pybis.py

        """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'] )
            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')


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


    def __call__(self, data):
        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
                import copy
                self.__dict__['_prev_tags'] = copy.deepcopy(tags)
            else:
                self.__dict__['_'+attr] = data.get(attr, None)


    def _new_attrs(self):
        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 == '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']:
                items = getattr(self, '_'+attr)
                if items is None:
                    items = []
            else:
                items = getattr(self, '_'+attr)

            key = None
            if attr in attr2ids:
                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):
        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 ]

                if self._is_new:
                    up_obj['attachments'] = atts_data
                else:
                    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
                    else:
                        isModified=False
                        if 'isModified' in value:
                            isModified=True
                            del value['isModified']
                        
                        up_obj[attr2ids[attr]] = {
                           "@type": "as.dto.common.update.FieldUpdateValue",
                           "isModified": isModified,
                           "value": value,
                        }

        # 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']:
                return self.__dict__[int_name].get('userId', None)
            elif int_name in ['_registrationDate', '_modificationDate']:
                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):
        if name in ["parents", "children", "components"]:
            if not isinstance(value, list):
                value = [value]
            objs = []
            for val in value:
                # fetch objects in openBIS, make sure they actually exists
                obj = getattr(self._openbis, 'get_'+self._entity.lower())(val)
                objs.append(obj)
            self.__dict__['_'+name] = {
                "@type": "as.dto.common.update.IdListUpdateValue",
                "actions": [{
                    "@type": "as.dto.common.update.ListUpdateActionSet",
                    "items": [item._permId for item in objs]
                }]
            }
        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 ["sample", "experiment"]:
            if isinstance(value, object):
                obj = value
            else:
                # fetch object in openBIS, make sure it actually exists
                obj = getattr(self._openbis, "get_"+name)(value)

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

            # mark attribute as modified, if it's an existing entity
            if self.is_new:
                pass
            else:
                self.__dict__['_'+name]['isModified'] = True

        elif name in ["space"]:
            # fetch object in openBIS, make sure it actually exists
            obj = getattr(self._openbis, "get_"+name)(value)
            self.__dict__['_'+name] = obj.data['permId']

                # mark attribute as modified, if it's an existing entity
            if self.is_new:
                pass
            else:
                self.__dict__['_'+name]['isModified'] = True

        elif name in ["project"]:
            # fetch object in openBIS, make sure it actually exists
            obj = getattr(self._openbis, "get_"+name)(value)
            self.__dict__['_'+name] = obj.data['identifier']

                # mark attribute as modified, if it's an existing entity
            if self.is_new:
                pass
            else:
                self.__dict__['_'+name]['isModified'] = True

        elif name in ["identifier"]:
            raise KeyError("you can not modify the {}".format(name))
        elif name == "code":
            if getattr(self, '_type') and self.__dict__['_type'].data['autoGeneratedCode']:
                raise KeyError("for this {}Type you can not set a code".format(self.__dict__['_entity']))
            else:
                self.__dict__['_code'] = value
        elif name == "description":
            self.__dict__['_description'] = value
        else:
            raise KeyError("no such attribute: {}".format(name))

    def get_type(self):
        return self._type

    def get_parents(self):
        # e.g. self._openbis.get_samples(withChildren=self.identifier)
        return getattr(self._openbis, 'get_'+self._entity.lower()+'s')(withChildren=self.identifier)

    def get_children(self):
        # e.g. self._openbis.get_samples(withParents=self.identifier)
        return getattr(self._openbis, 'get_'+self._entity.lower()+'s')(withParents=self.identifier)

    @property
    def tags(self):
        if getattr(self, '_tags') is not None:
            return [ x['code'] for x in self._tags ]

    def set_tags(self, tags):
        if getattr(self, '_tags') is None:
            self.__dict__['_tags'] = []

        tagIds = _create_tagIds(tags)

        # remove tags that are not in the new tags list
        for tagId in self.__dict__['_tags']:
            if tagId not in tagIds:
                self.__dict__['_tags'].remove(tagId)

        # add all new tags that are not in the list yet
        for tagId in tagIds:
            if tagId not in self.__dict__['_tags']:
                self.__dict__['_tags'].append(tagId)        

    def add_tags(self, tags):
        if getattr(self, '_tags') is None:
            self.__dict__['_tags'] = []

        # add the new tags to the _tags and _new_tags list,
        # if not listed yet
        tagIds = _create_tagIds(tags)
        for tagId in tagIds:
            if not tagId in self.__dict__['_tags']:
                self.__dict__['_tags'].append(tagId)        

    def del_tags(self, tags):
        if getattr(self, '_tags') is None:
            self.__dict__['_tags'] = []

        # remove the tags from the _tags and _del_tags list,
        # if listed there
        tagIds = _create_tagIds(tags)
        for tagId in tagIds:
            if tagId in self.__dict__['_tags']:
                self.__dict__['_tags'].remove(tagId)        

    def get_attachments(self):
        if getattr(self, '_attachments') is None:
            return None
        else:
            return DataFrame(self._attachments)[['fileName','title','description','version']]

    def add_attachment(self, fileName, title=None, description=None):
        att = Attachment(filename=fileName, title=title, description=description)
        if getattr(self, '_attachments') is None:
            self.__dict__['_attachments'] = []
        self._attachments.append(att.get_data_short())

        if getattr(self, '_new_attachments') is None:
            self.__dict__['_new_attachments'] = []
        self._new_attachments.append(att)

    def download_attachments(self):
        method = 'get'+self.entity+'s'
        entity = self.entity.lower()
        request = {
            "method": method,
            "params": [ self._openbis.token,
                [ self._permId ],
                {
                    "attachments": fetch_option['attachmentsWithContent'],
                    **fetch_option[entity]
                }
            ]
        }
        resp = self._openbis._post_request(self._openbis.as_v3, request)
        attachments = resp[self.permId]['attachments']
        file_list = []
        for attachment in attachments:
            filename = os.path.join(
                self._openbis.hostname, 
                self.permId,
                attachment['fileName']
            )
            os.makedirs(os.path.dirname(filename), exist_ok=True)
            with open(filename, 'wb') as att:
                content = base64.b64decode(attachment['content'])
                att.write(content)    
            file_list.append(filename)
        return file_list


    def _repr_html_(self):
        def nvl(val, string=''):
            if val is None:
                return string
            return val

        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._allowed_attrs:
            if attr == 'attachments':
                continue
            html += "<tr> <td>{}</td> <td>{}</td> </tr>".format(
                attr, nvl(getattr(self, attr, ''),'') 
            )
        if getattr(self, '_attachments') is not None:
            html += "<tr><td>attachments</td><td>"
            html += "<br/>".join(att['fileName'] for att in self._attachments)
            html += "</td></tr>"

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


class Sample():
    """ A Sample is one of the most commonly used objects in openBIS.
    """

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

        if data is not None:
            self._set_data(data)

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

    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)
            for key, value in data['properties'].items():
                self.p.__dict__[key.lower()] = value

    def __dir__(self):
        return [
            'props', 'get_parents()', 'get_children()',
            'get_datasets()', 'get_experiment()',
            'space', 'project', 'experiment', 'project', 'tags', 
            'set_tags()', 'add_tags()', 'del_tags()',
            'add_attachment()', 'get_attachments()', 'download_attachments()'
        ]

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

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

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

    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):
        html = self.a._repr_html_()
        return html

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

    def save(self):
        props = self.p._all_props()
        attrs = self.a._up_attrs()
        attrs["properties"] = props

        if self.identifier is None:
            # create a new sample
            attrs["@type"] = "as.dto.sample.create.SampleCreation"
            attrs["typeId"] = self.__dict__['type'].data['permId']
            request = {
                "method": "createSamples",
                "params": [ self.openbis.token,
                    [ attrs ]
                ]
            }
            resp = self.openbis._post_request(self.openbis.as_v3, request)
            new_sample_data = self.openbis.get_sample(resp[0]['permId'], only_data=True)
            self._set_data(new_sample_data)
            return self
            
        else:
            attrs["@type"] = "as.dto.sample.update.SampleUpdate"
            attrs["sampleId"] = {
                "permId": self.permId,
                "@type": "as.dto.sample.id.SamplePermId"
            }
            request = {
                "method": "updateSamples",
                "params": [ self.openbis.token,
                    [ attrs ]
                ]
            }
            resp = self.openbis._post_request(self.openbis.as_v3, request)
            print('Sample successfully updated')

    def delete(self, reason):
        self.openbis.delete_entity('sample', self.permId, reason)

    def get_datasets(self):
        return self.openbis.get_datasets(sample=self.permId)

    def get_projects(self):
        return self.openbis.get_project(withSamples=[self.permId])

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

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

class Space(OpenBisObject):
    """ managing openBIS spaces
    """

    def __init__(self, openbis_obj, type=None, data=None, **kwargs):
        self.__dict__['openbis'] = openbis_obj
        self.__dict__['a'] = AttrHolder(openbis_obj, 'Space', type)

        if data is not None:
            self.a(data)
            self.__dict__['data'] = data

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

    def __dir__(self):
        """all the available methods and attributes that should be displayed
        when using the autocompletion feature (TAB) in Jupyter
        """
        return['code','permId', 'description', 'registrator', 'registrationDate',
        'modificationDate', 'get_projects()', 'new_project()', 'get_samples()', 'delete()']

    def __str__(self):
        return self.data.get('code', None)

    def get_samples(self):
        return self.openbis.get_samples(space=self.code)

    def get_projects(self):
        return self.openbis.get_projects(space=self.code)

    def new_project(self, code, description=None, **kwargs):
        return self.openbis.new_project(self.code, code, description, **kwargs)

    def delete(self, reason):
        self.openbis.delete_entity('Space', self.permId, reason)


class Things():
    """An object that contains a DataFrame object about an entity  available in openBIS.
       
    """

    def __init__(self, openbis_obj, entity, df, identifier_name='code'):
        self.openbis = openbis_obj
        self.entity = entity
        self.df = df
        self.identifier_name = identifier_name

    def _repr_html_(self):
        return self.df._repr_html_()

    def __getitem__(self, key):
        if self.df is not None and len(self.df) > 0:
            row = None
            if isinstance(key, int):
                # get thing by rowid
                row = self.df.loc[[key]]
            elif isinstance(key, list):
                # treat it as a normal dataframe
                return self.df[key]
            else:
                # get thing by code
                row = self.df[self.df[self.identifier_name]==key.upper()]

            if row is not None:
                # invoke the openbis.get_entity() method
                return getattr(self.openbis, 'get_'+self.entity)(row[self.identifier_name].values[0])


class Experiment(OpenBisObject):
    """ 
    """

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

        if data is not None:
            self._set_data(data)

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

    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)
            for key, value in data['properties'].items():
                self.p.__dict__[key.lower()] = value

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

    def __dir__(self):
        # the list of possible methods/attributes displayed
        # when invoking TAB-completition
        return [
            'props', 'space', 'project', 
            'project','tags', 'attachments', 'data',
            'get_datasets()', 'get_samples()', 
            'set_tags()', 'add_tags()', 'del_tags()',
            'add_attachment()', 'get_attachments()', 'download_attachments()'
        ]

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

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

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

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

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

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

    def _repr_html_(self):
        html = self.a._repr_html_()
        return html

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

    def save(self):
        props = self.p._all_props()
        attrs = self.a._up_attrs()
        attrs["properties"] = props

        if self.identifier is None:
            # create a new experiment
            attrs["@type"] = "as.dto.experiment.create.ExperimentCreation"
            attrs["typeId"] = self.__dict__['type'].data['permId']
            request = {
                "method": "createExperiments",
                "params": [ self.openbis.token,
                    [ attrs ]
                ]
            }
            resp = self.openbis._post_request(self.openbis.as_v3, request)
            new_experiment_data = self.openbis.get_experiment(resp[0]['permId'], only_data=True)
            self._set_data(new_experiment_data)
            return self
            
        else:
            attrs["@type"] = "as.dto.experiment.update.ExperimentUpdate"
            attrs["experimentId"] = {
                "permId": self.permId,
                "@type": "as.dto.experiment.id.ExperimentPermId"
            }
            request = {
                "method": "updateExperiments",
                "params": [ self.openbis.token,
                    [ attrs ]
                ]
            }
            resp = self.openbis._post_request(self.openbis.as_v3, request)
            print('Experiment successfully updated')

    def delete(self, reason):
        self.openbis.delete_entity('experiment', self.permId, reason)

    def get_datasets(self):
        return self.openbis.get_datasets(experiment=self.permId)

    def get_projects(self):
        return self.openbis.get_project(experiment=self.permId)

    def get_samples(self):
        return self.openbis.get_samples(experiment=self.permId)


class Attachment():

    def __init__(self, filename, title=None, description=None):
        if not os.path.exists(filename):
            raise ValueError("File not found: {}".format(filename))
        self.fileName = filename
        self.title = title
        self.description = description

    def get_data_short(self):
        return {
            "fileName"    : self.fileName,
            "title"       : self.title,
            "description" : self.description,
        }

    def get_data(self):
        with open(self.fileName, 'rb') as att:
            content = att.read()
            contentb64 = base64.b64encode(content).decode()
        return {
            "fileName"    : self.fileName,
            "title"       : self.title,
            "description" : self.description,
            "content"     : contentb64,
            "@type"       : "as.dto.attachment.create.AttachmentCreation",
        }


class Project(OpenBisObject):

    def __init__(self, openbis_obj, data=None, **kwargs):
        self.__dict__['openbis'] = openbis_obj
        self.__dict__['a'] = AttrHolder(openbis_obj, 'Project')

        if data is not None:
            self.a(data)
            self.__dict__['data'] = data

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

    def _modifiable_attrs(self):
        return
 
    def __dir__(self):
        """all the available methods and attributes that should be displayed
        when using the autocompletion feature (TAB) in Jupyter
        """
        return['code','permId', 'identifier', 'description', 'space', 'registrator',
        'registrationDate', 'modifier', 'modificationDate', 'add_attachment()',
        'get_attachments()', 'download_attachments()',
        'get_experiments()', 'get_samples()', 'get_datasets()',
        'delete()'
        ]

    def get_samples(self):
        return self.openbis.get_samples(project=self.permId)

    def get_experiments(self):
        return self.openbis.get_experiments(project=self.permId)

    def get_datasets(self):
        return self.openbis.get_datasets(project=self.permId)

    def delete(self, reason):
        self.openbis.delete_entity('project', self.permId, reason) 

    def save(self):
        if self.is_new:
            request = self._new_attrs()
            self.openbis._post_request(self.openbis.as_v3, request)
            self.a.__dict__['_is_new'] = False
            print("Project successfully created.")
        else:
            request = self._up_attrs()
            self.openbis._post_request(self.openbis.as_v3, request)
            print("Project successfully updated.")

        #attrs = self.a._up_attrs()

        #if self.identifier is None:
        #    attrs["@type"] = "as.dto.project.create.ProjectCreation"
        #    attrs["typeId"] = self.__dict__['type'].data['permId']
        #    request = {
        #        "method": "createProjects",
        #        "params": [ self.openbis.token, [ attrs ] ]
        #    }
        #    resp = self.openbis._post_request(self.openbis.as_v3, request)
        #    new_sample_data = self.openbis.get_sample(resp[0]['permId'], only_data=True)
        #    self._set_data(new_sample_data)
        #    return self
        #    
        #else:
        #    attrs["@type"] = "as.dto.project.update.ProjectUpdate"
        #    attrs["projectId"] = {
        #        "permId": self.permId,
        #        "@type": "as.dto.project.id.ProjectPermId"
        #    }
        #    request = {
        #        "method": "updateProjects",
        #        "params": [ self.openbis.token,
        #            [ attrs ]
        #        ]
        #    }
        #    resp = self.openbis._post_request(self.openbis.as_v3, request)
        #    print('Project successfully updated')