download.py

import bson
import json
import pytz
import os.path
import tarfile
import datetime
import cStringIO

from . import base
from . import config
from . import util
from . import validators

log = config.log


def _filter_check(property_filter, property_values):
    minus = set(property_filter.get('-', []))
    plus = set(property_filter.get('+', []))
    if not minus.isdisjoint(property_values):
        return False
    if plus and plus.isdisjoint(property_values):
        return False
    return True


def _append_targets(targets, container, prefix, total_size, total_cnt, optional, data_path, filters):
    for f in container.get('files', []):
        if filters:
            filtered = True
            for filter_ in filters:
                type_as_list = [f['type']] if f.get('type') else []
                if (
                    _filter_check(filter_.get('tags', {}), f.get('tags', [])) and
                    _filter_check(filter_.get('types', {}), type_as_list)
                    ):
                    filtered = False
                    break
            if filtered:
                continue
        if optional or not f.get('optional', False):
            filepath = os.path.join(data_path, util.path_from_hash(f['hash']))
            if os.path.exists(filepath): # silently skip missing files
                targets.append((filepath, prefix + '/' + f['name'], f['size']))
                total_size += f['size']
                total_cnt += 1
    return total_size, total_cnt

def symlinkarchivestream(ticket, data_path):
    for filepath, arcpath, _ in ticket['target']:
        t = tarfile.TarInfo(name=arcpath)
        t.type = tarfile.SYMTYPE
        t.linkname = os.path.relpath(filepath, data_path)
        yield t.tobuf()
    stream = cStringIO.StringIO()
    with tarfile.open(mode='w|', fileobj=stream) as archive:
        pass
    yield stream.getvalue() # get tar stream trailer
    stream.close()

def archivestream(ticket):
    BLOCKSIZE = 512
    CHUNKSIZE = 2**20  # stream files in 1MB chunks
    stream = cStringIO.StringIO()
    with tarfile.open(mode='w|', fileobj=stream) as archive:
        for filepath, arcpath, _ in ticket['target']:
            yield archive.gettarinfo(filepath, arcpath).tobuf()
            with open(filepath, 'rb') as fd:
                for chunk in iter(lambda: fd.read(CHUNKSIZE), ''):
                    yield chunk
                if len(chunk) % BLOCKSIZE != 0:
                    yield (BLOCKSIZE - (len(chunk) % BLOCKSIZE)) * b'\0'
    yield stream.getvalue() # get tar stream trailer
    stream.close()

class Download(base.RequestHandler):

    def _bulk_preflight_archivestream(self, file_refs):
        data_path = config.get_item('persistent', 'data_path')
        arc_prefix = 'sdm'
        file_cnt = 0
        total_size = 0
        targets = []

        for fref in file_refs:
            cont_name   = fref.get('container_name','')+'s'
            cont_id     = fref.get('container_id', '')
            filename    = fref.get('filename', '')

            if cont_name not in ['projects', 'sessions', 'acquisitions']:
                self.abort(400, 'Bulk download only supports files in projects, sessions and acquisitions')
            file_obj = None
            try:
                # Try to find the file reference in the database (filtering on user permissions)
                bid = bson.ObjectId(cont_id)
                query = {'_id': bid}
                if not self.superuser_request:
                    query['permissions._id'] = self.uid
                file_obj = config.db[cont_name].find_one(
                    query,
                    {'files': { '$elemMatch': {
                        'name': filename
                    }}
                })['files'][0]
            except:
                # self.abort(404, 'File {} on Container {} {} not found'.format(filename, cont_name, cont_id))
                # silently skip missing files/files user does not have access to
                continue

            filepath = os.path.join(data_path, util.path_from_hash(file_obj['hash']))
            if os.path.exists(filepath): # silently skip missing files
                targets.append((filepath, cont_name+'/'+cont_id+'/'+file_obj['name'], file_obj['size']))
                total_size += file_obj['size']
                file_cnt += 1

        if len(targets) > 0:
            filename = arc_prefix + datetime.datetime.utcnow().strftime('%Y%m%d_%H%M%S') + '.tar'
            ticket = util.download_ticket(self.request.client_addr, 'batch', targets, filename, total_size)
            config.db.downloads.insert_one(ticket)
            return {'ticket': ticket['_id'], 'file_cnt': file_cnt, 'size': total_size}
        else:
            self.abort(404, 'No files requested could be found')




    def _preflight_archivestream(self, req_spec, collection=None):
        data_path = config.get_item('persistent', 'data_path')
        arc_prefix = 'sdm'
        file_cnt = 0
        total_size = 0
        targets = []

        used_subpaths = {}
        base_query = {}
        if not self.superuser_request:
            base_query['permissions._id'] = self.uid

        for item in req_spec['nodes']:

            item_id = bson.ObjectId(item['_id'])
            base_query['_id'] = item_id

            if item['level'] == 'project':
                project = config.db.projects.find_one(base_query, ['group', 'label', 'files'])
                if not project:
                    # silently skip missing objects/objects user does not have access to
                    continue

                prefix = '/'.join([arc_prefix, project['group'], project['label']])
                total_size, file_cnt = _append_targets(targets, project, prefix, total_size, file_cnt, req_spec['optional'], data_path, req_spec.get('filters'))

                sessions = config.db.sessions.find({'project': item_id}, ['label', 'files', 'uid', 'timestamp', 'timezone'])
                session_dict = {session['_id']: session for session in sessions}
                acquisitions = config.db.acquisitions.find({'session': {'$in': session_dict.keys()}}, ['label', 'files', 'session', 'uid', 'timestamp', 'timezone'])
                session_prefixes = {}

                for session in session_dict.itervalues():
                    session_prefix = prefix + '/' + self._path_from_container(session, used_subpaths, project['_id'])
                    session_prefixes[session['_id']] = session_prefix
                    total_size, file_cnt = _append_targets(targets, session, session_prefix, total_size, file_cnt, req_spec['optional'], data_path, req_spec.get('filters'))

                for acq in acquisitions:
                    session = session_dict[acq['session']]
                    acq_prefix = session_prefixes[session['_id']] + '/' + self._path_from_container(acq, used_subpaths, session['_id'])
                    total_size, file_cnt = _append_targets(targets, acq, acq_prefix, total_size, file_cnt, req_spec['optional'], data_path, req_spec.get('filters'))

            elif item['level'] == 'session':
                session = config.db.sessions.find_one(base_query, ['project', 'label', 'files', 'uid', 'timestamp', 'timezone'])
                if not session:
                    # silently skip missing objects/objects user does not have access to
                    continue

                project = config.db.projects.find_one({'_id': session['project']}, ['group', 'label'])
                prefix = project['group'] + '/' + project['label'] + '/' + self._path_from_container(session, used_subpaths, project['_id'])
                total_size, file_cnt = _append_targets(targets, session, prefix, total_size, file_cnt, req_spec['optional'], data_path, req_spec.get('filters'))

                # If the param `collection` holding a collection id is not None, filter out acquisitions that are not in the collection
                a_query = {'session': item_id}
                if collection:
                    a_query['collections'] = bson.ObjectId(collection)
                acquisitions = config.db.acquisitions.find(a_query, ['label', 'files', 'uid', 'timestamp', 'timezone'])

                for acq in acquisitions:
                    acq_prefix = prefix + '/' + self._path_from_container(acq, used_subpaths, session['_id'])
                    total_size, file_cnt = _append_targets(targets, acq, acq_prefix, total_size, file_cnt, req_spec['optional'], data_path, req_spec.get('filters'))

            elif item['level'] == 'acquisition':
                acq = config.db.acquisitions.find_one(base_query, ['session', 'label', 'files', 'uid', 'timestamp', 'timezone'])
                if not acq:
                    # silently skip missing objects/objects user does not have access to
                    continue

                session = config.db.sessions.find_one({'_id': acq['session']}, ['project', 'label', 'uid', 'timestamp', 'timezone'])
                project = config.db.projects.find_one({'_id': session['project']}, ['group', 'label'])
                prefix = project['group'] + '/' + project['label'] + '/' + self._path_from_container(session, used_subpaths, project['_id']) + '/' + self._path_from_container(acq, used_subpaths, session['_id'])
                total_size, file_cnt = _append_targets(targets, acq, prefix, total_size, file_cnt, req_spec['optional'], data_path, req_spec.get('filters'))

        if len(targets) > 0:
            log.debug(json.dumps(targets, sort_keys=True, indent=4, separators=(',', ': ')))
            filename = 'sdm_' + datetime.datetime.utcnow().strftime('%Y%m%d_%H%M%S') + '.tar'
            ticket = util.download_ticket(self.request.client_addr, 'batch', targets, filename, total_size)
            config.db.downloads.insert_one(ticket)
            return {'ticket': ticket['_id'], 'file_cnt': file_cnt, 'size': total_size}
        else:
            self.abort(404, 'No requested containers could be found')

    def _path_from_container(self, container, used_subpaths, parent_id):
        def _find_new_path(path, list_used_subpaths):
            """from the input path finds a path that hasn't been used"""
            if path not in list_used_subpaths:
                return path
            i = 0
            while True:
                modified_path = path + '_' + str(i)
                if modified_path not in list_used_subpaths:
                    return modified_path
                i += 1
        path = None
        if not path and container.get('label'):
            path = container['label']
        if not path and container.get('timestamp'):
            timezone = container.get('timezone')
            if timezone:
                path = pytz.timezone('UTC').localize(container['timestamp']).astimezone(pytz.timezone(timezone)).strftime('%Y%m%d_%H%M')
            else:
                path = container['timestamp'].strftime('%Y%m%d_%H%M')
        if not path and container.get('uid'):
            path = container['uid']
        if not path:
            path = 'untitled'
        path = _find_new_path(path, used_subpaths.get(parent_id, []))
        used_subpaths[parent_id] = used_subpaths.get(parent_id, []) + [path]
        return path

    def download(self):
        """
        .. http:get::  /api/download

            Download GET Description...

            :statuscode 400: describe me
            :statuscode 404: describe me


        .. http:post:: /api/download

            Download POST Description...

            :statuscode 400: describe me
            :statuscode 404: describe me
        """


        """
        In downloads we use filters in the payload to exclude/include files.
        To pass a single filter, each of its conditions should be satisfied.
        If a file pass at least one filter, it is included in the targets.
        For example:

        download_payload = {
            'optional': True,
            'nodes': [{'level':'project', '_id':project_id}],
            'filters':[{
                'tags':{'+':['incomplete']}
            },
            {
                'types':{'-':['dicom']}
            }]
        }
        will download files with tag 'incomplete' OR type different from 'dicom'

        download_payload = {
            'optional': True,
            'nodes': [{'level':'project', '_id':project_id}],
            'filters':[{
                'tags':{'+':['incomplete']},
                'types':{'+':['dicom']}
            }]
        }
        will download only files with tag 'incomplete' AND type different from 'dicom'
        """
        ticket_id = self.get_param('ticket')
        if ticket_id:
            ticket = config.db.downloads.find_one({'_id': ticket_id})
            if not ticket:
                self.abort(404, 'no such ticket')
            if ticket['ip'] != self.request.client_addr:
                self.abort(400, 'ticket not for this source IP')
            if self.get_param('symlinks'):
                self.response.app_iter = symlinkarchivestream(ticket, config.get_item('persistent', 'data_path'))
            else:
                self.response.app_iter = archivestream(ticket)
            self.response.headers['Content-Type'] = 'application/octet-stream'
            self.response.headers['Content-Disposition'] = 'attachment; filename=' + str(ticket['filename'])
            for project_id in ticket['projects']:
                config.db.projects.update_one({'_id': project_id}, {'$inc': {'counter': 1}})
        else:
            req_spec = self.request.json_body

            if self.is_true('bulk'):
                return self._bulk_preflight_archivestream(req_spec.get('files', []))
            else:
                payload_schema_uri = validators.schema_uri('input', 'download.json')
                validator = validators.from_schema_path(payload_schema_uri)
                validator(req_spec, 'POST')
                log.debug(json.dumps(req_spec, sort_keys=True, indent=4, separators=(',', ': ')))

                return self._preflight_archivestream(req_spec, collection=self.get_param('collection'))