comparison webapollo.py @ 5:1a2976c6b161 draft

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

4:9968eec7430e

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

from BCBio import GFF

        return True
    else:
        raise Exception("User is not an administrator. Permission denied")


class WebApolloInstance(object):

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

            data['species'] = species

        return self.request('addOrganism', data)

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

    def findOrganismByCn(self, cn):
        orgs = self.findAllOrganisms()
        orgs = [x for x in orgs if x['commonName'] == cn]
        if len(orgs) == 0:

    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):
        data = {
            'firstName': firstName,
            'lastName': lastName,
            'email': email,
            'role': role,
            'groups': [] if groups is None else groups,
            # 'availableGroups': [],
            'newPassword': newPassword,
            # 'organismPermissions': [],
        }
        return self.request('createUser', data)

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

    def updateUser(self, user, email, firstName, lastName, newPassword):

    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 = '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, 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

        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, gx_user, *args, **kwargs)
        cache[cacheKey] = data
        return data


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

5:1a2976c6b161

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

from BCBio import GFF

        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

            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:

    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):

    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

        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))