JorgeVB/code_unlearning_dataset · Data Studio

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View handler decorator that adds SID resolve and PID validation. - For v1 calls, assume that ``did`` is a pid and raise NotFound exception if it's not valid. - For v2 calls, if DID is a valid PID, return it. If not, try to resolve it as a SID and, if successful, return the new PID. Else, raise NotF...
View handler decorator that decodes "%2f" ("/") in SID or PID extracted from URL path segment by Django. def decode_did(f): """View handler decorator that decodes "%2f" ("/") in SID or PID extracted from URL path segment by Django.""" @functools.wraps(f) def wrapper(request, did, args, *kwargs):...
Access only by D1 infrastructure. def trusted_permission(f): """Access only by D1 infrastructure.""" @functools.wraps(f) def wrapper(request, args, kwargs): trusted(request) return f(request, args, **kwargs) return wrapper
Access to listObjects() controlled by settings.PUBLIC_OBJECT_LIST. def list_objects_access(f): """Access to listObjects() controlled by settings.PUBLIC_OBJECT_LIST.""" @functools.wraps(f) def wrapper(request, args, *kwargs): if not django.conf.settings.PUBLIC_OBJECT_LIST: trusted(req...
Access to getLogRecords() controlled by settings.PUBLIC_LOG_RECORDS. def get_log_records_access(f): """Access to getLogRecords() controlled by settings.PUBLIC_LOG_RECORDS.""" @functools.wraps(f) def wrapper(request, args, *kwargs): if not django.conf.settings.PUBLIC_LOG_RECORDS: trus...
Access only by subjects with Create/Update/Delete permission and by trusted infrastructure (CNs). def assert_create_update_delete_permission(f): """Access only by subjects with Create/Update/Delete permission and by trusted infrastructure (CNs).""" @functools.wraps(f) def wrapper(request, args, ...
Access only with a valid session. def authenticated(f): """Access only with a valid session.""" @functools.wraps(f) def wrapper(request, args, *kwargs): if d1_common.const.SUBJECT_AUTHENTICATED not in request.all_subjects_set: raise d1_common.types.exceptions.NotAuthorized( ...
Assert that subject has access at given level or higher for object. def required_permission(f, level): """Assert that subject has access at given level or higher for object.""" @functools.wraps(f) def wrapper(request, pid, args, *kwargs): d1_gmn.app.auth.assert_allowed(request, level, pid) ...
Given a response body, try to create an instance of a DataONE type. The return value will be either an instance of a type or a DataONE exception. def _read_and_deserialize_dataone_type(self, response): """Given a response body, try to create an instance of a DataONE type. The return value wil...
Initiate a MNRead.get(). Return a Requests Response object from which the object bytes can be retrieved. When ``stream`` is False, Requests buffers the entire object in memory before returning the Response. This can exhaust available memory on the local machine when retrieving large sci...
Like MNRead.get(), but also retrieve the object bytes and store them in a stream. This method does not have the potential issue with excessive memory usage that get() with ``stream``=False has. Also see MNRead.get(). def get_and_save( self, pid, sciobj_stream, create_missing_dirs=False...
Note: If the server returns a status code other than 200 OK, a ServiceFailure will be raised, as this method is based on a HEAD request, which cannot carry exception information. def describe(self, pid, vendorSpecific=None): """Note: If the server returns a status code other than 200 OK, a Serv...
Return True if user is allowed to perform ``action`` on ``pid``, else False. def isAuthorized(self, pid, action, vendorSpecific=None): """Return True if user is allowed to perform ``action`` on ``pid``, else False.""" response = self.isAuthorizedResponse(pid, action, vendorSpecific) ...
Filter fields based on request query parameters. def fields(self): """Filter fields based on request query parameters.""" fields = super().fields return apply_subfield_projection(self, copy.copy(fields))
Iterate over all field values sub-fields. This will iterate over all field values. Some fields defined in the schema might not be visited. :param fields: field values to iterate over :type fields: dict :param schema: schema to iterate over :type schema: dict :return: (field schema, field v...
Iterate over all schema sub-fields. This will iterate over all field definitions in the schema. Some field v alues might be None. :param fields: field values to iterate over :type fields: dict :param schema: schema to iterate over :type schema: dict :param path_prefix: dot separated path p...
Iterate over a nested dictionary. The dictionary is iterated over in a depth first manner. :param container: Dictionary to iterate over :param exclude: Optional callable, which is given key and value as arguments and may return True to stop iteration of that branch :return: (path, key, value) ...
Get all subjects in the certificate. - Returns: primary_str (primary subject), equivalent_set (equivalent identities, groups and group memberships) - The primary subject is the certificate subject DN, serialized to a DataONE compliant subject string. def get_subjects(request): """Get all subje...
Return primary subject and set of equivalents authenticated by certificate. - ``cert_pem`` can be str or bytes def get_authenticated_subjects(cert_pem): """Return primary subject and set of equivalents authenticated by certificate. - ``cert_pem`` can be str or bytes """ if isinstance(cert_pem, s...
Augment base serializer class. Include permissions information with objects. def get_serializer_class(self): """Augment base serializer class. Include permissions information with objects. """ base_class = super().get_serializer_class() class SerializerWithPermission...
Get or set permissions API endpoint. def detail_permissions(self, request, pk=None): """Get or set permissions API endpoint.""" obj = self.get_object() if request.method == 'POST': content_type = ContentType.objects.get_for_model(obj) payload = request.data ...
Perform descriptor validation and save object. def save(self, args, *kwargs): """Perform descriptor validation and save object.""" if self.descriptor_schema: try: validate_schema(self.descriptor, self.descriptor_schema.schema) # pylint: disable=no-member s...
Duplicate (make a copy). def duplicate(self, contributor=None): """Duplicate (make a copy).""" duplicate = Collection.objects.get(id=self.id) duplicate.pk = None duplicate.slug = None duplicate.name = 'Copy of {}'.format(self.name) duplicate.duplicated = now() if...
Convert a dictionary with scalar elements and string indices '_1234' to a dictionary of arrays. Unspecified entries are np.nan. def _scalar2array(d): """Convert a dictionary with scalar elements and string indices '_1234' to a dictionary of arrays. Unspecified entries are np.nan.""" da = {} for k, ...
To get rid of NaNs produced by _scalar2array, symmetrize operators where C_ijkl = C_jilk* def _symm_herm(C): """To get rid of NaNs produced by _scalar2array, symmetrize operators where C_ijkl = C_jilk*""" nans = np.isnan(C) C[nans] = np.einsum('jilk', C)[nans].conj() return C
To get rid of NaNs produced by _scalar2array, symmetrize operators where C_ijkl = C_klij def _symm_current(C): """To get rid of NaNs produced by _scalar2array, symmetrize operators where C_ijkl = C_klij""" nans = np.isnan(C) C[nans] = np.einsum('klij', C)[nans] return C
To get rid of NaNs produced by _scalar2array, antisymmetrize the first two indices of operators where C_ijkl = -C_jikl def _antisymm_12(C): """To get rid of NaNs produced by _scalar2array, antisymmetrize the first two indices of operators where C_ijkl = -C_jikl""" nans = np.isnan(C) C[nans] = -np.e...
For a dictionary with JMS Wilson coefficients, return a dictionary of arrays. def JMS_to_array(C, sectors=None): """For a dictionary with JMS Wilson coefficients, return a dictionary of arrays.""" if sectors is None: wc_keys = wcxf.Basis['WET', 'JMS'].all_wcs else: try: ...
For a dictionary with JMS Wilson coefficients but keys that might not be in the non-redundant basis, return a dictionary with keys from the basis and values conjugated if necessary. def symmetrize_JMS_dict(C): """For a dictionary with JMS Wilson coefficients but keys that might not be in the non-redund...
Redefinition of all Wilson coefficients in the JMS basis when rotating down-type quark fields from the flavour to the mass basis. C_in is expected to be an array-valued dictionary containg a key for all Wilson coefficient matrices. def rotate_down(C_in, p): """Redefinition of all Wilson coefficients i...
To account for the fact that arXiv:Jenkins:2017jig uses a flavour non-redundant basis in contrast to WCxf, symmetry factors of two have to be introduced in several places for operators that are symmetric under the interchange of two currents. def scale_dict_wet(C): """To account for the fact that arXiv...
Undo the scaling applied in `scale_dict_wet`. def unscale_dict_wet(C): """Undo the scaling applied in `scale_dict_wet`.""" return {k: _scale_dict[k] * v for k, v in C.items()}
Args: req_path: req_list: def write_reqs(req_path, req_list): """ Args: req_path: req_list: """ with open(req_path, 'w') as f: f.write('\n'.join(req_list) + "\n")
Run process locally. For details, see :meth:`~resolwe.flow.managers.workload_connectors.base.BaseConnector.submit`. def submit(self, data, runtime_dir, argv): """Run process locally. For details, see :meth:`~resolwe.flow.managers.workload_connectors.base.BaseConnector.submit`....
Calculate the checksum of a stream. Args: f: file-like object Only requirement is a ``read()`` method that returns ``bytes``. algorithm: str Checksum algorithm, ``MD5`` or ``SHA1`` / ``SHA-1``. Returns: Populated Checksum PyXB object. def create_checksum_object_from_stream(...
Calculate the checksum of an iterator. Args: itr: iterable Object which supports the iterator protocol. algorithm: str Checksum algorithm, ``MD5`` or ``SHA1`` / ``SHA-1``. Returns: Populated Checksum PyXB object. def create_checksum_object_from_iterator( itr, algorithm=...
Calculate the checksum of ``bytes``. Warning: This method requires the entire object to be buffered in (virtual) memory, which should normally be avoided in production code. Args: b: bytes Raw bytes algorithm: str Checksum algorithm, ``MD5`` or ``SHA1`` / ``SHA-1``. ...
Calculate the checksum of a stream. Args: f: file-like object Only requirement is a ``read()`` method that returns ``bytes``. algorithm: str Checksum algorithm, ``MD5`` or ``SHA1`` / ``SHA-1``. chunk_size : int Number of bytes to read from the file and add to the checksu...
Calculate the checksum of an iterator. Args: itr: iterable Object which supports the iterator protocol. algorithm: str Checksum algorithm, ``MD5`` or ``SHA1`` / ``SHA-1``. Returns: str : Checksum as a hexadecimal string, with length decided by the algorithm. def calculate_c...
Calculate the checksum of ``bytes``. Warning: This method requires the entire object to be buffered in (virtual) memory, which should normally be avoided in production code. Args: b: bytes Raw bytes algorithm: str Checksum algorithm, ``MD5`` or ``SHA1`` / ``SHA-1``. Retur...
Determine if checksums are equal. Args: checksum_a_pyxb, checksum_b_pyxb: PyXB Checksum objects to compare. Returns: bool - True: The checksums contain the same hexadecimal values calculated with the same algorithm. Identical checksums guarantee (for all practical ...
Create string representation of a PyXB Checksum object. Args: PyXB Checksum object Returns: str : Combined hexadecimal value and algorithm name. def format_checksum(checksum_pyxb): """Create string representation of a PyXB Checksum object. Args: PyXB Checksum object Returns: ...
Run the executor listener. This method never returns. def handle(self, args, *kwargs): """Run the executor listener. This method never returns.""" listener = ExecutorListener(redis_params=getattr(settings, 'FLOW_MANAGER', {}).get('REDIS_CONNECTION', {})) def _killer(signum, frame): ...
Apply projection from request context. The passed dictionary may be mutated. :param field: An instance of `Field` or `Serializer` :type field: `Field` or `Serializer` :param value: Dictionary to apply the projection to :type value: dict :param deep: Also process all deep projections :type ...
Apply projection. def apply_projection(projection, value): """Apply projection.""" if isinstance(value, Sequence): # Apply projection to each item in the list. return [ apply_projection(projection, item) for item in value ] elif not isinstance(value, Mapping)...
Create partitions. def _create_partitions(self, instance, partitions): """Create partitions.""" for partition in partitions: RelationPartition.objects.create( relation=instance, entity=partition['entity'], label=partition.get('label', None), ...
Create ``Relation`` object and add partitions of ``Entities``. def create(self, validated_data): """Create ``Relation`` object and add partitions of ``Entities``.""" # `partitions` field is renamed to `relationpartition_set` based on source of nested serializer partitions = validated_data.pop('...
Update ``Relation``. def update(self, instance, validated_data): """Update ``Relation``.""" # `partitions` field is renamed to `relationpartition_set` based on source of nested serializer partitions = validated_data.pop('relationpartition_set', None) with transaction.atomic(): ...
Display or save file like object. def output(file_like_object, path, verbose=False): """Display or save file like object.""" if not path: for line in file_like_object: if verbose: print_info(line.rstrip()) else: print(line.rstrip()) else: ...
Print the information in Unicode safe manner. def _print_level(level, msg): """Print the information in Unicode safe manner.""" for l in str(msg.rstrip()).split("\n"): print("{0:<9s}{1}".format(level, str(l)))
Find the first line of process definition. The first line of process definition is the line with a slug. :param str fname: Path to filename with processes :param string slug: process slug :return: line where the process definiton starts :rtype: int def get_process_definition_start(fname, slug): ...
Find processes in path. :param str process_dir: Path to the directory where to search for processes :param str base_source_uri: Base URL of the source code repository with process definitions :return: Dictionary of processes where keys are URLs pointing to processes' source code and values are processe...
Register directives. When sphinx loads the extension (= imports the extension module) it also executes the setup() function. Setup is the way extension informs Sphinx about everything that the extension enables: which config_values are introduced, which custom nodes/directives/roles and which event...
Fill content into nodes. :param string field_name: Field name of the field :param field_name: Field body if the field :type field_name: str or instance of docutils.nodes :return: field instance filled with given name and body :rtype: nodes.field def make_field(self, field_name,...
Fill the ``field`` into a properties list and return it. :param dict field: the content of the property list to make :return: field_list instance filled with given field :rtype: nodes.field_list def make_properties_list(self, field): """Fill the ``field`` into a properties list and ret...
Generate a process definition header. :param str slug: process' slug :param str typ: process' type :param str version: process' version :param str source_uri: url to the process definition :param str description: process' description :param dict inputs: process' inputs ...
Fill the content of process definiton node. :param dict process: process data as given from yaml.load function :return: process node def make_process_node(self, process): """Fill the content of process definiton node. :param dict process: process data as given from yaml.load function ...
Create a list of process definitions. def run(self): """Create a list of process definitions.""" config = self.state.document.settings.env.config # Get all processes: processes = get_processes(config.autoprocess_process_dir, config.autoprocess_source_base_url) process_nodes = [...
Create a category tree. def run(self): """Create a category tree.""" config = self.state.document.settings.env.config # Group processes by category processes = get_processes(config.autoprocess_process_dir, config.autoprocess_source_base_url) processes.sort(key=itemgetter('categ...
Create a type list. def run(self): """Create a type list.""" config = self.state.document.settings.env.config # Group processes by category processes = get_processes(config.autoprocess_process_dir, config.autoprocess_source_base_url) processes.sort(key=itemgetter('type')) ...
MNRead.get() Retrieve the SciObj bytes and write them to a file or other stream. Args: file_stream: Open file-like object Stream to which the SciObj bytes will be written. pid: str vendor_specific: dict Custom HTTP headers to includ...
Send an object synchronization request to the CN. async def synchronize(self, pid, vendor_specific=None): """Send an object synchronization request to the CN.""" return await self._request_pyxb( "post", ["synchronize", pid], {}, mmp_dict={"pid": pid}, ...
Encode any datetime query parameters to ISO8601. def _datetime_to_iso8601(self, query_dict): """Encode any datetime query parameters to ISO8601.""" return { k: v if not isinstance(v, datetime.datetime) else v.isoformat() for k, v in list(query_dict.items()) }
Project outgoing native value. def to_representation(self, value): """Project outgoing native value.""" value = apply_subfield_projection(self, value, deep=True) return super().to_representation(value)
CNRead.synchronize(session, pid) → boolean POST /synchronize. Args: pid: vendorSpecific: def synchronizeResponse(self, pid, vendorSpecific=None): """CNRead.synchronize(session, pid) → boolean POST /synchronize. Args: pid: vendorSpecific: """ mmp_dict = {'pid': pid} ...
See Also: synchronizeResponse() Args: pid: vendorSpecific: Returns: def synchronize(self, pid, vendorSpecific=None): """See Also: synchronizeResponse() Args: pid: vendorSpecific: Returns: """ response = self.synchronizeResponse(pid, vendorSpecific) return self._read_b...
Command handle. def handle(self, args, *options): """Command handle.""" verbosity = int(options['verbosity']) if self.has_filter(options): self.filter_indices(options, verbosity) else: # Process all indices. index_builder.build()
Check if a BagIt file is valid. Raises: ServiceFailure If the BagIt zip archive file fails any of the following checks: - Is a valid zip file. - The tag and manifest files are correctly formatted. - Contains all the files listed in the manifests. ...
Create a stream containing a BagIt zip archive. Args: dir_name : str The name of the root directory in the zip file, under which all the files are placed (avoids "zip bombs"). payload_info_list: list List of payload_info_dict, each dict describing a file. ...
Add a key with the path to each payload_info_dict. def _add_path(dir_name, payload_info_list): """Add a key with the path to each payload_info_dict.""" for payload_info_dict in payload_info_list: file_name = payload_info_dict['filename'] or payload_info_dict['pid'] payload_info_dict['path'] = d...
Add the payload files to the zip. def _add_payload_files(zip_file, payload_info_list): """Add the payload files to the zip.""" payload_byte_count = 0 payload_file_count = 0 for payload_info_dict in payload_info_list: zip_file.write_iter(payload_info_dict['path'], payload_info_dict['iter']) ...
Generate the tag files and add them to the zip. def _add_tag_files( zip_file, dir_name, payload_info_list, payload_byte_count, payload_file_count ): """Generate the tag files and add them to the zip.""" tag_info_list = [] _add_tag_file(zip_file, dir_name, tag_info_list, _gen_bagit_text_file_tup()) ...
Generate the manifest files and add them to the zip. def _add_manifest_files(zip_file, dir_name, payload_info_list, tag_info_list): """Generate the manifest files and add them to the zip.""" for checksum_algorithm in _get_checksum_algorithm_set(payload_info_list): _add_tag_file( zip_file, ...
Generate the tag manifest file and add it to the zip. def _add_tag_manifest_file(zip_file, dir_name, tag_info_list): """Generate the tag manifest file and add it to the zip.""" _add_tag_file( zip_file, dir_name, tag_info_list, _gen_tag_manifest_file_tup(tag_info_list) )
Add a tag file to zip_file and record info for the tag manifest file. def _add_tag_file(zip_file, dir_name, tag_info_list, tag_tup): """Add a tag file to zip_file and record info for the tag manifest file.""" tag_name, tag_str = tag_tup tag_path = d1_common.utils.filesystem.gen_safe_path(dir_name, tag_name...
Command handle. def handle(self, args, *options): """Command handle.""" verbosity = int(options['verbosity']) skip_mapping = options['skip_mapping'] if self.has_filter(options): self.filter_indices(options, verbosity, skip_mapping=skip_mapping) else: #...
Returns: dict : Representation of ``node_list_pyxb``, keyed on the Node identifier (``urn:node:*``). Example:: { u'urn:node:ARCTIC': { 'base_url': u'https://arcticdata.io/metacat/d1/mn', 'description': u'The US National Science Foundation...', 'name': u'Arctic Data Center...
Filter permissions queryset. def filter_queryset(self, request, queryset, view): """Filter permissions queryset.""" user = request.user app_label = queryset.model._meta.app_label # pylint: disable=protected-access model_name = queryset.model._meta.model_name # pylint: disable=protect...
Check object permissions. def has_object_permission(self, request, view, obj): """Check object permissions.""" # admins can do anything if request.user.is_superuser: return True # `share` permission is required for editing permissions if 'permissions' in view.action...
Get a set containing all subjects for which the current connection has been successfully authenticated. def get_active_subject_set(self, request): """Get a set containing all subjects for which the current connection has been successfully authenticated.""" # Handle complete certificate ...
Set up logging. We output only to stdout. Instead of also writing to a log file, redirect stdout to a log file when the script is executed from cron. def log_setup(debug_bool): """Set up logging. We output only to stdout. Instead of also writing to a log file, redirect stdout to a log file when t...
Connect to DB. dbname: the database name user: user name used to authenticate password: password used to authenticate host: database host address (defaults to UNIX socket if not provided) port: connection port number (defaults to 5432 if not provided) def connect(self, dsn): ""...
Get query parameter uniformly for GET and POST requests. def get_query_param(self, key, default=None): """Get query parameter uniformly for GET and POST requests.""" value = self.request.query_params.get(key, None) if value is None: value = self.request.data.get(key, None) i...
Get combined query parameters (GET and POST). def get_query_params(self): """Get combined query parameters (GET and POST).""" params = self.request.query_params.copy() params.update(self.request.data) return params
Order given search by the ordering parameter given in request. :param search: ElasticSearch query object def order_search(self, search): """Order given search by the ordering parameter given in request. :param search: ElasticSearch query object """ ordering = self.get_query_p...
Filter given search by the filter parameter given in request. :param search: ElasticSearch query object def filter_search(self, search): """Filter given search by the filter parameter given in request. :param search: ElasticSearch query object """ builder = QueryBuilder( ...
Filter given query based on permissions of the user in the request. :param search: ElasticSearch query object def filter_permissions(self, search): """Filter given query based on permissions of the user in the request. :param search: ElasticSearch query object """ user = self...
Optionally return paginated response. If pagination parameters are provided in the request, then paginated response is returned, otherwise response is not paginated. def paginate_response(self, queryset, serializers_kwargs={}): """Optionally return paginated response. If pagination pa...
Handle the search request. def search(self): """Handle the search request.""" search = self.document_class().search() # pylint: disable=not-callable search = self.custom_filter(search) search = self.filter_search(search) search = self.order_search(search) search = sel...
Endpoint handler. def list_with_post(self, request): """Endpoint handler.""" if self.is_search_request(): search = self.search() page = self.paginate_queryset(search) if page is None: items = search else: items = page ...
Called by FUSE when the attributes for a file or directory are required. Returns a dictionary with keys identical to the stat C structure of stat(2). st_atime, st_mtime and st_ctime should be floats. On OSX, st_nlink should count all files inside the directory. On Linux, only the subdirectories...
Called by FUSE when a directory is opened. Returns a list of file and directory names for the directory. def readdir(self, path, fh): """Called by FUSE when a directory is opened. Returns a list of file and directory names for the directory. """ log.debug('readdir(): {}'.form...
Called by FUSE when a file is opened. Determines if the provided path and open flags are valid. def open(self, path, flags): """Called by FUSE when a file is opened. Determines if the provided path and open flags are valid. """ log.debug('open(): {}'.format(path)) # O...
Extract an inline expression from the given text. def get_inline_expression(self, text): """Extract an inline expression from the given text.""" text = text.strip() if not text.startswith(self.inline_tags[0]) or not text.endswith(self.inline_tags[1]): return return text[2:-...
Filter queryset by entity, label and position. Due to a bug in django-filter these filters have to be applied manually: https://github.com/carltongibson/django-filter/issues/883 def _filter_queryset(self, queryset): """Filter queryset by entity, label and position. Due to a bu...
Update the ``Relation`` object. Reject the update if user doesn't have ``EDIT`` permission on the collection referenced in the ``Relation``. def update(self, request, args, *kwargs): """Update the ``Relation`` object. Reject the update if user doesn't have ``EDIT`` permission on ...
Rebuild indexes affected by the given permission. def _process_permission(perm): """Rebuild indexes affected by the given permission.""" # XXX: Optimize: rebuild only permissions, not whole document codename = perm.permission.codename if not codename.startswith('view') and not codename.startswith('owne...
Parse a multipart Requests.Response into a tuple of BodyPart objects. Args: response: Requests.Response encoding: The parser will assume that any text in the HTML body is encoded with this encoding when decoding it for use in the ``text`` attribute. Returns: tuple of BodyPar...
Parse multipart document bytes into a tuple of BodyPart objects. Args: mmp_bytes: bytes Multipart document. content_type : str Must be on the form, ``multipart/form-data; boundary=<BOUNDARY>``, where ``<BOUNDARY>`` is the string that separates the parts of the multipart documen...
Normalize a tuple of BodyPart objects to a string. Normalization is done by sorting the body_parts by the Content- Disposition headers, which is typically on the form, ``form-data; name="name_of_part``. def normalize(body_part_tup,): """Normalize a tuple of BodyPart objects to a string. Normalization...

View handler decorator that adds SID resolve and PID validation. - For v1 calls, assume that ``did`` is a pid and raise NotFound exception if it's not valid. - For v2 calls, if DID is a valid PID, return it. If not, try to resolve it as a SID and, if successful, return the new PID. Else, raise NotF...

View handler decorator that decodes "%2f" ("/") in SID or PID extracted from URL path segment by Django. def decode_did(f): """View handler decorator that decodes "%2f" ("/") in SID or PID extracted from URL path segment by Django.""" @functools.wraps(f) def wrapper(request, did, *args, **kwargs):...

Access only by D1 infrastructure. def trusted_permission(f): """Access only by D1 infrastructure.""" @functools.wraps(f) def wrapper(request, *args, **kwargs): trusted(request) return f(request, *args, **kwargs) return wrapper

Access to listObjects() controlled by settings.PUBLIC_OBJECT_LIST. def list_objects_access(f): """Access to listObjects() controlled by settings.PUBLIC_OBJECT_LIST.""" @functools.wraps(f) def wrapper(request, *args, **kwargs): if not django.conf.settings.PUBLIC_OBJECT_LIST: trusted(req...

Access to getLogRecords() controlled by settings.PUBLIC_LOG_RECORDS. def get_log_records_access(f): """Access to getLogRecords() controlled by settings.PUBLIC_LOG_RECORDS.""" @functools.wraps(f) def wrapper(request, *args, **kwargs): if not django.conf.settings.PUBLIC_LOG_RECORDS: trus...

Access only by subjects with Create/Update/Delete permission and by trusted infrastructure (CNs). def assert_create_update_delete_permission(f): """Access only by subjects with Create/Update/Delete permission and by trusted infrastructure (CNs).""" @functools.wraps(f) def wrapper(request, *args, *...

Access only with a valid session. def authenticated(f): """Access only with a valid session.""" @functools.wraps(f) def wrapper(request, *args, **kwargs): if d1_common.const.SUBJECT_AUTHENTICATED not in request.all_subjects_set: raise d1_common.types.exceptions.NotAuthorized( ...

Assert that subject has access at given level or higher for object. def required_permission(f, level): """Assert that subject has access at given level or higher for object.""" @functools.wraps(f) def wrapper(request, pid, *args, **kwargs): d1_gmn.app.auth.assert_allowed(request, level, pid) ...

Given a response body, try to create an instance of a DataONE type. The return value will be either an instance of a type or a DataONE exception. def _read_and_deserialize_dataone_type(self, response): """Given a response body, try to create an instance of a DataONE type. The return value wil...

Initiate a MNRead.get(). Return a Requests Response object from which the object bytes can be retrieved. When ``stream`` is False, Requests buffers the entire object in memory before returning the Response. This can exhaust available memory on the local machine when retrieving large sci...

Like MNRead.get(), but also retrieve the object bytes and store them in a stream. This method does not have the potential issue with excessive memory usage that get() with ``stream``=False has. Also see MNRead.get(). def get_and_save( self, pid, sciobj_stream, create_missing_dirs=False...

Note: If the server returns a status code other than 200 OK, a ServiceFailure will be raised, as this method is based on a HEAD request, which cannot carry exception information. def describe(self, pid, vendorSpecific=None): """Note: If the server returns a status code other than 200 OK, a Serv...

Return True if user is allowed to perform ``action`` on ``pid``, else False. def isAuthorized(self, pid, action, vendorSpecific=None): """Return True if user is allowed to perform ``action`` on ``pid``, else False.""" response = self.isAuthorizedResponse(pid, action, vendorSpecific) ...

Filter fields based on request query parameters. def fields(self): """Filter fields based on request query parameters.""" fields = super().fields return apply_subfield_projection(self, copy.copy(fields))

Iterate over all field values sub-fields. This will iterate over all field values. Some fields defined in the schema might not be visited. :param fields: field values to iterate over :type fields: dict :param schema: schema to iterate over :type schema: dict :return: (field schema, field v...

Iterate over all schema sub-fields. This will iterate over all field definitions in the schema. Some field v alues might be None. :param fields: field values to iterate over :type fields: dict :param schema: schema to iterate over :type schema: dict :param path_prefix: dot separated path p...

Iterate over a nested dictionary. The dictionary is iterated over in a depth first manner. :param container: Dictionary to iterate over :param exclude: Optional callable, which is given key and value as arguments and may return True to stop iteration of that branch :return: (path, key, value) ...

Get all subjects in the certificate. - Returns: primary_str (primary subject), equivalent_set (equivalent identities, groups and group memberships) - The primary subject is the certificate subject DN, serialized to a DataONE compliant subject string. def get_subjects(request): """Get all subje...

Return primary subject and set of equivalents authenticated by certificate. - ``cert_pem`` can be str or bytes def get_authenticated_subjects(cert_pem): """Return primary subject and set of equivalents authenticated by certificate. - ``cert_pem`` can be str or bytes """ if isinstance(cert_pem, s...

Augment base serializer class. Include permissions information with objects. def get_serializer_class(self): """Augment base serializer class. Include permissions information with objects. """ base_class = super().get_serializer_class() class SerializerWithPermission...

Get or set permissions API endpoint. def detail_permissions(self, request, pk=None): """Get or set permissions API endpoint.""" obj = self.get_object() if request.method == 'POST': content_type = ContentType.objects.get_for_model(obj) payload = request.data ...

Perform descriptor validation and save object. def save(self, *args, **kwargs): """Perform descriptor validation and save object.""" if self.descriptor_schema: try: validate_schema(self.descriptor, self.descriptor_schema.schema) # pylint: disable=no-member s...

Duplicate (make a copy). def duplicate(self, contributor=None): """Duplicate (make a copy).""" duplicate = Collection.objects.get(id=self.id) duplicate.pk = None duplicate.slug = None duplicate.name = 'Copy of {}'.format(self.name) duplicate.duplicated = now() if...

Convert a dictionary with scalar elements and string indices '_1234' to a dictionary of arrays. Unspecified entries are np.nan. def _scalar2array(d): """Convert a dictionary with scalar elements and string indices '_1234' to a dictionary of arrays. Unspecified entries are np.nan.""" da = {} for k, ...

To get rid of NaNs produced by _scalar2array, symmetrize operators where C_ijkl = C_jilk* def _symm_herm(C): """To get rid of NaNs produced by _scalar2array, symmetrize operators where C_ijkl = C_jilk*""" nans = np.isnan(C) C[nans] = np.einsum('jilk', C)[nans].conj() return C

To get rid of NaNs produced by _scalar2array, symmetrize operators where C_ijkl = C_klij def _symm_current(C): """To get rid of NaNs produced by _scalar2array, symmetrize operators where C_ijkl = C_klij""" nans = np.isnan(C) C[nans] = np.einsum('klij', C)[nans] return C

To get rid of NaNs produced by _scalar2array, antisymmetrize the first two indices of operators where C_ijkl = -C_jikl def _antisymm_12(C): """To get rid of NaNs produced by _scalar2array, antisymmetrize the first two indices of operators where C_ijkl = -C_jikl""" nans = np.isnan(C) C[nans] = -np.e...

For a dictionary with JMS Wilson coefficients, return a dictionary of arrays. def JMS_to_array(C, sectors=None): """For a dictionary with JMS Wilson coefficients, return a dictionary of arrays.""" if sectors is None: wc_keys = wcxf.Basis['WET', 'JMS'].all_wcs else: try: ...

For a dictionary with JMS Wilson coefficients but keys that might not be in the non-redundant basis, return a dictionary with keys from the basis and values conjugated if necessary. def symmetrize_JMS_dict(C): """For a dictionary with JMS Wilson coefficients but keys that might not be in the non-redund...

Redefinition of all Wilson coefficients in the JMS basis when rotating down-type quark fields from the flavour to the mass basis. C_in is expected to be an array-valued dictionary containg a key for all Wilson coefficient matrices. def rotate_down(C_in, p): """Redefinition of all Wilson coefficients i...

To account for the fact that arXiv:Jenkins:2017jig uses a flavour non-redundant basis in contrast to WCxf, symmetry factors of two have to be introduced in several places for operators that are symmetric under the interchange of two currents. def scale_dict_wet(C): """To account for the fact that arXiv...

Undo the scaling applied in `scale_dict_wet`. def unscale_dict_wet(C): """Undo the scaling applied in `scale_dict_wet`.""" return {k: _scale_dict[k] * v for k, v in C.items()}

Args: req_path: req_list: def write_reqs(req_path, req_list): """ Args: req_path: req_list: """ with open(req_path, 'w') as f: f.write('\n'.join(req_list) + "\n")

Run process locally. For details, see :meth:`~resolwe.flow.managers.workload_connectors.base.BaseConnector.submit`. def submit(self, data, runtime_dir, argv): """Run process locally. For details, see :meth:`~resolwe.flow.managers.workload_connectors.base.BaseConnector.submit`....

Calculate the checksum of a stream. Args: f: file-like object Only requirement is a ``read()`` method that returns ``bytes``. algorithm: str Checksum algorithm, ``MD5`` or ``SHA1`` / ``SHA-1``. Returns: Populated Checksum PyXB object. def create_checksum_object_from_stream(...

Calculate the checksum of an iterator. Args: itr: iterable Object which supports the iterator protocol. algorithm: str Checksum algorithm, ``MD5`` or ``SHA1`` / ``SHA-1``. Returns: Populated Checksum PyXB object. def create_checksum_object_from_iterator( itr, algorithm=...

Calculate the checksum of ``bytes``. Warning: This method requires the entire object to be buffered in (virtual) memory, which should normally be avoided in production code. Args: b: bytes Raw bytes algorithm: str Checksum algorithm, ``MD5`` or ``SHA1`` / ``SHA-1``. ...

Calculate the checksum of a stream. Args: f: file-like object Only requirement is a ``read()`` method that returns ``bytes``. algorithm: str Checksum algorithm, ``MD5`` or ``SHA1`` / ``SHA-1``. chunk_size : int Number of bytes to read from the file and add to the checksu...

Calculate the checksum of an iterator. Args: itr: iterable Object which supports the iterator protocol. algorithm: str Checksum algorithm, ``MD5`` or ``SHA1`` / ``SHA-1``. Returns: str : Checksum as a hexadecimal string, with length decided by the algorithm. def calculate_c...

Calculate the checksum of ``bytes``. Warning: This method requires the entire object to be buffered in (virtual) memory, which should normally be avoided in production code. Args: b: bytes Raw bytes algorithm: str Checksum algorithm, ``MD5`` or ``SHA1`` / ``SHA-1``. Retur...

Determine if checksums are equal. Args: checksum_a_pyxb, checksum_b_pyxb: PyXB Checksum objects to compare. Returns: bool - **True**: The checksums contain the same hexadecimal values calculated with the same algorithm. Identical checksums guarantee (for all practical ...

Create string representation of a PyXB Checksum object. Args: PyXB Checksum object Returns: str : Combined hexadecimal value and algorithm name. def format_checksum(checksum_pyxb): """Create string representation of a PyXB Checksum object. Args: PyXB Checksum object Returns: ...

Run the executor listener. This method never returns. def handle(self, *args, **kwargs): """Run the executor listener. This method never returns.""" listener = ExecutorListener(redis_params=getattr(settings, 'FLOW_MANAGER', {}).get('REDIS_CONNECTION', {})) def _killer(signum, frame): ...

Apply projection from request context. The passed dictionary may be mutated. :param field: An instance of `Field` or `Serializer` :type field: `Field` or `Serializer` :param value: Dictionary to apply the projection to :type value: dict :param deep: Also process all deep projections :type ...

Apply projection. def apply_projection(projection, value): """Apply projection.""" if isinstance(value, Sequence): # Apply projection to each item in the list. return [ apply_projection(projection, item) for item in value ] elif not isinstance(value, Mapping)...

Create partitions. def _create_partitions(self, instance, partitions): """Create partitions.""" for partition in partitions: RelationPartition.objects.create( relation=instance, entity=partition['entity'], label=partition.get('label', None), ...

Create ``Relation`` object and add partitions of ``Entities``. def create(self, validated_data): """Create ``Relation`` object and add partitions of ``Entities``.""" # `partitions` field is renamed to `relationpartition_set` based on source of nested serializer partitions = validated_data.pop('...

Update ``Relation``. def update(self, instance, validated_data): """Update ``Relation``.""" # `partitions` field is renamed to `relationpartition_set` based on source of nested serializer partitions = validated_data.pop('relationpartition_set', None) with transaction.atomic(): ...

Display or save file like object. def output(file_like_object, path, verbose=False): """Display or save file like object.""" if not path: for line in file_like_object: if verbose: print_info(line.rstrip()) else: print(line.rstrip()) else: ...

Print the information in Unicode safe manner. def _print_level(level, msg): """Print the information in Unicode safe manner.""" for l in str(msg.rstrip()).split("\n"): print("{0:<9s}{1}".format(level, str(l)))

Find the first line of process definition. The first line of process definition is the line with a slug. :param str fname: Path to filename with processes :param string slug: process slug :return: line where the process definiton starts :rtype: int def get_process_definition_start(fname, slug): ...

Find processes in path. :param str process_dir: Path to the directory where to search for processes :param str base_source_uri: Base URL of the source code repository with process definitions :return: Dictionary of processes where keys are URLs pointing to processes' source code and values are processe...

Register directives. When sphinx loads the extension (= imports the extension module) it also executes the setup() function. Setup is the way extension informs Sphinx about everything that the extension enables: which config_values are introduced, which custom nodes/directives/roles and which event...

Fill content into nodes. :param string field_name: Field name of the field :param field_name: Field body if the field :type field_name: str or instance of docutils.nodes :return: field instance filled with given name and body :rtype: nodes.field def make_field(self, field_name,...

Fill the ``field`` into a properties list and return it. :param dict field: the content of the property list to make :return: field_list instance filled with given field :rtype: nodes.field_list def make_properties_list(self, field): """Fill the ``field`` into a properties list and ret...

Generate a process definition header. :param str slug: process' slug :param str typ: process' type :param str version: process' version :param str source_uri: url to the process definition :param str description: process' description :param dict inputs: process' inputs ...

Fill the content of process definiton node. :param dict process: process data as given from yaml.load function :return: process node def make_process_node(self, process): """Fill the content of process definiton node. :param dict process: process data as given from yaml.load function ...

Create a list of process definitions. def run(self): """Create a list of process definitions.""" config = self.state.document.settings.env.config # Get all processes: processes = get_processes(config.autoprocess_process_dir, config.autoprocess_source_base_url) process_nodes = [...

Create a category tree. def run(self): """Create a category tree.""" config = self.state.document.settings.env.config # Group processes by category processes = get_processes(config.autoprocess_process_dir, config.autoprocess_source_base_url) processes.sort(key=itemgetter('categ...

Create a type list. def run(self): """Create a type list.""" config = self.state.document.settings.env.config # Group processes by category processes = get_processes(config.autoprocess_process_dir, config.autoprocess_source_base_url) processes.sort(key=itemgetter('type')) ...

MNRead.get() Retrieve the SciObj bytes and write them to a file or other stream. Args: file_stream: Open file-like object Stream to which the SciObj bytes will be written. pid: str vendor_specific: dict Custom HTTP headers to includ...

Send an object synchronization request to the CN. async def synchronize(self, pid, vendor_specific=None): """Send an object synchronization request to the CN.""" return await self._request_pyxb( "post", ["synchronize", pid], {}, mmp_dict={"pid": pid}, ...

Encode any datetime query parameters to ISO8601. def _datetime_to_iso8601(self, query_dict): """Encode any datetime query parameters to ISO8601.""" return { k: v if not isinstance(v, datetime.datetime) else v.isoformat() for k, v in list(query_dict.items()) }

Project outgoing native value. def to_representation(self, value): """Project outgoing native value.""" value = apply_subfield_projection(self, value, deep=True) return super().to_representation(value)

CNRead.synchronize(session, pid) → boolean POST /synchronize. Args: pid: vendorSpecific: def synchronizeResponse(self, pid, vendorSpecific=None): """CNRead.synchronize(session, pid) → boolean POST /synchronize. Args: pid: vendorSpecific: """ mmp_dict = {'pid': pid} ...

See Also: synchronizeResponse() Args: pid: vendorSpecific: Returns: def synchronize(self, pid, vendorSpecific=None): """See Also: synchronizeResponse() Args: pid: vendorSpecific: Returns: """ response = self.synchronizeResponse(pid, vendorSpecific) return self._read_b...

Command handle. def handle(self, *args, **options): """Command handle.""" verbosity = int(options['verbosity']) if self.has_filter(options): self.filter_indices(options, verbosity) else: # Process all indices. index_builder.build()

Check if a BagIt file is valid. Raises: ServiceFailure If the BagIt zip archive file fails any of the following checks: - Is a valid zip file. - The tag and manifest files are correctly formatted. - Contains all the files listed in the manifests. ...

Create a stream containing a BagIt zip archive. Args: dir_name : str The name of the root directory in the zip file, under which all the files are placed (avoids "zip bombs"). payload_info_list: list List of payload_info_dict, each dict describing a file. ...

Add a key with the path to each payload_info_dict. def _add_path(dir_name, payload_info_list): """Add a key with the path to each payload_info_dict.""" for payload_info_dict in payload_info_list: file_name = payload_info_dict['filename'] or payload_info_dict['pid'] payload_info_dict['path'] = d...

Add the payload files to the zip. def _add_payload_files(zip_file, payload_info_list): """Add the payload files to the zip.""" payload_byte_count = 0 payload_file_count = 0 for payload_info_dict in payload_info_list: zip_file.write_iter(payload_info_dict['path'], payload_info_dict['iter']) ...

Generate the tag files and add them to the zip. def _add_tag_files( zip_file, dir_name, payload_info_list, payload_byte_count, payload_file_count ): """Generate the tag files and add them to the zip.""" tag_info_list = [] _add_tag_file(zip_file, dir_name, tag_info_list, _gen_bagit_text_file_tup()) ...

Generate the manifest files and add them to the zip. def _add_manifest_files(zip_file, dir_name, payload_info_list, tag_info_list): """Generate the manifest files and add them to the zip.""" for checksum_algorithm in _get_checksum_algorithm_set(payload_info_list): _add_tag_file( zip_file, ...

Generate the tag manifest file and add it to the zip. def _add_tag_manifest_file(zip_file, dir_name, tag_info_list): """Generate the tag manifest file and add it to the zip.""" _add_tag_file( zip_file, dir_name, tag_info_list, _gen_tag_manifest_file_tup(tag_info_list) )

Add a tag file to zip_file and record info for the tag manifest file. def _add_tag_file(zip_file, dir_name, tag_info_list, tag_tup): """Add a tag file to zip_file and record info for the tag manifest file.""" tag_name, tag_str = tag_tup tag_path = d1_common.utils.filesystem.gen_safe_path(dir_name, tag_name...

Command handle. def handle(self, *args, **options): """Command handle.""" verbosity = int(options['verbosity']) skip_mapping = options['skip_mapping'] if self.has_filter(options): self.filter_indices(options, verbosity, skip_mapping=skip_mapping) else: #...

Returns: dict : Representation of ``node_list_pyxb``, keyed on the Node identifier (``urn:node:*``). Example:: { u'urn:node:ARCTIC': { 'base_url': u'https://arcticdata.io/metacat/d1/mn', 'description': u'The US National Science Foundation...', 'name': u'Arctic Data Center...

Filter permissions queryset. def filter_queryset(self, request, queryset, view): """Filter permissions queryset.""" user = request.user app_label = queryset.model._meta.app_label # pylint: disable=protected-access model_name = queryset.model._meta.model_name # pylint: disable=protect...

Check object permissions. def has_object_permission(self, request, view, obj): """Check object permissions.""" # admins can do anything if request.user.is_superuser: return True # `share` permission is required for editing permissions if 'permissions' in view.action...

Get a set containing all subjects for which the current connection has been successfully authenticated. def get_active_subject_set(self, request): """Get a set containing all subjects for which the current connection has been successfully authenticated.""" # Handle complete certificate ...

Set up logging. We output only to stdout. Instead of also writing to a log file, redirect stdout to a log file when the script is executed from cron. def log_setup(debug_bool): """Set up logging. We output only to stdout. Instead of also writing to a log file, redirect stdout to a log file when t...

Connect to DB. dbname: the database name user: user name used to authenticate password: password used to authenticate host: database host address (defaults to UNIX socket if not provided) port: connection port number (defaults to 5432 if not provided) def connect(self, dsn): ""...

Get query parameter uniformly for GET and POST requests. def get_query_param(self, key, default=None): """Get query parameter uniformly for GET and POST requests.""" value = self.request.query_params.get(key, None) if value is None: value = self.request.data.get(key, None) i...

Get combined query parameters (GET and POST). def get_query_params(self): """Get combined query parameters (GET and POST).""" params = self.request.query_params.copy() params.update(self.request.data) return params

Order given search by the ordering parameter given in request. :param search: ElasticSearch query object def order_search(self, search): """Order given search by the ordering parameter given in request. :param search: ElasticSearch query object """ ordering = self.get_query_p...

Filter given search by the filter parameter given in request. :param search: ElasticSearch query object def filter_search(self, search): """Filter given search by the filter parameter given in request. :param search: ElasticSearch query object """ builder = QueryBuilder( ...

Filter given query based on permissions of the user in the request. :param search: ElasticSearch query object def filter_permissions(self, search): """Filter given query based on permissions of the user in the request. :param search: ElasticSearch query object """ user = self...

Optionally return paginated response. If pagination parameters are provided in the request, then paginated response is returned, otherwise response is not paginated. def paginate_response(self, queryset, serializers_kwargs={}): """Optionally return paginated response. If pagination pa...

Handle the search request. def search(self): """Handle the search request.""" search = self.document_class().search() # pylint: disable=not-callable search = self.custom_filter(search) search = self.filter_search(search) search = self.order_search(search) search = sel...

Endpoint handler. def list_with_post(self, request): """Endpoint handler.""" if self.is_search_request(): search = self.search() page = self.paginate_queryset(search) if page is None: items = search else: items = page ...

Called by FUSE when the attributes for a file or directory are required. Returns a dictionary with keys identical to the stat C structure of stat(2). st_atime, st_mtime and st_ctime should be floats. On OSX, st_nlink should count all files inside the directory. On Linux, only the subdirectories...

Called by FUSE when a directory is opened. Returns a list of file and directory names for the directory. def readdir(self, path, fh): """Called by FUSE when a directory is opened. Returns a list of file and directory names for the directory. """ log.debug('readdir(): {}'.form...

Called by FUSE when a file is opened. Determines if the provided path and open flags are valid. def open(self, path, flags): """Called by FUSE when a file is opened. Determines if the provided path and open flags are valid. """ log.debug('open(): {}'.format(path)) # O...

Extract an inline expression from the given text. def get_inline_expression(self, text): """Extract an inline expression from the given text.""" text = text.strip() if not text.startswith(self.inline_tags[0]) or not text.endswith(self.inline_tags[1]): return return text[2:-...

Filter queryset by entity, label and position. Due to a bug in django-filter these filters have to be applied manually: https://github.com/carltongibson/django-filter/issues/883 def _filter_queryset(self, queryset): """Filter queryset by entity, label and position. Due to a bu...

Update the ``Relation`` object. Reject the update if user doesn't have ``EDIT`` permission on the collection referenced in the ``Relation``. def update(self, request, *args, **kwargs): """Update the ``Relation`` object. Reject the update if user doesn't have ``EDIT`` permission on ...

Rebuild indexes affected by the given permission. def _process_permission(perm): """Rebuild indexes affected by the given permission.""" # XXX: Optimize: rebuild only permissions, not whole document codename = perm.permission.codename if not codename.startswith('view') and not codename.startswith('owne...

Parse a multipart Requests.Response into a tuple of BodyPart objects. Args: response: Requests.Response encoding: The parser will assume that any text in the HTML body is encoded with this encoding when decoding it for use in the ``text`` attribute. Returns: tuple of BodyPar...

Parse multipart document bytes into a tuple of BodyPart objects. Args: mmp_bytes: bytes Multipart document. content_type : str Must be on the form, ``multipart/form-data; boundary=<BOUNDARY>``, where ``<BOUNDARY>`` is the string that separates the parts of the multipart documen...

Normalize a tuple of BodyPart objects to a string. Normalization is done by sorting the body_parts by the Content- Disposition headers, which is typically on the form, ``form-data; name="name_of_part``. def normalize(body_part_tup,): """Normalize a tuple of BodyPart objects to a string. Normalization...