From 6a9ac69d047bf18d91486666da0f6ce89ef438e0 Mon Sep 17 00:00:00 2001
From: Pedro Mendes <mendes@copasi.org>
Date: Thu, 23 May 2024 21:17:59 -0400
Subject: [PATCH] tests a 100 gene network

---
 tests/0024_GRNCoopSW8_001/README.md |  2 +-
 tests/0024_GRNCoopSW8_001/run.sh    | 33 +++++++++++++++++++----------
 2 files changed, 23 insertions(+), 12 deletions(-)

diff --git a/tests/0024_GRNCoopSW8_001/README.md b/tests/0024_GRNCoopSW8_001/README.md
index 94c19af..ab3fffd 100644
--- a/tests/0024_GRNCoopSW8_001/README.md
+++ b/tests/0024_GRNCoopSW8_001/README.md
@@ -8,8 +8,8 @@ a gene regulatory network of 100 genes connected according to a small-world topo
 - cps file reads well
 - network file reads well
 - named output file
+- checks the regulated_by_2 rate law was created
 
-- checks the regulated_by_1 rate law was created
 - checks that there are exactly 3 species
 - checks that noise worked
 - checks no compartments created
diff --git a/tests/0024_GRNCoopSW8_001/run.sh b/tests/0024_GRNCoopSW8_001/run.sh
index 3c5a7ca..0be6e32 100755
--- a/tests/0024_GRNCoopSW8_001/run.sh
+++ b/tests/0024_GRNCoopSW8_001/run.sh
@@ -36,32 +36,43 @@ if ((n != 100)); then
   let "fail = $fail + 4"
 fi
 
-exit $fail
-
-# check that min and max of initial concentrations are different (meaning noise worked!)
-n=$(grep -Po "^G_[123]\s+reactions\s+([0-9]+\.[0-9]+\s)" repressilator.summary.txt | awk '(NR==1){Min=$3;Max=$3};(NR>=2){if(Min>$3) Min=$3;if(Max<$3) Max=$3} END {if(Min<Max) {print 0} else {print 1}}')
+# check that min and max of a_synth_G_i-j are within bounds
+n=$(grep -Po "^a_synth_G_\d+-\d+\s+fixed\s+(.[0-9]+\.[0-9]+\s)" CoopSW8_001.summary.txt | awk '(NR==1){Min=$3;Max=$3};(NR>=2){if(Min>$3) Min=$3;if(Max<$3) Max=$3} END {if(Min<-1.0 || Max>1.0) {print 1} else {print 0} }')
 if ((n != 0)) ; then
   printf 'FAIL %s\n' "${test}"
   let "fail = $fail + 8"
 fi
 
-# check that no new compartments were created
-n=$(grep -Pc "^cell_[123]\s+fixed" repressilator.summary.txt)
-if ((n != 0))  ; then
+# check that min and max of h_synth_G_i-j are within bounds
+n=$(grep -Po "^h_synth_G_\d+-\d+\s+fixed\s+(.[0-9]+\.[0-9]+\s)" CoopSW8_001.summary.txt | awk '(NR==1){Min=$3;Max=$3};(NR>=2){if(Min>$3) Min=$3;if(Max<$3) Max=$3} END {if(Min<1.0 || Max>10.0) {print 1} else {print 0} }')
+if ((n != 0)) ; then
   printf 'FAIL %s\n' "${test}"
   let "fail = $fail + 16"
 fi
 
-# checks that there are three synthesis reactions
-n=$(grep -Pc "synthesis (G_[123])\s+-> \1\;\s+G_[123]\s+regulated_by_1" repressilator.summary.txt)
-if ((n != 3))  ; then
+# check that V_synth_G_i-j is positive
+n=$(grep -Po "^V_synth_G_\d+\s+fixed\s+(.[0-9]+\.[0-9]+\s)" CoopSW8_001.summary.txt | awk '(NR==1){Min=$3};(NR>=2){if(Min>$3) Min=$3} END {if(Min<0.0) {print 1} else {print 0} }')
+if ((n != 0)) ; then
   printf 'FAIL %s\n' "${test}"
   let "fail = $fail + 32"
 fi
 
+# are there 300 reactions ?
+if ! grep -Pq "Reactions\: 300 =" CoopSW8_001.summary.txt ; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = $fail + 64"
+fi
+
+# check that no new compartments were created
+n=$(grep -Pc "^cell_[123]\s+fixed" CoopSW8_001.summary.txt)
+if ((n != 0))  ; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = $fail + 128"
+fi
+
 if [ "$fail" = 0 ] ; then
   printf 'PASS %s\n' "${test}"
-  rm repressilator.summary.txt output *.cps
+  rm CoopSW8_001.summary.txt output *.cps
 fi
 
 exit $fail