--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/bin/s3put	Sat May 02 07:14:21 2020 -0400
@@ -0,0 +1,438 @@
+#!/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()