--- a/env/bin/s3put	Thu May 14 16:47:39 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,438 +0,0 @@
-#!/Users/pldms/Development/Projects/2020/david-matthews-galaxy/guppy_basecaller/env/bin/python3
-# Copyright (c) 2006,2007,2008 Mitch Garnaat http://garnaat.org/
-#
-# Permission is hereby granted, free of charge, to any person obtaining a
-# copy of this software and associated documentation files (the
-# "Software"), to deal in the Software without restriction, including
-# without limitation the rights to use, copy, modify, merge, publish, dis-
-# tribute, sublicense, and/or sell copies of the Software, and to permit
-# persons to whom the Software is furnished to do so, subject to the fol-
-# lowing conditions:
-#
-# The above copyright notice and this permission notice shall be included
-# in all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
-# OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABIL-
-# ITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT
-# SHALL THE AUTHOR BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
-# WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS
-# IN THE SOFTWARE.
-#
-import getopt
-import sys
-import os
-import boto
-
-from boto.compat import six
-
-try:
-    # multipart portions copyright Fabian Topfstedt
-    # https://gist.github.com/924094
-
-    import math
-    import mimetypes
-    from multiprocessing import Pool
-    from boto.s3.connection import S3Connection
-    from filechunkio import FileChunkIO
-    multipart_capable = True
-    usage_flag_multipart_capable = """ [--multipart]"""
-    usage_string_multipart_capable = """
-        multipart - Upload files as multiple parts. This needs filechunkio.
-                    Requires ListBucket, ListMultipartUploadParts,
-                    ListBucketMultipartUploads and PutObject permissions."""
-except ImportError as err:
-    multipart_capable = False
-    usage_flag_multipart_capable = ""
-    if six.PY2:
-        attribute = 'message'
-    else:
-        attribute = 'msg'
-    usage_string_multipart_capable = '\n\n     "' + \
-        getattr(err, attribute)[len('No module named '):] + \
-        '" is missing for multipart support '
-
-
-DEFAULT_REGION = 'us-east-1'
-
-usage_string = """
-SYNOPSIS
-    s3put [-a/--access_key <access_key>] [-s/--secret_key <secret_key>]
-          -b/--bucket <bucket_name> [-c/--callback <num_cb>]
-          [-d/--debug <debug_level>] [-i/--ignore <ignore_dirs>]
-          [-n/--no_op] [-p/--prefix <prefix>] [-k/--key_prefix <key_prefix>]
-          [-q/--quiet] [-g/--grant grant] [-w/--no_overwrite] [-r/--reduced]
-          [--header] [--region <name>] [--host <s3_host>]""" + \
-          usage_flag_multipart_capable + """ path [path...]
-
-    Where
-        access_key - Your AWS Access Key ID.  If not supplied, boto will
-                     use the value of the environment variable
-                     AWS_ACCESS_KEY_ID
-        secret_key - Your AWS Secret Access Key.  If not supplied, boto
-                     will use the value of the environment variable
-                     AWS_SECRET_ACCESS_KEY
-        bucket_name - The name of the S3 bucket the file(s) should be
-                      copied to.
-        path - A path to a directory or file that represents the items
-               to be uploaded.  If the path points to an individual file,
-               that file will be uploaded to the specified bucket.  If the
-               path points to a directory, it will recursively traverse
-               the directory and upload all files to the specified bucket.
-        debug_level - 0 means no debug output (default), 1 means normal
-                      debug output from boto, and 2 means boto debug output
-                      plus request/response output from httplib
-        ignore_dirs - a comma-separated list of directory names that will
-                      be ignored and not uploaded to S3.
-        num_cb - The number of progress callbacks to display.  The default
-                 is zero which means no callbacks.  If you supplied a value
-                 of "-c 10" for example, the progress callback would be
-                 called 10 times for each file transferred.
-        prefix - A file path prefix that will be stripped from the full
-                 path of the file when determining the key name in S3.
-                 For example, if the full path of a file is:
-                     /home/foo/bar/fie.baz
-                 and the prefix is specified as "-p /home/foo/" the
-                 resulting key name in S3 will be:
-                     /bar/fie.baz
-                 The prefix must end in a trailing separator and if it
-                 does not then one will be added.
-        key_prefix - A prefix to be added to the S3 key name, after any
-                     stripping of the file path is done based on the
-                     "-p/--prefix" option.
-        reduced - Use Reduced Redundancy storage
-        grant - A canned ACL policy that will be granted on each file
-                transferred to S3.  The value of provided must be one
-                of the "canned" ACL policies supported by S3:
-                private|public-read|public-read-write|authenticated-read
-        no_overwrite - No files will be overwritten on S3, if the file/key
-                       exists on s3 it will be kept. This is useful for
-                       resuming interrupted transfers. Note this is not a
-                       sync, even if the file has been updated locally if
-                       the key exists on s3 the file on s3 will not be
-                       updated.
-        header - key=value pairs of extra header(s) to pass along in the
-                 request
-        region - Manually set a region for buckets that are not in the US
-                 classic region. Normally the region is autodetected, but
-                 setting this yourself is more efficient.
-        host - Hostname override, for using an endpoint other then AWS S3
-""" + usage_string_multipart_capable + """
-
-
-     If the -n option is provided, no files will be transferred to S3 but
-     informational messages will be printed about what would happen.
-"""
-
-
-def usage(status=1):
-    print(usage_string)
-    sys.exit(status)
-
-
-def submit_cb(bytes_so_far, total_bytes):
-    print('%d bytes transferred / %d bytes total' % (bytes_so_far, total_bytes))
-
-
-def get_key_name(fullpath, prefix, key_prefix):
-    if fullpath.startswith(prefix):
-        key_name = fullpath[len(prefix):]
-    else:
-        key_name = fullpath
-    l = key_name.split(os.sep)
-    return key_prefix + '/'.join(l)
-
-
-def _upload_part(bucketname, aws_key, aws_secret, multipart_id, part_num,
-                 source_path, offset, bytes, debug, cb, num_cb,
-                 amount_of_retries=10):
-    """
-    Uploads a part with retries.
-    """
-    if debug == 1:
-        print("_upload_part(%s, %s, %s)" % (source_path, offset, bytes))
-
-    def _upload(retries_left=amount_of_retries):
-        try:
-            if debug == 1:
-                print('Start uploading part #%d ...' % part_num)
-            conn = S3Connection(aws_key, aws_secret)
-            conn.debug = debug
-            bucket = conn.get_bucket(bucketname)
-            for mp in bucket.get_all_multipart_uploads():
-                if mp.id == multipart_id:
-                    with FileChunkIO(source_path, 'r', offset=offset,
-                                     bytes=bytes) as fp:
-                        mp.upload_part_from_file(fp=fp, part_num=part_num,
-                                                 cb=cb, num_cb=num_cb)
-                    break
-        except Exception as exc:
-            if retries_left:
-                _upload(retries_left=retries_left - 1)
-            else:
-                print('Failed uploading part #%d' % part_num)
-                raise exc
-        else:
-            if debug == 1:
-                print('... Uploaded part #%d' % part_num)
-
-    _upload()
-
-def check_valid_region(conn, region):
-    if conn is None:
-        print('Invalid region (%s)' % region)
-        sys.exit(1)
-
-def multipart_upload(bucketname, aws_key, aws_secret, source_path, keyname,
-                     reduced, debug, cb, num_cb, acl='private', headers={},
-                     guess_mimetype=True, parallel_processes=4,
-                     region=DEFAULT_REGION):
-    """
-    Parallel multipart upload.
-    """
-    conn = boto.s3.connect_to_region(region, aws_access_key_id=aws_key,
-                                     aws_secret_access_key=aws_secret)
-    check_valid_region(conn, region)
-    conn.debug = debug
-    bucket = conn.get_bucket(bucketname)
-
-    if guess_mimetype:
-        mtype = mimetypes.guess_type(keyname)[0] or 'application/octet-stream'
-        headers.update({'Content-Type': mtype})
-
-    mp = bucket.initiate_multipart_upload(keyname, headers=headers,
-                                          reduced_redundancy=reduced)
-
-    source_size = os.stat(source_path).st_size
-    bytes_per_chunk = max(int(math.sqrt(5242880) * math.sqrt(source_size)),
-                          5242880)
-    chunk_amount = int(math.ceil(source_size / float(bytes_per_chunk)))
-
-    pool = Pool(processes=parallel_processes)
-    for i in range(chunk_amount):
-        offset = i * bytes_per_chunk
-        remaining_bytes = source_size - offset
-        bytes = min([bytes_per_chunk, remaining_bytes])
-        part_num = i + 1
-        pool.apply_async(_upload_part, [bucketname, aws_key, aws_secret, mp.id,
-                                        part_num, source_path, offset, bytes,
-                                        debug, cb, num_cb])
-    pool.close()
-    pool.join()
-
-    if len(mp.get_all_parts()) == chunk_amount:
-        mp.complete_upload()
-        key = bucket.get_key(keyname)
-        key.set_acl(acl)
-    else:
-        mp.cancel_upload()
-
-
-def singlepart_upload(bucket, key_name, fullpath, *kargs, **kwargs):
-    """
-    Single upload.
-    """
-    k = bucket.new_key(key_name)
-    k.set_contents_from_filename(fullpath, *kargs, **kwargs)
-
-
-def expand_path(path):
-    path = os.path.expanduser(path)
-    path = os.path.expandvars(path)
-    return os.path.abspath(path)
-
-
-def main():
-
-    # default values
-    aws_access_key_id = None
-    aws_secret_access_key = None
-    bucket_name = ''
-    ignore_dirs = []
-    debug = 0
-    cb = None
-    num_cb = 0
-    quiet = False
-    no_op = False
-    prefix = '/'
-    key_prefix = ''
-    grant = None
-    no_overwrite = False
-    reduced = False
-    headers = {}
-    host = None
-    multipart_requested = False
-    region = None
-
-    try:
-        opts, args = getopt.getopt(
-            sys.argv[1:], 'a:b:c::d:g:hi:k:np:qs:wr',
-            ['access_key=', 'bucket=', 'callback=', 'debug=', 'help', 'grant=',
-             'ignore=', 'key_prefix=', 'no_op', 'prefix=', 'quiet',
-             'secret_key=', 'no_overwrite', 'reduced', 'header=', 'multipart',
-             'host=', 'region='])
-    except:
-        usage(1)
-
-    # parse opts
-    for o, a in opts:
-        if o in ('-h', '--help'):
-            usage(0)
-        if o in ('-a', '--access_key'):
-            aws_access_key_id = a
-        if o in ('-b', '--bucket'):
-            bucket_name = a
-        if o in ('-c', '--callback'):
-            num_cb = int(a)
-            cb = submit_cb
-        if o in ('-d', '--debug'):
-            debug = int(a)
-        if o in ('-g', '--grant'):
-            grant = a
-        if o in ('-i', '--ignore'):
-            ignore_dirs = a.split(',')
-        if o in ('-n', '--no_op'):
-            no_op = True
-        if o in ('-w', '--no_overwrite'):
-            no_overwrite = True
-        if o in ('-p', '--prefix'):
-            prefix = a
-            if prefix[-1] != os.sep:
-                prefix = prefix + os.sep
-            prefix = expand_path(prefix)
-        if o in ('-k', '--key_prefix'):
-            key_prefix = a
-        if o in ('-q', '--quiet'):
-            quiet = True
-        if o in ('-s', '--secret_key'):
-            aws_secret_access_key = a
-        if o in ('-r', '--reduced'):
-            reduced = True
-        if o == '--header':
-            (k, v) = a.split("=", 1)
-            headers[k] = v
-        if o == '--host':
-            host = a
-        if o == '--multipart':
-            if multipart_capable:
-                multipart_requested = True
-            else:
-                print("multipart upload requested but not capable")
-                sys.exit(4)
-        if o == '--region':
-            regions = boto.s3.regions()
-            for region_info in regions:
-                if region_info.name == a:
-                    region = a
-                    break
-            else:
-                raise ValueError('Invalid region %s specified' % a)
-
-    if len(args) < 1:
-        usage(2)
-
-    if not bucket_name:
-        print("bucket name is required!")
-        usage(3)
-
-    connect_args = {
-        'aws_access_key_id': aws_access_key_id,
-        'aws_secret_access_key': aws_secret_access_key
-    }
-
-    if host:
-        connect_args['host'] = host
-
-    c = boto.s3.connect_to_region(region or DEFAULT_REGION, **connect_args)
-    check_valid_region(c, region or DEFAULT_REGION)
-    c.debug = debug
-    b = c.get_bucket(bucket_name, validate=False)
-
-    # Attempt to determine location and warn if no --host or --region
-    # arguments were passed. Then try to automagically figure out
-    # what should have been passed and fix it.
-    if host is None and region is None:
-        try:
-            location = b.get_location()
-
-            # Classic region will be '', any other will have a name
-            if location:
-                print('Bucket exists in %s but no host or region given!' % location)
-
-                # Override for EU, which is really Ireland according to the docs
-                if location == 'EU':
-                    location = 'eu-west-1'
-
-                print('Automatically setting region to %s' % location)
-
-                # Here we create a new connection, and then take the existing
-                # bucket and set it to use the new connection
-                c = boto.s3.connect_to_region(location, **connect_args)
-                c.debug = debug
-                b.connection = c
-        except Exception as e:
-            if debug > 0:
-                print(e)
-            print('Could not get bucket region info, skipping...')
-
-    existing_keys_to_check_against = []
-    files_to_check_for_upload = []
-
-    for path in args:
-        path = expand_path(path)
-        # upload a directory of files recursively
-        if os.path.isdir(path):
-            if no_overwrite:
-                if not quiet:
-                    print('Getting list of existing keys to check against')
-                for key in b.list(get_key_name(path, prefix, key_prefix)):
-                    existing_keys_to_check_against.append(key.name)
-            for root, dirs, files in os.walk(path):
-                for ignore in ignore_dirs:
-                    if ignore in dirs:
-                        dirs.remove(ignore)
-                for path in files:
-                    if path.startswith("."):
-                        continue
-                    files_to_check_for_upload.append(os.path.join(root, path))
-
-        # upload a single file
-        elif os.path.isfile(path):
-            fullpath = os.path.abspath(path)
-            key_name = get_key_name(fullpath, prefix, key_prefix)
-            files_to_check_for_upload.append(fullpath)
-            existing_keys_to_check_against.append(key_name)
-
-        # we are trying to upload something unknown
-        else:
-            print("I don't know what %s is, so i can't upload it" % path)
-
-    for fullpath in files_to_check_for_upload:
-        key_name = get_key_name(fullpath, prefix, key_prefix)
-
-        if no_overwrite and key_name in existing_keys_to_check_against:
-            if b.get_key(key_name):
-                if not quiet:
-                    print('Skipping %s as it exists in s3' % fullpath)
-                continue
-
-        if not quiet:
-            print('Copying %s to %s/%s' % (fullpath, bucket_name, key_name))
-
-        if not no_op:
-            # 0-byte files don't work and also don't need multipart upload
-            if os.stat(fullpath).st_size != 0 and multipart_capable and \
-                    multipart_requested:
-                multipart_upload(bucket_name, aws_access_key_id,
-                                 aws_secret_access_key, fullpath, key_name,
-                                 reduced, debug, cb, num_cb,
-                                 grant or 'private', headers,
-                                 region=region or DEFAULT_REGION)
-            else:
-                singlepart_upload(b, key_name, fullpath, cb=cb, num_cb=num_cb,
-                                  policy=grant, reduced_redundancy=reduced,
-                                  headers=headers)
-
-if __name__ == "__main__":
-    main()