annotate webapollo.py @ 5:207c1c281360 draft

planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2

from __future__ import print_function

import argparse
import collections
import json
import logging
import os
import random
import time
from abc import abstractmethod

from BCBio import GFF

from Bio import SeqIO

import requests

from six.moves.builtins import next
from six.moves.builtins import object
from six.moves.builtins import str


try:
    import StringIO as io
except BaseException:
    import io
logging.getLogger("requests").setLevel(logging.CRITICAL)
log = logging.getLogger()


#############################################
#      BEGIN IMPORT OF CACHING LIBRARY      #
#############################################
# This code is licensed under the MIT       #
# License and is a copy of code publicly    #
# available in rev.                         #
# e27332bc82f4e327aedaec17c9b656ae719322ed  #
# of https://github.com/tkem/cachetools/    #
#############################################

class DefaultMapping(collections.MutableMapping):

    __slots__ = ()

    @abstractmethod
    def __contains__(self, key):  # pragma: nocover
        return False

    @abstractmethod
    def __getitem__(self, key):  # pragma: nocover
        if hasattr(self.__class__, '__missing__'):
            return self.__class__.__missing__(self, key)
        else:
            raise KeyError(key)

    def get(self, key, default=None):
        if key in self:
            return self[key]
        else:
            return default

    __marker = object()

    def pop(self, key, default=__marker):
        if key in self:
            value = self[key]
            del self[key]
        elif default is self.__marker:
            raise KeyError(key)
        else:
            value = default
        return value

    def setdefault(self, key, default=None):
        if key in self:
            value = self[key]
        else:
            self[key] = value = default
        return value


DefaultMapping.register(dict)


class _DefaultSize(object):
    def __getitem__(self, _):
        return 1

    def __setitem__(self, _, value):
        assert value == 1

    def pop(self, _):
        return 1


class Cache(DefaultMapping):
    """Mutable mapping to serve as a simple cache or cache base class."""

    __size = _DefaultSize()

    def __init__(self, maxsize, missing=None, getsizeof=None):
        if missing:
            self.__missing = missing
        if getsizeof:
            self.__getsizeof = getsizeof
            self.__size = dict()
        self.__data = dict()
        self.__currsize = 0
        self.__maxsize = maxsize

    def __repr__(self):
        return '%s(%r, maxsize=%r, currsize=%r)' % (
            self.__class__.__name__,
            list(self.__data.items()),
            self.__maxsize,
            self.__currsize,
        )

    def __getitem__(self, key):
        try:
            return self.__data[key]
        except KeyError:
            return self.__missing__(key)

    def __setitem__(self, key, value):
        maxsize = self.__maxsize
        size = self.getsizeof(value)
        if size > maxsize:
            raise ValueError('value too large')
        if key not in self.__data or self.__size[key] < size:
            while self.__currsize + size > maxsize:
                self.popitem()
        if key in self.__data:
            diffsize = size - self.__size[key]
        else:
            diffsize = size
        self.__data[key] = value
        self.__size[key] = size
        self.__currsize += diffsize

    def __delitem__(self, key):
        size = self.__size.pop(key)
        del self.__data[key]
        self.__currsize -= size

    def __contains__(self, key):
        return key in self.__data

    def __missing__(self, key):
        value = self.__missing(key)
        try:
            self.__setitem__(key, value)
        except ValueError:
            pass  # value too large
        return value

    def __iter__(self):
        return iter(self.__data)

    def __len__(self):
        return len(self.__data)

    @staticmethod
    def __getsizeof(value):
        return 1

    @staticmethod
    def __missing(key):
        raise KeyError(key)

    @property
    def maxsize(self):
        """The maximum size of the cache."""
        return self.__maxsize

    @property
    def currsize(self):
        """The current size of the cache."""
        return self.__currsize

    def getsizeof(self, value):
        """Return the size of a cache element's value."""
        return self.__getsizeof(value)


class _Link(object):

    __slots__ = ('key', 'expire', 'next', 'prev')

    def __init__(self, key=None, expire=None):
        self.key = key
        self.expire = expire

    def __reduce__(self):
        return _Link, (self.key, self.expire)

    def unlink(self):
        next = self.next
        prev = self.prev
        prev.next = next
        next.prev = prev


class _Timer(object):

    def __init__(self, timer):
        self.__timer = timer
        self.__nesting = 0

    def __call__(self):
        if self.__nesting == 0:
            return self.__timer()
        else:
            return self.__time

    def __enter__(self):
        if self.__nesting == 0:
            self.__time = time = self.__timer()
        else:
            time = self.__time
        self.__nesting += 1
        return time

    def __exit__(self, *exc):
        self.__nesting -= 1

    def __reduce__(self):
        return _Timer, (self.__timer,)

    def __getattr__(self, name):
        return getattr(self.__timer, name)


class TTLCache(Cache):
    """LRU Cache implementation with per-item time-to-live (TTL) value."""

    def __init__(self, maxsize, ttl, timer=time.time, missing=None,
                 getsizeof=None):
        Cache.__init__(self, maxsize, missing, getsizeof)
        self.__root = root = _Link()
        root.prev = root.next = root
        self.__links = collections.OrderedDict()
        self.__timer = _Timer(timer)
        self.__ttl = ttl

    def __contains__(self, key):
        try:
            link = self.__links[key]  # no reordering
        except KeyError:
            return False
        else:
            return not (link.expire < self.__timer())

    def __getitem__(self, key, cache_getitem=Cache.__getitem__):
        try:
            link = self.__getlink(key)
        except KeyError:
            expired = False
        else:
            expired = link.expire < self.__timer()
        if expired:
            return self.__missing__(key)
        else:
            return cache_getitem(self, key)

    def __setitem__(self, key, value, cache_setitem=Cache.__setitem__):
        with self.__timer as time:
            self.expire(time)
            cache_setitem(self, key, value)
        try:
            link = self.__getlink(key)
        except KeyError:
            self.__links[key] = link = _Link(key)
        else:
            link.unlink()
        link.expire = time + self.__ttl
        link.next = root = self.__root
        link.prev = prev = root.prev
        prev.next = root.prev = link

    def __delitem__(self, key, cache_delitem=Cache.__delitem__):
        cache_delitem(self, key)
        link = self.__links.pop(key)
        link.unlink()
        if link.expire < self.__timer():
            raise KeyError(key)

    def __iter__(self):
        root = self.__root
        curr = root.next
        while curr is not root:
            # "freeze" time for iterator access
            with self.__timer as time:
                if not (curr.expire < time):
                    yield curr.key
            curr = curr.next

    def __len__(self):
        root = self.__root
        curr = root.next
        time = self.__timer()
        count = len(self.__links)
        while curr is not root and curr.expire < time:
            count -= 1
            curr = curr.next
        return count

    def __setstate__(self, state):
        self.__dict__.update(state)
        root = self.__root
        root.prev = root.next = root
        for link in sorted(self.__links.values(), key=lambda obj: obj.expire):
            link.next = root
            link.prev = prev = root.prev
            prev.next = root.prev = link
        self.expire(self.__timer())

    def __repr__(self, cache_repr=Cache.__repr__):
        with self.__timer as time:
            self.expire(time)
            return cache_repr(self)

    @property
    def currsize(self):
        with self.__timer as time:
            self.expire(time)
            return super(TTLCache, self).currsize

    @property
    def timer(self):
        """The timer function used by the cache."""
        return self.__timer

    @property
    def ttl(self):
        """The time-to-live value of the cache's items."""
        return self.__ttl

    def expire(self, time=None):
        """Remove expired items from the cache."""
        if time is None:
            time = self.__timer()
        root = self.__root
        curr = root.next
        links = self.__links
        cache_delitem = Cache.__delitem__
        while curr is not root and curr.expire < time:
            cache_delitem(self, curr.key)
            del links[curr.key]
            next = curr.next
            curr.unlink()
            curr = next

    def clear(self):
        with self.__timer as time:
            self.expire(time)
            Cache.clear(self)

    def get(self, *args, **kwargs):
        with self.__timer:
            return Cache.get(self, *args, **kwargs)

    def pop(self, *args, **kwargs):
        with self.__timer:
            return Cache.pop(self, *args, **kwargs)

    def setdefault(self, *args, **kwargs):
        with self.__timer:
            return Cache.setdefault(self, *args, **kwargs)

    def popitem(self):
        """Remove and return the `(key, value)` pair least recently used that
        has not already expired.

        """
        with self.__timer as time:
            self.expire(time)
            try:
                key = next(iter(self.__links))
            except StopIteration:
                raise KeyError('%s is empty' % self.__class__.__name__)
            else:
                return (key, self.pop(key))

    if hasattr(collections.OrderedDict, 'move_to_end'):
        def __getlink(self, key):
            value = self.__links[key]
            self.__links.move_to_end(key)
            return value
    else:
        def __getlink(self, key):
            value = self.__links.pop(key)
            self.__links[key] = value
            return value


#############################################
#       END IMPORT OF CACHING LIBRARY       #
#############################################


cache = TTLCache(
    100,  # Up to 100 items
    5 * 60  # 5 minute cache life
)
userCache = TTLCache(
    2,  # Up to 2 items
    60  # 1 minute cache life
)


class UnknownUserException(Exception):
    pass


def WAAuth(parser):
    parser.add_argument('apollo', help='Complete Apollo URL')
    parser.add_argument('username', help='WA Username')
    parser.add_argument('password', help='WA Password')


def OrgOrGuess(parser):
    parser.add_argument('--org_json', type=argparse.FileType("r"), help='Apollo JSON output, source for common name')
    parser.add_argument('--org_raw', help='Common Name')
    parser.add_argument('--org_id', help='Organism ID')


def CnOrGuess(parser):
    OrgOrGuess(parser)
    parser.add_argument('--seq_fasta', type=argparse.FileType("r"), help='Fasta file, IDs used as sequence sources')
    parser.add_argument('--seq_raw', nargs='*', help='Sequence Names')


def GuessOrg(args, wa):
    if args.org_json:
        orgs = [x.get('commonName', None)
                for x in json.load(args.org_json)]
        orgs = [x for x in orgs if x is not None]
        return orgs
    elif args.org_raw:
        org = args.org_raw.strip()
        if len(org) > 0:
            return [org]
        else:
            raise Exception("Organism Common Name not provided")
    elif args.org_id:
        return [wa.organisms.findOrganismById(args.org_id).get('commonName', None)]
    else:
        raise Exception("Organism Common Name not provided")


def GuessCn(args, wa):
    org = GuessOrg(args, wa)
    seqs = []
    if args.seq_fasta:
        # If we have a fasta, pull all rec ids from that.
        for rec in SeqIO.parse(args.seq_fasta, 'fasta'):
            seqs.append(rec.id)
    elif args.seq_raw:
        # Otherwise raw list.
        seqs = [x.strip() for x in args.seq_raw if len(x.strip()) > 0]

    return org, seqs


def AssertUser(user_list):
    if len(user_list) == 0:
        raise UnknownUserException()
    elif len(user_list) == 1:
        return user_list[0]
    else:
        raise Exception("Too many users!")


def AssertAdmin(user):
    if user.role == 'ADMIN':
        return True
    else:
        raise Exception("User is not an administrator. Permission denied")


def PermissionCheck(user, org_cn, permission_type):
    return any(org["organism"] == org_cn and permission_type in org["permissions"] for org in user.organismPermissions)


def PasswordGenerator(length):
    chars = list('qwrtpsdfghjklzxcvbnm')
    return ''.join(random.choice(chars) for _ in range(length))


def IsRemoteUser():
    if 'GALAXY_WEBAPOLLO_REMOTE_USER' not in os.environ:
        return False
    value = os.environ['GALAXY_WEBAPOLLO_REMOTE_USER']
    if value.lower() in ('true', 't', '1'):
        return True
    else:
        return False


class WebApolloInstance(object):

    def __init__(self, url, username, password):
        self.apollo_url = url
        self.username = username
        self.password = password

        self.annotations = AnnotationsClient(self)
        self.groups = GroupsClient(self)
        self.io = IOClient(self)
        self.organisms = OrganismsClient(self)
        self.users = UsersClient(self)
        self.metrics = MetricsClient(self)
        self.bio = RemoteRecord(self)
        self.status = StatusClient(self)
        self.canned_comments = CannedCommentsClient(self)
        self.canned_keys = CannedKeysClient(self)
        self.canned_values = CannedValuesClient(self)

    def __str__(self):
        return '<WebApolloInstance at %s>' % self.apollo_url

    def requireUser(self, email):
        cacheKey = 'user-list'
        try:
            # Get the cached value
            data = userCache[cacheKey]
        except KeyError:
            # If we hit a key error above, indicating that
            # we couldn't find the key, we'll simply re-request
            # the data
            data = self.users.loadUsers()
            userCache[cacheKey] = data

        return AssertUser([x for x in data if x.username == email])


class GroupObj(object):
    def __init__(self, **kwargs):
        self.name = kwargs['name']

        if 'id' in kwargs:
            self.groupId = kwargs['id']


class UserObj(object):
    ROLE_USER = 'USER'
    ROLE_ADMIN = 'ADMIN'

    def __init__(self, **kwargs):
        # Generally expect 'userId', 'firstName', 'lastName', 'username' (email)
        for attr in kwargs.keys():
            setattr(self, attr, kwargs[attr])

        if 'groups' in kwargs:
            groups = []
            for groupData in kwargs['groups']:
                groups.append(GroupObj(**groupData))
            self.groups = groups

        self.__props = kwargs.keys()

    def isAdmin(self):
        if hasattr(self, 'role'):
            return self.role == self.ROLE_ADMIN
        return False

    def refresh(self, wa):
        # This method requires some sleeping usually.
        newU = wa.users.loadUser(self).toDict()
        for prop in newU:
            setattr(self, prop, newU[prop])

    def toDict(self):
        data = {}
        for prop in self.__props:
            data[prop] = getattr(self, prop)
        return data

    def orgPerms(self):
        for orgPer in self.organismPermissions:
            if len(orgPer['permissions']) > 2:
                orgPer['permissions'] = json.loads(orgPer['permissions'])
                yield orgPer

    def __str__(self):
        return '<User %s: %s %s <%s>>' % (self.userId, self.firstName,
                                          self.lastName, self.username)


class Client(object):

    def __init__(self, webapolloinstance, **requestArgs):
        self._wa = webapolloinstance

        self.__verify = requestArgs.get('verify', True)
        self._requestArgs = requestArgs

        if 'verify' in self._requestArgs:
            del self._requestArgs['verify']

    def request(self, clientMethod, data, post_params={}, isJson=True):
        url = self._wa.apollo_url + self.CLIENT_BASE + clientMethod

        headers = {
            'Content-Type': 'application/json'
        }

        data.update({
            'username': self._wa.username,
            'password': self._wa.password,
        })

        r = requests.post(url, data=json.dumps(data), headers=headers,
                          verify=self.__verify, params=post_params, allow_redirects=False, **self._requestArgs)

        if r.status_code == 200 or r.status_code == 302:
            if isJson:
                d = r.json()
                if 'username' in d:
                    del d['username']
                if 'password' in d:
                    del d['password']
                return d
            else:
                return r.text

        # @see self.body for HTTP response body
        raise Exception("Unexpected response from apollo %s: %s" %
                        (r.status_code, r.text))

    def get(self, clientMethod, get_params):
        url = self._wa.apollo_url + self.CLIENT_BASE + clientMethod
        headers = {}

        r = requests.get(url, headers=headers, verify=self.__verify,
                         params=get_params, **self._requestArgs)
        if r.status_code == 200:
            d = r.json()
            if 'username' in d:
                del d['username']
            if 'password' in d:
                del d['password']
            return d
        # @see self.body for HTTP response body
        raise Exception("Unexpected response from apollo %s: %s" %
                        (r.status_code, r.text))


class MetricsClient(Client):
    CLIENT_BASE = '/metrics/'

    def getServerMetrics(self):
        return self.get('metrics', {})


class AnnotationsClient(Client):
    CLIENT_BASE = '/annotationEditor/'

    def _update_data(self, data):
        if not hasattr(self, '_extra_data'):
            raise Exception("Please call setSequence first")

        data.update(self._extra_data)
        return data

    def setSequence(self, sequence, organism):
        self._extra_data = {
            'sequence': sequence,
            'organism': organism,
        }

    def setDescription(self, featureDescriptions):
        data = {
            'features': featureDescriptions,
        }
        data = self._update_data(data)
        return self.request('setDescription', data)

    def setName(self, uniquename, name):
        # TODO
        data = {
            'features': [
                {
                    'uniquename': uniquename,
                    'name': name,
                }
            ],
        }
        data = self._update_data(data)
        return self.request('setName', data)

    def setNames(self, features):
        # TODO
        data = {
            'features': features,
        }
        data = self._update_data(data)
        return self.request('setName', data)

    def setStatus(self, statuses):
        # TODO
        data = {
            'features': statuses,
        }
        data = self._update_data(data)
        return self.request('setStatus', data)

    def setSymbol(self, symbols):
        data = {
            'features': symbols,
        }
        data.update(self._extra_data)
        return self.request('setSymbol', data)

    def getComments(self, feature_id):
        data = {
            'features': [{'uniquename': feature_id}],
        }
        data = self._update_data(data)
        return self.request('getComments', data)

    def addComments(self, feature_id, comments):
        # TODO: This is probably not great and will delete comments, if I had to guess...
        data = {
            'features': [
                {
                    'uniquename': feature_id,
                    'comments': comments
                }
            ],
        }
        data = self._update_data(data)
        return self.request('addComments', data)

    def addAttributes(self, feature_id, attributes):
        nrps = []
        for (key, values) in attributes.items():
            for value in values:
                nrps.append({
                    'tag': key,
                    'value': value
                })

        data = {
            'features': [
                {
                    'uniquename': feature_id,
                    'non_reserved_properties': nrps
                }
            ]
        }
        data = self._update_data(data)
        return self.request('addAttribute', data)

    def deleteAttribute(self, feature_id, key, value):
        data = {
            'features': [
                {
                    'uniquename': feature_id,
                    'non_reserved_properties': [
                        {'tag': key, 'value': value}
                    ]
                }
            ]
        }
        data = self._update_data(data)
        return self.request('addAttribute', data)

    def getFeatures(self):
        data = self._update_data({})
        return self.request('getFeatures', data)

    def getSequence(self, uniquename):
        data = {
            'features': [
                {'uniquename': uniquename}
            ]
        }
        data = self._update_data(data)
        return self.request('getSequence', data)

    def addFeature(self, feature, trustme=False):
        if not trustme:
            raise NotImplementedError("Waiting on better docs from project. If you know what you are doing, pass trustme=True to this function.")

        data = {
            'features': feature,
        }
        data = self._update_data(data)
        return self.request('addFeature', data)

    def addTranscript(self, transcript, trustme=False):
        if not trustme:
            raise NotImplementedError("Waiting on better docs from project. If you know what you are doing, pass trustme=True to this function.")

        data = {}
        data.update(transcript)
        data = self._update_data(data)
        return self.request('addTranscript', data)

    # addExon, add/delete/updateComments, addTranscript skipped due to docs

    def duplicateTranscript(self, transcriptId):
        data = {
            'features': [{'uniquename': transcriptId}]
        }

        data = self._update_data(data)
        return self.request('duplicateTranscript', data)

    def setTranslationStart(self, uniquename, start):
        data = {
            'features': [{
                'uniquename': uniquename,
                'location': {
                    'fmin': start
                }
            }]
        }
        data = self._update_data(data)
        return self.request('setTranslationStart', data)

    def setTranslationEnd(self, uniquename, end):
        data = {
            'features': [{
                'uniquename': uniquename,
                'location': {
                    'fmax': end
                }
            }]
        }
        data = self._update_data(data)
        return self.request('setTranslationEnd', data)

    def setLongestOrf(self, uniquename):
        data = {
            'features': [{
                'uniquename': uniquename,
            }]
        }
        data = self._update_data(data)
        return self.request('setLongestOrf', data)

    def setBoundaries(self, uniquename, start, end):
        data = {
            'features': [{
                'uniquename': uniquename,
                'location': {
                    'fmin': start,
                    'fmax': end,
                }
            }]
        }
        data = self._update_data(data)
        return self.request('setBoundaries', data)

    def getSequenceAlterations(self):
        data = {
        }
        data = self._update_data(data)
        return self.request('getSequenceAlterations', data)

    def setReadthroughStopCodon(self, uniquename):
        data = {
            'features': [{
                'uniquename': uniquename,
            }]
        }
        data = self._update_data(data)
        return self.request('setReadthroughStopCodon', data)

    def deleteSequenceAlteration(self, uniquename):
        data = {
            'features': [{
                'uniquename': uniquename,
            }]
        }
        data = self._update_data(data)
        return self.request('deleteSequenceAlteration', data)

    def flipStrand(self, uniquenames):
        data = {
            'features': [
                {'uniquename': x} for x in uniquenames
            ]
        }
        data = self._update_data(data)
        return self.request('flipStrand', data)

    def mergeExons(self, exonA, exonB):
        data = {
            'features': [
                {'uniquename': exonA},
                {'uniquename': exonB},
            ]
        }
        data = self._update_data(data)
        return self.request('mergeExons', data)

    # def splitExon(): pass

    def deleteFeatures(self, uniquenames):
        assert isinstance(uniquenames, collections.Iterable)
        data = {
            'features': [
                {'uniquename': x} for x in uniquenames
            ]
        }
        data = self._update_data(data)
        return self.request('deleteFeature', data)

    # def deleteExon(): pass

    # def makeIntron(self, uniquename, ): pass

    def getSequenceSearchTools(self):
        return self.get('getSequenceSearchTools', {})

    def getCannedComments(self):
        return self.get('getCannedComments', {})

    def searchSequence(self, searchTool, sequence, database):
        data = {
            'key': searchTool,
            'residues': sequence,
            'database_id': database,
        }
        return self.request('searchSequences', data)

    def getGff3(self, uniquenames):
        assert isinstance(uniquenames, collections.Iterable)
        data = {
            'features': [
                {'uniquename': x} for x in uniquenames
            ]
        }
        data = self._update_data(data)
        return self.request('getGff3', data, isJson=False)


class GroupsClient(Client):
    CLIENT_BASE = '/group/'

    def createGroup(self, name):
        data = {'name': name}
        return self.request('createGroup', data)

    def getOrganismPermissionsForGroup(self, group):
        data = {
            'id': group.groupId,
            'name': group.name,
        }
        return self.request('getOrganismPermissionsForGroup', data)

    def loadGroup(self, group):
        return self.loadGroupById(group.groupId)

    def loadGroupById(self, groupId):
        res = self.request('loadGroups', {'groupId': groupId})
        if isinstance(res, list):
            # We can only match one, right?
            return GroupObj(**res[0])
        else:
            return res

    def loadGroupByName(self, name):
        res = self.request('loadGroups', {'name': name})
        if isinstance(res, list):
            # We can only match one, right?
            return GroupObj(**res[0])
        else:
            return res

    def loadGroups(self, group=None):
        res = self.request('loadGroups', {})
        data = [GroupObj(**x) for x in res]
        if group is not None:
            data = [x for x in data if x.name == group]

        return data

    def deleteGroup(self, group):
        data = {
            'id': group.groupId,
            'name': group.name,
        }
        return self.request('deleteGroup', data)

    def updateGroup(self, group, newName):
        # TODO: Sure would be nice if modifying ``group.name`` would invoke
        # this?
        data = {
            'id': group.groupId,
            'name': newName,
        }
        return self.request('updateGroup', data)

    def updateOrganismPermission(self, group, organismName,
                                 administrate=False, write=False, read=False,
                                 export=False):
        data = {
            'groupId': group.groupId,
            'organism': organismName,
            'ADMINISTRATE': administrate,
            'WRITE': write,
            'EXPORT': export,
            'READ': read,
        }
        return self.request('updateOrganismPermission', data)

    def updateMembership(self, group, users):
        data = {
            'groupId': group.groupId,
            'user': [user.email for user in users]
        }
        return self.request('updateMembership', data)


class IOClient(Client):
    CLIENT_BASE = '/IOService/'

    def write(self, exportType='FASTA', seqType='peptide',
              exportFormat='text', sequences=None, organism=None,
              output='text', exportAllSequences=False,
              exportGff3Fasta=False):
        if exportType not in ('FASTA', 'GFF3'):
            raise Exception("exportType must be one of FASTA, GFF3")

        if seqType not in ('peptide', 'cds', 'cdna', 'genomic'):
            raise Exception("seqType must be one of peptide, cds, dna, genomic")

        if exportFormat not in ('gzip', 'text'):
            raise Exception("exportFormat must be one of gzip, text")

        if output not in ('file', 'text'):
            raise Exception("output must be one of file, text")

        data = {
            'type': exportType,
            'seqType': seqType,
            'format': exportFormat,
            'sequences': sequences,
            'organism': organism,
            'output': output,
            'exportAllSequences': exportAllSequences,
            'exportGff3Fasta': exportGff3Fasta,
        }

        return self.request('write', data, isJson=output == 'file')

    def download(self, uuid, outputFormat='gzip'):

        if outputFormat.lower() not in ('gzip', 'text'):
            raise Exception("outputFormat must be one of file, text")

        data = {
            'format': outputFormat,
            'uuid': uuid,
        }
        return self.request('write', data)


class StatusClient(Client):
    CLIENT_BASE = '/availableStatus/'

    def addStatus(self, value):
        data = {
            'value': value
        }

        return self.request('createStatus', data)

    def findAllStatuses(self):
        return self.request('showStatus', {})

    def findStatusByValue(self, value):
        statuses = self.findAllStatuses()
        statuses = [x for x in statuses if x['value'] == value]
        if len(statuses) == 0:
            raise Exception("Unknown status value")
        else:
            return statuses[0]

    def findStatusById(self, id_number):
        statuses = self.findAllStatuses()
        statuses = [x for x in statuses if str(x['id']) == str(id_number)]
        if len(statuses) == 0:
            raise Exception("Unknown ID")
        else:
            return statuses[0]

    def updateStatus(self, id_number, new_value):
        data = {
            'id': id_number,
            'new_value': new_value
        }

        return self.request('updateStatus', data)

    def deleteStatus(self, id_number):
        data = {
            'id': id_number
        }

        return self.request('deleteStatus', data)


class CannedCommentsClient(Client):
    CLIENT_BASE = '/cannedComment/'

    def addComment(self, comment, metadata=""):
        data = {
            'comment': comment,
            'metadata': metadata
        }

        return self.request('createComment', data)

    def findAllComments(self):
        return self.request('showComment', {})

    def findCommentByValue(self, value):
        comments = self.findAllComments()
        comments = [x for x in comments if x['comment'] == value]
        if len(comments) == 0:
            raise Exception("Unknown comment")
        else:
            return comments[0]

    def findCommentById(self, id_number):
        comments = self.findAllComments()
        comments = [x for x in comments if str(x['id']) == str(id_number)]
        if len(comments) == 0:
            raise Exception("Unknown ID")
        else:
            return comments[0]

    def updateComment(self, id_number, new_value, metadata=None):
        data = {
            'id': id_number,
            'new_comment': new_value
        }

        if metadata is not None:
            data['metadata'] = metadata

        return self.request('updateComment', data)

    def deleteComment(self, id_number):
        data = {
            'id': id_number
        }

        return self.request('deleteComment', data)


class CannedKeysClient(Client):
    CLIENT_BASE = '/cannedKey/'

    def addKey(self, key, metadata=""):
        data = {
            'key': key,
            'metadata': metadata
        }

        return self.request('createKey', data)

    def findAllKeys(self):
        return self.request('showKey', {})

    def findKeyByValue(self, value):
        keys = self.findAllKeys()
        keys = [x for x in keys if x['label'] == value]
        if len(keys) == 0:
            raise Exception("Unknown key")
        else:
            return keys[0]

    def findKeyById(self, id_number):
        keys = self.findAllKeys()
        keys = [x for x in keys if str(x['id']) == str(id_number)]
        if len(keys) == 0:
            raise Exception("Unknown ID")
        else:
            return keys[0]

    def updateKey(self, id_number, new_key, metadata=None):
        data = {
            'id': id_number,
            'new_key': new_key
        }

        if metadata is not None:
            data['metadata'] = metadata

        return self.request('updateKey', data)

    def deleteKey(self, id_number):
        data = {
            'id': id_number
        }

        return self.request('deleteKey', data)


class CannedValuesClient(Client):
    CLIENT_BASE = '/cannedValue/'

    def addValue(self, value, metadata=""):
        data = {
            'value': value,
            'metadata': metadata
        }

        return self.request('createValue', data)

    def findAllValues(self):
        return self.request('showValue', {})

    def findValueByValue(self, value):
        values = self.findAllValues()
        values = [x for x in values if x['label'] == value]
        if len(values) == 0:
            raise Exception("Unknown value")
        else:
            return values[0]

    def findValueById(self, id_number):
        values = self.findAllValues()
        values = [x for x in values if str(x['id']) == str(id_number)]
        if len(values) == 0:
            raise Exception("Unknown ID")
        else:
            return values[0]

    def updateValue(self, id_number, new_value, metadata=None):
        data = {
            'id': id_number,
            'new_value': new_value
        }

        if metadata is not None:
            data['metadata'] = metadata

        return self.request('updateValue', data)

    def deleteValue(self, id_number):
        data = {
            'id': id_number
        }

        return self.request('deleteValue', data)


class OrganismsClient(Client):
    CLIENT_BASE = '/organism/'

    def addOrganism(self, commonName, directory, blatdb=None, species=None,
                    genus=None, public=False):
        data = {
            'commonName': commonName,
            'directory': directory,
            'publicMode': public,
        }

        if blatdb is not None:
            data['blatdb'] = blatdb
        if genus is not None:
            data['genus'] = genus
        if species is not None:
            data['species'] = species

        return self.request('addOrganism', data)

    def findAllOrganisms(self):
        orgs = self.request('findAllOrganisms', {})
        if not isinstance(orgs, (list,)):
            orgs = []
        return orgs

    def findOrganismByCn(self, cn):
        orgs = self.findAllOrganisms()
        orgs = [x for x in orgs if x['commonName'] == cn]
        if len(orgs) == 0:
            raise Exception("Unknown common name")
        else:
            return orgs[0]

    def findOrganismById(self, id_number):
        orgs = self.findAllOrganisms()
        orgs = [x for x in orgs if str(x['id']) == str(id_number)]
        if len(orgs) == 0:
            raise Exception("Unknown ID")
        else:
            return orgs[0]

    def deleteOrganism(self, organismId):
        return self.request('deleteOrganism', {'id': organismId})

    def deleteOrganismFeatures(self, organismId):
        return self.request('deleteOrganismFeatures', {'id': organismId})

    def getSequencesForOrganism(self, commonName):
        return self.request('getSequencesForOrganism', {'organism': commonName})

    def updateOrganismInfo(self, organismId, commonName, directory, blatdb=None, species=None, genus=None, public=False):
        data = {
            'id': organismId,
            'name': commonName,
            'directory': directory,
            'publicMode': public,
        }

        if blatdb is not None:
            data['blatdb'] = blatdb
        if genus is not None:
            data['genus'] = genus
        if species is not None:
            data['species'] = species

        return self.request('updateOrganismInfo', data)


class UsersClient(Client):
    CLIENT_BASE = '/user/'

    # Real one
    # def getOrganismPermissionsForUser(self, user):
    # data = {
    # 'userId': user.userId,
    # }
    # return self.request('getOrganismPermissionsForUser', data)

    # Utter frigging hack
    def getOrganismPermissionsForUser(self, user):
        return self.loadUser(user).organismPermissions

    def updateOrganismPermission(self, user, organism, administrate=False,
                                 write=False, export=False, read=False):
        data = {
            'userId': user.userId,
            'organism': organism,
            'ADMINISTRATE': administrate,
            'WRITE': write,
            'EXPORT': export,
            'READ': read,
        }
        return self.request('updateOrganismPermission', data)

    def loadUser(self, user):
        return self.loadUserById(user.userId)

    def loadUserById(self, userId):
        res = self.request('loadUsers', {'userId': userId})
        if isinstance(res, list):
            # We can only match one, right?
            return UserObj(**res[0])
        else:
            return res

    def loadUsers(self, email=None):
        res = self.request('loadUsers', {})
        data = [UserObj(**x) for x in res]
        if email is not None:
            data = [x for x in data if x.username == email]

        return data

    def addUserToGroup(self, group, user):
        data = {'group': group.name, 'userId': user.userId}
        return self.request('addUserToGroup', data)

    def removeUserFromGroup(self, group, user):
        data = {'group': group.name, 'userId': user.userId}
        return self.request('removeUserFromGroup', data)

    def createUser(self, email, firstName, lastName, newPassword, role="user", groups=None, addToHistory=False):
        data = {
            'firstName': firstName,
            'lastName': lastName,
            'email': email,
            'role': role,
            'groups': [] if groups is None else groups,
            # 'availableGroups': [],
            'newPassword': newPassword,
            # 'organismPermissions': [],
        }
        returnData = self.request('createUser', data)
        if addToHistory and not IsRemoteUser():
            f = open("Apollo_credentials.txt", "w")
            f.write('Username: %s\tPassword: %s' % (email, newPassword))
        return returnData

    def assertOrCreateUser(self, email):
        try:
            gx_user = AssertUser(self.loadUsers(email))
        except Exception:
            self.createUser(email, email, email, PasswordGenerator(12), role='user', addToHistory=True)
            gx_user = AssertUser(self.loadUsers(email))
        return gx_user

    def deleteUser(self, user):
        return self.request('deleteUser', {'userId': user.userId})

    def updateUser(self, user, email, firstName, lastName, newPassword):
        data = {
            'userId': user.userId,
            'email': email,
            'firstName': firstName,
            'lastName': lastName,
            'newPassword': newPassword,
        }
        return self.request('updateUser', data)


class RemoteRecord(Client):
    CLIENT_BASE = None

    def ParseRecord(self, cn):
        org = self._wa.organisms.findOrganismByCn(cn)
        self._wa.annotations.setSequence(org['commonName'], org['id'])

        data = io.StringIO(self._wa.io.write(
            exportType='GFF3',
            seqType='genomic',
            exportAllSequences=False,
            exportGff3Fasta=True,
            output="text",
            exportFormat="text",
            sequences=cn,
        ))
        data.seek(0)

        for record in GFF.parse(data):
            yield WebApolloSeqRecord(record, self._wa)


class WebApolloSeqRecord(object):
    def __init__(self, sr, wa):
        self._sr = sr
        self._wa = wa

    def __dir__(self):
        return dir(self._sr)

    def __getattr__(self, key):
        if key in ('_sr', '_wa'):
            return self.__dict__[key]
        else:
            if key == 'features':
                return (WebApolloSeqFeature(x, self._wa)
                        for x in self._sr.__dict__[key])
            else:
                return self._sr.__dict__[key]

    def __setattr__(self, key, value):
        if key in ('_sd', '_wa'):
            self.__dict__[key] = value
        else:
            self._sr.__dict__[key] = value
            # Methods acting on the SeqRecord object


class WebApolloSeqFeature(object):
    def __init__(self, sf, wa):
        self._sf = sf
        self._wa = wa

    def __dir__(self):
        return dir(self._sf)

    def __getattr__(self, key):
        if key in ('_sf', '_wa'):
            return self.__dict__[key]
        else:
            return self._sf.__dict__[key]

    def __setattr__(self, key, value):
        if key in ('_sf', '_wa'):
            self.__dict__[key] = value
        else:
            # Methods acting on the SeqFeature object
            if key == 'location':
                if value.strand != self._sf.location.strand:
                    self.wa.annotations.flipStrand(
                        self._sf.qualifiers['ID'][0]
                    )

                self.wa.annotations.setBoundaries(
                    self._sf.qualifiers['ID'][0],
                    value.start,
                    value.end,
                )

                self._sf.__dict__[key] = value
            else:
                self._sf.__dict__[key] = value


def _tnType(feature):
    if feature.type in ('gene', 'mRNA', 'exon', 'CDS', 'terminator', 'tRNA'):
        return feature.type
    else:
        return 'exon'


def _yieldFeatData(features):
    for f in features:
        current = {
            'location': {
                'strand': f.strand,
                'fmin': int(f.location.start),
                'fmax': int(f.location.end),
            },
            'type': {
                'name': _tnType(f),
                'cv': {
                    'name': 'sequence',
                }
            },
        }
        if f.type in ('gene', 'mRNA'):
            current['name'] = f.qualifiers.get('Name', [f.id])[0]
        if hasattr(f, 'sub_features') and len(f.sub_features) > 0:
            current['children'] = [x for x in _yieldFeatData(f.sub_features)]

        yield current


def featuresToFeatureSchema(features):
    compiled = []
    for feature in features:
        # if feature.type != 'gene':
            # log.warn("Not able to handle %s features just yet...", feature.type)
            # continue

        for x in _yieldFeatData([feature]):
            compiled.append(x)
    return compiled


def accessible_organisms(user, orgs):
    permissionMap = {
        x['organism']: x['permissions']
        for x in user.organismPermissions
        if 'WRITE' in x['permissions'] or
        'READ' in x['permissions'] or
        'ADMINISTRATE' in x['permissions'] or
        user.role == 'ADMIN'
    }

    if 'error' in orgs:
        raise Exception("Error received from Apollo server: \"%s\"" % orgs['error'])

    return [
        (org['commonName'], org['id'], False)
        for org in sorted(orgs, key=lambda x: x['commonName'])
        if org['commonName'] in permissionMap
    ]


def galaxy_list_groups(trans, *args, **kwargs):
    email = trans.get_user().email
    wa = WebApolloInstance(
        os.environ['GALAXY_WEBAPOLLO_URL'],
        os.environ['GALAXY_WEBAPOLLO_USER'],
        os.environ['GALAXY_WEBAPOLLO_PASSWORD']
    )

    # Key for cached data
    cacheKey = 'groups-' + email
    # We don't want to trust "if key in cache" because between asking and fetch
    # it might through key error.
    if cacheKey not in cache:
        # However if it ISN'T there, we know we're safe to fetch + put in
        # there.
        data = _galaxy_list_groups(wa, *args, **kwargs)
        cache[cacheKey] = data
        return data
    try:
        # The cache key may or may not be in the cache at this point, it
        # /likely/ is. However we take no chances that it wasn't evicted between
        # when we checked above and now, so we reference the object from the
        # cache in preparation to return.
        data = cache[cacheKey]
        return data
    except KeyError:
        # If access fails due to eviction, we will fail over and can ensure that
        # data is inserted.
        data = _galaxy_list_groups(wa, *args, **kwargs)
        cache[cacheKey] = data
        return data


def _galaxy_list_groups(wa, *args, **kwargs):
    # Fetch the groups.
    group_data = []
    for group in wa.groups.loadGroups():
        # Reformat
        group_data.append((group.name, group.name, False))
    return group_data


def galaxy_list_orgs(trans, *args, **kwargs):
    email = trans.get_user().email
    wa = WebApolloInstance(
        os.environ['GALAXY_WEBAPOLLO_URL'],
        os.environ['GALAXY_WEBAPOLLO_USER'],
        os.environ['GALAXY_WEBAPOLLO_PASSWORD']
    )
    try:
        gx_user = wa.requireUser(email)
    except UnknownUserException:
        return []

    # Key for cached data
    cacheKey = 'orgs-' + email
    if cacheKey not in cache:
        data = _galaxy_list_orgs(wa, gx_user, *args, **kwargs)
        cache[cacheKey] = data
        return data
    try:
        data = cache[cacheKey]
        return data
    except KeyError:
        data = _galaxy_list_orgs(wa, gx_user, *args, **kwargs)
        cache[cacheKey] = data
        return data


def _galaxy_list_orgs(wa, gx_user, *args, **kwargs):
    # Fetch all organisms
    all_orgs = wa.organisms.findAllOrganisms()
    # Figure out which are accessible to the user
    orgs = accessible_organisms(gx_user, all_orgs)
    # Return org list
    return orgs


def galaxy_list_users(trans, *args, **kwargs):
    email = trans.get_user().email
    wa = WebApolloInstance(
        os.environ['GALAXY_WEBAPOLLO_URL'],
        os.environ['GALAXY_WEBAPOLLO_USER'],
        os.environ['GALAXY_WEBAPOLLO_PASSWORD']
    )
    # Assert that the email exists in apollo
    try:
        gx_user = wa.requireUser(email)
    except UnknownUserException:
        return []

    # Key for cached data
    cacheKey = 'users-' + email
    # We don't want to trust "if key in cache" because between asking and fetch
    # it might through key error.
    if cacheKey not in cache:
        # However if it ISN'T there, we know we're safe to fetch + put in
        # there.
        data = _galaxy_list_users(wa, gx_user, *args, **kwargs)
        cache[cacheKey] = data
        return data
    try:
        # The cache key may or may not be in the cache at this point, it
        # /likely/ is. However we take no chances that it wasn't evicted between
        # when we checked above and now, so we reference the object from the
        # cache in preparation to return.
        data = cache[cacheKey]
        return data
    except KeyError:
        # If access fails due to eviction, we will fail over and can ensure that
        # data is inserted.
        data = _galaxy_list_users(wa, gx_user, *args, **kwargs)
        cache[cacheKey] = data
        return data


def _galaxy_list_users(wa, gx_user, *args, **kwargs):
    # Fetch the users.
    user_data = []
    for user in wa.users.loadUsers():
        # Reformat
        user_data.append((user.username, user.username, False))
    return user_data


# This is all for implementing the command line interface for testing.
class obj(object):
    pass


class fakeTrans(object):

    def __init__(self, username):
        self.un = username

    def get_user(self):
        o = obj()
        o.email = self.un
        return o


def retry(closure, sleep=1, limit=5):
    """
    Apollo has the bad habit of returning 500 errors if you call APIs
    too quickly, largely because of the unholy things that happen in
    grails.

    To deal with the fact that we cannot send an addComments call too
    quickly after a createFeature call, we have this function that will
    keep calling a closure until it works.
    """
    count = 0
    while True:
        count += 1

        if count >= limit:
            return False
        try:
            # Try calling it
            closure()
            # If successful, exit
            return True
        except Exception as e:
            log.info(str(e)[0:100])
            time.sleep(sleep)


if __name__ == '__main__':
    parser = argparse.ArgumentParser(description='Test access to apollo server')
    parser.add_argument('email', help='Email of user to test')
    parser.add_argument('--action', choices=['org', 'group', 'users'], default='org', help='Data set to test, fetch a list of groups or users known to the requesting user.')
    args = parser.parse_args()

    trans = fakeTrans(args.email)
    if args.action == 'org':
        for f in galaxy_list_orgs(trans):
            print(f)
    elif args.action == 'group':
        for f in galaxy_list_groups(trans):
            print(f)
    else:
        for f in galaxy_list_users(trans):
            print(f)