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libcifpp/test/unit-v2-test.cpp
Maarten L. Hekkelman 84af564aee More documentation 
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2023-09-13 10:22:28 +02:00

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/*-
* SPDX-License-Identifier: BSD-2-Clause
*
* Copyright (c) 2020 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.
*/
#define BOOST_TEST_ALTERNATIVE_INIT_API
#include <boost/test/included/unit_test.hpp>
#include <stdexcept>
#include <cif++.hpp>
#include "cif++/dictionary_parser.hpp"
namespace tt = boost::test_tools;
std::filesystem::path gTestDir = std::filesystem::current_path(); // filled in first test
// --------------------------------------------------------------------
cif::file operator""_cf(const char *text, size_t length)
{
struct membuf : public std::streambuf
{
membuf(char *text, size_t length)
{
this->setg(text, text, text + length);
}
} buffer(const_cast<char *>(text), length);
std::istream is(&buffer);
return cif::file(is);
}
// --------------------------------------------------------------------
bool init_unit_test()
{
cif::VERBOSE = 1;
// not a test, just initialize test dir
if (boost::unit_test::framework::master_test_suite().argc == 2)
gTestDir = boost::unit_test::framework::master_test_suite().argv[1];
// do this now, avoids the need for installing
cif::add_file_resource("mmcif_pdbx.dic", gTestDir / ".." / "rsrc" / "mmcif_pdbx.dic");
// initialize CCD location
cif::add_file_resource("components.cif", gTestDir / ".." / "data" / "ccd-subset.cif");
return true;
}
// --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(id_1)
{
BOOST_TEST(cif::cif_id_for_number(0) == "A");
BOOST_TEST(cif::cif_id_for_number(25) == "Z");
BOOST_TEST(cif::cif_id_for_number(26) == "AA");
BOOST_TEST(cif::cif_id_for_number(26 + 1) == "AB");
BOOST_TEST(cif::cif_id_for_number(26 + 26 * 26 - 1) == "ZZ");
BOOST_TEST(cif::cif_id_for_number(26 + 26 * 26) == "AAA");
BOOST_TEST(cif::cif_id_for_number(26 + 26 * 26 + 1) == "AAB");
std::set<std::string> testset;
for (int i = 0; i < 100000; ++i)
{
std::string id = cif::cif_id_for_number(i);
BOOST_TEST(testset.count(id) == 0);
testset.insert(id);
}
BOOST_TEST(testset.size() == 100000);
}
// --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(cc_1)
{
std::tuple<std::string_view, float, char> tests[] = {
{ "1.0", 1.0f, 0 },
{ "1.0e10", 1.0e10f, 0 },
{ "-1.1e10", -1.1e10f, 0 },
{ "-.2e11", -.2e11f, 0 },
{ "1.3e-10", 1.3e-10f, 0 },
{ "1.0 ", 1.0f, ' ' },
{ "1.0e10 ", 1.0e10f, ' ' },
{ "-1.1e10 ", -1.1e10f, ' ' },
{ "-.2e11 ", -.2e11f, ' ' },
{ "1.3e-10 ", 1.3e-10f, ' ' },
{ "3.0", 3.0f, 0 },
{ "3.0 ", 3.0f, ' ' },
{ "3.000000", 3.0f, 0 },
{ "3.000000 ", 3.0f, ' ' },
};
for (const auto &[txt, val, ch] : tests)
{
float tv;
const auto &[ptr, ec] = cif::from_chars(txt.data(), txt.data() + txt.length(), tv);
BOOST_CHECK(ec == std::errc());
BOOST_CHECK_EQUAL(tv, val);
if (ch != 0)
BOOST_CHECK_EQUAL(*ptr, ch);
}
}
BOOST_AUTO_TEST_CASE(cc_2)
{
std::tuple<float, int, std::string_view> tests[] = {
{ 1.1f, 1, "1.1" }
};
for (const auto &[val, prec, test] : tests)
{
char buffer[64];
const auto &[ptr, ec] = cif::to_chars(buffer, buffer + sizeof(buffer), val, cif::chars_format::fixed, prec);
BOOST_CHECK(ec == std::errc());
BOOST_CHECK_EQUAL(buffer, test);
}
}
BOOST_AUTO_TEST_CASE(item_1)
{
using namespace cif;
item i1("1", "1");
item i2("2", 2.0f);
item i3("3", '3');
item ci1(i1);
item ci2(i2);
item ci3(i3);
BOOST_CHECK_EQUAL(i1.value(), ci1.value());
BOOST_CHECK_EQUAL(i2.value(), ci2.value());
BOOST_CHECK_EQUAL(i3.value(), ci3.value());
item mi1(std::move(ci1));
item mi2(std::move(ci2));
item mi3(std::move(ci3));
BOOST_CHECK_EQUAL(i1.value(), mi1.value());
BOOST_CHECK_EQUAL(i2.value(), mi2.value());
BOOST_CHECK_EQUAL(i3.value(), mi3.value());
BOOST_CHECK(ci1.empty());
BOOST_CHECK(ci2.empty());
BOOST_CHECK(ci3.empty());
}
// --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(r_1)
{
cif::category c("foo");
c.emplace({
{ "f-1", 1 },
{ "f-2", "two" },
{ "f-3", 3.0f, 3 },
});
auto row = c.front();
BOOST_CHECK_EQUAL(row["f-1"].compare(1), 0);
BOOST_CHECK_EQUAL(row["f-2"].compare("two"), 0);
BOOST_CHECK_EQUAL(row["f-3"].compare(3.0f), 0); // This fails when running in valgrind... sigh
const auto &[f1, f2, f3] = row.get<int, std::string, float>("f-1", "f-2", "f-3");
BOOST_CHECK_EQUAL(f1, 1);
BOOST_CHECK_EQUAL(f2, "two");
BOOST_CHECK_EQUAL(f3, 3.0f); // This fails when running in valgrind... sigh
BOOST_CHECK_EQUAL(row.get<int>("f-1"), 1);
BOOST_CHECK_EQUAL(row.get<std::string>("f-2"), "two");
BOOST_CHECK_EQUAL(row.get<float>("f-3"), 3.0f);
int f_1;
std::string f_2;
float f_3;
cif::tie(f_1, f_2, f_3) = row.get("f-1", "f-2", "f-3");
BOOST_CHECK_EQUAL(f_1, 1);
BOOST_CHECK_EQUAL(f_2, "two");
BOOST_CHECK_EQUAL(f_3, 3.0f); // This fails when running in valgrind... sigh
}
BOOST_AUTO_TEST_CASE(r_2)
{
cif::category c("foo");
for (size_t i = 1; i < 256; ++i)
{
c.emplace({ { "id", i },
{ "txt", std::string(i, 'x') } });
}
}
BOOST_AUTO_TEST_CASE(c_1)
{
cif::category c("foo");
c.emplace({ { "id", 1 }, { "s", "aap" } });
c.emplace({ { "id", 2 }, { "s", "noot" } });
c.emplace({ { "id", 3 }, { "s", "mies" } });
int n = 1;
const char *ts[] = { "aap", "noot", "mies" };
for (auto r : c)
{
BOOST_CHECK_EQUAL(r["id"].as<int>(), n);
BOOST_CHECK_EQUAL(r["s"].compare(ts[n - 1]), 0);
++n;
}
n = 1;
for (auto r : c)
{
int i;
std::string s;
cif::tie(i, s) = r.get("id", "s");
BOOST_CHECK_EQUAL(i, n);
BOOST_CHECK_EQUAL(s.compare(ts[n - 1]), 0);
++n;
}
n = 1;
for (const auto &[i, s] : c.rows<int, std::string>("id", "s"))
{
BOOST_CHECK_EQUAL(i, n);
BOOST_CHECK_EQUAL(s.compare(ts[n - 1]), 0);
++n;
}
}
BOOST_AUTO_TEST_CASE(c_2)
{
std::tuple<int, const char *> D[] = {
{ 1, "aap" },
{ 2, "noot" },
{ 3, "mies" }
};
cif::category c("foo");
for (const auto &[id, s] : D)
c.emplace({ { "id", id }, { "s", s } });
BOOST_CHECK(not c.empty());
BOOST_CHECK_EQUAL(c.size(), 3);
cif::category c2(c);
BOOST_CHECK(not c2.empty());
BOOST_CHECK_EQUAL(c2.size(), 3);
cif::category c3(std::move(c));
BOOST_CHECK(not c3.empty());
BOOST_CHECK_EQUAL(c3.size(), 3);
BOOST_CHECK(c.empty());
BOOST_CHECK_EQUAL(c.size(), 0);
c = c3;
BOOST_CHECK(not c.empty());
BOOST_CHECK_EQUAL(c.size(), 3);
c = std::move(c2);
BOOST_CHECK(not c.empty());
BOOST_CHECK_EQUAL(c.size(), 3);
}
BOOST_AUTO_TEST_CASE(c_3)
{
std::tuple<int, const char *> D[] = {
{ 1, "aap" },
{ 2, "noot" },
{ 3, "mies" }
};
cif::category c("foo");
for (const auto &[id, s] : D)
c.emplace({ { "id", id }, { "s", s } });
cif::category c2("bar");
for (auto r : c)
c2.emplace(r);
// BOOST_CHECK(c == c2);
}
BOOST_AUTO_TEST_CASE(ci_1)
{
cif::category c("foo");
c.emplace({ { "id", 1 }, { "s", "aap" } });
c.emplace({ { "id", 2 }, { "s", "noot" } });
c.emplace({ { "id", 3 }, { "s", "mies" } });
cif::category::iterator i1 = c.begin();
cif::category::const_iterator i2 = c.cbegin();
cif::category::const_iterator i3 = c.begin();
cif::category::const_iterator i4 = i2;
cif::category::const_iterator i5 = i1;
BOOST_CHECK(i1 == i2);
BOOST_CHECK(i1 == i3);
BOOST_CHECK(i1 == i4);
BOOST_CHECK(i1 == i5);
}
BOOST_AUTO_TEST_CASE(os_1)
{
using namespace cif::literals;
using namespace std::literals;
std::tuple<int, const char *> D[] = {
{ 1, "aap" },
{ 2, "noot" },
{ 3, "mies" }
};
cif::category c("foo");
for (const auto &[id, s] : D)
c.emplace({ { "id", id }, { "s", s } });
for (auto rh : c)
{
rh["o"].os(1, ',', 2, ": ", rh.get<std::string>("s"));
}
for (const auto &[id, s] : D)
{
auto rh = c.find1("id"_key == id);
BOOST_CHECK_EQUAL(rh.get<int>("id"), id);
BOOST_CHECK_EQUAL(rh.get<std::string>("s"), s);
BOOST_CHECK_EQUAL(rh.get<std::string>("o"), "1,2: "s + s);
}
}
// --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(get_1)
{
auto f = R"(data_TEST
#
loop_
_test.id
_test.name
1 aap
2 noot
3 mies
4 ?
5 .
)"_cf;
for (auto r : f.front()["test"])
{
int id;
std::optional<std::string> name;
cif::tie(id, name) = r.get("id", "name");
switch (id)
{
case 1: BOOST_CHECK_EQUAL(*name, "aap"); break;
case 2: BOOST_CHECK_EQUAL(*name, "noot"); break;
case 3: BOOST_CHECK_EQUAL(*name, "mies"); break;
default: BOOST_CHECK(name.has_value() == false);
}
}
}
// --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(f_1)
{
// using namespace mmcif;
auto f = R"(data_TEST
#
loop_
_test.id
_test.name
1 aap
2 noot
3 mies
)"_cf;
BOOST_ASSERT(not f.empty());
BOOST_ASSERT(f.size() == 1);
auto &db = f.front();
BOOST_CHECK_EQUAL(db.name(), "TEST");
auto &test = db["test"];
BOOST_CHECK_EQUAL(test.size(), 3);
const char *ts[] = { "aap", "noot", "mies" };
int n = 1;
for (const auto &[i, s] : test.rows<int, std::string>("id", "name"))
{
BOOST_CHECK_EQUAL(i, n);
BOOST_CHECK_EQUAL(s.compare(ts[n - 1]), 0);
++n;
}
auto n2 = test.erase(cif::key("id") == 1, [](cif::row_handle r)
{
BOOST_CHECK_EQUAL(r["id"].as<int>(), 1);
BOOST_CHECK_EQUAL(r["name"].as<std::string>(), "aap"); });
BOOST_CHECK_EQUAL(n2, 1);
// for (auto r: test)
// test.erase(r);
test.clear();
BOOST_CHECK(test.empty());
// fill again.
test.emplace({ { "id", "1" }, { "name", "aap" } });
test.emplace({ { "id", "2" }, { "name", "noot" } });
test.emplace({ { "id", "3" }, { "name", "mies" } });
n = 1;
for (const auto &[i, s] : test.rows<int, std::string>("id", "name"))
{
BOOST_CHECK_EQUAL(i, n);
BOOST_CHECK_EQUAL(s.compare(ts[n - 1]), 0);
++n;
}
}
// --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(ut2)
{
// using namespace mmcif;
auto f = R"(data_TEST
#
loop_
_test.id
_test.name
_test.value
1 aap 1.0
2 noot 1.1
3 mies 1.2
)"_cf;
auto &db = f.front();
BOOST_CHECK_EQUAL(db.name(), "TEST");
auto &test = db["test"];
BOOST_CHECK_EQUAL(test.size(), 3);
int n = 0;
for (auto r : test.find(cif::key("name") == "aap"))
{
BOOST_CHECK_EQUAL(++n, 1);
BOOST_CHECK_EQUAL(r["id"].as<int>(), 1);
BOOST_CHECK_EQUAL(r["name"].as<std::string>(), "aap");
BOOST_CHECK_EQUAL(r["value"].as<float>(), 1.0f);
}
auto t = test.find(cif::key("id") == 1);
BOOST_CHECK(not t.empty());
BOOST_CHECK_EQUAL(t.front()["name"].as<std::string>(), "aap");
auto t2 = test.find(cif::key("value") == 1.2f);
BOOST_CHECK(not t2.empty());
BOOST_CHECK_EQUAL(t2.front()["name"].as<std::string>(), "mies");
}
BOOST_AUTO_TEST_CASE(ut3)
{
using namespace cif::literals;
auto f = R"(data_TEST
#
loop_
_test.id
_test.name
_test.value
1 aap 1.0
2 noot 1.1
3 mies 1.2
4 boom .
5 roos ?
)"_cf;
auto &db = f.front();
BOOST_CHECK_EQUAL(db.name(), "TEST");
auto &test = db["test"];
BOOST_CHECK_EQUAL(test.size(), 5);
BOOST_CHECK(test.exists("value"_key == cif::null));
BOOST_CHECK_EQUAL(test.find("value"_key == cif::null).size(), 2);
}
// --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(sw_1)
{
using namespace cif::literals;
auto f = R"(data_TEST
#
loop_
_test.id
_test.name
_test.value
1 aap 1.0
2 noot 1.1
3 mies 1.2
)"_cf;
auto &db = f.front();
auto &test = db["test"];
swap(test.front()["name"], test.back()["name"]);
BOOST_CHECK_EQUAL(test.find1<std::string>("id"_key == 1, "name"), "mies");
BOOST_CHECK_EQUAL(test.find1<std::string>("id"_key == 3, "name"), "aap");
swap(test.front()["name"], test.back()["name"]);
BOOST_CHECK_EQUAL(test.find1<std::string>("id"_key == 1, "name"), "aap");
BOOST_CHECK_EQUAL(test.find1<std::string>("id"_key == 3, "name"), "mies");
}
// --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(d1)
{
const char dict[] = R"(
data_test_dict.dic
_datablock.id test_dict.dic
_datablock.description
;
A test dictionary
;
_dictionary.title test_dict.dic
_dictionary.datablock_id test_dict.dic
_dictionary.version 1.0
loop_
_item_type_list.code
_item_type_list.primitive_code
_item_type_list.construct
_item_type_list.detail
code char
'[][_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types/single words ...
;
text char
'[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*'
; text item types / multi-line text ...
;
int numb
'[+-]?[0-9]+'
; int item types are the subset of numbers that are the negative
or positive integers.
;
save_cat_1
_category.description 'A simple test category'
_category.id cat_1
_category.mandatory_code no
_category_key.name '_cat_1.id'
save_
save__cat_1.id
_item.name '_cat_1.id'
_item.category_id cat_1
_item.mandatory_code yes
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_linked.child_name '_cat_2.parent_id'
_item_linked.parent_name '_cat_1.id'
_item_type.code code
save_
save__cat_1.name
_item.name '_cat_1.name'
_item.category_id cat_1
_item.mandatory_code yes
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
save_cat_2
_category.description 'A second simple test category'
_category.id cat_2
_category.mandatory_code no
_category_key.name '_cat_2.id'
save_
save__cat_2.id
_item.name '_cat_2.id'
_item.category_id cat_2
_item.mandatory_code yes
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code int
save_
save__cat_2.parent_id
_item.name '_cat_2.parent_id'
_item.category_id cat_2
_item.mandatory_code yes
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code code
save_
save__cat_2.desc
_item.name '_cat_2.desc'
_item.category_id cat_2
_item.mandatory_code yes
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
)";
struct membuf : public std::streambuf
{
membuf(char *text, size_t length)
{
this->setg(text, text, text + length);
}
} buffer(const_cast<char *>(dict), sizeof(dict) - 1);
std::istream is_dict(&buffer);
auto validator = cif::parse_dictionary("test", is_dict);
cif::file f;
f.set_validator(&validator);
// --------------------------------------------------------------------
const char data[] = R"(
data_test
loop_
_cat_1.id
_cat_1.name
1 Aap
2 Noot
3 Mies
loop_
_cat_2.id
_cat_2.parent_id
_cat_2.desc
1 1 'Een dier'
2 1 'Een andere aap'
3 2 'walnoot bijvoorbeeld'
)";
struct data_membuf : public std::streambuf
{
data_membuf(char *text, size_t length)
{
this->setg(text, text, text + length);
}
} data_buffer(const_cast<char *>(data), sizeof(data) - 1);
std::istream is_data(&data_buffer);
f.load(is_data);
auto &cat1 = f.front()["cat_1"];
auto &cat2 = f.front()["cat_2"];
BOOST_CHECK_EQUAL(cat1.size(), 3);
BOOST_CHECK_EQUAL(cat2.size(), 3);
cat1.erase(cif::key("id") == 1);
BOOST_CHECK_EQUAL(cat1.size(), 2);
BOOST_CHECK_EQUAL(cat2.size(), 1);
// BOOST_CHECK_THROW(cat2.emplace({
// { "id", 4 },
// { "parent_id", 4 },
// { "desc", "moet fout gaan" }
// }), std::exception);
BOOST_CHECK_THROW(cat2.emplace({ { "id", "vijf" }, // <- invalid value
{ "parent_id", 2 },
{ "desc", "moet fout gaan" } }),
std::exception);
}
// --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(d2)
{
const char dict[] = R"(
data_test_dict.dic
_datablock.id test_dict.dic
_datablock.description
;
A test dictionary
;
_dictionary.title test_dict.dic
_dictionary.datablock_id test_dict.dic
_dictionary.version 1.0
loop_
_item_type_list.code
_item_type_list.primitive_code
_item_type_list.construct
_item_type_list.detail
code char
'[][_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types/single words ...
;
ucode uchar
'[][_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types/single words, case insensitive
;
text char
'[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*'
; text item types / multi-line text ...
;
int numb
'[+-]?[0-9]+'
; int item types are the subset of numbers that are the negative
or positive integers.
;
save_cat_1
_category.description 'A simple test category'
_category.id cat_1
_category.mandatory_code no
_category_key.name '_cat_1.id'
save_
save__cat_1.id
_item.name '_cat_1.id'
_item.category_id cat_1
_item.mandatory_code yes
_item_type.code code
save_
save__cat_1.c
_item.name '_cat_1.c'
_item.category_id cat_1
_item.mandatory_code yes
_item_type.code ucode
save_
)";
struct membuf : public std::streambuf
{
membuf(char *text, size_t length)
{
this->setg(text, text, text + length);
}
} buffer(const_cast<char *>(dict), sizeof(dict) - 1);
std::istream is_dict(&buffer);
auto validator = cif::parse_dictionary("test", is_dict);
cif::file f;
f.set_validator(&validator);
// --------------------------------------------------------------------
const char data[] = R"(
data_test
loop_
_cat_1.id
_cat_1.c
aap Aap
noot Noot
mies Mies
)";
struct data_membuf : public std::streambuf
{
data_membuf(char *text, size_t length)
{
this->setg(text, text, text + length);
}
} data_buffer(const_cast<char *>(data), sizeof(data) - 1);
std::istream is_data(&data_buffer);
f.load(is_data);
auto &cat1 = f.front()["cat_1"];
BOOST_CHECK_EQUAL(cat1.size(), 3);
cat1.erase(cif::key("id") == "AAP");
BOOST_CHECK_EQUAL(cat1.size(), 3);
cat1.erase(cif::key("id") == "noot");
BOOST_CHECK_EQUAL(cat1.size(), 2);
// should fail with duplicate key:
BOOST_CHECK_THROW(cat1.emplace({ { "id", "aap" },
{ "c", "2e-aap" } }),
std::exception);
cat1.erase(cif::key("id") == "aap");
BOOST_CHECK_EQUAL(cat1.size(), 1);
cat1.emplace({ { "id", "aap" },
{ "c", "2e-aap" } });
BOOST_CHECK_EQUAL(cat1.size(), 2);
}
// --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(d3)
{
const char dict[] = R"(
data_test_dict.dic
_datablock.id test_dict.dic
_datablock.description
;
A test dictionary
;
_dictionary.title test_dict.dic
_dictionary.datablock_id test_dict.dic
_dictionary.version 1.0
loop_
_item_type_list.code
_item_type_list.primitive_code
_item_type_list.construct
code char
'[][_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]*'
text char
'[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*'
int numb
'[+-]?[0-9]+'
save_cat_1
_category.description 'A simple test category'
_category.id cat_1
_category.mandatory_code no
_category_key.name '_cat_1.id'
save_
save__cat_1.id
_item.name '_cat_1.id'
_item.category_id cat_1
_item.mandatory_code yes
_item_linked.child_name '_cat_2.parent_id'
_item_linked.parent_name '_cat_1.id'
_item_type.code code
save_
save__cat_1.name1
_item.name '_cat_1.name1'
_item.category_id cat_1
_item.mandatory_code yes
_item_type.code text
save_
save__cat_1.name2
_item.name '_cat_1.name2'
_item.category_id cat_1
_item.mandatory_code no
_item_linked.child_name '_cat_2.name2'
_item_linked.parent_name '_cat_1.name2'
_item_type.code text
save_
save_cat_2
_category.description 'A second simple test category'
_category.id cat_2
_category.mandatory_code no
_category_key.name '_cat_2.id'
save_
save__cat_2.id
_item.name '_cat_2.id'
_item.category_id cat_2
_item.mandatory_code yes
_item_type.code int
save_
save__cat_2.parent_id
_item.name '_cat_2.parent_id'
_item.category_id cat_2
_item.mandatory_code yes
_item_type.code code
save_
save__cat_2.name2
_item.name '_cat_2.name2'
_item.category_id cat_2
_item.mandatory_code no
_item_type.code text
save_
save__cat_2.desc
_item.name '_cat_2.desc'
_item.category_id cat_2
_item.mandatory_code yes
_item_type.code text
save_
)";
struct membuf : public std::streambuf
{
membuf(char *text, size_t length)
{
this->setg(text, text, text + length);
}
} buffer(const_cast<char *>(dict), sizeof(dict) - 1);
std::istream is_dict(&buffer);
auto validator = cif::parse_dictionary("test", is_dict);
cif::file f;
f.set_validator(&validator);
// --------------------------------------------------------------------
const char data[] = R"(
data_test
loop_
_cat_1.id
_cat_1.name1
_cat_1.name2
1 Aap aap
2 Noot noot
3 Mies mies
loop_
_cat_2.id
_cat_2.parent_id
_cat_2.name2
_cat_2.desc
1 1 aap 'Een dier'
2 1 . 'Een andere aap'
3 2 noot 'walnoot bijvoorbeeld'
4 2 n2 hazelnoot
)";
struct data_membuf : public std::streambuf
{
data_membuf(char *text, size_t length)
{
this->setg(text, text, text + length);
}
} data_buffer(const_cast<char *>(data), sizeof(data) - 1);
std::istream is_data(&data_buffer);
f.load(is_data);
auto &cat1 = f.front()["cat_1"];
auto &cat2 = f.front()["cat_2"];
// check a rename in parent and child
for (auto r : cat1.find(cif::key("id") == 1))
{
r["id"] = 10;
break;
}
BOOST_CHECK_EQUAL(cat1.size(), 3);
BOOST_CHECK_EQUAL(cat2.size(), 4);
BOOST_CHECK_EQUAL(cat1.find(cif::key("id") == 1).size(), 0);
BOOST_CHECK_EQUAL(cat1.find(cif::key("id") == 10).size(), 1);
BOOST_CHECK_EQUAL(cat2.find(cif::key("parent_id") == 1).size(), 0);
BOOST_CHECK_EQUAL(cat2.find(cif::key("parent_id") == 10).size(), 2);
// check a rename in parent and child, this time only one child should be renamed
for (auto r : cat1.find(cif::key("id") == 2))
{
r["id"] = 20;
break;
}
BOOST_CHECK_EQUAL(cat1.size(), 3);
BOOST_CHECK_EQUAL(cat2.size(), 4);
BOOST_CHECK_EQUAL(cat1.find(cif::key("id") == 2).size(), 0);
BOOST_CHECK_EQUAL(cat1.find(cif::key("id") == 20).size(), 1);
BOOST_CHECK_EQUAL(cat2.find(cif::key("parent_id") == 2).size(), 1);
BOOST_CHECK_EQUAL(cat2.find(cif::key("parent_id") == 20).size(), 1);
BOOST_CHECK_EQUAL(cat2.find(cif::key("parent_id") == 2 and cif::key("name2") == "noot").size(), 0);
BOOST_CHECK_EQUAL(cat2.find(cif::key("parent_id") == 2 and cif::key("name2") == "n2").size(), 1);
BOOST_CHECK_EQUAL(cat2.find(cif::key("parent_id") == 20 and cif::key("name2") == "noot").size(), 1);
BOOST_CHECK_EQUAL(cat2.find(cif::key("parent_id") == 20 and cif::key("name2") == "n2").size(), 0);
// --------------------------------------------------------------------
cat1.erase(cif::key("id") == 10);
BOOST_CHECK_EQUAL(cat1.size(), 2);
BOOST_CHECK_EQUAL(cat2.size(), 2); // TODO: Is this really what we want?
cat1.erase(cif::key("id") == 20);
BOOST_CHECK_EQUAL(cat1.size(), 1);
BOOST_CHECK_EQUAL(cat2.size(), 1); // TODO: Is this really what we want?
}
// --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(d4)
{
const char dict[] = R"(
data_test_dict.dic
_datablock.id test_dict.dic
_datablock.description
;
A test dictionary
;
_dictionary.title test_dict.dic
_dictionary.datablock_id test_dict.dic
_dictionary.version 1.0
loop_
_item_type_list.code
_item_type_list.primitive_code
_item_type_list.construct
code char
'[][_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]*'
text char
'[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*'
int numb
'[+-]?[0-9]+'
save_cat_1
_category.description 'A simple test category'
_category.id cat_1
_category.mandatory_code no
_category_key.name '_cat_1.id'
save_
save__cat_1.id
_item.name '_cat_1.id'
_item.category_id cat_1
_item.mandatory_code yes
_item_linked.child_name '_cat_2.parent_id'
_item_linked.parent_name '_cat_1.id'
_item_type.code int
save_
save__cat_1.id2
_item.name '_cat_1.id2'
_item.category_id cat_1
_item.mandatory_code no
_item_linked.child_name '_cat_2.parent_id2'
_item_linked.parent_name '_cat_1.id2'
_item_type.code code
save_
save__cat_1.id3
_item.name '_cat_1.id3'
_item.category_id cat_1
_item.mandatory_code no
_item_linked.child_name '_cat_2.parent_id3'
_item_linked.parent_name '_cat_1.id3'
_item_type.code text
save_
save_cat_2
_category.description 'A second simple test category'
_category.id cat_2
_category.mandatory_code no
_category_key.name '_cat_2.id'
save_
save__cat_2.id
_item.name '_cat_2.id'
_item.category_id cat_2
_item.mandatory_code yes
_item_type.code int
save_
save__cat_2.parent_id
_item.name '_cat_2.parent_id'
_item.category_id cat_2
_item.mandatory_code yes
_item_type.code int
save_
save__cat_2.parent_id2
_item.name '_cat_2.parent_id2'
_item.category_id cat_2
_item.mandatory_code no
_item_type.code code
save_
save__cat_2.parent_id3
_item.name '_cat_2.parent_id3'
_item.category_id cat_2
_item.mandatory_code no
_item_type.code code
save_
)";
struct membuf : public std::streambuf
{
membuf(char *text, size_t length)
{
this->setg(text, text, text + length);
}
} buffer(const_cast<char *>(dict), sizeof(dict) - 1);
std::istream is_dict(&buffer);
auto validator = cif::parse_dictionary("test", is_dict);
cif::file f;
f.set_validator(&validator);
// --------------------------------------------------------------------
const char data[] = R"(
data_test
loop_
_cat_1.id
_cat_1.id2
_cat_1.id3
1 aap aap
2 . noot
3 mies .
4 . .
loop_
_cat_2.id
_cat_2.parent_id
_cat_2.parent_id2
_cat_2.parent_id3
1 1 aap aap
2 1 . x
3 1 aap .
4 2 noot noot
5 2 . noot
6 2 noot .
7 2 . .
8 3 mies mies
9 3 . mies
10 3 mies .
11 4 roos roos
12 4 . roos
13 4 roos .
)";
struct data_membuf : public std::streambuf
{
data_membuf(char *text, size_t length)
{
this->setg(text, text, text + length);
}
} data_buffer(const_cast<char *>(data), sizeof(data) - 1);
std::istream is_data(&data_buffer);
f.load(is_data);
auto &cat1 = f.front()["cat_1"];
auto &cat2 = f.front()["cat_2"];
// check a rename in parent and child
for (auto r : cat1.find(cif::key("id") == 1))
{
r["id"] = 10;
break;
}
BOOST_CHECK_EQUAL(cat1.size(), 4);
BOOST_CHECK_EQUAL(cat2.size(), 13);
BOOST_CHECK_EQUAL(cat1.find(cif::key("id") == 1).size(), 0);
BOOST_CHECK_EQUAL(cat1.find(cif::key("id") == 10).size(), 1);
BOOST_CHECK_EQUAL(cat2.find(cif::key("parent_id") == 1).size(), 1);
BOOST_CHECK_EQUAL(cat2.find(cif::key("parent_id") == 10).size(), 2);
for (auto r : cat1.find(cif::key("id") == 2))
{
r["id"] = 20;
break;
}
BOOST_CHECK_EQUAL(cat1.size(), 4);
BOOST_CHECK_EQUAL(cat2.size(), 13);
BOOST_CHECK_EQUAL(cat1.find(cif::key("id") == 2).size(), 0);
BOOST_CHECK_EQUAL(cat1.find(cif::key("id") == 20).size(), 1);
BOOST_CHECK_EQUAL(cat2.find(cif::key("parent_id") == 2).size(), 2);
BOOST_CHECK_EQUAL(cat2.find(cif::key("parent_id") == 20).size(), 2);
for (auto r : cat1.find(cif::key("id") == 3))
{
r["id"] = 30;
break;
}
BOOST_CHECK_EQUAL(cat1.size(), 4);
BOOST_CHECK_EQUAL(cat2.size(), 13);
BOOST_CHECK_EQUAL(cat1.find(cif::key("id") == 3).size(), 0);
BOOST_CHECK_EQUAL(cat1.find(cif::key("id") == 30).size(), 1);
BOOST_CHECK_EQUAL(cat2.find(cif::key("parent_id") == 3).size(), 2);
BOOST_CHECK_EQUAL(cat2.find(cif::key("parent_id") == 30).size(), 1);
for (auto r : cat1.find(cif::key("id") == 4))
{
r["id"] = 40;
break;
}
BOOST_CHECK_EQUAL(cat1.size(), 4);
BOOST_CHECK_EQUAL(cat2.size(), 13);
BOOST_CHECK_EQUAL(cat1.find(cif::key("id") == 4).size(), 0);
BOOST_CHECK_EQUAL(cat1.find(cif::key("id") == 10).size(), 1);
BOOST_CHECK_EQUAL(cat2.find(cif::key("parent_id") == 4).size(), 3);
BOOST_CHECK_EQUAL(cat2.find(cif::key("parent_id") == 40).size(), 0);
}
// --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(d5)
{
const char dict[] = R"(
data_test_dict.dic
_datablock.id test_dict.dic
_datablock.description
;
A test dictionary
;
_dictionary.title test_dict.dic
_dictionary.datablock_id test_dict.dic
_dictionary.version 1.0
loop_
_item_type_list.code
_item_type_list.primitive_code
_item_type_list.construct
code char
'[][_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]*'
text char
'[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*'
int numb
'[+-]?[0-9]+'
save_cat_1
_category.description 'A simple test category'
_category.id cat_1
_category.mandatory_code no
_category_key.name '_cat_1.id'
save_
save__cat_1.id
_item.name '_cat_1.id'
_item.category_id cat_1
_item.mandatory_code yes
_item_type.code int
save_
save_cat_2
_category.description 'A second simple test category'
_category.id cat_2
_category.mandatory_code no
_category_key.name '_cat_2.id'
save_
save__cat_2.id
_item.name '_cat_2.id'
_item.category_id cat_2
_item.mandatory_code yes
_item_type.code int
save_
save__cat_2.parent_id
_item.name '_cat_2.parent_id'
_item.category_id cat_2
_item.mandatory_code yes
_item_type.code int
save_
save__cat_2.parent_id2
_item.name '_cat_2.parent_id2'
_item.category_id cat_2
_item.mandatory_code no
_item_type.code code
save_
save__cat_2.parent_id3
_item.name '_cat_2.parent_id3'
_item.category_id cat_2
_item.mandatory_code no
_item_type.code code
save_
loop_
_pdbx_item_linked_group_list.child_category_id
_pdbx_item_linked_group_list.link_group_id
_pdbx_item_linked_group_list.child_name
_pdbx_item_linked_group_list.parent_name
_pdbx_item_linked_group_list.parent_category_id
cat_2 1 '_cat_2.parent_id' '_cat_1.id' cat_1
cat_2 2 '_cat_2.parent_id2' '_cat_1.id' cat_1
cat_2 3 '_cat_2.parent_id3' '_cat_1.id' cat_1
loop_
_pdbx_item_linked_group.category_id
_pdbx_item_linked_group.link_group_id
_pdbx_item_linked_group.label
cat_2 1 cat_2:cat_1:1
cat_2 2 cat_2:cat_1:2
cat_2 3 cat_2:cat_1:3
)";
struct membuf : public std::streambuf
{
membuf(char *text, size_t length)
{
this->setg(text, text, text + length);
}
} buffer(const_cast<char *>(dict), sizeof(dict) - 1);
std::istream is_dict(&buffer);
auto validator = cif::parse_dictionary("test", is_dict);
cif::file f;
f.set_validator(&validator);
// --------------------------------------------------------------------
const char data[] = R"(
data_test
loop_
_cat_1.id
1
2
3
loop_
_cat_2.id
_cat_2.parent_id
_cat_2.parent_id2
_cat_2.parent_id3
1 1 ? ?
2 ? 1 ?
3 ? ? 1
4 2 2 ?
5 2 ? 2
6 ? 2 2
7 3 3 3
)";
// --------------------------------------------------------------------
struct data_membuf : public std::streambuf
{
data_membuf(char *text, size_t length)
{
this->setg(text, text, text + length);
}
} data_buffer(const_cast<char *>(data), sizeof(data) - 1);
std::istream is_data(&data_buffer);
f.load(is_data);
auto &cat1 = f.front()["cat_1"];
auto &cat2 = f.front()["cat_2"];
// --------------------------------------------------------------------
// check iterate children
auto PR2set = cat1.find(cif::key("id") == 2);
BOOST_ASSERT(PR2set.size() == 1);
auto PR2 = PR2set.front();
BOOST_CHECK_EQUAL(PR2["id"].as<int>(), 2);
auto CR2set = cat1.get_children(PR2, cat2);
BOOST_CHECK_EQUAL(CR2set.size(), 3);
BOOST_ASSERT(CR2set.size() == 3);
std::vector<int> CRids;
std::transform(CR2set.begin(), CR2set.end(), std::back_inserter(CRids), [](cif::row_handle r)
{ return r["id"].as<int>(); });
std::sort(CRids.begin(), CRids.end());
BOOST_CHECK(CRids == std::vector<int>({ 4, 5, 6 }));
// check a rename in parent and child
for (auto r : cat1.find(cif::key("id") == 1))
{
r["id"] = 10;
break;
}
BOOST_CHECK_EQUAL(cat1.size(), 3);
BOOST_CHECK_EQUAL(cat2.size(), 7);
BOOST_CHECK_EQUAL(cat1.find(cif::key("id") == 1).size(), 0);
BOOST_CHECK_EQUAL(cat1.find(cif::key("id") == 10).size(), 1);
BOOST_CHECK_EQUAL(cat2.find(cif::key("parent_id") == 1).size(), 0);
BOOST_CHECK_EQUAL(cat2.find(cif::key("parent_id2") == 1).size(), 0);
BOOST_CHECK_EQUAL(cat2.find(cif::key("parent_id3") == 1).size(), 0);
BOOST_CHECK_EQUAL(cat2.find(cif::key("parent_id") == 10).size(), 1);
BOOST_CHECK_EQUAL(cat2.find(cif::key("parent_id2") == 10).size(), 1);
BOOST_CHECK_EQUAL(cat2.find(cif::key("parent_id3") == 10).size(), 1);
for (auto r : cat1.find(cif::key("id") == 2))
{
r["id"] = 20;
break;
}
BOOST_CHECK_EQUAL(cat1.size(), 3);
BOOST_CHECK_EQUAL(cat2.size(), 7);
BOOST_CHECK_EQUAL(cat1.find(cif::key("id") == 2).size(), 0);
BOOST_CHECK_EQUAL(cat1.find(cif::key("id") == 20).size(), 1);
BOOST_CHECK_EQUAL(cat2.find(cif::key("parent_id") == 2).size(), 0);
BOOST_CHECK_EQUAL(cat2.find(cif::key("parent_id2") == 2).size(), 0);
BOOST_CHECK_EQUAL(cat2.find(cif::key("parent_id3") == 2).size(), 0);
BOOST_CHECK_EQUAL(cat2.find(cif::key("parent_id") == 20).size(), 2);
BOOST_CHECK_EQUAL(cat2.find(cif::key("parent_id2") == 20).size(), 2);
BOOST_CHECK_EQUAL(cat2.find(cif::key("parent_id3") == 20).size(), 2);
for (auto r : cat1.find(cif::key("id") == 3))
{
r["id"] = 30;
break;
}
BOOST_CHECK_EQUAL(cat1.size(), 3);
BOOST_CHECK_EQUAL(cat2.size(), 7);
BOOST_CHECK_EQUAL(cat1.find(cif::key("id") == 3).size(), 0);
BOOST_CHECK_EQUAL(cat1.find(cif::key("id") == 30).size(), 1);
BOOST_CHECK_EQUAL(cat2.find(cif::key("parent_id") == 3).size(), 0);
BOOST_CHECK_EQUAL(cat2.find(cif::key("parent_id2") == 3).size(), 0);
BOOST_CHECK_EQUAL(cat2.find(cif::key("parent_id3") == 3).size(), 0);
BOOST_CHECK_EQUAL(cat2.find(cif::key("parent_id") == 30).size(), 1);
BOOST_CHECK_EQUAL(cat2.find(cif::key("parent_id2") == 30).size(), 1);
BOOST_CHECK_EQUAL(cat2.find(cif::key("parent_id3") == 30).size(), 1);
// test delete
cat1.erase(cif::key("id") == 10);
BOOST_CHECK_EQUAL(cat1.size(), 2);
BOOST_CHECK_EQUAL(cat2.size(), 4);
cat1.erase(cif::key("id") == 20);
BOOST_CHECK_EQUAL(cat1.size(), 1);
BOOST_CHECK_EQUAL(cat2.size(), 1);
cat1.erase(cif::key("id") == 30);
BOOST_CHECK_EQUAL(cat1.size(), 0);
BOOST_CHECK_EQUAL(cat2.size(), 0);
}
// --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(d6)
{
const char dict[] = R"(
data_test_dict.dic
_datablock.id test_dict.dic
_datablock.description
;
A test dictionary
;
_dictionary.title test_dict.dic
_dictionary.datablock_id test_dict.dic
_dictionary.version 1.0
loop_
_item_type_list.code
_item_type_list.primitive_code
_item_type_list.construct
code char
'[][_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]*'
text char
'[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*'
int numb
'[+-]?[0-9]+'
save_cat_1
_category.description 'A simple test category'
_category.id cat_1
_category.mandatory_code yes
_category_key.name '_cat_1.id'
save_
save__cat_1.id
_item.name '_cat_1.id'
_item.category_id cat_1
_item.mandatory_code yes
_item_type.code int
save_
save__cat_1.id_2
_item.name '_cat_1.id_2'
_item.category_id cat_1
_item.mandatory_code no
_item_type.code int
save_
save_cat_2
_category.description 'A second simple test category'
_category.id cat_2
_category.mandatory_code no
_category_key.name '_cat_2.id'
save_
save__cat_2.id
_item.name '_cat_2.id'
_item.category_id cat_2
_item.mandatory_code yes
_item_type.code int
save_
save__cat_2.parent_id
_item.name '_cat_2.parent_id'
_item.category_id cat_2
_item.mandatory_code yes
_item_type.code int
save_
save__cat_2.parent_id_2
_item.name '_cat_2.parent_id_2'
_item.category_id cat_2
_item.mandatory_code no
_item_type.code code
save_
loop_
_pdbx_item_linked_group_list.child_category_id
_pdbx_item_linked_group_list.link_group_id
_pdbx_item_linked_group_list.child_name
_pdbx_item_linked_group_list.parent_name
_pdbx_item_linked_group_list.parent_category_id
cat_2 1 '_cat_2.parent_id' '_cat_1.id' cat_1
cat_2 1 '_cat_2.parent_id_2' '_cat_1.id_2' cat_1
loop_
_pdbx_item_linked_group.category_id
_pdbx_item_linked_group.link_group_id
_pdbx_item_linked_group.label
cat_2 1 cat_2:cat_1:1
)";
struct membuf : public std::streambuf
{
membuf(char *text, size_t length)
{
this->setg(text, text, text + length);
}
} buffer(const_cast<char *>(dict), sizeof(dict) - 1);
std::istream is_dict(&buffer);
auto validator = cif::parse_dictionary("test", is_dict);
cif::file f;
f.set_validator(&validator);
// --------------------------------------------------------------------
const char data[] = R"(
data_test
loop_
_cat_1.id
_cat_1.id_2
1 1
2 2
3 ?
loop_
_cat_2.id
_cat_2.parent_id
_cat_2.parent_id_2
0 1 1
1 1 ?
2 ? 1
3 ? ?
4 2 2
5 3 1
6 3 ?
)";
// --------------------------------------------------------------------
struct data_membuf : public std::streambuf
{
data_membuf(char *text, size_t length)
{
this->setg(text, text, text + length);
}
} data_buffer(const_cast<char *>(data), sizeof(data) - 1);
std::istream is_data(&data_buffer);
f.load(is_data);
// auto &cat1 = f.front()["cat_1"];
auto &cat2 = f.front()["cat_2"];
// f.front().validate_links();
// BOOST_CHECK(not );
using namespace cif::literals;
BOOST_CHECK( cat2.has_parents(cat2.find1("id"_key == 0)));
BOOST_CHECK( cat2.has_parents(cat2.find1("id"_key == 1)));
BOOST_CHECK( cat2.has_parents(cat2.find1("id"_key == 2)));
BOOST_CHECK(not cat2.has_parents(cat2.find1("id"_key == 3)));
BOOST_CHECK( cat2.has_parents(cat2.find1("id"_key == 4)));
BOOST_CHECK(not cat2.has_parents(cat2.find1("id"_key == 5)));
BOOST_CHECK( cat2.has_parents(cat2.find1("id"_key == 6)));
}
// --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(c1)
{
cif::VERBOSE = 1;
auto f = R"(data_TEST
#
loop_
_test.id
_test.name
1 aap
2 noot
3 mies
4 .
5 ?
)"_cf;
auto &db = f.front();
for (auto r : db["test"].find(cif::key("id") == 1))
{
const auto &[id, name] = r.get<int, std::string>("id", "name");
BOOST_CHECK_EQUAL(id, 1);
BOOST_CHECK_EQUAL(name, "aap");
}
for (auto r : db["test"].find(cif::key("id") == 4))
{
const auto &[id, name] = r.get<int, std::string>("id", "name");
BOOST_CHECK_EQUAL(id, 4);
BOOST_CHECK(name.empty());
}
for (auto r : db["test"].find(cif::key("id") == 5))
{
const auto &[id, name] = r.get<int, std::string>("id", "name");
BOOST_CHECK_EQUAL(id, 5);
BOOST_CHECK(name.empty());
}
// optional
for (auto r : db["test"])
{
const auto &[id, name] = r.get<int, std::optional<std::string>>("id", "name");
switch (id)
{
case 1: BOOST_CHECK(name == "aap"); break;
case 2: BOOST_CHECK(name == "noot"); break;
case 3: BOOST_CHECK(name == "mies"); break;
case 4:
case 5: BOOST_CHECK(not name); break;
default:
BOOST_CHECK(false);
}
}
}
BOOST_AUTO_TEST_CASE(c2)
{
cif::VERBOSE = 1;
auto f = R"(data_TEST
#
loop_
_test.id
_test.name
1 aap
2 noot
3 mies
4 .
5 ?
)"_cf;
auto &db = f.front();
// query tests
for (const auto &[id, name] : db["test"].rows<int, std::optional<std::string>>("id", "name"))
{
switch (id)
{
case 1: BOOST_CHECK(name == "aap"); break;
case 2: BOOST_CHECK(name == "noot"); break;
case 3: BOOST_CHECK(name == "mies"); break;
case 4:
case 5: BOOST_CHECK(not name); break;
default:
BOOST_CHECK(false);
}
}
}
BOOST_AUTO_TEST_CASE(c3)
{
auto f = R"(data_TEST
#
loop_
_test.id
_test.name
1 aap
2 noot
3 mies
4 .
5 ?
)"_cf;
auto &db = f.front();
// query tests
for (const auto &[id, name] : db["test"].find<int, std::optional<std::string>>(cif::all(), "id", "name"))
{
switch (id)
{
case 1: BOOST_CHECK(name == "aap"); break;
case 2: BOOST_CHECK(name == "noot"); break;
case 3: BOOST_CHECK(name == "mies"); break;
case 4:
case 5: BOOST_CHECK(not name); break;
default:
BOOST_CHECK(false);
}
}
const auto &[id, name] = db["test"].find1<int, std::string>(cif::key("id") == 1, "id", "name");
BOOST_CHECK_EQUAL(id, 1);
BOOST_CHECK_EQUAL(name, "aap");
}
BOOST_AUTO_TEST_CASE(c4)
{
auto f = R"(data_TEST
#
loop_
_test.id
_test.name
1 aap
2 noot
3 mies
4 .
5 ?
)"_cf;
auto &db = f.front();
// query tests
BOOST_TEST(db["test"].find_max<int>("id") == 5);
BOOST_TEST(db["test"].find_max<int>("id", cif::key("name") != cif::null) == 3);
BOOST_TEST(db["test"].find_min<int>("id") == 1);
BOOST_TEST(db["test"].find_min<int>("id", cif::key("name") == cif::null) == 4);
// count tests
BOOST_TEST(db["test"].count(cif::all()) == 5);
BOOST_TEST(db["test"].count(cif::key("name") != cif::null) == 3);
BOOST_TEST(db["test"].count(cif::key("name") == cif::null) == 2);
// find_first tests
BOOST_TEST(db["test"].find_first<int>(cif::key("id") == 1, "id") == 1);
BOOST_TEST(db["test"].find_first<int>(cif::all(), "id") == 1);
std::optional<int> v;
v = db["test"].find_first<std::optional<int>>(cif::key("id") == 1, "id");
BOOST_TEST(v.has_value());
BOOST_TEST(*v == 1);
v = db["test"].find_first<std::optional<int>>(cif::key("id") == 6, "id");
BOOST_TEST(not v.has_value());
// find1 tests
BOOST_TEST(db["test"].find1<int>(cif::key("id") == 1, "id") == 1);
BOOST_CHECK_THROW(db["test"].find1<int>(cif::all(), "id"), cif::multiple_results_error);
}
// --------------------------------------------------------------------
// rename test
BOOST_AUTO_TEST_CASE(r1)
{
/*
Rationale:
The pdbx_mmcif dictionary contains inconsistent child-parent relations. E.g. atom_site is parent
of pdbx_nonpoly_scheme which itself is a parent of pdbx_entity_nonpoly. If I want to rename a residue
I cannot update pdbx_nonpoly_scheme since changing a parent changes children, but not vice versa.
But if I change the comp_id in atom_site, the pdbx_nonpoly_scheme is updated, that's good, and then
pdbx_entity_nonpoly is updated and that's bad.
The idea is now that if we update a parent and a child that must change as well, we first check
if there are more parents of this child that will not change. In that case we have to split the
child into two, one with the new value and one with the old. We then of course have to split all
children of this split row that are direct children.
*/
const char dict[] = R"(
data_test_dict.dic
_datablock.id test_dict.dic
_datablock.description
;
A test dictionary
;
_dictionary.title test_dict.dic
_dictionary.datablock_id test_dict.dic
_dictionary.version 1.0
loop_
_item_type_list.code
_item_type_list.primitive_code
_item_type_list.construct
code char
'[][_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]*'
text char
'[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*'
int numb
'[+-]?[0-9]+'
save_cat_1
_category.description 'A simple test category'
_category.id cat_1
_category.mandatory_code no
_category_key.name '_cat_1.id'
save_
save__cat_1.id
_item.name '_cat_1.id'
_item.category_id cat_1
_item.mandatory_code yes
_item_linked.child_name '_cat_2.parent_id'
_item_linked.parent_name '_cat_1.id'
_item_type.code int
save_
save__cat_1.name
_item.name '_cat_1.name'
_item.category_id cat_1
_item.mandatory_code yes
_item_type.code code
save_
save__cat_1.desc
_item.name '_cat_1.desc'
_item.category_id cat_1
_item.mandatory_code yes
_item_type.code text
save_
save_cat_2
_category.description 'A second simple test category'
_category.id cat_2
_category.mandatory_code no
_category_key.name '_cat_2.id'
save_
save__cat_2.id
_item.name '_cat_2.id'
_item.category_id cat_2
_item.mandatory_code yes
_item_type.code int
save_
save__cat_2.name
_item.name '_cat_2.name'
_item.category_id cat_2
_item.mandatory_code yes
_item_type.code code
save_
save__cat_2.num
_item.name '_cat_2.num'
_item.category_id cat_2
_item.mandatory_code yes
_item_type.code int
save_
save__cat_2.desc
_item.name '_cat_2.desc'
_item.category_id cat_2
_item.mandatory_code yes
_item_type.code text
save_
save_cat_3
_category.description 'A third simple test category'
_category.id cat_3
_category.mandatory_code no
_category_key.name '_cat_3.id'
save_
save__cat_3.id
_item.name '_cat_3.id'
_item.category_id cat_3
_item.mandatory_code yes
_item_type.code int
save_
save__cat_3.name
_item.name '_cat_3.name'
_item.category_id cat_3
_item.mandatory_code yes
_item_type.code code
save_
save__cat_3.num
_item.name '_cat_3.num'
_item.category_id cat_3
_item.mandatory_code yes
_item_type.code int
save_
loop_
_pdbx_item_linked_group_list.child_category_id
_pdbx_item_linked_group_list.link_group_id
_pdbx_item_linked_group_list.child_name
_pdbx_item_linked_group_list.parent_name
_pdbx_item_linked_group_list.parent_category_id
cat_1 1 '_cat_1.name' '_cat_2.name' cat_2
cat_2 1 '_cat_2.name' '_cat_3.name' cat_3
cat_2 1 '_cat_2.num' '_cat_3.num' cat_3
)";
struct membuf : public std::streambuf
{
membuf(char *text, size_t length)
{
this->setg(text, text, text + length);
}
} buffer(const_cast<char *>(dict), sizeof(dict) - 1);
std::istream is_dict(&buffer);
auto validator = cif::parse_dictionary("test", is_dict);
cif::file f;
f.set_validator(&validator);
// --------------------------------------------------------------------
const char data[] = R"(
data_test
loop_
_cat_1.id
_cat_1.name
_cat_1.desc
1 aap Aap
2 noot Noot
3 mies Mies
loop_
_cat_2.id
_cat_2.name
_cat_2.num
_cat_2.desc
1 aap 1 'Een dier'
2 aap 2 'Een andere aap'
3 noot 1 'walnoot bijvoorbeeld'
loop_
_cat_3.id
_cat_3.name
_cat_3.num
1 aap 1
2 aap 2
)";
using namespace cif::literals;
struct data_membuf : public std::streambuf
{
data_membuf(char *text, size_t length)
{
this->setg(text, text, text + length);
}
} data_buffer(const_cast<char *>(data), sizeof(data) - 1);
std::istream is_data(&data_buffer);
f.load(is_data);
auto &cat1 = f.front()["cat_1"];
auto &cat2 = f.front()["cat_2"];
auto &cat3 = f.front()["cat_3"];
cat3.update_value("name"_key == "aap" and "num"_key == 1, "name", "aapje");
BOOST_CHECK_EQUAL(cat3.size(), 2);
{
int id, num;
std::string name;
cif::tie(id, name, num) = cat3.front().get("id", "name", "num");
BOOST_CHECK_EQUAL(id, 1);
BOOST_CHECK_EQUAL(num, 1);
BOOST_CHECK_EQUAL(name, "aapje");
cif::tie(id, name, num) = cat3.back().get("id", "name", "num");
BOOST_CHECK_EQUAL(id, 2);
BOOST_CHECK_EQUAL(num, 2);
BOOST_CHECK_EQUAL(name, "aap");
}
int i = 0;
for (const auto &[id, name, num, desc] : cat2.rows<int, std::string, int, std::string>("id", "name", "num", "desc"))
{
switch (++i)
{
case 1:
BOOST_CHECK_EQUAL(id, 1);
BOOST_CHECK_EQUAL(num, 1);
BOOST_CHECK_EQUAL(name, "aapje");
BOOST_CHECK_EQUAL(desc, "Een dier");
break;
case 2:
BOOST_CHECK_EQUAL(id, 2);
BOOST_CHECK_EQUAL(num, 2);
BOOST_CHECK_EQUAL(name, "aap");
BOOST_CHECK_EQUAL(desc, "Een andere aap");
break;
case 3:
BOOST_CHECK_EQUAL(id, 3);
BOOST_CHECK_EQUAL(num, 1);
BOOST_CHECK_EQUAL(name, "noot");
BOOST_CHECK_EQUAL(desc, "walnoot bijvoorbeeld");
break;
default:
BOOST_FAIL("Unexpected record");
}
}
BOOST_CHECK_EQUAL(cat1.size(), 4);
i = 0;
for (const auto &[id, name, desc] : cat1.rows<int, std::string, std::string>("id", "name", "desc"))
{
switch (++i)
{
case 1:
BOOST_CHECK_EQUAL(id, 1);
BOOST_CHECK_EQUAL(name, "aapje");
BOOST_CHECK_EQUAL(desc, "Aap");
break;
case 2:
BOOST_CHECK_EQUAL(id, 2);
BOOST_CHECK_EQUAL(name, "noot");
BOOST_CHECK_EQUAL(desc, "Noot");
break;
case 3:
BOOST_CHECK_EQUAL(id, 3);
BOOST_CHECK_EQUAL(name, "mies");
BOOST_CHECK_EQUAL(desc, "Mies");
break;
case 4:
BOOST_CHECK_EQUAL(id, 4);
BOOST_CHECK_EQUAL(name, "aap");
BOOST_CHECK_EQUAL(desc, "Aap");
break;
default:
BOOST_FAIL("Unexpected record");
}
}
// f.save(std::cout);
}
BOOST_AUTO_TEST_CASE(pc_1)
{
/*
Parent/child tests
Note that the dictionary is different than the one in test r1
*/
const char dict[] = R"(
data_test_dict.dic
_datablock.id test_dict.dic
_datablock.description
;
A test dictionary
;
_dictionary.title test_dict.dic
_dictionary.datablock_id test_dict.dic
_dictionary.version 1.0
loop_
_item_type_list.code
_item_type_list.primitive_code
_item_type_list.construct
code char
'[][_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]*'
text char
'[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*'
int numb
'[+-]?[0-9]+'
save_cat_1
_category.description 'A simple test category'
_category.id cat_1
_category.mandatory_code no
_category_key.name '_cat_1.id'
save_
save__cat_1.id
_item.name '_cat_1.id'
_item.category_id cat_1
_item.mandatory_code yes
_item_linked.child_name '_cat_2.parent_id'
_item_linked.parent_name '_cat_1.id'
_item_type.code int
save_
save__cat_1.name
_item.name '_cat_1.name'
_item.category_id cat_1
_item.mandatory_code yes
_item_type.code code
save_
save__cat_1.desc
_item.name '_cat_1.desc'
_item.category_id cat_1
_item.mandatory_code yes
_item_type.code text
save_
save_cat_2
_category.description 'A second simple test category'
_category.id cat_2
_category.mandatory_code no
_category_key.name '_cat_2.id'
save_
save__cat_2.id
_item.name '_cat_2.id'
_item.category_id cat_2
_item.mandatory_code yes
_item_type.code int
save_
save__cat_2.name
_item.name '_cat_2.name'
_item.category_id cat_2
_item.mandatory_code yes
_item_type.code code
save_
save__cat_2.num
_item.name '_cat_2.num'
_item.category_id cat_2
_item.mandatory_code yes
_item_type.code int
save_
save__cat_2.desc
_item.name '_cat_2.desc'
_item.category_id cat_2
_item.mandatory_code yes
_item_type.code text
save_
save_cat_3
_category.description 'A third simple test category'
_category.id cat_3
_category.mandatory_code no
_category_key.name '_cat_3.id'
save_
save__cat_3.id
_item.name '_cat_3.id'
_item.category_id cat_3
_item.mandatory_code yes
_item_type.code int
save_
save__cat_3.name
_item.name '_cat_3.name'
_item.category_id cat_3
_item.mandatory_code yes
_item_type.code code
save_
save__cat_3.num
_item.name '_cat_3.num'
_item.category_id cat_3
_item.mandatory_code yes
_item_type.code int
save_
loop_
_pdbx_item_linked_group_list.parent_category_id
_pdbx_item_linked_group_list.link_group_id
_pdbx_item_linked_group_list.parent_name
_pdbx_item_linked_group_list.child_name
_pdbx_item_linked_group_list.child_category_id
cat_1 1 '_cat_1.name' '_cat_2.name' cat_2
cat_2 1 '_cat_2.name' '_cat_3.name' cat_3
cat_2 1 '_cat_2.num' '_cat_3.num' cat_3
)";
struct membuf : public std::streambuf
{
membuf(char *text, size_t length)
{
this->setg(text, text, text + length);
}
} buffer(const_cast<char *>(dict), sizeof(dict) - 1);
std::istream is_dict(&buffer);
auto validator = cif::parse_dictionary("test", is_dict);
cif::file f;
f.set_validator(&validator);
// --------------------------------------------------------------------
const char data[] = R"(
data_test
loop_
_cat_1.id
_cat_1.name
_cat_1.desc
1 aap Aap
2 noot Noot
3 mies Mies
loop_
_cat_2.id
_cat_2.name
_cat_2.num
_cat_2.desc
1 aap 1 'Een dier'
2 aap 2 'Een andere aap'
3 noot 1 'walnoot bijvoorbeeld'
loop_
_cat_3.id
_cat_3.name
_cat_3.num
1 aap 1
2 aap 2
)";
using namespace cif::literals;
struct data_membuf : public std::streambuf
{
data_membuf(char *text, size_t length)
{
this->setg(text, text, text + length);
}
} data_buffer(const_cast<char *>(data), sizeof(data) - 1);
std::istream is_data(&data_buffer);
f.load(is_data);
auto &cat1 = f.front()["cat_1"];
auto &cat2 = f.front()["cat_2"];
auto &cat3 = f.front()["cat_3"];
// some parent/child tests
// find all children in cat2 for the row with id == 1 in cat1
auto rs1 = cat1.get_children(cat1.find1("id"_key == 1), cat2);
BOOST_TEST(rs1.size() == 2);
auto rs2 = cat1.get_children(cat1.find1("id"_key == 2), cat2);
BOOST_TEST(rs2.size() == 1);
auto rs3 = cat1.get_children(cat1.find1("id"_key == 3), cat2);
BOOST_TEST(rs3.size() == 0);
// finding parents
auto rs4 = cat2.get_parents(cat2.find1("id"_key == 1), cat1);
BOOST_TEST(rs4.size() == 1);
auto rs5 = cat3.get_parents(cat3.find1("id"_key == 1), cat2);
BOOST_TEST(rs5.size() == 1);
// This link is not defined:
auto rs6 = cat3.get_parents(cat3.find1("id"_key == 1), cat1);
BOOST_TEST(rs6.size() == 0);
}
// --------------------------------------------------------------------
// BOOST_AUTO_TEST_CASE(bondmap_1)
// {
// cif::VERBOSE = 2;
// // sections taken from CCD compounds.cif
// auto components = R"(
// data_ASN
// loop_
// _chem_comp_bond.comp_id
// _chem_comp_bond.atom_id_1
// _chem_comp_bond.atom_id_2
// _chem_comp_bond.value_order
// _chem_comp_bond.pdbx_aromatic_flag
// _chem_comp_bond.pdbx_stereo_config
// _chem_comp_bond.pdbx_ordinal
// ASN N CA SING N N 1
// ASN N H SING N N 2
// ASN N H2 SING N N 3
// ASN CA C SING N N 4
// ASN CA CB SING N N 5
// ASN CA HA SING N N 6
// ASN C O DOUB N N 7
// ASN C OXT SING N N 8
// ASN CB CG SING N N 9
// ASN CB HB2 SING N N 10
// ASN CB HB3 SING N N 11
// ASN CG OD1 DOUB N N 12
// ASN CG ND2 SING N N 13
// ASN ND2 HD21 SING N N 14
// ASN ND2 HD22 SING N N 15
// ASN OXT HXT SING N N 16
// data_PHE
// loop_
// _chem_comp_bond.comp_id
// _chem_comp_bond.atom_id_1
// _chem_comp_bond.atom_id_2
// _chem_comp_bond.value_order
// _chem_comp_bond.pdbx_aromatic_flag
// _chem_comp_bond.pdbx_stereo_config
// _chem_comp_bond.pdbx_ordinal
// PHE N CA SING N N 1
// PHE N H SING N N 2
// PHE N H2 SING N N 3
// PHE CA C SING N N 4
// PHE CA CB SING N N 5
// PHE CA HA SING N N 6
// PHE C O DOUB N N 7
// PHE C OXT SING N N 8
// PHE CB CG SING N N 9
// PHE CB HB2 SING N N 10
// PHE CB HB3 SING N N 11
// PHE CG CD1 DOUB Y N 12
// PHE CG CD2 SING Y N 13
// PHE CD1 CE1 SING Y N 14
// PHE CD1 HD1 SING N N 15
// PHE CD2 CE2 DOUB Y N 16
// PHE CD2 HD2 SING N N 17
// PHE CE1 CZ DOUB Y N 18
// PHE CE1 HE1 SING N N 19
// PHE CE2 CZ SING Y N 20
// PHE CE2 HE2 SING N N 21
// PHE CZ HZ SING N N 22
// PHE OXT HXT SING N N 23
// data_PRO
// loop_
// _chem_comp_bond.comp_id
// _chem_comp_bond.atom_id_1
// _chem_comp_bond.atom_id_2
// _chem_comp_bond.value_order
// _chem_comp_bond.pdbx_aromatic_flag
// _chem_comp_bond.pdbx_stereo_config
// _chem_comp_bond.pdbx_ordinal
// PRO N CA SING N N 1
// PRO N CD SING N N 2
// PRO N H SING N N 3
// PRO CA C SING N N 4
// PRO CA CB SING N N 5
// PRO CA HA SING N N 6
// PRO C O DOUB N N 7
// PRO C OXT SING N N 8
// PRO CB CG SING N N 9
// PRO CB HB2 SING N N 10
// PRO CB HB3 SING N N 11
// PRO CG CD SING N N 12
// PRO CG HG2 SING N N 13
// PRO CG HG3 SING N N 14
// PRO CD HD2 SING N N 15
// PRO CD HD3 SING N N 16
// PRO OXT HXT SING N N 17
// )"_cf;
// const std::filesystem::path example(gTestDir / ".." / "examples" / "1cbs.cif.gz");
// mmcif::File file(example.string());
// mmcif::Structure structure(file);
// (void)file.isValid();
// mmcif::BondMap bm(structure);
// // Test the bonds of the first three residues, that's PRO A 1, ASN A 2, PHE A 3
// for (const auto &[compound, seqnr] : std::initializer_list<std::tuple<std::string, int>>{{"PRO", 1}, {"ASN", 2}, {"PHE", 3}})
// {
// auto &res = structure.get_residue("A", compound, seqnr, "");
// auto atoms = res.atoms();
// auto dc = components.get(compound);
// BOOST_ASSERT(dc != nullptr);
// auto cc = dc->get("chem_comp_bond");
// BOOST_ASSERT(cc != nullptr);
// std::set<std::tuple<std::string, std::string>> bonded;
// for (const auto &[atom_id_1, atom_id_2] : cc->rows<std::string, std::string>("atom_id_1", "atom_id_2"))
// {
// if (atom_id_1 > atom_id_2)
// bonded.insert({atom_id_2, atom_id_1});
// else
// bonded.insert({atom_id_1, atom_id_2});
// }
// for (size_t i = 0; i + 1 < atoms.size(); ++i)
// {
// auto label_i = atoms[i].labelAtomID();
// for (size_t j = i + 1; j < atoms.size(); ++j)
// {
// auto label_j = atoms[j].labelAtomID();
// bool bonded_1 = bm(atoms[i], atoms[j]);
// bool bonded_1_i = bm(atoms[j], atoms[i]);
// bool bonded_t = label_i > label_j
// ? bonded.count({label_j, label_i})
// : bonded.count({label_i, label_j});
// BOOST_CHECK(bonded_1 == bonded_t);
// BOOST_CHECK(bonded_1_i == bonded_t);
// }
// }
// }
// // And check the inter-aminoacid links
// auto &poly = structure.polymers().front();
// for (size_t i = 0; i + 1 < poly.size(); ++i)
// {
// auto C = poly[i].atomByID("C");
// auto N = poly[i + 1].atomByID("N");
// BOOST_CHECK(bm(C, N));
// BOOST_CHECK(bm(N, C));
// }
// }
// BOOST_AUTO_TEST_CASE(bondmap_2)
// {
// BOOST_CHECK_THROW(mmcif::BondMap::atomIDsForCompound("UN_"), mmcif::BondMapException);
// mmcif::CompoundFactory::instance().pushDictionary(gTestDir / "UN_.cif");
// BOOST_CHECK(mmcif::BondMap::atomIDsForCompound("UN_").empty() == false);
// }
BOOST_AUTO_TEST_CASE(reading_file_1)
{
std::istringstream is("Hello, world!");
cif::file file;
BOOST_CHECK_THROW(file.load(is), std::runtime_error);
}
BOOST_AUTO_TEST_CASE(parser_test_1)
{
auto data1 = R"(
data_QM
_test.text ??
)"_cf;
auto &db1 = data1.front();
auto &test1 = db1["test"];
BOOST_CHECK_EQUAL(test1.size(), 1);
for (auto r : test1)
{
auto text = r.get<std::string>("text");
BOOST_CHECK_EQUAL(text, "??");
}
std::stringstream ss;
data1.save(ss);
auto data2 = cif::file(ss);
auto &db2 = data2.front();
auto &test2 = db2["test"];
BOOST_CHECK_EQUAL(test2.size(), 1);
for (auto r : test2)
{
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
'data_.whatever'
'stop_'
'loop_'
'global_'
'_with.leading_underscore'
)"_cf;
auto &db1 = data1.front();
auto &test1 = db1["test"];
struct T
{
const char *s;
bool q;
} kS[] = {
{ "stop_the_crap", true },
{ "and stop_ this too", false },
{ "data_dinges", false },
{ "blablaglobal_bla", true },
{ "boo.data_.whatever", true },
{ "data_.whatever", false },
{ "stop_", false },
{ "loop_", false },
{ "global_", false },
{ "_with.leading_underscore", false }
};
BOOST_CHECK_EQUAL(test1.size(), sizeof(kS) / sizeof(T));
size_t i = 0;
for (auto r : test1)
{
auto text = r.get<std::string>("text");
BOOST_CHECK_EQUAL(text, kS[i].s);
BOOST_CHECK_EQUAL(cif::sac_parser::is_unquoted_string(kS[i].s), kS[i].q);
++i;
}
std::stringstream ss;
data1.save(ss);
auto data2 = cif::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)
{
auto text = r.get<std::string>("text");
BOOST_CHECK_EQUAL(text, kS[i++].s);
}
}
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 }
};
BOOST_CHECK_EQUAL(test1.size(), sizeof(kS) / sizeof(T));
size_t i = 0;
for (auto r : test1)
{
auto text = r.get<std::string>("text");
BOOST_CHECK_EQUAL(text, kS[i].s);
BOOST_CHECK_EQUAL(cif::sac_parser::is_unquoted_string(kS[i].s), kS[i].q);
++i;
}
std::stringstream ss;
data1.save(ss);
auto data2 = cif::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)
{
auto text = r.get<std::string>("text");
BOOST_CHECK_EQUAL(text, kS[i++].s);
}
}
BOOST_AUTO_TEST_CASE(trim_test)
{
BOOST_CHECK_EQUAL(cif::trim_copy("aap"), "aap");
BOOST_CHECK_EQUAL(cif::trim_copy(" aap"), "aap");
BOOST_CHECK_EQUAL(cif::trim_copy(" aap "), "aap");
BOOST_CHECK_EQUAL(cif::trim_copy("aap "), "aap");
BOOST_CHECK_EQUAL(cif::trim_copy(" aap "), "aap");
BOOST_CHECK_EQUAL(cif::trim_left_copy("aap"), "aap");
BOOST_CHECK_EQUAL(cif::trim_left_copy(" aap"), "aap");
BOOST_CHECK_EQUAL(cif::trim_left_copy(" aap "), "aap ");
BOOST_CHECK_EQUAL(cif::trim_left_copy("aap "), "aap ");
BOOST_CHECK_EQUAL(cif::trim_left_copy("aap "), "aap ");
BOOST_CHECK_EQUAL(cif::trim_right_copy("aap"), "aap");
BOOST_CHECK_EQUAL(cif::trim_right_copy(" aap"), " aap");
BOOST_CHECK_EQUAL(cif::trim_right_copy(" aap "), " aap");
BOOST_CHECK_EQUAL(cif::trim_right_copy("aap "), "aap");
BOOST_CHECK_EQUAL(cif::trim_right_copy(" aap "), " aap");
std::string s;
s = "aap";
cif::trim(s);
BOOST_CHECK_EQUAL(s, "aap");
s = " aap";
cif::trim(s);
BOOST_CHECK_EQUAL(s, "aap");
s = " aap ";
cif::trim(s);
BOOST_CHECK_EQUAL(s, "aap");
s = "aap ";
cif::trim(s);
BOOST_CHECK_EQUAL(s, "aap");
s = " aap ";
cif::trim(s);
BOOST_CHECK_EQUAL(s, "aap");
s = "aap";
cif::trim_left(s);
BOOST_CHECK_EQUAL(s, "aap");
s = " aap";
cif::trim_left(s);
BOOST_CHECK_EQUAL(s, "aap");
s = " aap ";
cif::trim_left(s);
BOOST_CHECK_EQUAL(s, "aap ");
s = "aap ";
cif::trim_left(s);
BOOST_CHECK_EQUAL(s, "aap ");
s = "aap ";
cif::trim_left(s);
BOOST_CHECK_EQUAL(s, "aap ");
s = "aap";
cif::trim_right(s);
BOOST_CHECK_EQUAL(s, "aap");
s = " aap";
cif::trim_right(s);
BOOST_CHECK_EQUAL(s, " aap");
s = " aap ";
cif::trim_right(s);
BOOST_CHECK_EQUAL(s, " aap");
s = "aap ";
cif::trim_right(s);
BOOST_CHECK_EQUAL(s, "aap");
s = " aap ";
cif::trim_right(s);
BOOST_CHECK_EQUAL(s, " aap");
}
BOOST_AUTO_TEST_CASE(split_test)
{
std::vector<std::string_view> v, t;
v = cif::split<>("aap;noot;mies", ";");
t = std::vector<std::string_view>{ "aap", "noot", "mies" };
BOOST_CHECK(v == t);
v = cif::split("aap;noot,mies", ";,");
// t = std::vector<std::string>{ "aap", "noot", "mies" };
BOOST_CHECK(v == t);
v = cif::split(";aap;noot,mies;", ";,");
t = std::vector<std::string_view>{ "", "aap", "noot", "mies", "" };
BOOST_CHECK(v == t);
v = cif::split(";aap;noot,mies;", ";,", true);
t = std::vector<std::string_view>{ "aap", "noot", "mies" };
BOOST_CHECK(v == t);
}
BOOST_AUTO_TEST_CASE(join_test)
{
BOOST_CHECK_EQUAL(cif::join(std::vector<std::string>{ "aap" }, ", "), "aap");
BOOST_CHECK_EQUAL(cif::join(std::vector<std::string>{ "aap", "noot" }, ", "), "aap, noot");
BOOST_CHECK_EQUAL(cif::join(std::vector<std::string>{ "aap", "noot", "mies" }, ", "), "aap, noot, mies");
}
BOOST_AUTO_TEST_CASE(replace_all_test)
{
std::string s("aap, noot, mies");
cif::replace_all(s, ", ", ",");
BOOST_CHECK_EQUAL(s, "aap,noot,mies");
cif::replace_all(s, ",", ", ");
BOOST_CHECK_EQUAL(s, "aap, noot, mies");
cif::replace_all(s, ", ", ", ");
BOOST_CHECK_EQUAL(s, "aap, noot, mies");
}
// --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(reorder_test)
{
const char dict[] = R"(
data_test_dict.dic
_datablock.id test_dict.dic
_datablock.description
;
A test dictionary
;
_dictionary.title test_dict.dic
_dictionary.datablock_id test_dict.dic
_dictionary.version 1.0
loop_
_item_type_list.code
_item_type_list.primitive_code
_item_type_list.construct
_item_type_list.detail
code char
'[][_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types/single words ...
;
text char
'[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*'
; text item types / multi-line text ...
;
int numb
'[+-]?[0-9]+'
; int item types are the subset of numbers that are the negative
or positive integers.
;
save_cat_1
_category.description 'A simple test category'
_category.id cat_1
_category.mandatory_code no
_category_key.name '_cat_1.id'
save_
save__cat_1.id
_item.name '_cat_1.id'
_item.category_id cat_1
_item.mandatory_code yes
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code code
save_
save__cat_1.name
_item.name '_cat_1.name'
_item.category_id cat_1
_item.mandatory_code yes
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
)";
struct membuf : public std::streambuf
{
membuf(char *text, size_t length)
{
this->setg(text, text, text + length);
}
} buffer(const_cast<char *>(dict), sizeof(dict) - 1);
std::istream is_dict(&buffer);
auto validator = cif::parse_dictionary("test", is_dict);
cif::file f;
f.set_validator(&validator);
// --------------------------------------------------------------------
const char data[] = R"(
data_test
loop_
_cat_1.id
_cat_1.name
2 Noot
1 Aap
3 Mies
)";
struct data_membuf : public std::streambuf
{
data_membuf(char *text, size_t length)
{
this->setg(text, text, text + length);
}
} data_buffer(const_cast<char *>(data), sizeof(data) - 1);
std::istream is_data(&data_buffer);
f.load(is_data);
BOOST_ASSERT(f.is_valid());
auto &cat1 = f.front()["cat_1"];
cat1.reorder_by_index();
int n = 1;
const char *ts[] = { "Aap", "Noot", "Mies" };
for (const auto &[id, name] : cat1.rows<int, std::string>("id", "name"))
{
BOOST_CHECK_EQUAL(id, n);
BOOST_CHECK_EQUAL(name, ts[n - 1]);
++n;
}
}
// --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(audit_conform_test)
{
const char dict[] = R"(
data_test_dict.dic
_datablock.id test_dict.dic
_datablock.description
;
A test dictionary
;
_dictionary.title test_dict.dic
_dictionary.datablock_id test_dict.dic
_dictionary.version 1.0
loop_
_item_type_list.code
_item_type_list.primitive_code
_item_type_list.construct
_item_type_list.detail
code char
'[][_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types/single words ...
;
text char
'[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*'
; text item types / multi-line text ...
;
int numb
'[+-]?[0-9]+'
; int item types are the subset of numbers that are the negative
or positive integers.
;
###################
## AUDIT_CONFORM ##
###################
save_audit_conform
_category.description
; Data items in the AUDIT_CONFORM category describe the
dictionary versions against which the data names appearing in
the current data block are conformant.
;
_category.id audit_conform
_category.mandatory_code no
loop_
_category_key.name '_audit_conform.dict_name'
'_audit_conform.dict_version'
loop_
_category_group.id 'inclusive_group'
'audit_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - any file conforming to the current CIF core dictionary.
;
;
_audit_conform.dict_name cif_core.dic
_audit_conform.dict_version 2.3.1
_audit_conform.dict_location
ftp://ftp.iucr.org/pub/cif_core.2.3.1.dic
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__audit_conform.dict_location
_item_description.description
; A file name or uniform resource locator (URL) for the
dictionary to which the current data block conforms.
;
_item.name '_audit_conform.dict_location'
_item.category_id audit_conform
_item.mandatory_code no
_item_aliases.alias_name '_audit_conform_dict_location'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
save__audit_conform.dict_name
_item_description.description
; The string identifying the highest-level dictionary defining
data names used in this file.
;
_item.name '_audit_conform.dict_name'
_item.category_id audit_conform
_item.mandatory_code yes
_item_aliases.alias_name '_audit_conform_dict_name'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
save__audit_conform.dict_version
_item_description.description
; The version number of the dictionary to which the current
data block conforms.
;
_item.name '_audit_conform.dict_version'
_item.category_id audit_conform
_item.mandatory_code yes
_item_aliases.alias_name '_audit_conform_dict_version'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
save_cat_1
_category.description 'A simple test category'
_category.id cat_1
_category.mandatory_code no
_category_key.name '_cat_1.id'
save_
save__cat_1.id
_item.name '_cat_1.id'
_item.category_id cat_1
_item.mandatory_code yes
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code code
save_
save__cat_1.name
_item.name '_cat_1.name'
_item.category_id cat_1
_item.mandatory_code yes
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
)";
struct membuf : public std::streambuf
{
membuf(char *text, size_t length)
{
this->setg(text, text, text + length);
}
} buffer(const_cast<char *>(dict), sizeof(dict) - 1);
std::istream is_dict(&buffer);
auto &validator = cif::validator_factory::instance().construct_validator("test_dict.dic", is_dict);
cif::file f;
f.set_validator(&validator);
// --------------------------------------------------------------------
const char data[] = R"(
data_test
#
_audit_conform.dict_name test_dict.dic
_audit_conform.dict_version 1.0
#
loop_
_cat_1.id
_cat_1.name
2 Noot
1 Aap
3 Mies
)";
struct data_membuf : public std::streambuf
{
data_membuf(char *text, size_t length)
{
this->setg(text, text, text + length);
}
} data_buffer(const_cast<char *>(data), sizeof(data) - 1);
std::istream is_data(&data_buffer);
f.load(is_data);
BOOST_ASSERT(f.is_valid());
std::stringstream ss;
ss << f;
cif::file f2(ss);
BOOST_ASSERT(f2.is_valid());
auto &audit_conform = f2.front()["audit_conform"];
BOOST_CHECK_EQUAL(audit_conform.front()["dict_name"].as<std::string>(), "test_dict.dic");
BOOST_CHECK_EQUAL(audit_conform.front()["dict_version"].as<float>(), 1.0);
}
// --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(ix_op_1)
{
const char dict[] = R"(
data_test_dict.dic
_datablock.id test_dict.dic
_datablock.description
;
A test dictionary
;
_dictionary.title test_dict.dic
_dictionary.datablock_id test_dict.dic
_dictionary.version 1.0
loop_
_item_type_list.code
_item_type_list.primitive_code
_item_type_list.construct
code char
'[][_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]*'
text char
'[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*'
int numb
'[+-]?[0-9]+'
save_cat_1
_category.description 'A simple test category'
_category.id cat_1
_category.mandatory_code yes
loop_
_category_key.name '_cat_1.id'
'_cat_1.id_2'
save_
save__cat_1.id
_item.name '_cat_1.id'
_item.category_id cat_1
_item.mandatory_code yes
_item_type.code int
save_
save__cat_1.id_2
_item.name '_cat_1.id_2'
_item.category_id cat_1
_item.mandatory_code no
_item_type.code int
save_
)";
struct membuf : public std::streambuf
{
membuf(char *text, size_t length)
{
this->setg(text, text, text + length);
}
} buffer(const_cast<char *>(dict), sizeof(dict) - 1);
std::istream is_dict(&buffer);
auto validator = cif::parse_dictionary("test", is_dict);
cif::file f;
f.set_validator(&validator);
// --------------------------------------------------------------------
const char data[] = R"(
data_test
loop_
_cat_1.id
_cat_1.id_2
1 10
2 20
3 ?
)";
// --------------------------------------------------------------------
struct data_membuf : public std::streambuf
{
data_membuf(char *text, size_t length)
{
this->setg(text, text, text + length);
}
} data_buffer(const_cast<char *>(data), sizeof(data) - 1);
std::istream is_data(&data_buffer);
f.load(is_data);
auto &cat1 = f.front()["cat_1"];
using key_type = cif::category::key_type;
using test_tuple_type = std::tuple<key_type,bool>;
test_tuple_type TESTS[] = {
{ {{"id", 1}, {"id_2", 10}}, true },
{ {{"id_2", 10}, {"id", 1}}, true },
{ {{"id", 1}, {"id_2", 20}}, false },
{ {{"id", 3} }, true },
};
for (const auto &[key, test] : TESTS)
BOOST_CHECK_EQUAL((bool)cat1[key], test);
}
// --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(cifv1_0_1)
{
auto f = R"(data_TEST
#
loop_
_id
_name
1 aap
2 noot
3 mies
4 ?
5 .
)"_cf;
auto &db = f.front();
auto &cat = db[""];
for (auto r : cat)
{
int id;
std::optional<std::string> name;
cif::tie(id, name) = r.get("id", "name");
switch (id)
{
case 1: BOOST_CHECK_EQUAL(*name, "aap"); break;
case 2: BOOST_CHECK_EQUAL(*name, "noot"); break;
case 3: BOOST_CHECK_EQUAL(*name, "mies"); break;
default: BOOST_CHECK(name.has_value() == false);
}
}
std::stringstream ss;
ss << db;
auto f2 = cif::file(ss);
auto &db2 = f2.front();
BOOST_TEST(db == db2);
}
// BOOST_AUTO_TEST_CASE(cifv1_0_2)
// {
// BOOST_CHECK_THROW(R"(data_TEST
// #
// _version 1.0
// loop_
// _id
// _name
// 1 aap
// 2 noot
// 3 mies
// 4 ?
// 5 .
// )"_cf, cif::parse_error);
// }
BOOST_AUTO_TEST_CASE(cifv1_0_3)
{
auto f = R"(data_TEST
#
_version 1.0
_date today
)"_cf;
auto &db = f.front();
auto &cat = db[""];
BOOST_CHECK(not cat.empty());
auto r = cat.front();
BOOST_CHECK_EQUAL(r["version"].as<std::string>(), "1.0");
BOOST_CHECK_EQUAL(r["date"].as<std::string>(), "today");
std::stringstream ss;
ss << db;
auto f2 = cif::file(ss);
auto &db2 = f2.front();
BOOST_TEST(db == db2);
}
BOOST_AUTO_TEST_CASE(find1_opt_1)
{
using namespace cif::literals;
using namespace std::literals;
auto f = R"(data_TEST
#
loop_
_test.id
_test.name
_test.value
1 aap 1.0
2 noot 1.1
3 mies 1.2
)"_cf;
auto &db = f.front();
auto &test = db["test"];
auto v = test.find1<std::optional<float>>("id"_key == 1, "value");
BOOST_CHECK(v.has_value());
BOOST_TEST(*v == 1.0f);
v = test.find1<std::optional<float>>("id"_key == 4, "value");
BOOST_CHECK(v.has_value() == false);
}
// --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(compound_test_1)
{
cif::compound_factory::instance().push_dictionary(gTestDir / "REA_v2.cif");
auto compound = cif::compound_factory::instance().create("REA_v2");
BOOST_ASSERT(compound != nullptr);
BOOST_CHECK(compound->id() == "REA_v2");
}
// --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(pdb_parser_test_1)
{
char k1CBS[] = R"(HEADER RETINOIC-ACID TRANSPORT 28-SEP-94 1CBS
TITLE CRYSTAL STRUCTURE OF CELLULAR RETINOIC-ACID-BINDING
TITLE 2 PROTEINS I AND II IN COMPLEX WITH ALL-TRANS-RETINOIC ACID
TITLE 3 AND A SYNTHETIC RETINOID
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: CELLULAR RETINOIC ACID BINDING PROTEIN TYPE II;
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 CELL_LINE: BL21;
SOURCE 6 GENE: HUMAN CRABP-II;
SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3);
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-3A
KEYWDS RETINOIC-ACID TRANSPORT
EXPDTA X-RAY DIFFRACTION
AUTHOR G.J.KLEYWEGT,T.BERGFORS,T.A.JONES
ATOM 1 N PRO A 1 16.979 13.301 44.555 1.00 30.05 N
ATOM 2 CA PRO A 1 18.150 13.525 43.680 1.00 28.82 C
ATOM 3 C PRO A 1 18.656 14.966 43.784 1.00 26.59 C
ATOM 4 O PRO A 1 17.890 15.889 44.078 1.00 26.84 O
ATOM 5 CB PRO A 1 17.678 13.270 42.255 1.00 29.24 C
ATOM 6 CG PRO A 1 16.248 13.734 42.347 1.00 29.29 C
ATOM 7 CD PRO A 1 15.762 13.216 43.724 1.00 30.71 C)";
struct membuf : public std::streambuf
{
membuf(char *text, size_t length)
{
this->setg(text, text, text + length);
}
} buffer(k1CBS, sizeof(k1CBS) - 1);
std::istream is(&buffer);
auto f = cif::pdb::read(is);
}
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