comparison webapollo.py @ 10:dca2fb399ee6 draft

"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"

9:d8bb1f9b85b2

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()


#############################################

    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):

            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)

        # @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']

    ]


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.

    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 []

    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

        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)

10:dca2fb399ee6

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

import requests

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

import yaml

logging.getLogger("requests").setLevel(logging.CRITICAL)
log = logging.getLogger()


#############################################

    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 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!")


class WebApolloInstance(object):

    def __init__(self):

        if 'ARROW_GLOBAL_CONFIG_PATH' in os.environ:

            with open(os.environ['ARROW_GLOBAL_CONFIG_PATH'], 'r') as config:
                conf = yaml.safe_load(config)
                try:
                    instance_name = conf['__default']
                except KeyError:
                    raise Exception("Unknown Apollo instance and no __default provided")
                self.apollo_url = conf[instance_name]['url']
                self.username = conf[instance_name]['username']
                self.password = conf[instance_name]['password']
        else:
            self.apollo_url = os.environ['GALAXY_WEBAPOLLO_URL']
            self.username = os.environ['GALAXY_WEBAPOLLO_USER']
            self.password = os.environ['GALAXY_WEBAPOLLO_PASSWORD']

        self.groups = GroupsClient(self)
        self.organisms = OrganismsClient(self)
        self.users = UsersClient(self)

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

    def requireUser(self, email):

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

        self.__props = kwargs.keys()

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

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


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

    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


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

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


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

    def loadUsers(self):
        res = self.request('loadUsers', {})

        data = [UserObj(**x) for x in res]

        return data


def handle_credentials(user):
    if hasattr(user, 'new_password'):
        f = open("Apollo_credentials.txt", "w")
        f.write('Username:\t%s\nPassword:\t%s' % (user.username, user.new_password))


def accessible_organisms(user, orgs):
    permissionMap = {
        x['organism']: x['permissions']

    ]


def galaxy_list_groups(trans, *args, **kwargs):
    email = trans.get_user().email
    wa = WebApolloInstance()

    # 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.

    return group_data


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

    orgs = accessible_organisms(gx_user, all_orgs)
    # Return org list
    return orgs


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

        o = obj()
        o.email = self.un
        return o


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'], default='org', help='Data set to test, fetch a list of groups or orgs known to the requesting user.')
    args = parser.parse_args()

    trans = fakeTrans(args.email)
    if args.action == 'org':
        print(galaxy_list_orgs(trans))
    elif args.action == 'group':
        print(galaxy_list_groups(trans))