<commit_before><?xml version="1.0" encoding="UTF-8" ?>
<!DOCTYPE log4j:configuration SYSTEM "log4j.dtd">

<!-- Note that this file is refreshed by the server every 60seconds, as specified in web.xml -->

<log4j:configuration debug="true">

<!-- RollingFileAppender -->
<!--  
        <appender name="ROLL" class="org.apache.log4j.rolling.RollingFileAppender">
-->
        <appender name="ROLL" class="org.apache.log4j.RollingFileAppender">

                <!-- The active file to log to -->
                <!--  Have to comment 'RollingFileAppender file specification' block
                	  out to make the filename be controlled by the class specified by < rollingPolicy -->
                
			    <!--  Start RollingFileAppender file specification -->              
                <param name="file" value="${catalina.base}/logs/proxl_generic.log" />
			    <param name="MaxFileSize" value="500KB"/>
			    <!-- Number of backup files -->
			    <param name="MaxBackupIndex" value="5"/>   
			    <!--  End RollingFileAppender file specification -->              


                <param name="append" value="true" />
                <param name="encoding" value="UTF-8" />

<!-- No longer create filename with dates.  Using base RollingFileAppender will limit total size of logs for this module -->
<!--  
                <rollingPolicy class="org.apache.log4j.rolling.TimeBasedRollingPolicy">
-->                
                        <!-- The file to roll to, this is a fairly intelligent parameter, if the file
                        ends in .gz, it gzips it, based on the date stamp it rolls at that time,
                        default is yyyy-MM-dd, (rolls at midnight)
                        See: http://logging.apache.org/log4j/companions/extras/apidocs/org/apache/log4j/rolling/TimeBasedRollingPolicy.html -->
                        <!--  <param name="FileNamePattern" value="/applogs/myportal/portal.%d.log.gz" /> -->
<!--  
                        <param name="FileNamePattern" value="${catalina.base}/logs/proxl.%d.log" />
                </rollingPolicy>
-->
                <layout class="org.apache.log4j.PatternLayout">
                        <!-- The log message pattern -->
                        <param name="ConversionPattern" value="%5p %d{ISO8601} [%t][%x] %c - %m%n" /> <!-- from .properties:  %d [%t] %-5p %c - %m %n -->
                </layout>
        </appender>


<!-- RollingFileAppender -->
<!--  
        <appender name="ROLL_ERROR" class="org.apache.log4j.rolling.RollingFileAppender">
-->
        <appender name="ROLL_ERROR" class="org.apache.log4j.RollingFileAppender">

                <!-- The active file to log to -->
                <!--  Have to comment 'RollingFileAppender file specification' block
                	  out to make the filename be controlled by the class specified by < rollingPolicy -->
                
			    <!--  Start RollingFileAppender file specification -->              
                <param name="file" value="${catalina.base}/logs/proxl_generic.errors.log" />
			    <param name="MaxFileSize" value="500KB"/>
			    <!-- Number of backup files -->
			    <param name="MaxBackupIndex" value="5"/>   
			    <!--  End RollingFileAppender file specification -->              


                <param name="append" value="true" />
                <param name="encoding" value="UTF-8" />
                
				<param name="Threshold" value="WARN" />  <!-- Only WARN, ERROR, and FATAL messages -->


<!-- No longer create filename with dates.  Using base RollingFileAppender will limit total size of logs for this module -->
<!--  
                <rollingPolicy class="org.apache.log4j.rolling.TimeBasedRollingPolicy">
-->                
                        <!-- The file to roll to, this is a fairly intelligent parameter, if the file
                        ends in .gz, it gzips it, based on the date stamp it rolls at that time,
                        default is yyyy-MM-dd, (rolls at midnight)
                        See: http://logging.apache.org/log4j/companions/extras/apidocs/org/apache/log4j/rolling/TimeBasedRollingPolicy.html -->
                        <!--  <param name="FileNamePattern" value="/applogs/myportal/portal.%d.log.gz" /> -->
<!--                          
                        <param name="FileNamePattern" value="${catalina.base}/logs/proxl.errors.%d.log" />
                </rollingPolicy>
-->

                <layout class="org.apache.log4j.PatternLayout">
                        <!-- The log message pattern -->
                        <param name="ConversionPattern" value="%5p %d{ISO8601} [%t][%x] %c - %m%n" /> <!-- from .properties:  %d [%t] %-5p %c - %m %n -->
                </layout>

        </appender>



    <!--                          -->
    <!-- Declare the SMTPAppender -->
    <!--                          -->

<!--
    <appender name="EMAIL"  class="org.apache.log4j.net.SMTPAppender">
        <param name="BufferSize" value="512" />
        <param name="SMTPHost" value="localhost" />
        <param name="From" value="<EMAIL>" />
        <param name="To" value="<EMAIL>" />
        <param name="Subject" value="Error from SSSSSSSSSSSSS - check main program in stack trace" />
        <layout class="org.apache.log4j.PatternLayout">
            <param name="ConversionPattern"
              value="[%d{ISO8601}]%n%n%-5p%n%n%c%n%n%m%n%n" />
        </layout>
        <filter class="org.apache.log4j.varia.LevelRangeFilter">
            <param name="LevelMin" value="ERROR"/>
            <param name="LevelMax" value="FATAL"/>
        </filter>
    </appender>
-->
        <!-- Loggers to filter out various class paths -->

<!--

        <logger name="org.yeastrc.xlink" additivity="false">
        
                <level value="INFO"/>
                
                <appender-ref ref="ROLL" />

                <appender-ref ref="ROLL_ERROR" />



        </logger>

-->

<!--
        <logger name="org.yeastrc.auth" additivity="false">
        
                <level value="INFO"/>
                
                <appender-ref ref="ROLL" />

                <appender-ref ref="ROLL_ERROR" />



        </logger>
 -->
        
        
        <!-- Debugging loggers -->

        <!-- Uncomment to enable debug on specific code only -->
        <!--
        <logger name="org.yeastrc.xlink.www.actions.ViewSearchPeptidesAction" additivity="false">
                <level value="debug"/>
                <appender-ref ref="ROLL" />
                <appender-ref ref="ROLL_ERROR" />
        </logger>
        -->


		<!--    Uncomment debug for the following to get Timing info written to the log file  -->
        <!--
        <logger name="org.yeastrc.xlink.www.actions.ViewSearchPeptidesAction" additivity="false">
                <level value="debug"/>
                <appender-ref ref="ROLL" />
                <appender-ref ref="ROLL_ERROR" />
        </logger>

        <logger name="org.yeastrc.xlink.www.actions.ViewSearchProteinsAction" additivity="false">
                <level value="debug"/>
                <appender-ref ref="ROLL" />
                <appender-ref ref="ROLL_ERROR" />
        </logger>


        <logger name="org.yeastrc.xlink.www.actions.ViewMergedSearchPeptidesAction" additivity="false">
                <level value="debug"/>
                <appender-ref ref="ROLL" /><commit_msg>Add logging at debug, commented out<commit_after><?xml version="1.0" encoding="UTF-8" ?>
<!DOCTYPE log4j:configuration SYSTEM "log4j.dtd">

<!-- Note that this file is refreshed by the server every 60seconds, as specified in web.xml -->

<log4j:configuration debug="true">

<!-- RollingFileAppender -->
<!--  
        <appender name="ROLL" class="org.apache.log4j.rolling.RollingFileAppender">
-->
        <appender name="ROLL" class="org.apache.log4j.RollingFileAppender">

                <!-- The active file to log to -->
                <!--  Have to comment 'RollingFileAppender file specification' block
                	  out to make the filename be controlled by the class specified by < rollingPolicy -->
                
			    <!--  Start RollingFileAppender file specification -->              
                <param name="file" value="${catalina.base}/logs/proxl_generic.log" />
			    <param name="MaxFileSize" value="500KB"/>
			    <!-- Number of backup files -->
			    <param name="MaxBackupIndex" value="5"/>   
			    <!--  End RollingFileAppender file specification -->              


                <param name="append" value="true" />
                <param name="encoding" value="UTF-8" />

<!-- No longer create filename with dates.  Using base RollingFileAppender will limit total size of logs for this module -->
<!--  
                <rollingPolicy class="org.apache.log4j.rolling.TimeBasedRollingPolicy">
-->                
                        <!-- The file to roll to, this is a fairly intelligent parameter, if the file
                        ends in .gz, it gzips it, based on the date stamp it rolls at that time,
                        default is yyyy-MM-dd, (rolls at midnight)
                        See: http://logging.apache.org/log4j/companions/extras/apidocs/org/apache/log4j/rolling/TimeBasedRollingPolicy.html -->
                        <!--  <param name="FileNamePattern" value="/applogs/myportal/portal.%d.log.gz" /> -->
<!--  
                        <param name="FileNamePattern" value="${catalina.base}/logs/proxl.%d.log" />
                </rollingPolicy>
-->
                <layout class="org.apache.log4j.PatternLayout">
                        <!-- The log message pattern -->
                        <param name="ConversionPattern" value="%5p %d{ISO8601} [%t][%x] %c - %m%n" /> <!-- from .properties:  %d [%t] %-5p %c - %m %n -->
                </layout>
        </appender>


<!-- RollingFileAppender -->
<!--  
        <appender name="ROLL_ERROR" class="org.apache.log4j.rolling.RollingFileAppender">
-->
        <appender name="ROLL_ERROR" class="org.apache.log4j.RollingFileAppender">

                <!-- The active file to log to -->
                <!--  Have to comment 'RollingFileAppender file specification' block
                	  out to make the filename be controlled by the class specified by < rollingPolicy -->
                
			    <!--  Start RollingFileAppender file specification -->              
                <param name="file" value="${catalina.base}/logs/proxl_generic.errors.log" />
			    <param name="MaxFileSize" value="500KB"/>
			    <!-- Number of backup files -->
			    <param name="MaxBackupIndex" value="5"/>   
			    <!--  End RollingFileAppender file specification -->              


                <param name="append" value="true" />
                <param name="encoding" value="UTF-8" />
                
				<param name="Threshold" value="WARN" />  <!-- Only WARN, ERROR, and FATAL messages -->


<!-- No longer create filename with dates.  Using base RollingFileAppender will limit total size of logs for this module -->
<!--  
                <rollingPolicy class="org.apache.log4j.rolling.TimeBasedRollingPolicy">
-->                
                        <!-- The file to roll to, this is a fairly intelligent parameter, if the file
                        ends in .gz, it gzips it, based on the date stamp it rolls at that time,
                        default is yyyy-MM-dd, (rolls at midnight)
                        See: http://logging.apache.org/log4j/companions/extras/apidocs/org/apache/log4j/rolling/TimeBasedRollingPolicy.html -->
                        <!--  <param name="FileNamePattern" value="/applogs/myportal/portal.%d.log.gz" /> -->
<!--                          
                        <param name="FileNamePattern" value="${catalina.base}/logs/proxl.errors.%d.log" />
                </rollingPolicy>
-->

                <layout class="org.apache.log4j.PatternLayout">
                        <!-- The log message pattern -->
                        <param name="ConversionPattern" value="%5p %d{ISO8601} [%t][%x] %c - %m%n" /> <!-- from .properties:  %d [%t] %-5p %c - %m %n -->
                </layout>

        </appender>



    <!--                          -->
    <!-- Declare the SMTPAppender -->
    <!--                          -->

<!--
    <appender name="EMAIL"  class="org.apache.log4j.net.SMTPAppender">
        <param name="BufferSize" value="512" />
        <param name="SMTPHost" value="localhost" />
        <param name="From" value="<EMAIL>" />
        <param name="To" value="<EMAIL>" />
        <param name="Subject" value="Error from SSSSSSSSSSSSS - check main program in stack trace" />
        <layout class="org.apache.log4j.PatternLayout">
            <param name="ConversionPattern"
              value="[%d{ISO8601}]%n%n%-5p%n%n%c%n%n%m%n%n" />
        </layout>
        <filter class="org.apache.log4j.varia.LevelRangeFilter">
            <param name="LevelMin" value="ERROR"/>
            <param name="LevelMax" value="FATAL"/>
        </filter>
    </appender>
-->
        <!-- Loggers to filter out various class paths -->

<!--

        <logger name="org.yeastrc.xlink" additivity="false">
        
                <level value="INFO"/>
                
                <appender-ref ref="ROLL" />

                <appender-ref ref="ROLL_ERROR" />



        </logger>

-->

<!--
        <logger name="org.yeastrc.auth" additivity="false">
        
                <level value="INFO"/>
                
                <appender-ref ref="ROLL" />

                <appender-ref ref="ROLL_ERROR" />



        </logger>
 -->
        
        
        <!-- Debugging loggers -->


        <!-- Uncomment to enable debug on specific code only -->
        <!--
        <logger name="org.yeastrc.xlink.www.actions.ViewSearchPeptidesAction" additivity="false">
                <level value="debug"/>
                <appender-ref ref="ROLL" />
                <appender-ref ref="ROLL_ERROR" />
        </logger>
        -->
		<!--  
        <logger name="org.yeastrc.xlink.www.searcher.ScoreCountFromPsmTblSearcher" additivity="false">
                <level value="debug"/>
                <appender-ref ref="ROLL" />
                <appender-ref ref="ROLL_ERROR" />
        </logger>
        -->

		<!--    Uncomment debug for the following to get Timing info written to the log file  -->
        <!--
        <logger name="org.yeastrc.xlink.www.actions.ViewSearchPeptidesAction" additivity="false">
                <level value="debug"/>
                <appender-ref ref="ROLL" />
                <appender-ref ref="ROLL_ERROR" />
        </logger>

        <logger name="org.yeastrc.xlink.www.actions.ViewSearchProteinsAction" additivity="false">
                <level value="debug"/>
                <appender-ref ref="ROLL" />
                <appender-ref ref="ROLL_ERROR" />
        </logger>


        <logger name="org.yeastrc.xlink.www.actions.ViewMergedSearchPeptidesAction" additivity="false">
                <level value="debug"/>
                <appender-ref ref="ROLL" />
{'fraction_non_alphanumeric': 0.14510663743272872, 'fraction_numerical': 0.007042721413859544, 'mean_word_length': 1.7273056713172676, 'pattern_counts': {'":': 0, '<': 253, '<?xml version=': 2, '>': 247, 'https://': 0, 'lorem ipsum': 0, 'www.': 9, 'xml': 4}, 'pii_count': 0, 'substrings_counts': 2, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '5265953', 'n_tokens_mistral': 4374, 'n_tokens_neox': 4041, 'n_words': 939}