caosadvancedtools.models package
Submodules
caosadvancedtools.models.data_model module
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class
caosadvancedtools.models.data_model.DataModel(*args) Bases:
dictProvides tools for managing a data model.
When constructing a data model the CaosDB representation can easily be created using the classes RecordType and Propery, storing them in a Container and inserting it in CaoSDB. However, this has one drawback: You cannot simply change someting and update the container. The container will insist on having valid ids for all contained Entities.
This class allows you to define your model as easily but also provides you with a method (sync_data_model) that will sync with the data model in an existing CaosDB instance.
This is possible because entities, defined in this model, are identified with entities in CaosDB using names. I.e. a RecordType “Experiment” in this model will update an existing RecordType with name “Experiment” in CaosDB. Thus, be carefull not to change existing Entities that were created for a different purpose (e.g. someone else’s experiment).
DataModel inherits from dict. The keys are always the names of the entities. Thus you cannot have unnamed entities in your model.
Example:
# Create a DataModel with a RecordType and a Property, not assuming any # relation between the two. dm = DataModel([db.RecordType(name=”myRecordType”),
db.Property(name=”myProperty”)])
# Sync the DataModel with the server, so that the server state is consistent # with this DataModel’s content. dm.sync_data_model() # Now the DataModel’s IDs are the same as on the server.
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append(entity: caosdb.common.models.Entity)
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collect_entities() Collects all entities: explicitly defined RecordTypes and Properties and those mentioned as Properties
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static
entities_without(entities, names) Return a new list with all entities which do not have certain names.
- Parameters
entities (iterable) – A iterable with entities.
names (iterable of str) – Only entities which do not have one of these names will end up in the returned iterable.
- Returns
A list with entities.
- Return type
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extend(entities: List[caosdb.common.models.Entity])
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static
get_existing_entities(entities) Return a list with those entities of the supplied iterable that exist in the CaosDB instance.
- Parameters
entities (iterable) – The entities to be retrieved. This object will not be moidified.
- Raises
TransactionError – If the retrieval fails.
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sync_data_model(noquestion: bool = False, verbose: bool = True) Synchronize this DataModel with a CaosDB instance.
Updates existing entities from the CaosDB instance and inserts non-existing entities into the instance. Note: This allows to easily overwrite changes that were made to an existing data model. Use this function with care and double check its effect.
- Raises
TransactionError – If one of the involved transactions fails.
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sync_ids_by_name(valid_entities) Add IDs from valid_entities to the entities in this DataModel.
“By name” means that the valid IDs (from the valid_entities) are assigned to the entities, their properties in this DataModel by their names, also parents are replaced by equally named entities in valid_entities. These changes happen in place to this DataModel!
- Parameters
valid_entities (list of Entity) – A list (e.g. a Container) of valid entities.
- Returns
- Return type
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caosadvancedtools.models.parser module
This module (and script) provides methods to read a DataModel from a YAML file.
If a file name is passed to parse_model_from_yaml it is parsed and a DataModel is created. The yaml file needs to be structured in a certain way which will be described in the following.
The file should only contain a dictionary. The keys are the names of RecordTypes or Properties. The values are again dictionaries describing the entities. This information can be defined via the keys listed in KEYWORDS. Notably, properties can be given in a dictionary under the xxxx_properties keys and will be added with the respective importance. These properties can be RecordTypes or Properties and can be defined right there. Every Property or RecordType only needs to be defined once anywhere. When it is not defined, simply the name can be supplied with no value. Parents can be provided under the ‘inherit_from_xxxx’ keywords. The value needs to be a list with the names. Here, NO NEW entities can be defined.
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exception
caosadvancedtools.models.parser.JsonSchemaDefinitionError(msg) Bases:
RuntimeError
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class
caosadvancedtools.models.parser.JsonSchemaParser(types_for_missing_array_items={}, ignore_unspecified_array_items=False) Bases:
caosadvancedtools.models.parser.ParserExtends the yaml parser to read in datamodels defined in a json schema.
EXPERIMENTAL: While this class can already be used to create data models from basic json schemas, there are the following limitations and missing features:
Due to limitations of json-schema itself, we currently do not support inheritance in the imported data models
The same goes for suggested properties of RecordTypes
Already defined RecordTypes and (scalar) Properties can’t be re-used as list properties
Reference properties that are different from the referenced RT. (Although this is possible for list of references)
Values
Roles
The extern keyword from the yaml parser
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class
caosadvancedtools.models.parser.Parser Bases:
object-
parse_model_from_string(string) Create and return a data model from the given YAML string.
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class
caosadvancedtools.models.parser.SafeLineLoader(stream) Bases:
yaml.loader.SafeLoaderLoad a line and keep meta-information.
Note that this will add a __line__ element to all the dicts.
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construct_mapping(node, deep=False) Overwritung the parent method.
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exception
caosadvancedtools.models.parser.YamlDefinitionError(line, template=None) Bases:
RuntimeError
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caosadvancedtools.models.parser.parse_model_from_json_schema(filename: str, top_level_recordtype: bool = True, types_for_missing_array_items: dict = {}, ignore_unspecified_array_items: bool = False) Return a datamodel parsed from a json schema definition.
- Parameters
filename (str) – The path of the json schema file that is to be parsed
top_level_recordtype (bool, optional) – Whether there is a record type defined at the top level of the schema. Default is true.
types_for_missing_array_items (dict, optional) – dictionary containing fall-back types for json entries with type: array but without items specification. Default is an empty dict.
ignore_unspecified_array_items (bool, optional) – Whether to ignore type: array entries the type of which is not specified by their items property or given in types_for_missing_array_items. An error is raised if they are not ignored. Default is False.
- Returns
out – The datamodel generated from the input schema which then can be used for synchronizing with CaosDB.
- Return type
Datamodel
Note
This is an experimental feature, see
JsonSchemaParserfor information about the limitations of the current implementation.
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caosadvancedtools.models.parser.parse_model_from_string(string) Shortcut if the Parser object is not needed.
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caosadvancedtools.models.parser.parse_model_from_yaml(filename) Shortcut if the Parser object is not needed.
Module contents
Submodule for working with data models.