLEncoder" %> -<%@ page import="org.apache.commons.lang3.*" %> -<%@ page import="org.mskcc.cbio.portal.util.GlobalProperties" %> -<%@ page import="java.util.ArrayList" %> -<%@ page import="java.util.Map" %> -<%@ page import="java.util.Set" %> -<%@ page import="java.util.List" %> - -<% - org.mskcc.cbio.portal.servlet.ServletXssUtil localXssUtil = ServletXssUtil.getInstance(); - String localCancerTypeId = - (String) request.getAttribute(QueryBuilder.CANCER_STUDY_ID); - String localSampleSetId = - (String) request.getAttribute(QueryBuilder.CASE_SET_ID); - String localCancerStudyList = (String) request.getParameter(QueryBuilder.CANCER_STUDY_LIST); - if (localCancerStudyList == null) { - localCancerStudyList = ""; - } - HashSet localGeneticProfileIdSet = (HashSet) request.getAttribute - (QueryBuilder.GENETIC_PROFILE_IDS); - String localCaseIds = request.getParameter(QueryBuilder.CASE_IDS); - //String localGeneList = localXssUtil.getCleanInput(request, QueryBuilder.GENE_LIST); - String localGeneList = request.getParameter(QueryBuilder.GENE_LIST); - - if (request instanceof XssRequestWrapper) - { - localGeneList = localXssUtil.getCleanInput( - ((XssRequestWrapper)request).getRawParameter(QueryBuilder.GENE_LIST)); - } - - String localTabIndex = request.getParameter(QueryBuilder.TAB_INDEX); - String localzScoreThreshold = request.getParameter(QueryBuilder.Z_SCORE_THRESHOLD); - if (localzScoreThreshold == null) { - localzScoreThreshold = "2.0"; - } - String localRppaScoreThreshold = request.getParameter(QueryBuilder.RPPA_SCORE_THRESHOLD); - if (localRppaScoreThreshold == null) { - localRppaScoreThreshold = "2.0"; - } - if (localTabIndex == null) { - localTabIndex = QueryBuilder.TAB_VISUALIZE; - } else { - localTabIndex = URLEncoder.encode(localTabIndex); - } - - String localGeneSetChoice = request.getParameter(QueryBuilder.GENE_SET_CHOICE); - //String clientTranspose = localXssUtil.getCleanInput(request, QueryBuilder.CLIENT_TRANSPOSE_MATRIX); - String clientTranspose = request.getParameter(QueryBuilder.CLIENT_TRANSPOSE_MATRIX); - if (localGeneSetChoice == null) { - localGeneSetChoice = "user-defined-list"; - } - // Get prioritized studies for study selector - - List priorityStudies = GlobalProperties.getPriorityStudies(); -%> - -<% - /** - * Put together global parameters - * - */ -// HashSet geneticProfileIdSet = -// (HashSet) request.getAttribute(QueryBuilder.GENETIC_PROFILE_IDS); - - // put geneticProfileIds into the proper form for the JSON request -// HashSet geneticProfileIdSet = (HashSet) request.getAttribute -// (QueryBuilder.GENETIC_PROFILE_IDS); -// String geneticProfiles = StringUtils.join(geneticProfileIdSet.iterator(), " "); -// geneticProfiles = geneticProfiles.trim(); -// -// // put gene string into a form that javascript can swallow -// String genes = (String) request.getAttribute(QueryBuilder.RAW_GENE_STR); -// genes = StringEscapeUtils.escapeEcmaScript(genes); -// -// // get cases -// String cases = (String) request.getAttribute(QueryBuilder.SET_OF_CASE_IDS); -// cases = StringEscapeUtils.escapeEcmaScript(cases); -// -// String caseSetId = (String) request.getAttribute(QueryBuilder.CASE_SET_ID); -// String caseIdsKey = (String) request.getAttribute(QueryBuilder.CASE_IDS_KEY); -%> - - - -
-
-
- <%@ include file="src/main/webapp/jsp/step1_json.jsp" %> - <%@ include file="src/main/webapp/jsp/step2_json.jsp" %> - <%@ include file="src/main/webapp/jsp/step3_json.jsp" %> - <%@ include file="src/main/webapp/jsp/step4_json.jsp" %> - <%@ include file="src/main/webapp/jsp/step5_json.jsp" %> - - -

- <% conditionallyOutputTransposeMatrixOption (localTabIndex, clientTranspose, out); %> -

-

- - <% conditionallyOutputGenomespaceOption(localTabIndex, out); %> -

-
-
-
- -<%! - private void conditionallyOutputTransposeMatrixOption(String localTabIndex, - String clientTranspose, JspWriter out) - throws IOException { - if (localTabIndex.equals(QueryBuilder.TAB_DOWNLOAD)) { - outputTransposeMatrixOption(clientTranspose, out); - } - } - - private void outputTransposeMatrixOption(String clientTranspose, JspWriter out) throws IOException { - String checked = hasUserSelectedTheTransposeOption(clientTranspose); - out.println (" Clicking submit will generate a tab-delimited file " - + " containing your requested data."); - out.println ("
"); - } - - private String hasUserSelectedTheTransposeOption(String clientTranspose) { - if (clientTranspose != null) { - return "checked"; - } else { - return ""; - } - } - - private void conditionallyOutputGenomespaceOption(String localTabIndex, JspWriter out) - throws IOException { - if (GlobalProperties.genomespaceEnabled() && localTabIndex.equals(QueryBuilder.TAB_DOWNLOAD)) { - out.println("\"Send"); - } - } -%> diff --git a/src/main/resources/webapp/jsp/step1_json.jsp b/src/main/resources/webapp/jsp/step1_json.jsp deleted file mode 100644 index 7eb9b990316..00000000000 --- a/src/main/resources/webapp/jsp/step1_json.jsp +++ /dev/null @@ -1,149 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - -<%@ taglib prefix="c" uri="http://java.sun.com/jsp/jstl/core" %> -<%@taglib prefix="s" uri="http://www.springframework.org/tags" %> - -<% - String step1ErrorMsg = (String) request.getAttribute(QueryBuilder.STEP1_ERROR_MSG); -%> -
- Select Cancer Study: -
-
- - -
- - <%-- loop over the configured query suggestions --%> - -
-
-
- No studies selected. - Deselect all -
- - - -
- - - - - - -
-
- - - - - - -<% -if (step1ErrorMsg != null) { - out.println("
" - + "" - + "" + step1ErrorMsg + ""); -} -%> - -<% -if (step1ErrorMsg != null) { - out.println ("
"); -} -%> - -
- diff --git a/src/main/resources/webapp/jsp/step2_json.jsp b/src/main/resources/webapp/jsp/step2_json.jsp deleted file mode 100644 index 29eabbfa7ee..00000000000 --- a/src/main/resources/webapp/jsp/step2_json.jsp +++ /dev/null @@ -1,89 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - -<%@ page import="org.mskcc.cbio.portal.servlet.QueryBuilder" %> -<%@ page import="static org.mskcc.cbio.portal.servlet.QueryBuilder.DATA_PRIORITY" %> -<% - String step2ErrorMsg = (String) request.getAttribute(QueryBuilder.STEP2_ERROR_MSG); -%> - -
- Select Genomic Profiles: - -<% -if (step2ErrorMsg != null) { - out.println("
" - + "" - + "" + step2ErrorMsg + ""); -} -%> - -
-
- -<% -if (step2ErrorMsg != null) { - out.println ("
"); -} -%> - -
- - -<% - Integer priority; - try { - priority = Integer.parseInt(request.getParameter(DATA_PRIORITY)); - } catch (NumberFormatException e) { - priority = 0; - } - - String checked[] = {"", "", ""}; - if(priority == null) - priority = 0; - - checked[priority] = " checked"; -%> - -
- Select Data Type Priority: - > - - - > - - - > - -
- - diff --git a/src/main/resources/webapp/jsp/step3_json.jsp b/src/main/resources/webapp/jsp/step3_json.jsp deleted file mode 100644 index 188f2d72dae..00000000000 --- a/src/main/resources/webapp/jsp/step3_json.jsp +++ /dev/null @@ -1,205 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - -<%@ page import="org.mskcc.cbio.portal.servlet.QueryBuilder" %> -<% - String step3ErrorMsg = (String) request.getAttribute(QueryBuilder.STEP3_ERROR_MSG); -%> - -
- - - - - - - - - - - -
- Select Patient/Case Set: - - - - -
- -
- -
- - - - - - - - - - - - - -
Build a Custom Case Set for: Number of Matching Cases:
 
-
- - - - - - -
- -
- loading - - - - - - - - - - - -
Gene SymbolNum MutationsQ-ValueAll
- -
- -
-
loading
-
- -
- - -<% -String customCaseListStyle = "none"; -// Output step 3 form validation error -if (step3ErrorMsg != null) { - out.println("
" - + "" - + "" + step3ErrorMsg + ""); - customCaseListStyle = "block"; -} -%> -
-

Enter case IDs below:

- -
-By sample ID -
-By patient ID -
- -<% -if (step3ErrorMsg != null) { - out.println("
"); -} -%> -
diff --git a/src/main/resources/webapp/jsp/step4_json.jsp b/src/main/resources/webapp/jsp/step4_json.jsp deleted file mode 100644 index 52b8f554798..00000000000 --- a/src/main/resources/webapp/jsp/step4_json.jsp +++ /dev/null @@ -1,87 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - -<%@ page import="org.mskcc.cbio.portal.servlet.QueryBuilder" %> -<% - String step4ErrorMsg = (String) request.getAttribute(QueryBuilder.STEP4_ERROR_MSG); -%> - -
- Enter Gene Set: - - - - <% if (localTabIndex.equals(QueryBuilder.TAB_VISUALIZE)) { %> - <% out.println("      Advanced: Onco Query Language (OQL)"); %> - <% } %> - -
- -
- -
- - -
- - - - - -

- -
- diff --git a/src/main/resources/webapp/jsp/step5_json.jsp b/src/main/resources/webapp/jsp/step5_json.jsp deleted file mode 100644 index f792df2ec7f..00000000000 --- a/src/main/resources/webapp/jsp/step5_json.jsp +++ /dev/null @@ -1,48 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - -<% - if (localTabIndex != null && localTabIndex.equals(QueryBuilder.TAB_VISUALIZE)) { -%> - -<% } %> \ No newline at end of file diff --git a/src/main/resources/webapp/jsp/survival_tab.jsp b/src/main/resources/webapp/jsp/survival_tab.jsp deleted file mode 100644 index a4682dc5b55..00000000000 --- a/src/main/resources/webapp/jsp/survival_tab.jsp +++ /dev/null @@ -1,63 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - -
-
-
- - \ No newline at end of file diff --git a/src/main/resources/webapp/jsp/testimonials.jsp b/src/main/resources/webapp/jsp/testimonials.jsp deleted file mode 100644 index c39ed26d13b..00000000000 --- a/src/main/resources/webapp/jsp/testimonials.jsp +++ /dev/null @@ -1,108 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - -<%-- - Created by IntelliJ IDEA. - User: byrne - Date: Dec 2, 2011 - Time: 12:16:49 PM - To change this template use File | Settings | File Templates. ---%> -<%@ page contentType="text/html;charset=UTF-8" language="java" %> - -
-
-

"Whenever bench scientists ask me how they can look at TCGA data, I've never - had a good answer for them. Now I do. The cBio Portal meets a critical need--it is the - interface that the cancer research community needs to access the wealth of TCGA. Even as a - computational biologist, I use it to follow-up on genes of interest. It makes querying - the data much less painful." -

- – Postdoctoral Fellow, Oregon Health & Science University -
-
-

"I would like to congratulate you and the team of the cBio portal. - It's just an amazing tool to work with, and we at Mass General really appreciate it." -

- – Research Fellow at Massachusetts General Hospital -
- -
-

"As a bench biologist with primary aim of determining gene aberrations in GBM, I found - your site absolutely fantastic! Thank you! I have to reiterate how awesome and user-friendly - your group has made this site - finally accomplishing the goal of having data easily accessible - and meaningful." -

- – Sr. Research Associate at Knight Cancer Institute/OHSU -
- -
-

"Thank you for your incredible resource that has helped greatly in accessing the TCGA - genomics data." -

- – Postdoctoral Fellow, Johns Hopkins University School of Medicine, - Dept Radiation Oncology and Molecular Radiation Sciences - -
- -
-

"I have been enjoying the ease with which TCGA data can be extracted in R using your CGDS package. - Very nice work!" -

- – Sr. Software Engineer, Institute for Systems Biology -
- -
-

"Thank you for generating such an excellent software. It is very useful for our research." -

- – Research Fellow, Memorial Sloan-Kettering Cancer Center -
- -
-

"Thank you very much for providing and maintaining this great resource." -

- – Scientist, Discovery Bioinformatics, Biotechnology Company -
- -
-

"I want to thank you for the nice, useful and user-friendly interface you have generated - and shared with the community." -

- – Postdoctoral Fellow, Harvard Medical School, Children's Hospital Boston -
- -
-

"This portal is truly the greatest thing since sliced bread. I am making discoveries with it not only in glioblastoma, my primary focus, but in other cancers as well -- it's all so easy with this fantastic tool. And I am enjoying showing it to my colleagues, whose jaws also drop. Thank you a thousand times over for this beautiful public resource. I am looking forward to citing this soon in an upcoming paper..." -

- – Associate Professor, University of Virginia -
-
diff --git a/src/main/resources/webapp/jsp/visualize.jsp b/src/main/resources/webapp/jsp/visualize.jsp deleted file mode 100644 index 6c0bdc19499..00000000000 --- a/src/main/resources/webapp/jsp/visualize.jsp +++ /dev/null @@ -1,575 +0,0 @@ -<%-- - - Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center. - - - - This library is distributed in the hope that it will be useful, but WITHOUT - - ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS - - FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder - - is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no - - obligations to provide maintenance, support, updates, enhancements or - - modifications. In no event shall Memorial Sloan-Kettering Cancer Center be - - liable to any party for direct, indirect, special, incidental or - - consequential damages, including lost profits, arising out of the use of this - - software and its documentation, even if Memorial Sloan-Kettering Cancer - - Center has been advised of the possibility of such damage. - --%> - -<%@page import="java.net.URLDecoder"%> -<%-- - - This file is part of cBioPortal. - - - - cBioPortal is free software: you can redistribute it and/or modify - - it under the terms of the GNU Affero General Public License as - - published by the Free Software Foundation, either version 3 of the - - License. - - - - This program is distributed in the hope that it will be useful, - - but WITHOUT ANY WARRANTY; without even the implied warranty of - - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - - GNU Affero General Public License for more details. - - - - You should have received a copy of the GNU Affero General Public License - - along with this program. If not, see . ---%> - - - - -<%@ include file="src/main/webapp/jsp/global/global_variables.jsp" %> - - - - - - -<%@ page import="java.util.Map" %> - -<% - // we have session service running AND this was a post, - // then modify URL to include session service id so bookmarking will work - if (useSessionServiceBookmark && "POST".equals(request.getMethod())) { -%> - -<% } // end if isPost and we have session service running %> - -
-
-
-
- -
-
    - <% - Boolean showMutTab = false; - Boolean showCancerTypesSummary = false; - Boolean showEnrichmentsTab = true; - Boolean showSurvivalTab = true; - Boolean showPlotsTab = true; - Boolean showDownloadTab = true; - Boolean showBookmarkTab = true; - List disabledTabs = GlobalProperties.getDisabledTabs(); - - Enumeration paramEnum = request.getParameterNames(); - StringBuffer buf = new StringBuffer(request.getAttribute(QueryBuilder.ATTRIBUTE_URL_BEFORE_FORWARDING) + "?"); - - while (paramEnum.hasMoreElements()) - { - String paramName = (String) paramEnum.nextElement(); - String values[] = request.getParameterValues(paramName); - - if (values != null && values.length >0) - { - for (int i=0; i' if we decide to add this - // parameter in the future - continue; - } - - // this is required to prevent XSS attacks - currentValue = xssUtil.getCleanInput(currentValue); - //currentValue = StringEscapeUtils.escapeEcmaScript(currentValue); - //currentValue = StringEscapeUtils.escapeHtml(currentValue); - currentValue = URLEncoder.encode(currentValue); - - buf.append (paramName + "=" + currentValue + "&"); - } - } - } - - if(isVirtualStudy){ - showCoexpTab = false; - showIGVtab = false; - showEnrichmentsTab = false; - has_survival = false; - includeNetworks = false; - showPlotsTab = false; - } - if(geneticProfiles.contains("mutation")) { - // hacky but consistent with how currently being done - showMutTab = true; - } - String[] geneList = URLDecoder.decode((String) request.getAttribute(QueryBuilder.GENE_LIST), "UTF-8").split("( )|(\\n)|(;)"); - if (geneList.length <= 1) { - computeLogOddsRatio = false; - } - - // determine whether to show the cancerTypesSummaryTab - // retrieve the cancerTypesMap and create an iterator for the values - showCancerTypesSummary = (Boolean) request.getAttribute(QueryBuilder.HAS_CANCER_TYPES); - - out.println ("
  • OncoPrint
    • "); - // if showCancerTypesSummary is try, add the list item - if(showCancerTypesSummary){ - out.println ("
  • Cancer Types Summary
    • "); - } - - if (computeLogOddsRatio) { - out.println ("
  • " - + "Mutual Exclusivity
    • "); - } - if (showPlotsTab) { - out.println ("
  • Plots
    • "); - } else { - out.println ("
  • Expression
    • "); - } - if (showMutTab){ - out.println ("
  • Mutations
    • "); - } - if (showCoexpTab) { - out.println ("
  • Co-Expression
    • "); - } - if ((has_mrna || has_copy_no || showMutTab && showEnrichmentsTab) && !isVirtualStudy) { - out.println("
  • Enrichments
    • "); - } - if (has_survival) { - out.println ("
  • Survival
    • "); - } - if (includeNetworks) { - out.println ("
  • Network
    • "); - } - if (showIGVtab){ - out.println ("
  • CN Segments
    • "); - } - if (showDownloadTab) { - out.println ("
  • Download
    • "); - } - if (showBookmarkTab) { - out.print ("
  • Bookmark
    • "); - } - out.println ("
"); - %> - -
- -
- -
- <% //contents of fingerprint.jsp now come from attribute on request object %> - <%@ include file="src/main/webapp/jsp/oncoprint/main.jsp" %> -
- - - <% if(showCancerTypesSummary) { %> - <%@ include file="src/main/webapp/jsp/pancancer_study_summary.jsp"%> - <%}%> - - <% if(showPlotsTab) { %> - <%@ include file="src/main/webapp/jsp/plots_tab.jsp" %> - <% } else { %> - <%@ include file="src/main/webapp/jsp/cross_cancer_plots_tab.jsp" %> - <% }%> - - <% if (showIGVtab) { %> - <%@ include file="src/main/webapp/jsp/igv.jsp" %> - <% } %> - - <% if (has_survival) { %> - <%@ include file="src/main/webapp/jsp/survival_tab.jsp" %> - <% } %> - - <% if (computeLogOddsRatio) { %> - <%@ include file="src/main/webapp/jsp/mutex_tab.jsp" %> - <% } %> - - <% if (mutationDetailLimitReached != null) { - out.println("
"); - out.println("

To retrieve mutation details, please specify " - + QueryBuilder.MUTATION_DETAIL_LIMIT + " or fewer genes.
"); - out.println("

"); - } else if (showMutTab) { %> - <%@ include file="src/main/webapp/jsp/mutation_details.jsp" %> - <% } %> - - <% if (includeNetworks) { %> - <%@ include file="src/main/webapp/jsp/networks.jsp" %> - <% } %> - - <% if (showCoexpTab) { %> - <%@ include file="src/main/webapp/jsp/co_expression.jsp" %> - <% } %> - - <% if ((has_mrna || has_copy_no || showMutTab) && !isVirtualStudy) { %> - <%@ include file="src/main/webapp/jsp/enrichments_tab.jsp" %> - <% } %> - <% if(showDownloadTab) { %> - <%@ include file="src/main/webapp/jsp/data_download.jsp" %> - <% } %> - -
- - -
- - - - - - - - -
- - - - - - - - - - - - -