From cdb30491b8c9781fb53cea4fdc4f316a9a53015b Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Mon, 13 Aug 2018 15:10:27 +0200
Subject: [PATCH] Ensure that RuleBasedProcessor is never created with a
None/NULL library.
---
modules/conop/doc/compoundlib.rst | 2 +-
modules/conop/src/rule_based.cc | 10 +++++--
modules/conop/src/rule_based.hh | 14 ++++++++--
modules/conop/tests/test_rule_based_conop.cc | 29 +++++++++++++++-----
4 files changed, 41 insertions(+), 14 deletions(-)
diff --git a/modules/conop/doc/compoundlib.rst b/modules/conop/doc/compoundlib.rst
index caca8445b..41f859e7a 100644
--- a/modules/conop/doc/compoundlib.rst
+++ b/modules/conop/doc/compoundlib.rst
@@ -45,7 +45,7 @@ build the compound library manually.
write mode, the programs can deadlock.
:type readonly: :class:`bool`
- :returns: The loaded compound lib
+ :returns: The loaded compound lib or None if it failed.
.. staticmethod:: Create(database)
diff --git a/modules/conop/src/rule_based.cc b/modules/conop/src/rule_based.cc
index 6e8b712fe..fe2013e25 100644
--- a/modules/conop/src/rule_based.cc
+++ b/modules/conop/src/rule_based.cc
@@ -19,6 +19,7 @@
#include <limits>
#include <ost/log.hh>
#include <ost/profile.hh>
+#include <ost/message.hh>
#include <ost/mol/xcs_editor.hh>
#include <ost/mol/bond_handle.hh>
#include <ost/mol/torsion_handle.hh>
@@ -30,8 +31,6 @@
namespace ost { namespace conop {
-
-
void RuleBasedProcessor::DoProcess(DiagnosticsPtr diags,
mol::EntityHandle ent) const
{
@@ -199,6 +198,11 @@ String RuleBasedProcessor::ToString() const {
return ss.str();
}
-
+void RuleBasedProcessor::_CheckLib() const {
+ if (!lib_) {
+ throw Error("Cannot initialize RuleBasedProcessor without a valid "
+ "CompoundLib object!");
+ }
+}
}}
diff --git a/modules/conop/src/rule_based.hh b/modules/conop/src/rule_based.hh
index 3b91771a2..719ba7803 100644
--- a/modules/conop/src/rule_based.hh
+++ b/modules/conop/src/rule_based.hh
@@ -40,13 +40,19 @@ public:
lib_(compound_lib), fix_element_(true), strict_hydrogens_(false),
unk_res_treatment_(CONOP_WARN), unk_atom_treatment_(CONOP_WARN)
{
+ _CheckLib();
}
- RuleBasedProcessor(CompoundLibPtr compound_lib, bool fe, bool sh, ConopAction ur,
- ConopAction ua, bool bf, bool at, bool cn, bool aa, ConopAction zo):
+ RuleBasedProcessor(CompoundLibPtr compound_lib, bool fe, bool sh,
+ ConopAction ur, ConopAction ua, bool bf, bool at, bool cn,
+ bool aa, ConopAction zo):
Processor(bf, at, cn, aa, zo), lib_(compound_lib), fix_element_(fe),
strict_hydrogens_(sh), unk_res_treatment_(ur),
- unk_atom_treatment_(ua) {}
+ unk_atom_treatment_(ua)
+ {
+ _CheckLib();
+ }
+
ConopAction GetUnkResidueTreatment() const {
return unk_res_treatment_;
}
@@ -91,6 +97,8 @@ protected:
virtual void DoProcess(DiagnosticsPtr diags,
mol::EntityHandle ent) const;
private:
+ void _CheckLib() const;
+
CompoundLibPtr lib_;
bool fix_element_;
bool strict_hydrogens_;
diff --git a/modules/conop/tests/test_rule_based_conop.cc b/modules/conop/tests/test_rule_based_conop.cc
index 6444695d9..1ce4ebe24 100644
--- a/modules/conop/tests/test_rule_based_conop.cc
+++ b/modules/conop/tests/test_rule_based_conop.cc
@@ -50,9 +50,24 @@ CompoundLibPtr load_lib()
BOOST_AUTO_TEST_SUITE(conop);
+BOOST_AUTO_TEST_CASE(rule_based_init_check)
+{
+ CompoundLibPtr lib; // null ptr is return value when library loading failed
+ BOOST_CHECK_THROW(RuleBasedProcessor rbc1(lib), ost::Error);
+ BOOST_CHECK_THROW(RuleBasedProcessor rbc2(lib, true, false, CONOP_WARN,
+ CONOP_WARN, false, true, true, true,
+ CONOP_WARN), ost::Error);
+ lib = load_lib();
+ if (!lib) { return; }
+ BOOST_CHECK_NO_THROW(RuleBasedProcessor rbc3(lib));
+ BOOST_CHECK_NO_THROW(RuleBasedProcessor rbc4(lib, true, false, CONOP_WARN,
+ CONOP_WARN, false, true, true,
+ true, CONOP_WARN));
+}
+
BOOST_AUTO_TEST_CASE(rule_based_set_get_flags)
{
- CompoundLibPtr lib=load_lib();
+ CompoundLibPtr lib = load_lib();
if (!lib) { return; }
RuleBasedProcessor rbc(lib);
// check the defaults
@@ -76,7 +91,7 @@ BOOST_AUTO_TEST_CASE(rule_based_set_get_flags)
BOOST_AUTO_TEST_CASE(rule_based_connect)
{
- CompoundLibPtr lib=load_lib();
+ CompoundLibPtr lib = load_lib();
if (!lib) { return; }
RuleBasedProcessor rbc(lib);
EntityHandle ent = CreateEntity();
@@ -94,7 +109,7 @@ BOOST_AUTO_TEST_CASE(rule_based_connect)
BOOST_AUTO_TEST_CASE(rule_based_unk_atoms)
{
- CompoundLibPtr lib = load_lib();
+ CompoundLibPtr lib = load_lib();
if (!lib) { return; }
RuleBasedProcessor rbc(lib);
EntityHandle ent = CreateEntity();
@@ -125,7 +140,7 @@ BOOST_AUTO_TEST_CASE(rule_based_unk_atoms)
BOOST_AUTO_TEST_CASE(guesses_elements_of_unknown_atoms)
{
- CompoundLibPtr lib = load_lib();
+ CompoundLibPtr lib = load_lib();
if (!lib) { return; }
RuleBasedProcessor rbc(lib);
EntityHandle ent = CreateEntity();
@@ -142,7 +157,7 @@ BOOST_AUTO_TEST_CASE(guesses_elements_of_unknown_atoms)
BOOST_AUTO_TEST_CASE(fills_properties_of_unknown_residues)
{
- CompoundLibPtr lib = load_lib();
+ CompoundLibPtr lib = load_lib();
if (!lib) { return; }
RuleBasedProcessor rbc(lib);
EntityHandle ent = CreateEntity();
@@ -160,7 +175,7 @@ BOOST_AUTO_TEST_CASE(fills_properties_of_unknown_residues)
BOOST_AUTO_TEST_CASE(connects_atoms_of_unknown_residues_based_on_distance)
{
- CompoundLibPtr lib = load_lib();
+ CompoundLibPtr lib = load_lib();
if (!lib) { return; }
RuleBasedProcessor rbc(lib);
EntityHandle ent = CreateEntity();
@@ -177,7 +192,7 @@ BOOST_AUTO_TEST_CASE(connects_atoms_of_unknown_residues_based_on_distance)
BOOST_AUTO_TEST_CASE(rule_based_unk_res)
{
- CompoundLibPtr lib = load_lib();
+ CompoundLibPtr lib = load_lib();
if (!lib) { return; }
RuleBasedProcessor rbc(lib);
EntityHandle ent = CreateEntity();
--
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