# Process with autom4te to create an -*- Autotest -*- test suite.
#
# see regression/... subdirs wherein for each of the cases and each check (enumerated) is a pre and post dir. 
# In pre initial files are placed, in post results can be found to be checked by diff in this testsuite.

AT_INIT([Molecular Builder])

# Checking if command line options are parsed correctly
AT_BANNER([MoleCuilder - standard options])
AT_SETUP([Standard Options])
AT_KEYWORDS([options])
AT_CHECK([pwd],[ignore],[ignore])
AT_CHECK([../../molecuilder -v], 0, [stdout], [ignore])
AT_CHECK([fgrep olecuilder stdout], 0, [ignore], [ignore])
AT_CHECK([../../molecuilder -h], 0, [stdout], [ignore])
AT_CHECK([fgrep "Give this help screen" stdout], 0, [ignore], [ignore])
AT_CHECK([../../molecuilder -e], 255, [ignore], [stderr])
AT_CHECK([fgrep "Not enough or invalid arguments" stderr], 0, [ignore], [ignore])
AT_CHECK([../../molecuilder test.conf], 0, [stdout], [stderr])
AT_CHECK([fgrep "Element list loading failed" stdout], 0, [ignore], [ignore])
AT_CLEANUP


AT_BANNER([MoleCuilder - molecular config creation from xyz file and atom adding])
AT_KEYWORDS([Atom handling])
# 1. create some simplest molecular geometry
AT_SETUP([Simple configuration - xyz file generation])
AT_DATA([test.xyz], [[1
 # test configuration, created by molecuilder test suite
H	10.	10.	10.
]])
AT_CHECK([file=test.xyz; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/1/post/$file], 0, [ignore], [ignore])
AT_CLEANUP

# 2. parsing an xyz
AT_SETUP([Simple configuration - parsing xyz file])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/2/pre/test.xyz .], 0)
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -p test.xyz], 0, [ignore], [ignore])
AT_CHECK([fgrep "Ion_Type1_1" test.conf], 0, [Ion_Type1_1	10.000000000	10.000000000	10.000000000	0 # molecule nr 0
], [ignore])
AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/2/post/$file], 0, [ignore], [ignore])
AT_CHECK([file=test.conf.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/2/post/$file], 0, [ignore], [ignore])
AT_CHECK([file=test.conf.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/2/post/$file], 0, [ignore], [ignore])

# 3. add atom
AT_CLEANUP
AT_SETUP([Simple configuration - adding atom])
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -a 1 10. 10. 10.], 0, [ignore], [ignore])
AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
AT_CHECK([file=test.conf.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
AT_CHECK([file=test.conf.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
AT_CLEANUP

# 4. change the element
AT_SETUP([Simple configuration - Changing element])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/4/pre/test.conf test.conf], 0)
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -E 0 6], 0, [ignore], [ignore])
AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/4/post/$file], 0, [ignore], [ignore])
AT_CLEANUP

# 5. remove atom
AT_SETUP([Simple configuration - Atom removal])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/5/pre/test.conf .], 0)
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -r 0], 0, [ignore], [ignore])
AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/5/post/$file], 0, [ignore], [ignore])
AT_CHECK([file=test.conf.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/5/post/$file], 0, [ignore], [ignore])
AT_CHECK([file=test.conf.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/5/post/$file], 0, [ignore], [ignore])
AT_CLEANUP

# 6. test some more configuration that all desire parameters and count how many complain
AT_SETUP([Simple configuration - invalid commands on empty configs])
AT_CHECK([../../molecuilder empty.conf -e ${abs_top_srcdir}/src/ -t -s -b -E -c -b -a -U -T -u], 255, [ignore], [stderr])
AT_CHECK([fgrep -c "Not enough or invalid" stderr], 0, [1
], [ignore])
AT_CLEANUP

# 7. test some more configuration that all need parameters and count how many complain
AT_SETUP([Simple configuration - invalid commands on present configs])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/7/pre/test.conf .], 0)
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -t], 255, [ignore], [stderr])
AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -s -b -E -c -b -a -U -T -u], 255, [ignore], [stderr])
AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -b -E -c -b -a -U -T -u], 255, [ignore], [stderr])
AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -E -c -b -a -U -T -u], 255, [ignore], [stderr])
AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -c -b -a -U -T -u], 255, [ignore], [stderr])
AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -b -a -U -T -u], 255, [ignore], [stderr])
AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -a -U -T -u], 255, [ignore], [stderr])
AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -U -T -u], 255, [ignore], [stderr])
AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -T -u], 255, [ignore], [stderr])
AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -u], 255, [ignore], [stderr])
AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
AT_CLEANUP


AT_BANNER([MoleCuilder - Graph routines test])
AT_KEYWORDS([graph])
AT_SETUP([Graph - DFS analysis])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Graph/1/pre/test.conf .], 0)
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -vvv -D 2.], 0, [stdout], [stderr])
AT_CHECK([fgrep -c "No rings were detected in the molecular structure." stdout], 0, [1
], [ignore])
AT_CLEANUP

AT_BANNER([MoleCuilder - Fragmentation and Re-fragmentation test])
AT_KEYWORDS([fragmentation])
# 1. check config
AT_SETUP([Fragmentation - Checking present config])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Fragmentation/1/pre/test.conf .], 0)
AT_CHECK([fgrep "Ion_Type1_4" test.conf], 0, [Ion_Type1_4	8.532785963	4.787886018	2.645886050	0 # molecule nr 6
], [ignore])
AT_CHECK([fgrep "Ion_Type2_4" test.conf], 1, [ignore], [ignore])
AT_CLEANUP
# 2. fragment the molecule and check the number of configs
AT_SETUP([Fragmentation - Fragmentation])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Fragmentation/2/pre/test.conf .], 0)
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -f 1.55 2], 0, [ignore], [ignore], [mkdir std; mv BondFragment*.conf* std/])
AT_CHECK([mkdir std; mv BondFragment*.conf* std/], 0)
AT_CHECK([ls -l std/BondFragment*.conf | wc -l], 0, [5
], [ignore])
AT_CLEANUP
# 3. check whether parsing of BondFragment files and re-rwriting config files is working (exit code is 2 as we don't need to continue wrt to ...OrderAtSite)
AT_SETUP([Fragmentation - Fragmentation is at MaxOrder])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Fragmentation/3/pre/* .], 0)
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -f 1.55 2], 2, [ignore], [ignore], [mkdir new; mv BondFragment*.conf* new/])
AT_CHECK([mkdir new; mv BondFragment*.conf* new/], 0)
AT_CLEANUP


AT_BANNER([MoleCuilder - Tesselation test])
AT_KEYWORDS([Tesselation])
# 1. Non convex tesselation
AT_SETUP([Tesselation - Non-Convex Envelope])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/1/pre/* .], 0)
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -N 4. NonConvexEnvelope], 0, [stdout], [stderr])
AT_CHECK([file=NonConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/1/post/$file], 0, [ignore], [ignore])
AT_CHECK([file=NonConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/1/post/$file], 0, [ignore], [ignore])
AT_CLEANUP

# 2. convex tesselation (where the non-convex is already convex)
AT_SETUP([Tesselation - Convex Envelope])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/2/pre/* .], 0)
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -o ConvexEnvelope NonConvexEnvelope], 0, [stdout], [stderr])
AT_CHECK([file=ConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/2/post/$file], 0, [ignore], [ignore])
AT_CHECK([file=ConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/2/post/$file], 0, [ignore], [ignore])
AT_CHECK([fgrep "tesselated volume area is 16.4016 angstrom^3" stdout], 0, [ignore], [ignore])
AT_CHECK([diff ConvexEnvelope.dat NonConvexEnvelope.dat], 0, [ignore], [ignore])
AT_CLEANUP

# 3. Big Non convex tesselation
AT_SETUP([Tesselation - Big non-Convex Envelope])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/3/pre/* .], 0)
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -N 4. NonConvexEnvelope], 0, [stdout], [stderr])
AT_CHECK([file=NonConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/3/post/$file], 0, [ignore], [ignore])
AT_CHECK([file=NonConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/3/post/$file], 0, [ignore], [ignore])
AT_CLEANUP

# 4. Big convex tesselation - is not working yet 
#AT_SETUP([Tesselation - big convex Envelope])
#AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/4/pre/* .], 0)
#AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -o ConvexEnvelope NonConvexEnvelope], 0, [stdout], [stderr])
#AT_CHECK([file=ConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/4/post/$file], 0, [ignore], [ignore])
#AT_CHECK([file=ConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/4/post/$file], 0, [ignore], [ignore])
#AT_CHECK([fgrep "tesselated volume area is 16.4016 angstrom^3" stdout], 0, [ignore], [ignore])
#AT_CLEANUP