From 2c7a6a7a64bf6ce5920dff2446ffb9a21cac02ef Mon Sep 17 00:00:00 2001
From: Marco Biasini <marco.biasini@unibas.ch>
Date: Tue, 12 Jul 2011 15:35:22 +0200
Subject: [PATCH] introduce FormatDiagnostic routine
---
modules/io/src/mol/star_parser.cc | 45 +++++++++++++++++++++++-----
modules/io/src/mol/star_parser.hh | 16 +++++++++-
modules/io/tests/test_star_parser.cc | 28 +++++++++++++++++
3 files changed, 81 insertions(+), 8 deletions(-)
diff --git a/modules/io/src/mol/star_parser.cc b/modules/io/src/mol/star_parser.cc
index d21d00278..b440181c9 100644
--- a/modules/io/src/mol/star_parser.cc
+++ b/modules/io/src/mol/star_parser.cc
@@ -28,12 +28,45 @@
namespace ost { namespace io {
StarParser::StarParser(std::istream& stream, bool items_as_row):
- stream_(stream), line_num_(0), has_current_line_(false), current_line_(),
+ stream_(stream), filename_("<stream>"), line_num_(0),
+ has_current_line_(false), current_line_(),
+ items_row_header_(), items_row_columns_(),
+ items_row_values_()
+{
+ items_as_row_ = items_as_row;
+}
+
+StarParser::StarParser(const String& filename, bool items_as_row):
+ fstream_(filename.c_str()), stream_(fstream_), filename_(filename),
+ line_num_(0), has_current_line_(false), current_line_(),
items_row_header_(), items_row_columns_(), items_row_values_()
{
items_as_row_ = items_as_row;
}
+String StarParser::FormatDiagnostic(StarDiagType type, const String& message,
+ int line)
+{
+ std::stringstream ss;
+ ss << filename_ << ":";
+ if (line!=-1) {
+ ss << line << ": ";
+ } else {
+ ss << " ";
+ }
+ switch (type) {
+ case STAR_DIAG_ERROR:
+ ss << "error: ";
+ break;
+ case STAR_DIAG_WARNING:
+ ss << "warning: ";
+ break;
+ }
+ ss << message;
+ return ss.str();
+}
+
+
bool StarParser::SplitLine(const StringRef& line,
std::vector<StringRef>& parts, bool clear)
{
@@ -363,10 +396,9 @@ void StarParser::DiagnoseUnknown()
StringRef line;
bool r=this->GetLine(line);
assert(r);r=r;
-
- ss << "unknown control structure '"<< line.rtrim() << "' on line "
- << line_num_ << "." << std::endl;
- throw IOException(ss.str());
+ ss << "unknown control structure '"<< line.rtrim() << "'";
+ throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR, ss.str(),
+ line_num_));
}
void StarParser::ParseGlobal()
@@ -400,8 +432,7 @@ void StarParser::Parse()
this->ConsumeLine();
break;
default:
- ss << "Missing 'data_' control structure." << std::endl;
- throw IOException(ss.str());
+ throw IOException("Missing 'data_' control structure");
break;
}
}
diff --git a/modules/io/src/mol/star_parser.hh b/modules/io/src/mol/star_parser.hh
index 47aa98b0e..e151e6c09 100644
--- a/modules/io/src/mol/star_parser.hh
+++ b/modules/io/src/mol/star_parser.hh
@@ -24,6 +24,7 @@
Author: Marco Biasini
*/
#include <iostream>
+#include <fstream>
#include <vector>
#include <map>
#include <ost/string_ref.hh>
@@ -31,6 +32,13 @@
namespace ost { namespace io {
+
+typedef enum {
+ STAR_DIAG_WARNING,
+ STAR_DIAG_ERROR
+} StarDiagType;
+
+
class DLLEXPORT_OST_IO StarDataItem {
public:
StarDataItem(const StringRef& category, const StringRef& name,
@@ -108,7 +116,7 @@ public:
/// header, values as row) and then parsed like a loop
/// (OnBeginLoop(), OnDataRow(), OnEndLoop())
explicit StarParser(std::istream& stream, bool items_as_row=false);
-
+ explicit StarParser(const String& filename, bool items_as_row=false);
virtual ~StarParser() { }
// callback interface
public:
@@ -139,6 +147,10 @@ public:
/// \brief called when leaving a datasection. Will only be invoked when
/// OnBeginData() returned true.
virtual void OnEndData() { }
+
+ /// \brief format diagnostic and returns it as a string.
+ String FormatDiagnostic(StarDiagType type, const String& message,
+ int line=-1);
public:
void Parse();
@@ -187,7 +199,9 @@ private:
void ParseDataItem();
void DiagnoseUnknown();
bool ParseMultilineValue(String& value, bool skip=false);
+ std::ifstream fstream_;
std::istream& stream_;
+ String filename_;
int line_num_;
bool has_current_line_;
String current_line_;
diff --git a/modules/io/tests/test_star_parser.cc b/modules/io/tests/test_star_parser.cc
index fc58a63b6..67a818fc2 100644
--- a/modules/io/tests/test_star_parser.cc
+++ b/modules/io/tests/test_star_parser.cc
@@ -37,6 +37,9 @@ class DataItemTestParser: public StarParser {
public:
DataItemTestParser(std::istream& stream): StarParser(stream)
{ }
+
+ DataItemTestParser(const String& filename): StarParser(filename)
+ { }
virtual void OnDataItem(const StarDataItem& item)
{
BOOST_CHECK_EQUAL(item.GetCategory().str(), "data-item");
@@ -242,6 +245,31 @@ BOOST_AUTO_TEST_CASE(star_data_item)
BOOST_CHECK_EQUAL(star_p.s4, "a'b");
}
+BOOST_AUTO_TEST_CASE(format_diag_stream)
+{
+ BOOST_MESSAGE(" Running star_data_item tests...");
+ std::ifstream s("testfiles/data-item.cif");
+ DataItemTestParser star_p(s);
+ BOOST_CHECK_EQUAL(star_p.FormatDiagnostic(STAR_DIAG_WARNING, "bad", -1),
+ "<stream>: warning: bad");
+ BOOST_CHECK_EQUAL(star_p.FormatDiagnostic(STAR_DIAG_ERROR, "really bad", -1),
+ "<stream>: error: really bad");
+ BOOST_CHECK_EQUAL(star_p.FormatDiagnostic(STAR_DIAG_ERROR, "bad", 55),
+ "<stream>:55: error: bad");
+}
+
+BOOST_AUTO_TEST_CASE(format_diag_filename)
+{
+ BOOST_MESSAGE(" Running star_data_item tests...");
+ DataItemTestParser star_p("testfiles/data-item.cif");
+ BOOST_CHECK_EQUAL(star_p.FormatDiagnostic(STAR_DIAG_WARNING, "bad", -1),
+ "testfiles/data-item.cif: warning: bad");
+ BOOST_CHECK_EQUAL(star_p.FormatDiagnostic(STAR_DIAG_ERROR, "really bad", -1),
+ "testfiles/data-item.cif: error: really bad");
+ BOOST_CHECK_EQUAL(star_p.FormatDiagnostic(STAR_DIAG_ERROR, "bad", 55),
+ "testfiles/data-item.cif:55: error: bad");
+}
+
BOOST_AUTO_TEST_CASE(star_multi)
{
std::ifstream s("testfiles/multi-data.cif");
--
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