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url.h
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url.h
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/*
Pheniqs : PHilology ENcoder wIth Quality Statistics
Copyright (C) 2018 Lior Galanti
NYU Center for Genetics and System Biology
Author: Lior Galanti <lior.galanti@nyu.edu>
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as
published by the Free Software Foundation, either version 3 of the
License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Affero General Public License for more details.
You should have received a copy of the GNU Affero General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef PHENIQS_URL_H
#define PHENIQS_URL_H
#include "include.h"
#include "json.h"
#define STANDARD_STREAM_ALIAS "-"
#define CANONICAL_STDIN_PATH "/dev/stdin"
#define CANONICAL_STDOUT_PATH "/dev/stdout"
#define CANONICAL_STDERR_PATH "/dev/stderr"
#define CANONICAL_NULL_DEVICE_PATH "/dev/null"
enum class IoDirection : uint8_t {
IN,
OUT,
UNKNOWN,
};
string to_string(const IoDirection& value);
bool from_string(const char* value, IoDirection& result);
bool from_string(const string& value, IoDirection& result);
ostream& operator<<(ostream& o, const IoDirection& direction);
void encode_key_value(const string& key, const IoDirection& value, Value& container, Document& document);
enum class FormatType : uint8_t {
UNKNOWN,
NONE,
FASTQ,
SAM,
BAM,
BAI,
CRAM,
CRAI,
VCF,
BCF,
CSI,
GZI,
TBI,
BED,
JSON,
};
string to_string(const FormatType& value);
bool from_string(const char* value, FormatType& result);
bool from_string(const string& value, FormatType& result);
ostream& operator<<(ostream& o, const FormatType& value);
void encode_key_value(const string& key, const FormatType& value, Value& container, Document& document);
template<> bool decode_value_by_key< FormatType >(const Value::Ch* key, FormatType& value, const Value& container);
template<> FormatType decode_value_by_key< FormatType >(const Value::Ch* key, const Value& container);
enum class FormatCompression : uint8_t {
UNKNOWN,
NONE,
GZIP,
BGZF,
BZ2,
XZ,
};
string to_string(const FormatCompression& value);
bool from_string(const char* value, FormatCompression& result);
bool from_string(const string& value, FormatCompression& result);
ostream& operator<<(ostream& o, const FormatCompression& value);
void encode_key_value(const string& key, const FormatCompression& value, Value& container, Document& document);
template<> bool decode_value_by_key< FormatCompression >(const Value::Ch* key, FormatCompression& value, const Value& container);
template<> FormatCompression decode_value_by_key< FormatCompression >(const Value::Ch* key, const Value& container);
enum class CompressionLevel : uint8_t {
LEVEL_0,
LEVEL_1,
LEVEL_2,
LEVEL_3,
LEVEL_4,
LEVEL_5,
LEVEL_6,
LEVEL_7,
LEVEL_8,
LEVEL_9,
UNKNOWN,
};
string to_string(const CompressionLevel& value);
bool from_string(const char* value, CompressionLevel& result);
bool from_string(const string& value, CompressionLevel& result);
ostream& operator<<(ostream& o, const CompressionLevel& value);
void encode_key_value(const string& key, const CompressionLevel& value, Value& container, Document& document);
template<> bool decode_value_by_key< CompressionLevel >(const Value::Ch* key, CompressionLevel& value, const Value& container);
template<> CompressionLevel decode_value_by_key< CompressionLevel >(const Value::Ch* key, const Value& container);
enum class URLQueryParameter : uint8_t {
UNKNOWN,
FORMAT_TYPE,
FORMAT_COMPRESSION,
COMPRESSION_LEVEL,
};
string to_string(const URLQueryParameter& value);
bool from_string(const char* value, URLQueryParameter& result);
bool from_string(const string& value, URLQueryParameter& result);
ostream& operator<<(ostream& o, const URLQueryParameter& value);
string& expand_shell(string& expression);
void normalize_standard_stream(string& path, const IoDirection& direction);
class URL {
friend ostream& operator<<(ostream& o, const URL& url);
friend bool operator<(const URL& lhs, const URL& rhs);
public:
URL();
URL(const URL& other);
URL(const string& encoded);
void parse(const string& encoded);
void set_type(const FormatType type);
void set_compression(const FormatCompression& compression);
void set_compression_level(const CompressionLevel& level);
void override_query(const URL& other);
void relocate_child(const URL& base);
void relocate_sibling(const URL& base);
inline const string& encoded() const {
return _encoded;
};
inline const string& path() const {
return _path;
};
inline const string& basename() const {
return _basename;
};
inline const string& dirname() const {
return _dirname;
};
inline const string& query() const {
return _query;
};
inline const FormatType& type() const {
return _format_type;
};
inline const FormatCompression& implicit_compression() const {
return _implicit_compression;
};
inline const FormatCompression& explicit_compression() const {
return _explicit_compression;
};
inline const FormatCompression& compression() const {
return _explicit_compression != FormatCompression::UNKNOWN ? _explicit_compression: _implicit_compression;
};
inline const CompressionLevel& compression_level() const {
return _compression_level;
};
inline bool empty() const {
return _encoded.empty();
};
inline bool is_file() const {
return !_basename.empty();
};
inline bool is_directory() const {
return _basename.empty() && !_dirname.empty();
};
inline bool is_stdin() const {
return _path == CANONICAL_STDIN_PATH;
};
inline bool is_stdout() const {
return _path == CANONICAL_STDOUT_PATH;
};
inline bool is_stderr() const {
return _path == CANONICAL_STDERR_PATH;
};
inline bool is_dev_null() const {
return _path == CANONICAL_NULL_DEVICE_PATH;
};
inline bool is_standard_stream() const {
return is_stdin() || is_stdout() || is_stderr() || is_dev_null();
};
inline bool is_absolute() const {
return !_dirname.empty() && _dirname[0] == '/';
};
inline const char* const hfile_name() const {
if(is_file()) {
if(is_stdout() || is_stdin()) {
return STANDARD_STREAM_ALIAS;
} else if(is_stderr()) {
return NULL;
} else if(is_dev_null()) {
return NULL;
} else {
return _path.c_str();
}
} else {
return NULL;
}
};
inline void clear() {
_encoded.clear();
_path.clear();
_basename.clear();
_dirname.clear();
_query.clear();
_format_type = FormatType::UNKNOWN;
_explicit_compression = FormatCompression::UNKNOWN;
_implicit_compression = FormatCompression::UNKNOWN;
_compression_level = CompressionLevel::UNKNOWN;
};
bool is_readable() const;
bool is_writable() const;
bool operator==(const URL& other) const;
URL& operator=(const URL& other);
operator string() const;
string description() const;
private:
string _encoded;
string _path;
string _basename;
string _dirname;
string _query;
FormatType _format_type;
FormatCompression _implicit_compression;
FormatCompression _explicit_compression;
CompressionLevel _compression_level;
void refresh();
void parse_query();
void apply_query_parameter(const string& key, const string& value);
void append_query_parameter(const URLQueryParameter& name, const string& value);
};
bool operator<(const URL& lhs, const URL& rhs);
namespace std {
template <> struct hash< URL > {
size_t operator()(const URL& url) const {
return hash< string >()(url.path());
};
};
};
template<> URL decode_value(const Value& container);
template<> URL decode_value_by_key(const Value::Ch* key, const Value& container);
template<> bool decode_value< URL >(URL& value, const Value& container);
template<> list< URL > decode_value_by_key(const Value::Ch* key, const Value& container);
template<> bool decode_value_by_key< URL >(const Value::Ch* key, URL& value, const Value& container);
template<> bool decode_value_by_key< list< URL > >(const Value::Ch* key, list< URL >& value, const Value& container);
void encode_value(const URL& value, Value& container, Document& document);
bool encode_key_value(const string& key, const URL& value, Value& container, Document& document);
bool encode_key_value(const string& key, const list< URL >& value, Value& container, Document& document);
void standardize_url_value_by_key(const Value::Ch* key, Value& container, Document& document, const IoDirection& direction);
void standardize_url_array_by_key(const Value::Ch* key, Value& container, Document& document, const IoDirection& direction);
void relocate_url_by_key(const Value::Ch* key, Value& container, Document& document, const URL& base);
void relocate_url_array_by_key(const Value::Ch* key, Value& container, Document& document, const URL& base);
#endif /* PHENIQS_URL_H */