pybis.py

                "@type": identifierType
            }
        return object_id

    @staticmethod
    def data_set_to_data_set_id(data_set):
        if isinstance(data_set, str):
            code = data_set
        else:
            code = data_set.permId
        return {
            "permId": code,
            "@type": "as.dto.dataset.id.DataSetPermId"
        }

    def external_data_managment_system_to_dms_id(self, dms):
        if isinstance(dms, str):
            dms_id = {
                "permId": dms,
                "@type": "as.dto.externaldms.id.ExternalDmsPermId"
            }
        else:
            dms_id = {
                "identifier": dms.code,
                "@type": "as.dto.sample.id.SampleIdentifier"
            }
        return dms_id

    def new_sample(self, type, props=None, **kwargs):
        """ Creates a new sample of a given sample type.
        """
        return Sample(self, self.get_sample_type(type), None, props, **kwargs)

    new_object = new_sample # Alias

    def new_dataset(self, type=None, files=None, props=None, folder=None, **kwargs):
        """ Creates a new dataset of a given sample type.
        """
        if files is None:
            raise ValueError('please provide at least one file')
        elif isinstance(files, str):
            files = [files]

        type_obj = self.get_dataset_type(type.upper())

        return DataSet(self, type=type_obj, files=files, folder=folder, props=props, **kwargs)
    
    def new_semantic_annotation(self, entityType=None, propertyType=None, **kwargs):
        return SemanticAnnotation(openbis_obj=self, isNew=True, entityType=entityType, propertyType=propertyType, **kwargs)    

    def _get_dss_url(self, dss_code=None):
        """ internal method to get the downloadURL of a datastore.
        """
        dss = self.get_datastores()
        if dss_code is None:
            return dss['downloadUrl'][0]
        else:
            return dss[dss['code'] == dss_code]['downloadUrl'][0]

    def upload_files(self, datastore_url=None, files=None, folder=None, wait_until_finished=False):

        if datastore_url is None:
            datastore_url = self._get_dss_url()

        if files is None:
            raise ValueError("Please provide a filename.")

        if folder is None:
            # create a unique foldername
            folder = time.strftime('%Y-%m-%d_%H-%M-%S')

        if isinstance(files, str):
            files = [files]

        self.files = files
        self.startByte = 0
        self.endByte = 0

        # define a queue to handle the upload threads
        queue = DataSetUploadQueue()

        real_files = []
        for filename in files:
            if os.path.isdir(filename):
                real_files.extend(
                    [os.path.join(dp, f) for dp, dn, fn in os.walk(os.path.expanduser(filename)) for f in fn])
            else:
                real_files.append(os.path.join(filename))

        # compose the upload-URL and put URL and filename in the upload queue 
        for filename in real_files:
            file_in_wsp = os.path.join(folder, filename)
            self.files_in_wsp.append(file_in_wsp)
            upload_url = (
                datastore_url + '/session_workspace_file_upload'
                + '?filename=' + os.path.join(folder, quote(filename))
                + '&id=1'
                + '&startByte=0&endByte=0'
                + '&sessionID=' + self.token
            )
            queue.put([upload_url, filename, self.verify_certificates])

        # wait until all files have uploaded
        if wait_until_finished:
            queue.join()

        # return files with full path in session workspace
        return self.files_in_wsp


class DataSetUploadQueue():
    def __init__(self, workers=20):
        # maximum files to be uploaded at once
        self.upload_queue = Queue()

        # define number of threads and start them
        for t in range(workers):
            t = Thread(target=self.upload_file)
            t.daemon = True
            t.start()

    def put(self, things):
        """ expects a list [url, filename] which is put into the upload queue
        """
        self.upload_queue.put(things)

    def join(self):
        """ needs to be called if you want to wait for all uploads to be finished
        """
        self.upload_queue.join()

    def upload_file(self):
        while True:
            # get the next item in the queue
            upload_url, filename, verify_certificates = self.upload_queue.get()

            filesize = os.path.getsize(filename)

            # upload the file to our DSS session workspace
            with open(filename, 'rb') as f:
                resp = requests.post(upload_url, data=f, verify=verify_certificates)
                resp.raise_for_status()
                data = resp.json()
                assert filesize == int(data['size'])

            # Tell the queue that we are done
            self.upload_queue.task_done()


class DataSetDownloadQueue():
    def __init__(self, workers=20):
        # maximum files to be downloaded at once
        self.download_queue = Queue()

        # define number of threads
        for t in range(workers):
            t = Thread(target=self.download_file)
            t.daemon = True
            t.start()

    def put(self, things):
        """ expects a list [url, filename] which is put into the download queue
        """
        self.download_queue.put(things)

    def join(self):
        """ needs to be called if you want to wait for all downloads to be finished
        """
        self.download_queue.join()

    def download_file(self):
        while True:
            url, filename, file_size, verify_certificates = self.download_queue.get()
            # create the necessary directory structure if they don't exist yet
            os.makedirs(os.path.dirname(filename), exist_ok=True)

            # request the file in streaming mode
            r = requests.get(url, stream=True, verify=verify_certificates)
            with open(filename, 'wb') as f:
                for chunk in r.iter_content(chunk_size=1024):
                    if chunk:  # filter out keep-alive new chunks
                        f.write(chunk)

            assert os.path.getsize(filename) == int(file_size)
            self.download_queue.task_done()


class OpenBisObject():
    def __init__(self, openbis_obj, type, data=None, props=None, **kwargs):
        self.__dict__['openbis'] = openbis_obj
        self.__dict__['type'] = type
        self.__dict__['p'] = PropertyHolder(openbis_obj, type)
        self.__dict__['a'] = AttrHolder(openbis_obj, 'DataSet', type)

        # existing OpenBIS object
        if data is not None:
            self._set_data(data)

        if props is not None:
            for key in props:
                setattr(self.p, key, props[key])

        if kwargs is not None:
            for key in kwargs:
                setattr(self, key, kwargs[key])

    def __eq__(self, other):
        return str(self) == str(other)

    def __ne__(self, other):
        return str(self) != str(other)

    def _set_data(self, data):
        # assign the attribute data to self.a by calling it
        # (invoking the AttrHolder.__call__ function)
        self.a(data)
        self.__dict__['data'] = data

        # put the properties in the self.p namespace (without checking them)
        if 'properties' in data:
            for key, value in data['properties'].items():
                self.p.__dict__[key.lower()] = value

    @property
    def attrs(self):
        return self.__dict__['a']

    @property
    def space(self):
        try:
            return self.openbis.get_space(self._space['permId'])
        except Exception:
            pass

    @property
    def project(self):
        try:
            return self.openbis.get_project(self._project['identifier'])
        except Exception:
            pass

    @property
    def experiment(self):
        try:
            return self.openbis.get_experiment(self._experiment['identifier'])
        except Exception:
            pass

    @property
    def sample(self):
        try:
            return self.openbis.get_sample(self._sample['identifier'])
        except Exception:
            pass

    object = sample # Alias

    def __getattr__(self, name):
        return getattr(self.__dict__['a'], name)

    def __setattr__(self, name, value):
        if name in ['set_properties', 'set_tags', 'add_tags']:
            raise ValueError("These are methods which should not be overwritten")

        setattr(self.__dict__['a'], name, value)

    def _repr_html_(self):
        """Print all the assigned attributes (identifier, tags, etc.) in a nicely formatted table. See
        AttributeHolder class.
        """
        return self.a._repr_html_()

    def __repr__(self):
        """same thing as _repr_html_() but for IPython
        """
        return self.a.__repr__()


class LinkedData():
    def __init__(self, data=None):
        self.data = data if data is not None else []
        self.attrs = ['externalCode', 'contentCopies']

    def __dir__(self):
        return self.attrs

    def __getattr__(self, name):
        if name in self.attrs:
            if name in self.data:
                return self.data[name]
        else:
            return ''


class PhysicalData():
    def __init__(self, data=None):
        if data is None:
            data = []
        self.data = data
        self.attrs = ['speedHint', 'complete', 'shareId', 'size',
                      'fileFormatType', 'storageFormat', 'location', 'presentInArchive',
                      'storageConfirmation', 'locatorType', 'status']

    def __dir__(self):
        return self.attrs

    def __getattr__(self, name):
        if name in self.attrs:
            if name in self.data:
                return self.data[name]
        else:
            return ''

    def _repr_html_(self):
        html = """
            <table border="1" class="dataframe">
            <thead>
                <tr style="text-align: right;">
                <th>attribute</th>
                <th>value</th>
                </tr>
            </thead>
            <tbody>
        """

        for attr in self.attrs:
            html += "<tr> <td>{}</td> <td>{}</td> </tr>".format(
                attr, getattr(self, attr, '')
            )

        html += """
            </tbody>
            </table>
        """
        return html

    def __repr__(self):

        headers = ['attribute', 'value']
        lines = []
        for attr in self.attrs:
            lines.append([
                attr,
                getattr(self, attr, '')
            ])
        return tabulate(lines, headers=headers)


class DataSet(OpenBisObject):
    """ DataSet are openBIS objects that contain the actual files.
    """

    def __init__(self, openbis_obj, type=type, data=None, files=None, folder=None, props=None, **kwargs):
        super(DataSet, self).__init__(openbis_obj, type, data, props, **kwargs)

        # existing DataSet
        if data is not None:
            if data['physicalData'] is None:
                self.__dict__['shareId'] = None
                self.__dict__['location'] = None
            else:
                self.__dict__['shareId'] = data['physicalData']['shareId']
                self.__dict__['location'] = data['physicalData']['location']
        
        # new DataSet
        if files is not None:
            self.__dict__['files'] = files

        self.__dict__['folder'] = folder


    def __str__(self):
        return self.data['code']

    def __dir__(self):
        return [
            'props', 'get_parents()', 'get_children()', 
            'add_parents()', 'add_children()', 'del_parents()', 'del_children()',
            'sample', 'experiment', 'physicalData', 'linkedData',
            'tags', 'set_tags()', 'add_tags()', 'del_tags()',
            'add_attachment()', 'get_attachments()', 'download_attachments()',
            "get_files(start_folder='/')", 'file_list',
            'download(files=None, destination=None, wait_until_finished=True)', 
            'status', 'archive()', 'unarchive()', 'data'
        ]

    def __setattr__(self, name, value):
        if name in ['folder']:
            self.__dict__[name] = value
        else:
            super(DataSet, self).__setattr__(name, value)

    @property
    def props(self):
        return self.__dict__['p']

    @property
    def type(self):
        return self.__dict__['type']

    @type.setter
    def type(self, type_name):
        dataset_type = self.openbis.get_dataset_type(type_name.upper())
        self.p.__dict__['_type'] = dataset_type
        self.a.__dict__['_type'] = dataset_type

    @property
    def physicalData(self):
        if 'physicalData' in self.data:
            return PhysicalData(self.data['physicalData'])

    @property
    def linkedData(self):
        if 'linkedData' in self.data:
            return LinkedData(self.data['linkedData'])

    @property
    def status(self):
        ds = self.openbis.get_dataset(self.permId)
        self.data['physicalData'] = ds.data['physicalData']
        try:
            return self.data['physicalData']['status']
        except Exception:
            return None

    def archive(self, remove_from_data_store=True):
        fetchopts = {
            "removeFromDataStore": remove_from_data_store,
            "@type": "as.dto.dataset.archive.DataSetArchiveOptions"
        }
        self.archive_unarchive('archiveDataSets', fetchopts)
        print("DataSet {} archived".format(self.permId))

    def unarchive(self):
        fetchopts = {
            "@type": "as.dto.dataset.unarchive.DataSetUnarchiveOptions"
        }
        self.archive_unarchive('unarchiveDataSets', fetchopts)
        print("DataSet {} unarchived".format(self.permId))

    def archive_unarchive(self, method, fetchopts):
        dss = self.get_datastore
        payload = {}

        request = {
            "method": method,
            "params": [
                self.openbis.token,
                [{
                    "permId": self.permId,
                    "@type": "as.dto.dataset.id.DataSetPermId"
                }],
                dict(fetchopts)
            ],
        }
        resp = self.openbis._post_request(self._openbis.as_v3, request)
        return

    def set_properties(self, properties):
        self.openbis.update_dataset(self.permId, properties=properties)

    def download(self, files=None, destination=None, wait_until_finished=True, workers=10):
        """ download the actual files and put them by default in the following folder:
        __current_dir__/destination/dataset_permId/
        If no files are specified, all files of a given dataset are downloaded.
        If no destination is specified, the hostname is chosen instead.
        Files are usually downloaded in parallel, using 10 workers by default. If you want to wait until
        all the files are downloaded, set the wait_until_finished option to True.
        """

        if files == None:
            files = self.file_list
        elif isinstance(files, str):
            files = [files]

        if destination is None:
            destination = self.openbis.hostname

        base_url = self.data['dataStore']['downloadUrl'] + '/datastore_server/' + self.permId + '/'

        queue = DataSetDownloadQueue(workers=workers)

        # get file list and start download
        for filename in files:
            file_info = self.get_file_list(start_folder=filename)
            file_size = file_info[0]['fileSize']
            download_url = base_url + filename + '?sessionID=' + self.openbis.token
            filename_dest = os.path.join(destination, self.permId, filename)
            queue.put([download_url, filename_dest, file_size, self.openbis.verify_certificates])

        # wait until all files have downloaded
        if wait_until_finished:
            queue.join()

        print("Files downloaded to: %s" % os.path.join(destination, self.permId))

    @property
    def folder(self):
        return self.__dict__['folder']

    @property
    def file_list(self):
        """returns the list of files including their directories as an array of strings. Just folders are not
        listed.
        """
        files = []
        for file in self.get_file_list(recursive=True):
            if file['isDirectory']:
                pass
            else:
                files.append(file['pathInDataSet'])
        return files

    def get_files(self, start_folder='/'):
        """Returns a DataFrame of all files in this dataset
        """

        def createRelativePath(pathInDataSet):
            if self.shareId is None:
                return ''
            else:
                return os.path.join(self.shareId, self.location, pathInDataSet)

        def signed_to_unsigned(sig_int):
            """openBIS delivers crc32 checksums as signed integers.
            If the number is negative, we just have to add 2**32
            We display the hex number to match with the classic UI
            """
            if sig_int < 0:
                sig_int += 2 ** 32
            return "%x" % (sig_int & 0xFFFFFFFF)

        files = self.get_file_list(start_folder=start_folder)
        df = DataFrame(files)
        df['relativePath'] = df['pathInDataSet'].map(createRelativePath)
        df['crc32Checksum'] = df['crc32Checksum'].fillna(0.0).astype(int).map(signed_to_unsigned)
        return df[['isDirectory', 'pathInDataSet', 'fileSize', 'crc32Checksum']]

    def get_file_list(self, recursive=True, start_folder="/"):
        """Lists all files of a given dataset. You can specifiy a start_folder other than "/".
        By default, all directories and their containing files are listed recursively. You can
        turn off this option by setting recursive=False.
        """
        request = {
            "method": "listFilesForDataSet",
            "params": [
                self.openbis.token,
                self.permId,
                start_folder,
                recursive,
            ],
            "id": "1"
        }

        resp = requests.post(
            self.data["dataStore"]["downloadUrl"] + '/datastore_server/rmi-dss-api-v1.json',
            json.dumps(request),
            verify=self.openbis.verify_certificates
        )

        if resp.ok:
            data = resp.json()
            if 'error' in data:
                raise ValueError('Error from openBIS: ' + data['error']['message'])
            elif 'result' in data:
                return data['result']
            else:
                raise ValueError('request to openBIS did not return either result nor error')
        else:
            raise ValueError('internal error while performing post request')


    def _generate_plugin_request(self, dss):
        """generates a request to activate the dataset-uploader ingestion plugin to
        register our files as a new dataset
        """

        sample_identifier = None
        if self.sample is not None:
            sample_identifier = self.sample.identifier

        experiment_identifier = None
        if self.experiment is not None:
            experiment_identifier = self.experiment.identifier

        parentIds = self.parents

        dataset_type = self.type.code
        properties = self.props.all_nonempty()

        request = {
            "method": "createReportFromAggregationService",
            "params": [
                self.openbis.token,
                dss,
                PYBIS_PLUGIN,
                {
                    "method" : "insertDataSet",
                    "sampleIdentifier" : sample_identifier,
                    "experimentIdentifier" : experiment_identifier,
                    "dataSetType" : dataset_type,
                    "folderName" : self.folder,
                    "fileNames" : self.files,
                    "isZipDirectoryUpload" : False,
                    "properties" : properties,
                    "parentIdentifiers": parentIds
                }
            ],
        }
        return request


    def save(self):
        if self.is_new:
            if self.files is None or len(self.files) == 0:
                raise ValueError('Cannot register a dataset without a file. Please provide at least one file')

            if self.sample is None and self.experiment is None:
                raise ValueError('A DataSet must be either connected to a Sample or an Experiment')

            # upload the data to the user session workspace
            datastores = self.openbis.get_datastores()

            self.openbis.upload_files(
                datastore_url= datastores['downloadUrl'][0],
                files=self.files,
                folder='',
                wait_until_finished=True
            )

            # activate the ingestion plugin, as soon as the data is uploaded
            request = self._generate_plugin_request(dss=datastores['code'][0])

            resp = self.openbis._post_request(self.openbis.reg_v1, request)

            if resp['rows'][0][0]['value'] == 'OK':
                permId = resp['rows'][0][2]['value']
                if permId is None or permId == '': 
                    self.__dict__['is_new'] = False
                    print("DataSet successfully created. Because you connected to an openBIS version older than 16.05.04, you cannot update the object.")
                else:
                    new_dataset_data = self.openbis.get_dataset(permId, only_data=True)
                    self._set_data(new_dataset_data)
                    print("DataSet successfully created.")
            else:
                raise ValueError('Error while creating the DataSet: ' + resp['rows'][0][1]['value'])

            self.__dict__['_is_new'] = False

            
        else:
            request = self._up_attrs()
            props = self.p._all_props()
            request["params"][1][0]["properties"] = props
            request["params"][1][0].pop('parentIds')
            request["params"][1][0].pop('childIds')

            self.openbis._post_request(self.openbis.as_v3, request)
            print("DataSet successfully updated.")


class AttrHolder():
    """ General class for both samples and experiments that hold all common attributes, such as:
    - space
    - project
    - experiment (sample)
    - samples (experiment)
    - dataset
    - parents (sample, dataset)
    - children (sample, dataset)
    - tags
    """

    def __init__(self, openbis_obj, entity, type=None):
        self.__dict__['_openbis'] = openbis_obj
        self.__dict__['_entity'] = entity

        if type is not None:
            self.__dict__['_type'] = type.data

        self.__dict__['_allowed_attrs'] = _definitions(entity)['attrs']
        self.__dict__['_identifier'] = None
        self.__dict__['_is_new'] = True
        self.__dict__['_tags'] = []

    def __call__(self, data):
        """This internal method is invoked when an existing object is loaded.
        Instead of invoking a special method we «call» the object with the data
           self(data)
        which automatically invokes this method.
        Since the data comes from openBIS, we do not have to check it (hence the
        self.__dict__ statements to prevent invoking the __setattr__ method)
        Internally data is stored with an underscore, e.g.
            sample._space --> { '@id': 4,
                                '@type': 'as.dto.space.id.SpacePermId',
                                'permId': 'MATERIALS' }
        but when fetching the attribute without the underscore, we only return
        the relevant data for the user:
            sample.space  --> 'MATERIALS'
        """
        self.__dict__['_is_new'] = False
        for attr in self._allowed_attrs:
            if attr in ["code", "permId", "identifier",
                        "type", "container", "components"]:
                self.__dict__['_' + attr] = data.get(attr, None)

            elif attr in ["space"]:
                d = data.get(attr, None)
                if d is not None:
                    d = d['permId']
                self.__dict__['_' + attr] = d

            elif attr in ["sample", "experiment", "project"]:
                d = data.get(attr, None)
                if d is not None:
                    d = d['identifier']
                self.__dict__['_' + attr] = d

            elif attr in ["parents", "children", "samples"]:
                self.__dict__['_' + attr] = []
                for item in data[attr]:
                    if 'identifier' in item:
                        self.__dict__['_' + attr].append(item['identifier'])
                    elif 'permId' in item:
                        self.__dict__['_' + attr].append(item['permId'])

            elif attr in ["tags"]:
                tags = []
                for item in data[attr]:
                    tags.append({
                        "code": item['code'],
                        "@type": "as.dto.tag.id.TagCode"
                    })
                self.__dict__['_tags'] = tags
                self.__dict__['_prev_tags'] = copy.deepcopy(tags)
            else:
                self.__dict__['_' + attr] = data.get(attr, None)

    def _new_attrs(self):
        """Returns the Python-equivalent JSON request when a new object is created.
        It is used internally by the save() method of a newly created object.
        """
        defs = _definitions(self.entity)
        attr2ids = _definitions('attr2ids')

        new_obj = {
            "@type": "as.dto.{}.create.{}Creation".format(self.entity.lower(), self.entity)
        }

        for attr in defs['attrs_new']:
            items = None

            if attr == 'type':
                new_obj['typeId'] = self._type['permId']
                continue

            elif attr == 'attachments':
                attachments = getattr(self, '_new_attachments')
                if attachments is None:
                    continue
                atts_data = [attachment.get_data() for attachment in attachments]
                items = atts_data

            elif attr in defs['multi']:
                # parents, children, components, container, tags, attachments
                items = getattr(self, '_' + attr)
                if items is None:
                    items = []
            else:
                items = getattr(self, '_' + attr)

            key = None
            if attr in attr2ids:
                # translate parents into parentIds, children into childIds etc.
                key = attr2ids[attr]
            else:
                key = attr

            new_obj[key] = items

        # create a new entity
        request = {
            "method": "create{}s".format(self.entity),
            "params": [
                self.openbis.token,
                [new_obj]
            ]
        }
        return request


    def _up_attrs(self):
        """Returns the Python-equivalent JSON request when a new object is updated.
        It is used internally by the save() method of an object to be updated.
        """
        defs = _definitions(self._entity)
        attr2ids = _definitions('attr2ids')

        up_obj = {
            "@type": "as.dto.{}.update.{}Update".format(self.entity.lower(), self.entity),
            defs["identifier"]: self._permId
        }

        # look at all attributes available for that entity
        # that can be updated
        for attr in defs['attrs_up']:
            items = None

            if attr == 'attachments':
                # v3 API currently only supports adding attachments
                attachments = self.__dict__.get('_new_attachments', None)
                if attachments is None:
                    continue
                atts_data = [attachment.get_data() for attachment in attachments]

                up_obj['attachments'] = {
                    "actions": [{
                        "items": atts_data,
                        "@type": "as.dto.common.update.ListUpdateActionAdd"
                    }],
                    "@type": "as.dto.attachment.update.AttachmentListUpdateValue"
                }

            elif attr == 'tags':
                # look which tags have been added or removed and update them
                if getattr(self, '_prev_tags') is None:
                    self.__dict__['_prev_tags'] = []
                actions = []
                for tagId in self._prev_tags:
                    if tagId not in self._tags:
                        actions.append({
                            "items": [tagId],
                            "@type": "as.dto.common.update.ListUpdateActionRemove"
                        })

                for tagId in self._tags:
                    if tagId not in self._prev_tags:
                        actions.append({
                            "items": [tagId],
                            "@type": "as.dto.common.update.ListUpdateActionAdd"
                        })

                up_obj['tagIds'] = {
                    "@type": "as.dto.common.update.IdListUpdateValue",
                    "actions": actions
                }

            elif '_' + attr in self.__dict__:
                # handle multivalue attributes (parents, children, tags etc.)
                # we only cover the Set mechanism, which means we always update 
                # all items in a list
                if attr in defs['multi']:
                    items = self.__dict__.get('_' + attr, [])
                    if items == None:
                        items = []
                    up_obj[attr2ids[attr]] = {
                        "actions": [
                            {
                                "items": items,
                                "@type": "as.dto.common.update.ListUpdateActionSet",
                            }
                        ],
                        "@type": "as.dto.common.update.IdListUpdateValue"
                    }
                else:
                    # handle single attributes (space, experiment, project, container, etc.)
                    value = self.__dict__.get('_' + attr, {})
                    if value is None:
                        pass
                    elif len(value) == 0:
                        # value is {}: it means that we want this attribute to be
                        # deleted, not updated.
                        up_obj[attr2ids[attr]] = {
                            "@type": "as.dto.common.update.FieldUpdateValue",
                            "isModified": True,
                        }
                    elif 'isModified' in value and value['isModified'] == True:
                        val = {}
                        for x in ['identifier','permId','@type']:
                            if x in value:
                                val[x] = value[x]

                        up_obj[attr2ids[attr]] = {
                            "@type": "as.dto.common.update.FieldUpdateValue",
                            "isModified": True,
                            "value": val
                        }

        # update a new entity
        request = {
            "method": "update{}s".format(self.entity),
            "params": [
                self.openbis.token,
                [up_obj]
            ]
        }
        return request

    def __getattr__(self, name):
        """ handles all attribute requests dynamically. Values are returned in a sensible way,
            for example the identifiers of parents, children and components are returned
            as an array of values.
        """

        int_name = '_' + name
        if int_name in self.__dict__:
            if int_name in ['_attachments']:
                return [
                    {
                        "fileName": x['fileName'],
                        "title": x['title'],
                        "description": x['description']
                    } for x in self._attachments
                    ]
            if int_name in ['_registrator', '_modifier', '_dataProducer']:
                return self.__dict__[int_name].get('userId', None)
            elif int_name in ['_registrationDate', '_modificationDate', '_accessDate', '_dataProductionDate']:
                return format_timestamp(self.__dict__[int_name])
            # if the attribute contains a list, 
            # return a list of either identifiers, codes or
            # permIds (whatever is available first)
            elif isinstance(self.__dict__[int_name], list):
                values = []
                for item in self.__dict__[int_name]:
                    if "identifier" in item:
                        values.append(item['identifier'])
                    elif "code" in item:
                        values.append(item['code'])
                    elif "permId" in item:
                        values.append(item['permId'])
                    else:
                        pass
                return values
            # attribute contains a dictionary: same procedure as above.
            elif isinstance(self.__dict__[int_name], dict):
                if "identifier" in self.__dict__[int_name]:
                    return self.__dict__[int_name]['identifier']
                elif "code" in self.__dict__[int_name]:
                    return self.__dict__[int_name]['code']
                elif "permId" in self.__dict__[int_name]:
                    return self.__dict__[int_name]['permId']
            else:
                return self.__dict__[int_name]
        else:
            return None

    def __setattr__(self, name, value):
        """This method is always invoked whenever we assign an attribute to an
        object, e.g.
            new_sample.space = 'MATERIALS'
            new_sample.parents = ['/MATERIALS/YEAST747']
        """
        if name in ["parents", "children", "components"]:
            if not isinstance(value, list):
                value = [value]
            objs = []
            for val in value:
                if isinstance(val, str):
                    # fetch objects in openBIS, make sure they actually exists
                    obj = getattr(self._openbis, 'get_' + self._entity.lower())(val)
                    objs.append(obj)
                elif getattr(val, '_permId'):
                    # we got an existing object
                    objs.append(val)

            permids = []
            for item in objs:
                permid = item._permId
                # remove any existing @id keys to prevent jackson parser errors
                if '@id' in permid: permid.pop('@id')
                permids.append(permid)

            # setting self._parents = [{ 
            #    '@type': 'as.dto.sample.id.SampleIdentifier',
            #    'identifier': '/SPACE_NAME/SAMPLE_NAME'
            # }]
            self.__dict__['_' + name] = permids
        elif name in ["tags"]:
            self.set_tags(value)

        elif name in ["attachments"]:
            if isinstance(value, list):
                for item in value:
                    if isinstance(item, dict):
                        self.add_attachment(**item)
                    else:
                        self.add_attachment(item)

            else:
                self.add_attachment(value)

        elif name in ["space"]:
            obj = None
            if isinstance(value, str):
                # fetch object in openBIS, make sure it actually exists
                obj = getattr(self._openbis, "get_" + name)(value)
            else:
                obj = value

            self.__dict__['_' + name] = obj.data['permId']