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tsv.hpp
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tsv.hpp
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// tsv.hpp
/*===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
* Author: Vyacheslav Brover
*
* File Description:
* TSV-table
*
*/
#ifndef TSV_HPP
#define TSV_HPP
#include "common.hpp"
using namespace Common_sp;
namespace Common_sp
{
struct Date : Root
{
enum Format {fmt_Year, fmt_YMD, fmt_None}; // not complete list ??
short year {0};
char month {0};
// 0 .. 12 - 1
char day {0};
// 0 .. days[month] - 1 // leap year ??
Date () = default;
explicit Date (short year_arg,
char month_arg = 0,
char day_arg = 0)
: year (year_arg)
, month (month_arg)
, day (day_arg)
{}
static bool isYear (short n)
{ return n > 1000 && n < 2500; } // PAR
static bool isMonth (short n)
{ return between<short> (n, 0, 12); }
static bool isDay (short n)
{ return between<short> (n, 0, 31); } // Must depend on month ??
static Date parse (const string &s,
Format fmt);
// Return: !empty() <=> success
bool empty () const final
{ return ! year
&& ! month
&& ! day;
}
void saveText (ostream &os) const final
{ os << std::setfill('0') << std::setw(4) << year << '-'
<< std::setfill('0') << std::setw(2) << (int) month + 1 << '-'
<< std::setfill('0') << std::setw(2) << (int) day + 1;
}
JsonMap* toJson (JsonContainer* parent,
const string& name = noString) const override
{ auto j = new JsonMap (parent, name);
new JsonInt (year, j, "year");
new JsonInt (month, j, "month");
new JsonInt (day, j, "day");
return j;
}
bool operator== (const Date &other) const
{ return year == other. year
&& month == other. month
&& day == other. day;
}
bool less (const Date &other,
bool equal) const;
bool operator<= (const Date &other) const
{ return less (other, true); }
bool operator< (const Date &other) const
{ return less (other, false); }
Date operator- (const Date &other) const;
// Requires: other <= *this
bool year_divisible () const
{ return ! month && ! day; }
bool quarter_divisible () const
{ return ! (month % 3) && ! day; }
bool month_divisible () const
{ return ! day; }
};
struct TextTable : Named
// Tab-delimited (tsv) table with a header
// name: file name or empty()
{
bool pound {false};
// '#' in the beginning of header
bool saveHeader {true};
struct Header : Named
{
size_t len_max {0};
// Type
bool numeric {true};
// Valid if numeric
bool scientific {false};
streamsize decimals {0};
bool null {false};
// = can be empty()
static constexpr size_t choices_max {7}; // PAR
Set<string> choices;
// size() <= choices_max + 1
Header () = default;
explicit Header (const string &name_arg)
: Named (name_arg)
{}
void qc () const override;
void saveText (ostream& os) const override
{ os << name
<< '\t' << len_max
<< '\t' << (numeric ? ((scientific ? "float" : "int") + string ("(") + to_string (decimals) + ")") : "char")
<< '\t' << (null ? "null" : "not null");
}
void saveSql (ostream& os) const
{ os << name << ' ';
if (numeric)
{ if (scientific)
os << "float";
else
os << "numeric(" << len_max << ',' << decimals << ")";
}
else
os << "varchar(" << len_max << ")";
if (! null)
os << " not null";
os << endl;
}
};
Vector<Header> header;
// Header::name's are unique
// size() = number of columns
Vector<StringVector> rows;
// StringVector::size() = header.size()
// Values are trim()'ed
typedef size_t ColNum;
// no_index <=> no column
typedef size_t RowNum;
// no_index <=> no row
static constexpr char aggr_sep {','}; // PAR
struct Error : runtime_error
{
Error (const TextTable &tab,
const string &what)
: runtime_error (what + "\nIn table file: " + tab. name)
{}
};
explicit TextTable (const string &tableFName,
const string &columnSynonymsFName = noString);
// Input: tableFName: format: [{'#' <comment> <EOL>}* '#'] <header> <EOL> {<row> <EOL>>}*
// empty lines are skipped
// columnSynonymsFName: <syn_format>
// Rows where number of columns < header size are added empty values
static constexpr const char* syn_format {"Column synonyms file with the format: {<main synonym> <eol> {<synonym> <eol>}* {<eol>|<eof>}}*"};
TextTable () = default;
TextTable (bool pound_arg,
const Vector<Header> &header_arg)
: pound (pound_arg)
, header (header_arg)
{}
private:
void setHeader ();
public:
void qc () const override;
void saveText (ostream &os) const override;
static bool getDecimals (string s,
bool &hasPoint,
streamsize &decimals);
// Return: true => scientific number
void printHeader (ostream &os) const;
ColNum col2num_ (const string &columnName) const;
// Retuirn: no_index <=> no columnName
ColNum col2num (const string &columnName) const
{ const ColNum i = col2num_ (columnName);
if (i == no_index)
throw Error (*this, "Table has no column " + strQuote (columnName));
return i;
}
Vector<ColNum> columns2nums (const StringVector &columns) const
{ Vector<ColNum> nums; nums. reserve (columns. size ());
for (const string &s : columns)
nums << col2num (s);
return nums;
}
bool hasColumn (const string &columnName) const
{ return col2num_ (columnName) != no_index; }
void duplicateColumn (const string &columnName_from,
const string &columnName_to);
void substitueColumn (string &columnName_from,
const string &columnName_to)
{ duplicateColumn (columnName_from, columnName_to);
columnName_from = columnName_to;
}
ColNum findDate (Date::Format &fmt) const;
// Date column is not empty and has the same format fmt in all rows
// Return: no_index <=> not found
// Output: fmt, valid if return != no_index
bool isKey (ColNum colNum) const;
private:
int compare (const StringVector& row1,
const StringVector& row2,
ColNum column) const;
public:
void filterColumns (const StringVector &newColumnNames);
// Input: newColumnNames: in header::name's
// can be repeated
// ordered
void sort (const StringVector &by);
void group (const StringVector &by,
const StringVector &sum,
const StringVector &minV,
const StringVector &maxV,
const StringVector &aggr);
// aggr: slow
// Invokes: filterColumns(by + sum + aggr)
private:
void merge (RowNum toRowNum,
RowNum fromRowNum,
const Vector<ColNum> &sum,
const Vector<ColNum> &minV,
const Vector<ColNum> &maxV,
const Vector<ColNum> &aggr);
public:
static StringVector aggr2values (const string &aggr)
{ StringVector v (aggr, aggr_sep, true);
v. sort ();
v. uniq ();
return v;
}
void colNumsRow2values (const Vector<ColNum> &colNums,
RowNum row_num,
StringVector &values) const;
// Output: values
RowNum find (const Vector<ColNum> &colNums,
const StringVector &targetValues,
RowNum rowNum_start) const;
StringVector col2values (ColNum col) const;
struct Key
{
const Vector<ColNum> colNums;
unordered_map<StringVector,RowNum,StringVector::Hasher> data;
Key (const TextTable &tab,
const StringVector &columns);
RowNum find (const StringVector &values) const
{ const auto& it = data. find (values);
if (it != data. end ())
return it->second;
return no_index;
}
};
struct Index
{
const Vector<ColNum> colNums;
unordered_map<StringVector,Vector<RowNum>,StringVector::Hasher> data;
Index (const TextTable &tab,
const StringVector &columns);
const Vector<RowNum>* find (const StringVector &values) const
{ const auto& it = data. find (values);
if (it == data. end ())
return nullptr;
return & it->second;
}
};
};
struct TsvOut
{
private:
ostream* os {nullptr};
unique_ptr<const ONumber> on;
size_t lines {0};
size_t fields_max {0};
size_t fields {0};
public:
bool usePound {true};
explicit TsvOut (ostream* os_arg,
streamsize precision = 6,
bool scientific = false)
: os (os_arg)
, on (os_arg ? new ONumber (*os_arg, precision, scientific) : nullptr)
{}
// !os_arg <=> disabled
explicit TsvOut (ostream &os_arg,
streamsize precision = 6,
bool scientific = false)
: TsvOut (& os_arg, precision, scientific)
{}
~TsvOut ()
{ if (fields)
errorExitStr ("TsvOut: unfinished line with " + to_string (fields) + " fields");
}
bool live () const
{ return os; }
bool empty () const
{ return ! lines
&& ! fields_max
&& ! fields;
}
template <typename T>
TsvOut& operator<< (const T &field)
{ if (os)
{ if (lines && fields >= fields_max)
throw runtime_error ("TsvOut: fields_max = " + to_string (fields_max));
if (fields)
*os << '\t';
else if (! lines && usePound)
*os << '#';
*os << field;
fields++;
}
return *this;
}
void newLn ()
{ if (! os)
return;
*os << endl;
if (! lines)
fields_max = fields;
lines++;
if (fields != fields_max)
throw runtime_error ("TsvOut: fields_max = " + to_string (fields_max) + ", but fields = " + to_string (fields));
fields = 0;
}
};
}
#endif