From 9169bbc879b11b55610c417cacb8008eba6cf844 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavalias-github@xavier.robin.name>
Date: Mon, 5 Feb 2024 10:15:23 +0100
Subject: [PATCH] refactor: make error messages more pythonic and consistent
---
modules/io/src/mol/pdb_reader.cc | 4 +++-
modules/io/src/mol/pdb_writer.cc | 4 +++-
modules/io/src/mol/sdf_reader.cc | 4 +++-
modules/io/src/mol/sdf_writer.cc | 30 +++++++++++++++++++++++++-----
modules/io/src/mol/sdf_writer.hh | 1 +
modules/io/src/mol/star_parser.cc | 6 +++---
modules/io/src/mol/star_writer.cc | 14 ++++++--------
7 files changed, 44 insertions(+), 19 deletions(-)
diff --git a/modules/io/src/mol/pdb_reader.cc b/modules/io/src/mol/pdb_reader.cc
index 5b047c3aa..78b6bec4d 100644
--- a/modules/io/src/mol/pdb_reader.cc
+++ b/modules/io/src/mol/pdb_reader.cc
@@ -92,7 +92,9 @@ void PDBReader::Init(const boost::filesystem::path& loc)
in_.push(boost::iostreams::gzip_decompressor());
}
in_.push(instream_);
- if(!infile_) throw IOException("could not open "+loc.string());
+ if(!infile_) throw IOException("[Errno " + std::to_string(errno) + "] " +
+ std::string(strerror(errno)) +
+ ": '" + loc.string() + "'");
line_num_=0;
if(boost::iequals(boost::filesystem::extension(loc), ".pqr")) {
is_pqr_=true;
diff --git a/modules/io/src/mol/pdb_writer.cc b/modules/io/src/mol/pdb_writer.cc
index d4461402c..265a8a024 100644
--- a/modules/io/src/mol/pdb_writer.cc
+++ b/modules/io/src/mol/pdb_writer.cc
@@ -407,7 +407,9 @@ PDBWriter::PDBWriter(const String& filename, const IOProfile& profile):
is_pqr_(false), profile_(profile), filename_(filename)
{
if (!outfile_.is_open()) {
- throw IOException("Failed to open: " + filename);
+ throw IOException("[Errno " + std::to_string(errno) + "] " +
+ std::string(strerror(errno)) +
+ ": '" + filename + "'");
}
if (boost::iequals(".pqr", boost::filesystem::extension(filename))) {
is_pqr_=true;
diff --git a/modules/io/src/mol/sdf_reader.cc b/modules/io/src/mol/sdf_reader.cc
index 660a9dcb5..76c7091a2 100644
--- a/modules/io/src/mol/sdf_reader.cc
+++ b/modules/io/src/mol/sdf_reader.cc
@@ -124,7 +124,9 @@ void SDFReader::ClearState(const boost::filesystem::path& loc)
in_.push(boost::iostreams::gzip_decompressor());
}
in_.push(instream_);
- if(!infile_) throw IOException("could not open "+loc.string());
+ if(!infile_) throw IOException("[Errno " + std::to_string(errno) + "] " +
+ std::string(strerror(errno)) +
+ ": '" + loc.string() + "'");
curr_chain_=mol::ChainHandle();
curr_residue_=mol::ResidueHandle();
chain_count_=0;
diff --git a/modules/io/src/mol/sdf_writer.cc b/modules/io/src/mol/sdf_writer.cc
index c0241211a..e9fd0ded4 100644
--- a/modules/io/src/mol/sdf_writer.cc
+++ b/modules/io/src/mol/sdf_writer.cc
@@ -171,28 +171,48 @@ namespace {
}
SDFWriter::SDFWriter(std::ostream& ostream)
- : outfile_(), ostr_(ostream), counter_(0), atom_indices_() {
+ : outfile_(), ostr_(ostream), counter_(0), atom_indices_(), filename_("") {
}
SDFWriter::SDFWriter(const String& filename)
- : outfile_(filename.c_str()), ostr_(outfile_), counter_(0), atom_indices_() {
+ : outfile_(filename.c_str()), ostr_(outfile_), counter_(0), atom_indices_(),
+ filename_(filename){
}
SDFWriter::SDFWriter(const boost::filesystem::path& filename):
outfile_(BFPathToString(filename).c_str()),
- ostr_(outfile_), counter_(0), atom_indices_() {}
+ ostr_(outfile_), counter_(0), atom_indices_(), filename_("") {}
void SDFWriter::Write(const mol::EntityView& ent) {
if (!ostr_) {
- throw IOException("Can't write SDF file. Bad output stream");
+ if (!filename_.empty()) {
+ throw IOException("[Errno " + std::to_string(errno) + "] " +
+ std::string(strerror(errno)) +
+ ": '" + filename_ + "'");
+ }
+ else {
+ throw IOException("[Errno " + std::to_string(errno) + "] " +
+ std::string(strerror(errno)) +
+ ": <stream>");
+ }
}
+
mol::EntityView non_const_view = ent;
non_const_view.Apply(*this);
}
void SDFWriter::Write(const mol::EntityHandle& ent) {
if (!ostr_) {
- throw IOException("Can't write SDF file. Bad output stream");
+ if (!filename_.empty()) {
+ throw IOException("[Errno " + std::to_string(errno) + "] " +
+ std::string(strerror(errno)) +
+ ": '" + filename_ + "'");
+ }
+ else {
+ throw IOException("[Errno " + std::to_string(errno) + "] " +
+ std::string(strerror(errno)) +
+ ": <stream>");
+ }
}
mol::EntityView non_const_view = ent.CreateFullView();
non_const_view.Apply(*this);
diff --git a/modules/io/src/mol/sdf_writer.hh b/modules/io/src/mol/sdf_writer.hh
index 8ca166d97..929be1d35 100644
--- a/modules/io/src/mol/sdf_writer.hh
+++ b/modules/io/src/mol/sdf_writer.hh
@@ -54,6 +54,7 @@ private:
std::ostream& ostr_;
int counter_;
std::map<long,int> atom_indices_;
+ String filename_;
};
}}
diff --git a/modules/io/src/mol/star_parser.cc b/modules/io/src/mol/star_parser.cc
index f22857a8f..c16bc2483 100644
--- a/modules/io/src/mol/star_parser.cc
+++ b/modules/io/src/mol/star_parser.cc
@@ -549,9 +549,9 @@ void StarParser::ParseGlobal()
void StarParser::Parse()
{
if (!file_open_) {
- throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
- "Failed to open file '" +
- filename_ + "'!"));
+ throw IOException("[Errno " + std::to_string(errno) + "] " +
+ std::string(strerror(errno)) +
+ ": '" + filename_ + "'");
}
StringRef line;
std::stringstream ss;
diff --git a/modules/io/src/mol/star_writer.cc b/modules/io/src/mol/star_writer.cc
index 4b64bd370..73ff08f94 100644
--- a/modules/io/src/mol/star_writer.cc
+++ b/modules/io/src/mol/star_writer.cc
@@ -27,10 +27,9 @@ namespace ost{ namespace io{
void StarWriter::Write(const String& data_name, std::ostream& stream) {
if(!stream) {
- std::stringstream ss;
- ss << "Cannot open stream: [Errno " << errno << "] "
- << strerror(errno) << std::endl;
- throw IOException(ss.str());
+ throw IOException("[Errno " + std::to_string(errno) + "] " +
+ std::string(strerror(errno)) +
+ ": <stream>");
}
// write data header
stream << "data_" << data_name << std::endl;
@@ -45,10 +44,9 @@ void StarWriter::Write(const String& data_name, std::ostream& stream) {
void StarWriter::Write(const String& data_name, const String& filename) {
std::ofstream fstream(filename.c_str());
if (!fstream) {
- std::stringstream ss;
- ss << "Cannot open " << filename << ": [Errno " << errno << "] "
- << strerror(errno) << std::endl;
- throw IOException(ss.str());
+ throw IOException("[Errno " + std::to_string(errno) + "] " +
+ std::string(strerror(errno)) +
+ ": '" + filename + "'");
}
boost::iostreams::filtering_stream<boost::iostreams::output> stream;
if (boost::iequals(".gz", boost::filesystem::extension(filename))) {
--
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