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NCBI C++ ToolKit: src/objtools/readers/unit_test/unit_test_mod_adder.cpp Source File

95 if

( ! dirEntry.

IsFile

() ) {

100 string

name =

file

.GetName();

106 const string

sFileName =

file

.GetName();

107

vector<CTempString> vecFileNamePieces;

108 NStr::Split

( sFileName,

"."

, vecFileNamePieces );

109

BOOST_REQUIRE(vecFileNamePieces.size() == 2);

112

BOOST_REQUIRE(!tsTestName.

empty

());

114

BOOST_REQUIRE(!tsFileType.

empty

());

137

BOOST_FAIL(

"Unknown file type "

<< sFileName <<

"."

);

169 if

(!mod_name.empty()) {

170

mod_info.

name

= mod_name;

173 if

(!mod_value.empty()) {

187

BOOST_FAIL(

"input file "

input

" does not exist."

);

189

cerr <<

"Creating new test case from "

input

" ..."

<< endl;

195

pSeqEntry->Parentize();

197 auto

& bioseq = pSeqEntry->IsSeq() ?

198

pSeqEntry->SetSeq() :

199 const_cast<CBioseq

>

(pSeqEntry->SetSet().GetNucFromNucProtSet());

203 auto

fReportError = [&] (

const CModData

& modData,

const string

msg

EDiagSev

sev,

int

subcode)

208

pMessageListener->PutMessage(

225 for

(

string

line; getline(ifstr, line);) {

228 auto

it = handle_existing_map.

find

(line);

229 if

(it != handle_existing_map.

end

()) {

231

mod_handler.

AddMods

(mods, handle_existing, rejected_mods, fReportError);

234

handle_existing = it->second;

239

mods.emplace_back(mod_info.

name

, mod_info.

value

);

242

mod_handler.

AddMods

(mods, handle_existing, rejected_mods, fReportError);

247

BOOST_FAIL(

"Error: "

input

" failed during conversion."

);

254

cerr <<

" Produced new ASN1 file "

output

"."

<< endl;

257 if

(pMessageListener->Count() > 0) {

258

pMessageListener->Dump(errstr);

261

cerr <<

" Produced new error listing "

<< errors <<

"."

<< endl;

262

cerr <<

" ... Done."

<< endl;

267 const

vector<string> kEmptyStringVec;

279 const string

& sName = name_to_info_it->first;

287

cerr <<

"Testing "

<< testInfo.

mInFile

GetName

() <<

" and "

300

pSeqEntry->Parentize();

302 auto

& bioseq = pSeqEntry->IsSeq() ?

303

pSeqEntry->SetSeq() :

304 const_cast<CBioseq

>

(pSeqEntry->SetSet().GetNucFromNucProtSet());

307 auto

fReportError = [&] (

const CModData

& modData,

const string

msg

EDiagSev

sev,

int

subcode)

312

pMessageListener->PutMessage(

330 for

(

string

line; getline(ifstr, line);) {

333 auto

it = handle_existing_map.

find

(line);

334 if

(it != handle_existing_map.

end

()) {

336

mod_handler.

AddMods

(mods, handle_existing, rejected_mods, fReportError);

339

handle_existing = it->second;

344

mods.emplace_back(mod_info.

name

, mod_info.

value

);

347

mod_handler.

AddMods

(mods, handle_existing, rejected_mods, fReportError);

351

BOOST_ERROR(

"Error: "

<< sTestName <<

" failed during conversion."

);

356

cout <<

"# skipped mods : "

<< skipped_mods.size() << endl;

359 if

(pMessageListener->Count() > 0) {

360

pMessageListener->Dump(errstr);

376

BOOST_ERROR(

"Error: "

<< sTestName <<

" failed due to post processing diffs."

);

388

BOOST_ERROR(

"Error: "

<< sTestName <<

" failed due to error handling diffs."

);

399

arg_descrs->AddDefaultKey(

"test-dir"

"TEST_FILE_DIRECTORY"

400 "Set the root directory under which all test files can be found."

403

arg_descrs->AddDefaultKey(

"update-case"

"UPDATE_CASE"

404 "Produce .asn and .error files from given name for new or updated test case."

407

arg_descrs->AddFlag(

"update-all"

408 "Update all test cases to current reader code (dangerous)."

410

arg_descrs->AddFlag(

"keep-diffs"

411 "Keep output files that are different from the expected."

423 CDir

test_cases_dir( args[

"test-dir"

].AsDirectory() );

424

BOOST_REQUIRE_MESSAGE( test_cases_dir.

IsDir

(),

425 "Cannot find dir: "

<< test_cases_dir.

GetPath

() );

426 bool

update_all = args[

"update-all"

].AsBoolean();

432 string

update_case = args[

"update-case"

].AsString();

433 if

(!update_case.empty()) {

437 const

vector<string> kEmptyStringVec;

449 const string

& sName = name_to_info_it->first;

450 const STestInfo

& testInfo = name_to_info_it->second;

451

cout <<

"Verifying: "

<< sName << endl;

460 const string

& sName = name_to_info_it->first;

461 const STestInfo

& testInfo = name_to_info_it->second;

463

cout <<

"Running test: "

<< sName << endl;

465

BOOST_CHECK_NO_THROW(

sRunTest

(sName, testInfo, args[

"keep-diffs"

]));

static void Apply(const CModHandler &mod_handler, CBioseq &bioseq, TSkippedMods &skipped_mods, FPostMessage fPostMessage=nullptr)

list< CModData > TSkippedMods

list< CModData > TModList

void AddMods(const TModList &mods, EHandleExisting handle_existing, TModList &rejected_mods, FReportError fReportError=nullptr)

static CNcbiApplication * Instance(void)

Singleton method.

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

TTestNameToInfoMap & m_TestNameToInfoMap

void operator()(const CDirEntry &dirEntry)

CTestNameToInfoMapLoader(TTestNameToInfoMap &testNameToInfoMap, const string &extTemplate, const string &extInput, const string &extOutput, const string &extErrors)

const_iterator end() const

const_iterator find(const key_type &key) const

static SQLCHAR output[256]

static int RunTests(void)

Code to iterate through all tests to run.

static char test_name[128]

virtual const CArgs & GetArgs(void) const

Get parsed command line arguments.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

@ eString

An arbitrary string.

@ eDirectory

Name of file directory.

EDiagSev

Severity level for the posted diagnostics.

void FindFilesInDir(const CDir &dir, const vector< string > &masks, const vector< string > &masks_subdir, TFindFunc &find_func, TFindFiles flags=fFF_Default)

Find files in the specified directory.

virtual bool Remove(TRemoveFlags flags=eRecursive) const

Remove a directory entry.

bool IsDir(EFollowLinks follow=eFollowLinks) const

Check whether a directory entry is a directory.

bool CompareTextContents(const string &file, ECompareText mode, size_t buf_size=0) const

Compare files contents in text form.

bool IsFile(EFollowLinks follow=eFollowLinks) const

Check whether a directory entry is a file.

static string GetTmpName(ETmpFileCreationMode mode=eTmpFileGetName)

Get temporary file name.

static string ConcatPath(const string &first, const string &second)

Concatenate two parts of the path for the current OS.

string GetName(void) const

Get the base entry name with extension (if any).

const string & GetPath(void) const

Get entry path.

virtual bool Copy(const string &new_path, TCopyFlags flags=fCF_Default, size_t buf_size=0) const

Copy the entry to a location specified by "new_path".

virtual bool Exists(void) const

Check existence of file.

@ fFF_Recursive

descend into sub-dirs

@ fFF_Default

default behavior

#define MSerial_AsnText

I/O stream manipulators â.

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

IO_PREFIX::ofstream CNcbiOfstream

Portable alias for ofstream.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

static bool EndsWith(const CTempString str, const CTempString end, ECase use_case=eCase)

Check if a string ends with a specified suffix value.

static bool IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

bool empty(void) const

Return true if the represented string is empty (i.e., the length is zero)

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

static bool SplitInTwo(const CTempString str, const CTempString delim, string &str1, string &str2, TSplitFlags flags=0)

Split a string into two pieces using the specified delimiters.

static string TruncateSpaces(const string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string.

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

CModHandler::EHandleExisting handle_existing

Utility stuff for more convenient using of Boost.Test library.

BOOST_AUTO_TEST_CASE(RunTests)

const string extErrors("errors")

void sUpdateAll(CDir &test_cases_dir)

map< TTestName, STestInfo > TTestNameToInfoMap

const string dirTestFiles("mod_adder_test_cases")

const string extTemplate("template")

const string extInput("mods")

const string extOutput("asn")

void sUpdateCase(CDir &test_cases_dir, const string &test_name)

static void sGetModInfo(const string &line, SModInfo &mod_info)

const string extKeep("new")

void sRunTest(const string &sTestName, const STestInfo &testInfo, bool keep)

NCBITEST_INIT_CMDLINE(arg_descrs)

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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/unit__test__mod__adder_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/readers/unit_test/unit_test_mod_adder.cpp Source File

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/unittestmod__adder_8cpp_source.html below: