#!/usr/local/bin/perl
# build.pl for srsldap software
# for biodata directories, using SRSv6, LDAP and SOAP(Glue)
# d.gilbert, oct. 2002
# Trivial Build Script - changed to Perl 

use Getopt::Long;

print <<HEADER;
# Trivial Build Script for SRSv6-LDAP/SOAP interface software
# so far this only has been tested on Solaris w/ a SRS v6 library
# to build and use, you need an active SRS v6 (maybe v7) installation
# from Lion Biosciences.  You should have run its srs/etc/prep_srs 

HEADER

# configure choices 

# compile srs6ldap.cc and link w/ srs library
$MAKE_SRSLIB=0;

# compile java -- these should be already compiled
$MAKE_JAVA=0;

# dont make openldap backend unless want it; java ldap server is ok (a bit slower)
$MAKE_SLAPD=0;

$SHOW_TESTS=0;

$pcrs= 0; $pthreads= 0; $gzip= 1;

# ldap=/c7/soft/net/ldap/openldap-2.0.19/servers/slapd/
$ldap="/usr/local/openldap-2.0.19/servers/slapd/";

$srsroot=$ENV{SRSROOT} || "/bio/mb/srs61/";

my $ok= Getopt::Long::GetOptions( 
		'srslib!' => \$MAKE_SRSLIB,
		'java!' => \$MAKE_JAVA,
		'slapd!' => \$MAKE_SLAPD,
		'tests!' => \$SHOW_TESTS,

		'pcrs!' => \$pcrs,
		'pthreads!' => \$pthreads,
		'gzip!' => \$gzip,

		'ldap!' => \$ldap,
		);

usage() unless($MAKE_SRSLIB||$MAKE_JAVA||$MAKE_SLAPD||$SHOW_TESTS);

sub usage() {
  my $usage= <<HERE;
  $O -- options
'srslib!' => $MAKE_SRSLIB, -- make srs library
'java!' => $MAKE_JAVA,     -- make java classes
'slapd!' => $MAKE_SLAPD,   -- make openldap slapd srs backend
'tests!' => $SHOW_TESTS,   -- show test commands

  -- srslib compile options --
'pcrs!' => $pcrs,        -- make and use pcrs C regex package
'pthreads!' => $pthreads, -- use pthreads lib
'gzip!' => $gzip,        -- use zlib compression lib

'ldap!' => $ldap      
	 -- path to openLdap installation (for slapd make)
  
  -- ENV settings --
ENV{SRSROOT}   -- SRSROOT + environ paths [SRSROOT='$ENV{SRSROOT}']
ENV{JAVA_HOME} -- java home (java 1.4+ recommended)
ENV{CPP}       -- c++ compiler
  
HERE
	die $usage;
}

# Edit paths as needed

# installation folder
$ho=`pwd`; chomp($ho);

$java=$ENV{JAVA_HOME} || "/usr/java";

# GLUE java soap server libs - copy these for distrib. w/ this srs-ldap-soap server
$glu="$ho/lib";
$jld="$ho/lib";

# C++ and C compilers
$CPP=$ENV{CPP} || "CC";
$CC=$ENV{CC} || "cc";

# compile flags for srs6ldap.cc
# avoid pcrs? - may be memory crasher - used for ldap2srs filter conversion
$MAKE_NOPCRS= ($pcrs) ? "" : "-DSRS6LDAP_NOPCRS=1";

# dont need threaded calls in srs6ldap.cc ?
$MAKE_PTHREADS= ($pthreads) ? "-DSRS6LDAP_PTHREADS=1" : ''; 

# define -DSRS6LDAP_NOGZIP=1 for no zlib/gzip compression
$MAKE_GZIP= ($gzip) ? '' : "-DSRS6LDAP_NOGZIP=1"; # 

$TARGET_OS = "unknown";
$OS = `uname`; chomp($OS);
if ($OS eq 'SunOS' && (`uname -r` !~ /^[1-4]/)) { $OS = 'Solaris'; }
$_= $OS;
OSCASE: {
	if (/Solaris/){ $TARGET_OS = "solaris"; last OSCASE; }
	if (/SunOS/)  { $TARGET_OS = "sunos"; last OSCASE; }
	if (/OSF1/)   { $TARGET_OS = "osf"; last OSCASE; }
	if (/ULTRIX/) { $TARGET_OS = "ultrix"; last OSCASE; }
	if (/IRIX/)   { $TARGET_OS = "irix"; last OSCASE; }
	if (/IRIX64/) { $TARGET_OS = "irix64"; last OSCASE; }
	if (/Linux/)  { $TARGET_OS = "linux"; last OSCASE; }
	if (/AIX/)    { $TARGET_OS = "aix"; last OSCASE; }
	if (/HP-UX/)  { $TARGET_OS = "hpux"; last OSCASE; }
	$TARGET_OS = $OS;
	warn "Unsupported operating system: $OS";
	}

## require use have run srs/prep_srs to set env
unless($ENV{SRSSOU} && $ENV{SRSEXE}) {
	warn "SRS env settings not here. Using '$srsroot' path. This may not work well.";
	}
# locate srs6 directory & libraries - get from ENV if there
$sxsrc=$ENV{SRSSOU} || "$srsroot/src";
$sxbin=$ENV{SRSEXE} || "$srsroot/bin/$TARGET_OS";



# ------------------------
# Java compile for GLUE SOAP server
# Java source is in iubio/srs/
if ( $MAKE_JAVA ) {
	print "# Java compile for GLUE SOAP + JavaLDAP servers\n";
	
	chdir( $ho);

	$GLUEBASE="$glu/GLUE-STD.jar:$glu/dom.jar:$glu/jcert.jar:$glu/jnet.jar:$glu/jsse.jar:$glu/sax.jar:$glu/saxpath.jar:$glu/servlet.jar:$glu/xerces.jar";

	$JAVALDAP="$jld/javaldap.jar:$jld/xss4j.jar";
	 ## also $jld/xerces.jar:$jld/hsqldb-1.61.jar
	
	my $cp= ".:$GLUEBASE:$JAVALDAP";
	$ENV{CLASSPATH}= $cp;
	#export CLASSPATH
	
	# Compile all .java files under org
	my @jf= `find iubio -name '*.java' -print`;
	for my $j (@jf) {
	 	chomp $j;
		print "javac $j\n";
		print `javac -classpath $cp $j`;
	}
	
	print "# --- make iubio_jni_SRS.h if need be ---\n";
	print " javah iubio.srs.SRSjni\n";
	print " mv iubio_srs_SRSjni.h iubio/lib-srs/\n";
	
	print "# Done java\n";
	print "\n";
}

# ------------------------
# C++ compile libpcrs/pcre - C perl-like regex
# pcre-3.9.tar.gz by Philip Hazel <ph10@cam.ac.uk>
#  ftp://ftp.csx.cam.ac.uk/pub/software/programming/pcre/pcre-xxx.tar.gz
# pcrs-0.0.1-src.tar.gz  by Andreas S. Oesterhelt <andreas@oesterhelt.org>, LGPL - Written and Copyright (C) 2000, 2001 
# -- include and build these (in tar.gz)

if (! $MAKE_NOPCRS ) {
	print "\n";
	print "# Build C perl-like regex\n";
	
	my $script=<<HERE;
	cd $ho/etc
	gtar -zxf pcre-3.9.tar.gz
	cd pcre-3.9
	env  CC=gcc ./configure --enable-static --disable-shared
	make
	cp pcre.h ../
	cp .libs/libpcre.a ../
	
	cd $ho/etc
	ranlib libpcre.a 
	
	gtar -zxf pcrs-0.0.1-src.tar.gz
	cd pcrs-0.0.1
	env  CC=gcc CFLAGS=-I.. LDFLAGS=-L.. CPPFLAGS=-I..  ./configure  
	perl -pi -e 's/all: shared static pcrsed/all: pcrsed static/' Makefile
	make
	cp pcrs.h ../
	cp libpcrs.a ../
	cd $ho/etc
	mv pc*.h libpc*.a $ho/iubio/lib-srs
HERE
	print `$script`;
	
	print "# Done C regex\n";
	print "\n";
}

# ------------------------
# C++ compile for Java JNI and OpenLDAP slapd server
# LDAP build is based on OpenLDAP v2.0.19 / v2.1.5
# mods for openldap/servers/slapd/back-srs
# assumes ldap has been compiled 

if ( $MAKE_SRSLIB ) {
	print "# C++ compile for Java JNI and OpenLDAP slapd server\n";
	
	chdir("$ho");
	chdir("iubio/lib-srs");
	
	## add -DSRS6LDAP_NOPCRS for no pcre/rs
	## add -DSRS6LDAP_PTHREADS for pthread locks
	## patch $sxsrc/ctreep.h - non-functional, used by src/Index.h
	## /bio/mb/srs61/src/Index.h:    /* dgg: notfound: pIFIL  newIndexFile;*/
	# -DCTREEPH=1 - block non-functional srs/src/ctreep.h header

	$CFLAGS="-DCTREEPH=1 $MAKE_NOPCRS $MAKE_PTHREADS $MAKE_GZIP";
	
	$SRSLIBS="$sxbin/libsrs.a $sxbin/libctreestd.a $sxbin/libgd.a $sxbin/Monitor.o";
	if ( $MAKE_NOPCRS ) {
		$XLIBS=""; }
	else {
		$XLIBS="libpcrs.a libpcre.a"; }
	
	my ($cmd,$err);
        $cmd  ="/bin/cp -rp $sxsrc ./srssrc ; ";
        $cmd .="echo '#define pIFIL void*' | cat - $sxsrc/Index.h  > ./srssrc/Index.h";
	print "# patch copy of srs/src/Index.h \n";
	print $cmd; $err= `$cmd`; warn($err) if ($err);
	$sxsrcold= $sxsrc; $sxsrc= './srssrc';

	print "# make srs6 main routines\n";
	$cmd= "$CPP -w -g -I./ -I$sxsrc -I$sxbin $CFLAGS -c srs6ldap.cc -o srs6ldapmain.o \n";
	print $cmd; $err= `$cmd`; warn($err) if ($err);
	
	print "# link as stand-alone srs6ldap\n";
	$cmd= "$CPP -o srs6ldap  srs6ldapmain.o -lm -lz  $XLIBS $SRSLIBS \n";
	print $cmd; $err= `$cmd`; warn($err) if ($err);
		
	print "# re-make for JNI and slapd-back w/o main \n";
	$cmd=  "$CPP -w -g -I./ -I$sxsrc  -I$sxbin $CFLAGS -DSRS6LDAP_NOMAIN -c srs6ldap.cc \n";
	print $cmd; $err= `$cmd`; warn($err) if ($err);
	
	print "# make jni interface to srs6ldap\n";
	$cmd= "$CPP -g -I./ -I$java/include -I$java/include/$TARGET_OS -c srs6ldap_jni.cc \n";
	print $cmd; $err= `$cmd`; warn($err) if ($err);
	
	# link as shared lib for java use
	# need /usr/lib/libCstd specified as noted below (used by libsrs)
	print "# link libsrsjni -- need change for non-solaris systems  \n";
	$cmd= "$CPP -G -o libsrsjni.so srs6ldap_jni.o srs6ldap.o -lm -lz "
		." /usr/lib/libCstd.so.1 $XLIBS $SRSLIBS \n";
	print $cmd; $err= `$cmd`; warn($err) if ($err);
	
	print "# ----- If okay, DO THIS: -------\n";
	print " mkdir $ho/lib/$TARGET_OS\n";
	print " cp $ho/iubio/lib-srs/libsrsjni.so $ho/lib/$TARGET_OS\n";
	print "\n";
}


if ( $MAKE_SLAPD ) {
	# build as slapd backend
	# Makefile for back-srs/ set? uses SRS6 path
	# SRS6=/bio/mb/srs61
	# AC_LIBS = >> add these >> -lsrs -lpcre -lpcrs -lz
	# SRCS    = search.c config.c init.c srs6ldap2.cc
	# OBJS    = search.lo config.lo init.lo srs6ldap2.o Monitor.o 
	# XLIBS = libsrs.a  libpcrs.a libpcre.a libctreestd.a libgd.a  Monitor.o
	# also need in $ldap/../../include/portable.h
	#  ../../include/portable.h:#define SLAPD_SRS 1

	print "# compile OpenLDAP slapd server back-srs backend\n";
	if (! -d $ldap ) {
		print ">>> expecting OpenLDAP source in $ldap\n";
		}	
	else {
	
	chdir($ho);
	my $script=<<HERE;
	cp -rp iubio/openldap-back-srs $ldap/back-srs
	cp -p iubio/lib-srs/* $ldap/back-srs
	cd $ldap/back-srs/
	make
HERE
	# make slapd back parts - gmake should handle ?
	# $CC -g -I../../../include -I..  -xCC -I/usr/local/include -c search.c -o search.o
	# $CC -g -I../../../include -I..  -xCC -I/usr/local/include -c config.c -o config.o
	# $CC -g -I../../../include -I..  -xCC -I/usr/local/include -c init.c -o init.o
	# $CC -g -I../../../include -I..  -xCC -I/usr/local/include -c version.c -o version.o
	# 
	# ar ruv libback_srs.a search.o config.o init.o srs6ldap.o version.o

	print `$script\n`;
	
	## !!for slapd Makefile to link srs libs properly, srs/bin/xxx/lib*.a need to be in back-srs/
	## ?? do I want to cp -p $sxbin/*.a . OR ln -s $sxbin/*.a . + Monitor.o  ??
	print "\n";
	print "# Makefile for openldap/slapd/ needs editing to compile back-srs properly\n";
	$script=<<HERE;
	cd $ldap
	make
HERE
	print `$script\n`;
	
	print "# Done openldap/slapd/back-srs\n";
	print "\n";
	}

}

## ------------------

## ?? need to make java client shell scripts w/ JAR path settings

if ( $SHOW_TESTS ) {
chdir ( $ho);
print <<HERE;
# -------- TESTS ------------------------

# test standalone srs6ldap
./iubio/lib-srs/srs6ldap
./iubio/lib-srs/srs6ldap -d 1 -m 2 -f '(&(objectclass=*)(lib=swissprot)(des=kinase))' 
./iubio/lib-srs/srs6ldap -d 1 -m 2 -g '[swissprot-des:kinase]' -o '*'
./iubio/lib-srs/srs6ldap -d 1 -m 2 -g '[swissprot-des:kinase]' -o 'BioseqEntry'
./iubio/lib-srs/srs6ldap -d 1 -m 2 -g '[swissprot-des:kinase]' -o 'BioseqRecord'
./iubio/lib-srs/srs6ldap -d 1 -m 2 -g '[swissprot-des:kinase]' -o 'BinaryBioseqRecord'

# locate libsrsjni.so for SRSjni & soap server -- system specific?
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:$ho/lib/$TARGET_OS

# test java JNI interface
java iubio.srs.SRSjni
java iubio.srs.SRSjni -d 1 -m 2 -f '(&(objectclass=*)(lib=swissprot)(des=kinase))' 
# or
java -Diubio.srsjni.libfile=$ho/lib/$TARGET_OS/libsrsjni.so  iubio.srs.SRSjni 
java iubio.srs.LdapBackendSRS

# run LDAP server, ldap://localhost:10389/
cd jldapserver ; ./javaldap.sh ; cd ..

java iubio.srs.ldapsearch
java iubio.srs.ldapsearch \\
 'ldap://localhost:10389/srv=srs??sub?(&(objectclass=*)(lib=swissprot)(des=kinase))' 
java iubio.srs.ldapsearch \\
 'ldap://localhost:10389/srv=srs??sub?(&(objectclass=BioseqRecord)(lib=swissprot)(des=kinase))?sizelimit=2' 

# run GLUE Web server,  http://localhost:8004/bionames
cd jwebserver ; ./bionames.sh ; cd ..

# open web browser to http://localhost:8004/bionames/ for servlet web pages

# get wsdl from bionames server
lynx -source http://localhost:8004/bionames/services/srs.wsdl > srs.wsdl

# run GLUE soap client
etc/runglue iubio.srs.SRSsoapclient -w file://srs.wsdl
etc/runglue iubio.srs.SRSsoapclient -w file://srs.wsdl getzq1

## if desired, run GLUE SRSsoap only as http://localhost:8004/glue/srs.wsdl
## same as http://localhost:8004/bionames/services/srs.wsdl
# cd jwebserver ; ./srssoap.sh ; cd ..

HERE

}