Breaking changes
The switch from odML version 1.3 to 1.4 contains many cool updates which should make work more comfortable, but also includes some breaking changes.
Update of the odML file format version
- The odML format version number in odML files has changed from "1" to "1.1".
Changes in odML classes
- The odML class hierarchy has been flattened:
- removing `base._baseobj` class, leaving `BaseObject` as the root odML class.
- removing `doc.Document` class, leaving `BaseDocument` as the only odML Document class.
- removing `section.Section` class, leaving `BaseSection` as the only odML Section class.
- removing `property.Property` class leaving `BaseProperty` as the only odML Property class.
- `baseobject` and `sectionable` are renamed to `BaseObject` and `Sectionable` respectively.
- `base.SafeList` and `base.SmartList` have been merged, `base.SafeList` has been removed.
- `base.SmartList` can now only contain Sections or Properties. See 272.
- The `reorder` method is moved from the `base` to the `Section` class. See 267.
Changes in Value handling:
- The `Value` class has been removed.
- `Property.value` now always holds a list of uniform values. `Property.value` always
returns a copy of the actual value list. See 227.
- Values can only be changed directly via the `__setitem__` method of a `Property`
- `Value` attributes `uncertainty`, `unit`, `dtype` and `reference` have been moved to
`Property` and now apply to all values of the `Property.value` list.
- The `Value` attributes `filename`, `encoder` and `checksum` have been removed.
DType changes:
- The `binary` dtype has been removed. Providing binary content via odML files is
discouraged in favor of providing a reference to the origin files using the `URL`
dtype instead.
Mapping
- Any `mapping` functionality has been removed.
Minor breaking changes
- `XMLReader.fromFile()` and `.fromString()` have been renamed to `.from_file()` and `.from_string()` respectively.
Features and changes
Required odML entity attributes handling
- Required attributes of odML entities in `odml.format` where changed: `Section.name`,
`Section.type` and `Property.name` are the only attributes set to be required for
their respective odML entities. See 240.
- `Section.name` and `Property.name` can now be `None` on init. If this is the case, the
entities' `id` value is used as `name` value.
- Hardcoded checks for existing `name` attributes in the XML Parser are removed. Only
attributes set as required in `format` are now used to check for missing required odML
entity attributes. See 241.
- The `name` attribute of a `Section` or a `Property` can now only be rewritten if there
is no sibling with the same name on the same hierarchical level. See 283.
Addition of the 'id' attribute
- `Document`, `Section` and `Property` now have an `id` attribute to uniquely identify any
entity. If no valid id is provided when an entity is initialized, an id is
automatically generated and assigned.
- Adding the `new_id()` method to `Document`, `Section` and `Property` which generates
and sets a new valid id for any entity. See 262.
Changes in DType handling
- Setting a dtype now also supports odML style tuple types. See 254.
- DTypes now always return the defined default values if a value is `None` or `""`.
- Any boolean dtype value other than `"false", "f", 0, False, "true", "t", 1` or `True`
will now raise a `ValueError`. See 224
'base.Sectionable' (Document and Section) changes
- Adds a `base.Sectionable.extend` method for child Sections and Properties. See 237.
- Refactors the `base.Sectionable.insert` and `.append` methods. Only proper
`BaseSections` with a unique name can be added to the Section child list of a
`Sectionable`.
- Appending multiple Sections or Properties has been removed from the `append` method to
mirror Property `append` functionality and since `extend` now serves this need.
'Section' and 'Property' merge
- `Property` now provides a `merge` method to merge two properties. This will sync all but
the dependency and dependencyValue attributes. ValueErrors are raised, if information
is set in both properties but are in conflict. See 221.
- Adds a `Section.merge_check()` method which validates whether a Section including all
its sub-sections and sub-properties can properly be merged. A `ValueError` is raised
if any potential merge problem arises. This is necessary since a recursive Section
merge cannot be easily rolled back once begun.
- A Section merge imports `reference` and `definition` from the "source" Section if they
were `None` in the "destination" Section. See 273.
- Adds a `strict` flag to any `merge` method. Now all `Section` and `Property` attribute
checks during a merge will only be done, if `strict=True`. On `strict=False` a
`Section` or `Property` attribute will only be replaced with the "source" value, if
the "destination" value is `None`. Otherwise the "destination" value will be kept and
the "source" value lost. See 270.
Changes of 'Section' and 'Property' clone
- When a `Section` or a `Property` is cloned, a new id is set for the clone and of any
cloned children. See 259.
'Document' changes
- Tuples of Sections can now no longer be used with `Document.append` since
`Document.extend` should be used to add multiple new Sections to a Document.
'Section' changes
- Adds a `Section.extend` method.
'Property' changes
- `Property` has the new attribute `value_origin` which may contain the origin of the
property's value e.g. a filename.
- `Property` init now supports setting all attributes as well as its parent.
- `Property` now provides `append`, `extend` and `remove` methods to change the actual
value list. This approach is required to ensure DType checks when adding new values
to an existing list. See 223.
- Only valid dtypes can now be set on `Property` init. See 253.
Terminology changes
- The default odML terminology repository is set to `http://portal.g-node.org/odml/terminologies/v1.1/terminologies.xml`.
Changes in Tools and IO
- The `XMLParser` can now be run in warning mode: any errors encountered during parsing
will just print a warning, but will not stop and exit during the parsing process.
- An odML document can now only be saved, if the validation does not show any errors.
Saving an invalid document will stop the process before saving and print all
encountered errors.
- All parsers are now more relaxed when encountering unsupported or missing tags and only
print warnings instead of ending with an exception. Warnings are collected and can be
accessed via the parser object.
- When trying to open a file with any of the odML parsers, the document format version
number is checked. If the version number does not match the supported one, file
loading will fail with an exception.
New tools
- Added the `tools.RDFWriter` and `toosl.RDFReader` classes, which enable the export of
odML documents to RDF and also provides the used ontology OWL file at `doc/odml_terminology/`.
- Added the `tools.ODMLWriter` and `tools.ODMLReader` classes which serve as an easy
entry point to saving and loading for all the supported file formats `XML`, `YAML`,
`JSON` and `RDF`.
- Added the `tools.DictWriter` and `tools.DictReader` classes which convert Python
dictionary data to odML data and vice versa, which in turn is required for both YAML
and JSON format loading and saving.
- Removed the `tools.jsonparser` file which is no longer required due to the classes in
`tools.odmlparser` and `tools.dict_parser`.
- Added the `tools.FormatConverter` class which enables batch conversion of one odML
format into another.
- Added the `tools.VersionConverter` class which enables conversion of pre-v1.4 odML files
into valid v1.4 odML.
- The `VersionConverter` converts `XML`, `JSON` and `YAML` based odML files of odML file
version 1.0 to odML file version 1.1.
- Only attributes supported by `Document`, `Section` and `Property` are exported. Any
non supported attribute will produce a warning message, the content will be
discarded.
- The value content is moved from a `Value` object to its parent `Property` value list.
- The first encountered `unit` or `uncertainty` of values of a `Property` will be moved
to its parent `Property`. Any differing subsequent `unit` or `uncertainty` of
values of the same `Property` will produce a warning message, the content will be
discarded.
- The first `filename` attribute content of a `Value` is moved to the `value_origin`
attribute of its parent `Property`.
- Any g-node terminology URL in `repository` or `link` is updated from v1.0 to their
v1.1 counterparts if available.
- A `VersionConverter` object provides a `.conversion_log` list attribute to access all
info and warning messages after a conversion has taken place. See 234.
Fixes
- Various installation issues have been resolved for Linux and MacOS.
- `False` as well as `F` are now properly converted to bool values in both
Python 2 and 3. See 222.
- Fixes saving datetime related values to JSON. See 248.
- odML style custom tuples can now properly be saved using the `XMLParser`.
- `Document` now properly uses the dtypes date setter on init. See 249.
- Fixes load errors on Empty and `None` boolean and datetime related values. See 245.
- Excludes `id` when comparing odML entities for equality. See 260.
- When a `Property` is cloned, the parent of the clone is now properly set to `None`.
- Avoids an `AttributeError` on `get_path()` when a `Property` has no parent. See 256.
- Avoids an `AttributeError` on `get_merged_equivalent()` when a `Property`
has no parent. See 257.
- Avoids an error on `Property.append()`, if the dtype was not set. See 266.
- Makes sure that `Property.append()` exits on empty values but accepts `0` and `False`.
- Sets `Property.uncertainty` to `None` if an empty string is passed to it.
- Changes the `Property.__init__` set attributes order: In the previous set attribute
order, the repository attribute was overwritten with `None` by the `super.__init__`
after it had been set.
- Fixes set `Property.parent = None` bugs in `remove()` and `insert()` methods.
- Consistently use relative imports to address circular imports and remove code that
circumvents previous circular import errors in the `ODMLParser` class. See 199.
- Consistently uses `BaseSection` or `BaseDocument` for isinstance checks throughout
`base` instead of a mixture of `BaseSection` and `Section`.