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<%-- $Id$ |
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------------------------------------------------------------------ |
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Copyright (C) 2006 Johan Enell, Nicklas Nordborg |
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Copyright (C) 2007 Nicklas Nordborg |
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|
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This file is part of BASE - BioArray Software Environment. |
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Available at http://base.thep.lu.se/ |
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|
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BASE is free software; you can redistribute it and/or |
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modify it under the terms of the GNU General Public License |
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as published by the Free Software Foundation; either version 3 |
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of the License, or (at your option) any later version. |
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|
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BASE is distributed in the hope that it will be useful, |
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but WITHOUT ANY WARRANTY; without even the implied warranty of |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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GNU General Public License for more details. |
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|
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You should have received a copy of the GNU General Public License |
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along with BASE. If not, see <http://www.gnu.org/licenses/>. |
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------------------------------------------------------------------ |
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|
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@author Nicklas |
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@version 2.0 |
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--%> |
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<%@ page pageEncoding="UTF-8" session="false" |
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contentType="text/html; charset=UTF-8" |
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import="net.sf.basedb.core.SessionControl" |
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import="net.sf.basedb.core.DbControl" |
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import="net.sf.basedb.core.Item" |
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enell |
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import="net.sf.basedb.core.Config" |
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import="net.sf.basedb.core.Location" |
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import="net.sf.basedb.util.parser.FlatFileParser" |
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import="net.sf.basedb.clients.web.Base" |
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import="net.sf.basedb.util.Values" |
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import="net.sf.basedb.plugins.util.Parameters" |
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import="net.sf.basedb.clients.web.util.HTML" |
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import="java.nio.charset.Charset" |
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%> |
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<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %> |
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<%@ taglib prefix="m" uri="/WEB-INF/menu.tld" %> |
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|
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<% |
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final SessionControl sc = Base.getExistingSessionControl(pageContext, true); |
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final String ID = sc.getId(); |
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final DbControl dc = sc.newDbControl(":Test with file"); |
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try |
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{ |
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%> |
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22 Sep 06 |
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<base:page type="popup" title="Test with file"> |
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15 Mar 19 |
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<base:head scripts="menu.js,~test_with_file.js" styles="menu.css"> |
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15 Mar 19 |
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<style> |
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15 Mar 19 |
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body:not([data-filemode="csv"]) .csv-mode |
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15 Mar 19 |
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{ |
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15 Mar 19 |
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display: none; |
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15 Mar 19 |
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} |
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15 Mar 19 |
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body:not([data-filemode="excel"]) .excel-mode |
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15 Mar 19 |
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{ |
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display: none; |
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} |
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</style> |
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15 Mar 19 |
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</base:head> |
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<base:body data-filemode="csv"> |
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|
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<m:menu |
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id="predefinedSplitters" |
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style="display: none;"> |
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|
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<m:menuitem |
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subclass="auto-init" |
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data-auto-init="set-preset" |
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data-field="dataSplitter" |
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data-value="\t" |
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title="Tab" |
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tooltip="Splits data on tab" |
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/> |
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<m:menuitem |
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subclass="auto-init" |
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data-auto-init="set-preset" |
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data-field="dataSplitter" |
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data-value="," |
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title="Comma" |
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tooltip="Splits data on comma" |
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/> |
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<m:menuitem |
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subclass="auto-init" |
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data-auto-init="set-preset" |
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data-field="dataSplitter" |
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data-value=";" |
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title="Semicolon" |
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tooltip="Splits data on semicolon" |
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/> |
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<m:menuseparator /> |
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<m:menuitem |
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subclass="auto-init" |
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data-auto-init="set-preset" |
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11 Sep 13 |
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data-field="dataSplitter" |
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11 Sep 13 |
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data-value="(?!")\t(?=")" |
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22 Sep 06 |
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title="Tab with quotes" |
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tooltip="Splits data on tab, but only if it is has quotes before and after" |
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22 Sep 06 |
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/> |
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22 Sep 06 |
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<m:menuitem |
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11 Sep 13 |
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subclass="auto-init" |
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11 Sep 13 |
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data-auto-init="set-preset" |
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11 Sep 13 |
nicklas |
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data-field="dataSplitter" |
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11 Sep 13 |
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data-value="(?!"),(?=")" |
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22 Sep 06 |
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title="Comma with quotes" |
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22 Sep 06 |
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tooltip="Splits data on comma, but only if it is has quotes before and after" |
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22 Sep 06 |
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/> |
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22 Sep 06 |
nicklas |
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<m:menuitem |
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11 Sep 13 |
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subclass="auto-init" |
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11 Sep 13 |
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data-auto-init="set-preset" |
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11 Sep 13 |
nicklas |
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data-field="dataSplitter" |
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11 Sep 13 |
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data-value="(?!");(?=")" |
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22 Sep 06 |
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title="Semicolon with quotes" |
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22 Sep 06 |
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tooltip="Splits data on semicolon, but only if it is has quotes before and after" |
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22 Sep 06 |
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/> |
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02 Aug 07 |
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<m:menuseparator /> |
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02 Aug 07 |
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<m:menuitem |
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11 Sep 13 |
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subclass="auto-init" |
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11 Sep 13 |
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data-auto-init="set-preset" |
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11 Sep 13 |
nicklas |
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data-field="dataSplitter" |
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11 Sep 13 |
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data-value=",(?=(?:[^"]*"[^"]*")*(?![^"]*"))" |
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02 Aug 07 |
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title="Comma; ignored inside quotes" |
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02 Aug 07 |
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tooltip="Splits data on comma, but not if they are inside quotes" |
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02 Aug 07 |
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/> |
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02 Aug 07 |
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<m:menuitem |
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11 Sep 13 |
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subclass="auto-init" |
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11 Sep 13 |
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data-auto-init="set-preset" |
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11 Sep 13 |
nicklas |
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data-field="dataSplitter" |
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11 Sep 13 |
nicklas |
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data-value=";(?=(?:[^"]*"[^"]*")*(?![^"]*"))" |
6321 |
11 Sep 13 |
nicklas |
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title="Semicolon; ignored inside quotes" |
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02 Aug 07 |
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tooltip="Splits data on semicolon, but not if they are inside quotes" |
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02 Aug 07 |
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/> |
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22 Sep 06 |
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</m:menu> |
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22 Sep 06 |
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|
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22 Sep 06 |
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137 |
<m:menu |
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22 Sep 06 |
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id="predefinedHeaders" |
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22 Sep 06 |
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style="display: none;"> |
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22 Sep 06 |
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<m:menuitem |
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11 Sep 13 |
nicklas |
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subclass="auto-init" |
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11 Sep 13 |
nicklas |
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data-auto-init="set-preset" |
6321 |
11 Sep 13 |
nicklas |
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data-field="header" |
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11 Sep 13 |
nicklas |
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data-value="(.+)=(.*)" |
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22 Sep 06 |
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title="Key = value" |
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22 Sep 06 |
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tooltip="Headers have a key and value separated by an equal sign" |
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22 Sep 06 |
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/> |
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22 Sep 06 |
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<m:menuitem |
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11 Sep 13 |
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subclass="auto-init" |
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11 Sep 13 |
nicklas |
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data-auto-init="set-preset" |
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11 Sep 13 |
nicklas |
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data-field="header" |
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11 Sep 13 |
nicklas |
152 |
data-value="[\s\"]*(.+?)[\s\"]*=[\s\"]*(.*?)[\s\"]*" |
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22 Sep 06 |
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title="Key = value; remove whitespace and quotes" |
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22 Sep 06 |
nicklas |
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tooltip="Header have a key and value separated by an equal sign; whitespace and quotes are removed" |
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22 Sep 06 |
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/> |
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22 Sep 06 |
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</m:menu> |
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22 Sep 06 |
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|
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22 Sep 06 |
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<m:menu |
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22 Sep 06 |
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id="predefinedIgnore" |
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22 Sep 06 |
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style="display: none;"> |
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22 Sep 06 |
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<m:menuitem |
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11 Sep 13 |
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subclass="auto-init" |
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11 Sep 13 |
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data-auto-init="set-preset" |
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11 Sep 13 |
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data-field="ignore" |
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11 Sep 13 |
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data-value="#.*" |
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22 Sep 06 |
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title="# Comment" |
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22 Sep 06 |
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tooltip="Ignore all lines starting with #" |
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22 Sep 06 |
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/> |
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01 Sep 08 |
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<m:menuitem |
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11 Sep 13 |
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subclass="auto-init" |
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11 Sep 13 |
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data-auto-init="set-preset" |
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11 Sep 13 |
nicklas |
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data-field="ignore" |
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11 Sep 13 |
nicklas |
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data-value="\s*" |
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01 Sep 08 |
nicklas |
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title="Empty line" |
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01 Sep 08 |
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tooltip="Ignore all lines that contains nothing but white-space" |
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01 Sep 08 |
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/> |
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22 Sep 06 |
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</m:menu> |
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13 Feb 12 |
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<h1>Test with file <base:help helpid="runplugin.testwithfile" /></h1> |
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10 Oct 12 |
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<form name="testwithfile" action="parse_file.jsp?ID=<%=ID%>" target="parsed" method="post"> |
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22 Sep 06 |
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<input type="hidden" name="file_id" value=""> |
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15 Mar 19 |
nicklas |
181 |
<input type="hidden" name="filemode" value="csv"> |
7655 |
19 Mar 19 |
nicklas |
182 |
<input type="hidden" name="decimalSeparator" value=""> |
7654 |
15 Mar 19 |
nicklas |
183 |
<input type="hidden" name="dateFormat" value=""> |
7655 |
19 Mar 19 |
nicklas |
184 |
<input type="hidden" name="timestampFormat" value=""> |
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22 Sep 06 |
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185 |
|
5955 |
13 Feb 12 |
nicklas |
186 |
<div class="content"> |
5955 |
13 Feb 12 |
nicklas |
187 |
<div class="absolutefull" style="height: 15em;"> |
5955 |
13 Feb 12 |
nicklas |
188 |
<table class="fullform input100 bottomborder"> |
5955 |
13 Feb 12 |
nicklas |
189 |
<tr> |
7654 |
15 Mar 19 |
nicklas |
190 |
<th>File (CSV or Excel)</th> |
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22 Sep 06 |
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<td colspan="3"> |
5955 |
13 Feb 12 |
nicklas |
192 |
<table style="width: 100%;"> |
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22 Sep 06 |
nicklas |
193 |
<tr> |
6322 |
11 Sep 13 |
nicklas |
194 |
<td><input type="text" class="text required" name="path" id="path" value=""></td> |
6200 |
05 Nov 12 |
nicklas |
195 |
<td style="width: 11em;"><base:button id="btnBrowse" title="Browse…" style="width: 10em;" /></td> |
6200 |
05 Nov 12 |
nicklas |
196 |
<td style="width: 11em;"><base:button id="btnParse" title="Parse the file" style="width: 10em;" image="gonext.png"/></td> |
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22 Sep 06 |
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197 |
</tr> |
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22 Sep 06 |
nicklas |
198 |
</table> |
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22 Sep 06 |
nicklas |
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</td> |
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22 Sep 06 |
nicklas |
200 |
</tr> |
5955 |
13 Feb 12 |
nicklas |
201 |
<tr> |
5955 |
13 Feb 12 |
nicklas |
202 |
<th>Lines to parse</th> |
2992 |
01 Dec 06 |
enell |
203 |
<td> |
6200 |
05 Nov 12 |
nicklas |
204 |
<input type="text" class="text" name="maxLines" |
6200 |
05 Nov 12 |
nicklas |
205 |
id="maxLines" style="width: 15em;" maxlength="10" |
6200 |
05 Nov 12 |
nicklas |
206 |
value="<%=FlatFileParser.DEFAULT_MAX_UNKNOWN_LINES%>"> |
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22 Sep 06 |
nicklas |
207 |
</td> |
7656 |
19 Mar 19 |
nicklas |
208 |
<th class="leftborder">Excel sheet</th> |
7654 |
15 Mar 19 |
nicklas |
209 |
<td> |
7654 |
15 Mar 19 |
nicklas |
210 |
<select id="sheet" name="sheet" style="min-width: 20em;" disabled> |
7654 |
15 Mar 19 |
nicklas |
211 |
</select> |
7656 |
19 Mar 19 |
nicklas |
212 |
<base:icon image="warning.png" id="noSheetSupportWarning" |
7656 |
19 Mar 19 |
nicklas |
213 |
tooltip="This plug-in only support import from the first sheet" |
7656 |
19 Mar 19 |
nicklas |
214 |
style="display: none;" |
7656 |
19 Mar 19 |
nicklas |
215 |
/> |
7654 |
15 Mar 19 |
nicklas |
216 |
</td> |
7654 |
15 Mar 19 |
nicklas |
217 |
</tr> |
7654 |
15 Mar 19 |
nicklas |
218 |
<tr > |
7654 |
15 Mar 19 |
nicklas |
219 |
<th>Header regexp</th> |
7654 |
15 Mar 19 |
nicklas |
220 |
<td> |
7654 |
15 Mar 19 |
nicklas |
221 |
<table style="width: 100%;"> |
7654 |
15 Mar 19 |
nicklas |
222 |
<tr> |
7654 |
15 Mar 19 |
nicklas |
223 |
<td><input type="text" class="text" name="header"></td> |
7654 |
15 Mar 19 |
nicklas |
224 |
<td style="width: 11em;"> |
7654 |
15 Mar 19 |
nicklas |
225 |
<base:button title="Predefined…" style="width: 10em;" |
7654 |
15 Mar 19 |
nicklas |
226 |
id="btnHeaderRegexp" data-predefined="predefinedHeaders" /> |
7654 |
15 Mar 19 |
nicklas |
227 |
</td> |
7654 |
15 Mar 19 |
nicklas |
228 |
</tr> |
7654 |
15 Mar 19 |
nicklas |
229 |
</table> |
7654 |
15 Mar 19 |
nicklas |
230 |
</td> |
5955 |
13 Feb 12 |
nicklas |
231 |
<th class="leftborder">Character set</th> |
2992 |
01 Dec 06 |
enell |
232 |
<td> |
7654 |
15 Mar 19 |
nicklas |
233 |
<select name="charset" style="min-width: 20em;"> |
2992 |
01 Dec 06 |
enell |
234 |
<% |
2992 |
01 Dec 06 |
enell |
235 |
String defaultCharset = Config.getCharset(); |
5570 |
16 Feb 11 |
nicklas |
236 |
int numCommon = Config.getCommonCharsets().size(); |
5570 |
16 Feb 11 |
nicklas |
237 |
int i = 0; |
5570 |
16 Feb 11 |
nicklas |
238 |
for (String charset : Config.getAllCharsets()) |
2992 |
01 Dec 06 |
enell |
239 |
{ |
2992 |
01 Dec 06 |
enell |
240 |
%> |
2992 |
01 Dec 06 |
enell |
241 |
<option value="<%=charset%>" |
5570 |
16 Feb 11 |
nicklas |
242 |
<%=defaultCharset.equalsIgnoreCase(charset) ? "selected" : ""%> |
5570 |
16 Feb 11 |
nicklas |
243 |
<%=i==numCommon ? "style=\"border-top: 1px solid #666666;\"" : "" %>><%=charset%> |
2992 |
01 Dec 06 |
enell |
244 |
<% |
5570 |
16 Feb 11 |
nicklas |
245 |
i++; |
2992 |
01 Dec 06 |
enell |
246 |
} |
2992 |
01 Dec 06 |
enell |
247 |
%> |
2992 |
01 Dec 06 |
enell |
248 |
</select> |
2992 |
01 Dec 06 |
enell |
249 |
</td> |
2655 |
22 Sep 06 |
nicklas |
250 |
</tr> |
7654 |
15 Mar 19 |
nicklas |
251 |
<tr> |
7654 |
15 Mar 19 |
nicklas |
252 |
<th>Data splitter regexp</th> |
2655 |
22 Sep 06 |
nicklas |
253 |
<td> |
5955 |
13 Feb 12 |
nicklas |
254 |
<table style="width: 100%;"> |
2655 |
22 Sep 06 |
nicklas |
255 |
<tr> |
7654 |
15 Mar 19 |
nicklas |
256 |
<td><input type="text" class="text required" name="dataSplitter"></td> |
5955 |
13 Feb 12 |
nicklas |
257 |
<td style="width: 11em;"> |
5955 |
13 Feb 12 |
nicklas |
258 |
<base:button title="Predefined…" style="width: 10em;" |
7654 |
15 Mar 19 |
nicklas |
259 |
id="btnSplitterRegexp" data-predefined="predefinedSplitters" /> |
2655 |
22 Sep 06 |
nicklas |
260 |
</td> |
2655 |
22 Sep 06 |
nicklas |
261 |
</tr> |
2655 |
22 Sep 06 |
nicklas |
262 |
</table> |
2655 |
22 Sep 06 |
nicklas |
263 |
</td> |
5955 |
13 Feb 12 |
nicklas |
264 |
<th class="leftborder">Min data columns</th> |
2655 |
22 Sep 06 |
nicklas |
265 |
<td> |
6200 |
05 Nov 12 |
nicklas |
266 |
<input type="text" class="text" name="minDataColumns" |
6200 |
05 Nov 12 |
nicklas |
267 |
id="minDataColumns" style="width: 15em;" maxlength="10"> |
2655 |
22 Sep 06 |
nicklas |
268 |
</td> |
2655 |
22 Sep 06 |
nicklas |
269 |
</tr> |
5905 |
12 Dec 11 |
nicklas |
270 |
<tr > |
7654 |
15 Mar 19 |
nicklas |
271 |
<th>Ignore regexp</th> |
2655 |
22 Sep 06 |
nicklas |
272 |
<td> |
5955 |
13 Feb 12 |
nicklas |
273 |
<table style="width: 100%;"> |
2655 |
22 Sep 06 |
nicklas |
274 |
<tr> |
7654 |
15 Mar 19 |
nicklas |
275 |
<td><input type="text" class="text" name="ignore"></td> |
5955 |
13 Feb 12 |
nicklas |
276 |
<td style="width: 11em;"> |
5955 |
13 Feb 12 |
nicklas |
277 |
<base:button title="Predefined…" style="width: 10em;" |
7654 |
15 Mar 19 |
nicklas |
278 |
id="btnIgnoreRegexp" data-predefined="predefinedIgnore" /> |
2655 |
22 Sep 06 |
nicklas |
279 |
</td> |
2655 |
22 Sep 06 |
nicklas |
280 |
</tr> |
2655 |
22 Sep 06 |
nicklas |
281 |
</table> |
2655 |
22 Sep 06 |
nicklas |
282 |
</td> |
5955 |
13 Feb 12 |
nicklas |
283 |
<th class="leftborder">Max data columns</th> |
2655 |
22 Sep 06 |
nicklas |
284 |
<td> |
6200 |
05 Nov 12 |
nicklas |
285 |
<input type="text" class="text" name="maxDataColumns" |
6200 |
05 Nov 12 |
nicklas |
286 |
id="maxDataColumns" style="width: 15em;" maxlength="10"> |
2655 |
22 Sep 06 |
nicklas |
287 |
</td> |
2655 |
22 Sep 06 |
nicklas |
288 |
</tr> |
5905 |
12 Dec 11 |
nicklas |
289 |
<tr > |
7654 |
15 Mar 19 |
nicklas |
290 |
<th>Data header regexp</th> |
7654 |
15 Mar 19 |
nicklas |
291 |
<td><input type="text" class="text" name="dataHeader"></td> |
5955 |
13 Feb 12 |
nicklas |
292 |
<th class="leftborder"><label for="trimQuotes">Remove quotes</label></th> |
5812 |
17 Oct 11 |
nicklas |
293 |
<td><input type="checkbox" name="trimQuotes" id="trimQuotes" value="1"></td> |
2655 |
22 Sep 06 |
nicklas |
294 |
</tr> |
5955 |
13 Feb 12 |
nicklas |
295 |
<tr class="dynamic"> |
5955 |
13 Feb 12 |
nicklas |
296 |
<th>Data footer regexp</th> |
5955 |
13 Feb 12 |
nicklas |
297 |
<td><input type="text" class="text" name="dataFooter"></td> |
5955 |
13 Feb 12 |
nicklas |
298 |
<th class="subprompt leftborder"></th> |
5955 |
13 Feb 12 |
nicklas |
299 |
<td></td> |
2655 |
22 Sep 06 |
nicklas |
300 |
</tr> |
5955 |
13 Feb 12 |
nicklas |
301 |
|
2655 |
22 Sep 06 |
nicklas |
302 |
</table> |
5955 |
13 Feb 12 |
nicklas |
303 |
</div> |
2655 |
22 Sep 06 |
nicklas |
304 |
|
6139 |
19 Sep 12 |
nicklas |
305 |
<div class="absolutefull" style="top: 16em;"><iframe class="absolutefull" |
6021 |
19 Mar 12 |
nicklas |
306 |
name="parsed" id="idParsed" src="parse_file.jsp?ID=<%=ID%>" |
6021 |
19 Mar 12 |
nicklas |
307 |
style="width: 100%; height: 100%;"></iframe></div> |
5955 |
13 Feb 12 |
nicklas |
308 |
|
5955 |
13 Feb 12 |
nicklas |
309 |
</div> |
2655 |
22 Sep 06 |
nicklas |
310 |
</form> |
2655 |
22 Sep 06 |
nicklas |
311 |
|
5955 |
13 Feb 12 |
nicklas |
312 |
<base:buttongroup subclass="dialogbuttons"> |
6200 |
05 Nov 12 |
nicklas |
313 |
<base:button id="btnSave" title="Ok" /> |
6200 |
05 Nov 12 |
nicklas |
314 |
<base:button id="close" title="Cancel" /> |
5955 |
13 Feb 12 |
nicklas |
315 |
</base:buttongroup> |
2655 |
22 Sep 06 |
nicklas |
316 |
</base:body> |
2655 |
22 Sep 06 |
nicklas |
317 |
</base:page> |
2655 |
22 Sep 06 |
nicklas |
318 |
<% |
2655 |
22 Sep 06 |
nicklas |
319 |
} |
2655 |
22 Sep 06 |
nicklas |
320 |
finally |
2655 |
22 Sep 06 |
nicklas |
321 |
{ |
2655 |
22 Sep 06 |
nicklas |
322 |
if (dc != null) dc.close(); |
2655 |
22 Sep 06 |
nicklas |
323 |
} |
2655 |
22 Sep 06 |
nicklas |
324 |
%> |
2655 |
22 Sep 06 |
nicklas |
325 |
|