Merge pull request #14 from pgdurand/prepV5

Prep v5

TODOs.txt

@@ -1,6 +1,3 @@
-- MaJ descripteurs avec dépendances ; temporairement virer pfam (marche plus ?)
-- MaJ doc: formatdb->makeblastdb 
-
 remote: warning: GH001: Large files detected. You may want to try Git Large File Storage - https://git-lfs.github.com.
 remote: warning: See http://git.io/iEPt8g for more information.
 remote: warning: File tests/junit/databank/fasta_multi2/fasta4.faa is 64.63 MB; this is larger than GitHub's recommended maximum file size of 50.00 MB

build.xml

@@ -38,13 +38,8 @@
 
 	<property name="rootpkg" value="bzh.plealog.dbmirror.main" />
 	<property name="KLMirrorClass" value="${rootpkg}.CmdLineInstaller" />
-	<property name="KLUIMirrorClass" value="${rootpkg}.UiInstaller" />
-	<property name="KLQueryMirrorClass" value="${rootpkg}.CmdLineQuery" />
-	<property name="KLMirrorAnnot" value="${rootpkg}.Annotate" />
-  <property name="KLMirrorInfo" value="${rootpkg}.DumpBankList" />
-  <property name="KLMirrorDelete" value="${rootpkg}.DeleteBank" />
-  <property name="KLMirrorCheck" value="${rootpkg}.AutoCheckDescriptors" />
-
+	<property name="KANT_ZIP" value="ant-1.9.4.zip" />
+
 	<path id="class.path">
 		<pathelement path="${classpath}" />
 		<fileset dir="${jar}">
@@ -216,17 +211,8 @@
 	<!-- ============================================================= -->
   <!-- Compile code and make software dustribution package           -->
 	<target name="makedistrib" depends="makejar">
-		<!-- Copy the DBMS scripts for Mac, Linux and Windows -->
-		<copy file="${scripts}/bdm.sh" todir="${Dscripts}">
-			<filterset>
-				<filter token="APP_MAIN_CLASS" value="${KLMirrorClass}" />
-			</filterset>
-		</copy>
-		<copy file="${scripts}/bdm.bat" todir="${Dscripts}">
-			<filterset>
-				<filter token="APP_MAIN_CLASS" value="${KLMirrorClass}" />
-			</filterset>
-		</copy>
+		<!-- Copy the DBMS scripts for Mac, Linux -->
+		<copy file="${scripts}/bdm.sh" todir="${Dscripts}" />
     <copy file="${scripts}/test_bdm.sh" todir="${Dscripts}" />
 		<!-- Galaxy wrapper to list available DBs -->
     <copy file="${scripts}/beedeem_info.xml" todir="${Dconf}/system">
@@ -266,7 +252,7 @@
 		<!-- in case Ant will not be available on the target system,
          we provide it. -->
 		<mkdir dir="${distrib}/ant" />
-		<copy file="${scripts}/ant-1.9.4.zip" todir="${distrib}/ant" />
+		<copy file="${scripts}/${KANT_ZIP}" todir="${distrib}/ant" />
 		<!-- Package the whole stuff in a zip (natively readable on 
 		     all OS, including Windows)
 		 -->

scripts/bdm.sh

@@ -29,10 +29,14 @@
 # Proxy configuration: update configuration file: 
 #      ${beedeemHome}/conf/system/network.config.
 
-# *** Bank installation scripts of BeeDeeM (conf/scripts) requires BASH 5
-BASH_VER=$(bash --version | grep ", version" | cut -d' ' -f4 | cut -d'.' -f1)
-if [ "$BASH_VER" -lt "5" ]; then
-  echo "/!\ ERROR: BeeDeeM requires BASH release 5 (yours is: $BASH_VER)"
+# *** Bank installation scripts of BeeDeeM (conf/scripts) requires realpath:
+#     available in BASH 5 for macOS
+#     or available from Linux:coreutils
+which realpath
+if [ ! $? -eq 0 ]; then
+  echo "/!\ ERROR: realpath command not found"
+  echo "           macOS: install bash 5"
+  echo "           Linux: install coreutils"
   exit 1
 fi
 

scripts/deploy-std.xml

@@ -1,7 +1,11 @@
 <?xml version="1.0" encoding="utf-8"?>
 <!-- This is the Ant configuration file used to deploy, install and configure
      the DataBank Manager System (BeeDeeM).
-     Copyright (c) 2007-2022, Patrick G. Durand
+     
+     Documentation:
+       https://pgdurand.gitbook.io/beedeem/installation/installation#legacy-installation
+     
+     Copyright (c) 2007-2023, Patrick G. Durand
 -->
 
 <project name="BeeDeeM_installer" default="help" basedir=".">
@@ -13,10 +17,6 @@
 		<os family="unix"/>
 	</condition>
 
-	<condition property="winOS">
-		<os family="windows"/>
-	</condition>
-
 	<!-- ============================================================= -->
 	<target name="help">
 		<echo>This is the Ant project file to install BeeDeeM.</echo>
@@ -81,7 +81,6 @@
 
 	<!-- ============================================================= -->
 	<target name="copyScripts">
-		<antcall target="copyScriptsWin" />
 		<antcall target="copyScriptsUnix" />
 	</target>
 
@@ -97,37 +96,13 @@
 
 			</filterset>
 		</copy>
-		<antcall target="updateWinPath">
-			<param name="sourceF" value="${installDir}/${kscript}.tmp"/>
-			<param name="targetF" value="${installDir}/${kscript}.${kext}"/>
-		</antcall>
 		<antcall target="updateUnixPath">
 			<param name="sourceF" value="${installDir}/${kscript}.tmp"/>
 			<param name="targetF" value="${installDir}/${kscript}"/>
 		</antcall>
 		<delete file="${installDir}/${kscript}.tmp"/>
 	</target>
 
-	<!-- ============================================================= -->
-	<target name="copyScriptsWin" if="winOS">
-		<!-- Copy and configure the KDBMS starter script (Windows) -->
-		<antcall target="prepareScript">
-			<param name="kscript" value="bdm"/>
-			<param name="kext" value="bat"/>
-		</antcall>
-		<!-- Copy and configure the DBMS main config file-->
-		<copy file="${installDir}/scripts/dbms.config" tofile="${installDir}/conf/dbms.tmp">
-			<filterset>
-				<filter token="BIOBASE_ROOTDIR" value="${biobaseRootDir}"/>
-			</filterset>
-		</copy>
-		<antcall target="updateWinPath">
-			<param name="sourceF" value="${installDir}/conf/dbms.tmp"/>
-			<param name="targetF" value="${installDir}/conf/dbms.config"/>
-		</antcall>
-		<delete file="${installDir}/conf/dbms.tmp"/>
-	</target>
-
 	<!-- ============================================================= -->
 	<target name="copyScriptsUnix" if="unixOS">
 		<!-- Copy and configure the KDBMS starter script (Unix) -->
@@ -148,23 +123,6 @@
 		</copy>
 	</target>
 
-	<!-- ============================================================= -->
-	<target name="updateWinPath" if="winOS">
-		<path id="distribClass.path">
-			<fileset dir="${installDir}/bin">
-				<include name="**/*.jar"/>
-			</fileset>
-		</path>
-		<java fork="true" 
-          classname="bzh.plealog.dbmirror.main.SetupConfiguration" 
-          classpathref="distribClass.path" >
-			<arg value="${sourceF}"/>
-			<arg value="${targetF}"/>
-			<arg value="\"/>
-			<arg value="\\"/>
-		</java>
-	</target>
-
 	<!-- ============================================================= -->
 	<target name="updateUnixPath" if="unixOS">
 		<copy file="${sourceF}" tofile="${targetF}"/>

scripts/test_bdm.sh

@@ -1,7 +1,7 @@
 #!/usr/bin/env bash
 
 # =================================================
-# Test script for BeeDeeM legacy installer.
+# Test script for BeeDeeM legacy installer or Conda.
 # To be used directly on the command-line.
 # DO NOT use for Singularity/Docker installations.
 #
@@ -10,21 +10,28 @@
 # Step 1: install BeeDeeM as stated at:
 #         https://pgdurand.gitbook.io/beedeem/installation/installation#legacy-installation 
 #
-# Step 2: run test as follows: 
-#         ./test_bdm.sh
+# Step 2: run test as follows:
+#         cd /path/to/beedeem 
+#         export PATH=$PWD:$PATH
+#         ./test_bdm
 # --
 # P. Durand (SeBiMER, Ifremer), last updated on Jan 2023
 # =================================================
 
+
 # == TEST 1 =========================================== 
 echo "*** TEST 1: Start simple bank installation"
-# set log mode to console (otherwise default is a log file located in KL_WORKING_DIR
+
+# set BeeDeeM log mode to console (otherwise default is a log file located in KL_WORKING_DIR)
 export KL_LOG_TYPE=console
+
 # Set the bank to install
 # This is a '.dsc' file located in BeeDeeM installation path at ${beedeem-home}/conf/descriptors
 DESCRIPTOR="SwissProt_human"
+
 # start BeeDeeM with 'install' command
-./bdm install -desc ${DESCRIPTOR} 
+bdm install -desc ${DESCRIPTOR} 
+
 # check whether command succeeded or not
 if [ $? -eq 0 ]; then
   echo "TEST 1: SUCCESS"
@@ -33,26 +40,34 @@ else
   exit 1
 fi
 
+
 # == TEST 2 =========================================== 
 echo "*** TEST 2: list installed bank"
-# reset log mode to file
+
+# reset BeeDeeM log mode to file (default)
 export KL_LOG_TYPE=file
+
 # start BeeDeeM with 'info' command
-./bdm info -d all -f txt
+bdm info -d all -f txt
+
 if [ $? -eq 0 ]; then
   echo "TEST 2: SUCCESS"
 else
   echo "TEST 2: FAILED. Review log file in: @KL_WORKING_DIR@"
   exit 1
 fi
 
+
 # == TEST 3 =========================================== 
-# Change default log file name to something else
+# Change default BeeDeeM log file name to something else
 export KL_LOG_FILE=query.log
+
 SW_ENTRY="ZZZ3_HUMAN"
 echo "*** TEST 3: query bank for entry: $SW_ENTRY"
+
 # start BeeDeeM with 'query' command
-./bdm query -d protein -f txt -i $SW_ENTRY
+bdm query -d protein -f txt -i $SW_ENTRY
+
 if [ $? -eq 0 ]; then
   echo "TEST 3: SUCCESS"
 else

src/bzh/plealog/dbmirror/util/log/LoggerCentral.java

@@ -336,7 +336,6 @@ private static void configureRollingFileLogger(Level aLevel, String logName) {
     userPath = getLogAppPath();
     szLogFileName = userPath + _logAppFile;
     szLogFilePattern = userPath + "%d{MM-dd-yy}-" + _logAppFile;
-    System.out.println("**** LogFile: "+szLogFileName);
     try {
       cleanSystemLogs(userPath, _logAppFile);
     } catch (Exception e) {