--- a/env/bin/mturk	Thu May 14 16:47:39 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,514 +0,0 @@
-#!/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()