void CVMappingFile::load(const String & filename, CVMappings & cv_mappings, bool strip_namespaces)
{
//File name for error messages in XMLHandler
file_ = filename;
strip_namespaces_ = strip_namespaces;
parse_(filename, this);
cv_mappings.setCVReferences(cv_references_);
cv_mappings.setMappingRules(rules_);
cv_references_.clear();
rules_.clear();
return;
}
TEST_EQUAL(CVMappings(cvm).getMappingRules() == rules, true)
CVReference ref1, ref2;
ref1.setIdentifier("Ref1");
ref2.setIdentifier("Ref2");
vector<CVReference> refs;
refs.push_back(ref1);
refs.push_back(ref2);
cvm.setCVReferences(refs);
TEST_EQUAL(CVMappings(cvm).getCVReferences() == refs, true)
}
END_SECTION
START_SECTION((CVMappings& operator=(const CVMappings &rhs)))
{
CVMappings cvm, cvm_copy;
CVMappingRule r1, r2;
vector<CVMappingRule> rules;
rules.push_back(r1);
rules.push_back(r2);
cvm.setMappingRules(rules);
cvm_copy = cvm;
TEST_EQUAL(cvm_copy.getMappingRules() == rules, true)
CVReference ref1, ref2;
ref1.setIdentifier("Ref1");
ref2.setIdentifier("Ref2");
vector<CVReference> refs;
refs.push_back(ref1);
refs.push_back(ref2);
cvm.setCVReferences(refs);
START_SECTION(CVMappingFile())
{
ptr = new CVMappingFile();
TEST_NOT_EQUAL(ptr, nullPointer)
}
END_SECTION
START_SECTION(virtual ~CVMappingFile())
{
delete ptr;
}
END_SECTION
START_SECTION((void load(const String &filename, CVMappings &cv_mappings, bool strip_namespaces=false)))
{
CVMappings mappings;
CVMappingFile().load(OPENMS_GET_TEST_DATA_PATH("cv_mapping_test_file.xml"), mappings);
TEST_EQUAL(mappings.getMappingRules().size(), 9)
vector<CVMappingRule> rules = mappings.getMappingRules();
TEST_STRING_EQUAL(rules[0].getIdentifier(), "0")
TEST_STRING_EQUAL(rules[1].getIdentifier(), "1")
TEST_STRING_EQUAL(rules[2].getIdentifier(), "2")
TEST_STRING_EQUAL(rules[3].getIdentifier(), "3")
TEST_STRING_EQUAL(rules[4].getIdentifier(), "4")
TEST_STRING_EQUAL(rules[5].getIdentifier(), "5")
TEST_STRING_EQUAL(rules[6].getIdentifier(), "6")
TEST_STRING_EQUAL(rules[7].getIdentifier(), "7")
TEST_STRING_EQUAL(rules[8].getIdentifier(), "8")
ExitCodes main_(int, const char**)
{
StringList cv_files = getStringList_("cv_files");
StringList cv_names = getStringList_("cv_names");
if (cv_files.size() != cv_names.size())
{
cerr << "Error: You have to specify an identifier for each CV file. Aborting!" << endl;
return ILLEGAL_PARAMETERS;
}
// load cv terms
ControlledVocabulary cv;
for (Size i = 0; i < cv_files.size(); ++i)
{
cv.loadFromOBO(cv_names[i], cv_files[i]);
}
Map<String, ControlledVocabulary::CVTerm> terms = cv.getTerms();
// load mappings from mapping file
String mapping_file = getStringOption_("mapping_file");
CVMappings mappings;
CVMappingFile().load(mapping_file, mappings);
//store HTML version of mapping and CV
if (getStringOption_("html") != "")
{
TextFile file;
file.addLine("<HTML>");
file.addLine(" <HEAD>");
file.addLine(" <TITLE>CV mapping file</TITLE>");
file.addLine(" <SCRIPT language=javascript type='text/javascript'>");
file.addLine(" function toggleDiv(layer_ref,force_state) ");
file.addLine(" {");
file.addLine(" if (document.getElementById(layer_ref).style.display=='none' || force_state=='true')");
file.addLine(" {");
file.addLine(" document.getElementById(layer_ref).style.display = 'block';");
file.addLine(" }");
file.addLine(" else if (document.getElementById(layer_ref).style.display=='block' || force_state=='false')");
file.addLine(" {");
file.addLine(" document.getElementById(layer_ref).style.display = 'none';");
file.addLine(" }");
file.addLine(" }");
file.addLine(" </SCRIPT>");
file.addLine(" </HEAD>");
file.addLine(" <BODY>");
//count the number of terms and add button to expend/collaps all terms
Int term_count = 0;
for (vector<CVMappingRule>::const_iterator it = mappings.getMappingRules().begin(); it != mappings.getMappingRules().end(); ++it)
{
for (vector<CVMappingTerm>::const_iterator tit = it->getCVTerms().begin(); tit != it->getCVTerms().end(); ++tit)
{
++term_count;
}
}
String expand_all = " <a href=\"javascript:toggleDiv('div0','true')";
String collapse_all = " <a href=\"javascript:toggleDiv('div0','false')";
for (Int i = 1; i < term_count; ++i)
{
expand_all += String(";toggleDiv('div") + i + "','true')";
collapse_all += String(";toggleDiv('div") + i + "','false')";
}
file.addLine(expand_all + "\">Expand all</a><BR>");
file.addLine(collapse_all + "\">Collapse all</a>");
file.addLine(" <TABLE width=100% border=0>");
term_count = -1;
for (vector<CVMappingRule>::const_iterator it = mappings.getMappingRules().begin(); it != mappings.getMappingRules().end(); ++it)
{
//create rule line
file.addLine(" <TR><TD colspan=\"2\"><HR></TD></TR>");
file.addLine(String(" <TR><TD>Identifier:</TD><TD><B>") + it->getIdentifier() + "</B></TD></TR>");
file.addLine(String(" <TR><TD>Element:</TD><TD><B>") + it->getElementPath() + "</B></TD></TR>");
if (it->getRequirementLevel() == CVMappingRule::MUST)
{
file.addLine(" <TR><TD>Requirement level:</TD><TD><FONT color=\"red\">MUST</FONT></TD></TR>");
}
else if (it->getRequirementLevel() == CVMappingRule::SHOULD)
{
file.addLine(" <TR><TD>Requirement level:</TD><TD><FONT color=\"orange\">SHOULD</FONT></TD></TR>");
}
else if (it->getRequirementLevel() == CVMappingRule::MAY)
{
file.addLine(" <TR><TD>Requirement level:</TD><TD><FONT color=\"green\">MAY</FONT></TD></TR>");
}
if (it->getCombinationsLogic() == CVMappingRule::AND)
{
file.addLine(" <TR><TD>Combination logic:</TD><TD><FONT color=\"red\">AND</FONT></TD></TR>");
}
else if (it->getCombinationsLogic() == CVMappingRule::XOR)
{
file.addLine(" <TR><TD>Combination logic:</TD><TD><FONT color=\"orange\">XOR</FONT></TD></TR>");
}
else if (it->getCombinationsLogic() == CVMappingRule::OR)
{
file.addLine(" <TR><TD>Combination logic:</TD><TD><FONT color=\"green\">OR</FONT></TD></TR>");
}
//create table with terms
for (vector<CVMappingTerm>::const_iterator tit = it->getCVTerms().begin(); tit != it->getCVTerms().end(); ++tit)
{
//create term line
String term_line = String(" <TR><TD valign=\"top\">Term:</TD><TD>");
if (tit->getAllowChildren())
{
++term_count;
term_line += String("<a href=\"javascript:toggleDiv('div") + term_count + "','')\" style=\"text-decoration:none\" >+</a> ";
}
else
{
term_line += String(" ");
}
//add Term accession, name and description (as popup)
if (cv.exists(tit->getAccession()))
{
const ControlledVocabulary::CVTerm& child_term = cv.getTerm(tit->getAccession());
String description = child_term.description;
if (child_term.synonyms.size() != 0)
{
description += String(" -- Synonyms: '") + ListUtils::concatenate(child_term.synonyms, ", ") + "'";
}
term_line += "<span title=\"" + description + "\">";
}
term_line += tit->getAccession() + " ! " + tit->getTermName();
if (cv.exists(tit->getAccession()))
{
term_line += "</span>";
//check if term accession and term name correspond to the CV
const ControlledVocabulary::CVTerm& main_term = cv.getTerm(tit->getAccession());
if (main_term.name != tit->getTermName())
{
cerr << "Warning: Accession '" << tit->getAccession() << "' and name '" << tit->getTermName() << "' do not match. Name should be '" << main_term.name << "'." << endl;
}
}
//tags
StringList tags;
if (!tit->getUseTerm())
{
tags.push_back("children only");
}
if (tit->getIsRepeatable())
{
tags.push_back("repeatable");
}
if (cv.exists(tit->getAccession()))
{
const ControlledVocabulary::CVTerm& term = cv.getTerm(tit->getAccession());
if (term.obsolete)
{
tags.push_back("<font color=darkred>obsolete</font>");
}
if (term.xref_type != ControlledVocabulary::CVTerm::NONE)
{
tags.push_back("value-type=" + ControlledVocabulary::CVTerm::getXRefTypeName(term.xref_type));
}
if (term.units.size() > 0)
{
StringList units;
for (set<String>::const_iterator u_it = term.units.begin(); u_it != term.units.end(); ++u_it)
{
units.push_back(*u_it + "!" + cv.getTerm(*u_it).name);
}
tags.push_back(String("units=") + ListUtils::concatenate(units, ","));
}
if (term.xref_binary.size() > 0)
{
StringList types;
for (StringList::const_iterator u_it = term.xref_binary.begin(); u_it != term.xref_binary.end(); ++u_it)
{
types.push_back(*u_it + "!" + cv.getTerm(*u_it).name);
}
tags.push_back(String("binary-array-types=") + ListUtils::concatenate(types, ","));
}
}
if (tags.size() != 0)
{
term_line += String("<FONT color=\"grey\"> (") + ListUtils::concatenate(tags, ", ") + ")</FONT>";
}
file.addLine(term_line);
// check whether we need the whole tree, or just the term itself
if (tit->getAllowChildren())
{
file.addLine(String(" <div id=\"div") + term_count + "\" style=\"display: none\">");
if (cv.exists(tit->getAccession()))
{
writeTermTree_(tit->getAccession(), cv, file, 1);
//BEGIN - THIS IS NEEDED FOR WRITING PARSERS ONLY
/*
set<String> allowed_terms;
cv.getAllChildTerms(allowed_terms, tit->getAccession());
for (set<String>::const_iterator atit=allowed_terms.begin(); atit!=allowed_terms.end(); ++atit)
{
const ControlledVocabulary::CVTerm& child_term = cv.getTerm(*atit);
String parser_string = String("os << \"<cvParam cvRef=\\\"MS\\\" accession=\\\"") + child_term.id + "\\\" name=\\\"" + child_term.name + "\\\"";
for (Size i=0; i<child_term.unparsed.size(); ++i)
{
//TODO this does not work anymore. The type is now stored as a member
if (child_term.unparsed[i].hasSubstring("value-type:xsd\\:int") || child_term.unparsed[i].hasSubstring("value-type:xsd\\:float") || child_term.unparsed[i].hasSubstring("value-type:xsd\\:string"))
{
parser_string += " value=\\\"\" << << \"\\\"";
}
}
parser_string += "/>\\n\";<BR>";
file.push_back(parser_string);
}*/
}
else
{
file.addLine(" - Missing terms, CV not loaded...");
cerr << "Warning: no child terms for " << tit->getAccession() << " found!" << endl;
}
file.addLine(" </div>");
file.addLine(" </TD></TD></TR>");
}
}
}
file.addLine(" </TABLE>");
file.addLine(" </BODY>");
file.addLine("</HTML>");
file.store(getStringOption_("html"));
return EXECUTION_OK;
}
// iterator over all mapping rules and store the mentioned terms
StringList ignore_namespaces = getStringList_("ignore_cv");
set<String> ignore_cv_list;
for (StringList::const_iterator it = ignore_namespaces.begin(); it != ignore_namespaces.end(); ++it)
{
ignore_cv_list.insert(*it);
}
set<String> used_terms;
for (vector<CVMappingRule>::const_iterator it = mappings.getMappingRules().begin(); it != mappings.getMappingRules().end(); ++it)
{
set<String> allowed_terms;
// iterate over all allowed terms
for (vector<CVMappingTerm>::const_iterator tit = it->getCVTerms().begin(); tit != it->getCVTerms().end(); ++tit)
{
// check whether the term itself it allowed, or only its children
if (tit->getUseTerm())
{
allowed_terms.insert(tit->getAccession());
}
// check whether we need the whole tree, or just the term itself
if (tit->getAllowChildren())
{
// check whether we want to ignore this term
if (!(tit->getAccession().has(':') && ignore_cv_list.find(tit->getAccession().prefix(':')) != ignore_cv_list.end()))
{
cv.getAllChildTerms(allowed_terms, tit->getAccession());
}
// also add the term itself to the used_terms, because all the children are allowed
used_terms.insert(tit->getAccession());
}
}
// print the allowed terms for the rule
cout << "MappingRule: id=" << it->getIdentifier() << ", elementPath=" << it->getElementPath() << ", #terms=" << it->getCVTerms().size() << endl;
for (set<String>::const_iterator ait = allowed_terms.begin(); ait != allowed_terms.end(); ++ait)
{
cout << *ait << " " << terms[*ait].name << endl;
}
used_terms.insert(allowed_terms.begin(), allowed_terms.end());
}
// find unused terms, which CANNOT be used in the XML due to the mapping file
set<String> unused_terms;
for (Map<String, ControlledVocabulary::CVTerm>::ConstIterator it = terms.begin(); it != terms.end(); ++it)
{
if (used_terms.find(it->first) == used_terms.end())
{
unused_terms.insert(it->first);
}
}
cout << "\n\nCVTerms which are unused in the mapping file and therefore MUST NOT be used in an instance document" << endl;
for (set<String>::const_iterator it = unused_terms.begin(); it != unused_terms.end(); ++it)
{
cout << *it << " " << terms[*it].name;
// print also parent names
for (set<String>::const_iterator pit = terms[*it].parents.begin(); pit != terms[*it].parents.end(); ++pit)
{
cout << " " << terms[*pit].id << " " << terms[*pit].name;
}
cout << endl;
}
return EXECUTION_OK;
}
