pybis.py

                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],
                       dict(
                           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

    def __repr__(self):

        headers = ['attribute', 'value']
        lines = []
        for attr in self._allowed_attrs:
            if attr == 'attachments':
                continue
            lines.append([
                attr,
                nvl(getattr(self, attr, ''))
            ])
        return tabulate(lines, headers=headers)


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

    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, 'Sample', 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 __dir__(self):
        return [
            'props', 'get_parents()', 'get_children()', 
            'add_parents()', 'add_children()', 'del_parents()', 'del_children()',
            'get_datasets()', 'get_experiment()',
            'space', 'project', 'experiment', 'tags',
            'set_tags()', 'add_tags()', 'del_tags()',
            'add_attachment()', 'get_attachments()', 'download_attachments()',
            'save()', 'delete()'
        ]

    @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):
        return self.a._repr_html_()

    def __repr__(self):
        return self.a.__repr__()

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

    def save(self):
        props = self.p._all_props()

        if self.is_new:
            request = self._new_attrs()
            request["params"][1][0]["properties"] = props
            resp = self.openbis._post_request(self.openbis.as_v3, request)

            print("Sample successfully created.")
            new_sample_data = self.openbis.get_sample(resp[0]['permId'], only_data=True)
            self._set_data(new_sample_data)
            return self

        else:
            request = self._up_attrs()
            self.openbis._post_request(self.openbis.as_v3, request)
            print("Sample successfully updated.")
            new_sample_data = self.openbis.get_sample(self.permId, only_data=True)
            self._set_data(new_sample_data)

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

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

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

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

        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(code='', description='')", 
            'get_samples()', 
            'delete()'
        ]

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

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

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

    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)

    def save(self):
        if self.is_new:
            request = self._new_attrs()
            resp = self.openbis._post_request(self.openbis.as_v3, request)
            print("Space successfully created.")
            new_space_data = self.openbis.get_space(resp[0]['permId'], only_data=True)
            self._set_data(new_space_data)
            return self

        else:
            request = self._up_attrs()
            self.openbis._post_request(self.openbis.as_v3, request)
            print("Space successfully updated.")
            new_space_data = self.openbis.get_space(self.permId, only_data=True)
            self._set_data(new_space_data)


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 __len__(self):
        return len(self.df)

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

    def get_parents(self, **kwargs):
        if self.entity not in ['sample', 'dataset']:
            raise ValueError("{}s do not have parents".format(self.entity))

        if self.df is not None and len(self.df) > 0:
            dfs = []
            for ident in self.df[self.identifier_name]:
                # get all objects that have this object as a child == parent
                try:
                    parents = getattr(self.openbis, 'get_' + self.entity.lower() + 's')(withChildren=ident, **kwargs)
                    dfs.append(parents.df)
                except ValueError:
                    pass

            if len(dfs) > 0:
                return Things(self.openbis, self.entity, pd.concat(dfs), self.identifier_name)
            else:
                return Things(self.openbis, self.entity, DataFrame(), self.identifier_name)

    def get_children(self, **kwargs):
        if self.entity not in ['sample', 'dataset']:
            raise ValueError("{}s do not have children".format(self.entity))

        if self.df is not None and len(self.df) > 0:
            dfs = []
            for ident in self.df[self.identifier_name]:
                # get all objects that have this object as a child == parent
                try:
                    parents = getattr(self.openbis, 'get_' + self.entity.lower() + 's')(withParent=ident, **kwargs)
                    dfs.append(parents.df)
                except ValueError:
                    pass

            if len(dfs) > 0:
                return Things(self.openbis, self.entity, pd.concat(dfs), self.identifier_name)
            else:
                return Things(self.openbis, self.entity, DataFrame(), self.identifier_name)

    def get_samples(self, **kwargs):
        if self.entity not in ['space', 'project', 'experiment']:
            raise ValueError("{}s do not have samples".format(self.entity))

        if self.df is not None and len(self.df) > 0:
            dfs = []
            for ident in self.df[self.identifier_name]:
                args = {}
                args[self.entity.lower()] = ident
                try:
                    samples = self.openbis.get_samples(**args, **kwargs)
                    dfs.append(samples.df)
                except ValueError:
                    pass

            if len(dfs) > 0:
                return Things(self.openbis, 'sample', pd.concat(dfs), 'identifier')
            else:
                return Things(self.openbis, 'sample', DataFrame(), 'identifier')

    def get_datasets(self, **kwargs):
        if self.entity not in ['sample', 'experiment']:
            raise ValueError("{}s do not have datasets".format(self.entity))

        if self.df is not None and len(self.df) > 0:
            dfs = []
            for ident in self.df[self.identifier_name]:
                args = {}
                args[self.entity.lower()] = ident
                try:
                    datasets = self.openbis.get_datasets(**args, **kwargs)
                    dfs.append(datasets.df)
                except ValueError:
                    pass

            if len(dfs) > 0:
                return Things(self.openbis, 'dataset', pd.concat(dfs), 'permId')
            else:
                return Things(self.openbis, 'dataset', DataFrame(), 'permId')

    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, code=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 code is not None:
            self.code = code

        if kwargs is not None:
            defs = _definitions('Experiment')
            for key in kwargs:
                if key in defs['attrs']:
                    setattr(self, key, kwargs[key])
                else:
                    raise ValueError("{attr} is not a known attribute for an Experiment".format(attr=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()',
            'save()'
        ]

    @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
            resp = self.openbis._post_request(self.openbis.as_v3, request)

            print("Experiment successfully created.")
            new_exp_data = self.openbis.get_experiment(resp[0]['permId'], only_data=True)
            self._set_data(new_exp_data)
            return self
        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.")
            new_exp_data = self.openbis.get_experiment(resp[0]['permId'], only_data=True)
            self._set_data(new_exp_data)

    def delete(self, reason):
        if self.permId is None:
            return None
        self.openbis.delete_entity('experiment', self.permId, reason)

    def get_datasets(self, **kwargs):
        if self.permId is None:
            return None
        return self.openbis.get_datasets(experiment=self.permId, **kwargs)

    def get_projects(self, **kwargs):
        if self.permId is None:
            return None
        return self.openbis.get_project(experiment=self.permId, **kwargs)

    def get_samples(self, **kwargs):
        if self.permId is None:
            return None
        return self.openbis.get_samples(experiment=self.permId, **kwargs)

    def add_samples(self, *samples):

        for sample in samples:
            if isinstance(sample, str):
                obj = self.openbis.get_sample(sample)
            else:
                # we assume we got a sample object
                obj = sample

            # a sample can only belong to exactly one experiment
            if obj.experiment is not None:
                raise ValueError(
                    "sample {} already belongs to experiment {}".format(
                        obj.code, obj.experiment
                    )
                )
            else:
                if self.is_new:
                    raise ValueError("You need to save this experiment first before you can assign any samples to it")
                else:
                    # update the sample directly
                    obj.experiment = self.identifier
                    obj.save()
                    self.a.__dict__['_samples'].append(obj._identifier)


    def del_samples(self, samples):
        if not isinstance(samples, list):
            samples = [samples]

        
        for sample in samples:
            if isinstance(sample, str):
                obj = self.openbis.get_sample(sample)
                objects.append(obj)
            else:
                # we assume we got an object
                objects.append(obj)
        
        self.samples = objects

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()',
                'save()', 'delete()'
                ]

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

    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.")