Merge branch '18947-githttpd'

[arvados.git] / sdk / python / arvados / commands / get.py

diff --git a/sdk/python/arvados/commands/get.py b/sdk/python/arvados/commands/get.py
index b23f2d07ede2db407a6815bf69eedb9ae0815032..c4262c59c9daa6bc8687bd7f6e360e26088e4914 100755 (executable)
--- a/sdk/python/arvados/commands/get.py
+++ b/sdk/python/arvados/commands/get.py
@@ -1,4 +1,7 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0

 
 import argparse
 import hashlib
 
 import argparse
 import hashlib


@@ -10,14 +13,12 @@ import logging
 
 import arvados
 import arvados.commands._util as arv_cmd
 
 import arvados
 import arvados.commands._util as arv_cmd

+import arvados.util as util

 
 from arvados._version import __version__
 
 api_client = None
 
 from arvados._version import __version__
 
 api_client = None

-
-def abort(msg, code=1):
-    print >>sys.stderr, "arv-get:", msg
-    exit(code)
+logger = logging.getLogger('arvados.arv-get')

 
 parser = argparse.ArgumentParser(
     description='Copy data from Keep to a local file or pipe.',
 
 parser = argparse.ArgumentParser(
     description='Copy data from Keep to a local file or pipe.',


@@ -80,6 +81,10 @@ Overwrite existing files while writing. The default behavior is to
 refuse to write *anything* if any of the output files already
 exist. As a special case, -f is not needed to write to stdout.
 """)
 refuse to write *anything* if any of the output files already
 exist. As a special case, -f is not needed to write to stdout.
 """)

+group.add_argument('-v', action='count', default=0,
+                    help="""
+Once for verbose mode, twice for debug mode.
+""")

 group.add_argument('--skip-existing', action='store_true',
                    help="""
 Skip files that already exist. The default behavior is to refuse to
 group.add_argument('--skip-existing', action='store_true',
                    help="""
 Skip files that already exist. The default behavior is to refuse to


@@ -87,9 +92,23 @@ write *anything* if any files exist that would have to be
 overwritten. This option causes even devices, sockets, and fifos to be
 skipped.
 """)
 overwritten. This option causes even devices, sockets, and fifos to be
 skipped.
 """)

+group.add_argument('--strip-manifest', action='store_true', default=False,
+                   help="""
+When getting a collection manifest, strip its access tokens before writing
+it.
+""")

 
 

-def parse_arguments(arguments, logger):
-    args = parser.parse_args()
+parser.add_argument('--threads', type=int, metavar='N', default=4,
+                    help="""
+Set the number of download threads to be used. Take into account that
+using lots of threads will increase the RAM requirements. Default is
+to use 4 threads.
+On high latency installations, using a greater number will improve
+overall throughput.
+""")
+
+def parse_arguments(arguments, stdout, stderr):
+    args = parser.parse_args(arguments)

 
     if args.locator[-1] == os.sep:
         args.r = True
 
     if args.locator[-1] == os.sep:
         args.r = True


@@ -120,27 +139,35 @@ def parse_arguments(arguments, logger):
     # either going to a named file, or going (via stdout) to something
     # that isn't a tty.
     if (not (args.batch_progress or args.no_progress)
     # either going to a named file, or going (via stdout) to something
     # that isn't a tty.
     if (not (args.batch_progress or args.no_progress)

-        and sys.stderr.isatty()
+        and stderr.isatty()

         and (args.destination != '-'
         and (args.destination != '-'

-             or not sys.stdout.isatty())):
+             or not stdout.isatty())):

         args.progress = True
     return args
 
 def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr):
     global api_client
         args.progress = True
     return args
 
 def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr):
     global api_client

-    
-    logger = logging.getLogger('arvados.arv-get')
-    args = parse_arguments(arguments, logger)
+
+    if stdout is sys.stdout and hasattr(stdout, 'buffer'):
+        # in Python 3, write to stdout as binary
+        stdout = stdout.buffer
+
+    args = parse_arguments(arguments, stdout, stderr)
+    logger.setLevel(logging.WARNING - 10 * args.v)
+
+    request_id = arvados.util.new_request_id()
+    logger.info('X-Request-Id: '+request_id)
+

     if api_client is None:
     if api_client is None:

-        api_client = arvados.api('v1')
+        api_client = arvados.api('v1', request_id=request_id)

 
     r = re.search(r'^(.*?)(/.*)?$', args.locator)
 
     r = re.search(r'^(.*?)(/.*)?$', args.locator)

-    collection = r.group(1)
+    col_loc = r.group(1)

     get_prefix = r.group(2)
     if args.r and not get_prefix:
         get_prefix = os.sep
     get_prefix = r.group(2)
     if args.r and not get_prefix:
         get_prefix = os.sep

-    reader = arvados.CollectionReader(collection, num_retries=args.retries)

 
 

+    # User asked to download the collection's manifest

     if not get_prefix:
         if not args.n:
             open_flags = os.O_CREAT | os.O_WRONLY
     if not get_prefix:
         if not args.n:
             open_flags = os.O_CREAT | os.O_WRONLY


@@ -148,57 +175,86 @@ def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr):
                 open_flags |= os.O_EXCL
             try:
                 if args.destination == "-":
                 open_flags |= os.O_EXCL
             try:
                 if args.destination == "-":

-                    sys.stdout.write(reader.manifest_text())
+                    write_block_or_manifest(
+                        dest=stdout, src=col_loc,
+                        api_client=api_client, args=args)

                 else:
                     out_fd = os.open(args.destination, open_flags)
                     with os.fdopen(out_fd, 'wb') as out_file:
                 else:
                     out_fd = os.open(args.destination, open_flags)
                     with os.fdopen(out_fd, 'wb') as out_file:

-                        out_file.write(reader.manifest_text())
+                        write_block_or_manifest(
+                            dest=out_file, src=col_loc,
+                            api_client=api_client, args=args)

             except (IOError, OSError) as error:
             except (IOError, OSError) as error:

-                abort("can't write to '{}': {}".format(args.destination, error))
+                logger.error("can't write to '{}': {}".format(args.destination, error))
+                return 1

             except (arvados.errors.ApiError, arvados.errors.KeepReadError) as error:
             except (arvados.errors.ApiError, arvados.errors.KeepReadError) as error:

-                abort("failed to download '{}': {}".format(collection, error))
-        sys.exit(0)
+                logger.error("failed to download '{}': {}".format(col_loc, error))
+                return 1
+            except arvados.errors.ArgumentError as error:
+                if 'Argument to CollectionReader' in str(error):
+                    logger.error("error reading collection: {}".format(error))
+                    return 1
+                else:
+                    raise
+        return 0

 
 

-    reader.normalize()
+    try:
+        reader = arvados.CollectionReader(
+            col_loc, api_client=api_client, num_retries=args.retries,
+            keep_client=arvados.keep.KeepClient(block_cache=arvados.keep.KeepBlockCache((args.threads+1)*64 * 1024 * 1024)),
+            get_threads=args.threads)
+    except Exception as error:
+        logger.error("failed to read collection: {}".format(error))
+        return 1

 
     # Scan the collection. Make an array of (stream, file, local
     # destination filename) tuples, and add up total size to extract.
     todo = []
     todo_bytes = 0
     try:
 
     # Scan the collection. Make an array of (stream, file, local
     # destination filename) tuples, and add up total size to extract.
     todo = []
     todo_bytes = 0
     try:

-        for s in reader.all_streams():
-            for f in s.all_files():
-                if get_prefix and get_prefix[-1] == os.sep:
-                    if 0 != string.find(os.path.join(s.name(), f.name()),
-                                        '.' + get_prefix):
-                        continue
-                    if args.destination == "-":
-                        dest_path = "-"
-                    else:
-                        dest_path = os.path.join(
-                            args.destination,
-                            os.path.join(s.name(), f.name())[len(get_prefix)+1:])
-                        if (not (args.n or args.f or args.skip_existing) and
-                            os.path.exists(dest_path)):
-                            abort('Local file %s already exists.' % (dest_path,))
-                else:
-                    if os.path.join(s.name(), f.name()) != '.' + get_prefix:
-                        continue
-                    dest_path = args.destination
+        if get_prefix == os.sep:
+            item = reader
+        else:
+            item = reader.find('.' + get_prefix)
+
+        if isinstance(item, arvados.collection.Subcollection) or isinstance(item, arvados.collection.CollectionReader):
+            # If the user asked for a file and we got a subcollection, error out.
+            if get_prefix[-1] != os.sep:
+                logger.error("requested file '{}' is in fact a subcollection. Append a trailing '/' to download it.".format('.' + get_prefix))
+                return 1
+            # If the user asked stdout as a destination, error out.
+            elif args.destination == '-':
+                logger.error("cannot use 'stdout' as destination when downloading multiple files.")
+                return 1
+            # User asked for a subcollection, and that's what was found. Add up total size
+            # to download.
+            for s, f in files_in_collection(item):
+                dest_path = os.path.join(
+                    args.destination,
+                    os.path.join(s.stream_name(), f.name)[len(get_prefix)+1:])
+                if (not (args.n or args.f or args.skip_existing) and
+                    os.path.exists(dest_path)):
+                    logger.error('Local file %s already exists.' % (dest_path,))
+                    return 1

                 todo += [(s, f, dest_path)]
                 todo_bytes += f.size()
                 todo += [(s, f, dest_path)]
                 todo_bytes += f.size()

-    except arvados.errors.NotFoundError as e:
-        abort(e)
-
-    # Read data, and (if not -n) write to local file(s) or pipe.
+        elif isinstance(item, arvados.arvfile.ArvadosFile):
+            todo += [(item.parent, item, args.destination)]
+            todo_bytes += item.size()
+        else:
+            logger.error("'{}' not found.".format('.' + get_prefix))
+            return 1
+    except (IOError, arvados.errors.NotFoundError) as e:
+        logger.error(e)
+        return 1

 
     out_bytes = 0
 
     out_bytes = 0

-    for s,f,outfilename in todo:
+    for s, f, outfilename in todo:

         outfile = None
         digestor = None
         if not args.n:
             if outfilename == "-":
         outfile = None
         digestor = None
         if not args.n:
             if outfilename == "-":

-                outfile = sys.stdout
+                outfile = stdout

             else:
                 if args.skip_existing and os.path.exists(outfilename):
                     logger.debug('Local file %s exists. Skipping.', outfilename)
             else:
                 if args.skip_existing and os.path.exists(outfilename):
                     logger.debug('Local file %s exists. Skipping.', outfilename)


@@ -207,40 +263,70 @@ def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr):
                                    os.path.isdir(outfilename)):
                     # Good thing we looked again: apparently this file wasn't
                     # here yet when we checked earlier.
                                    os.path.isdir(outfilename)):
                     # Good thing we looked again: apparently this file wasn't
                     # here yet when we checked earlier.

-                    abort('Local file %s already exists.' % (outfilename,))
+                    logger.error('Local file %s already exists.' % (outfilename,))
+                    return 1

                 if args.r:
                     arvados.util.mkdir_dash_p(os.path.dirname(outfilename))
                 try:
                     outfile = open(outfilename, 'wb')
                 except Exception as error:
                 if args.r:
                     arvados.util.mkdir_dash_p(os.path.dirname(outfilename))
                 try:
                     outfile = open(outfilename, 'wb')
                 except Exception as error:

-                    abort('Open(%s) failed: %s' % (outfilename, error))
+                    logger.error('Open(%s) failed: %s' % (outfilename, error))
+                    return 1

         if args.hash:
             digestor = hashlib.new(args.hash)
         try:
         if args.hash:
             digestor = hashlib.new(args.hash)
         try:

-            for data in f.readall():
-                if outfile:
-                    outfile.write(data)
-                if digestor:
-                    digestor.update(data)
-                out_bytes += len(data)
-                if args.progress:
-                    sys.stderr.write('\r%d MiB / %d MiB %.1f%%' %
+            with s.open(f.name, 'rb') as file_reader:
+                for data in file_reader.readall():
+                    if outfile:
+                        outfile.write(data)
+                    if digestor:
+                        digestor.update(data)
+                    out_bytes += len(data)
+                    if args.progress:
+                        stderr.write('\r%d MiB / %d MiB %.1f%%' %

                                      (out_bytes >> 20,
                                       todo_bytes >> 20,
                                       (100
                                        if todo_bytes==0
                                        else 100.0*out_bytes/todo_bytes)))
                                      (out_bytes >> 20,
                                       todo_bytes >> 20,
                                       (100
                                        if todo_bytes==0
                                        else 100.0*out_bytes/todo_bytes)))

-                elif args.batch_progress:
-                    sys.stderr.write('%s %d read %d total\n' %
+                    elif args.batch_progress:
+                        stderr.write('%s %d read %d total %d\n' %

                                      (sys.argv[0], os.getpid(),
                                       out_bytes, todo_bytes))
             if digestor:
                                      (sys.argv[0], os.getpid(),
                                       out_bytes, todo_bytes))
             if digestor:

-                sys.stderr.write("%s  %s/%s\n"
-                                 % (digestor.hexdigest(), s.name(), f.name()))
+                stderr.write("%s  %s/%s\n"
+                             % (digestor.hexdigest(), s.stream_name(), f.name))

         except KeyboardInterrupt:
             if outfile and (outfile.fileno() > 2) and not outfile.closed:
                 os.unlink(outfile.name)
             break
         except KeyboardInterrupt:
             if outfile and (outfile.fileno() > 2) and not outfile.closed:
                 os.unlink(outfile.name)
             break

+        finally:
+            if outfile != None and outfile != stdout:
+                outfile.close()

 
     if args.progress:
 
     if args.progress:

-        sys.stderr.write('\n')
+        stderr.write('\n')
+    return 0
+
+def files_in_collection(c):
+    # Sort first by file type, then alphabetically by file path.
+    for i in sorted(list(c.keys()),
+                    key=lambda k: (
+                        isinstance(c[k], arvados.collection.Subcollection),
+                        k.upper())):
+        if isinstance(c[i], arvados.arvfile.ArvadosFile):
+            yield (c, c[i])
+        elif isinstance(c[i], arvados.collection.Subcollection):
+            for s, f in files_in_collection(c[i]):
+                yield (s, f)
+
+def write_block_or_manifest(dest, src, api_client, args):
+    if '+A' in src:
+        # block locator
+        kc = arvados.keep.KeepClient(api_client=api_client)
+        dest.write(kc.get(src, num_retries=args.retries))
+    else:
+        # collection UUID or portable data hash
+        reader = arvados.CollectionReader(
+            src, api_client=api_client, num_retries=args.retries)
+        dest.write(reader.manifest_text(strip=args.strip_manifest).encode())