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libcifpp
Commit dfff8c95 by Maarten L. Hekkelman
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condition work (children, parents)

parent cc5d52bb
Showing with 150 additions and 190 deletions
include/cif++/cif/category.hpp
...@@ -381,18 +381,7 @@ class category ...@@ -381,18 +381,7 @@ class category
return insert_impl(cend(), r); return insert_impl(cend(), r);
} }
void clear() void clear();
{
auto i = m_head;
while (i != nullptr)
{
auto t = i;
i = i->m_next;
delete_row(t);
}
m_head = m_tail = nullptr;
}
// -------------------------------------------------------------------- // --------------------------------------------------------------------
/// \brief generate a new, unique ID. Pass it an ID generating function /// \brief generate a new, unique ID. Pass it an ID generating function
...@@ -497,7 +486,6 @@ class category ...@@ -497,7 +486,6 @@ class category
void update_value(row *row, size_t column, std::string_view value, bool updateLinked, bool validate = true); void update_value(row *row, size_t column, std::string_view value, bool updateLinked, bool validate = true);
private: private:
bool is_orphan(row_handle r) const;
void erase_orphans(condition &&cond); void erase_orphans(condition &&cond);
using allocator_type = std::allocator<void>; using allocator_type = std::allocator<void>;
...@@ -580,44 +568,9 @@ class category ...@@ -580,44 +568,9 @@ class category
return p; return p;
} }
row *clone_row(const row &r) row *clone_row(const row &r);
{
row *result = create_row();
try void delete_row(row *r);
{
for (auto i = r.m_head; i != nullptr; i = i->m_next)
{
item_value *v = create_item(i->m_column_ix, i->text());
result->append(v);
}
}
catch (...)
{
delete_row(result);
throw;
}
return result;
}
void delete_row(row *r)
{
if (r != nullptr)
{
auto i = r->m_head;
while (i != nullptr)
{
auto t = i;
i = i->m_next;
delete_item(t);
}
row_allocator_type ra(get_allocator());
row_allocator_traits::destroy(ra, r);
row_allocator_traits::deallocate(ra, r, 1);
}
}
row_handle create_copy(row_handle r); row_handle create_copy(row_handle r);
...@@ -651,6 +604,11 @@ class category ...@@ -651,6 +604,11 @@ class category
// -------------------------------------------------------------------- // --------------------------------------------------------------------
condition get_parents_condition(row_handle rh, const category &parentCat) const;
condition get_children_condition(row_handle rh, const category &childCat) const;
// --------------------------------------------------------------------
std::string m_name; std::string m_name;
std::vector<item_column> m_columns; std::vector<item_column> m_columns;
const validator *m_validator = nullptr; const validator *m_validator = nullptr;
......
include/cif++/cif/condition.hpp
...@@ -77,7 +77,8 @@ class condition ...@@ -77,7 +77,8 @@ class condition
: m_impl(nullptr) : m_impl(nullptr)
{ {
} }
condition(condition_impl *impl)
explicit condition(condition_impl *impl)
: m_impl(impl) : m_impl(impl)
{ {
} }
...@@ -118,6 +119,7 @@ class condition ...@@ -118,6 +119,7 @@ class condition
return m_impl ? m_impl->test(r) : false; return m_impl ? m_impl->test(r) : false;
} }
explicit operator bool() { return not empty(); }
bool empty() const { return m_impl == nullptr; } bool empty() const { return m_impl == nullptr; }
friend condition operator||(condition &&a, condition &&b); friend condition operator||(condition &&a, condition &&b);
......
src/cif/category.cpp
...@@ -371,6 +371,8 @@ category_index::entry *category_index::insert(entry *h, row *v) ...@@ -371,6 +371,8 @@ category_index::entry *category_index::insert(entry *h, row *v)
void category_index::erase(row *k) void category_index::erase(row *k)
{ {
assert(find(k) == k);
m_root = erase(m_root, k); m_root = erase(m_root, k);
if (m_root != nullptr) if (m_root != nullptr)
m_root->m_red = false; m_root->m_red = false;
...@@ -813,125 +815,137 @@ bool category::is_valid() const ...@@ -813,125 +815,137 @@ bool category::is_valid() const
// -------------------------------------------------------------------- // --------------------------------------------------------------------
bool category::has_children(row_handle r) const condition category::get_parents_condition(row_handle rh, const category &parentCat) const
{ {
assert(m_validator != nullptr); if (m_validator == nullptr or m_cat_validator == nullptr)
assert(m_cat_validator != nullptr); throw std::runtime_error("No validator known for category " + m_name);
bool result = false; condition result;
for (auto &&[childCat, link] : m_child_links) for (auto &link : m_validator->get_links_for_child(m_name))
{ {
if (link->m_parent_category != parentCat.m_name)
continue;
condition cond; condition cond;
for (size_t ix = 0; ix < link->m_parent_keys.size(); ++ix) for (size_t ix = 0; ix < link->m_child_keys.size(); ++ix)
{ {
std::string_view value = r[link->m_parent_keys[ix]].text(); auto childValue = rh[link->m_child_keys[ix]];
// cond = std::move(cond) and (key(link->m_child_keys[ix]) == value or key(link->m_child_keys[ix]) == null); if (childValue.empty())
cond = std::move(cond) and (key(link->m_child_keys[ix]) == value); cond = std::move(cond) and key(link->m_parent_keys[ix]) == null;
else
cond = std::move(cond) and key(link->m_parent_keys[ix]) == childValue.text();
} }
result = not childCat->find(std::move(cond)).empty();
if (result) if (result)
break; result = std::move(result) or std::move(cond);
else
result = std::move(cond);
} }
return result; return result;
} }
bool category::has_parents(row_handle r) const condition category::get_children_condition(row_handle rh, const category &childCat) const
{ {
assert(m_validator != nullptr); if (m_validator == nullptr or m_cat_validator == nullptr)
assert(m_cat_validator != nullptr); throw std::runtime_error("No validator known for category " + m_name);
bool result = false; condition result;
for (auto &&[parentCat, link] : m_parent_links) for (auto &link : m_validator->get_links_for_parent(m_name))
{ {
if (link->m_child_category != childCat.m_name)
continue;
condition cond; condition cond;
for (size_t ix = 0; ix < link->m_child_keys.size(); ++ix) for (size_t ix = 0; ix < link->m_parent_keys.size(); ++ix)
{ {
std::string_view value = r[link->m_child_keys[ix]].text(); auto childKey = link->m_child_keys[ix];
auto parentKey = link->m_parent_keys[ix];
cond = std::move(cond) and (key(link->m_parent_keys[ix]) == value); auto parentValue = rh[parentKey];
}
result = not parentCat->find(std::move(cond)).empty(); if (parentValue.empty())
cond = std::move(cond) and key(childKey) == null;
else
cond = std::move(cond) and key(childKey) == parentValue.text();
}
if (result) if (result)
break; result = std::move(result) or std::move(cond);
else
result = std::move(cond);
} }
return result; return result;
} }
std::vector<row_handle> category::get_children(row_handle r, const category &childCat) const bool category::has_children(row_handle r) const
{ {
assert(m_validator != nullptr); bool result = false;
assert(m_cat_validator != nullptr);
std::vector<row_handle> result;
for (auto &link : m_validator->get_links_for_parent(m_name)) for (auto &&[childCat, link] : m_child_links)
{ {
if (link->m_child_category != childCat.m_name) if (not childCat->exists(get_children_condition(r, *childCat)))
continue; continue;
condition cond; result = true;
break;
}
for (size_t ix = 0; ix < link->m_parent_keys.size(); ++ix) return result;
{ }
if (r[link->m_parent_keys[ix]].empty())
cond = std::move(cond) and key(link->m_child_keys[ix]) == null;
else
{
std::string_view value = r[link->m_parent_keys[ix]].text();
cond = std::move(cond) and key(link->m_child_keys[ix]) == value;
}
}
for (auto child: childCat.find(std::move(cond))) bool category::has_parents(row_handle r) const
{ {
if (std::find(result.begin(), result.end(), child) == result.end()) bool result = false;
result.push_back(child);
} for (auto &&[parentCat, link] : m_parent_links)
{
if (not parentCat->exists(get_parents_condition(r, *parentCat)))
continue;
result = true;
break;
} }
return result; return result;
} }
std::vector<row_handle> category::get_parents(row_handle r, const category &parentCat) const std::vector<row_handle> category::get_children(row_handle r, const category &childCat) const
{ {
assert(m_validator != nullptr); if (m_validator == nullptr or m_cat_validator == nullptr)
assert(m_cat_validator != nullptr); throw std::runtime_error("No validator known for category " + m_name);
std::vector<row_handle> result; std::vector<row_handle> result;
for (auto &link : m_validator->get_links_for_child(m_name)) for (auto child : childCat.find(get_children_condition(r, childCat)))
{ {
if (link->m_parent_category != parentCat.m_name) if (std::find(result.begin(), result.end(), child) == result.end())
continue; result.push_back(child);
}
condition cond; return result;
}
for (size_t ix = 0; ix < link->m_child_keys.size(); ++ix) std::vector<row_handle> category::get_parents(row_handle r, const category &parentCat) const
{ {
std::string_view value = r[link->m_child_keys[ix]].text(); assert(m_validator != nullptr);
assert(m_cat_validator != nullptr);
cond = std::move(cond) and (key(link->m_parent_keys[ix]) == value); std::vector<row_handle> result;
}
for (auto parent: parentCat.find(std::move(cond))) for (auto parent : parentCat.find(get_parents_condition(r, parentCat)))
{ {
if (std::find(result.begin(), result.end(), parent) == result.end()) if (std::find(result.begin(), result.end(), parent) == result.end())
result.push_back(parent); result.push_back(parent);
}
} }
return result; return result;
} }
std::vector<row_handle> category::get_linked(row_handle r, const category &cat) const std::vector<row_handle> category::get_linked(row_handle r, const category &cat) const
...@@ -979,7 +993,7 @@ category::iterator category::erase(iterator pos) ...@@ -979,7 +993,7 @@ category::iterator category::erase(iterator pos)
} }
// links are created based on the _pdbx_item_linked_group_list entries // links are created based on the _pdbx_item_linked_group_list entries
// in mmcif_pdbx_v50.dic dictionary. // in mmcif_pdbx.dic dictionary.
// //
// For each link group in _pdbx_item_linked_group_list // For each link group in _pdbx_item_linked_group_list
// a std::set of keys from one category is mapped to another. // a std::set of keys from one category is mapped to another.
...@@ -989,23 +1003,7 @@ category::iterator category::erase(iterator pos) ...@@ -989,23 +1003,7 @@ category::iterator category::erase(iterator pos)
if (m_validator != nullptr) if (m_validator != nullptr)
{ {
for (auto &&[childCat, link] : m_child_links) for (auto &&[childCat, link] : m_child_links)
{ childCat->erase_orphans(get_children_condition(rh, *childCat));
condition cond;
for (size_t ix = 0; ix < link->m_parent_keys.size(); ++ix)
{
std::string_view value = rh[link->m_parent_keys[ix]].text();
auto childKey = link->m_child_keys[ix];
if (childCat->m_cat_validator and childCat->m_cat_validator->m_mandatory_fields.contains(childKey))
cond = std::move(cond) and key(childKey) == value;
else
cond = std::move(cond) and (key(childKey) == value or key(childKey) == null);
}
childCat->erase_orphans(std::move(cond));
}
} }
delete_row(r); delete_row(r);
...@@ -1065,36 +1063,10 @@ size_t category::erase(condition &&cond, std::function<void(row_handle)> &&visit ...@@ -1065,36 +1063,10 @@ size_t category::erase(condition &&cond, std::function<void(row_handle)> &&visit
return result; return result;
} }
bool category::is_orphan(row_handle r) const void category::clear()
{ {
// be safe while (m_head != nullptr)
if (m_cat_validator == nullptr) erase(begin());
return false;
bool isOrphan = true;
for (auto &&[parentCat, link] : m_parent_links)
{
condition cond;
for (size_t ix = 0; ix < link->m_child_keys.size(); ++ix)
{
std::string_view value = r[link->m_child_keys[ix]].text();
cond = std::move(cond) and (key(link->m_parent_keys[ix]) == value);
}
// if (VERBOSE > 2)
// std::cerr << "Check condition '" << cond << "' in parent category " << link->mParentcategory << " for child cat " << m_name << std::endl;
if (parentCat->exists(std::move(cond)))
{
if (VERBOSE > 2)
std::cerr << "Not removing because row has a parent in category " << link->m_parent_category << std::endl;
isOrphan = false;
break;
}
}
return isOrphan;
} }
void category::erase_orphans(condition &&cond) void category::erase_orphans(condition &&cond)
...@@ -1105,7 +1077,7 @@ void category::erase_orphans(condition &&cond) ...@@ -1105,7 +1077,7 @@ void category::erase_orphans(condition &&cond)
for (auto r : *this) for (auto r : *this)
{ {
if (cond(r) and is_orphan(r)) if (cond(r) and not has_parents(r))
{ {
if (VERBOSE > 1) if (VERBOSE > 1)
std::cerr << "Removing orphaned record: " << std::endl std::cerr << "Removing orphaned record: " << std::endl
...@@ -1191,8 +1163,6 @@ void category::update_value(const std::vector<row_handle> &rows, std::string_vie ...@@ -1191,8 +1163,6 @@ void category::update_value(const std::vector<row_handle> &rows, std::string_vie
std::string pk = linked->m_parent_keys[ix]; std::string pk = linked->m_parent_keys[ix];
std::string ck = linked->m_child_keys[ix]; std::string ck = linked->m_child_keys[ix];
// TODO: add code to *NOT* test mandatory fields for Empty
if (pk == tag) if (pk == tag)
{ {
childTag = ck; childTag = ck;
...@@ -1224,8 +1194,6 @@ void category::update_value(const std::vector<row_handle> &rows, std::string_vie ...@@ -1224,8 +1194,6 @@ void category::update_value(const std::vector<row_handle> &rows, std::string_vie
std::string pk = linked->m_parent_keys[ix]; std::string pk = linked->m_parent_keys[ix];
std::string ck = linked->m_child_keys[ix]; std::string ck = linked->m_child_keys[ix];
// TODO: add code to *NOT* test mandatory fields for Empty
cond_c = std::move(cond_c) && key(pk) == child[ck].text(); cond_c = std::move(cond_c) && key(pk) == child[ck].text();
} }
...@@ -1244,8 +1212,6 @@ void category::update_value(const std::vector<row_handle> &rows, std::string_vie ...@@ -1244,8 +1212,6 @@ void category::update_value(const std::vector<row_handle> &rows, std::string_vie
std::string pk = linked->m_parent_keys[ix]; std::string pk = linked->m_parent_keys[ix];
std::string ck = linked->m_child_keys[ix]; std::string ck = linked->m_child_keys[ix];
// TODO: add code to *NOT* test mandatory fields for Empty
if (pk == tag) if (pk == tag)
check = std::move(check) && key(ck) == value; check = std::move(check) && key(ck) == value;
else else
...@@ -1273,7 +1239,7 @@ void category::update_value(const std::vector<row_handle> &rows, std::string_vie ...@@ -1273,7 +1239,7 @@ void category::update_value(const std::vector<row_handle> &rows, std::string_vie
// finally, update the children // finally, update the children
if (not process.empty()) if (not process.empty())
childCat->update_value(std::move(process), childTag, value); childCat->update_value(process, childTag, value);
} }
} }
} }
...@@ -1408,7 +1374,7 @@ void category::update_value(row *row, size_t column, std::string_view value, boo ...@@ -1408,7 +1374,7 @@ void category::update_value(row *row, size_t column, std::string_view value, boo
// } // }
// Now, suppose there are already rows in child that conform to the new value, // Now, suppose there are already rows in child that conform to the new value,
// we then skip this renam // we then skip this rename
condition cond_n; condition cond_n;
...@@ -1417,8 +1383,6 @@ void category::update_value(row *row, size_t column, std::string_view value, boo ...@@ -1417,8 +1383,6 @@ void category::update_value(row *row, size_t column, std::string_view value, boo
std::string pk = linked->m_parent_keys[ix]; std::string pk = linked->m_parent_keys[ix];
std::string ck = linked->m_child_keys[ix]; std::string ck = linked->m_child_keys[ix];
// TODO: add code to *NOT* test mandatory fields for Empty
if (pk == iv->m_tag) if (pk == iv->m_tag)
cond_n = std::move(cond_n) and key(ck) == value; cond_n = std::move(cond_n) and key(ck) == value;
else else
...@@ -1427,7 +1391,7 @@ void category::update_value(row *row, size_t column, std::string_view value, boo ...@@ -1427,7 +1391,7 @@ void category::update_value(row *row, size_t column, std::string_view value, boo
if (pk_value.empty()) if (pk_value.empty())
cond_n = std::move(cond_n) and key(ck) == null; cond_n = std::move(cond_n) and key(ck) == null;
else else
cond_n = std::move(cond_n) and ((key(ck) == pk_value) or key(ck) == null); cond_n = std::move(cond_n) and key(ck) == pk_value;
} }
} }
...@@ -1446,6 +1410,45 @@ void category::update_value(row *row, size_t column, std::string_view value, boo ...@@ -1446,6 +1410,45 @@ void category::update_value(row *row, size_t column, std::string_view value, boo
} }
} }
row *category::clone_row(const row &r)
{
row *result = create_row();
try
{
for (auto i = r.m_head; i != nullptr; i = i->m_next)
{
item_value *v = create_item(i->m_column_ix, i->text());
result->append(v);
}
}
catch (...)
{
delete_row(result);
throw;
}
return result;
}
void category::delete_row(row *r)
{
if (r != nullptr)
{
auto i = r->m_head;
while (i != nullptr)
{
auto t = i;
i = i->m_next;
delete_item(t);
}
row_allocator_type ra(get_allocator());
row_allocator_traits::destroy(ra, r);
row_allocator_traits::deallocate(ra, r, 1);
}
}
row_handle category::create_copy(row_handle r) row_handle category::create_copy(row_handle r)
{ {
// copy the values // copy the values
...@@ -1564,7 +1567,7 @@ category::iterator category::insert_impl(const_iterator pos, row *n) ...@@ -1564,7 +1567,7 @@ category::iterator category::insert_impl(const_iterator pos, row *n)
return iterator(*this, n); return iterator(*this, n);
} }
catch(const std::exception& e) catch (const std::exception &e)
{ {
delete_row(n); delete_row(n);
throw; throw;
...@@ -1620,7 +1623,6 @@ category::iterator category::erase_impl(const_iterator pos) ...@@ -1620,7 +1623,6 @@ category::iterator category::erase_impl(const_iterator pos)
// return iterator(*this, cur); // return iterator(*this, cur);
} }
namespace detail namespace detail
{ {
...@@ -1631,7 +1633,7 @@ namespace detail ...@@ -1631,7 +1633,7 @@ namespace detail
if (offset > 0) if (offset > 0)
os << '\n'; os << '\n';
os << ';'; os << ';';
char pc = 0; char pc = 0;
for (auto ch : value) for (auto ch : value)
{ {
...@@ -1640,7 +1642,7 @@ namespace detail ...@@ -1640,7 +1642,7 @@ namespace detail
os << ch; os << ch;
pc = ch; pc = ch;
} }
if (value.back() != '\n') if (value.back() != '\n')
os << '\n'; os << '\n';
os << ';' << '\n'; os << ';' << '\n';
...@@ -1664,7 +1666,7 @@ namespace detail ...@@ -1664,7 +1666,7 @@ namespace detail
else else
{ {
bool done = false; bool done = false;
for (char q : {'\'', '"'}) for (char q : { '\'', '"' })
{ {
auto p = value.find(q); // see if we can use the quote character auto p = value.find(q); // see if we can use the quote character
while (p != std::string::npos and sac_parser::is_non_blank(value[p + 1]) and value[p + 1] != q) while (p != std::string::npos and sac_parser::is_non_blank(value[p + 1]) and value[p + 1] != q)
...@@ -1705,7 +1707,6 @@ namespace detail ...@@ -1705,7 +1707,6 @@ namespace detail
} // namespace detail } // namespace detail
std::vector<std::string> category::get_tag_order() const std::vector<std::string> category::get_tag_order() const
{ {
std::vector<std::string> result; std::vector<std::string> result;
......
src/dssp/DSSP.cpp
...@@ -1537,21 +1537,19 @@ std::string cif2pdbDate(const std::string &d) ...@@ -1537,21 +1537,19 @@ std::string cif2pdbDate(const std::string &d)
}; };
std::smatch m; std::smatch m;
std::string result; std::ostringstream os;
if (std::regex_match(d, m, rx)) if (std::regex_match(d, m, rx))
{ {
int year = std::stoi(m[1].str()); int year = std::stoi(m[1].str());
int month = std::stoi(m[2].str()); int month = std::stoi(m[2].str());
std::ostringstream os;
if (m[3].matched) if (m[3].matched)
os << std::setw(2) << std::setfill('0') << stoi(m[3].str()) << '-'; os << std::setw(2) << std::setfill('0') << stoi(m[3].str()) << '-';
os << kMonths[month - 1] << std::setw(2) << std::setfill('0') << (year % 100); os << kMonths[month - 1] << '-' << std::setw(2) << std::setfill('0') << (year % 100);
} }
return result; return os.str();
} }
std::string cif2pdbAuth(std::string name) std::string cif2pdbAuth(std::string name)
...@@ -1616,7 +1614,7 @@ std::string DSSP_impl::GetPDBHEADERLine() ...@@ -1616,7 +1614,7 @@ std::string DSSP_impl::GetPDBHEADERLine()
std::copy(id.begin(), id.end(), header + 62); std::copy(id.begin(), id.end(), header + 62);
return header; return FixStringLength(header);
} }
std::string DSSP_impl::GetPDBCOMPNDLine() std::string DSSP_impl::GetPDBCOMPNDLine()
......
test/unit-v2-test.cpp
...@@ -949,12 +949,12 @@ _cat_2.desc ...@@ -949,12 +949,12 @@ _cat_2.desc
cat1.erase(cif::key("id") == 10); cat1.erase(cif::key("id") == 10);
BOOST_CHECK_EQUAL(cat1.size(), 2); BOOST_CHECK_EQUAL(cat1.size(), 2);
BOOST_CHECK_EQUAL(cat2.size(), 2); BOOST_CHECK_EQUAL(cat2.size(), 3); // TODO: Is this really what we want?
cat1.erase(cif::key("id") == 20); cat1.erase(cif::key("id") == 20);
BOOST_CHECK_EQUAL(cat1.size(), 1); BOOST_CHECK_EQUAL(cat1.size(), 1);
BOOST_CHECK_EQUAL(cat2.size(), 1); BOOST_CHECK_EQUAL(cat2.size(), 2); // TODO: Is this really what we want?
} }
// -------------------------------------------------------------------- // --------------------------------------------------------------------
...@@ -1341,6 +1341,7 @@ _cat_2.parent_id3 ...@@ -1341,6 +1341,7 @@ _cat_2.parent_id3
BOOST_CHECK_EQUAL(PR2["id"].as<int>(), 2); BOOST_CHECK_EQUAL(PR2["id"].as<int>(), 2);
auto CR2set = cat1.get_children(PR2, cat2); auto CR2set = cat1.get_children(PR2, cat2);
BOOST_CHECK_EQUAL(CR2set.size(), 3);
BOOST_ASSERT(CR2set.size() == 3); BOOST_ASSERT(CR2set.size() == 3);
std::vector<int> CRids; std::vector<int> CRids;
......
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