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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/asndisc_8cpp_source.html below:

NCBI C++ ToolKit: src/app/discrepancy_report/asndisc.cpp Source File

48 #if __has_include(<multicall/multicall.hpp>) 49 #include <multicall/multicall.hpp> 51 #define asndisc_app_main main 63 void Init

()

override

;

101 string

PrintUsage

(

string

str

bool

detailed =

false

)

const override

;

111 for

(

auto

nm :

names

) {

115 for

(

auto

al : aliases) {

138

arg_desc->SetUsageContext(

""

"Discrepancy Report"

);

143

arg_desc->AddFlag(

"u"

"Recurse"

);

150

arg_desc->AddOptionalKey(

"d"

"DisableTests"

"List of disabled tests, separated by ','"

CArgDescriptions::eString

);

152

arg_desc->AddOptionalKey(

"a"

"Asn1Type"

"Asn.1 Type: a: Any, e: Seq-entry, b: Bioseq, s: Bioseq-set, m: Seq-submit, t: Batch Bioseq-set, u: Batch Seq-submit, c: Catenated seq-entry"

CArgDescriptions::eString

);

154

arg_desc->AddFlag(

"S"

"SummaryReport"

);

159

arg_desc->AddOptionalKey(

"X"

"ExpandCategories"

"Expand Report Categories (comma-delimited list of test names or ALL)"

CArgDescriptions::eString

);

160

arg_desc->AddFlag(

"N"

"Check Product Names"

);

161

arg_desc->AddFlag(

"F"

"Autofix"

);

162

arg_desc->AddFlag(

"XML"

"Generate XML output"

);

163

arg_desc->AddFlag(

"STDOUT"

"Copy the output to STDOUT"

);

164

arg_desc->AddFlag(

"LIST"

"List the tests without execution"

);

167

arg_desc->AddOptionalKey(

"P"

"ReportType"

"Report type: q - SMART genomes, u - Genome Submitter, b - Big Sequence, f - FATAL, t - Include FATAL Tag, s - FATAL Tag for Superuser"

CArgDescriptions::eString

);

168

arg_desc->AddOptionalKey(

"R"

"SevCount"

"0: always fail, 1: fail if severity is WARNING or above, 2 and higher: fail if severity is ERROR or above"

CArgDescriptions::eInteger

);

185 string

path = args[

"outdir"

] ? args[

"outdir"

].AsString() : fname.

GetDir

();

186 string

ext = args[

"s"

] ? args[

"s"

].AsString() :

".dr"

;

196

unique_ptr<CNcbiIstream> InputStream(

new CNcbiIfstream

(fname, ios::binary));

212

unique_ptr<CObjectIStream> objectStream;

230 if

(

type

"e"

)

return

CSeq_entry::GetTypeInfo()->GetName();

231 else if

(

type

"m"

)

return

CSeq_submit::GetTypeInfo()->GetName();

232 else if

(

type

"s"

)

return

CBioseq_set::GetTypeInfo()->GetName();

233 else if

(

type

"b"

)

return

CBioseq::GetTypeInfo()->GetName();

241 bool

compressed =

false

;

255 string

ext =

GetArgs

()[

"x"

].AsString();

256 if

(!ext.empty() && ext[0] !=

'.'

) {

259 string

autofixext =

".autofix"

+ ext;

263 auto

filename = entry->GetName();

264 if

(filename ==

"."

|| filename ==

".."

)

continue

;

265 if

(recursive && entry->IsDir())

x_ParseDirectory

(entry->GetPath(),

true

);

269 m_Files

.push_back(entry->GetPath());

282

Tests->AddTest(eTestNames::_SUSPECT_PRODUCT_NAMES);

283

Tests->ParseStrings(fname);

284

severity = Tests->Summarize();

288

Tests->AddTest(tname);

292

severity = Tests->Summarize();

298 x_Output

(outfilename, *Tests->GetProduct(), 0);

310

list<ostream*> olist{&out1};

312

olist.push_back(&std::cout);

321 unsigned

severity = 0;

325

Tests->AddTest(eTestNames::_SUSPECT_PRODUCT_NAMES);

326 for

(

const string

& fname :

m_Files

) {

331

Tests->ParseStrings(fname);

333

severity = Tests->Summarize();

336

Tests->AddTest(tname);

339 for

(

const string

& fname :

m_Files

) {

345

severity = Tests->Summarize();

349 for

(

const string

& fname :

m_Files

) {

351

Tests->AddTest(tname);

360

severity = Tests->Summarize();

380 const string

& s = args[

"P"

].AsString();

385 else if

(c ==

's'

) {

389 else if

(c ==

'q'

|| c ==

'b'

|| c ==

'u'

|| c ==

'f'

) {

413 for

(

const string

& s : List) {

415 if

(name == eTestNames::notset) {

427 else if

(!args[

"N"

]) {

454 for

(

const string

& s : List) {

456 if

(name == eTestNames::notset) {

478 for

(

const string

& s : List) {

489 if

(args[

"LIST"

]) {

496 string

abs_input_path;

498 m_Files

.push_back(args[

"i"

].AsString());

502 if

(args[

"indir"

])

x_ParseDirectory

(args[

"indir"

].AsString(), args[

"u"

].AsBoolean());

510 if

(args[

"L"

])

m_Lineage

= args[

"L"

].AsString();

511 if

(args[

"XML"

])

m_Xml

= args[

"XML"

].AsBoolean();

512 if

(args[

"STDOUT"

])

m_Print

= args[

"STDOUT"

].AsBoolean();

518 transform

(

m_Files

.begin(),

m_Files

.end(),

m_Files

.begin(), [](

string

& s) { for (auto n = s.find(

'\\'

); n != string::npos; n = s.find(

'\\'

)) s[n] =

'/'

; return s; });

528 unsigned

severity = 0;

540 for

(

const string

m_Files

) {

546

severity = sev > severity ? sev : severity;

556 int r

= args[

"R"

].AsInteger();

557 if

(

< 1 || (r < 2 && severity > 0) || severity > 1) {

572

list<string> split_args;

573

vector<const char*> new_argv;

575 if

(argc==2 && argv && argv[1] && strchr(argv[1],

' '

))

579

argc = 1 + split_args.size();

580

new_argv.reserve(argc);

581

new_argv.push_back(argv[0]);

582 for

(

auto

& s : split_args) {

583

new_argv.push_back(s.c_str());

585

std::cerr << s.c_str() <<

" "

;

590

argv = new_argv.data();

User-defined methods of the data storage class.

static void PrintMsg(EDiagSev sev, const string &msg)

USING_SCOPE(NDiscrepancy)

static unique_ptr< CObjectIStream > OpenUncompressedStream(const string &fname, bool &compressed)

void transform(Container &c, UnaryFunction *op)

static void SetupObjectManager(const CArgs &args, objects::CObjectManager &obj_mgr, TLoaders loaders=fDefault)

Set up the standard object manager data loaders according to the arguments provided above.

static void AddArgumentDescriptions(CArgDescriptions &arg_desc, TLoaders loaders=fDefault)

Add a standard set of arguments used to configure the object manager.

int Run() override

Run the application.

void Init() override

Initialize the application.

void x_Autofix(CDiscrepancySet &tests)

bool m_SuspectProductNames

unsigned x_ProcessAll(const string &outname)

string x_ConstructOutputName(const string &input)

void x_ParseDirectory(const string &name, bool recursive)

void x_ProcessFile(const string &filename, CDiscrepancySet &tests)

void x_Output(const string &fname, CDiscrepancyProduct &tests, unsigned short flags)

unsigned x_ProcessOne(const string &filename)

string & PrintUsage(string &str, bool detailed=false) const override

Print usage message to end of specified string.

static CRef< CDiscrepancySet > New(objects::CScope &scope)

EFormat

The formats are checked in the same order as declared here.

@ eBZip2

bzip2 compressed file

@ eBinaryASN

Binary ASN.1.

@ eLzo

lzo compressed file

@ eGZip

GNU zip compressed file.

static EFormat Format(const string &path, EOnError onerror=eDefault)

Guess file format.

IWriter which can write simultaneously to the different streams.

Writer-based output stream.

constexpr bool empty() const

eTestNames GetDiscrepancyCaseName(string_view)

vector< string_view > GetDiscrepancyAliases(eTestNames name)

TTestNamesSet GetDiscrepancyTests(TGroup group)

std::ofstream out("events_result.xml")

main entry point for tests

static const struct name_t names[]

static void AllTests(void)

static const char * str(char *buf, int n)

static DbTestEntry * tests

virtual const CArgs & GetArgs(void) const

Get parsed command line arguments.

int AppMain(int argc, const char *const *argv, const char *const *envp=0, EAppDiagStream diag=eDS_Default, const char *conf=NcbiEmptyCStr, const string &name=NcbiEmptyString)

Main function (entry point) for the NCBI application.

virtual void SetupArgDescriptions(CArgDescriptions *arg_desc)

Setup the command line argument descriptions.

void SetVersion(const CVersionInfo &version)

Set the version number for the program.

@ eTakeOwnership

An object can take ownership of another.

virtual string & PrintUsage(string &str, bool detailed=false) const

Print usage message to end of specified string.

@ eInputFile

Name of file (must exist and be readable)

@ eString

An arbitrary string.

@ eOutputFile

Name of file (must be writable)

@ eInteger

Convertible into an integer number (int or Int8)

EMethod

Compression/decompression methods.

@ eNone

no compression method (copy "as is")

@ eGZipFile

.gz file (including concatenated files)

@ fDefault

Use algorithm-specific defaults.

EDiagSev

Severity level for the posted diagnostics.

@ eDiag_Info

Informational message.

@ eDiag_Error

Error message.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

const string & GetMsg(void) const

Get message string.

TEntries GetEntries(const string &mask=kEmptyStr, TGetEntriesFlags flags=0) const

Get directory entries based on the specified "mask".

static string CreateAbsolutePath(const string &path, ERelativeToWhat rtw=eRelativeToCwd)

Get an absolute path from some, possibly relative, path.

string GetDir(EIfEmptyPath mode=eIfEmptyPath_Current) const

Get the directory component for this directory entry.

string GetBase(void) const

Get the base entry name without extension.

static string MakePath(const string &dir=kEmptyStr, const string &base=kEmptyStr, const string &ext=kEmptyStr)

Assemble a path from basic components.

virtual bool Exists(void) const

Check if directory "dirname" exists.

bool IsDir(EFollowLinks follow=eFollowLinks) const

Check whether a directory entry is a directory.

@ eSerial_AsnText

ASN.1 text.

@ eSerial_AsnBinary

ASN.1 binary.

static CObjectIStream * Open(ESerialDataFormat format, CNcbiIstream &inStream, bool deleteInStream)

Create serial object reader and attach it to an input stream.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

void Reset(void)

Reset reference object.

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.

@ fSplit_CanEscape

Allow \... escaping.

@ fSplit_Tokenize

All delimiters are merged and trimmed, to get non-empty tokens only.

@ fSplit_MergeDelimiters

Merge adjacent delimiters.

The blob sat and sat key Both must be positive integers</td > n< td > Non empty string The interpretation of the blob id depends on a processor Cassandra n processor expects the following format

Lightweight interface for getting lines of data with minimal memory copying.

constexpr auto sort(_Init &&init)

#define NCBI_SC_VERSION_PROXY

#define NCBI_TEAMCITY_BUILD_NUMBER_PROXY

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

std::istream & in(std::istream &in_, double &x_)

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

Reader-writer based streams.

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

C++ I/O stream wrappers to compress/decompress data on-the-fly.

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