ProteoWizard
Functions | Variables
cvtest.cpp File Reference
#include "pwiz/utility/misc/unit.hpp"
#include "cv.hpp"
#include "pwiz/utility/misc/Std.hpp"
#include "boost/thread/thread.hpp"
#include "boost/thread/barrier.hpp"
#include <cstring>

Go to the source code of this file.

Functions

void test ()
 
void testIsA ()
 
void testOtherRelations ()
 
void testSynonyms ()
 
void testIDTranslation ()
 
void testPropertyValues ()
 
void testThreadSafetyWorker (boost::barrier *testBarrier)
 
void testThreadSafety (const int &testThreadCount)
 
int main (int argc, char *argv[])
 

Variables

ostream * os_ = 0
 

Function Documentation

◆ test()

void test ( )

Definition at line 39 of file cvtest.cpp.

40{
41 if (os_)
42 {
43 *os_ << "name: " << cvTermInfo(MS_sample_number).name << endl
44 << "def: " << cvTermInfo(MS_sample_number).def << "\n\n";
45
46 *os_ << "name: " << cvTermInfo(MS_scan_polarity).name << endl
47 << "def: " << cvTermInfo(MS_scan_polarity).def << endl;
48 }
49
50 // some simple tests
51 unit_assert(cvTermInfo(MS_sample_number).name == "sample number");
52 unit_assert(cvTermInfo(MS_contact_email).name == "contact email");
53 unit_assert(cvTermInfo(MS_contact_email).def == "Email address of the contact person or organization.");
54
55 unit_assert(cvTermInfo(MS_zlib_compression).parentsIsA.size() == 1 &&
57
58 unit_assert(cvTermInfo(MS_instrument_model).parentsPartOf.size() == 1 &&
59 cvTermInfo(MS_instrument_model).parentsPartOf[0] == MS_instrument);
60
62
63 unit_assert(cvTermInfo(MS_regular_expressions_for_a_GUID).def == "([A-Fa-f0-9]\\{8\\}-([A-Fa-f0-9]\\{4\\}-)\\{3\\}[A-Fa-f0-9]\\{12\\}).");
64}
MS_scan_polarity
scan polarity: Relative orientation of the electromagnetic field during the selection and detection o...
Definition cv.hpp:1992
MS_None____OBSOLETE
None ??: None.
Definition cv.hpp:630
MS_instrument
instrument: Description of the instrument or the mass spectrometer.
Definition cv.hpp:1983
MS_instrument_model
instrument model: Instrument model name not including the vendor's name.
Definition cv.hpp:357
MS_zlib_compression
zlib compression: Zlib.
Definition cv.hpp:2331
MS_binary_data_compression_type
binary data compression type: Compression Type.
Definition cv.hpp:2325
MS_contact_email
contact email: Email address of the contact person or organization.
Definition cv.hpp:2418
MS_regular_expressions_for_a_GUID
).
Definition cv.hpp:7140
MS_sample_number
sample number: A reference number relevant to the sample under study.
Definition cv.hpp:264
ostream * os_
Definition cvtest.cpp:36
PWIZ_API_DECL const CVTermInfo & cvTermInfo(CVID cvid)
returns CV term info for the specified CVID
std::string name
Definition cv.hpp:14947
std::string def
Definition cv.hpp:14948
#define unit_assert(x)
Definition unit.hpp:85

References pwiz::cv::cvTermInfo(), pwiz::cv::CVTermInfo::def, MS_binary_data_compression_type, MS_contact_email, MS_instrument, MS_instrument_model, MS_None____OBSOLETE, MS_regular_expressions_for_a_GUID, MS_sample_number, MS_scan_polarity, MS_zlib_compression, pwiz::cv::CVTermInfo::name, os_, and unit_assert.

Referenced by testThreadSafetyWorker().

◆ testIsA()

void testIsA ( )

Definition at line 67 of file cvtest.cpp.

68{
81}
UO_unit
unit: A unit of measurement is a standardized quantity of a physical quality.
Definition cv.hpp:13803
MS_FT_ICR
FT_ICR (fourier transform ion cyclotron resonance mass spectrometer): A mass spectrometer based on th...
Definition cv.hpp:537
MS_mass_analyzer_type
mass analyzer type: Mass analyzer separates the ions according to their mass-to-charge ratio.
Definition cv.hpp:1911
MS_radial_ejection_linear_ion_trap
radial ejection linear ion trap: A linear ion trap mass spectrometer where ions are ejected along the...
Definition cv.hpp:558
MS_m_z
m/z: Three-character symbol m/z is used to denote the quantity formed by dividing the mass of an ion ...
Definition cv.hpp:384
UO_mass_unit
mass unit: A unit which is a standard measure of the amount of matter/energy of a physical object.
Definition cv.hpp:13809
UO_dalton
dalton: An independently to the base SI units defined mass unit which is equal to one twelfth of the ...
Definition cv.hpp:14460
MS_ion_trap
ion trap: A device for spatially confining ions using electric and magnetic fields alone or in combin...
Definition cv.hpp:1278
MS_linear_ion_trap
linear ion trap: A two dimensional Paul ion trap in which ions are confined in the axial dimension by...
Definition cv.hpp:1434
UO_energy_unit
energy unit: A unit which is a standard measure of the work done by a certain force (gravitational,...
Definition cv.hpp:14136
PWIZ_API_DECL bool cvIsA(CVID child, CVID parent)
returns true iff child IsA parent in the CV

References pwiz::cv::cvIsA(), MS_FT_ICR, MS_ion_trap, MS_linear_ion_trap, MS_m_z, MS_mass_analyzer_type, MS_radial_ejection_linear_ion_trap, unit_assert, UO_dalton, UO_energy_unit, UO_mass_unit, and UO_unit.

Referenced by testThreadSafetyWorker().

◆ testOtherRelations()

void testOtherRelations ( )

Definition at line 84 of file cvtest.cpp.

85{
86 const CVTermInfo& info = cvTermInfo(MS_accuracy);
87 unit_assert(info.otherRelations.size() == 2);
88 unit_assert(info.otherRelations.begin()->first == "has_units");
89 unit_assert(info.otherRelations.begin()->second == MS_m_z);
90 unit_assert(info.otherRelations.rbegin()->first == "has_units");
91 unit_assert(info.otherRelations.rbegin()->second == UO_parts_per_million);
92
93 const CVTermInfo& info2 = cvTermInfo(MS_Trypsin);
94 unit_assert(info2.otherRelations.size() == 1);
95 unit_assert(info2.otherRelations.begin()->first == "has_regexp");
96 unit_assert(info2.otherRelations.begin()->second == MS______KR_____P_);
97}
MS_Trypsin
Trypsin: Enzyme trypsin.
Definition cv.hpp:4179
MS_accuracy
accuracy: Accuracy is the degree of conformity of a measured mass to its actual value.
Definition cv.hpp:303
MS______KR_____P_
(?<=[KR])(?!P): Regular expression for Trypsin.
Definition cv.hpp:3987
UO_parts_per_million
parts per million: A dimensionless concentration notation which denotes the amount of a given substan...
Definition cv.hpp:14304
structure for holding CV term info
Definition cv.hpp:14944
std::multimap< std::string, CVID > otherRelations
Definition cv.hpp:14954

References pwiz::cv::cvTermInfo(), MS______KR_____P_, MS_accuracy, MS_m_z, MS_Trypsin, pwiz::cv::CVTermInfo::otherRelations, unit_assert, and UO_parts_per_million.

Referenced by testThreadSafetyWorker().

◆ testSynonyms()

void testSynonyms ( )

Definition at line 100 of file cvtest.cpp.

101{
102 const CVTermInfo& info = cvTermInfo(MS_B);
103 unit_assert(info.name == "magnetic field strength");
104 unit_assert(info.exactSynonyms.size() == 1);
105 unit_assert(info.exactSynonyms[0] == "B");
106 unit_assert(cvTermInfo(MS_QIT).exactSynonyms.size() == 3);
107
108 unit_assert(cvTermInfo(MS_chemical_ionization).shortName() == "CI");
109 unit_assert(cvTermInfo(MS_FT_ICR).shortName() == "FT_ICR");
111 unit_assert(cvTermInfo(CVID_Unknown).shortName() == "Unknown");
112}
MS_B
B (magnetic field strength): A property of space that produces a force on a charged particle equal to...
Definition cv.hpp:339
MS_fourier_transform_ion_cyclotron_resonance_mass_spectrometer
fourier transform ion cyclotron resonance mass spectrometer: A mass spectrometer based on the princip...
Definition cv.hpp:534
CVID_Unknown
Definition cv.hpp:114
MS_QIT
QIT (quadrupole ion trap): Quadrupole Ion Trap mass analyzer captures the ions in a three dimensional...
Definition cv.hpp:552
MS_chemical_ionization
chemical ionization: The formation of a new ion by the reaction of a neutral species with an ion....
Definition cv.hpp:495
std::vector< std::string > exactSynonyms
Definition cv.hpp:14955

References CVID_Unknown, pwiz::cv::cvTermInfo(), pwiz::cv::CVTermInfo::exactSynonyms, MS_B, MS_chemical_ionization, MS_fourier_transform_ion_cyclotron_resonance_mass_spectrometer, MS_FT_ICR, MS_QIT, pwiz::cv::CVTermInfo::name, and unit_assert.

Referenced by testThreadSafetyWorker().

◆ testIDTranslation()

void testIDTranslation ( )

Definition at line 115 of file cvtest.cpp.

116{
117 unit_assert(cvTermInfo("MS:1000025").cvid == MS_B);
118 unit_assert(cvTermInfo("MS:1000042").cvid == MS_peak_intensity);
119 unit_assert(cvTermInfo("UO:0000231").cvid == UO_information_unit);
120 unit_assert(cvTermInfo("XX:0000231").cvid == CVID_Unknown);
121 unit_assert(cvTermInfo("FOO:").cvid == CVID_Unknown);
122 unit_assert(cvTermInfo(":FOO").cvid == CVID_Unknown);
123 unit_assert(cvTermInfo("MS").cvid == CVID_Unknown);
124}
UO_information_unit
information unit: A unit which is a standard measure of the amount of information.
Definition cv.hpp:14490
MS_peak_intensity
peak intensity: Intensity of ions as measured by the height or area of a peak in a mass spectrum.
Definition cv.hpp:402

References CVID_Unknown, pwiz::cv::cvTermInfo(), MS_B, MS_peak_intensity, unit_assert, and UO_information_unit.

Referenced by testThreadSafetyWorker().

◆ testPropertyValues()

void testPropertyValues ( )

Definition at line 127 of file cvtest.cpp.

128{
130
131 unit_assert_operator_equal(1, phospho.propertyValues.count("delta_composition"));
132 unit_assert_operator_equal("H O(3) P", phospho.propertyValues.find("delta_composition")->second);
133
134 unit_assert_operator_equal(2, phospho.propertyValues.count("spec_1_site"));
135 unit_assert_operator_equal("T", phospho.propertyValues.equal_range("spec_1_site").first->second);
136 unit_assert_operator_equal("S", (--phospho.propertyValues.equal_range("spec_1_site").second)->second);
137
138 unit_assert_operator_equal(1, phospho.propertyValues.count("spec_2_site"));
139 unit_assert_operator_equal("Y", phospho.propertyValues.find("spec_2_site")->second);
140}
UNIMOD_Phospho
Phospho: Phosphorylation.
Definition cv.hpp:9417
std::multimap< std::string, std::string > propertyValues
Definition cv.hpp:14956
#define unit_assert_operator_equal(expected, actual)
Definition unit.hpp:92

References pwiz::cv::cvTermInfo(), pwiz::cv::CVTermInfo::propertyValues, UNIMOD_Phospho, and unit_assert_operator_equal.

Referenced by testThreadSafetyWorker().

◆ testThreadSafetyWorker()

void testThreadSafetyWorker ( boost::barrier *  testBarrier)

Definition at line 143 of file cvtest.cpp.

144{
145 testBarrier->wait(); // wait until all threads have started
146
147 try
148 {
149 test();
150 testIsA();
152 testSynonyms();
155 }
156 catch (exception& e)
157 {
158 cerr << "Exception in worker thread: " << e.what() << endl;
159 }
160 catch (...)
161 {
162 cerr << "Unhandled exception in worker thread." << endl;
163 }
164}
void testPropertyValues()
Definition cvtest.cpp:127
void testIDTranslation()
Definition cvtest.cpp:115
void testSynonyms()
Definition cvtest.cpp:100
void testOtherRelations()
Definition cvtest.cpp:84
void testIsA()
Definition cvtest.cpp:67
void test()
Definition cvtest.cpp:39

References test(), testIDTranslation(), testIsA(), testOtherRelations(), testPropertyValues(), and testSynonyms().

Referenced by testThreadSafety().

◆ testThreadSafety()

void testThreadSafety ( const int &  testThreadCount)

Definition at line 166 of file cvtest.cpp.

167{
168 boost::barrier testBarrier(testThreadCount);
169 boost::thread_group testThreadGroup;
170 for (int i=0; i < testThreadCount; ++i)
171 testThreadGroup.add_thread(new boost::thread(&testThreadSafetyWorker, &testBarrier));
172 testThreadGroup.join_all();
173}
void testThreadSafetyWorker(boost::barrier *testBarrier)
Definition cvtest.cpp:143

References testThreadSafetyWorker().

◆ main()

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

Definition at line 176 of file cvtest.cpp.

177{
178 TEST_PROLOG(argc, argv)
179
180 if (argc>1 && !strcmp(argv[1],"-v")) os_ = &cout;
181
182 try
183 {
184 //testThreadSafety(1); // does not test thread-safety of singleton initialization
189 }
190 catch (exception& e)
191 {
192 TEST_FAILED(e.what())
193 }
194 catch (...)
195 {
196 TEST_FAILED("Caught unknown exception.")
197 }
198
200}
void testThreadSafety()
#define TEST_EPILOG
Definition unit.hpp:183
#define TEST_FAILED(x)
Definition unit.hpp:177
#define TEST_PROLOG(argc, argv)
Definition unit.hpp:175

References os_, TEST_EPILOG, TEST_FAILED, TEST_PROLOG, and testThreadSafety().

Variable Documentation

◆ os_

ostream* os_ = 0

Definition at line 36 of file cvtest.cpp.

Referenced by main(), and test().