pybis.py

        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 Vocabulary():

    def __init__(self, data):
        self.data = data

    @property
    def terms_kv(self):
         return [ 
            {voc["code"]:voc["label"] }
            for voc 
            in sorted(self.data['objects'], key=lambda v: v["ordinal"]) 
        ]

    @property
    def terms(self):
         return [ 
            voc["code"]
            for voc 
            in sorted(self.data['objects'], key=lambda v: v["ordinal"]) 
        ]


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

        for voc in sorted(
            self.data['objects'], 
            key=lambda v: (v["permId"]["vocabularyCode"], v["ordinal"])
        ):

            html += "<tr> <td>{}</td> <td>{}</td> <td>{}</td> <td>{}</td> </tr>".format(
                voc['code'],
                voc['label'],
                voc['description'],
                voc['permId']['vocabularyCode']
            )

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


class PropertyHolder():

    def __init__(self, openbis_obj, type):
        self.__dict__['_openbis'] = openbis_obj
        self.__dict__['_type'] = type
        self.__dict__['_property_names'] = []
        for prop in type.data['propertyAssignments']:
            self._property_names.append(prop['propertyType']['code'].lower())

    def _get_terms(self, vocabulary):
        return self._openbis.get_terms(vocabulary)

    def _all_props(self):
        props = {}
        for code in self._type.codes():
            props[code] = getattr(self, code)
        return props

    def __getattr__(self, name):
        if name.endswith('_'):
            name = name.rstrip('_')
            property_type = self._type.prop[name]['propertyType']
            if property_type['dataType'] == 'CONTROLLEDVOCABULARY':
                return self._openbis.get_terms(name)
            else:
                return { property_type["label"] : property_type["dataType"]}
        else: return None

    def __setattr__(self, name, value):
        if name not in self._property_names:
            raise KeyError("No such property: {}".format(name)) 
        property_type = self._type.prop[name]['propertyType']
        data_type = property_type['dataType']
        if data_type == 'CONTROLLEDVOCABULARY':
            voc = self._openbis.get_terms(name)
            if value not in voc.terms:
                raise ValueError("Value must be one of these terms: " + ", ".join(voc.terms))
        elif data_type in ('INTEGER', 'BOOLEAN', 'VARCHAR'):
            if not check_datatype(data_type, value):
                raise ValueError("Value must be of type {}".format(data_type))
        self.__dict__[name] = value

    def __dir__(self):
        return self._property_names

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

        for prop in self._property_names:
            value = ''
            try:
                value = getattr(self, prop)
            except Exception:
                pass

            html += "<tr> <td>{}</td> <td>{}</td> </tr>".format(
                prop,
                value
            )

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


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

    def __init__(self, openbis_obj, type):
        self.__dict__['_openbis'] = openbis_obj
        self.__dict__['_type_obj'] = type

        entity_type = type.data['@type'].split('.')[2].capitalize()
        self.__dict__['_entity_type'] = entity_type
        self.__dict__['_allowed_attrs'] = _definitions(entity_type)['attrs']
        self.__dict__['_identifier'] = None
        self.__dict__['_is_new'] = True

    def __call__(self, data):
        self.__dict__['_is_new'] = False
        for key in  "code permId identifier type container components attachments".split():
            self.__dict__['_'+key] = data.get(key, None)

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

        for key in "experiment".split():
            d =  data.get(key, None)
            if d is not None:
                d = d['identifier']
            self.__dict__['_'+key] = d

        for key in "parents children".split():
            self.__dict__['_'+key] = []
            for item in data[key]:
                self.__dict__['_'+key].append(item['identifier'])

        for key in "tags".split():
            self.__dict__['_'+key] = []
            for item in data[key]:
                self.__dict__['_'+key].append({
                    "code": item['code'],
                    "@type": "as.dto.tag.id.TagCode"
                })


    def _all_attrs(self):
        defs = _definitions(self._entity_type)
        attr2ids = _definitions('attr2ids')
        ids2type = _definitions('ids2type')

        request = {}

        # look at all attributes available for that entity
        for attr in defs['attrs']:
            if '_'+attr in self.__dict__:
                # in inserts and updates, space becomes spaceId, dataset becomes dataSetId etc.
                ids = attr2ids[attr]
                if self._is_new:
                    # handle multivalue attributes (parents, children, tags etc.)
                    if attr in defs['multi']:
                        items = self.__dict__.get('_'+attr, [])
                        if items == None:
                            items = []
                        request[ids] = items
                    else:
                        request[ids] = self.__dict__.get('_'+attr, None)

                else:
                    # 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 = []
                        request[ids] = {
                            "actions": [
                                {
                                    "items": items,
                                    "@type": "as.dto.common.update.ListUpdateActionSet",
                                }
                            ],
                            "@type": "as.dto.common.update.IdListUpdateValue"
                        }
                    else:
                        # handle single attribut4es (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']
                            
                            request[ids] = {
                               "@type": "as.dto.common.update.FieldUpdateValue",
                               "isModified": isModified,
                               "value": value,
                            }

        if self.__dict__.get('_code', None) is None:
            request['autoGeneratedCode'] = True
        else:
            pass
            
        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 ["_experiment"]:
                exp = ''
                try:
                    exp = self.__dict__[int_name]['identifier']
                except Exception:
                    pass
                return exp
            elif isinstance(self.__dict__[int_name], list):
                values = []
                for item in self.__dict__[int_name]:
                    values.append(
                        item.get("code",
                            item.get("identifier",
                                item.get("permId", None)))
                    )
                return values
            elif isinstance(self.__dict__[int_name], dict):
                return self.__dict__[int_name].get(name,
                    self.__dict__[int_name].get("code",
                        self.__dict__[int_name].get("identifier",
                            self.__dict__[int_name].get("permId", None))))
            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_type.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"]:
            tags = []
            for val in value:
                tags.append({
                    "@type": "as.dto.tag.id.TagCode",
                    "code": val
                })

            self.__dict__['_tags'] = tags

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

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

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

    def get_type(self):
        return self._type_obj

    def get_parents(self):
        return getattr(self._openbis, 'get_'+self._entity_type.lower()+'s')(withChildren=self.identifier)

    def get_children(self):
        return getattr(self._openbis, 'get_'+self._entity_type.lower()+'s')(withParents=self.identifier)

    @property 
    def set_tags(self, tags):
        tagIds = _tagIds_for_tags(tags, 'Set')
        self.openbis.update_sample(self.permId, tagIds=tagIds)

    def add_tags(self, tags):
        tagIds = _tagIds_for_tags(tags, 'Add')
        self.openbis.update_sample(self.permId, tagIds=tagIds)

    def del_tags(self, tags):
        tagIds = _tagIds_for_tags(tags, 'Remove')
        self.openbis.update_sample(self.permId, tagIds=tagIds)

    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 key in ["identifier","permId", "code", "type", "space","project", "experiment", "parents", "children", "tags"]:
            html += "<tr> <td>{}</td> <td>{}</td> </tr>".format(key, getattr(self, key, None))

        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, 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 ['get_parents()', 'get_children()', 'a', 'space', 'project', 'experiment',
        'project','tags', 'data']

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

    @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._all_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(withSamples=[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
        
class Space(dict):
    """ managing openBIS spaces
    """

    def __init__(self, openbis_obj, *args, **kwargs):
        super(Space, self).__init__(*args, **kwargs)
        self.__dict__ = self
        self.openbis = openbis_obj


    def get_samples(self, *args, **kwargs):
        """ Lists all samples in a given space. A pandas DataFrame object is returned.
        """

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

    @property
    def projects(self):
        return self.openbis.get_projects(space=self.code)
    
    def new_project(self, **kwargs):
        return self.openbis.new_project(space=self.code, **kwargs)

    @property
    def experiments(self):
        return self.openbis.get_experiments(space=self.code)



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

    def __init__(self, openbis_obj, what, df, identifier_name='code'):
        self.openbis = openbis_obj
        self.what = what
        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_what() method
                return getattr(self.openbis, 'get_'+self.what)(row[self.identifier_name].values[0])


class Experiment():
    """ managing openBIS experiments
    """

    def __init__(self, openbis_obj, data):
        self.openbis = openbis_obj
        self.permId = data['permId']['permId']
        self.identifier  = data['identifier']['identifier']
        self.properties = data['properties']
        self.tags = extract_tags(data['tags'])
        self.attachments = extract_attachments(data['attachments'])
        self.project = data['project']['code']
        self.data = data

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

    def set_tags(self, tags):
        tagIds = _tagIds_for_tags(tags, 'Set')
        self.openbis.update_experiment(self.permId, tagIds=tagIds)

    def add_tags(self, tags):
        tagIds = _tagIds_for_tags(tags, 'Add')
        self.openbis.update_experiment(self.permId, tagIds=tagIds)

    def del_tags(self, tags):
        tagIds = _tagIds_for_tags(tags, 'Remove')
        self.openbis.update_experiment(self.permId, tagIds=tagIds)

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

    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>
    <tr> <th>permId</th> <td>{}</td> </tr>
    <tr> <th>identifier</th> <td>{}</td> </tr>
    <tr> <th>project</th> <td>{}</td> </tr>
    <tr> <th>properties</th> <td>{}</td> </tr>
    <tr> <th>tags</th> <td>{}</td> </tr>
    <tr> <th>attachments</th> <td>{}</td> </tr>
  </tbody>
</table>
        """
        return html.format(self.permId, self.identifier, self.project, self.properties, self.tags, self.attachments)

    def __repr__(self):
        data = {}
        data["identifier"] = self.identifier
        data["permId"] = self.permId
        data["properties"] = self.properties
        data["tags"] = self.tags
        return repr(data)


class PropertyAssignments():
    """ holds are properties, that are assigned to an entity, eg. sample or experiment
    """

    def __init__(self, openbis_obj, data):
        self.openbis = openbis_obj
        self.data = data
        self.prop = {}
        if self.data['propertyAssignments'] is None:
            self.data['propertyAssignments'] = []
        for pa in self.data['propertyAssignments']:
            self.prop[pa['propertyType']['code'].lower()] = pa

    def codes(self):
        codes = []
        for pa in self.data['propertyAssignments']:
            codes.append(pa['propertyType']['code'].lower())
        return codes

    def _repr_html_(self):
        html = """
<p>{}: <b>{}</b>
<p>description: {}</p>
<p>Code autogenerated: {}</p>
<table border="1" class="dataframe">
  <thead>
    <tr style="text-align: right;">
      <th>property</th>
      <th>label</th>
      <th>description</th>
      <th>dataType</th>
      <th>mandatory</th>
    </tr>
  </thead>
  <tbody>
        """.format(
            self.data['@type'].split('.')[-1],
            self.data['code'], 
            self.data['description'], 
            self.data['autoGeneratedCode']
        )

        for pa in self.data['propertyAssignments']:
            html += "<tr> <th>{}</th> <td>{}</td> <td>{}</td> <td>{}</td> <td>{}</td> </tr>".format(
                pa['propertyType']['code'].lower(),    
                pa['propertyType']['label'],    
                pa['propertyType']['description'],    
                pa['propertyType']['dataType'],    
                pa['mandatory']
            )

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