--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/bin/mturk	Sat May 02 07:14:21 2020 -0400
@@ -0,0 +1,514 @@
+#!/Users/pldms/Development/Projects/2020/david-matthews-galaxy/guppy_basecaller/env/bin/python3
+# Copyright 2012, 2014 Kodi Arfer
+#
+# 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
+
+import argparse # Hence, Python 2.7 is required.
+import sys
+import os.path
+import string
+import inspect
+import datetime, calendar
+import boto.mturk.connection, boto.mturk.price, boto.mturk.question, boto.mturk.qualification
+from boto.compat import json
+
+# --------------------------------------------------
+# Globals
+# -------------------------------------------------
+
+interactive = False
+con = None
+mturk_website = None
+
+default_nicknames_path = os.path.expanduser('~/.boto_mturkcli_hit_nicknames')
+nicknames = {}
+nickname_pool = set(string.ascii_lowercase)
+
+get_assignments_page_size = 100
+
+time_units = dict(
+    s = 1,
+    min = 60,
+    h = 60 * 60,
+    d = 24 * 60 * 60)
+
+qual_requirements = dict(
+    Adult = '00000000000000000060',
+    Locale = '00000000000000000071',
+    NumberHITsApproved = '00000000000000000040',
+    PercentAssignmentsSubmitted = '00000000000000000000',
+    PercentAssignmentsAbandoned = '00000000000000000070',
+    PercentAssignmentsReturned = '000000000000000000E0',
+    PercentAssignmentsApproved = '000000000000000000L0',
+    PercentAssignmentsRejected = '000000000000000000S0')
+
+qual_comparators = {v : k for k, v in dict(
+    LessThan = '<', LessThanOrEqualTo = '<=',
+    GreaterThan = '>', GreaterThanOrEqualTo = '>=',
+    EqualTo = '==', NotEqualTo = '!=',
+    Exists = 'exists').items()}
+
+example_config_file = '''Example configuration file:
+
+  {
+    "title": "Pick your favorite color",
+    "description": "In this task, you are asked to pick your favorite color.",
+    "reward": 0.50,
+    "assignments": 10,
+    "duration": "20 min",
+    "keywords": ["color", "favorites", "survey"],
+    "lifetime": "7 d",
+    "approval_delay": "14 d",
+    "qualifications": [
+        "PercentAssignmentsApproved > 90",
+        "Locale == US",
+        "2ARFPLSP75KLA8M8DH1HTEQVJT3SY6 exists"
+    ],
+    "question_url": "http://example.com/myhit",
+    "question_frame_height": 450
+  }'''
+
+# --------------------------------------------------
+# Subroutines
+# --------------------------------------------------
+
+def unjson(path):
+    with open(path) as o:
+        return json.load(o)
+
+def add_argparse_arguments(parser):
+    parser.add_argument('-P', '--production',
+        dest = 'sandbox', action = 'store_false', default = True,
+        help = 'use the production site (default: use the sandbox)')
+    parser.add_argument('--nicknames',
+        dest = 'nicknames_path', metavar = 'PATH',
+        default = default_nicknames_path,
+        help = 'where to store HIT nicknames (default: {})'.format(
+            default_nicknames_path))
+
+def init_by_args(args):
+    init(args.sandbox, args.nicknames_path)
+
+def init(sandbox = False, nicknames_path = default_nicknames_path):
+    global con, mturk_website, nicknames, original_nicknames
+
+    mturk_website = 'workersandbox.mturk.com' if sandbox else 'www.mturk.com'
+    con = boto.mturk.connection.MTurkConnection(
+        host = 'mechanicalturk.sandbox.amazonaws.com' if sandbox else 'mechanicalturk.amazonaws.com')
+
+    try:
+        nicknames = unjson(nicknames_path)
+    except IOError:
+        nicknames = {}
+    original_nicknames = nicknames.copy()
+
+def save_nicknames(nicknames_path = default_nicknames_path):
+    if nicknames != original_nicknames:
+        with open(nicknames_path, 'w') as o:
+            json.dump(nicknames, o, sort_keys = True, indent = 4)
+            print >>o
+
+def parse_duration(s):
+    '''Parses durations like "2 d", "48 h", "2880 min",
+"172800 s", or "172800".'''
+    x = s.split()
+    return int(x[0]) * time_units['s' if len(x) == 1 else x[1]]
+def display_duration(n):
+    for unit, m in sorted(time_units.items(), key = lambda x: -x[1]):
+        if n % m == 0:
+            return '{} {}'.format(n / m, unit)
+
+def parse_qualification(inp):
+    '''Parses qualifications like "PercentAssignmentsApproved > 90",
+"Locale == US", and "2ARFPLSP75KLA8M8DH1HTEQVJT3SY6 exists".'''
+    inp = inp.split()
+    name, comparator, value = inp.pop(0), inp.pop(0), (inp[0] if len(inp) else None)
+    qtid = qual_requirements.get(name)
+    if qtid is None:
+      # Treat "name" as a Qualification Type ID.
+        qtid = name
+    if qtid == qual_requirements['Locale']:
+        return boto.mturk.qualification.LocaleRequirement(
+            qual_comparators[comparator],
+            value,
+            required_to_preview = False)
+    return boto.mturk.qualification.Requirement(
+        qtid,
+        qual_comparators[comparator],
+        value,
+        required_to_preview = qtid == qual_requirements['Adult'])
+          # Thus required_to_preview is true only for the
+          # Worker_Adult requirement.
+
+def preview_url(hit):
+    return 'https://{}/mturk/preview?groupId={}'.format(
+        mturk_website, hit.HITTypeId)
+
+def parse_timestamp(s):
+    '''Takes a timestamp like "2012-11-24T16:34:41Z".
+
+Returns a datetime object in the local time zone.'''
+    return datetime.datetime.fromtimestamp(
+        calendar.timegm(
+        datetime.datetime.strptime(s, '%Y-%m-%dT%H:%M:%SZ').timetuple()))
+
+def get_hitid(nickname_or_hitid):
+    return nicknames.get(nickname_or_hitid) or nickname_or_hitid
+
+def get_nickname(hitid):
+    for k, v in nicknames.items():
+        if v == hitid:
+            return k
+    return None
+
+def display_datetime(dt):
+    return dt.strftime('%e %b %Y, %l:%M %P')
+
+def display_hit(hit, verbose = False):
+    et = parse_timestamp(hit.Expiration)
+    return '\n'.join([
+        '{} - {} ({}, {}, {})'.format(
+            get_nickname(hit.HITId),
+            hit.Title,
+            hit.FormattedPrice,
+            display_duration(int(hit.AssignmentDurationInSeconds)),
+            hit.HITStatus),
+        'HIT ID: ' + hit.HITId,
+        'Type ID: ' + hit.HITTypeId,
+        'Group ID: ' + hit.HITGroupId,
+        'Preview: ' + preview_url(hit),
+        'Created {}   {}'.format(
+            display_datetime(parse_timestamp(hit.CreationTime)),
+            'Expired' if et <= datetime.datetime.now() else
+                'Expires ' + display_datetime(et)),
+        'Assignments: {} -- {} avail, {} pending, {} reviewable, {} reviewed'.format(
+            hit.MaxAssignments,
+            hit.NumberOfAssignmentsAvailable,
+            hit.NumberOfAssignmentsPending,
+            int(hit.MaxAssignments) - (int(hit.NumberOfAssignmentsAvailable) + int(hit.NumberOfAssignmentsPending) + int(hit.NumberOfAssignmentsCompleted)),
+            hit.NumberOfAssignmentsCompleted)
+            if hasattr(hit, 'NumberOfAssignmentsAvailable')
+            else 'Assignments: {} total'.format(hit.MaxAssignments),
+            # For some reason, SearchHITs includes the
+            # NumberOfAssignmentsFoobar fields but GetHIT doesn't.
+        ] + ([] if not verbose else [
+            '\nDescription: ' + hit.Description,
+            '\nKeywords: ' + hit.Keywords
+        ])) + '\n'
+
+def digest_assignment(a):
+    return dict(
+        answers = {str(x.qid): str(x.fields[0]) for x in a.answers[0]},
+        **{k: str(getattr(a, k)) for k in (
+            'AcceptTime', 'SubmitTime',
+            'HITId', 'AssignmentId', 'WorkerId',
+            'AssignmentStatus')})
+
+# --------------------------------------------------
+# Commands
+# --------------------------------------------------
+
+def get_balance():
+    return con.get_account_balance()
+
+def show_hit(hit):
+    return display_hit(con.get_hit(hit)[0], verbose = True)
+
+def list_hits():
+    'Lists your 10 most recently created HITs, with the most recent last.'
+    return '\n'.join(reversed(map(display_hit, con.search_hits(
+        sort_by = 'CreationTime',
+        sort_direction = 'Descending',
+        page_size = 10))))
+
+def make_hit(title, description, keywords, reward, question_url, question_frame_height, duration, assignments, approval_delay, lifetime, qualifications = []):
+    r = con.create_hit(
+        title = title,
+        description = description,
+        keywords = con.get_keywords_as_string(keywords),
+        reward = con.get_price_as_price(reward),
+        question = boto.mturk.question.ExternalQuestion(
+            question_url,
+            question_frame_height),
+        duration = parse_duration(duration),
+        qualifications = boto.mturk.qualification.Qualifications(
+            map(parse_qualification, qualifications)),
+        max_assignments = assignments,
+        approval_delay = parse_duration(approval_delay),
+        lifetime = parse_duration(lifetime))
+    nick = None
+    available_nicks = nickname_pool - set(nicknames.keys())
+    if available_nicks:
+        nick = min(available_nicks)
+        nicknames[nick] = r[0].HITId
+    if interactive:
+        print 'Nickname:', nick
+        print 'HIT ID:', r[0].HITId
+        print 'Preview:', preview_url(r[0])
+    else:
+        return r[0]
+
+def extend_hit(hit, assignments_increment = None, expiration_increment = None):
+    con.extend_hit(hit, assignments_increment, expiration_increment)
+
+def expire_hit(hit):
+    con.expire_hit(hit)
+
+def delete_hit(hit):
+    '''Deletes a HIT using DisableHIT.
+
+Unreviewed assignments get automatically approved. Unsubmitted
+assignments get automatically approved upon submission.
+
+The API docs say DisableHIT doesn't work with Reviewable HITs,
+but apparently, it does.'''
+    con.disable_hit(hit)
+    global nicknames
+    nicknames = {k: v for k, v in nicknames.items() if v != hit}
+
+def list_assignments(hit, only_reviewable = False):
+    # Accumulate all relevant assignments, one page of results at
+    # a time.
+    assignments = []
+    page = 1
+    while True:
+        rs = con.get_assignments(
+            hit_id = hit,
+            page_size = get_assignments_page_size,
+            page_number = page,
+            status = 'Submitted' if only_reviewable else None)
+        assignments += map(digest_assignment, rs)
+        if len(assignments) >= int(rs.TotalNumResults):
+            break
+        page += 1
+    if interactive:
+        print json.dumps(assignments, sort_keys = True, indent = 4)
+        print ' '.join([a['AssignmentId'] for a in assignments])
+        print ' '.join([a['WorkerId'] + ',' + a['AssignmentId'] for a in assignments])
+    else:
+        return assignments
+
+def grant_bonus(message, amount, pairs):
+    for worker, assignment in pairs:
+        con.grant_bonus(worker, assignment, con.get_price_as_price(amount), message)
+        if interactive: print 'Bonused', worker
+
+def approve_assignments(message, assignments):
+    for a in assignments:
+        con.approve_assignment(a, message)
+        if interactive: print 'Approved', a
+
+def reject_assignments(message, assignments):
+    for a in assignments:
+        con.reject_assignment(a, message)
+        if interactive: print 'Rejected', a
+
+def unreject_assignments(message, assignments):
+    for a in assignments:
+        con.approve_rejected_assignment(a, message)
+        if interactive: print 'Unrejected', a
+
+def notify_workers(subject, text, workers):
+    con.notify_workers(workers, subject, text)
+
+def give_qualification(qualification, workers, value = 1, notify = True):
+    for w in workers:
+        con.assign_qualification(qualification, w, value, notify)
+        if interactive: print 'Gave to', w
+
+def revoke_qualification(qualification, workers, message = None):
+    for w in workers:
+        con.revoke_qualification(w, qualification, message)
+        if interactive: print 'Revoked from', w
+
+# --------------------------------------------------
+# Mainline code
+# --------------------------------------------------
+
+if __name__ == '__main__':
+    interactive = True
+
+    parser = argparse.ArgumentParser()
+    add_argparse_arguments(parser)
+    subs = parser.add_subparsers()
+
+    sub = subs.add_parser('bal',
+        help = 'display your prepaid balance')
+    sub.set_defaults(f = get_balance, a = lambda: [])
+
+    sub = subs.add_parser('hit',
+        help = 'get information about a HIT')
+    sub.add_argument('HIT',
+        help = 'nickname or ID of the HIT to show')
+    sub.set_defaults(f = show_hit, a = lambda:
+        [get_hitid(args.HIT)])
+
+    sub = subs.add_parser('hits',
+        help = 'list all your HITs')
+    sub.set_defaults(f = list_hits, a = lambda: [])
+
+    sub = subs.add_parser('new',
+        help = 'create a new HIT (external questions only)',
+        epilog = example_config_file,
+        formatter_class = argparse.RawDescriptionHelpFormatter)
+    sub.add_argument('JSON_PATH',
+        help = 'path to JSON configuration file for the HIT')
+    sub.add_argument('-u', '--question-url', dest = 'question_url',
+        metavar = 'URL',
+        help = 'URL for the external question')
+    sub.add_argument('-a', '--assignments', dest = 'assignments',
+        type = int, metavar = 'N',
+        help = 'number of assignments')
+    sub.add_argument('-r', '--reward', dest = 'reward',
+        type = float, metavar = 'PRICE',
+        help = 'reward amount, in USD')
+    sub.set_defaults(f = make_hit, a = lambda: dict(
+        unjson(args.JSON_PATH).items() + [(k, getattr(args, k))
+            for k in ('question_url', 'assignments', 'reward')
+            if getattr(args, k) is not None]))
+
+    sub = subs.add_parser('extend',
+        help = 'add assignments or time to a HIT')
+    sub.add_argument('HIT',
+        help = 'nickname or ID of the HIT to extend')
+    sub.add_argument('-a', '--assignments', dest = 'assignments',
+        metavar = 'N', type = int,
+        help = 'number of assignments to add')
+    sub.add_argument('-t', '--time', dest = 'time',
+        metavar = 'T',
+        help = 'amount of time to add to the expiration date')
+    sub.set_defaults(f = extend_hit, a = lambda:
+        [get_hitid(args.HIT), args.assignments,
+            args.time and parse_duration(args.time)])
+
+    sub = subs.add_parser('expire',
+        help = 'force a HIT to expire without deleting it')
+    sub.add_argument('HIT',
+        help = 'nickname or ID of the HIT to expire')
+    sub.set_defaults(f = expire_hit, a = lambda:
+        [get_hitid(args.HIT)])
+
+    sub = subs.add_parser('rm',
+        help = 'delete a HIT')
+    sub.add_argument('HIT',
+        help = 'nickname or ID of the HIT to delete')
+    sub.set_defaults(f = delete_hit, a = lambda:
+        [get_hitid(args.HIT)])
+
+    sub = subs.add_parser('as',
+        help = "list a HIT's submitted assignments")
+    sub.add_argument('HIT',
+        help = 'nickname or ID of the HIT to get assignments for')
+    sub.add_argument('-r', '--reviewable', dest = 'only_reviewable',
+        action = 'store_true',
+        help = 'show only unreviewed assignments')
+    sub.set_defaults(f = list_assignments, a = lambda:
+        [get_hitid(args.HIT), args.only_reviewable])
+
+    for command, fun, helpmsg in [
+            ('approve', approve_assignments, 'approve assignments'),
+            ('reject', reject_assignments, 'reject assignments'),
+            ('unreject', unreject_assignments, 'approve previously rejected assignments')]:
+        sub = subs.add_parser(command, help = helpmsg)
+        sub.add_argument('ASSIGNMENT', nargs = '+',
+            help = 'ID of an assignment')
+        sub.add_argument('-m', '--message', dest = 'message',
+            metavar = 'TEXT',
+            help = 'feedback message shown to workers')
+        sub.set_defaults(f = fun, a = lambda:
+            [args.message, args.ASSIGNMENT])
+
+    sub = subs.add_parser('bonus',
+        help = 'give some workers a bonus')
+    sub.add_argument('AMOUNT', type = float,
+        help = 'bonus amount, in USD')
+    sub.add_argument('MESSAGE',
+        help = 'the reason for the bonus (shown to workers in an email sent by MTurk)')
+    sub.add_argument('WIDAID', nargs = '+',
+        help = 'a WORKER_ID,ASSIGNMENT_ID pair')
+    sub.set_defaults(f = grant_bonus, a = lambda:
+        [args.MESSAGE, args.AMOUNT,
+            [p.split(',') for p in args.WIDAID]])
+
+    sub = subs.add_parser('notify',
+        help = 'send a message to some workers')
+    sub.add_argument('SUBJECT',
+        help = 'subject of the message')
+    sub.add_argument('MESSAGE',
+        help = 'text of the message')
+    sub.add_argument('WORKER', nargs = '+',
+        help = 'ID of a worker')
+    sub.set_defaults(f = notify_workers, a = lambda:
+        [args.SUBJECT, args.MESSAGE, args.WORKER])
+
+    sub = subs.add_parser('give-qual',
+        help = 'give a qualification to some workers')
+    sub.add_argument('QUAL',
+        help = 'ID of the qualification')
+    sub.add_argument('WORKER', nargs = '+',
+        help = 'ID of a worker')
+    sub.add_argument('-v', '--value', dest = 'value',
+        metavar = 'N', type = int, default = 1,
+        help = 'value of the qualification')
+    sub.add_argument('--dontnotify', dest = 'notify',
+        action = 'store_false', default = True,
+        help = "don't notify workers")
+    sub.set_defaults(f = give_qualification, a = lambda:
+        [args.QUAL, args.WORKER, args.value, args.notify])
+
+    sub = subs.add_parser('revoke-qual',
+        help = 'revoke a qualification from some workers')
+    sub.add_argument('QUAL',
+        help = 'ID of the qualification')
+    sub.add_argument('WORKER', nargs = '+',
+        help = 'ID of a worker')
+    sub.add_argument('-m', '--message', dest = 'message',
+        metavar = 'TEXT',
+        help = 'the reason the qualification was revoked (shown to workers in an email sent by MTurk)')
+    sub.set_defaults(f = revoke_qualification, a = lambda:
+        [args.QUAL, args.WORKER, args.message])
+
+    args = parser.parse_args()
+
+    init_by_args(args)
+
+    f = args.f
+    a = args.a()
+    if isinstance(a, dict):
+        # We do some introspective gymnastics so we can produce a
+        # less incomprehensible error message if some arguments
+        # are missing.
+        spec = inspect.getargspec(f)
+        missing = set(spec.args[: len(spec.args) - len(spec.defaults)]) - set(a.keys())
+        if missing:
+            raise ValueError('Missing arguments: ' + ', '.join(missing))
+        doit = lambda: f(**a)
+    else:
+        doit = lambda: f(*a)
+
+    try:
+        x = doit()
+    except boto.mturk.connection.MTurkRequestError as e:
+        print 'MTurk error:', e.error_message
+        sys.exit(1)
+
+    if x is not None:
+        print x
+
+    save_nicknames()