[med-svn] [Git][med-team/libarb][master] 5 commits: Leave lib/arb_tcp_org.dat in libarb source tarball
Andreas Tille
gitlab at salsa.debian.org
Fri Jun 14 08:02:06 BST 2019
Andreas Tille pushed to branch master at Debian Med / libarb
Commits:
5bdd8731 by Andreas Tille at 2019-06-14T06:00:59Z
Leave lib/arb_tcp_org.dat in libarb source tarball
- - - - -
ac2e90b8 by Andreas Tille at 2019-06-14T06:01:32Z
New upstream version 6.0.6
- - - - -
f7d1883d by Andreas Tille at 2019-06-14T06:01:34Z
Update upstream source from tag 'upstream/6.0.6'
Update to upstream version '6.0.6'
with Debian dir 389c089b53f025eaa0afa9eeffa430bf98d493cf
- - - - -
18c525c5 by Andreas Tille at 2019-06-14T06:17:03Z
Install arb_tcp.dat
- - - - -
4ad93462 by Andreas Tille at 2019-06-14T06:23:18Z
Fix links
- - - - -
9 changed files:
- + UNIT_TESTER/log_result.pl
- debian/copyright
- debian/libarb-dev.links
- debian/libarb.install
- debian/libarb.links
- debian/rules
- + lib/GPL.txt
- + lib/Makefile
- + lib/arb_tcp_org.dat
Changes:
=====================================
UNIT_TESTER/log_result.pl
=====================================
@@ -0,0 +1,81 @@
+#!/usr/bin/perl
+use strict;
+use warnings;
+
+my $reg_summary = qr/^UnitTester:.*\stests=([0-9]+)\s/;
+my $reg_interrupted = qr/interrupting.*deadlocked.*test/i;
+
+sub log_summary($) {
+ my ($log) = @_;
+ my $interrupted = 0;
+
+ open(LOG,$log) || die "Failed to read '$log' (Reason: $!)";
+ my $line;
+ LINE: while (defined ($line=<LOG>)) {
+ if ($line =~ $reg_summary) {
+ my $testCount = $1;
+ if ($testCount==0) {
+ ; # looks like all tests in this module have been skipped
+ }
+ else {
+ chomp($line);
+ $line =~ s/^UnitTester:\s*//;
+ my @items = split /\s+/, $line;
+ my $module = undef;
+ my $passed = undef;
+ foreach (@items) {
+ my ($key,$value) = split /=/, $_;
+ if ($key eq 'target') {
+ $value =~ s/\.a//;
+ $module = $value;
+ }
+ elsif ($key eq 'passed') {
+ $passed = $value;
+ if ($passed eq 'ALL') { $passed = $testCount; }
+ }
+ }
+ print "- $module ($passed/$testCount)\n";
+ }
+
+ close(LOG);
+ return;
+ }
+ elsif ($line =~ $reg_interrupted) {
+ $interrupted = 1;
+ last LINE;
+ }
+ }
+
+ close(LOG);
+
+ # no summary found -> problem
+ my $module = $log; # fallback
+ my $extraMsg = '; invalid logname';
+
+ if ($log =~ /logs\//o) {
+ my $name = $';
+ if ($name =~ /^([^\.]+)\.test/o) {
+ $module = $1;
+ $extraMsg = '';
+ }
+ else {
+ $module = $name;
+ }
+ }
+
+ my $msg = 'no summary; crashed?';
+ if ($interrupted==1) { $msg = 'interrupted; deadlock?'; }
+
+ print "- $module ($msg$extraMsg)\n";
+}
+
+sub main() {
+ my $args = scalar(@ARGV);
+ if ($args!=1) {
+ die "Usage: log_result.pl unittest.log";
+ }
+ else {
+ log_summary($ARGV[0]);
+ }
+}
+main();
=====================================
debian/copyright
=====================================
@@ -11,7 +11,9 @@ Files-Excluded: arbsrc*/AISC_COM/Makefile
arbsrc*/CON*
arbsrc*/D*
arbsrc*/E*
- arbsrc*/G*
+ arbsrc*/GD*
+ arbsrc*/GE*
+ arbsrc*/GL*
arbsrc*/HEADERLIBS
arbsrc*/HELP_SOURCE
arbsrc*/I*
@@ -123,7 +125,25 @@ Files-Excluded: arbsrc*/AISC_COM/Makefile
arbsrc*/doc
arbsrc*/demo.arb
arbsrc*/etc
- arbsrc*/l*
+ arbsrc*/lib/BUGS
+ arbsrc*/lib/addlibs
+ arbsrc*/lib/arb_default
+ arbsrc*/lib/desktop
+ arbsrc*/lib/dtd
+ arbsrc*/lib/export
+ arbsrc*/lib/gde
+ arbsrc*/lib/import
+ arbsrc*/lib/inputMasks
+ arbsrc*/lib/macros
+ arbsrc*/lib/motifHack
+ arbsrc*/lib/nas
+ arbsrc*/lib/pictures
+ arbsrc*/lib/pixmaps
+ arbsrc*/lib/rna3d
+ arbsrc*/lib/sellists
+ arbsrc*/lib/submit
+ arbsrc*/lib/LoVPBN.*
+ arbsrc*/lib/macro.head
arbsrc*/ptpan*
arbsrc*/util
=====================================
debian/libarb-dev.links
=====================================
@@ -1,2 +1,3 @@
+#!/usr/bin/dh-exec
# Add symlink for tools expecting upstream non FHS location of header files
usr/include/arb usr/lib/${DEB_HOST_MULTIARCH}/arb/INCLUDE
\ No newline at end of file
=====================================
debian/libarb.install
=====================================
@@ -1,2 +1,3 @@
#!/usr/bin/dh-exec
-lib/*.so usr/lib/${DEB_HOST_MULTIARCH}/arb
+lib/*.so usr/lib/${DEB_HOST_MULTIARCH}/arb
+lib/arb_tcp.dat etc/arb
=====================================
debian/libarb.links
=====================================
@@ -1,2 +1,4 @@
+#!/usr/bin/dh-exec
# ARB expects a folder $ARBHOME to contain lib/libARBDB.so
-usr/lib/${DEB_HOST_MULTIARCH}/arb usr/lib/${DEB_HOST_MULTIARCH}/arb/lib
\ No newline at end of file
+usr/lib/${DEB_HOST_MULTIARCH}/arb usr/lib/${DEB_HOST_MULTIARCH}/arb/lib
+etc/arb/arb_tcp.dat usr/lib/${DEB_HOST_MULTIARCH}/arb/arb_tcp.dat
=====================================
debian/rules
=====================================
@@ -50,9 +50,9 @@ override_dh_auto_build:
ln -s ../SL/HELIX/BI_basepos.hxx INCLUDE/BI_basepos.hxx
ln -s ../SL/HELIX/BI_helix.hxx INCLUDE/BI_helix.hxx
mkdir bin
- mkdir lib
dh_auto_build -- all # --sourcedirectory=CORE
make bin/arb_pt_server
+ cd lib && make tcpdat
override_dh_auto_configure: config.makefile
@@ -64,7 +64,7 @@ override_dh_auto_clean: config.makefile
$(MAKE) clean
cd PROBE_COM; $(MAKE) clean; rm -f PT_*.h
rm -rf bin
- rm -rf lib
+ rm -rf lib/lib*
rm -rf NAMES_COM
rm -rf PROBE_COM/AISC
rm -rf INCLUDE
@@ -72,6 +72,7 @@ override_dh_auto_clean: config.makefile
rm -rf AISC_MKPTPS/aisc_mkpt
rm -rf PROBE_COM/DUMP PROBE_COM/GENC PROBE_COM/GENH
rm config.makefile
+ rm -rf lib/arb_tcp.dat
# ARB does not have "distclean" or "realclean". Remove some leftovers:
rm -f UNIT_TESTER/Makefile.setup.local
find -name \*.log -a ! -name phyml-manual.log -print0 | xargs -0 rm -f
=====================================
lib/GPL.txt
=====================================
@@ -0,0 +1,350 @@
+
+Below is a copy of the GPL. It does NOT apply to the ARB source code!
+
+It's only provided because ARB is distributed together with some GPLed
+software. You can get the source of that software together with the
+ARB source code from http://arb-home.de/
+
+--------------------------------------------------------------------------------
+
+
+ GNU GENERAL PUBLIC LICENSE
+ Version 2, June 1991
+
+ Copyright (C) 1989, 1991 Free Software Foundation, Inc.
+ 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+ Preamble
+
+ The licenses for most software are designed to take away your
+freedom to share and change it. By contrast, the GNU General Public
+License is intended to guarantee your freedom to share and change free
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+Foundation's software and to any other program whose authors commit to
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+ When we speak of free software, we are referring to freedom, not
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+Public License instead of this License.
=====================================
lib/Makefile
=====================================
@@ -0,0 +1,36 @@
+help.make:
+ @echo 'options'
+ @echo ' nameserver create nameserver from template'
+ @echo ' tcpdat create arb_tcp.dat from template'
+ @echo ''
+ @echo ' all all above'
+ @echo ' clean cleanup'
+
+all: tcpdat nameserver
+
+# ----------------------------------------
+# READ THIS!
+#
+# Please be very careful here to NOT
+# touch the following files/directories if
+# they are links:
+#
+# ./arb_tcp.dat
+# ./nas
+# ./pts
+#
+# ----------------------------------------
+
+tcpdat:
+ ( (test -e arb_tcp.dat || test -h arb_tcp.dat) \
+ && echo "lib/arb_tcp.dat is a link - skipped" ) \
+ || cp -p arb_tcp_org.dat arb_tcp.dat
+
+nameserver:
+ ( test -h nas && echo "lib/nas is a link - skipped" ) || (cd nas;$(MAKE) all)
+
+clean:
+ rm -f *.so
+ ( test -h nas && echo "lib/nas is a link - skipped" ) || (cd nas;$(MAKE) clean)
+ ( test -h pts && echo "lib/pts is a link - skipped" ) || rm -rf pts
+ ( test -h arb_tcp.dat && echo "lib/arb_tcp.dat is a link - skipped" ) || rm -f arb_tcp.dat
=====================================
lib/arb_tcp_org.dat
=====================================
@@ -0,0 +1,80 @@
+#******************* Syntax ***********************************
+#
+# [USER:]SERVER_ID HOST:IP_NR [programm args]
+# [USER:]SERVER_ID :SOCKETPATH [programm args]
+# [xxx] means optional field
+# all $(enviroment_variable) are replaced by the value of the 'enviroment_variable'.
+# if host is localhost then it is replaced by the result of `hostname`.
+#
+# Specifying an username before the SERVER_ID makes the server user specific.
+#
+# This file is searched at several locations:
+# - in the current directory
+# - in the $(HOME) (=home directory of the current user)
+# - in $(ARBHOME)/lib
+# The first occurrance found is taken.
+#
+# Existing SERVER_IDs:
+#
+# ARB_DB_SERVER Your private database server. It is automatically started
+# ARB_PT_SERVER Default PT_SERVER for PB_RETRIEVE (privat TU_Munich server)
+# ARB_PT_SERVERn Global PT_SERVERs. Needed for fast database search (align seq, probe des.)
+# n starts from 0 to max, no number can be excluded !!!
+# ARB_NAME_SERVER Generates short names for species (using 'acc')
+# ARB_NAME_SERVER_field Generates short names for species (using 'acc' and 'field')
+#
+#*****************************************************************
+
+# version of arb_tcp.dat
+ARB_TCP_DAT_VERSION 2
+
+#*********** Test Servers ******************
+
+ARB_TEST_PT_SERVER :$(ARBHOME)/UNIT_TESTER/sockets/pt.socket arb_pt_server -D$(ARBHOME)/UNIT_TESTER/run/TEST_pt.arb
+ARB_TEST_PT_SERVER_GENE :$(ARBHOME)/UNIT_TESTER/sockets/ptgene.socket arb_pt_server -D$(ARBHOME)/UNIT_TESTER/run/TEST_gpt.arb
+
+#*********** Private Servers (for each user) ******************
+#
+# This is a local server, running on one machine. Each user has his own socket:
+# ARB_PID is an Enviroment Variable which is set by the command 'arb' to its own process id
+# see programm $ARBHOME/SH/arb_clean to remove the sockets
+
+ARB_DB_SERVER :/tmp/arb_db_$(USER)_$(ARB_PID)
+
+# If you want to run programs on a workstation cluster, you have to assign your arbdb server
+# and one ip-id for each user. To choose an ip_id choose any number between 1000 and 4000 and
+# examine /etc/services whether this ip-id has not yet been allocated by another programm
+# smith:ARB_DB_SERVER myhost:4011 // socket for smith ('arb' has to be started on 'myhost')
+# ludwig:ARB_DB_SERVER myhost:4012 // socket for ludwig
+# ARB_DB_SERVER :/tmp/arb_db_$(USER)_$(ARB_PID) // and sockets for all others
+
+#*********** Global Servers (for all users) ******************
+#
+#*********** Nameserver The server should run on the nfs server ******************
+# The primary nameserver (ARB_NAME_SERVER) uses the field 'acc' for species identification
+#
+# You may define additional nameservers, using one additional field for identification.
+# The defined nameserver 'ARB_NAME_SERVER_START' uses the fields 'acc' and 'start'.
+
+ARB_NAME_SERVER localhost:3020 arb_name_server -d$(ARBHOME)/lib/nas/names.dat
+ARB_NAME_SERVER_START localhost:3021 arb_name_server -d$(ARBHOME)/lib/nas/names_start.dat -fstart=1
+# ARB_NAME_SERVER_STRAIN localhost:3022 arb_name_server -d$(ARBHOME)/lib/nas/names_strain.dat -fstrain=
+# ARB_NAME_SERVER_POS_START localhost:3023 arb_name_server -d$(ARBHOME)/lib/nas/names_pos_start.dat -fpos_start=1
+
+#*********** PT_SERVERS The server should run on the nfs server ******************
+#******* You may add new pt_servers here: (numbers must be continued) *********
+# Note: If the database name is '!ASSUME_RUNNING' (i.e. -D!ASSUME_RUNNING), ARB will not
+# try to start/stop/update/... the server and will not check DB for existance.
+# To use such a PT-Server you'll have to start it manually on the remote host
+
+ARB_PT_SERVER0 localhost:3030 arb_pt_server -D$(ARBHOME)/lib/pts/probe_server.arb
+ARB_PT_SERVER1 localhost:3031 arb_pt_server -D$(ARBHOME)/lib/pts/LSU_rRNA.arb
+ARB_PT_SERVER2 localhost:3032 arb_pt_server -D$(ARBHOME)/lib/pts/SSU_rRNA.arb
+ARB_PT_SERVER3 :$(HOME)/.arb_pts/$(USER)1.socket arb_pt_server -D$(HOME)/.arb_pts/$(USER)1.arb
+ARB_PT_SERVER4 :$(HOME)/.arb_pts/$(USER)2.socket arb_pt_server -D$(HOME)/.arb_pts/$(USER)2.arb
+ARB_PT_SERVER5 :$(HOME)/.arb_pts/$(USER)3.socket arb_pt_server -D$(HOME)/.arb_pts/$(USER)3.arb
+ARB_PT_SERVER6 localhost:3033 arb_pt_server -D$(ARBHOME)/lib/pts/user1.arb
+ARB_PT_SERVER7 localhost:3034 arb_pt_server -D$(ARBHOME)/lib/pts/user2.arb
+ARB_PT_SERVER8 localhost:3035 arb_pt_server -D$(ARBHOME)/lib/pts/user3.arb
+ARB_PT_SERVER9 localhost:3036 arb_pt_server -D$(ARBHOME)/lib/pts/user4.arb
+ARB_PT_SERVER10 localhost:3037 arb_pt_server -D$(ARBHOME)/lib/pts/user5.arb
View it on GitLab: https://salsa.debian.org/med-team/libarb/compare/5284f1188dbbb3b1a957f817177010234eb9e3a9...4ad9346240f1c6d66ec7a5b61bdcfb9ea5625e0c
--
View it on GitLab: https://salsa.debian.org/med-team/libarb/compare/5284f1188dbbb3b1a957f817177010234eb9e3a9...4ad9346240f1c6d66ec7a5b61bdcfb9ea5625e0c
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