obotest.cpp File Reference

#include "obo.hpp"
#include "pwiz/utility/misc/unit.hpp"
#include <boost/filesystem/operations.hpp>
#include "pwiz/utility/misc/Std.hpp"
#include <cstring>

Go to the source code of this file.

Functions
void	test ()
int	main (int argc, char *argv[])

Variables
ostream *	os_ = 0
const char *	oboText_ = "\n"

---

Function Documentation

void test

(

)

Definition at line 133 of file obotest.cpp.

References pwiz::data::OBO::filename, pwiz::data::OBO::header, oboText_, os_, pwiz::data::OBO::prefix, pwiz::data::OBO::terms, and unit_assert.

{
    const string& filename = "obotest_temp.txt";
    ofstream temp(filename.c_str());
    temp << oboText_ << endl; 
    temp.close();

    OBO obo(filename);

    if (os_) *os_ << obo << endl; 
   
    unit_assert(obo.filename == filename);    
    unit_assert(obo.header.size() == 5); 
    unit_assert(obo.prefix == "MS");
    unit_assert(obo.terms.size() == 12); // including obsolete terms

    set<Term>::const_iterator term = obo.terms.begin();
    unit_assert(term->prefix == "MS");
    unit_assert(term->id == 0);
    unit_assert(term->name == "MZ controlled vocabularies");
    unit_assert(term->def == "MZ controlled vocabularies.");
    unit_assert(term->parentsPartOf.empty());
    unit_assert(term->parentsIsA.empty());

    ++term;
    unit_assert(term->id == 1);
    unit_assert(term->name == "sample number");
    unit_assert(term->parentsPartOf.size() == 1);
    unit_assert(term->parentsPartOf[0] == 1000548);
 
    ++term;
    unit_assert(term->id == 11);
    unit_assert(term->name == "mass resolution");
    unit_assert(term->parentsIsA.size() == 1);
    unit_assert(term->parentsIsA[0] == 1000503);

    ++term;
    unit_assert(term->id == 1000025);
    unit_assert(term->exactSynonyms.size() == 1);
    unit_assert(term->exactSynonyms[0] == "B");

    ++term;
    unit_assert(term->id == 1000030);
    unit_assert(term->isObsolete);

    ++term;
    unit_assert(term->id == 1000035);
    unit_assert(term->isObsolete);

    // test unescaping "\!"
    ++term;
    unit_assert(term->id == 1001272);
    unit_assert(term->name == "(?<=R)(?!P)");

    // test other relationships
    ++term;
    unit_assert(term->id == 1001280);
    unit_assert(term->relations.size() == 2);
    unit_assert(term->relations.begin()->first == "has_units");
    unit_assert(term->relations.begin()->second.first == "MS");
    unit_assert(term->relations.begin()->second.second == 1000040);
    unit_assert(term->relations.rbegin()->second.first == "UO");
    unit_assert(term->relations.rbegin()->second.second == 169);

    ++term;
    unit_assert(term->id == 1001303);
    unit_assert(term->name == "Arg-C");
    unit_assert(term->relations.size() == 1);
    unit_assert(term->relations.begin()->first == "has_regexp");
    unit_assert(term->relations.begin()->second.first == "MS");
    unit_assert(term->relations.begin()->second.second == 1001272);

    // test term with OBO 1.2 synonym format
    ++term;
    unit_assert(term->id == 2000025);
    unit_assert(term->exactSynonyms.size() == 1);
    unit_assert(term->exactSynonyms[0] == "B");

    // test term with [stuff to ignore]
    ++term;
    unit_assert(term->id == 9999999);
    unit_assert(term->def == "description");
 
    ++term;
    // test property values
    unit_assert(term->id == 99999999);
    unit_assert(term->name == "Label:2H(4)+GlyGly");
    unit_assert(term->def == "Ubiquitination 2H4 lysine");
    unit_assert(term->propertyValues.size() == 9);
    unit_assert(term->propertyValues.find("record_id")->second == "853");
    unit_assert(term->propertyValues.find("delta_mono_mass")->second == "118.068034");
    unit_assert(term->propertyValues.find("delta_avge_mass")->second == "118.1273");
    unit_assert(term->propertyValues.find("delta_composition")->second == "H(2) 2H(4) C(4) N(2) O(2)");
    unit_assert(term->propertyValues.find("spec_classification_1")->second == "Post-translational");

    boost::filesystem::remove(filename); 
}

int main	(	int	argc,
		char *	argv[]
	)

Definition at line 232 of file obotest.cpp.

References e(), os_, test(), TEST_EPILOG, TEST_FAILED, and TEST_PROLOG.

{
    TEST_PROLOG(argc, argv)

    try
    {
        if (argc>1 && !strcmp(argv[1],"-v")) os_ = &cout;
        test();
    }
    catch (exception& e)
    {
        TEST_FAILED(e.what())
    }
    catch (...)
    {
        TEST_FAILED("Caught unknown exception.")
    }

    TEST_EPILOG
}

---

Variable Documentation

ostream* os_ = 0

Definition at line 35 of file obotest.cpp.

const char* oboText_ = "\n"

Definition at line 38 of file obotest.cpp.

Referenced by test().