tests for various gv files

tests/0028_GVVariations/README.md

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+# 0028_GVVariations
+
+tests various variations in graphviz files that represent valid networks for sbmodelr.
+
+## tests
+
+- cps file reads well
+- -o option works well
+- gv file reads well
+- test gv file with attributes on nodes and edges

tests/0028_GVVariations/run.sh

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+#!/bin/bash
+
+# work out our folder name
+test=${PWD##*/}          # to assign to a variable
+test=${test:-/}          # to correct for the case where PWD=/
+
+fail=0
+
+# undirected, 2 nodes with labels, etc.
+../../sbmodelr -t G -o t.cps -n ../sources/test08_2.gv ../sources/GeneExpressionUnit.cps 3 > output
+
+if ! grep -q "created new model t.cps with a set of 3 replicas of ../sources/GeneExpressionUnit.cps" output; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = 1"
+elif grep -q "Warning" output; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = 1"
+elif grep -q "Error" output; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = 1"
+fi
+
+# create model summary
+../model_report.py t.cps >/dev/null
+if ! [[ $? = 0 ]]; then
+  printf 'FAIL %s\n' "${test}"
+  exit -1
+fi
+
+# check that there is only 1 transport reaction
+n=$(grep -Pc "^t_G_[123]-[123]\s+G_[123] = G_[123]" t.summary.txt)
+if ((n != 1))  ; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = 1"
+fi
+
+# directed, 6 nodes with labels, etc.
+../../sbmodelr -g G --ignore-compartments -o t22.cps -n ../sources/test22_6.gv ../sources/GeneExpressionUnit.cps 6 > output
+
+if ! grep -q "created new model t22.cps with a set of 6 replicas of ../sources/GeneExpressionUnit.cps" output; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = $fail + 2"
+elif grep -q "Warning" output; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = $fail + 2"
+elif grep -q "Error" output; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = $fail + 2"
+fi
+
+# create model summary
+../model_report.py t22.cps >/dev/null
+if ! [[ $? = 0 ]]; then
+  printf 'FAIL %s\n' "${test}"
+  exit -1
+fi
+
+# check that there are exactly 4 regulated synthesis reactions
+n=$(grep -Pc "^synthesis G_(\d)\s+\-\>\s+G_\1;\s+G_\d" t22.summary.txt)
+if ((n != 4))  ; then
+  printf 'FAIL %s\n' "${test}"
+  if [[ $fail -lt 2 ]]; then
+   let "fail = $fail + 2"
+  fi
+fi
+
+# directed, 16 nodes with labels, landscape orientation etc.
+../../sbmodelr -g G --ignore-compartments -o t16.cps -n ../sources/test16_12.gv ../sources/GeneExpressionUnit.cps 12 > output
+
+if ! grep -q "created new model t16.cps with a set of 12 replicas of ../sources/GeneExpressionUnit.cps" output; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = $fail + 4"
+elif grep -q "Warning" output; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = $fail + 4"
+elif grep -q "Error" output; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = $fail + 4"
+fi
+
+# create model summary
+../model_report.py t16.cps >/dev/null
+if ! [[ $? = 0 ]]; then
+  printf 'FAIL %s\n' "${test}"
+  exit -1
+fi
+
+# check that there are exactly 11 regulated synthesis reactions
+n=$(grep -Pc "^synthesis G_(\d+)\s+\-\>\s+G_\1;\s+G_\d+" t16.summary.txt)
+if ((n != 11))  ; then
+  printf 'FAIL %s\n' "${test}"
+  if [[ $fail -lt 4 ]]; then
+   let "fail = $fail + 4"
+  fi
+fi
+
+# directed, 15 nodes with labels, landscape orientation etc.
+../../sbmodelr -g G --ignore-compartments -o t15.cps -n ../sources/test15_11.gv ../sources/GeneExpressionUnit.cps 11 > output
+
+if ! grep -q "created new model t15.cps with a set of 11 replicas of ../sources/GeneExpressionUnit.cps" output; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = $fail + 8"
+elif grep -q "Warning" output; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = $fail + 8"
+elif grep -q "Error" output; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = $fail + 8"
+fi
+
+# create model summary
+../model_report.py t15.cps >/dev/null
+if ! [[ $? = 0 ]]; then
+  printf 'FAIL %s\n' "${test}"
+  exit -1
+fi
+
+# check that there are exactly 11 regulated synthesis reactions
+n=$(grep -Pc "^synthesis G_(\d+)\s+\-\>\s+G_\1;\s+G_\d+" t15.summary.txt)
+if ((n != 11))  ; then
+  printf 'FAIL %s\n' "${test}"
+  if [[ $fail -lt 8 ]]; then
+   let "fail = $fail + 8"
+  fi
+fi
+
+# check that there are exactly 10 reactions with regulated_by_2 kinetics
+n=$(grep -Pc "^synthesis G_(\d+)\s+\-\>\s+G_\1.*regulated_by_2" t15.summary.txt)
+if ((n != 10))  ; then
+  printf 'FAIL %s\n' "${test}"
+  if [[ $fail -lt 8 ]]; then
+   let "fail = $fail + 8"
+  fi
+fi
+
+# check that there is exactly 1 reactions with regulated_by_5 kinetics
+n=$(grep -Pc "^synthesis G_(\d+)\s+\-\>\s+G_\1.*regulated_by_5" t15.summary.txt)
+if ((n != 1))  ; then
+  printf 'FAIL %s\n' "${test}"
+  if [[ $fail -lt 8 ]]; then
+   let "fail = $fail + 8"
+  fi
+fi
+
+
+if [ "$fail" = 0 ] ; then
+  printf 'PASS %s\n' "${test}"
+  rm *.summary.txt output *.cps
+fi
+
+exit $fail