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libcifpp
Commit ff62efe7 by Maarten L. Hekkelman
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More tests

parent 24078771
Showing with 349 additions and 206 deletions
CMakeLists.txt
......@@ -197,6 +197,7 @@ set(project_sources
${PROJECT_SOURCE_DIR}/src/cif/condition.cpp
${PROJECT_SOURCE_DIR}/src/cif/datablock.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/parser.cpp
${PROJECT_SOURCE_DIR}/src/cif/row.cpp
......
include/cif++/cif/file.hpp
......@@ -26,8 +26,6 @@
#pragma once
#include <cif++/cif/forward_decl.hpp>
#include <cif++/cif/datablock.hpp>
#include <cif++/cif/parser.hpp>
......@@ -39,7 +37,6 @@ namespace cif::v2
class file : public std::list<datablock>
{
public:
file() = default;
file(std::istream &is)
......@@ -52,126 +49,38 @@ class file : public std::list<datablock>
file &operator=(const file &) = default;
file &operator=(file &&) = default;
void set_validator(const validator *v)
{
m_validator = v;
for (auto &db : *this)
db.set_validator(v);
}
void set_validator(const validator *v);
const validator *get_validator() const
{
return m_validator;
}
bool 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 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;
bool is_valid() const;
bool is_valid();
return result;
}
void load_dictionary()
{
load_dictionary("mmcif_ddl");
}
void load_dictionary();
void load_dictionary(std::string_view name);
void load_dictionary(std::string_view name)
{
set_validator(&validator_factory::instance()[name]);
}
datablock &operator[](std::string_view name);
const datablock &operator[](std::string_view name) const;
datablock &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();
}
std::tuple<iterator, bool> emplace(std::string_view name);
const datablock &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;
}
void load(const std::filesystem::path &p);
void load(std::istream &is);
std::tuple<iterator, bool> 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 save(const std::filesystem::path &p) const;
void save(std::ostream &os) const;
void load(std::istream &is)
friend std::ostream &operator<<(std::ostream &os, const file &f)
{
auto saved = m_validator;
set_validator(nullptr);
parser p(is, *this);
p.parse_file();
if (saved != nullptr)
{
set_validator(saved);
(void)is_valid();
}
f.save(os);
return os;
}
private:
const validator* m_validator = nullptr;
const validator *m_validator = nullptr;
};
}
\ No newline at end of file
} // namespace cif::v2
\ No newline at end of file
include/cif++/cif/parser.hpp
......@@ -44,6 +44,8 @@ class parse_error : public std::runtime_error
// --------------------------------------------------------------------
// TODO: Need to implement support for transformed long lines
class sac_parser
{
public:
......@@ -228,6 +230,7 @@ class sac_parser
{
Start,
White,
Esc,
Comment,
QuestionMark,
Dot,
......
src/cif/category.cpp
......@@ -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 (offset > 0)
os << std::endl;
os << '\n';
os << ';';
char pc = 0;
......@@ -1639,8 +1639,8 @@ namespace detail
}
if (value.back() != '\n')
os << std::endl;
os << ';' << std::endl;
os << '\n';
os << ';' << '\n';
offset = 0;
}
else if (sac_parser::is_unquoted_string(value))
......@@ -1690,9 +1690,9 @@ namespace detail
if (not done)
{
if (offset > 0)
os << std::endl;
os << ';' << value << std::endl
<< ';' << std::endl;
os << '\n';
os << ';' << value << '\n'
<< ';' << '\n';
offset = 0;
}
}
......@@ -1749,14 +1749,14 @@ void category::write(std::ostream &os, const std::vector<uint16_t> &order, bool
if (needLoop)
{
os << "loop_" << std::endl;
os << "loop_" << '\n';
std::vector<size_t> columnWidths;
for (auto cix : order)
{
auto &col = m_columns[cix];
os << '_' << m_name << '.' << col.m_name << ' ' << std::endl;
os << '_' << m_name << '.' << col.m_name << ' ' << '\n';
columnWidths.push_back(2);
}
......@@ -1809,7 +1809,7 @@ void category::write(std::ostream &os, const std::vector<uint16_t> &order, bool
if (offset + l > 132 and offset > 0)
{
os << std::endl;
os << '\n';
offset = 0;
}
......@@ -1817,13 +1817,13 @@ void category::write(std::ostream &os, const std::vector<uint16_t> &order, bool
if (offset > 132)
{
os << std::endl;
os << '\n';
offset = 0;
}
}
if (offset > 0)
os << std::endl;
os << '\n';
}
}
else
......@@ -1863,16 +1863,16 @@ void category::write(std::ostream &os, const std::vector<uint16_t> &order, bool
size_t offset = l;
if (s.length() + l >= kMaxLineLength)
{
os << std::endl;
os << '\n';
offset = 0;
}
if (detail::write_value(os, s, offset, 1) != 0)
os << std::endl;
os << '\n';
}
}
os << "# " << std::endl;
os << "# " << '\n';
}
} // 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()
else
m_bol = (ch == '\n');
break;
case State::Comment:
if (ch == '\n')
{
......@@ -214,10 +214,17 @@ sac_parser::CIFToken sac_parser::get_next_token()
state = State::TextField + 1;
else if (ch == kEOF)
error("unterminated textfield");
// else if (ch == '\\')
// state = State::Esc;
else if (not is_any_print(ch))
warning("invalid character in text field '" + std::string({static_cast<char>(ch)}) + "' (" + std::to_string((int)ch) + ")");
break;
// case State::Esc:
// if (ch == '\n')
// break;
case State::TextField + 1:
if (is_text_lead(ch) or ch == ' ' or ch == '\t')
state = State::TextField;
......
test/unit-v2-test.cpp
......@@ -348,19 +348,18 @@ _test.name
++n;
}
// for (auto r: test)
// test.erase(r);
// BOOST_CHECK(test.empty());
auto n2 = test.erase(cif::v2::key("id") == 1, [](cif::v2::row_handle r)
{
BOOST_CHECK_EQUAL(r["id"].as<int>(), 1);
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)
// {
// BOOST_CHECK_EQUAL(r["id"].as<int>(), 1);
// BOOST_CHECK_EQUAL(r["name"].as<std::string>(), "aap"); });
// for (auto r: test)
// test.erase(r);
// BOOST_CHECK_EQUAL(n, 1);
test.clear();
BOOST_CHECK(test.empty());
}
// --------------------------------------------------------------------
......@@ -2002,96 +2001,150 @@ BOOST_AUTO_TEST_CASE(reading_file_1)
BOOST_CHECK_THROW(file.load(is), std::runtime_error);
}
// BOOST_AUTO_TEST_CASE(parser_test_1)
// {
// auto data1 = R"(
// data_QM
// _test.text ??
// )"_cf;
BOOST_AUTO_TEST_CASE(parser_test_1)
{
auto data1 = R"(
data_QM
_test.text ??
)"_cf;
// auto &db1 = data1.front();
// auto &test1 = db1["test"];
auto &db1 = data1.front();
auto &test1 = db1["test"];
// BOOST_CHECK_EQUAL(test1.size(), 1);
BOOST_CHECK_EQUAL(test1.size(), 1);
// for (auto r : test1)
// {
// const auto &[text] = r.get<std::string>({"text"});
// BOOST_CHECK_EQUAL(text, "??");
// }
for (auto r : test1)
{
const auto &[text] = r.get<std::string>({"text"});
BOOST_CHECK_EQUAL(text, "??");
}
// std::stringstream ss;
// data1.save(ss);
std::stringstream ss;
data1.save(ss);
// auto data2 = cif::File(ss);
auto data2 = cif::v2::file(ss);
// auto &db2 = data2.front();
// auto &test2 = db2["test"];
auto &db2 = data2.front();
auto &test2 = db2["test"];
// BOOST_CHECK_EQUAL(test2.size(), 1);
BOOST_CHECK_EQUAL(test2.size(), 1);
// for (auto r : test2)
// {
// const auto &[text] = r.get<std::string>({"text"});
// BOOST_CHECK_EQUAL(text, "??");
// }
// }
for (auto r : test2)
{
const auto &[text] = r.get<std::string>({"text"});
BOOST_CHECK_EQUAL(text, "??");
}
}
// BOOST_AUTO_TEST_CASE(output_test_1)
// {
// auto data1 = R"(
// data_Q
// loop_
// _test.text
// "stop_the_crap"
// 'and stop_ this too'
// 'data_dinges'
// 'blablaglobal_bla'
// boo.data_.whatever
// )"_cf;
BOOST_AUTO_TEST_CASE(output_test_1)
{
auto data1 = R"(
data_Q
loop_
_test.text
"stop_the_crap"
'and stop_ this too'
'data_dinges'
'blablaglobal_bla'
boo.data_.whatever
)"_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();
// auto &test1 = db1["test"];
BOOST_CHECK_EQUAL(test1.size(), sizeof(kS) / sizeof(T));
// 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 }
// };
size_t i = 0;
for (auto r : test1)
{
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;
}
// BOOST_CHECK_EQUAL(test1.size(), sizeof(kS) / sizeof(T));
std::stringstream ss;
data1.save(ss);
// size_t i = 0;
// 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;
// }
auto data2 = cif::v2::file(ss);
// std::stringstream ss;
// data1.save(ss);
auto &db2 = data2.front();
auto &test2 = db2["test"];
// auto data2 = cif::File(ss);
BOOST_CHECK_EQUAL(test2.size(), sizeof(kS) / sizeof(T));
// auto &db2 = data2.front();
// auto &test2 = db2["test"];
i = 0;
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;
// for (auto r : test2)
// {
// const auto &[text] = r.get<std::string>({"text"});
// BOOST_CHECK_EQUAL(text, kS[i++].s);
// }
// }
BOOST_CHECK_EQUAL(test1.size(), sizeof(kS) / sizeof(T));
size_t i = 0;
for (auto r : test1)
{
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)
......
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