24903485277

Committed 24 Apr 2026 05:42PM UTC coverage: 75.08%. Remained the same

Build # 24903485277

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push

github

Committed by

web-flow

Commit Message

Add public key authentication for dbgap sftp sync (#1334)

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fence/sync/sync_users.py

import paramiko.ssh_exception
import backoff
import glob

import httpx
import jwt
import os
import re
import subprocess as sp
import yaml
import copy
import datetime
import uuid
import collections
import hashlib

from contextlib import contextmanager
from collections import defaultdict
from csv import DictReader
from io import StringIO
from stat import S_ISDIR

import paramiko
from cdislogging import get_logger
from email_validator import validate_email, EmailNotValidError
from gen3authz.client.arborist.errors import ArboristError, ArboristTimeoutError
from gen3users.validation import validate_user_yaml
from paramiko.proxy import ProxyCommand
from sqlalchemy.exc import IntegrityError
from sqlalchemy import func

from fence.config import config
from fence.models import (
    AccessPrivilege,
    AuthorizationProvider,
    Project,
    Tag,
    User,
    query_for_user,
    Client,
    IdentityProvider,
    get_project_to_authz_mapping,
)
from fence.resources.google.utils import get_or_create_proxy_group_id
from fence.resources.storage import StorageManager
from fence.resources.google.access_utils import update_google_groups_for_users
from fence.resources.google.access_utils import GoogleUpdateException
from fence.sync import utils
from fence.sync.passport_sync.ras_sync import RASVisa
from fence.utils import get_SQLAlchemyDriver, DEFAULT_BACKOFF_SETTINGS


def _format_policy_id(path, privilege):
    resource = ".".join(name for name in path.split("/") if name)
    return "{}-{}".format(resource, privilege)


def download_dir(sftp, remote_dir, local_dir):
    """
    Recursively download file from remote_dir to local_dir
    Args:
        remote_dir(str)
        local_dir(str)
    Returns: None
    """
    dir_items = sftp.listdir_attr(remote_dir)

    for item in dir_items:
        remote_path = remote_dir + "/" + item.filename
        local_path = os.path.join(local_dir, item.filename)
        if S_ISDIR(item.st_mode):
            download_dir(sftp, remote_path, local_path)
        else:
            sftp.get(remote_path, local_path)


def arborist_role_for_permission(permission):
    """
    For the programs/projects in the existing fence access control model, in order to
    use arborist for checking permissions we generate a policy for each combination of
    program/project and privilege. The roles involved all contain only one permission,
    for one privilege from the project access model.
    """
    return {
        "id": permission,
        "permissions": [
            {"id": permission, "action": {"service": "*", "method": permission}}
        ],
    }


@contextmanager
def _read_file(filepath, encrypted=True, key=None, logger=None):
    """
    Context manager for reading and optionally decrypting file it only
    decrypts files encrypted by unix 'crypt' tool which is used by dbGaP.

    Args:
        filepath (str): path to the file
        encrypted (bool): whether the file is encrypted

    Returns:
        Generator[file-like class]: file like object for the file
    """
    if encrypted:
        p = sp.Popen(
            [
                "ccdecrypt",
                "-u",
                "-K",
                key,
                filepath,
            ],
            stdout=sp.PIPE,
            stderr=open(os.devnull, "w"),
            universal_newlines=True,
        )
        try:
            yield StringIO(p.communicate()[0])
        except UnicodeDecodeError:
            logger.error("Could not decode file. Check the decryption key.")
    else:
        f = open(filepath, "r")
        yield f
        f.close()


class UserYAML(object):
    """
    Representation of the information in a YAML file describing user, project, and ABAC
    information for access control.
    """

    def __init__(
        self,
        projects=None,
        user_info=None,
        policies=None,
        clients=None,
        authz=None,
        project_to_resource=None,
        logger=None,
        user_abac=None,
    ):
        self.projects = projects or {}
        self.user_info = user_info or {}
        self.user_abac = user_abac or {}
        self.policies = policies or {}
        self.clients = clients or {}
        self.authz = authz or {}
        self.project_to_resource = project_to_resource or {}
        self.logger = logger

    @classmethod
    def from_file(cls, filepath, encrypted=True, key=None, logger=None):
        """
        Add access by "auth_id" to "self.projects" to update the Fence DB.
        Add access by "resource" to "self.user_abac" to update Arborist.
        """
        data = {}
        if filepath:
            with _read_file(filepath, encrypted=encrypted, key=key, logger=logger) as f:
                file_contents = f.read()
                validate_user_yaml(file_contents)  # run user.yaml validation tests
                data = yaml.safe_load(file_contents)
        else:
            if logger:
                logger.info("Did not sync a user.yaml, no file path provided.")

        projects = dict()
        user_info = dict()
        policies = dict()

        # resources should be the resource tree to construct in arborist
        user_abac = dict()

        # Fall back on rbac block if no authz. Remove when rbac in useryaml fully deprecated.
        if not data.get("authz") and data.get("rbac"):
            if logger:
                logger.info(
                    "No authz block found but rbac block present. Using rbac block"
                )
            data["authz"] = data["rbac"]

        # get user project mapping to arborist resources if it exists
        project_to_resource = data.get("authz", dict()).get(
            "user_project_to_resource", dict()
        )

        # read projects and privileges for each user
        users = data.get("users", {})
        for username, details in users.items():
            # users should occur only once each; skip if already processed
            if username in projects:
                msg = "invalid yaml file: user `{}` occurs multiple times".format(
                    username
                )
                if logger:
                    logger.error(msg)
                raise EnvironmentError(msg)

            privileges = {}
            resource_permissions = dict()
            for project in details.get("projects", {}):
                try:
                    privileges[project["auth_id"]] = set(project["privilege"])
                except KeyError as e:
                    if logger:
                        logger.error("project {} missing field: {}".format(project, e))
                    continue

                # project may not have `resource` field.
                # prefer resource field;
                # if no resource or mapping, assume auth_id is resource.
                resource = project.get("resource", project["auth_id"])

                if project["auth_id"] not in project_to_resource:
                    project_to_resource[project["auth_id"]] = resource
                resource_permissions[resource] = set(project["privilege"])

            user_info[username] = {
                "email": details.get("email", ""),
                "display_name": details.get("display_name", ""),
                "phone_number": details.get("phone_number", ""),
                "tags": details.get("tags", {}),
                "admin": details.get("admin", False),
            }
            if not details.get("email"):
                try:
                    valid = validate_email(
                        username, allow_smtputf8=False, check_deliverability=False
                    )
                    user_info[username]["email"] = valid.email
                except EmailNotValidError:
                    pass
            projects[username] = privileges
            user_abac[username] = resource_permissions

            # list of policies we want to grant to this user, which get sent to arborist
            # to check if they're allowed to do certain things
            policies[username] = details.get("policies", [])

        if logger:
            logger.info(
                "Got user project to arborist resource mapping:\n{}".format(
                    str(project_to_resource)
                )
            )

        authz = data.get("authz", dict())
        if not authz:
            # older version: resources in root, no `authz` section or `rbac` section
            if logger:
                logger.warning(
                    "access control YAML file is using old format (missing `authz`/`rbac`"
                    " section in the root); assuming that if it exists `resources` will"
                    " be on the root level, and continuing"
                )
            # we're going to throw it into the `authz` dictionary anyways, so the rest of
            # the code can pretend it's in the normal place that we expect
            resources = data.get("resources", [])
            # keep authz empty dict if resources is not specified
            if resources:
                authz["resources"] = data.get("resources", [])

        clients = data.get("clients", {})

        return cls(
            projects=projects,
            user_info=user_info,
            user_abac=user_abac,
            policies=policies,
            clients=clients,
            authz=authz,
            project_to_resource=project_to_resource,
            logger=logger,
        )

    def persist_project_to_resource(self, db_session):
        """
        Store the mappings from Project.auth_id to authorization resource (Project.authz)

        The mapping comes from an external source, this function persists what was parsed
        into memory into the database for future use.
        """
        for auth_id, authz_resource in self.project_to_resource.items():
            project = (
                db_session.query(Project).filter(Project.auth_id == auth_id).first()
            )
            if project:
                project.authz = authz_resource
            else:
                project = Project(name=auth_id, auth_id=auth_id, authz=authz_resource)
                db_session.add(project)
        db_session.commit()


class UserSyncer(object):
    def __init__(
        self,
        dbGaP,
        DB,
        project_mapping,
        storage_credentials=None,
        db_session=None,
        is_sync_from_dbgap_server=False,
        sync_from_local_csv_dir=None,
        sync_from_local_yaml_file=None,
        arborist=None,
        folder=None,
    ):
        """
        Syncs ACL files from dbGap to auth database and storage backends
        Args:
            dbGaP: a list of dict containing creds to access dbgap sftp
            DB: database connection string
            project_mapping: a dict containing how dbgap ids map to projects
            storage_credentials: a dict containing creds for storage backends
            sync_from_dir: path to an alternative dir to sync from instead of
                           dbGaP
            arborist:
                ArboristClient instance if the syncer should also create
                resources in arborist
            folder: a local folder where dbgap telemetry files will sync to
        """
        self.sync_from_local_csv_dir = sync_from_local_csv_dir
        self.sync_from_local_yaml_file = sync_from_local_yaml_file
        self.is_sync_from_dbgap_server = is_sync_from_dbgap_server
        self.dbGaP = dbGaP
        self.session = db_session
        self.driver = get_SQLAlchemyDriver(DB)
        self.project_mapping = project_mapping or {}
        self._projects = dict()
        self._created_roles = set()
        self._created_policies = set()
        self._dbgap_study_to_resources = dict()
        self.logger = get_logger(
            "user_syncer", log_level="debug" if config["DEBUG"] is True else "info"
        )
        self.arborist_client = arborist
        self.folder = folder

        self.auth_source = defaultdict(set)
        # auth_source used for logging. username : [source1, source2]
        self.visa_types = config.get("USERSYNC", {}).get("visa_types", {})
        self.parent_to_child_studies_mapping = {}
        for dbgap_config in dbGaP:
            self.parent_to_child_studies_mapping.update(
                dbgap_config.get("parent_to_child_studies_mapping", {})
            )
        if storage_credentials:
            self.storage_manager = StorageManager(
                storage_credentials, logger=self.logger
            )
        self.id_patterns = []

    @staticmethod
    def _match_pattern(filepath, id_patterns, encrypted=True):
        """
        Check if the filename matches dbgap access control file pattern

        Args:
            filepath (str): path to file
            encrypted (bool): whether the file is encrypted

        Returns:
            bool: whether the pattern matches
        """
        id_patterns.append(r"authentication_file_phs(\d{6}).(csv|txt)")
        for pattern in id_patterns:
            if encrypted:
                pattern += r".enc"
            pattern += r"$"
            # when converting the YAML from fence-config,
            # python reads it as Python string literal. So "\" turns into "\\"
            # which messes with the regex match
            pattern.replace("\\\\", "\\")
            if re.match(pattern, os.path.basename(filepath)):
                return True
        return False

    def _get_from_sftp_with_proxy(self, server, path):
        """
        Download all data from sftp sever to a local dir

        Args:
            server (dict) : dictionary containing info to access sftp server
            path (str): path to local directory

        Returns:
            None
        """
        proxy = None
        if server.get("proxy", "") != "":
            command = "ssh -oHostKeyAlgorithms=+ssh-rsa -i ~/.ssh/id_rsa {user}@{proxy} nc {host} {port}".format(
                user=server.get("proxy_user", ""),
                proxy=server.get("proxy", ""),
                host=server.get("host", ""),
                port=server.get("port", 22),
            )
            self.logger.info("SSH proxy command: {}".format(command))

            proxy = ProxyCommand(command)

        with paramiko.SSHClient() as client:
            client.set_log_channel(self.logger.name)

            # Patch paramiko to use sha256 instead of md5 for enhanced security and fips compliance
            paramiko.PKey.get_fingerprint = lambda self: hashlib.sha256(
                self.asbytes()
            ).digest()

            # Load known host keys
            known_hosts_path = os.path.expanduser("~/.ssh/known_hosts")
            if os.path.exists(known_hosts_path):
                client.load_host_keys(known_hosts_path)
            else:
                self.logger.error(
                    "No known_hosts file found — rejecting unknown hosts - make sure the SFTP host key is present in known_hosts before attempting connection."
                )

            client.set_missing_host_key_policy(paramiko.RejectPolicy())
            parameters = {
                "hostname": str(server.get("host", "")),
                "username": str(server.get("username", "")),
                "port": int(server.get("port", 22)),
            }
            if server.get("private_key_filename"):
                parameters["key_filename"] = str(server.get("private_key_filename"))
            else:
                parameters["password"] = str(server.get("password", ""))
            if proxy:
                parameters["sock"] = proxy

            self.logger.info(
                "SSH connection hostname:post {}:{}".format(
                    parameters.get("hostname", "unknown"),
                    parameters.get("port", "unknown"),
                )
            )
            try:
                self._connect_with_ssh(ssh_client=client, parameters=parameters)

                with client.open_sftp() as sftp:
                    download_dir(sftp, "./", path)
            except paramiko.ssh_exception.SSHException as e:
                self.logger.error(f"SSH connection failed, error: {e}")

        if proxy:
            proxy.close()

    @backoff.on_exception(backoff.expo, Exception, **DEFAULT_BACKOFF_SETTINGS)
    def _connect_with_ssh(self, ssh_client, parameters):
        ssh_client.connect(**parameters)

    def _get_from_ftp_with_proxy(self, server, path):
        """
        Download data from ftp sever to a local dir

        Args:
            server (dict): dictionary containing information for accessing server
            path(str): path to local files

        Returns:
            None
        """
        execstr = (
            'lftp -u {},{}  {} -e "set ftp:proxy http://{}; mirror . {}; exit"'.format(
                server.get("username", ""),
                server.get("password", ""),
                server.get("host", ""),
                server.get("proxy", ""),
                path,
            )
        )
        os.system(execstr)

    def _get_parse_consent_code(self, dbgap_config={}):
        return dbgap_config.get(
            "parse_consent_code", True
        )  # Should this really be true?

    def _parse_csv(self, file_dict, sess, dbgap_config={}, encrypted=True):
        """
        parse csv files to python dict

        Args:
            file_dict: a dictionary with key(file path) and value(privileges)
            sess: sqlalchemy session
            dbgap_config: a dictionary containing information about the dbGaP sftp server
                (comes from fence config)
            encrypted: boolean indicating whether those files are encrypted


        Return:
            Tuple[[dict, dict]]:
                (user_project, user_info) where user_project is a mapping from
                usernames to project permissions and user_info is a mapping
                from usernames to user details, such as email

        Example:

            (
                {
                    username: {
                        'project1': {'read-storage','write-storage'},
                        'project2': {'read-storage'},
                    }
                },
                {
                    username: {
                        'email': 'email@mail.com',
                        'display_name': 'display name',
                        'phone_number': '123-456-789',
                        'tags': {'dbgap_role': 'PI'}
                    }
                },
            )

        """
        user_projects = dict()
        user_info = defaultdict(dict)

        # parse dbGaP sftp server information
        dbgap_key = dbgap_config.get("decrypt_key", None)

        self.id_patterns += (
            [
                item.replace("\\\\", "\\")
                for item in dbgap_config.get("allowed_whitelist_patterns", [])
            ]
            if dbgap_config.get("allow_non_dbGaP_whitelist", False)
            else []
        )

        enable_common_exchange_area_access = dbgap_config.get(
            "enable_common_exchange_area_access", False
        )
        study_common_exchange_areas = dbgap_config.get(
            "study_common_exchange_areas", {}
        )
        parse_consent_code = self._get_parse_consent_code(dbgap_config)

        if parse_consent_code and enable_common_exchange_area_access:
            self.logger.info(
                f"using study to common exchange area mapping: {study_common_exchange_areas}"
            )

        project_id_patterns = [r"phs(\d{6})"]
        if "additional_allowed_project_id_patterns" in dbgap_config:
            patterns = dbgap_config.get("additional_allowed_project_id_patterns")
            patterns = [
                pattern.replace("\\\\", "\\") for pattern in patterns
            ]  # when converting the YAML from fence-config, python reads it as Python string literal. So "\" turns into "\\" which messes with the regex match
            project_id_patterns += patterns

        self.logger.info(f"Using these file paths: {file_dict.items()}")
        for filepath, privileges in file_dict.items():
            self.logger.info("Reading file {}".format(filepath))
            if os.stat(filepath).st_size == 0:
                self.logger.warning("Empty file {}".format(filepath))
                continue
            if not self._match_pattern(
                filepath, id_patterns=self.id_patterns, encrypted=encrypted
            ):
                self.logger.warning(
                    "Filename {} does not match dbgap access control filename pattern;"
                    " this could mean that the filename has an invalid format, or has"
                    " an unexpected .enc extension, or lacks the .enc extension where"
                    " expected. This file is NOT being processed by usersync!".format(
                        filepath
                    )
                )
                continue

            with _read_file(
                filepath, encrypted=encrypted, key=dbgap_key, logger=self.logger
            ) as f:
                csv = DictReader(f, quotechar='"', skipinitialspace=True)

                for row in csv:
                    username = row.get("login") or ""
                    if username == "":
                        continue

                    if dbgap_config.get("allow_non_dbGaP_whitelist", False):
                        phsid = (
                            row.get("phsid") or (row.get("project_id") or "")
                        ).split(".")
                    else:
                        phsid = (row.get("phsid") or "").split(".")

                    dbgap_project = phsid[0]
                    # There are issues where dbgap has a wrong entry in their whitelist. Since we do a bulk arborist request, there are wrong entries in it that invalidates the whole request causing other correct entries not to be added
                    skip = False
                    for pattern in project_id_patterns:
                        self.logger.debug(
                            "Checking pattern:{} with project_id:{}".format(
                                pattern, dbgap_project
                            )
                        )
                        if re.match(pattern, dbgap_project):
                            skip = False
                            break
                        else:
                            skip = True
                    if skip:
                        self.logger.warning(
                            "Skip processing from file {}, user {} with project {}".format(
                                filepath,
                                username,
                                dbgap_project,
                            )
                        )
                        continue
                    if len(phsid) > 1 and parse_consent_code:
                        consent_code = phsid[-1]

                        # c999 indicates full access to all consents and access
                        # to a study-specific exchange area
                        # access to at least one study-specific exchange area implies access
                        # to the parent study's common exchange area
                        #
                        # NOTE: Handling giving access to all consents is done at
                        #       a later time, when we have full information about possible
                        #       consents
                        self.logger.debug(
                            f"got consent code {consent_code} from dbGaP project "
                            f"{dbgap_project}"
                        )
                        if (
                            consent_code == "c999"
                            and enable_common_exchange_area_access
                            and dbgap_project in study_common_exchange_areas
                        ):
                            self.logger.info(
                                "found study with consent c999 and Fence "
                                "is configured to parse exchange area data. Giving user "
                                f"{username} {privileges} privileges in project: "
                                f"{study_common_exchange_areas[dbgap_project]}."
                            )
                            self._add_dbgap_project_for_user(
                                study_common_exchange_areas[dbgap_project],
                                privileges,
                                username,
                                sess,
                                user_projects,
                                dbgap_config,
                            )

                        dbgap_project += "." + consent_code

                    self._add_children_for_dbgap_project(
                        dbgap_project,
                        privileges,
                        username,
                        sess,
                        user_projects,
                        dbgap_config,
                    )

                    display_name = row.get("user name") or ""
                    tags = {"dbgap_role": row.get("role") or ""}

                    # some dbgap telemetry files have information about a researchers PI
                    if "downloader for" in row:
                        tags["pi"] = row["downloader for"]

                    # prefer name over previous "downloader for" if it exists
                    if "downloader for names" in row:
                        tags["pi"] = row["downloader for names"]

                    user_info[username] = {
                        "email": row.get("email")
                        or user_info[username].get("email")
                        or "",
                        "display_name": display_name,
                        "phone_number": row.get("phone")
                        or user_info[username].get("phone_number")
                        or "",
                        "tags": tags,
                    }

                    self._process_dbgap_project(
                        dbgap_project,
                        privileges,
                        username,
                        sess,
                        user_projects,
                        dbgap_config,
                    )

        return user_projects, user_info

    def _get_children(self, dbgap_project):
        return self.parent_to_child_studies_mapping.get(dbgap_project.split(".")[0])

    def _add_children_for_dbgap_project(
        self, dbgap_project, privileges, username, sess, user_projects, dbgap_config
    ):
        """
        Adds the configured child studies for the given dbgap_project, adding it to the provided user_projects. If
        parse_consent_code is true, then the consents granted in the provided dbgap_project will also be granted to the
        child studies.
        """
        parent_phsid = dbgap_project
        parse_consent_code = self._get_parse_consent_code(dbgap_config)
        child_suffix = ""
        if parse_consent_code and re.match(
            config["DBGAP_ACCESSION_WITH_CONSENT_REGEX"], dbgap_project
        ):
            parent_phsid_parts = dbgap_project.split(".")
            parent_phsid = parent_phsid_parts[0]
            child_suffix = "." + parent_phsid_parts[1]

        if parent_phsid not in self.parent_to_child_studies_mapping:
            return

        self.logger.info(
            f"found parent study {parent_phsid} and Fence "
            "is configured to provide additional access to child studies. Giving user "
            f"{username} {privileges} privileges in projects: "
            f"{{k + child_suffix: v + child_suffix for k, v in self.parent_to_child_studies_mapping.items()}}."
        )
        child_studies = self.parent_to_child_studies_mapping.get(parent_phsid, [])
        for child_study in child_studies:
            self._add_dbgap_project_for_user(
                child_study + child_suffix,
                privileges,
                username,
                sess,
                user_projects,
                dbgap_config,
            )

    def _add_dbgap_project_for_user(
        self, dbgap_project, privileges, username, sess, user_projects, dbgap_config
    ):
        """
        Helper function for csv parsing that adds a given dbgap project to Fence/Arborist
        and then updates the dictionary containing all user's project access
        """
        if dbgap_project not in self._projects:
            self.logger.debug(
                "creating Project in fence for dbGaP study: {}".format(dbgap_project)
            )

            project = self._get_or_create(sess, Project, auth_id=dbgap_project)

            # need to add dbgap project to arborist
            if self.arborist_client:
                self._determine_arborist_resource(dbgap_project, dbgap_config)

            if project.name is None:
                project.name = dbgap_project
            self._projects[dbgap_project] = project
        phsid_privileges = {dbgap_project: set(privileges)}
        if username in user_projects:
            user_projects[username].update(phsid_privileges)
        else:
            user_projects[username] = phsid_privileges

    @staticmethod
    def sync_two_user_info_dict(user_info1, user_info2):
        """
        Merge user_info1 into user_info2. Values in user_info2 are overriden
        by values in user_info1. user_info2 ends up containing the merged dict.

        Args:
            user_info1 (dict): nested dict
            user_info2 (dict): nested dict

            Example:
            {username: {'email': 'abc@email.com'}}

        Returns:
            None
        """
        user_info2.update(user_info1)

    def sync_two_phsids_dict(
        self,
        phsids1,
        phsids2,
        source1=None,
        source2=None,
        phsids2_overrides_phsids1=True,
    ):
        """
        Merge phsids1 into phsids2. If `phsids2_overrides_phsids1`, values in
        phsids1 are overriden by values in phsids2. phsids2 ends up containing
        the merged dict (see explanation below).
        `source1` and `source2`: for logging.

        Args:
            phsids1, phsids2: nested dicts mapping phsids to sets of permissions

            source1, source2: source of authz information (eg. dbgap, user_yaml, visas)

            Example:
            {
                username: {
                    phsid1: {'read-storage','write-storage'},
                    phsid2: {'read-storage'},
                }
            }

        Return:
            None

        Explanation:
            Consider merging projects of the same user:

                {user1: {phsid1: privillege1}}

                {user1: {phsid2: privillege2}}

            case 1: phsid1 != phsid2. Output:

                {user1: {phsid1: privillege1, phsid2: privillege2}}

            case 2: phsid1 == phsid2 and privillege1! = privillege2. Output:

                {user1: {phsid1: union(privillege1, privillege2)}}

            For the other cases, just simple addition
        """

        for user, projects1 in phsids1.items():
            if not phsids2.get(user):
                if source1:
                    self.auth_source[user].add(source1)
                phsids2[user] = projects1
            elif phsids2_overrides_phsids1:
                if source1:
                    self.auth_source[user].add(source1)
                if source2:
                    self.auth_source[user].add(source2)
                for phsid1, privilege1 in projects1.items():
                    if phsid1 not in phsids2[user]:
                        phsids2[user][phsid1] = set()
                    phsids2[user][phsid1].update(privilege1)
            elif source2:
                self.auth_source[user].add(source2)

    def sync_to_db_and_storage_backend(
        self,
        user_project,
        user_info,
        sess,
        do_not_revoke_from_db_and_storage=False,
        expires=None,
    ):
        """
        sync user access control to database and storage backend

        Args:
            user_project (dict): a dictionary of

                {
                    username: {
                        'project1': {'read-storage','write-storage'},
                        'project2': {'read-storage'}
                    }
                }

            user_info (dict): a dictionary of {username: user_info{}}
            sess: a sqlalchemy session

        Return:
            None
        """
        google_bulk_mapping = None
        if config["GOOGLE_BULK_UPDATES"]:
            google_bulk_mapping = {}

        self._init_projects(user_project, sess)

        auth_provider_list = [
            self._get_or_create(sess, AuthorizationProvider, name="dbGaP"),
            self._get_or_create(sess, AuthorizationProvider, name="fence"),
        ]

        cur_db_user_project_list = {
            (ua.user.username.lower(), ua.project.auth_id)
            for ua in sess.query(AccessPrivilege).all()
        }

        # we need to compare db -> whitelist case-insensitively for username.
        # db stores case-sensitively, but we need to query case-insensitively
        user_project_lowercase = {}
        syncing_user_project_list = set()
        for username, projects in user_project.items():
            user_project_lowercase[username.lower()] = projects
            for project, _ in projects.items():
                syncing_user_project_list.add((username.lower(), project))

        user_info_lowercase = {
            username.lower(): info for username, info in user_info.items()
        }

        to_delete = set.difference(cur_db_user_project_list, syncing_user_project_list)
        to_add = set.difference(syncing_user_project_list, cur_db_user_project_list)
        to_update = set.intersection(
            cur_db_user_project_list, syncing_user_project_list
        )

        # when updating users we want to maintain case sesitivity in the username so
        # pass the original, non-lowered user_info dict
        self._upsert_userinfo(sess, user_info)

        if not do_not_revoke_from_db_and_storage:
            self._revoke_from_storage(
                to_delete, sess, google_bulk_mapping=google_bulk_mapping
            )
            self._revoke_from_db(sess, to_delete)

        self._grant_from_storage(
            to_add,
            user_project_lowercase,
            sess,
            google_bulk_mapping=google_bulk_mapping,
            expires=expires,
        )

        self._grant_from_db(
            sess,
            to_add,
            user_info_lowercase,
            user_project_lowercase,
            auth_provider_list,
        )

        # re-grant
        self._grant_from_storage(
            to_update,
            user_project_lowercase,
            sess,
            google_bulk_mapping=google_bulk_mapping,
            expires=expires,
        )
        self._update_from_db(sess, to_update, user_project_lowercase)

        if not do_not_revoke_from_db_and_storage:
            self._validate_and_update_user_admin(sess, user_info_lowercase)

        sess.commit()

        if config["GOOGLE_BULK_UPDATES"]:
            self.logger.info("Doing bulk Google update...")
            update_google_groups_for_users(google_bulk_mapping)
            self.logger.info("Bulk Google update done!")

        sess.commit()

    def sync_to_storage_backend(
        self, user_project, user_info, sess, expires, skip_google_updates=False
    ):
        """
        sync user access control to storage backend with given expiration

        Args:
            user_project (dict): a dictionary of

                {
                    username: {
                        'project1': {'read-storage','write-storage'},
                        'project2': {'read-storage'}
                    }
                }

            user_info (dict): a dictionary of attributes for a user.
            sess: a sqlalchemy session
            expires (int): time at which synced Arborist policies and
                   inclusion in any GBAG are set to expire
            skip_google_updates (bool): True if google group updates should be skipped. False if otherwise.
        Return:
            None
        """
        if not expires:
            raise Exception(
                f"sync to storage backend requires an expiration. you provided: {expires}"
            )

        google_group_user_mapping = None
        if config["GOOGLE_BULK_UPDATES"]:
            google_group_user_mapping = {}
            get_or_create_proxy_group_id(
                expires=expires,
                user_id=user_info["user_id"],
                username=user_info["username"],
                session=sess,
                storage_manager=self.storage_manager,
            )

        # TODO: eventually it'd be nice to remove this step but it's required
        #       so that grant_from_storage can determine what storage backends
        #       are needed for a project.
        self._init_projects(user_project, sess)

        # we need to compare db -> whitelist case-insensitively for username.
        # db stores case-sensitively, but we need to query case-insensitively
        user_project_lowercase = {}
        syncing_user_project_list = set()
        for username, projects in user_project.items():
            user_project_lowercase[username.lower()] = projects
            for project, _ in projects.items():
                syncing_user_project_list.add((username.lower(), project))

        to_add = set(syncing_user_project_list)

        # when updating users we want to maintain case sensitivity in the username so
        # pass the original, non-lowered user_info dict
        self._upsert_userinfo(sess, {user_info["username"].lower(): user_info})
        if not skip_google_updates:
            self._grant_from_storage(
                to_add,
                user_project_lowercase,
                sess,
                google_bulk_mapping=google_group_user_mapping,
                expires=expires,
            )

            if config["GOOGLE_BULK_UPDATES"]:
                self.logger.info("Updating user's google groups ...")
                update_google_groups_for_users(google_group_user_mapping)
                self.logger.info("Google groups update done!!")

        sess.commit()

    def _revoke_from_db(self, sess, to_delete):
        """
        Revoke user access to projects in the auth database

        Args:
            sess: sqlalchemy session
            to_delete: a set of (username, project.auth_id) to be revoked from db
        Return:
            None
        """
        for username, project_auth_id in to_delete:
            q = (
                sess.query(AccessPrivilege)
                .filter(AccessPrivilege.project.has(auth_id=project_auth_id))
                .join(AccessPrivilege.user)
                .filter(func.lower(User.username) == username)
                .all()
            )
            for access in q:
                self.logger.info(
                    "revoke {} access to {} in db".format(username, project_auth_id)
                )
                sess.delete(access)

    def _validate_and_update_user_admin(self, sess, user_info):
        """
        Make sure there is no admin user that is not in yaml/csv files

        Args:
            sess: sqlalchemy session
            user_info: a dict of
            {
                username: {
                    'email': email,
                    'display_name': display_name,
                    'phone_number': phonenum,
                    'tags': {'k1':'v1', 'k2': 'v2'}
                    'admin': is_admin
                }
            }
        Returns:
            None
        """
        for admin_user in sess.query(User).filter_by(is_admin=True).all():
            if admin_user.username.lower() not in user_info:
                admin_user.is_admin = False
                sess.add(admin_user)
                self.logger.info(
                    "remove admin access from {} in db".format(
                        admin_user.username.lower()
                    )
                )

    def _update_from_db(self, sess, to_update, user_project):
        """
        Update user access to projects in the auth database

        Args:
            sess: sqlalchemy session
            to_update:
                a set of (username, project.auth_id) to be updated from db

        Return:
            None
        """

        for username, project_auth_id in to_update:
            q = (
                sess.query(AccessPrivilege)
                .filter(AccessPrivilege.project.has(auth_id=project_auth_id))
                .join(AccessPrivilege.user)
                .filter(func.lower(User.username) == username)
                .all()
            )
            for access in q:
                access.privilege = user_project[username][project_auth_id]
                self.logger.info(
                    "update {} with {} access to {} in db".format(
                        username, access.privilege, project_auth_id
                    )
                )

    def _grant_from_db(self, sess, to_add, user_info, user_project, auth_provider_list):
        """
        Grant user access to projects in the auth database
        Args:
            sess: sqlalchemy session
            to_add: a set of (username, project.auth_id) to be granted
            user_project:
                a dictionary of {username: {project: {'read','write'}}
        Return:
            None
        """
        for username, project_auth_id in to_add:
            u = query_for_user(session=sess, username=username)

            auth_provider = auth_provider_list[0]
            if "dbgap_role" not in user_info[username]["tags"]:
                auth_provider = auth_provider_list[1]
            user_access = AccessPrivilege(
                user=u,
                project=self._projects[project_auth_id],
                privilege=list(user_project[username][project_auth_id]),
                auth_provider=auth_provider,
            )
            self.logger.info(
                "grant user {} to {} with access {}".format(
                    username, user_access.project, user_access.privilege
                )
            )
            sess.add(user_access)

    def _upsert_userinfo(self, sess, user_info):
        """
        update user info to database.

        Args:
            sess: sqlalchemy session
            user_info:
                a dict of {username: {display_name, phone_number, tags, admin}

        Return:
            None
        """

        for username in user_info:
            u = query_for_user(session=sess, username=username)

            if u is None:
                self.logger.info("create user {}".format(username))
                u = User(username=username)
                sess.add(u)

            if self.arborist_client:
                self.arborist_client.create_user({"name": username})

            u.email = user_info[username].get("email", "")
            u.display_name = user_info[username].get("display_name", "")
            u.phone_number = user_info[username].get("phone_number", "")
            u.is_admin = user_info[username].get("admin", False)

            idp_name = user_info[username].get("idp_name", "")
            if idp_name and not u.identity_provider:
                idp = (
                    sess.query(IdentityProvider)
                    .filter(IdentityProvider.name == idp_name)
                    .first()
                )
                if not idp:
                    idp = IdentityProvider(name=idp_name)
                u.identity_provider = idp

            # do not update if there is no tag
            if not user_info[username].get("tags"):
                continue

            # remove user db tags if they are not shown in new tags
            for tag in u.tags:
                if tag.key not in user_info[username]["tags"]:
                    u.tags.remove(tag)

            # sync
            for k, v in user_info[username]["tags"].items():
                found = False
                for tag in u.tags:
                    if tag.key == k:
                        found = True
                        tag.value = v
                # create new tag if not found
                if not found:
                    tag = Tag(key=k, value=v)
                    u.tags.append(tag)

    def _revoke_from_storage(self, to_delete, sess, google_bulk_mapping=None):
        """
        If a project have storage backend, revoke user's access to buckets in
        the storage backend.

        Args:
            to_delete: a set of (username, project.auth_id) to be revoked

        Return:
            None
        """
        for username, project_auth_id in to_delete:
            project = (
                sess.query(Project).filter(Project.auth_id == project_auth_id).first()
            )
            for sa in project.storage_access:
                if not hasattr(self, "storage_manager"):
                    self.logger.error(
                        (
                            "CANNOT revoke {} access to {} in {} because there is NO "
                            "configured storage accesses at all. See configuration. "
                            "Continuing anyway..."
                        ).format(username, project_auth_id, sa.provider.name)
                    )
                    continue

                self.logger.info(
                    "revoke {} access to {} in {}".format(
                        username, project_auth_id, sa.provider.name
                    )
                )
                self.storage_manager.revoke_access(
                    provider=sa.provider.name,
                    username=username,
                    project=project,
                    session=sess,
                    google_bulk_mapping=google_bulk_mapping,
                )

    def _grant_from_storage(
        self, to_add, user_project, sess, google_bulk_mapping=None, expires=None
    ):
        """
        If a project have storage backend, grant user's access to buckets in
        the storage backend.

        Args:
            to_add: a set of (username, project.auth_id)  to be granted
            user_project: a dictionary like:

                    {username: {phsid: {'read-storage','write-storage'}}}

        Return:
            dict of the users' storage usernames to their user_projects and the respective storage access.
        """
        storage_user_to_sa_and_user_project = defaultdict()
        for username, project_auth_id in to_add:
            project = self._projects[project_auth_id]
            for sa in project.storage_access:
                access = list(user_project[username][project_auth_id])
                if not hasattr(self, "storage_manager"):
                    self.logger.error(
                        (
                            "CANNOT grant {} access {} to {} in {} because there is NO "
                            "configured storage accesses at all. See configuration. "
                            "Continuing anyway..."
                        ).format(username, access, project_auth_id, sa.provider.name)
                    )
                    continue

                self.logger.info(
                    "grant {} access {} to {} in {}".format(
                        username, access, project_auth_id, sa.provider.name
                    )
                )
                storage_username = self.storage_manager.grant_access(
                    provider=sa.provider.name,
                    username=username,
                    project=project,
                    access=access,
                    session=sess,
                    google_bulk_mapping=google_bulk_mapping,
                    expires=expires,
                )

                storage_user_to_sa_and_user_project[storage_username] = (sa, project)
        return storage_user_to_sa_and_user_project

    def _init_projects(self, user_project, sess):
        """
        initialize projects
        """

        if self.project_mapping:
            for projects in list(self.project_mapping.values()):
                for p in projects:
                    self.logger.debug(
                        "creating Project with info from project_mapping: {}".format(p)
                    )
                    project = self._get_or_create(sess, Project, **p)
                    self._projects[p["auth_id"]] = project
        for _, projects in user_project.items():
            for auth_id in list(projects.keys()):
                project = sess.query(Project).filter(Project.auth_id == auth_id).first()
                if not project:
                    data = {"name": auth_id, "auth_id": auth_id}
                    try:
                        project = self._get_or_create(sess, Project, **data)
                    except IntegrityError as e:
                        sess.rollback()
                        self.logger.error(
                            f"Project {auth_id} already exists. Detail {str(e)}"
                        )
                        raise Exception(
                            "Project {} already exists. Detail {}. Please contact your system administrator.".format(
                                auth_id, str(e)
                            )
                        )
                if auth_id not in self._projects:
                    self._projects[auth_id] = project

    @staticmethod
    def _get_or_create(sess, model, **kwargs):
        instance = sess.query(model).filter_by(**kwargs).first()
        if not instance:
            instance = model(**kwargs)
            sess.add(instance)
        return instance

    def _process_dbgap_files(self, dbgap_config, sess):
        """
        Args:
            dbgap_config : a dictionary containing information about a single
                           dbgap sftp server (from fence config)
            sess: database session

        Return:
            user_projects (dict)
            user_info (dict)
        """
        dbgap_file_list = []
        hostname = dbgap_config["info"]["host"]
        username = dbgap_config["info"]["username"]
        encrypted = dbgap_config["info"].get("encrypted", True)
        folderdir = os.path.join(str(self.folder), str(hostname), str(username))

        try:
            if os.path.exists(folderdir):
                dbgap_file_list = glob.glob(
                    os.path.join(folderdir, "*")
                )  # get lists of file from folder
            else:
                self.logger.info("Downloading files from: {}".format(hostname))
                dbgap_file_list = self._download(dbgap_config)
        except Exception as e:
            self.logger.error(e)
            exit(1)
        self.logger.info("dbgap files: {}".format(dbgap_file_list))
        user_projects, user_info = self._get_user_permissions_from_csv_list(
            dbgap_file_list,
            encrypted=encrypted,
            session=sess,
            dbgap_config=dbgap_config,
        )

        user_projects = self.parse_projects(user_projects)
        return user_projects, user_info

    def _get_user_permissions_from_csv_list(
        self, file_list, encrypted, session, dbgap_config={}
    ):
        """
        Args:
            file_list: list of files (represented as strings)
            encrypted: boolean indicating whether those files are encrypted
            session: sqlalchemy session
            dbgap_config: a dictionary containing information about the dbGaP sftp server
                    (comes from fence config)

        Return:
            user_projects (dict)
            user_info (dict)
        """
        permissions = [{"read-storage", "read"} for _ in file_list]
        user_projects, user_info = self._parse_csv(
            dict(list(zip(file_list, permissions))),
            sess=session,
            dbgap_config=dbgap_config,
            encrypted=encrypted,
        )
        return user_projects, user_info

    def _merge_multiple_local_csv_files(
        self, dbgap_file_list, encrypted, dbgap_configs, session
    ):
        """
        Args:
            dbgap_file_list (list): a list of whitelist file locations stored locally
            encrypted (bool): whether the file is encrypted (comes from fence config)
            dbgap_configs (list): list of dictionaries containing information about the dbgap server (comes from fence config)
            session (sqlalchemy.Session): database session

        Return:
            merged_user_projects (dict)
            merged_user_info (dict)
        """
        merged_user_projects = {}
        merged_user_info = {}

        for dbgap_config in dbgap_configs:
            user_projects, user_info = self._get_user_permissions_from_csv_list(
                dbgap_file_list,
                encrypted,
                session=session,
                dbgap_config=dbgap_config,
            )
            self.sync_two_user_info_dict(user_info, merged_user_info)
            self.sync_two_phsids_dict(user_projects, merged_user_projects)
        return merged_user_projects, merged_user_info

    def _merge_multiple_dbgap_sftp(self, dbgap_servers, sess):
        """
        Args:
            dbgap_servers : a list of dictionaries each containging config on
                           dbgap sftp server (comes from fence config)
            sess: database session

        Return:
            merged_user_projects (dict)
            merged_user_info (dict)
        """
        merged_user_projects = {}
        merged_user_info = {}
        for dbgap in dbgap_servers:
            user_projects, user_info = self._process_dbgap_files(dbgap, sess)
            # merge into merged_user_info
            # user_info overrides original info in merged_user_info
            self.sync_two_user_info_dict(user_info, merged_user_info)

            # merge all access info dicts into "merged_user_projects".
            # the access info is combined - if the user_projects access is
            # ["read"] and the merged_user_projects is ["read-storage"], the
            # resulting access is ["read", "read-storage"].
            self.sync_two_phsids_dict(user_projects, merged_user_projects)
        return merged_user_projects, merged_user_info

    def parse_projects(self, user_projects):
        """
        helper function for parsing projects
        """
        return {key.lower(): value for key, value in user_projects.items()}

    def _process_dbgap_project(
        self, dbgap_project, privileges, username, sess, user_projects, dbgap_config
    ):
        if dbgap_project not in self.project_mapping:
            self._add_dbgap_project_for_user(
                dbgap_project,
                privileges,
                username,
                sess,
                user_projects,
                dbgap_config,
            )

        for element_dict in self.project_mapping.get(dbgap_project, []):
            try:
                phsid_privileges = {element_dict["auth_id"]: set(privileges)}

                # need to add dbgap project to arborist
                if self.arborist_client:
                    self._determine_arborist_resource(
                        element_dict["auth_id"], dbgap_config
                    )

                if username not in user_projects:
                    user_projects[username] = {}
                user_projects[username].update(phsid_privileges)

            except ValueError as e:
                self.logger.info(e)

    def _process_user_projects(
        self,
        user_projects,
        enable_common_exchange_area_access,
        study_common_exchange_areas,
        dbgap_config,
        sess,
    ):
        user_projects_to_modify = copy.deepcopy(user_projects)
        for username in user_projects.keys():
            for project in user_projects[username].keys():
                phsid = project.split(".")
                dbgap_project = phsid[0]
                privileges = user_projects[username][project]
                if len(phsid) > 1 and self._get_parse_consent_code(dbgap_config):
                    consent_code = phsid[-1]

                    # c999 indicates full access to all consents and access
                    # to a study-specific exchange area
                    # access to at least one study-specific exchange area implies access
                    # to the parent study's common exchange area
                    #
                    # NOTE: Handling giving access to all consents is done at
                    #       a later time, when we have full information about possible
                    #       consents
                    self.logger.debug(
                        f"got consent code {consent_code} from dbGaP project "
                        f"{dbgap_project}"
                    )
                    if (
                        consent_code == "c999"
                        and enable_common_exchange_area_access
                        and dbgap_project in study_common_exchange_areas
                    ):
                        self.logger.info(
                            "found study with consent c999 and Fence "
                            "is configured to parse exchange area data. Giving user "
                            f"{username} {privileges} privileges in project: "
                            f"{study_common_exchange_areas[dbgap_project]}."
                        )
                        self._add_dbgap_project_for_user(
                            study_common_exchange_areas[dbgap_project],
                            privileges,
                            username,
                            sess,
                            user_projects_to_modify,
                            dbgap_config,
                        )

                    dbgap_project += "." + consent_code

                self._add_children_for_dbgap_project(
                    dbgap_project,
                    privileges,
                    username,
                    sess,
                    user_projects_to_modify,
                    dbgap_config,
                )

                self._process_dbgap_project(
                    dbgap_project,
                    privileges,
                    username,
                    sess,
                    user_projects_to_modify,
                    dbgap_config,
                )
        for user in user_projects_to_modify.keys():
            user_projects[user] = user_projects_to_modify[user]

    def sync(self):
        if self.session:
            self._sync(self.session)
        else:
            with self.driver.session as s:
                self._sync(s)

    def download(self):
        for dbgap_server in self.dbGaP:
            self._download(dbgap_server)

    def _download(self, dbgap_config):
        """
        Download files from dbgap server.
        """
        server = dbgap_config["info"]
        protocol = dbgap_config["protocol"]
        hostname = server["host"]
        username = server["username"]
        folderdir = os.path.join(str(self.folder), str(hostname), str(username))

        if not os.path.exists(folderdir):
            os.makedirs(folderdir)

        self.logger.info("Download from server")
        try:
            if protocol == "sftp":
                self._get_from_sftp_with_proxy(server, folderdir)
            else:
                self._get_from_ftp_with_proxy(server, folderdir)
            dbgap_files = glob.glob(os.path.join(folderdir, "*"))
            return dbgap_files
        except Exception as e:
            self.logger.error(e)
            raise

    def _sync(self, sess):
        """
        Collect files from dbgap server(s), sync csv and yaml files to storage
        backend and fence DB
        """
        # get all dbgap files
        user_projects = {}
        user_info = {}
        if self.is_sync_from_dbgap_server:
            self.logger.debug(
                "Pulling telemetry files from {} dbgap sftp servers".format(
                    len(self.dbGaP)
                )
            )
            user_projects, user_info = self._merge_multiple_dbgap_sftp(self.dbGaP, sess)

        local_csv_file_list = []
        if self.sync_from_local_csv_dir:
            local_csv_file_list = glob.glob(
                os.path.join(self.sync_from_local_csv_dir, "*")
            )
            # Sort the list so the order of of files is consistent across platforms
            local_csv_file_list.sort()

        user_projects_csv, user_info_csv = self._merge_multiple_local_csv_files(
            local_csv_file_list,
            encrypted=False,
            session=sess,
            dbgap_configs=self.dbGaP,
        )

        try:
            user_yaml = UserYAML.from_file(
                self.sync_from_local_yaml_file, encrypted=False, logger=self.logger
            )
        except (EnvironmentError, AssertionError) as e:
            self.logger.error(str(e))
            self.logger.error("aborting early")
            raise

        # parse all projects
        user_projects_csv = self.parse_projects(user_projects_csv)
        user_projects = self.parse_projects(user_projects)
        user_yaml.projects = self.parse_projects(user_yaml.projects)

        # merge all user info dicts into "user_info".
        # the user info (such as email) in the user.yaml files
        # overrides the user info from the CSV files.
        self.sync_two_user_info_dict(user_info_csv, user_info)
        self.sync_two_user_info_dict(user_yaml.user_info, user_info)

        # merge all access info dicts into "user_projects".
        # the access info is combined - if the user.yaml access is
        # ["read"] and the CSV file access is ["read-storage"], the
        # resulting access is ["read", "read-storage"].
        self.sync_two_phsids_dict(
            user_projects_csv, user_projects, source1="local_csv", source2="dbgap"
        )
        self.sync_two_phsids_dict(
            user_yaml.projects, user_projects, source1="user_yaml", source2="dbgap"
        )

        # Note: if there are multiple dbgap sftp servers configured
        # this parameter is always from the config for the first dbgap sftp server
        # not any additional ones
        for dbgap_config in self.dbGaP:
            if self._get_parse_consent_code(dbgap_config):
                self._grant_all_consents_to_c999_users(
                    user_projects, user_yaml.project_to_resource
                )

        google_update_ex = None

        try:
            # update the Fence DB
            if user_projects:
                self.logger.info("Sync to db and storage backend")
                self.sync_to_db_and_storage_backend(user_projects, user_info, sess)
                self.logger.info("Finish syncing to db and storage backend")
            else:
                self.logger.info("No users for syncing")
        except GoogleUpdateException as ex:
            # save this to reraise later after all non-Google syncing has finished
            # this way, any issues with Google only affect Google data access and don't
            # cascade problems into non-Google AWS or Azure access
            google_update_ex = ex

        # update the Arborist DB (resources, roles, policies, groups)
        if user_yaml.authz:
            if not self.arborist_client:
                raise EnvironmentError(
                    "yaml file contains authz section but sync is not configured with"
                    " arborist client--did you run sync with --arborist <arborist client> arg?"
                )
            self.logger.info("Synchronizing arborist...")
            success = self._update_arborist(user_yaml)
            if success:
                self.logger.info("Finished synchronizing arborist")
            else:
                self.logger.error("Could not synchronize successfully")
                exit(1)
        else:
            self.logger.info("No `authz` section; skipping arborist sync")

        # update the Arborist DB (user access)
        if self.arborist_client:
            self.logger.info("Synchronizing arborist with authorization info...")
            success = self._update_authz_in_arborist(sess, user_projects, user_yaml)
            if success:
                self.logger.info(
                    "Finished synchronizing authorization info to arborist"
                )
            else:
                self.logger.error(
                    "Could not synchronize authorization info successfully to arborist"
                )
                exit(1)
        else:
            self.logger.error("No arborist client set; skipping arborist sync")

        # Logging authz source
        for u, s in self.auth_source.items():
            self.logger.info("Access for user {} from {}".format(u, s))

        self.logger.info(
            f"Persisting authz mapping to database: {user_yaml.project_to_resource}"
        )
        user_yaml.persist_project_to_resource(db_session=sess)
        if google_update_ex is not None:
            raise google_update_ex

    def _grant_all_consents_to_c999_users(
        self, user_projects, user_yaml_project_to_resources
    ):
        access_number_matcher = re.compile(config["DBGAP_ACCESSION_WITH_CONSENT_REGEX"])
        # combine dbgap/user.yaml projects into one big list (in case not all consents
        # are in either)
        all_projects = set(
            list(self._projects.keys()) + list(user_yaml_project_to_resources.keys())
        )

        self.logger.debug(f"all projects: {all_projects}")

        # construct a mapping from phsid (without consent) to all accessions with consent
        consent_mapping = {}
        for project in all_projects:
            phs_match = access_number_matcher.match(project)
            if phs_match:
                accession_number = phs_match.groupdict()

                # TODO: This is not handling the .v1.p1 at all
                consent_mapping.setdefault(accession_number["phsid"], set()).add(
                    ".".join([accession_number["phsid"], accession_number["consent"]])
                )
                children = self._get_children(accession_number["phsid"])
                if children:
                    for child_phs in children:
                        consent_mapping.setdefault(child_phs, set()).add(
                            ".".join(
                                [child_phs, accession_number["consent"]]
                            )  # Assign parent consent to child study
                        )

        self.logger.debug(f"consent mapping: {consent_mapping}")

        # go through existing access and find any c999's and make sure to give access to
        # all accessions with consent for that phsid
        for username, user_project_info in copy.deepcopy(user_projects).items():
            for project, _ in user_project_info.items():
                phs_match = access_number_matcher.match(project)
                if phs_match and phs_match.groupdict()["consent"] == "c999":
                    # give access to all consents
                    all_phsids_with_consent = consent_mapping.get(
                        phs_match.groupdict()["phsid"], []
                    )
                    self.logger.info(
                        f"user {username} has c999 consent group for: {project}. "
                        f"Granting access to all consents: {all_phsids_with_consent}"
                    )
                    # NOTE: Only giving read-storage at the moment (this is same
                    #       permission we give for other dbgap projects)
                    for phsid_with_consent in all_phsids_with_consent:
                        user_projects[username].update(
                            {phsid_with_consent: {"read-storage", "read"}}
                        )

    def _update_arborist(self, user_yaml):
        """
        Create roles, resources, policies, groups in arborist from the information in
        ``user_yaml``.

        The projects are sent to arborist as resources with paths like
        ``/projects/{project}``. Roles are created with just the original names
        for the privileges like ``"read-storage", "read"`` etc.

        Args:
            session (sqlalchemy.Session)
            user_yaml (UserYAML)

        Return:
            bool: success
        """
        healthy = self._is_arborist_healthy()
        if not healthy:
            return False

        # Set up the resource tree in arborist by combining provided resources with any
        # dbgap resources that were created before this.
        #
        # Why add dbgap resources if they've already been created?
        #   B/C Arborist's PUT update will override existing subresources. So if a dbgap
        #   resources was created under `/programs/phs000178` anything provided in
        #   user.yaml under `/programs` would completely wipe it out.
        resources = user_yaml.authz.get("resources", [])

        dbgap_resource_paths = []
        for path_list in self._dbgap_study_to_resources.values():
            dbgap_resource_paths.extend(path_list)

        self.logger.debug("user_yaml resources: {}".format(resources))
        self.logger.debug("dbgap resource paths: {}".format(dbgap_resource_paths))

        combined_resources = utils.combine_provided_and_dbgap_resources(
            resources, dbgap_resource_paths
        )

        for resource in combined_resources:
            try:
                self.logger.debug(
                    "attempting to update arborist resource: {}".format(resource)
                )
                self.arborist_client.update_resource("/", resource, merge=True)
            except ArboristError as e:
                self.logger.error(e)
                # keep going; maybe just some conflicts from things existing already

        # update roles
        roles = user_yaml.authz.get("roles", [])
        for role in roles:
            try:
                response = self.arborist_client.update_role(role["id"], role)
                if response:
                    self._created_roles.add(role["id"])
            except ArboristError as e:
                self.logger.info(
                    "couldn't update role '{}', creating instead".format(str(e))
                )
                try:
                    response = self.arborist_client.create_role(role)
                    if response:
                        self._created_roles.add(role["id"])
                except ArboristError as e:
                    self.logger.error(e)
                    # keep going; maybe just some conflicts from things existing already

        # update policies
        policies = user_yaml.authz.get("policies", [])
        for policy in policies:
            policy_id = policy.pop("id")
            try:
                self.logger.debug(
                    "Trying to upsert policy with id {}".format(policy_id)
                )
                response = self.arborist_client.update_policy(
                    policy_id, policy, create_if_not_exist=True
                )
            except ArboristError as e:
                self.logger.error(e)
                # keep going; maybe just some conflicts from things existing already
            else:
                if response:
                    self.logger.debug("Upserted policy with id {}".format(policy_id))
                    self._created_policies.add(policy_id)

        # update groups
        groups = user_yaml.authz.get("groups", [])

        # delete from arborist the groups that have been deleted
        # from the user.yaml
        arborist_groups = set(
            g["name"] for g in self.arborist_client.list_groups().get("groups", [])
        )
        useryaml_groups = set(g["name"] for g in groups)
        for deleted_group in arborist_groups.difference(useryaml_groups):
            # do not try to delete built in groups
            if deleted_group not in ["anonymous", "logged-in"]:
                self.arborist_client.delete_group(deleted_group)

        # create/update the groups defined in the user.yaml
        for group in groups:
            missing = {"name", "users", "policies"}.difference(set(group.keys()))
            if missing:
                name = group.get("name", "{MISSING NAME}")
                self.logger.error(
                    "group {} missing required field(s): {}".format(name, list(missing))
                )
                continue
            try:
                response = self.arborist_client.put_group(
                    group["name"],
                    # Arborist doesn't handle group descriptions yet
                    # description=group.get("description", ""),
                    users=group["users"],
                    policies=group["policies"],
                )
            except ArboristError as e:
                self.logger.info("couldn't put group: {}".format(str(e)))

        # Update policies for built-in (`anonymous` and `logged-in`) groups

        # First recreate these groups in order to clear out old, possibly deleted policies
        for builtin_group in ["anonymous", "logged-in"]:
            try:
                response = self.arborist_client.put_group(builtin_group)
            except ArboristError as e:
                self.logger.info("couldn't put group: {}".format(str(e)))

        # Now add back policies that are in the user.yaml
        for policy in user_yaml.authz.get("anonymous_policies", []):
            self.arborist_client.grant_group_policy("anonymous", policy)

        for policy in user_yaml.authz.get("all_users_policies", []):
            self.arborist_client.grant_group_policy("logged-in", policy)

        return True

    def _grant_arborist_policies(
        self,
        username,
        incoming_policies,
        user_yaml,
        expires=None,
        remove_users_with_no_policies=True,
    ):
        """
        Find the difference between the existing policies for a user and the incoming policies,
        and decide whether to add, remove, or keep policies.

        Args:
            username (str): the username of the user
            incoming_policies (set): set of policies to be applied to the user
            user_yaml (UserYAML): UserYAML object containing authz information
            expires (int): time at which authz info in Arborist should expire
            remove_users_with_no_policies (bool): whether to delete users with no access from
                the Arborist database
        """
        user_existing_policies = set()
        to_add = set()
        to_remove = set()
        is_revoke_all = False

        try:
            user_existing_policies = set(
                policy["policy"]
                for policy in self.arborist_client.get_user(username)["policies"]
            )
            self.logger.info(
                f"Fetched user {username} existing policies: {user_existing_policies}"
            )
        except ArboristError as e:
            self.logger.error(
                f"Could not get user {username} policies from Arborist: {e}. Revoking all policies..."
            )
            # if getting existing policies fails, revoke all policies and re-apply
            is_revoke_all = True

        if user_yaml:
            anonymous_policies = set(
                user_yaml.authz.get("anonymous_policies", [])
                + user_yaml.authz.get("all_users_policies", [])
            )
            user_existing_policies = user_existing_policies - anonymous_policies

        if is_revoke_all is False and len(incoming_policies) > 0:
            to_add = incoming_policies - user_existing_policies
            to_remove = user_existing_policies - incoming_policies
        else:
            # if incoming_policies is empty, we revoke all policies
            is_revoke_all = True

        if not is_revoke_all:
            success = not to_remove
            try:
                if to_remove:
                    for policy in to_remove:
                        self.logger.info(
                            f"Revoking policy {policy} for user {username}."
                        )
                        success = self.arborist_client.revoke_user_policy(
                            username, policy
                        )
            except ArboristError as e:
                self.logger.error(
                    f"Could not revoke user {username} policy {policy}: {e}"
                )
            if not success:
                # `revoke_user_policy` returns None in case of error
                self.logger.error(
                    f"Could not revoke user {username} policy. Revoking all instead."
                )
                is_revoke_all = True

        if is_revoke_all:
            if (
                remove_users_with_no_policies
                and not incoming_policies
                and not user_existing_policies
            ):
                # user without any access (other than anonymous and logged-in groups).
                # cleanup: remove from the arborist DB so we do not check their access again every
                # time this code runs.
                self.logger.info(
                    f"Deleting user {username} from Arborist (since they have no policies)."
                )
                self.arborist_client.delete_user(username)
                return
            success = False
            try:
                # Note: If a user only has group policies, we call `revoke_all_policies_for_user`
                # for nothing. Could be fixed by adding a flag to the arborist "get user" endpoint
                # to get the list of policies _excluding_ group policies, or by manually checking
                # which policies are group policies (not worth it atm).
                self.logger.info(f"Revoking all policies for user {username}.")
                success = self.arborist_client.revoke_all_policies_for_user(username)
            except ArboristError as e:
                self.logger.error(
                    f"Could not revoke all policies for user {username}. Error: {e}"
                )
            if not success:
                # `revoke_all_policies_for_user` returns None in case of error
                raise Exception(f"Could not revoke all policies for user {username}")
            to_add = incoming_policies  # if we revoke all, we need to add all incoming policies

        if (
            "mfa_policy" not in incoming_policies
            and "mfa_policy" in user_existing_policies
        ):
            to_add.add("mfa_policy")

        if to_add:
            self.logger.info(f"Bulk granting user {username} policies {to_add}.")
            self._grant_bulk_user_policies(username, to_add, expires)

    def _update_authz_in_arborist(
        self,
        session,
        user_projects,
        user_yaml=None,
        single_user_sync=False,
        expires=None,
    ):
        """
        Assign users policies in arborist from the information in
        ``user_projects`` and optionally a ``user_yaml``.

        The projects are sent to arborist as resources with paths like
        ``/projects/{project}``. Roles are created with just the original names
        for the privileges like ``"read-storage", "read"`` etc.

        Args:
            user_projects (dict)
            user_yaml (UserYAML) optional, if there are policies for users in a user.yaml
            single_user_sync (bool) whether authz update is for a single user
            expires (int) time at which authz info in Arborist should expire

        Return:
            bool: success
        """
        healthy = self._is_arborist_healthy()
        if not healthy:
            return False

        self.logger.debug("user_projects: {}".format(user_projects))

        if user_yaml:
            self.logger.debug(
                "useryaml abac before lowering usernames: {}".format(
                    user_yaml.user_abac
                )
            )
            user_yaml.user_abac = {
                key.lower(): value for key, value in user_yaml.user_abac.items()
            }
            # update the project info with `projects` specified in user.yaml
            self.sync_two_phsids_dict(user_yaml.user_abac, user_projects)

        # get list of users from arborist to make sure users that are completely removed
        # from authorization sources get policies revoked

        arborist_user_projects = {}
        if not single_user_sync:

            try:
                arborist_users = self.arborist_client.get_users().json["users"]

                # construct user information, NOTE the lowering of the username. when adding/
                # removing access, the case in the Fence db is used. For combining access, it is
                # case-insensitive, so we lower
                arborist_user_projects = {
                    user["name"].lower(): {} for user in arborist_users
                }
            except (ArboristError, KeyError, AttributeError) as error:
                # TODO usersync should probably exit with non-zero exit code at the end,
                #      but sync should continue from this point so there are no partial
                #      updates
                self.logger.warning(
                    "Could not get list of users in Arborist, continuing anyway. "
                    "WARNING: this sync will NOT remove access for users no longer in "
                    f"authorization sources. Error: {error}"
                )

            # update the project info with users from arborist
            self.sync_two_phsids_dict(arborist_user_projects, user_projects)

        # prefer in-memory if available from user_yaml, if not, get from database
        if user_yaml and user_yaml.project_to_resource:
            project_to_authz_mapping = user_yaml.project_to_resource
            self.logger.debug(
                f"using in-memory project to authz resource mapping from "
                f"user.yaml (instead of database): {project_to_authz_mapping}"
            )
        else:
            project_to_authz_mapping = get_project_to_authz_mapping(session)
            self.logger.debug(
                f"using persisted project to authz resource mapping from database "
                f"(instead of user.yaml - as it may not be available): {project_to_authz_mapping}"
            )

        self.logger.debug(
            f"_dbgap_study_to_resources: {self._dbgap_study_to_resources}"
        )
        all_resources = [
            r
            for resources in self._dbgap_study_to_resources.values()
            for r in resources
        ]
        all_resources.extend(r for r in project_to_authz_mapping.values())
        self._create_arborist_resources(all_resources)

        for username, user_project_info in user_projects.items():
            self.logger.info("processing user `{}`".format(username))
            user = query_for_user(session=session, username=username)
            idp = None
            if user:
                username = user.username
                idp = user.identity_provider.name if user.identity_provider else None

            self.arborist_client.create_user_if_not_exist(username)

            # as of 2/11/2022, for single_user_sync, as RAS visa parsing has
            # previously mapped each project to the same set of privileges
            # (i.e.{'read', 'read-storage'}), unique_policies will just be a
            # single policy with ('read', 'read-storage') being the single
            # key
            unique_policies = self._determine_unique_policies(
                user_project_info, project_to_authz_mapping
            )
            for roles in unique_policies.keys():
                for role in roles:
                    self._create_arborist_role(role)

            incoming_policies = set()  # set of policies for current user.

            if single_user_sync:
                for ordered_roles, ordered_resources in unique_policies.items():
                    policy_hash = self._hash_policy_contents(
                        ordered_roles, ordered_resources
                    )
                    self._create_arborist_policy(
                        policy_hash,
                        ordered_roles,
                        ordered_resources,
                        skip_if_exists=True,
                    )
                    # return here as it is not expected single_user_sync
                    # will need any of the remaining user_yaml operations
                    # left in _update_authz_in_arborist
                    return self._grant_arborist_policy(
                        username, policy_hash, expires=expires
                    )
            else:
                policy_ids_to_grant = set()
                for roles, resources in unique_policies.items():
                    for role in roles:
                        for resource in resources:
                            # grant a policy to this user which is a single
                            # role on a single resource

                            # format project '/x/y/z' -> 'x.y.z'
                            # so the policy id will be something like 'x.y.z-create'
                            policy_id = _format_policy_id(resource, role)
                            incoming_policies.add(policy_id)
                            if policy_id not in self._created_policies:
                                try:
                                    self.arborist_client.update_policy(
                                        policy_id,
                                        {
                                            "description": "policy created by fence sync",
                                            "role_ids": [role],
                                            "resource_paths": [resource],
                                        },
                                        create_if_not_exist=True,
                                    )
                                except ArboristError as e:
                                    self.logger.info(
                                        "not creating policy in arborist; {}".format(
                                            str(e)
                                        )
                                    )
                                self._created_policies.add(policy_id)
                            policy_ids_to_grant.add(policy_id)
                self._grant_arborist_policies(
                    username,
                    policy_ids_to_grant,
                    user_yaml=None,
                    expires=expires,
                    remove_users_with_no_policies=False,
                )

            if user_yaml:
                user_yaml_policies = set(user_yaml.policies.get(username, []))
                incoming_policies = (
                    incoming_policies | user_yaml_policies
                )  # add policies from whitelist and useryaml

            self._grant_arborist_policies(
                username,
                incoming_policies,
                user_yaml,
                expires=expires,
                remove_users_with_no_policies=True,
            )

        if user_yaml:
            for client_name, client_details in user_yaml.clients.items():
                client_policies = client_details.get("policies", [])
                clients = session.query(Client).filter_by(name=client_name).all()
                # update existing clients, do not create new ones
                if not clients:
                    self.logger.warning(
                        "client to update (`{}`) does not exist in fence: skipping".format(
                            client_name
                        )
                    )
                    continue
                self.logger.debug(
                    "updating client `{}` (found {} client IDs)".format(
                        client_name, len(clients)
                    )
                )
                # there may be more than 1 client with this name if credentials are being rotated,
                # so we grant access to each client ID
                for client in clients:
                    try:
                        self.arborist_client.update_client(
                            client.client_id, client_policies
                        )
                    except ArboristError as e:
                        self.logger.info(
                            "not granting policies {} to client `{}` (`{}`); {}".format(
                                client_policies, client_name, client.client_id, str(e)
                            )
                        )

        return True

    def _determine_unique_policies(self, user_project_info, project_to_authz_mapping):
        """
        Determine and return a dictionary of unique policies.

        Args (examples):
            user_project_info (dict):
            {
                'phs000002.c1': { 'read-storage', 'read' },
                'phs000001.c1': { 'read', 'read-storage' },
                'phs000004.c1': { 'write', 'read' },
                'phs000003.c1': { 'read', 'write' },
                'phs000006.c1': { 'write-storage', 'write', 'read-storage', 'read' }
                'phs000005.c1': { 'read', 'read-storage', 'write', 'write-storage' },
            }
            project_to_authz_mapping (dict):
            {
                'phs000001.c1': '/programs/DEV/projects/phs000001.c1'
            }

        Return (for examples):
            dict:
            {
                ('read', 'read-storage'): ('phs000001.c1', 'phs000002.c1'),
                ('read', 'write'): ('phs000003.c1', 'phs000004.c1'),
                ('read', 'read-storage', 'write', 'write-storage'): ('phs000005.c1', 'phs000006.c1'),
            }
        """
        roles_to_resources = collections.defaultdict(list)
        for study, roles in user_project_info.items():
            ordered_roles = tuple(sorted(roles))
            study_authz_paths = self._dbgap_study_to_resources.get(study, [study])
            if study in project_to_authz_mapping:
                study_authz_paths = [project_to_authz_mapping[study]]
            roles_to_resources[ordered_roles].extend(study_authz_paths)

        policies = {}
        for ordered_roles, unordered_resources in roles_to_resources.items():
            policies[ordered_roles] = tuple(sorted(unordered_resources))
        return policies

    def _create_arborist_role(self, role):
        """
        Wrapper around gen3authz's create_role with additional logging

        Args:
            role (str): what the Arborist identity should be of the created role

        Return:
            bool: True if the role was created successfully or it already
                  exists. False otherwise
        """
        if role in self._created_roles:
            return True
        try:
            response_json = self.arborist_client.create_role(
                arborist_role_for_permission(role)
            )
        except ArboristError as e:
            self.logger.error(
                "could not create `{}` role in Arborist: {}".format(role, e)
            )
            return False
        self._created_roles.add(role)

        if response_json is None:
            self.logger.info("role `{}` already exists in Arborist".format(role))
        else:
            self.logger.info("created role `{}` in Arborist".format(role))
        return True

    def _create_arborist_resources(self, resources):
        """
        Create resources in Arborist

        Args:
            resources (list): a list of full Arborist resource paths to create
            [
                "/programs/DEV/projects/phs000001.c1",
                "/programs/DEV/projects/phs000002.c1",
                "/programs/DEV/projects/phs000003.c1"
            ]

        Return:
            bool: True if the resources were successfully created, False otherwise


        As of 2/11/2022, for resources above,
        utils.combine_provided_and_dbgap_resources({}, resources) returns:
        [
            { 'name': 'programs', 'subresources': [
                { 'name': 'DEV', 'subresources': [
                    { 'name': 'projects', 'subresources': [
                        { 'name': 'phs000001.c1', 'subresources': []},
                        { 'name': 'phs000002.c1', 'subresources': []},
                        { 'name': 'phs000003.c1', 'subresources': []}
                    ]}
                ]}
            ]}
        ]
        Because this list has a single object, only a single network request gets
        sent to Arborist.

        However, for resources = ["/phs000001.c1", "/phs000002.c1", "/phs000003.c1"],
        utils.combine_provided_and_dbgap_resources({}, resources) returns:
        [
            {'name': 'phs000001.c1', 'subresources': []},
            {'name': 'phs000002.c1', 'subresources': []},
            {'name': 'phs000003.c1', 'subresources': []}
        ]
        Because this list has 3 objects, 3 network requests get sent to Arborist.

        As a practical matter, for sync_single_user_visas, studies
        should be nested under the `/programs` resource as in the former
        example (i.e. only one network request gets made).

        TODO for the sake of simplicity, it would be nice if only one network
        request was made no matter the input.
        """
        for request_body in utils.combine_provided_and_dbgap_resources({}, resources):
            try:
                response_json = self.arborist_client.update_resource(
                    "/", request_body, merge=True
                )
            except ArboristError as e:
                self.logger.error(
                    "could not create Arborist resources using request body `{}`. error: {}".format(
                        request_body, e
                    )
                )
                return False

        self.logger.debug(
            "created {} resource(s) in Arborist: `{}`".format(len(resources), resources)
        )
        return True

    def _create_arborist_policy(
        self, policy_id, roles, resources, skip_if_exists=False
    ):
        """
        Wrapper around gen3authz's create_policy with additional logging

        Args:
            policy_id (str): what the Arborist identity should be of the created policy
            roles (iterable): what roles the create policy should have
            resources (iterable): what resources the created policy should have
            skip_if_exists (bool): if True, this function will not treat an already
                                   existent policy as an error

        Return:
            bool: True if policy creation was successful. False otherwise
        """
        try:
            response_json = self.arborist_client.create_policy(
                {
                    "id": policy_id,
                    "role_ids": roles,
                    "resource_paths": resources,
                },
                skip_if_exists=skip_if_exists,
            )
        except ArboristError as e:
            self.logger.error(
                "could not create policy `{}` in Arborist: {}".format(policy_id, e)
            )
            return False

        if response_json is None:
            self.logger.info("policy `{}` already exists in Arborist".format(policy_id))
        else:
            self.logger.info("created policy `{}` in Arborist".format(policy_id))
        return True

    def _hash_policy_contents(self, ordered_roles, ordered_resources):
        """
        Generate a sha256 hexdigest representing ordered_roles and ordered_resources.

        Args:
            ordered_roles (iterable): policy roles in sorted order
            ordered_resources (iterable): policy resources in sorted order

        Return:
            str: SHA256 hex digest
        """

        def escape(s):
            return s.replace(",", "\\,")

        canonical_roles = ",".join(escape(r) for r in ordered_roles)
        canonical_resources = ",".join(escape(r) for r in ordered_resources)
        canonical_policy = f"{canonical_roles},,f{canonical_resources}"
        policy_hash = hashlib.sha256(canonical_policy.encode("utf-8")).hexdigest()

        return policy_hash

    def _grant_arborist_policy(self, username, policy_id, expires=None):
        """
        Wrapper around gen3authz's grant_user_policy with additional logging

        Args:
            username (str): username of user in Arborist who policy should be
                            granted to
            policy_id (str): Arborist policy id
            expires (int): POSIX timestamp for when policy should expire

        Return:
            bool: True if granting of policy was successful, False otherwise
        """
        try:
            resp = self.arborist_client.grant_user_policy(
                username,
                policy_id,
                expires_at=expires,
            )
            if not resp:
                self.logger.error(
                    "could not grant policy `{}` to user `{}`".format(
                        policy_id, username
                    )
                )
                return False
        except ArboristError as e:
            self.logger.error(
                "could not grant policy `{}` to user `{}`: {}".format(
                    policy_id, username, e
                )
            )
            return False

        self.logger.debug(
            "granted policy `{}` to user `{}`".format(policy_id, username)
        )
        return True

    def _grant_bulk_user_policies(self, username, policy_ids, expires=None):
        """
        Wrapper around gen3authz's grant_user_policies with additional logging

        Args:
            username (str): username of user in Arborist who policy should be
                            granted to
            policy_ids (set[str]): Arborist policy ids

        Return:
            bool: True if granting of policies was successful, False otherwise
        """
        try:
            resp = self.arborist_client.grant_bulk_user_policy(
                username, policy_ids, expires
            )
            if not resp:
                self.logger.error(
                    "could not grant bulk policies to user `{}`".format(username)
                )
                return False
        except ArboristError as e:
            self.logger.error(
                "could not grant bulk policies to user `{}`: {}".format(username, e)
            )
            return False
        except ArboristTimeoutError as e:
            self.logger.error(
                f"Timeout waiting for response to grant bulk policies  to user `{username}`: {e}"
                "This user will be skipped and usersync will continue."
                "As long as the timeout is not a pool/connection timeout, then "
            )
            return False
        return True

    def _determine_arborist_resource(self, dbgap_study, dbgap_config):
        """
        Determine the arborist resource path and add it to
        _self._dbgap_study_to_resources

        Args:
            dbgap_study (str): study phs identifier
            dbgap_config (dict): dictionary of config for dbgap server

        """
        default_namespaces = dbgap_config.get("study_to_resource_namespaces", {}).get(
            "_default", ["/"]
        )
        namespaces = dbgap_config.get("study_to_resource_namespaces", {}).get(
            dbgap_study, default_namespaces
        )

        self.logger.debug(f"dbgap study namespaces: {namespaces}")

        arborist_resource_namespaces = [
            namespace.rstrip("/") + "/programs/" for namespace in namespaces
        ]

        for resource_namespace in arborist_resource_namespaces:
            full_resource_path = resource_namespace + dbgap_study
            if dbgap_study not in self._dbgap_study_to_resources:
                self._dbgap_study_to_resources[dbgap_study] = []
            self._dbgap_study_to_resources[dbgap_study].append(full_resource_path)
        return arborist_resource_namespaces

    def _is_arborist_healthy(self):
        if not self.arborist_client:
            self.logger.warning("no arborist client set; skipping arborist dbgap sync")
            return False
        if not self.arborist_client.healthy():
            # TODO (rudyardrichter, 2019-01-07): add backoff/retry here
            self.logger.error(
                "arborist service is unavailable; skipping main arborist dbgap sync"
            )
            return False
        return True

    def _pick_sync_type(self, visa):
        """
        Pick type of visa to parse according to the visa provider
        """
        sync_client = None
        if visa.type in self.visa_types["ras"]:
            sync_client = self.ras_sync_client
        else:
            raise Exception(
                "Visa type {} not recognized. Configure in fence-config".format(
                    visa.type
                )
            )
        if not sync_client:
            raise Exception("Sync client for {} not configured".format(visa.type))

        return sync_client

    def sync_single_user_visas(
        self, user, ga4gh_visas, sess=None, expires=None, skip_google_updates=False
    ):
        """
        Sync a single user's visas during login or DRS/data access

        IMPORTANT NOTE: THIS DOES NOT VALIDATE THE VISA. ENSURE THIS IS DONE
                        BEFORE THIS.

        Args:
            user (userdatamodel.user.User): Fence user whose visas'
                                            authz info is being synced
            ga4gh_visas (list): a list of fence.models.GA4GHVisaV1 objects
                                that are ALREADY VALIDATED
            sess (sqlalchemy.orm.session.Session): database session
            expires (int): time at which synced Arborist policies and
                           inclusion in any GBAG are set to expire
            skip_google_updates (bool): True if google group updates should be skipped. False if otherwise.

        Return:
            list of successfully parsed visas
        """
        self.ras_sync_client = RASVisa(logger=self.logger)
        dbgap_config = self.dbGaP[0]
        parse_consent_code = self._get_parse_consent_code(dbgap_config)
        enable_common_exchange_area_access = dbgap_config.get(
            "enable_common_exchange_area_access", False
        )
        study_common_exchange_areas = dbgap_config.get(
            "study_common_exchange_areas", {}
        )

        try:
            user_yaml = UserYAML.from_file(
                self.sync_from_local_yaml_file, encrypted=False, logger=self.logger
            )
        except (EnvironmentError, AssertionError) as e:
            self.logger.error(str(e))
            self.logger.error("aborting early")
            raise

        user_projects = dict()
        projects = {}
        info = {}
        parsed_visas = []

        for visa in ga4gh_visas:
            project = {}
            visa_type = self._pick_sync_type(visa)
            encoded_visa = visa.ga4gh_visa

            try:
                project, info = visa_type._parse_single_visa(
                    user,
                    encoded_visa,
                    visa.expires,
                    parse_consent_code,
                )
            except Exception:
                self.logger.warning(
                    f"ignoring unsuccessfully parsed or expired visa: {encoded_visa}"
                )
                continue

            projects = {**projects, **project}
            parsed_visas.append(visa)

        info["user_id"] = user.id
        info["username"] = user.username
        user_projects[user.username] = projects

        user_projects = self.parse_projects(user_projects)

        if parse_consent_code and enable_common_exchange_area_access:
            self.logger.info(
                f"using study to common exchange area mapping: {study_common_exchange_areas}"
            )

        self._process_user_projects(
            user_projects,
            enable_common_exchange_area_access,
            study_common_exchange_areas,
            dbgap_config,
            sess,
        )

        if parse_consent_code:
            self._grant_all_consents_to_c999_users(
                user_projects, user_yaml.project_to_resource
            )

        if user_projects:
            self.sync_to_storage_backend(
                user_projects,
                info,
                sess,
                expires=expires,
                skip_google_updates=skip_google_updates,
            )
        else:
            self.logger.info("No users for syncing")

        # update arborist db (user access)
        if self.arborist_client:
            self.logger.info("Synchronizing arborist with authorization info...")
            success = self._update_authz_in_arborist(
                sess,
                user_projects,
                user_yaml=user_yaml,
                single_user_sync=True,
                expires=expires,
            )
            if success:
                self.logger.info(
                    "Finished synchronizing authorization info to arborist"
                )
            else:
                self.logger.error(
                    "Could not synchronize authorization info successfully to arborist"
                )
        else:
            self.logger.error("No arborist client set; skipping arborist sync")

        return parsed_visas

uc-cdis / fence / 24903485277

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