tests various gv files with problems

tests/0503_GvIssues/README.md

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+# 0503_GvIssues
+
+tests various graphviz network files that should raise warnings or errors
+
+## tests
+
+- 1D, network, transport
+- appropriate warning for an empty network file
+- appropriate warning for a network file without edges
+- appropriate warning for test a network file with repeated edges
+- ensure that repeated edges are added exactly once to model
+- appropriate warning for a network file with non-numeric nodes

tests/0503_GvIssues/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
+
+# test an empty network file
+../../sbmodelr -t G -n ../sources/empty.gv -o t.cps ../sources/GeneExpressionUnit.cps 2 > output
+
+# check that the correct warning is issued
+if ! grep -q " Warning: ../sources/empty.gv did not contain any valid edges, no connections added" output; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = 1"
+fi
+
+# test a network file without edges
+../../sbmodelr -t G -n ../sources/no-edges.gv -o t.cps ../sources/GeneExpressionUnit.cps 2 > output
+
+# check that the correct warning is issued
+if ! grep -q " Warning: ../sources/no-edges.gv did not contain any valid edges, no connections added" output; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = $fail + 2"
+fi
+
+# test a network file with repeated edges
+../../sbmodelr -t G -n ../sources/duplicates.gv -o t.cps ../sources/GeneExpressionUnit.cps 4 > output
+
+# check that the correct warning is issued
+if ! grep -q " Warning: duplicate entry for connection 1 to 3, ignored" output; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = $fail + 4"
+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 exactly one transport reaction 1->3 (the duplicate)
+n=$(grep -Pc "^t_G_1-3\s+G_1 = G_3\s+Mass action" t.summary.txt )
+if ((n != 1))  ; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = $fail + 8"
+fi
+
+# test a network file with non-numeric nodes
+../../sbmodelr -t G -n ../sources/non-numeric-nodes.gv -o t.cps ../sources/GeneExpressionUnit.cps 3 > output
+
+# check that the correct warning is issued
+if ! grep -q " Warning: ../sources/non-numeric-nodes.gv did not contain any valid edges, no connections added" output; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = $fail + 16"
+fi
+
+if [ "$fail" = 0 ] ; then
+  printf 'PASS %s\n' "${test}"
+  rm t.summary.txt output *.cps
+fi
+
+exit $fail