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add command to display installed banks list
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,117 @@ | ||
| <!DOCTYPE html> | ||
| <html lang="en"> | ||
| <head> | ||
| <title>$bdminfo.config.name</title> | ||
| <meta charset="UTF-8"> | ||
| </head> | ||
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||
| <body> | ||
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| <!-- CONFIGURATION --> | ||
| <div id="conf"> | ||
| <h4>Banks managed by $bdminfo.config.name</h4> | ||
| <h5>Configuration</h5> | ||
| <p> | ||
| <ul> | ||
| <li><i>Install path: </i>$bdminfo.config.instpath</li> | ||
| <li><i>Master configuration: </i>$bdminfo.config.instconfpath</li> | ||
| <li><i>Logs path: </i>$bdminfo.config.logpath</li> | ||
| <li><i>Working path: </i>$bdminfo.config.wkpath</li> | ||
| <li><i>Bank configuration: </i>$bdminfo.config.confpath</li> | ||
| <li><i>Bank storage path: </i>$bdminfo.config.dbpath</li> | ||
| <li><i>Bank repository size: </i>$bdminfo.config.reposize</i></li> | ||
| </ul> | ||
| </p> | ||
| </div> | ||
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| <div id="db"> | ||
| <!-- DATABANK: protein --> | ||
| #set( $dbTable = $bdminfo.databases2.mirror_p ) | ||
| <h4>Protein banks: <span>${dbTable.size()}</span></h4> | ||
| #if( ${dbTable.size()} == 0 ) | ||
| <p>none</p> | ||
| #else | ||
| <table border="1"> | ||
| <tr> | ||
| <th>Name</th> | ||
| <!-- <th>Code</th> --> | ||
| <th>Description</th> | ||
| <th>Annotated</th> | ||
| <th>Size (sequences)</th> | ||
| <th>Size on disk</th> | ||
| <th>Install date</th> | ||
| </tr> | ||
| #foreach( $db in $dbTable ) | ||
| <tr> | ||
| <td>$db.getName()</td> | ||
| <!-- <td>$db.getCode()</td> --> | ||
| <td>$db.getDescription()</br>BLAST+ use: -db $db.getDbPath().substring(0, $db.getDbPath().lastIndexOf("."))</td> | ||
| <td>$db.hasAnnotation()</td> | ||
| <td>$db.getNbSequence()</td> | ||
| <td>$db.getDiskSize()</td> | ||
| <td>$db.getTimeStamp()</td> | ||
| </tr> | ||
| #end | ||
| </table> | ||
| #end | ||
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| <!-- DATABANK: nucleotide --> | ||
| #set( $dbTable = $bdminfo.databases2.mirror_n ) | ||
| <h4>Nucleotide banks: <span>${dbTable.size()}</span></h4> | ||
| #if( ${dbTable.size()} == 0 ) | ||
| <p>none</p> | ||
| #else | ||
| <table border="1"> | ||
| <tr> | ||
| <th>Name</th> | ||
| <!-- <th>Code</th> --> | ||
| <th>Description</th> | ||
| <th>Annotated</th> | ||
| <th>Size (sequences)</th> | ||
| <th>Size on disk</th> | ||
| <th>Install date</th> | ||
| </tr> | ||
| #foreach( $db in $dbTable ) | ||
| <tr> | ||
| <td>$db.getName()</td> | ||
| <!-- <td>$db.getCode()</td> --> | ||
| <td>$db.getDescription()</br>BLAST+ use: -db $db.getDbPath().substring(0, $db.getDbPath().lastIndexOf("."))</td> | ||
| <td>$db.hasAnnotation()</td> | ||
| <td>$db.getNbSequence()</td> | ||
| <td>$db.getDiskSize()</td> | ||
| <td>$db.getTimeStamp()</td> | ||
| </tr> | ||
| #end | ||
| </table> | ||
| #end | ||
| <!-- DATABANK: bco --> | ||
| #set( $dbTable = $bdminfo.databases2.mirror_d ) | ||
| <h4>Biological classification banks: <span>${dbTable.size()}</span></h4> | ||
| #if( ${dbTable.size()} == 0 ) | ||
| <p>none</p> | ||
| #else | ||
| <table border="1"> | ||
| <tr> | ||
| <th>Name</th> | ||
| <!-- <th>Code</th> --> | ||
| <th>Description</th> | ||
| <th>Size (sequences)</th> | ||
| <th>Size on disk</th> | ||
| <th>Install date</th> | ||
| </tr> | ||
| #foreach( $db in $dbTable ) | ||
| <tr> | ||
| <td>$db.getName()</td> | ||
| <!-- <td>$db.getCode()</td> --> | ||
| <td>$db.getDescription()</td> | ||
| <td>$db.getNbSequence()</td> | ||
| <td>$db.getDiskSize()</td> | ||
| <td>$db.getTimeStamp()</td> | ||
| </tr> | ||
| #end | ||
| </table> | ||
| #end | ||
| </div> | ||
|
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||
| </body> | ||
| </html> |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,52 @@ | ||
| $bdminfo.config.name | ||
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| Configuration: | ||
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| Install path : $bdminfo.config.instpath | ||
| Master configuration : $bdminfo.config.instconfpath | ||
| Log path : $bdminfo.config.logpath | ||
| Work path : $bdminfo.config.wkpath | ||
| Bank configuration file: $bdminfo.config.confpath | ||
| Bank repository path : $bdminfo.config.dbpath | ||
| Bank repository size : $bdminfo.config.reposize | ||
|
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| Installed banks | ||
| #set( $pTable = $bdminfo.databases2.mirror_p ) | ||
| - Protein banks: ${pTable.size()} | ||
| #if( ${pTable.size()} != 0 ) | ||
| #foreach( $db in $pTable ) | ||
| * $db.getName() | ||
| Description: $db.getDescription() | ||
| BLAST+ use: -db $db.getDbPath().substring(0, $db.getDbPath().lastIndexOf(".")) | ||
| Annotated bank: $db.hasAnnotation() | ||
| Size (sequences): $db.getNbSequence() | ||
| Size on disk: $db.getDiskSize() | ||
| Install date: $db.getTimeStamp() | ||
| #end | ||
| #end | ||
|
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| #set( $nTable = $bdminfo.databases2.mirror_n ) | ||
| - Nucleotide banks: ${nTable.size()} | ||
| #if( ${nTable.size()} != 0 ) | ||
| #foreach( $db in $nTable ) | ||
| * $db.getName() | ||
| Description: $db.getDescription() | ||
| BLAST+ use: -db $db.getDbPath().substring(0, $db.getDbPath().lastIndexOf(".")) | ||
| Annotated bank: $db.hasAnnotation() | ||
| Size (sequences): $db.getNbSequence() | ||
| Size on disk: $db.getDiskSize() | ||
| Install date: $db.getTimeStamp() | ||
| #end | ||
| #end | ||
|
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| #set( $dTable = $bdminfo.databases2.mirror_d ) | ||
| - Biological classification banks: ${dTable.size()} | ||
| #if( ${dTable.size()} != 0 ) | ||
| #foreach( $db in $dTable ) | ||
| * $db.getName() | ||
| Description: $db.getDescription() | ||
| Size (terms): $db.getNbSequence() | ||
| Size on disk: $db.getDiskSize() | ||
| Install date: $db.getTimeStamp() | ||
| #end | ||
| #end |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,45 @@ | ||
| @echo off | ||
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| rem | ||
| rem DBMS program to list installed banks ; for Windows | ||
| rem Copyright (c) - Patrick G. Durand, 2007-2017 | ||
| rem ------------------------------------------------------------------- | ||
| rem User manual: | ||
| rem https://pgdurand.gitbooks.io/beedeem/ | ||
| rem ------------------------------------------------------------------- | ||
| rem The program can be used to list installed banks. | ||
| rem | ||
| rem In addition, some parameters can be passed to the JVM for special | ||
| rem configuration purposes: | ||
| rem -DKL_DEBUG=true ; if true, if set, log will be in debug mode | ||
| rem -DKL_WORKING_DIR=an_absolute_path ; if not set, log and working | ||
| rem directories are set to java.io.tmp | ||
| rem -DKL_LOG_FILE=a_file_name ; if set, creates a log file with that | ||
| rem name within KL_WORKING_DIR | ||
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| set CUR_DIR=%cd% | ||
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| rem *** Application home | ||
| set KL_APP_HOME=@KL_INSTALL_DIR@ | ||
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| rem *** Working directory | ||
| set KL_WORKING_DIR=@KL_WORKING_DIR@ | ||
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| rem *** Java VM | ||
| set JAVA_HOME=@JAVA_ROOT_DIR@ | ||
| set KL_JAVA_VM=%JAVA_HOME%\bin\java | ||
| set KL_JAVA_ARGS=-Xms128M -Xmx1024M -DKL_HOME="%KL_APP_HOME%" -DKL_WORKING_DIR="%KL_WORKING_DIR%" | ||
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| rem *** Create classpath | ||
| SETLOCAL ENABLEDELAYEDEXPANSION | ||
| set FILES= | ||
| set BIN_HOME=%KL_APP_HOME%\\bin | ||
| cd %BIN_HOME% | ||
| for /F %%f in ('dir /b *.jar') do set FILES=!FILES!;%KL_APP_HOME%\\bin\\%%f | ||
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| rem *** Start application | ||
| cd %CUR_DIR% | ||
| "%KL_JAVA_VM%" %KL_JAVA_ARGS% -classpath "%FILES%" bzh.plealog.dbmirror.main.DumpBankList | ||
|
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||
| rem *** do not leave immediately (to check potential cmd line messages coming from the application) | ||
| pause |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,37 @@ | ||
| #!/bin/sh | ||
| # | ||
| # | ||
| # DBMS program to list installed banks ; for Unix | ||
| # Copyright (c) - Patrick G. Durand, 2007-2017 | ||
| # ------------------------------------------------------------------- | ||
| # User manual: | ||
| # https://pgdurand.gitbooks.io/beedeem/ | ||
| # ------------------------------------------------------------------- | ||
| # The program can be used to list installed banks. | ||
| # | ||
| # In addition, some parameters can be passed to the JVM for special | ||
| # configuration purposes:<br> | ||
| # -DKL_DEBUG=true ; if true, if set, log will be in debug mode<br> | ||
| # -DKL_WORKING_DIR=an_absolute_path ; if not set, log and working | ||
| # directories are set to java.io.tmp<br> | ||
| # -DKL_LOG_FILE=a_file_name ; if set, creates a log file with that | ||
| # name within KL_WORKING_DIR<br><br> | ||
|
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| # *** Application home | ||
| KL_APP_HOME=@KL_INSTALL_DIR@ | ||
|
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| # *** Working directory | ||
| KL_WORKING_DIR=@KL_WORKING_DIR@ | ||
|
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| # *** Java VM | ||
| JAVA_HOME=@JAVA_ROOT_DIR@ | ||
| KL_JAVA_VM=$JAVA_HOME/bin/java | ||
| KL_JAVA_ARGS="@JAVA_ARGS@ -DKL_HOME=$KL_APP_HOME -DKL_WORKING_DIR=$KL_WORKING_DIR" | ||
|
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| # *** JARs section | ||
| KL_JAR_LIST_TMP=`\ls $KL_APP_HOME/bin/*.jar` | ||
| KL_JAR_LIST=`echo $KL_JAR_LIST_TMP | sed 's/ /:/g'` | ||
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| # *** start application | ||
| KL_APP_MAIN_CLASS=bzh.plealog.dbmirror.main.DumpBankList | ||
| $KL_JAVA_VM $KL_JAVA_ARGS -classpath $KL_JAR_LIST $KL_APP_MAIN_CLASS |
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