filesystem.py

"""

Copyright (c) 2017-2022, Vanessa Sochat
All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:

* Redistributions of source code must retain the above copyright notice, this
  list of conditions and the following disclaimer.

* Redistributions in binary form must reproduce the above copyright notice,
  this list of conditions and the following disclaimer in the documentation
  and/or other materials provided with the distribution.

* Neither the name of the copyright holder nor the names of its
  contributors may be used to endorse or promote products derived from
  this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

"""
from flask import session
from expfactory.utils import write_json, mkdir_p
from expfactory.defaults import EXPFACTORY_SUBID, EXPFACTORY_DATA
from glob import glob
import uuid
import os
import sys


# DEFAULT FLAT #################################################################
# Default "database" is flat files written to the system
################################################################################
# This is an Expfactory Flask Server database plugin. It implements common
# functions (generate_subid, save_data, init_db) that should prepare a
# database and perform actions to save data to it. The functions are added
# to the main application upon initialization of the server.


def generate_subid(self, token=None):
    """assumes a flat (file system) database, organized by experiment id, and
    subject id, with data (json) organized by subject identifier
    """

    # Not headless auto-increments
    if not token:
        token = str(uuid.uuid4())

    # Headless doesn't use any folder_id, just generated token folder
    return "%s/%s" % (self.study_id, token)


def list_users(self):
    """list users, each associated with a filesystem folder"""
    folders = glob("%s/*" % (self.database))
    folders.sort()
    return [self.print_user(x) for x in folders]


def print_user(self, user):
    """print a filesystem database user. A "database" folder that might end with
    the participant status (e.g. _finished) is extracted to print in format

    [folder]                        [identifier][studyid]
    /scif/data/expfactory/xxxx-xxxx   xxxx-xxxx[studyid]

    """
    status = "active"

    if user.endswith("_finished"):
        status = "finished"

    elif user.endswith("_revoked"):
        status = "revoked"

    subid = os.path.basename(user)
    for ext in ["_revoked", "_finished"]:
        subid = subid.replace(ext, "")

    subid = "%s\t%s[%s]" % (user, subid, status)
    print(subid)
    return subid


# Actions ######################################################################


def generate_user(self, subid=None):
    """generate a new user on the filesystem, still session based so we
    create a new identifier. This function is called from the users new
    entrypoint, and it assumes we want a user generated with a token.
    since we don't have a database proper, we write the folder name to
    the filesystem
    """
    # Only generate token if subid being created
    if subid is None:
        token = str(uuid.uuid4())
        subid = self.generate_subid(token=token)

    if os.path.exists(self.data_base):  # /scif/data
        data_base = "%s/%s" % (self.data_base, subid)
        # expfactory/00001
        if not os.path.exists(data_base):
            mkdir_p(data_base)

    return data_base


def finish_user(self, subid, ext="finished"):
    """finish user will append "finished" (or other) to the data folder when
    the user has completed (or been revoked from) the battery.
    For headless, this means that the session is ended and the token
    will not work again to rewrite the result. If the user needs to update
    or redo an experiment, this can be done with a new session. Note that if
    this function is called internally by the application at experiment
    finish, the subid includes a study id (e.g., expfactory/xxxx-xxxx)
    but if called by the user, it may not (e.g., xxxx-xxxx). We check
    for this to ensure it works in both places.
    """
    if os.path.exists(self.data_base):  # /scif/data

        # Only relevant to filesystem save - the studyid is the top folder
        if subid.startswith(self.study_id):
            data_base = "%s/%s" % (self.data_base, subid)
        else:
            data_base = "%s/%s/%s" % (self.data_base, self.study_id, subid)

        # The renamed file will be here
        finished = "%s_%s" % (data_base, ext)

        # Participant already finished
        if os.path.exists(finished):
            self.logger.warning("[%s] is already finished: %s" % (subid, data_base))

        # Exists and can finish
        elif os.path.exists(data_base):
            os.rename(data_base, finished)

        # Not finished, doesn't exist
        else:
            finished = None
            self.logger.warning(
                "%s does not exist, cannot finish. %s" % (data_base, subid)
            )

    return finished


def restart_user(self, subid):
    """restart user will remove any "finished" or "revoked" extensions from
    the user folder to restart the session. This command always comes from
    the client users function, so we know subid does not start with the
    study identifer first
    """
    if os.path.exists(self.data_base):  # /scif/data/<study_id>
        data_base = "%s/%s" % (self.data_base, subid)
        for ext in ["revoked", "finished"]:
            folder = "%s_%s" % (data_base, ext)
            if os.path.exists(folder):
                os.rename(folder, data_base)
                self.logger.info("Restarting %s, folder is %s." % (subid, data_base))

        self.logger.warning(
            "%s does not have revoked or finished folder, no changes necessary."
            % (subid)
        )
        return data_base

    self.logger.warning(
        "%s does not exist, cannot restart. %s" % (self.database, subid)
    )


# Tokens #######################################################################


def validate_token(self, token):
    """retrieve a subject based on a token. Valid means we return a participant
    invalid means we return None
    """
    # A token that is finished or revoked is not valid
    subid = None
    if not token.endswith(("finished", "revoked")):
        subid = self.generate_subid(token=token)
        data_base = "%s/%s" % (self.data_base, subid)
        if not os.path.exists(data_base):
            subid = None
    return subid


def refresh_token(self, subid):
    """refresh or generate a new token for a user. If the user is finished,
    this will also make the folder available again for using."""
    if os.path.exists(self.data_base):  # /scif/data
        data_base = "%s/%s" % (self.data_base, subid)
        if os.path.exists(data_base):
            refreshed = "%s/%s" % (self.database, str(uuid.uuid4()))
            os.rename(data_base, refreshed)
            return refreshed
        self.logger.warning("%s does not exist, cannot rename %s" % (data_base, subid))
    else:
        self.logger.warning(
            "%s does not exist, cannot rename %s" % (self.database, subid)
        )


def revoke_token(self, subid):
    """revoke a presently active token, meaning append _revoked to it."""
    return self.finish_user(subid, ext="revoked")


def save_data(self, session, exp_id, content):
    """save data will obtain the current subid from the session, and save it
    depending on the database type. Currently we just support flat files"""

    subid = session.get("subid")

    # We only attempt save if there is a subject id, set at start
    data_file = None
    if subid is not None:

        data_base = "%s/%s" % (self.data_base, subid)

        # If not running in headless, ensure path exists
        if not self.headless and not os.path.exists(data_base):
            mkdir_p(data_base)

        # Conditions for saving:
        do_save = False

        # If headless with token pre-generated OR not headless
        if self.headless and os.path.exists(data_base) or not self.headless:
            do_save = True
        if data_base.endswith(("revoked", "finished")):
            do_save = False

        # If headless with token pre-generated OR not headless
        if do_save is True:
            data_file = "%s/%s-results.json" % (data_base, exp_id)
            if os.path.exists(data_file):
                self.logger.warning("%s exists, and is being overwritten." % data_file)
            write_json(content, data_file)

    return data_file


def init_db(self):
    """init_db for the filesystem ensures that the base folder (named
    according to the studyid) exists.
    """
    self.session = None

    if not os.path.exists(self.data_base):
        mkdir_p(self.data_base)

    self.database = "%s/%s" % (self.data_base, self.study_id)
    if not os.path.exists(self.database):
        mkdir_p(self.database)