QDir d;
String dirname = File::getTempDirectory() + "/" + File::getUniqueName() + "/";
TEST_EQUAL(d.mkpath(dirname.toQString()), TRUE);
#ifdef OPENMS_WINDOWSPLATFORM
_putenv_s("OPENMS_HOME_PATH", dirname.c_str());
#else
setenv("OPENMS_HOME_PATH", dirname.c_str(), 0);
#endif
TEST_EQUAL(File::getUserDirectory(), dirname)
// Note: this does not guarantee any more that the user directory or an
// OpenMS.ini file exists at the new location.
END_SECTION
START_SECTION(static Param getSystemParameters())
Param p = File::getSystemParameters();
TEST_EQUAL(p.size()>0, true)
TEST_EQUAL(p.getValue("version"), VersionInfo::getVersion())
END_SECTION
START_SECTION(static String findDatabase(const String &db_name))
TEST_EXCEPTION(Exception::FileNotFound, File::findDatabase("filedoesnotexists"))
String db = File::findDatabase("./CV/unimod.obo");
//TEST_EQUAL(db,"wtf")
TEST_EQUAL(db.hasSubstring("share/OpenMS"), true)
END_SECTION
START_SECTION(static String findExecutable(const OpenMS::String& toolName))
{
TEST_EXCEPTION(Exception::FileNotFound, File::findExecutable("executable_does_not_exist"))
void createFragment_(String & fragment, const Param & param)
{
//std::cerr << "FRAGMENT: " << fragment << "\n\n";
// e.g.: -input %BASENAME[%%in].mzML
// we have to make this little detour param -> vector<String>
// to sort the param names by length, otherwise we have a
// problem with parameter substitution
// i.e., if A is a prefix of B and gets replaced first, the
// suffix of B remains and will cause trouble!
vector<String> param_names;
param_names.reserve(param.size());
for (Param::ParamIterator it = param.begin(); it != param.end(); ++it)
{
param_names.push_back(it->name);
}
// sort by length
std::sort(param_names.begin(), param_names.end(), reverseComparator(StringSizeLess()));
// iterate through all input params and replace with values:
SignedSize allowed_percent(0); // filenames might contain '%', which are allowed to remain there (and even must remain)
for (vector<String>::iterator it = param_names.begin(); it != param_names.end(); ++it)
{
if (!fragment.hasSubstring("%%" + *it)) continue;
String s_new = paramToString_(param.getEntry(*it));
allowed_percent += s_new.length() - String(s_new).substitute("%", "").length();
//std::cerr << "IN: " << s_new << "(" << allowed_percent << "\n";
fragment.substitute("%%" + *it, s_new);
}
if (fragment.hasSubstring("%%")) throw Exception::InvalidValue(__FILE__, __LINE__, __PRETTY_FUNCTION__, "Invalid '%%' found in '" + fragment + "' after replacing all parameters!", fragment);
// %TMP replace:
fragment.substitute("%TMP", File::getTempDirectory());
// %RND replace:
fragment.substitute("%RND", String(UniqueIdGenerator::getUniqueId()));
// %WORKINGDIR replace:
fragment.substitute("%WORKINGDIR", tde_.working_directory);
// %DIR% replace
{
QRegExp rx("%DIR\\[(.*)\\]");
rx.setMinimal(true);
int pos = 0;
QString t_tmp = fragment.toQString();
//std::cout << "fragment is:" << fragment << std::endl;
while ((pos = rx.indexIn(t_tmp, pos)) != -1)
{
String value = rx.cap(1); // param name (hopefully)
// replace in fragment:
QFileInfo qfi(value.toQString());
//std::cout << "match @ " << pos << " " << value << " --> " << qfi.canonicalPath() << "\n";
t_tmp = t_tmp.replace(String("%DIR[" + value + "]").toQString(), qfi.canonicalPath());
}
fragment = String(t_tmp);
//std::cout << "NEW fragment is:" << fragment << std::endl;
}
// %BASENAME% replace
{
QRegExp rx("%BASENAME\\[(.*)\\]");
rx.setMinimal(true);
int pos = 0, count = 0;
QString t_tmp = fragment.toQString();
while ((pos = rx.indexIn(t_tmp, pos)) != -1)
{
//std::cout << "match @ " << pos << "\n";
String value = rx.cap(1); // param name (hopefully)
// replace in fragment:
QFileInfo qfi(value.toQString());
//std::cout << "match @ " << pos << " " << value << " --> " << qfi.completeBaseName() << "\n";
t_tmp = t_tmp.replace(String("%BASENAME[" + value + "]").toQString(), qfi.completeBaseName());
++count;
}
// update expected count of valid '%'
allowed_percent -= (fragment.length() - String(fragment).substitute("%", "").length()) // original # of %
- (t_tmp.length() - String(t_tmp).substitute("%", "").length()) // new # of %
- count; // expected # of % due to %BASENAME
fragment = String(t_tmp);
}
SignedSize diff = (fragment.length() - String(fragment).substitute("%", "").length()) - allowed_percent;
//std::cerr << "allowed: " << allowed_percent << "\n" << "diff: " << diff << " in: " << fragment << "\n";
if (diff > 0) throw Exception::InvalidValue(__FILE__, __LINE__, __PRETTY_FUNCTION__, "Mapping still contains '%' after substitution! Did you use % instead of %%?", fragment);
else if (diff < 0) throw Exception::InvalidValue(__FILE__, __LINE__, __PRETTY_FUNCTION__, "Error: '%' from a filename where accidentally considered command tags! "
"This is a bug! Remove '%' from input filesnames to fix, but please report this as well!", fragment);
//std::cout << fragment << "'\n";
}
parameters.setValue(String("scaling_bucket_size"), 0.01);
parameters.setValue(String("shift_bucket_size"), 0.1);
// If hashing goes wrong, get debug output with the following:
// parameters.setValue(String("dump_buckets"),"pcast_buckets");
// parameters.setValue(String("dump_pairs"),"pcast_pairs");
TransformationDescription transformation;
PoseClusteringAffineSuperimposer pcat;
pcat.setParameters(parameters);
// That's a precondition for run()! Now even documented :-)
input[0].updateRanges();
input[1].updateRanges();
pcat.run(input[0], input[1], transformation);
TEST_STRING_EQUAL(transformation.getModelType(), "linear")
transformation.getModelParameters(parameters);
TEST_EQUAL(parameters.size(), 2)
TEST_REAL_SIMILAR(parameters.getValue("slope"), 1.0)
TEST_REAL_SIMILAR(parameters.getValue("intercept"), -0.4)
END_SECTION
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
feat3.setPosition(pos3);
feat3.setIntensity(100.0f);
feat4.setPosition(pos4);
feat4.setIntensity(100.0f);
input[1].push_back(ConsensusFeature(feat3));
input[1].push_back(ConsensusFeature(feat4));
TransformationDescription transformation;
PoseClusteringShiftSuperimposer pcat;
Param params;
#if 0 // switch this on for debugging
params.setValue("dump_buckets","tmp_PoseClusteringShiftSuperimposer_buckets");
params.setValue("dump_pairs","tmp_PoseClusteringShiftSuperimposer_pairs");
pcat.setParameters(params);
#endif
pcat.run(input[0], input[1], transformation);
TEST_STRING_EQUAL(transformation.getModelType(), "linear")
params = transformation.getModelParameters();
TEST_EQUAL(params.size(), 2)
TEST_REAL_SIMILAR(params.getValue("slope"), 1.0)
TEST_REAL_SIMILAR(params.getValue("intercept"), -20.4)
END_SECTION
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
p.setValue("item1", 7);
p.setValue("intlist3", ListUtils::create<Int>("1"));
p.setValue("stringlist3", ListUtils::create<String>("1"));
p.setValue("item3", 7.6);
p.setValue("doublelist", ListUtils::create<double>("1.22,2.33,4.55"));
p.setValue("doublelist2", ListUtils::create<double>(""));
p.setValue("doublelist3", ListUtils::create<double>("1.4"));
//store
String filename;
NEW_TMP_FILE(filename);
paramFile.store(filename,p);
//load
Param p2;
paramFile.load(filename,p2);
TEST_EQUAL(p2.size(),12);
TEST_EQUAL(p2.getValue("stringlist").valueType(), DataValue::STRING_LIST)
StringList list = p2.getValue("stringlist");
TEST_EQUAL(list.size(),3)
TEST_EQUAL(list[0],"a")
TEST_EQUAL(list[1],"bb")
TEST_EQUAL(list[2],"ccc")
TEST_EQUAL(p2.getValue("stringlist2").valueType(), DataValue::STRING_LIST)
list = p2.getValue("stringlist2");
TEST_EQUAL(list.size(),0)
TEST_EQUAL(p2.getValue("stringlist").valueType(), DataValue::STRING_LIST)
list = p2.getValue("stringlist3");
TEST_EQUAL(list.size(),1)