pybis.py

    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 ExternalDMS():
    """ managing openBIS external data management systems
    """

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

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

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

    def __getattr__(self, name):
        return self.__dict__['data'].get(name)

    def __dir__(self):
        """all the available methods and attributes that should be displayed
        when using the autocompletion feature (TAB) in Jupyter
        """
        return ['code', 'label', 'urlTemplate', 'address', 'addressType', 'openbis']

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


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__(self):
        return tabulate(self.df, headers=list(self.df))

    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])

    def __iter__(self):
        for item in self.df[[self.identifier_name]][self.identifier_name].iteritems():
            yield getattr(self.openbis, 'get_' + self.entity)(item[1])

            # return self.df[[self.identifier_name]].to_dict()[self.identifier_name]


class Experiment(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, 'Experiment', type)

        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 _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):
        if self.is_new:
            request = self._new_attrs()
            props = self.p._all_props()
            request["params"][1][0]["properties"] = props
            self.openbis._post_request(self.openbis.as_v3, request)
            self.a.__dict__['_is_new'] = False
            print("Experiment successfully created.")
        else:
            request = self._up_attrs()
            props = self.p._all_props()
            request["params"][1][0]["properties"] = props
            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.")