MikkelSchubert / adapterremoval / #39

Committed 20 Aug 2024 01:31PM UTC coverage: 79.602% (-3.8%) from 83.365%

Build # #39

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travis-ci

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MikkelSchubert

Commit Message

update schema URL to use github pages

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/src/managed_io.cpp

/*************************************************************************\
 * AdapterRemoval - cleaning next-generation sequencing reads            *
 *                                                                       *
 * Copyright (C) 2015 by Mikkel Schubert - mikkelsch@gmail.com           *
 *                                                                       *
 * This program is free software: you can redistribute it and/or modify  *
 * it under the terms of the GNU 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 General Public License for more details.                          *
 *                                                                       *
 * You should have received a copy of the GNU General Public License     *
 * along with this program.  If not, see <http://www.gnu.org/licenses/>. *
\*************************************************************************/
#include "managed_io.hpp" // declarations
#include "debug.hpp"      // for AR_REQUIRE
#include "errors.hpp"     // for io_error
#include "logging.hpp"    // for log::warn
#include "strutils.hpp"   // for log_escape
#include <algorithm>      // for any_of
#include <cerrno>         // for EMFILE, errno
#include <cstddef>        // for size_t
#include <cstdio>         // for fopen, fread, fwrite, ...
#include <exception>      // for std::exception
#include <fcntl.h>        // for posix_fadvise
#include <mutex>          // for mutex, lock_guard
#include <string>         // for string
#include <sys/stat.h>     // for fstat

namespace adapterremoval {

class io_manager
{
public:
  static void open(managed_reader* reader)
  {
    if (reader->m_file) {
      return;
    } else if (reader->filename() == "/dev/stdin") {
      reader->m_file = stdin;
    } else if (reader->filename() != "-") {
      reader->m_file = io_manager::fopen(reader->filename(), "rb");

#if _XOPEN_SOURCE >= 600 || _POSIX_C_SOURCE >= 200112L
      posix_fadvise(fileno(reader->m_file), 0, 0, POSIX_FADV_WILLNEED);
      posix_fadvise(fileno(reader->m_file), 0, 0, POSIX_FADV_SEQUENTIAL);
#endif
    } else {
      // Merged I/O depends on filenames being identical
      AR_FAIL("unhandled STDIN marker");
    }
  }

  static void open(managed_writer* writer)
  {
    if (writer->m_file) {
      return;
    } else if (writer->filename() == "/dev/stdout") {
      writer->m_file = stdout;
    } else if (writer->filename() == "/dev/stderr") {
      // Not sure why anyone would do this, but ¯\_(ツ)_/¯
      writer->m_file = stderr;
    } else if (writer->filename() != "-") {
      writer->m_file =
        io_manager::fopen(writer->filename(), writer->m_created ? "ab" : "wb");
    } else {
      // Merged I/O depends on filenames being identical
      AR_FAIL("unhandled STDOUT marker");
    }

    writer->m_created = true;
    writer->m_stream =
      io_manager::is_stream(writer->filename(), writer->m_file);
  }

  /** Adds writer to list of inactive writers */
  static void add(managed_writer* writer)
  {
    std::lock_guard<std::mutex> lock(m_lock);

    AR_REQUIRE(!writer->m_prev);
    AR_REQUIRE(!writer->m_next);
    AR_REQUIRE(!m_head == !m_tail);
    if (m_head) {
      writer->m_next = m_head;
      m_head->m_prev = writer;
    }

    m_head = writer;

    if (!m_tail) {
      m_tail = writer;
    }

    AR_REQUIRE(m_head && m_tail);
    AR_REQUIRE(!m_head->m_prev);
    AR_REQUIRE(!m_tail->m_next);
  }

  /* Removes the writer from the list of inactive writers */
  static void remove(managed_writer* writer)
  {
    std::lock_guard<std::mutex> lock(m_lock);

    AR_REQUIRE(!m_head == !m_tail);
    AR_REQUIRE(!m_head || !m_head->m_prev);
    AR_REQUIRE(!m_tail || !m_tail->m_next);

    if (writer == m_head) {
      m_head = writer->m_next;
    }

    if (writer == m_tail) {
      m_tail = writer->m_prev;
    }

    AR_REQUIRE(!m_head == !m_tail);

    if (writer->m_prev) {
      writer->m_prev->m_next = writer->m_next;
    }

    if (writer->m_next) {
      writer->m_next->m_prev = writer->m_prev;
    }

    writer->m_prev = nullptr;
    writer->m_next = nullptr;

    AR_REQUIRE(writer != m_head);
    AR_REQUIRE(writer != m_tail);
    AR_REQUIRE(!writer->m_prev);
    AR_REQUIRE(!writer->m_next);
    AR_REQUIRE(!m_head || !m_head->m_prev);
    AR_REQUIRE(!m_tail || !m_tail->m_next);
  }

  io_manager() = delete;
  ~io_manager() = delete;
  io_manager(const io_manager&) = delete;
  io_manager(io_manager&&) = delete;
  io_manager& operator=(const io_manager&) = delete;
  io_manager& operator=(io_manager&&) = delete;

private:
  static FILE* fopen(const std::string& filename, const char* mode)
  {
    while (true) {
      FILE* handle = ::fopen(filename.c_str(), mode);

      if (handle) {
        AR_REQUIRE(!::ferror(handle));
        return handle;
      } else if (errno == EMFILE) {
        close_one();
      } else {
        throw io_error("failed to open file", errno);
      }
    }
  }

  static bool is_stream(const std::string& filename, FILE* handle)
  {
    if (handle == stdin || handle == stdout || handle == stderr) {
      return true;
    }

    struct stat statbuf = {};
    if (fstat(fileno(handle), &statbuf) == 0) {
      return S_ISFIFO(statbuf.st_mode);
    }

    log::warn() << "Could not fstat " << log_escape(filename);

    // Assumed to be a stream to be safe
    return true;
  }

  /** Try to close the least recently used writer */
  static void close_one()
  {
    AR_REQUIRE(!m_head == !m_tail);
    if (!m_warning_printed) {
      log::warn() << "Number of available file-handles (ulimit -n) is too low. "
                  << "AdapterRemoval will dynamically close/re-open files as "
                  << "required, but performance may suffer as a result.";

      m_warning_printed = true;
    }

    if (m_tail) {
      if (fclose(m_tail->m_file)) {
        m_tail->m_file = nullptr;
        throw io_error("failed to close file", errno);
      }
      m_tail->m_file = nullptr;

      remove(m_tail);
    } else {
      throw io_error(
        "available number of file-handles too low; could not open any files");
    }
  }

  //! Indicates if a performance warning has been printed
  static bool m_warning_printed;
  //! Most recently used managed_writer
  static managed_writer* m_head;
  //! Least recently used managed_writer
  static managed_writer* m_tail;
  //! Lock used to control access to internal state
  static std::mutex m_lock;
};

bool io_manager::m_warning_printed = false;
managed_writer* io_manager::m_head = nullptr;
managed_writer* io_manager::m_tail = nullptr;
std::mutex io_manager::m_lock{};

///////////////////////////////////////////////////////////////////////////////

managed_reader::managed_reader(FILE* handle)
  : m_filename("<unknown file>")
  , m_file(handle)
{
  AR_REQUIRE(handle);
}

managed_reader::managed_reader(std::string filename)
  : m_filename(std::move(filename))
{
  io_manager::open(this);
}

managed_reader::~managed_reader()
{
  if (m_file && ::fclose(m_file) != 0) {
    AR_FAIL(format_io_error("error closing " + log_escape(m_filename), errno));
  }
}

void
managed_reader::close()
{
  if (m_file) {
    if (::fclose(m_file) != 0) {
      m_file = nullptr;
      throw io_error("error closing " + log_escape(m_filename), errno);
    }

    m_file = nullptr;
  }
}

size_t
managed_reader::read(void* buffer, size_t size)
{
  AR_REQUIRE(buffer);
  const auto nread = ::fread(buffer, 1, size, m_file);
  if (ferror(m_file)) {
    throw io_error("error reading " + log_escape(m_filename), errno);
  }

  return nread;
}

///////////////////////////////////////////////////////////////////////////////

/** Locker  */
class writer_lock
{
public:
  explicit writer_lock(managed_writer* writer)
    : m_writer(writer)
  {
    AR_REQUIRE(m_writer);

    // Remove from global queue to prevent other threads from manipulating it
    io_manager::remove(m_writer);
    io_manager::open(m_writer);
  };

  ~writer_lock()
  {
    // Streams cannot be managed, since they cannot be reopened
    if (m_writer->m_file && !m_writer->m_stream) {
      // Allow this writer to be closed if we run out of file handles
      io_manager::add(m_writer);
    }
  }

  void write(const void* buffer, size_t size)
  {
    AR_REQUIRE(buffer || size == 0);
    AR_REQUIRE(m_writer && m_writer->m_file);
    if (size) {
      const auto ret = ::fwrite(buffer, 1, size, m_writer->m_file);
      if (ret != size) {
        throw io_error("error writing to " + log_escape(m_writer->m_filename),
                       errno);
      }
    }
  }

  void flush()
  {
    AR_REQUIRE(m_writer && m_writer->m_file);
    if (::fflush(m_writer->m_file)) {
      throw io_error("error flushing file " + log_escape(m_writer->filename()),
                     errno);
    }
  }

  writer_lock(const writer_lock&) = delete;
  writer_lock(writer_lock&&) = delete;
  writer_lock& operator=(const writer_lock&) = delete;
  writer_lock& operator=(writer_lock&&) = delete;

private:
  managed_writer* m_writer;
};

///////////////////////////////////////////////////////////////////////////////

namespace {

bool
any_nonempty_buffers(const buffer_vec& buffers)
{
  return std::any_of(buffers.begin(), buffers.end(), [](const auto& it) {
    return it.size() != 0;
  });
}

} // namespace

managed_writer::managed_writer(std::string filename)
  : m_filename(std::move(filename))
{
}

managed_writer::~managed_writer()
{
  try {
    close();
  } catch (const std::exception&) {
    AR_FAIL("unhandled exception");
  }
}

void
managed_writer::write(const buffer& buf, const flush mode)
{
  if (buf.size() || mode == flush::on) {
    writer_lock writer{ this };

    writer.write(buf.data(), buf.size());

    if (mode == flush::on) {
      writer.flush();
    }
  }
}

void
managed_writer::write(const buffer_vec& buffers, const flush mode)
{
  if (mode == flush::on || any_nonempty_buffers(buffers)) {
    writer_lock writer{ this };

    for (const auto& buf : buffers) {
      writer.write(buf.data(), buf.size());
    }

    if (mode == flush::on) {
      writer.flush();
    }
  }
}

void
managed_writer::write(const std::string& buf, const flush mode)
{
  if (!buf.empty() || mode == flush::on) {
    writer_lock writer{ this };

    writer.write(buf.data(), buf.length());

    if (mode == flush::on) {
      writer.flush();
    }
  }
}

void
managed_writer::close()
{
  io_manager::remove(this);
  if (m_file) {
    if (fclose(m_file)) {
      m_file = nullptr;
      throw io_error("failed to close file", errno);
    }

    m_file = nullptr;
  }
}

} // namespace adapterremoval

1	/*************************************************************************\
2	* AdapterRemoval - cleaning next-generation sequencing reads *
3	* *
4	* Copyright (C) 2015 by Mikkel Schubert - mikkelsch@gmail.com *
5	* *
6	* This program is free software: you can redistribute it and/or modify *
7	* it under the terms of the GNU General Public License as published by *
8	* the Free Software Foundation, either version 3 of the License, or *
9	* (at your option) any later version. *
10	* *
11	* This program is distributed in the hope that it will be useful, *
12	* but WITHOUT ANY WARRANTY; without even the implied warranty of *
13	* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
14	* GNU General Public License for more details. *
15	* *
16	* You should have received a copy of the GNU General Public License *
17	* along with this program. If not, see <http://www.gnu.org/licenses/>. *
18	\*************************************************************************/
19	#include "managed_io.hpp" // declarations
20	#include "debug.hpp" // for AR_REQUIRE
21	#include "errors.hpp" // for io_error
22	#include "logging.hpp" // for log::warn
23	#include "strutils.hpp" // for log_escape
24	#include <algorithm> // for any_of
25	#include <cerrno> // for EMFILE, errno
26	#include <cstddef> // for size_t
27	#include <cstdio> // for fopen, fread, fwrite, ...
28	#include <exception> // for std::exception
29	#include <fcntl.h> // for posix_fadvise
30	#include <mutex> // for mutex, lock_guard
31	#include <string> // for string
32	#include <sys/stat.h> // for fstat
33
34	namespace adapterremoval {
35
36	class io_manager
37	{
38	public:
39	static void open(managed_reader* reader)	1✔
40	{
41	if (reader->m_file) {	1✔
42	return;
43	} else if (reader->filename() == "/dev/stdin") {	3✔
44	reader->m_file = stdin;	×
45	} else if (reader->filename() != "-") {	3✔
46	reader->m_file = io_manager::fopen(reader->filename(), "rb");	2✔
47
48	#if _XOPEN_SOURCE >= 600 \|\| _POSIX_C_SOURCE >= 200112L
49	posix_fadvise(fileno(reader->m_file), 0, 0, POSIX_FADV_WILLNEED);	×
50	posix_fadvise(fileno(reader->m_file), 0, 0, POSIX_FADV_SEQUENTIAL);	×
51	#endif
52	} else {
53	// Merged I/O depends on filenames being identical
54	AR_FAIL("unhandled STDIN marker");	×
55	}
56	}
57
58	static void open(managed_writer* writer)
59	{
60	if (writer->m_file) {	×
61	return;
62	} else if (writer->filename() == "/dev/stdout") {	×
63	writer->m_file = stdout;	×
64	} else if (writer->filename() == "/dev/stderr") {	×
65	// Not sure why anyone would do this, but ¯\_(ツ)_/¯
66	writer->m_file = stderr;	×
67	} else if (writer->filename() != "-") {	×
68	writer->m_file =	×
69	io_manager::fopen(writer->filename(), writer->m_created ? "ab" : "wb");	×
70	} else {
71	// Merged I/O depends on filenames being identical
72	AR_FAIL("unhandled STDOUT marker");	×
73	}
74
75	writer->m_created = true;	×
76	writer->m_stream =	×
77	io_manager::is_stream(writer->filename(), writer->m_file);	×
78	}
79
80	/** Adds writer to list of inactive writers */
81	static void add(managed_writer* writer)
82	{
83	std::lock_guard<std::mutex> lock(m_lock);	×
84
85	AR_REQUIRE(!writer->m_prev);	×
86	AR_REQUIRE(!writer->m_next);	×
87	AR_REQUIRE(!m_head == !m_tail);	×
88	if (m_head) {	×
89	writer->m_next = m_head;	×
90	m_head->m_prev = writer;	×
91	}
92
93	m_head = writer;	×
94
95	if (!m_tail) {	×
96	m_tail = writer;	×
97	}
98
99	AR_REQUIRE(m_head && m_tail);	×
100	AR_REQUIRE(!m_head->m_prev);	×
101	AR_REQUIRE(!m_tail->m_next);	×
102	}
103
104	/* Removes the writer from the list of inactive writers */
105	static void remove(managed_writer* writer)
106	{
107	std::lock_guard<std::mutex> lock(m_lock);	×
108
109	AR_REQUIRE(!m_head == !m_tail);	×
110	AR_REQUIRE(!m_head \|\| !m_head->m_prev);	×
111	AR_REQUIRE(!m_tail \|\| !m_tail->m_next);	×
112
113	if (writer == m_head) {	×
114	m_head = writer->m_next;	×
115	}
116
117	if (writer == m_tail) {	×
118	m_tail = writer->m_prev;	×
119	}
120
121	AR_REQUIRE(!m_head == !m_tail);	×
122
123	if (writer->m_prev) {	×
124	writer->m_prev->m_next = writer->m_next;	×
125	}
126
127	if (writer->m_next) {	×
128	writer->m_next->m_prev = writer->m_prev;	×
129	}
130
131	writer->m_prev = nullptr;	×
132	writer->m_next = nullptr;	×
133
134	AR_REQUIRE(writer != m_head);	×
135	AR_REQUIRE(writer != m_tail);	×
136	AR_REQUIRE(!writer->m_prev);	×
137	AR_REQUIRE(!writer->m_next);	×
138	AR_REQUIRE(!m_head \|\| !m_head->m_prev);	×
139	AR_REQUIRE(!m_tail \|\| !m_tail->m_next);	×
140	}
141
142	io_manager() = delete;
143	~io_manager() = delete;
144	io_manager(const io_manager&) = delete;
145	io_manager(io_manager&&) = delete;
146	io_manager& operator=(const io_manager&) = delete;
147	io_manager& operator=(io_manager&&) = delete;
148
149	private:
150	static FILE* fopen(const std::string& filename, const char* mode)	1✔
151	{
152	while (true) {	1✔
153	FILE* handle = ::fopen(filename.c_str(), mode);	2✔
154
155	if (handle) {	1✔
156	AR_REQUIRE(!::ferror(handle));	×
157	return handle;	×
158	} else if (errno == EMFILE) {	1✔
159	close_one();	×
160	} else {
161	throw io_error("failed to open file", errno);	2✔
162	}
163	}
164	}
165
166	static bool is_stream(const std::string& filename, FILE* handle)
167	{
168	if (handle == stdin \|\| handle == stdout \|\| handle == stderr) {	×
169	return true;
170	}
171
172	struct stat statbuf = {};	×
173	if (fstat(fileno(handle), &statbuf) == 0) {	×
174	return S_ISFIFO(statbuf.st_mode);	×
175	}
176
177	log::warn() << "Could not fstat " << log_escape(filename);	×
178
179	// Assumed to be a stream to be safe
180	return true;	×
181	}
182
183	/** Try to close the least recently used writer */
184	static void close_one()
185	{
186	AR_REQUIRE(!m_head == !m_tail);	×
187	if (!m_warning_printed) {	×
188	log::warn() << "Number of available file-handles (ulimit -n) is too low. "	×
189	<< "AdapterRemoval will dynamically close/re-open files as "	×
190	<< "required, but performance may suffer as a result.";	×
191
192	m_warning_printed = true;	×
193	}
194
195	if (m_tail) {	×
196	if (fclose(m_tail->m_file)) {	×
197	m_tail->m_file = nullptr;	×
198	throw io_error("failed to close file", errno);	×
199	}
200	m_tail->m_file = nullptr;	×
201
202	remove(m_tail);	×
203	} else {
204	throw io_error(	×
205	"available number of file-handles too low; could not open any files");	×
206	}
207	}
208
209	//! Indicates if a performance warning has been printed
210	static bool m_warning_printed;
211	//! Most recently used managed_writer
212	static managed_writer* m_head;
213	//! Least recently used managed_writer
214	static managed_writer* m_tail;
215	//! Lock used to control access to internal state
216	static std::mutex m_lock;
217	};
218
219	bool io_manager::m_warning_printed = false;
220	managed_writer* io_manager::m_head = nullptr;
221	managed_writer* io_manager::m_tail = nullptr;
222	std::mutex io_manager::m_lock{};
223
224	///////////////////////////////////////////////////////////////////////////////
225
226	managed_reader::managed_reader(FILE* handle)	14✔
227	: m_filename("<unknown file>")	29✔
228	, m_file(handle)	14✔
229	{
230	AR_REQUIRE(handle);	18✔
231	}	14✔
232
233	managed_reader::managed_reader(std::string filename)	1✔
234	: m_filename(std::move(filename))	2✔
235	{
236	io_manager::open(this);	1✔
237	}	1✔
238
239	managed_reader::~managed_reader()	13✔
240	{
241	if (m_file && ::fclose(m_file) != 0) {	13✔
242	AR_FAIL(format_io_error("error closing " + log_escape(m_filename), errno));	×
243	}
244	}	13✔
245
246	void
247	managed_reader::close()	×
248	{
249	if (m_file) {	×
250	if (::fclose(m_file) != 0) {	×
251	m_file = nullptr;	×
252	throw io_error("error closing " + log_escape(m_filename), errno);	×
253	}
254
255	m_file = nullptr;	×
256	}
257	}
258
259	size_t
260	managed_reader::read(void* buffer, size_t size)	33✔
261	{
262	AR_REQUIRE(buffer);	33✔
263	const auto nread = ::fread(buffer, 1, size, m_file);	33✔
264	if (ferror(m_file)) {	33✔
265	throw io_error("error reading " + log_escape(m_filename), errno);	×
266	}
267
268	return nread;	33✔
269	}
270
271	///////////////////////////////////////////////////////////////////////////////
272
273	/** Locker */
274	class writer_lock
275	{
276	public:
277	explicit writer_lock(managed_writer* writer)	×
278	: m_writer(writer)	×
279	{
280	AR_REQUIRE(m_writer);	×
281
282	// Remove from global queue to prevent other threads from manipulating it
283	io_manager::remove(m_writer);	×
284	io_manager::open(m_writer);	×
285	};
286
287	~writer_lock()	×
288	{
289	// Streams cannot be managed, since they cannot be reopened
290	if (m_writer->m_file && !m_writer->m_stream) {	×
291	// Allow this writer to be closed if we run out of file handles
292	io_manager::add(m_writer);	×
293	}
294	}
295
296	void write(const void* buffer, size_t size)	×
297	{
298	AR_REQUIRE(buffer \|\| size == 0);	×
299	AR_REQUIRE(m_writer && m_writer->m_file);	×
300	if (size) {	×
301	const auto ret = ::fwrite(buffer, 1, size, m_writer->m_file);	×
302	if (ret != size) {	×
303	throw io_error("error writing to " + log_escape(m_writer->m_filename),	×
304	errno);	×
305	}
306	}
307	}
308
309	void flush()	×
310	{
311	AR_REQUIRE(m_writer && m_writer->m_file);	×
312	if (::fflush(m_writer->m_file)) {	×
313	throw io_error("error flushing file " + log_escape(m_writer->filename()),	×
314	errno);	×
315	}
316	}
317
318	writer_lock(const writer_lock&) = delete;
319	writer_lock(writer_lock&&) = delete;
320	writer_lock& operator=(const writer_lock&) = delete;
321	writer_lock& operator=(writer_lock&&) = delete;
322
323	private:
324	managed_writer* m_writer;
325	};
326
327	///////////////////////////////////////////////////////////////////////////////
328
329	namespace {
330
331	bool
332	any_nonempty_buffers(const buffer_vec& buffers)	×
333	{
334	return std::any_of(buffers.begin(), buffers.end(), [](const auto& it) {	×
335	return it.size() != 0;	×
336	});	×
337	}
338
339	} // namespace
340
341	managed_writer::managed_writer(std::string filename)	×
342	: m_filename(std::move(filename))	×
343	{
344	}
345
346	managed_writer::~managed_writer()	×
347	{
348	try {	×
349	close();	×
350	} catch (const std::exception&) {	×
351	AR_FAIL("unhandled exception");	×
352	}
353	}
354
355	void
356	managed_writer::write(const buffer& buf, const flush mode)	×
357	{
358	if (buf.size() \|\| mode == flush::on) {	×
359	writer_lock writer{ this };	×
360
361	writer.write(buf.data(), buf.size());	×
362
363	if (mode == flush::on) {	×
364	writer.flush();	×
365	}
366	}
367	}
368
369	void
370	managed_writer::write(const buffer_vec& buffers, const flush mode)	×
371	{
372	if (mode == flush::on \|\| any_nonempty_buffers(buffers)) {	×
373	writer_lock writer{ this };	×
374
375	for (const auto& buf : buffers) {	×
376	writer.write(buf.data(), buf.size());	×
377	}
378
379	if (mode == flush::on) {	×
380	writer.flush();	×
381	}
382	}
383	}
384
385	void
386	managed_writer::write(const std::string& buf, const flush mode)	×
387	{
388	if (!buf.empty() \|\| mode == flush::on) {	×
389	writer_lock writer{ this };	×
390
391	writer.write(buf.data(), buf.length());	×
392
393	if (mode == flush::on) {	×
394	writer.flush();	×
395	}
396	}
397	}
398
399	void
400	managed_writer::close()	×
401	{
402	io_manager::remove(this);	×
403	if (m_file) {	×
404	if (fclose(m_file)) {	×
405	m_file = nullptr;	×
406	throw io_error("failed to close file", errno);	×
407	}
408
409	m_file = nullptr;	×
410	}
411	}
412
413	} // namespace adapterremoval

MikkelSchubert / adapterremoval / #39

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