ProteoWizard
ReaderTest.cpp
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1 //
2 // $Id: ReaderTest.cpp 5759 2014-02-19 22:26:29Z chambm $
3 //
4 //
5 // Original author: Darren Kessner <darren@proteowizard.org>
6 //
7 // Copyright 2008 Spielberg Family Center for Applied Proteomics
8 // Cedars-Sinai Medical Center, Los Angeles, California 90048
9 //
10 // Licensed under the Apache License, Version 2.0 (the "License");
11 // you may not use this file except in compliance with the License.
12 // You may obtain a copy of the License at
13 //
14 // http://www.apache.org/licenses/LICENSE-2.0
15 //
16 // Unless required by applicable law or agreed to in writing, software
17 // distributed under the License is distributed on an "AS IS" BASIS,
18 // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
19 // See the License for the specific language governing permissions and
20 // limitations under the License.
21 //
22 
23 
27 #include "Reader.hpp"
28 #include "examples.hpp"
29 #include "MSDataFile.hpp"
31 #include <cstring>
32 
33 
34 using namespace pwiz::util;
35 using namespace pwiz::cv;
36 using namespace pwiz::msdata;
37 
38 
39 ostream* os_ = 0;
40 
41 
42 class Reader1 : public Reader
43 {
44  public:
45 
46  struct ReaderConfig
47  {
48  string name;
49  mutable bool done;
50  ReaderConfig() : name("default"), done(false) {}
51  };
52 
54 
55  virtual std::string identify(const std::string& filename, const std::string& head) const
56  {
57  bool result = (filename == "1");
58  if (os_) *os_ << "Reader1::identify(): " << boolalpha << result << endl;
59  return std::string (result?filename:std::string(""));
60  }
61 
62  virtual void read(const std::string& filename,
63  const std::string& head,
64  MSData& result,
65  int runIndex = 0,
66  const Config& config = Config()) const
67  {
68  if (os_) *os_ << "Reader1::read()\n";
69  readerConfig.done = true;
70  }
71 
72  virtual void read(const std::string& filename,
73  const std::string& head,
74  std::vector<MSDataPtr>& results,
75  const Config& config = Config()) const
76  {
77  results.push_back(MSDataPtr(new MSData));
78  read(filename, head, *results.back(), 0, config);
79  }
80 
81  virtual const char *getType() const {return "Reader1";} // satisfy inheritance
82 };
83 
84 
85 class Reader2 : public Reader
86 {
87  public:
88 
89  struct ReaderConfig
90  {
91  string color;
92  mutable bool done;
93  ReaderConfig() : color("orange"), done(false) {}
94  };
95 
97 
98  virtual std::string identify(const std::string& filename, const std::string& head) const
99  {
100  bool result = (filename == "2");
101  if (os_) *os_ << "Reader2::identify(): " << boolalpha << result << endl;
102  return std::string (result?filename:std::string(""));
103  }
104 
105  virtual void read(const std::string& filename,
106  const std::string& head,
107  MSData& result,
108  int runIndex = 0,
109  const Config& config = Config()) const
110  {
111  if (os_) *os_ << "Reader2::read()\n";
112  readerConfig.done = true;
113  }
114 
115  virtual void read(const std::string& filename,
116  const std::string& head,
117  std::vector<MSDataPtr>& results,
118  const Config& config = Config()) const
119  {
120  results.push_back(MSDataPtr(new MSData));
121  read(filename, head, *results.back(), 0, config);
122  }
123 
124  const char *getType() const {return "Reader2";} // satisfy inheritance
125 };
126 
127 
128 void testGet()
129 {
130  if (os_) *os_ << "testGet()\n";
131 
132  ReaderList readers;
133  readers.push_back(ReaderPtr(new Reader1));
134  readers.push_back(ReaderPtr(new Reader2));
135 
136  unit_assert(readers.size() == 2);
137 
138  Reader1* reader1 = readers.get<Reader1>();
139  unit_assert(reader1);
140  if (os_) *os_ << "reader1 config: " << reader1->readerConfig.name << endl;
141  unit_assert(reader1->readerConfig.name == "default");
142  reader1->readerConfig.name = "raw";
143  if (os_) *os_ << "reader1 config: " << reader1->readerConfig.name << endl;
144  unit_assert(reader1->readerConfig.name == "raw");
145 
146  Reader2* reader2 = readers.get<Reader2>();
147  unit_assert(reader2);
148  if (os_) *os_ << "reader2 config: " << reader2->readerConfig.color << endl;
149  unit_assert(reader2->readerConfig.color == "orange");
150  reader2->readerConfig.color = "purple";
151  if (os_) *os_ << "reader2 config: " << reader2->readerConfig.color << endl;
152  unit_assert(reader2->readerConfig.color == "purple");
153 
154  const ReaderList& const_readers = readers;
155  const Reader2* constReader2 = const_readers.get<Reader2>();
156  unit_assert(constReader2);
157  if (os_) *os_ << "constReader2 config: " << constReader2->readerConfig.color << endl;
158 
159  if (os_) *os_ << endl;
160 }
161 
162 
164 {
165  if (os_) *os_ << "testAccept()\n";
166 
167  ReaderList readers;
168  readers.push_back(ReaderPtr(new Reader1));
169  readers.push_back(ReaderPtr(new Reader2));
170 
171  if (os_) *os_ << "accept 1:\n";
172  unit_assert(readers.accept("1", "head"));
173  if (os_) *os_ << "accept 2:\n";
174  unit_assert(readers.accept("2", "head"));
175  if (os_) *os_ << "accept 3:\n";
176  unit_assert(!readers.accept("3", "head"));
177 
178  if (os_) *os_ << endl;
179 }
180 
181 
182 void testRead()
183 {
184  if (os_) *os_ << "testRead()\n";
185 
186  ReaderList readers;
187  readers.push_back(ReaderPtr(new Reader1));
188  readers.push_back(ReaderPtr(new Reader2));
189 
190  MSData msd;
191 
192  // note: composite pattern with accept/read will cause two calls
193  // to accept(); the alternative is to maintain state between accept()
194  // and read(), which opens possibility for misuse.
195 
196  unit_assert(readers.get<Reader1>()->readerConfig.done == false);
197  if (readers.accept("1", "head"))
198  readers.read("1", "head", msd);
199  unit_assert(readers.get<Reader1>()->readerConfig.done == true);
200 
201  readers.get<Reader1>()->readerConfig.done = false;
202  unit_assert(readers.get<Reader2>()->readerConfig.done == false);
203  if (readers.accept("2", "head"))
204  readers.read("2", "head", msd);
205  unit_assert(readers.get<Reader1>()->readerConfig.done == false);
206  unit_assert(readers.get<Reader2>()->readerConfig.done == true);
207 
208  if (os_) *os_ << endl;
209 }
210 
211 
213 {
214  ReaderPtr readers(new ExtendedReaderList);
215 
216  {ofstream fs("testSpectraDataFile.mzedML"); fs << "<?xml?><mzML>";}
217  unit_assert_operator_equal(MS_mzML_format, identifyFileFormat(readers, "testSpectraDataFile.mzedML"));
218  bfs::remove("testSpectraDataFile.mzedML");
219 
220  {ofstream fs("testSpectraDataFile.mzedXML"); fs << "<?xml?><mzXML>";}
221  unit_assert_operator_equal(MS_ISB_mzXML_format, identifyFileFormat(readers, "testSpectraDataFile.mzedXML"));
222  bfs::remove("testSpectraDataFile.mzedXML");
223 
224 
225  {
226  MSData msd;
229  config.format = MSDataFile::Format_MZ5;
230 #ifndef WITHOUT_MZ5
231  MSDataFile::write(msd, "testSpectraDataFile.Mz5", config);
232  unit_assert_operator_equal(MS_mz5_format, identifyFileFormat(readers, "testSpectraDataFile.Mz5"));
233 #endif
234  }
235  bfs::remove("testSpectraDataFile.Mz5");
236 
237  {ofstream fs("testSpectraDataFile.mGF"); fs << "MGF";}
238  unit_assert_operator_equal(MS_Mascot_MGF_format, identifyFileFormat(readers, "testSpectraDataFile.mGF"));
239  bfs::remove("testSpectraDataFile.mGF");
240 
241  {ofstream fs("testSpectraDataFile.Ms2"); fs << "MS2";}
242  unit_assert_operator_equal(MS_MS2_format, identifyFileFormat(readers, "testSpectraDataFile.Ms2"));
243  bfs::remove("testSpectraDataFile.Ms2");
244 
245  {ofstream fs("testSpectraDataFile.wiFF"); fs << "WIFF";}
246  unit_assert_operator_equal(MS_ABI_WIFF_format, identifyFileFormat(readers, "testSpectraDataFile.wiFF"));
247  bfs::remove("testSpectraDataFile.wiFF");
248 
249  {ofstream fs("_FUNC42.DAT"); fs << "Life, the Universe, and Everything";}
251  bfs::remove("_FUNC42.DAT");
252 }
253 
254 
255 void test()
256 {
257  testGet();
258  testAccept();
259  testRead();
261 }
262 
263 
264 int main(int argc, char* argv[])
265 {
266  TEST_PROLOG_EX(argc, argv, "_MSData")
267 
268  try
269  {
270  if (argc==2 && !strcmp(argv[1],"-v")) os_ = &cout;
271  test();
272  }
273  catch (exception& e)
274  {
275  TEST_FAILED(e.what())
276  }
277  catch (...)
278  {
279  TEST_FAILED("Caught unknown exception.")
280  }
281 
283 }
284 
virtual void read(const std::string &filename, const std::string &head, MSData &result, int runIndex=0, const Config &config=Config()) const
Definition: ReaderTest.cpp:105
ReaderConfig readerConfig
Definition: ReaderTest.cpp:96
virtual void read(const std::string &filename, MSData &result, int runIndex=0, const Config &config=Config()) const
delegates to first child that identifies
MS_MS2_format
MS2 format: MS2 file format for MS2 spectral data.
Definition: cv.hpp:4636
MS_mzML_format
mzML format: Proteomics Standards Inititative mzML file format.
Definition: cv.hpp:2251
MS_Mascot_MGF_format
Mascot MGF format: Mascot MGF file format.
Definition: cv.hpp:3517
virtual std::string identify(const std::string &filename, const std::string &head) const
return file type iff Reader recognizes the file, else empty;
Definition: ReaderTest.cpp:55
virtual std::string identify(const std::string &filename, const std::string &head) const
return file type iff Reader recognizes the file, else empty;
Definition: ReaderTest.cpp:98
#define TEST_EPILOG
Definition: unit.hpp:182
virtual const char * getType() const
fill in a vector of MSData.Id values; provides support for multi-run input files
Definition: ReaderTest.cpp:81
virtual void read(const std::string &filename, const std::string &head, std::vector< MSDataPtr > &results, const Config &config=Config()) const
Definition: ReaderTest.cpp:115
void testGet()
Definition: ReaderTest.cpp:117
Reader container (composite pattern).
Definition: Reader.hpp:134
configuration for write()
Definition: MSDataFile.hpp:52
boost::shared_ptr< Reader > ReaderPtr
Definition: Reader.hpp:125
default ReaderList, extended to include vendor readers
MS_Waters_raw_format
Waters raw format: Waters data file format found in a Waters RAW directory, generated from an MS acqu...
Definition: cv.hpp:2032
#define unit_assert_operator_equal(expected, actual)
Definition: unit.hpp:92
void testAccept()
Definition: ReaderTest.cpp:137
virtual void read(const std::string &filename, const std::string &head, MSData &result, int runIndex=0, const Config &config=Config()) const
Definition: ReaderTest.cpp:62
PWIZ_API_DECL void write(minimxml::XMLWriter &writer, const CV &cv)
void test()
Definition: ReaderTest.cpp:186
PWIZ_API_DECL CVID identifyFileFormat(const ReaderPtr &reader, const std::string &filepath)
tries to identify a filepath using the provided Reader or ReaderList; returns the CVID file format of...
interface for file readers
Definition: Reader.hpp:37
boost::shared_ptr< MSData > MSDataPtr
Definition: MSData.hpp:909
ostream * os_
Definition: ReaderTest.cpp:34
void testRead()
Definition: ReaderTest.cpp:156
int main(int argc, char *argv[])
Definition: ReaderTest.cpp:194
MS_ISB_mzXML_format
ISB mzXML format: Institute of Systems Biology mzXML file format.
Definition: cv.hpp:2155
virtual void read(const std::string &filename, const std::string &head, std::vector< MSDataPtr > &results, const Config &config=Config()) const
Definition: ReaderTest.cpp:72
bool accept(const std::string &filename, const std::string &head) const
return true iff Reader recognizes the file as one it should handle
Definition: Reader.hpp:70
#define TEST_PROLOG_EX(argc, argv, suffix)
Definition: unit.hpp:157
PWIZ_API_DECL void read(std::istream &is, CV &cv)
#define TEST_FAILED(x)
Definition: unit.hpp:176
PWIZ_API_DECL void initializeTiny(IdentData &mzid)
ReaderConfig readerConfig
Definition: ReaderTest.cpp:53
MS_mz5_format
mz5 format: mz5 file format, modelled after mzML.
Definition: cv.hpp:5899
boost::shared_ptr< Reader > ReaderPtr
Definition: Reader.hpp:110
void testIdentifyFileFormat()
Definition: ReaderTest.cpp:212
MS_ABI_WIFF_format
ABI WIFF format: Applied Biosystems WIFF file format.
Definition: cv.hpp:2143
reader_type * get()
returns pointer to Reader of the specified type
Definition: Reader.hpp:199
This is the root element of ProteoWizard; it represents the mzML element, defined as: intended to cap...
Definition: MSData.hpp:845
#define unit_assert(x)
Definition: unit.hpp:85
const char * getType() const
fill in a vector of MSData.Id values; provides support for multi-run input files
Definition: ReaderTest.cpp:124
Definition: cv.hpp:91