From 6be3ccd951033a3dfc2ea461b5eafa4293130df0 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Tue, 23 Jul 2024 14:28:03 +0200
Subject: [PATCH] fix: exit with error code if nothing was read
---
modules/conop/src/chemdict_tool.cc | 5 +++++
modules/io/src/mol/chemdict_parser.cc | 1 +
modules/io/src/mol/chemdict_parser.hh | 10 +++++++++-
3 files changed, 15 insertions(+), 1 deletion(-)
diff --git a/modules/conop/src/chemdict_tool.cc b/modules/conop/src/chemdict_tool.cc
index 89499b698..9ca3729ca 100644
--- a/modules/conop/src/chemdict_tool.cc
+++ b/modules/conop/src/chemdict_tool.cc
@@ -116,6 +116,11 @@ int main(int argc, char const *argv[])
compound_lib.reset();
cdp.SetCompoundLib(in_mem_lib);
cdp.Parse();
+ if (cdp.GetImportedCount() == 0)
+ {
+ std::cout << "No compound imported from " << argv[2] << std::endl;
+ return 1;
+ }
in_mem_lib->SetChemLibInfo();
conop::CompoundLibPtr copy = in_mem_lib->Copy(argv[3]);
if (! copy) {
diff --git a/modules/io/src/mol/chemdict_parser.cc b/modules/io/src/mol/chemdict_parser.cc
index 3f97a49b5..f1b2610ad 100644
--- a/modules/io/src/mol/chemdict_parser.cc
+++ b/modules/io/src/mol/chemdict_parser.cc
@@ -215,6 +215,7 @@ void ChemdictParser::OnEndData()
}
}
lib_->AddCompound(compound_);
+ ++imported_count_;
}
}
}
diff --git a/modules/io/src/mol/chemdict_parser.hh b/modules/io/src/mol/chemdict_parser.hh
index 46a83ec3b..fe4981c11 100644
--- a/modules/io/src/mol/chemdict_parser.hh
+++ b/modules/io/src/mol/chemdict_parser.hh
@@ -44,7 +44,8 @@ public:
bool ignore_reserved=false, bool ignore_obsolete=false):
StarParser(stream), compound_(new conop::Compound("UNK")),
last_(0), loop_type_(DONT_KNOW), dialect_(dialect),
- ignore_reserved_(ignore_reserved), ignore_obsolete_(ignore_obsolete)
+ ignore_reserved_(ignore_reserved), ignore_obsolete_(ignore_obsolete),
+ imported_count_(0)
{
this->InitTypeMap();
this->InitPDBXTypeMap();
@@ -65,6 +66,12 @@ public:
{
lib_=lib;
}
+
+ /// \brief Get the number of compounds that were successfully parsed
+ int GetImportedCount()
+ {
+ return imported_count_;
+ }
private:
void InitTypeMap();
void InitPDBXTypeMap();
@@ -98,6 +105,7 @@ private:
conop::Compound::Dialect dialect_;
bool ignore_reserved_;
bool ignore_obsolete_;
+ int imported_count_;
};
--
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