comparison webapollo.py @ 7:f9a6e151b3b4 draft

planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174

6:8f76685cdfc8

import requests
import json
import os
import collections
try:
    import StringIO as io
except:
    import io
import logging
import time
import argparse
from abc import abstractmethod
from BCBio import GFF
from Bio import SeqIO
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

        if key in self:
            value = self[key]
        else:
            self[key] = value = default
        return value

DefaultMapping.register(dict)


class _DefaultSize(object):

            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 __init__(self, url, username, password):
        self.apollo_url = url
        self.username = username
        self.password = password
        # TODO: Remove after apollo 2.0.6.
        self.clientToken = time.time()

        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)

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

    def requireUser(self, email):

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

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

        }

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

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

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

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

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

    def getFeatures(self):

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


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

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


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

    # Figure out which are accessible to the user
    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


class fakeTrans(object):

    def get_user(self):
        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 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)
    else:
        for f in galaxy_list_groups(trans):
            print(f)

7:f9a6e151b3b4

from __future__ import print_function
import argparse
import collections
import json
import logging
import os
import requests
import time
from future import standard_library
from builtins import next
from builtins import str
from builtins import object
from abc import abstractmethod
from BCBio import GFF
from Bio import SeqIO
standard_library.install_aliases()
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

        if key in self:
            value = self[key]
        else:
            self[key] = value = default
        return value


DefaultMapping.register(dict)


class _DefaultSize(object):

            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 __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):

        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)

        }

        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)

            '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 = {
            '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/'

            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'

    # 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 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)