Skip to content

L
libcifpp
Commit ff62efe7 by Maarten L. Hekkelman
Options

More tests

parent 24078771
Showing with 349 additions and 206 deletions
CMakeLists.txt
...@@ -197,6 +197,7 @@ set(project_sources ...@@ -197,6 +197,7 @@ set(project_sources
${PROJECT_SOURCE_DIR}/src/cif/condition.cpp ${PROJECT_SOURCE_DIR}/src/cif/condition.cpp
${PROJECT_SOURCE_DIR}/src/cif/datablock.cpp ${PROJECT_SOURCE_DIR}/src/cif/datablock.cpp
${PROJECT_SOURCE_DIR}/src/cif/dictionary_parser.cpp ${PROJECT_SOURCE_DIR}/src/cif/dictionary_parser.cpp
${PROJECT_SOURCE_DIR}/src/cif/file.cpp
${PROJECT_SOURCE_DIR}/src/cif/item.cpp ${PROJECT_SOURCE_DIR}/src/cif/item.cpp
${PROJECT_SOURCE_DIR}/src/cif/parser.cpp ${PROJECT_SOURCE_DIR}/src/cif/parser.cpp
${PROJECT_SOURCE_DIR}/src/cif/row.cpp ${PROJECT_SOURCE_DIR}/src/cif/row.cpp
......
include/cif++/cif/file.hpp
...@@ -26,8 +26,6 @@ ...@@ -26,8 +26,6 @@
#pragma once #pragma once
#include <cif++/cif/forward_decl.hpp>
#include <cif++/cif/datablock.hpp> #include <cif++/cif/datablock.hpp>
#include <cif++/cif/parser.hpp> #include <cif++/cif/parser.hpp>
...@@ -39,7 +37,6 @@ namespace cif::v2 ...@@ -39,7 +37,6 @@ namespace cif::v2
class file : public std::list<datablock> class file : public std::list<datablock>
{ {
public: public:
file() = default; file() = default;
file(std::istream &is) file(std::istream &is)
...@@ -52,126 +49,38 @@ class file : public std::list<datablock> ...@@ -52,126 +49,38 @@ class file : public std::list<datablock>
file &operator=(const file &) = default; file &operator=(const file &) = default;
file &operator=(file &&) = default; file &operator=(file &&) = default;
void set_validator(const validator *v) void set_validator(const validator *v);
{
m_validator = v;
for (auto &db : *this)
db.set_validator(v);
}
const validator *get_validator() const const validator *get_validator() const
{ {
return m_validator; return m_validator;
} }
bool is_valid() const bool is_valid() const;
{ bool is_valid();
if (m_validator == nullptr)
std::runtime_error("No validator loaded explicitly, cannot continue");
bool result = true;
for (auto &d : *this)
result = d.is_valid() and result;
return result;
}
bool is_valid()
{
if (m_validator == nullptr)
{
if (VERBOSE > 0)
std::cerr << "No dictionary loaded explicitly, loading default" << std::endl;
load_dictionary();
}
bool result = true;
for (auto &d : *this)
result = d.is_valid() and result;
return result; void load_dictionary();
} void load_dictionary(std::string_view name);
void load_dictionary()
{
load_dictionary("mmcif_ddl");
}
void load_dictionary(std::string_view name) datablock &operator[](std::string_view name);
{ const datablock &operator[](std::string_view name) const;
set_validator(&validator_factory::instance()[name]);
}
datablock &operator[](std::string_view name) std::tuple<iterator, bool> emplace(std::string_view name);
{
auto i = std::find_if(begin(), end(), [name](const datablock &c)
{ return iequals(c.name(), name); });
if (i != end())
return *i;
emplace_back(name);
return back();
}
const datablock &operator[](std::string_view name) const void load(const std::filesystem::path &p);
{ void load(std::istream &is);
static const datablock s_empty;
auto i = std::find_if(begin(), end(), [name](const datablock &c)
{ return iequals(c.name(), name); });
return i == end() ? s_empty : *i;
}
std::tuple<iterator, bool> emplace(std::string_view name) void save(const std::filesystem::path &p) const;
{ void save(std::ostream &os) const;
bool is_new = true;
auto i = begin();
while (i != end())
{
if (iequals(name, i->name()))
{
is_new = false;
if (i != begin())
{
auto n = std::next(i);
splice(begin(), *this, i, n);
}
break;
}
++i;
}
if (is_new)
{
auto &db = emplace_front(name);
db.set_validator(m_validator);
}
return std::make_tuple(begin(), is_new);
}
void load(std::istream &is) friend std::ostream &operator<<(std::ostream &os, const file &f)
{ {
auto saved = m_validator; f.save(os);
set_validator(nullptr); return os;
parser p(is, *this);
p.parse_file();
if (saved != nullptr)
{
set_validator(saved);
(void)is_valid();
}
} }
private: private:
const validator* m_validator = nullptr; const validator *m_validator = nullptr;
}; };
} } // namespace cif::v2
\ No newline at end of file \ No newline at end of file
include/cif++/cif/parser.hpp
...@@ -44,6 +44,8 @@ class parse_error : public std::runtime_error ...@@ -44,6 +44,8 @@ class parse_error : public std::runtime_error
// -------------------------------------------------------------------- // --------------------------------------------------------------------
// TODO: Need to implement support for transformed long lines
class sac_parser class sac_parser
{ {
public: public:
...@@ -228,6 +230,7 @@ class sac_parser ...@@ -228,6 +230,7 @@ class sac_parser
{ {
Start, Start,
White, White,
Esc,
Comment, Comment,
QuestionMark, QuestionMark,
Dot, Dot,
......
src/cif/category.cpp
...@@ -1626,7 +1626,7 @@ namespace detail ...@@ -1626,7 +1626,7 @@ namespace detail
if (value.find('\n') != std::string::npos or width == 0 or value.length() > 132) // write as text field if (value.find('\n') != std::string::npos or width == 0 or value.length() > 132) // write as text field
{ {
if (offset > 0) if (offset > 0)
os << std::endl; os << '\n';
os << ';'; os << ';';
char pc = 0; char pc = 0;
...@@ -1639,8 +1639,8 @@ namespace detail ...@@ -1639,8 +1639,8 @@ namespace detail
} }
if (value.back() != '\n') if (value.back() != '\n')
os << std::endl; os << '\n';
os << ';' << std::endl; os << ';' << '\n';
offset = 0; offset = 0;
} }
else if (sac_parser::is_unquoted_string(value)) else if (sac_parser::is_unquoted_string(value))
...@@ -1690,9 +1690,9 @@ namespace detail ...@@ -1690,9 +1690,9 @@ namespace detail
if (not done) if (not done)
{ {
if (offset > 0) if (offset > 0)
os << std::endl; os << '\n';
os << ';' << value << std::endl os << ';' << value << '\n'
<< ';' << std::endl; << ';' << '\n';
offset = 0; offset = 0;
} }
} }
...@@ -1749,14 +1749,14 @@ void category::write(std::ostream &os, const std::vector<uint16_t> &order, bool ...@@ -1749,14 +1749,14 @@ void category::write(std::ostream &os, const std::vector<uint16_t> &order, bool
if (needLoop) if (needLoop)
{ {
os << "loop_" << std::endl; os << "loop_" << '\n';
std::vector<size_t> columnWidths; std::vector<size_t> columnWidths;
for (auto cix : order) for (auto cix : order)
{ {
auto &col = m_columns[cix]; auto &col = m_columns[cix];
os << '_' << m_name << '.' << col.m_name << ' ' << std::endl; os << '_' << m_name << '.' << col.m_name << ' ' << '\n';
columnWidths.push_back(2); columnWidths.push_back(2);
} }
...@@ -1809,7 +1809,7 @@ void category::write(std::ostream &os, const std::vector<uint16_t> &order, bool ...@@ -1809,7 +1809,7 @@ void category::write(std::ostream &os, const std::vector<uint16_t> &order, bool
if (offset + l > 132 and offset > 0) if (offset + l > 132 and offset > 0)
{ {
os << std::endl; os << '\n';
offset = 0; offset = 0;
} }
...@@ -1817,13 +1817,13 @@ void category::write(std::ostream &os, const std::vector<uint16_t> &order, bool ...@@ -1817,13 +1817,13 @@ void category::write(std::ostream &os, const std::vector<uint16_t> &order, bool
if (offset > 132) if (offset > 132)
{ {
os << std::endl; os << '\n';
offset = 0; offset = 0;
} }
} }
if (offset > 0) if (offset > 0)
os << std::endl; os << '\n';
} }
} }
else else
...@@ -1863,16 +1863,16 @@ void category::write(std::ostream &os, const std::vector<uint16_t> &order, bool ...@@ -1863,16 +1863,16 @@ void category::write(std::ostream &os, const std::vector<uint16_t> &order, bool
size_t offset = l; size_t offset = l;
if (s.length() + l >= kMaxLineLength) if (s.length() + l >= kMaxLineLength)
{ {
os << std::endl; os << '\n';
offset = 0; offset = 0;
} }
if (detail::write_value(os, s, offset, 1) != 0) if (detail::write_value(os, s, offset, 1) != 0)
os << std::endl; os << '\n';
} }
} }
os << "# " << std::endl; os << "# " << '\n';
} }
} // namespace cif::v2 } // namespace cif::v2
\ No newline at end of file
src/cif/file.cpp 0 → 100644
/*-
* SPDX-License-Identifier: BSD-2-Clause
*
* Copyright (c) 2022 NKI/AVL, Netherlands Cancer Institute
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice, this
* list of conditions and the following disclaimer
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
* ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
#include <gzstream/gzstream.hpp>
#include <cif++/cif/file.hpp>
namespace cif::v2
{
// --------------------------------------------------------------------
void file::set_validator(const validator *v)
{
m_validator = v;
for (auto &db : *this)
db.set_validator(v);
}
bool file::is_valid() const
{
if (m_validator == nullptr)
std::runtime_error("No validator loaded explicitly, cannot continue");
bool result = true;
for (auto &d : *this)
result = d.is_valid() and result;
return result;
}
bool file::is_valid()
{
if (m_validator == nullptr)
{
if (VERBOSE > 0)
std::cerr << "No dictionary loaded explicitly, loading default" << std::endl;
load_dictionary();
}
bool result = true;
for (auto &d : *this)
result = d.is_valid() and result;
return result;
}
void file::load_dictionary()
{
load_dictionary("mmcif_ddl");
}
void file::load_dictionary(std::string_view name)
{
set_validator(&validator_factory::instance()[name]);
}
datablock &file::operator[](std::string_view name)
{
auto i = std::find_if(begin(), end(), [name](const datablock &c)
{ return iequals(c.name(), name); });
if (i != end())
return *i;
emplace_back(name);
return back();
}
const datablock &file::operator[](std::string_view name) const
{
static const datablock s_empty;
auto i = std::find_if(begin(), end(), [name](const datablock &c)
{ return iequals(c.name(), name); });
return i == end() ? s_empty : *i;
}
std::tuple<file::iterator, bool> file::emplace(std::string_view name)
{
bool is_new = true;
auto i = begin();
while (i != end())
{
if (iequals(name, i->name()))
{
is_new = false;
if (i != begin())
{
auto n = std::next(i);
splice(begin(), *this, i, n);
}
break;
}
++i;
}
if (is_new)
{
auto &db = emplace_front(name);
db.set_validator(m_validator);
}
return std::make_tuple(begin(), is_new);
}
void file::load(std::istream &is)
{
auto saved = m_validator;
set_validator(nullptr);
parser p(is, *this);
p.parse_file();
if (saved != nullptr)
{
set_validator(saved);
(void)is_valid();
}
}
void file::save(const std::filesystem::path &p) const
{
if (p.extension() == ".gz")
{
gzstream::ofstream outFile(p);
save(outFile);
}
else
{
std::ofstream outFile(p, std::ios_base::binary);
save(outFile);
}
}
void file::save(std::ostream &os) const
{
for (auto &db : *this)
db.write(os);
}
} // namespace cif::v2
\ No newline at end of file
src/cif/parser.cpp
...@@ -195,7 +195,7 @@ sac_parser::CIFToken sac_parser::get_next_token() ...@@ -195,7 +195,7 @@ sac_parser::CIFToken sac_parser::get_next_token()
else else
m_bol = (ch == '\n'); m_bol = (ch == '\n');
break; break;
case State::Comment: case State::Comment:
if (ch == '\n') if (ch == '\n')
{ {
...@@ -214,10 +214,17 @@ sac_parser::CIFToken sac_parser::get_next_token() ...@@ -214,10 +214,17 @@ sac_parser::CIFToken sac_parser::get_next_token()
state = State::TextField + 1; state = State::TextField + 1;
else if (ch == kEOF) else if (ch == kEOF)
error("unterminated textfield"); error("unterminated textfield");
// else if (ch == '\\')
// state = State::Esc;
else if (not is_any_print(ch)) else if (not is_any_print(ch))
warning("invalid character in text field '" + std::string({static_cast<char>(ch)}) + "' (" + std::to_string((int)ch) + ")"); warning("invalid character in text field '" + std::string({static_cast<char>(ch)}) + "' (" + std::to_string((int)ch) + ")");
break; break;
// case State::Esc:
// if (ch == '\n')
// break;
case State::TextField + 1: case State::TextField + 1:
if (is_text_lead(ch) or ch == ' ' or ch == '\t') if (is_text_lead(ch) or ch == ' ' or ch == '\t')
state = State::TextField; state = State::TextField;
......
test/unit-v2-test.cpp
...@@ -348,19 +348,18 @@ _test.name ...@@ -348,19 +348,18 @@ _test.name
++n; ++n;
} }
// for (auto r: test) auto n2 = test.erase(cif::v2::key("id") == 1, [](cif::v2::row_handle r)
// test.erase(r); {
BOOST_CHECK_EQUAL(r["id"].as<int>(), 1);
// BOOST_CHECK(test.empty()); BOOST_CHECK_EQUAL(r["name"].as<std::string>(), "aap"); });
// test.clear(); BOOST_CHECK_EQUAL(n2, 1);
// auto n = test.erase(cif::v2::key("id") == 1, [](const cif::Row &r) // for (auto r: test)
// { // test.erase(r);
// BOOST_CHECK_EQUAL(r["id"].as<int>(), 1);
// BOOST_CHECK_EQUAL(r["name"].as<std::string>(), "aap"); });
// BOOST_CHECK_EQUAL(n, 1); test.clear();
BOOST_CHECK(test.empty());
} }
// -------------------------------------------------------------------- // --------------------------------------------------------------------
...@@ -2002,96 +2001,150 @@ BOOST_AUTO_TEST_CASE(reading_file_1) ...@@ -2002,96 +2001,150 @@ BOOST_AUTO_TEST_CASE(reading_file_1)
BOOST_CHECK_THROW(file.load(is), std::runtime_error); BOOST_CHECK_THROW(file.load(is), std::runtime_error);
} }
// BOOST_AUTO_TEST_CASE(parser_test_1) BOOST_AUTO_TEST_CASE(parser_test_1)
// { {
// auto data1 = R"( auto data1 = R"(
// data_QM data_QM
// _test.text ?? _test.text ??
// )"_cf; )"_cf;
// auto &db1 = data1.front(); auto &db1 = data1.front();
// auto &test1 = db1["test"]; auto &test1 = db1["test"];
// BOOST_CHECK_EQUAL(test1.size(), 1); BOOST_CHECK_EQUAL(test1.size(), 1);
// for (auto r : test1) for (auto r : test1)
// { {
// const auto &[text] = r.get<std::string>({"text"}); const auto &[text] = r.get<std::string>({"text"});
// BOOST_CHECK_EQUAL(text, "??"); BOOST_CHECK_EQUAL(text, "??");
// } }
// std::stringstream ss; std::stringstream ss;
// data1.save(ss); data1.save(ss);
// auto data2 = cif::File(ss); auto data2 = cif::v2::file(ss);
// auto &db2 = data2.front(); auto &db2 = data2.front();
// auto &test2 = db2["test"]; auto &test2 = db2["test"];
// BOOST_CHECK_EQUAL(test2.size(), 1); BOOST_CHECK_EQUAL(test2.size(), 1);
// for (auto r : test2) for (auto r : test2)
// { {
// const auto &[text] = r.get<std::string>({"text"}); const auto &[text] = r.get<std::string>({"text"});
// BOOST_CHECK_EQUAL(text, "??"); BOOST_CHECK_EQUAL(text, "??");
// } }
// } }
// BOOST_AUTO_TEST_CASE(output_test_1) BOOST_AUTO_TEST_CASE(output_test_1)
// { {
// auto data1 = R"( auto data1 = R"(
// data_Q data_Q
// loop_ loop_
// _test.text _test.text
// "stop_the_crap" "stop_the_crap"
// 'and stop_ this too' 'and stop_ this too'
// 'data_dinges' 'data_dinges'
// 'blablaglobal_bla' 'blablaglobal_bla'
// boo.data_.whatever boo.data_.whatever
// )"_cf; )"_cf;
auto &db1 = data1.front();
auto &test1 = db1["test"];
struct T {
const char *s;
bool q;
} kS[] = {
{ "stop_the_crap", false },
{ "and stop_ this too", false },
{ "data_dinges", false },
{ "blablaglobal_bla", false },
{ "boo.data_.whatever", true }
};
// auto &db1 = data1.front(); BOOST_CHECK_EQUAL(test1.size(), sizeof(kS) / sizeof(T));
// auto &test1 = db1["test"];
// struct T { size_t i = 0;
// const char *s; for (auto r : test1)
// bool q; {
// } kS[] = { const auto &[text] = r.get<std::string>({"text"});
// { "stop_the_crap", false }, BOOST_CHECK_EQUAL(text, kS[i].s);
// { "and stop_ this too", false }, BOOST_CHECK_EQUAL(cif::v2::sac_parser::is_unquoted_string(kS[i].s), kS[i].q);
// { "data_dinges", false }, ++i;
// { "blablaglobal_bla", false }, }
// { "boo.data_.whatever", true }
// };
// BOOST_CHECK_EQUAL(test1.size(), sizeof(kS) / sizeof(T)); std::stringstream ss;
data1.save(ss);
// size_t i = 0; auto data2 = cif::v2::file(ss);
// for (auto r : test1)
// {
// const auto &[text] = r.get<std::string>({"text"});
// BOOST_CHECK_EQUAL(text, kS[i].s);
// BOOST_CHECK_EQUAL(cif::isUnquotedString(kS[i].s), kS[i].q);
// ++i;
// }
// std::stringstream ss; auto &db2 = data2.front();
// data1.save(ss); auto &test2 = db2["test"];
// auto data2 = cif::File(ss); BOOST_CHECK_EQUAL(test2.size(), sizeof(kS) / sizeof(T));
// auto &db2 = data2.front(); i = 0;
// auto &test2 = db2["test"]; for (auto r : test2)
{
const auto &[text] = r.get<std::string>({"text"});
BOOST_CHECK_EQUAL(text, kS[i++].s);
}
}
// BOOST_CHECK_EQUAL(test2.size(), sizeof(kS) / sizeof(T)); BOOST_AUTO_TEST_CASE(output_test_2)
{
auto data1 = R"(
data_Q
loop_
_test.text
;A very, very loooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooong line
;
;A line with a newline, look:
There it was!
;
)"_cf;
auto &db1 = data1.front();
auto &test1 = db1["test"];
struct T {
const char *s;
bool q;
} kS[] = {
{ "A very, very loooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooong line", false },
{ R"(A line with a newline, look:
There it was!)", false}
};
// i = 0; BOOST_CHECK_EQUAL(test1.size(), sizeof(kS) / sizeof(T));
// for (auto r : test2)
// { size_t i = 0;
// const auto &[text] = r.get<std::string>({"text"}); for (auto r : test1)
// BOOST_CHECK_EQUAL(text, kS[i++].s); {
// } const auto &[text] = r.get<std::string>({"text"});
// } BOOST_CHECK_EQUAL(text, kS[i].s);
BOOST_CHECK_EQUAL(cif::v2::sac_parser::is_unquoted_string(kS[i].s), kS[i].q);
++i;
}
std::stringstream ss;
data1.save(ss);
auto data2 = cif::v2::file(ss);
auto &db2 = data2.front();
auto &test2 = db2["test"];
BOOST_CHECK_EQUAL(test2.size(), sizeof(kS) / sizeof(T));
i = 0;
for (auto r : test2)
{
const auto &[text] = r.get<std::string>({"text"});
BOOST_CHECK_EQUAL(text, kS[i++].s);
}
}
BOOST_AUTO_TEST_CASE(trim_test) BOOST_AUTO_TEST_CASE(trim_test)
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment