From a3f3f3ab842dd8608f2d5197258117dc482a7972 Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Tue, 9 Jul 2019 17:23:36 +0200
Subject: [PATCH] SCHWED-4246: Add mol.QueryQuoteName function.
---
modules/mol/base/pymod/export_query.cc | 2 +-
modules/mol/base/src/query.hh | 19 +++++++++++
modules/mol/base/tests/test_query.cc | 46 +++++++++++++++++++++++++-
3 files changed, 65 insertions(+), 2 deletions(-)
diff --git a/modules/mol/base/pymod/export_query.cc b/modules/mol/base/pymod/export_query.cc
index 7930cd426..8f1fc9460 100644
--- a/modules/mol/base/pymod/export_query.cc
+++ b/modules/mol/base/pymod/export_query.cc
@@ -68,5 +68,5 @@ void export_Query()
return_value_policy<copy_const_reference>())
;
-
+ def("QueryQuoteName", &QueryQuoteName);
}
diff --git a/modules/mol/base/src/query.hh b/modules/mol/base/src/query.hh
index c76454670..d855703c3 100644
--- a/modules/mol/base/src/query.hh
+++ b/modules/mol/base/src/query.hh
@@ -117,6 +117,25 @@ private:
impl::QueryImplP impl_;
};
+// inlined helper function to quote strings for use in queries (e.g. cname=..).
+// throws Error if string cannot be quoted
+inline String DLLEXPORT_OST_MOL QueryQuoteName(const String& name) {
+ // check what quotation marks to use
+ char quote = '\'';
+ if (name.find('\'') != String::npos) {
+ if (name.find('"') != String::npos) {
+ throw Error("Cannot quote chain name " + name + " because it contains '"
+ " and \" in its name.");
+ }
+ quote = '"';
+ }
+ // check problematic \ at end (escapes quotation mark and breaks logic)
+ if (name[name.length() - 1] == '\\') {
+ throw Error("Cannot quote chain name " + name + "because it ends in \\.");
+ }
+ return quote + name + quote;
+}
+
}} // ns
#endif
diff --git a/modules/mol/base/tests/test_query.cc b/modules/mol/base/tests/test_query.cc
index 57fc557bf..5f8865ae5 100644
--- a/modules/mol/base/tests/test_query.cc
+++ b/modules/mol/base/tests/test_query.cc
@@ -286,7 +286,7 @@ BOOST_AUTO_TEST_CASE(test_query_throw)
BOOST_CHECK_NO_THROW(e.Select("gcnotsetprop:0=1"));
}
-BOOST_AUTO_TEST_CASE(test_glob)
+BOOST_AUTO_TEST_CASE(test_glob)
{
EntityHandle e=make_query_test_entity();
ensure_counts(e, "rname=MET and aname=C*", 1, 1, 5);
@@ -299,4 +299,48 @@ BOOST_AUTO_TEST_CASE(test_glob)
ensure_counts(e, "rname=LEU and aname=?D?", 1, 1, 2);
}
+BOOST_AUTO_TEST_CASE(test_quoting)
+{
+ // possible letters taken from mmCIF dictionary
+ // -> http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_atom_site.label_asym_id.html
+ // not ok for us: '\' alone
+ String single_letters = " ][_,.;:\"&<>()/{}'`~!@#$\%|+-"
+ "ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789abcdefgh"
+ "ijklmnopqrstuvwxyz";
+ // put into vector
+ std::vector<String> chain_names;
+ for (size_t i = 0; i < single_letters.length(); ++i) {
+ chain_names.push_back(String(1, single_letters[i]));
+ }
+ // add some multi letter names and empty chain name too
+ // not ok: mixing ' and ", '\' at end
+ chain_names.push_back("\\ ][_,.;:&<>()/{}'`~!@#$\%|+-");
+ chain_names.push_back("ABCDEFGHIJKLMNOPQRSTU'VWXYZ0123456789abcdefgh");
+ chain_names.push_back("ijklmno\"pqrstuvwxyz");
+ chain_names.push_back("");
+ // setup entity
+ EntityHandle ent = CreateEntity();
+ XCSEditor edi = ent.EditXCS();
+ for (size_t i = 0; i < chain_names.size(); ++i) {
+ edi.InsertChain(chain_names[i]);
+ }
+ // test quoting
+ String query_all = "cname=";
+ for (size_t i = 0; i < chain_names.size(); ++i) {
+ const String quoted_name = QueryQuoteName(chain_names[i]);
+ BOOST_CHECK_EQUAL(ent.Select("cname=" + quoted_name).GetChainCount(), 1);
+ query_all += quoted_name;
+ if (i != chain_names.size() - 1) query_all += ",";
+ }
+ BOOST_CHECK_EQUAL(ent.Select(query_all).GetChainCount(),
+ int(chain_names.size()));
+ // note: quoting * keeps it as wild card!
+ BOOST_CHECK_EQUAL(ent.Select("cname=" + QueryQuoteName("*")).GetChainCount(),
+ int(chain_names.size()));
+ // expected failures (mixing ' and ", '\' at end)
+ BOOST_CHECK_THROW(QueryQuoteName("'\""), Error);
+ BOOST_CHECK_THROW(QueryQuoteName("\\"), Error);
+ BOOST_CHECK_THROW(QueryQuoteName("a\\"), Error);
+}
+
BOOST_AUTO_TEST_SUITE_END();
--
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