Used to document all changes from previous releases and collect changes until the next release.
RDF subclasses are now properly added by default to any written RDF document. The RDF document will now also include RDF Subclass definitions in addition to the actual data to enable Subclass specific queries. See PR #400 and issue #397 for details.
"(x;x;...)" syntax as well. See PR #393 and issue #392 for details.A Python 2 deprecation warning for August 2020 has been added. See issue #387 for details.
See issues #377, #378 and #379 as well as Pull Request #389 for details.
An IssueID enum class as been added to provide identifiers to individual ValidationErrors. The Validation class itself has been refactored to provide the option to create standalone Validation instances with a different set of registered validations than the default library validation.
The Validation class now features the new register_custom_handler, run_validationand report methods to add custom validation handlers to an instance, re-run the validations of an existing Instance and provide a brief report of encountered errors and warnings. The general ValidationError.__repr__ string has been shortened to make the individual ValidationErrors more convenient to print and read. The default Validation is always run when a Document is saved or loaded via the ODMLParser and the Validation.report method is used to provide a warnings.warn message of the following format:
UserWarning: The saved Document contains formal issues. Run 'odml.validation.Validation(doc)' to resolve them.
Validation found 0 errors and 3 warnings in 1 Sections and 1 Properties.
Further changes to the Validation class and behavior include:
Document now provides a validate method that will run a default Validation and return the Validation instance to provide users with access to encountered issues.validation_id field has been added to the ValidationError class.section_repository_present validation has been removed from the default validation list. Since Sections rarely have repositories set, this validation can lead to spam when validating a Document.Property and Section now provide a cardinality feature. Users can now define a range how many Values a Property and how many Properties or Sections a Section should have. A cardinality can be set and read via its accessor method and can be set via an additional convenience method. Whenever a cardinality or an affected Value, Section or Property is set, a corresponding validation is triggered. If this a set cardinality for a Property or Section is violated, a message is printed to the command line directly and a warning is issued when a Document is saved or loaded. Every cardinality is saved to and loaded from all available file formats. The full functionality of all cardinality features are documented in the tutorial and is available via readthedocs. For additional details see pull requests #374, #382, #383, #384 and issue #361.
With recent updates the library now respects and enforces Section.type as a required attribute and allows save only with documents where this requirement is satisfied.
To allow backwards file compatibility and ease usage, Section.type is by default set to the string n.s. (not specified), which means files where no Section.type had been specified can be loaded and saved, but will contain n.s. as value for every Sections.type that was previously not specified.
Further the validation run before a document can be saved will issue a warning, if a Section.type with value n.s. is encountered and will still refuse to save with an error, if an empty Section.type is encountered. See PR #376 for details.
DictParser.DictReader is now able to ignore errors, collect warnings and print corresponding notifications and works now analogous to the xmlparser.XMLReader behaviour. See issue #367 for details.ODMLParser.ODMLReader for JSON and YAML now uses ignore_errors by default e.g. when using the odml.load function for JSON and YAML odml files.Property with dtype tuple. See issue #364 for details.name attribute to None, it now silently sets the name to id instead, since name must not be empty. It would be set to id on load and can cause AttributeError exceptions with some methods if its not set.format.revmap where the reverse mapping of an odml attribute would always return the case that the attribute is part of the format, even if it was not.Property.value attribute deprecation warnings have been unified. See issue #360 for details.base.Sectionable.create_section method has been updated to conform with Section.__init__. See issue #368 for details.Property and Section names has been added. See issue #365 for details.odml.Document.origin_file_name attribute. See issue #358 for details.odml.tools.converters.VersionConverter is changed to odml.tools.parser_utils.ParserException. See issue #359 for details.odml.Property.export_leaf method now also includes sibling Properties on export.rdf_converter has been cleaned up, see issues #211 and #345 for details.Section/Property order in documents obtained via the RDFReader has been expanded. See issue #265 for details.Section or Property init have been added. See issue #369 for details.pprint method and a link to the odML templates hosting site. Further the tutorial has been updated to include descriptions of the cardinality feature and Validation usage.yaml.load calls are replaced with yaml.save_load. This also prepares for Python 3.9 compatibility. See also issue #350 and pull request #356 for details.assertRegexpMatches and assertRegex depending on the Python version used to prepare for Python 3.9 compatibility while still keeping the Python 2 tests running.The XMLWriter can now be used to save an XML odML document with an inline XSL stylesheet for rendered viewing via a web browser.
The document can be saved with the current default G-Node odML document style or with a custom style. When a document containing such a stylesheet is loaded, the style is lost and needs to be provided again as described above. See issue #331 for details.
Subsets of odML documents can now be exported using the introduced export_leaf features for Section and Property.
When invoked on a Section or a Property, the method will return all direct ancestor Sections including all their direct Properties up to the root of the document and return a new, cloned document containing only this particular direct branch. See issue #340 for details.
Since issue #291 the odml package had its pyyaml dependency fixed to version 4.2b4.
This release fixes the original problem with the pyyaml distribution and removes the fix to pyyaml version 4.2b4.
See issue #343 and pull request #344 for details.
The package structure was changed to reduce the number of import cycles and make various parser classes more easily available via the __init__ files. See issues #317 and #333 for details.
The changes to the package structure should not affect any of the main parsers and how they were previously imported nor affect any of the command line scripts provided with this package.
The following changes have been introduced to the package structure:
odml.tools.converters is added.format_converter and version_converter are moved into this directory.version_converter, a dummy file is left at its original location. It imports the VersionConverter class from its new location and prints a deprecation warning.RDFConversionFormats from file tools.utils has been moved to RDF_CONVERSION_FORMATS in file tools.parser_utils and all usages have been switched to the new dict.ConversionFormats from file tools.utils has been moved to the only file its using it, tools.converters.format_converter.tools.utils has been removed.odml.rdf was added and the files fuzzy_finder and query_creator were moved into this directory. Both files provide convenience and additional functions for odML specific RDF and are fairly independent from the rest of the library. Conceptually they are best kept separate from other convenience tools and parsers.section_subclasses.yaml file is moved from the doc folder to the new odml/resources folder. This allows usage of the file with all install options. See issue #212 for details.rdf_converter now features a new load_rdf_subclasses function, that either provides the content of the resources/subclasses.yml file or, if it cannot be accessed, deals with it without breaking the RDFWriter.odml.Property.value attribute in the rdf_converter.RDFWriter will now call every odml documents finalize method to ensure that all links and includes are resolved before exporting to RDF.doc/root-ontology.ttl to odml/resources/odml-ontology.ttl and included in Manifest.in.resources/section_subclasses.yaml.resources/odml-ontology.ttl has been restructured:
resources/section_subclasses.yaml file have been added to the ontology file as well.date, time and datetime now contain a message providing the required format. See issue #341 for details.Support for importing and working with odML templates is added:
TemplateHandler class to handle import and usage of odML templates.https://templates.g-node.org.https://terminology.g-node.org.Currently most web browsers no longer support viewing local files that include further local files like stylesheets; check here for additional details. The console script odmlview provides a local webserver that is able to properly serve odML XML files from a local directory and render them correctly, if the appropriate stylesheets are present in the same directory.
'odmlview' sets up a minimal webserver to view odml files saved in the
XML format via the webbrowser. After it is started, the webserver will
open a new tab in the default webbrowser and display the content of
the directory the server was started from. odML files can then be
viewed from there.
To properly render XML, an odML file may contain the element
'<?xml-stylesheet type="text/xsl" href="odmlDocument.xsl"?>' where the
'odmlDocument.xsl' stylesheet should reside in the same directory as the
odML file to be rendered. By using the '--fetch' flag the latest version
of this stylesheet will be downloaded from `templates.g-node.org` to
the current directory when starting up the service.
The console script odmlconversion is renamed to odmlconvert. For backwards compatibility the script will be available as odmlconversion with a deprecation notice.
The pyyaml dependency has been changed to the non-breaking beta version 4.2b4. See issue #291 for details.
Document, Section and Property elements. If an ID already exists, it stays the same, if it is compatible with the Python UUID types. Otherwise (also if empty) a new ID is created for the odML entity.Property can now be set as int with value 0. See issue #314 for details.Property values of dtypes person, url and text is now possible. See issue #318 for details.RDFWriter format is set to turtle. See issue #214 for details.RDFWriter now checks for a given file extension within the RDF document name if accidentally given there. See issue #213 for details.RDFWriter now throws a ValueError if an unsupported RDF format is given. See issue #215 for details.XMLReader now properly handles entity creation failures when started with option ignore_errors=True. See issue #276 for details.pprint method has been added to Document to print while document section. See issue #319 for details.rst to the md format.pprint methods have been added to both Section and Property
to print whole Section trees with their child sections and properties.
The __repr__ style of Section and Property has been changed to
be more similar to the nixpy __repr__ style.
Printing a Section now also features the immediate Property child count
in addition to the immediate Section child count. See #309.
To make working with odML more similar to working with the
metadata part of nixpy, the Property.value
attribute has been marked deprecated and the Property.values
attribute has been added. See #308.
Uncertainty is now limited to float only. See #294.
The VersionConverter dealt with an edge case of XML test files with opening tags that were missing their closing tag rendering them broken. Catching this one edge case circumvented opening XML files via lxml, leaving the resulting document open to various encoding problems.
Support to resolve the specific tag edge cases is dropped in favour of properly opening XML files via lxml. See #301.
The odmlconversion convenience console script has been added to convert multiple
previous odML version files to the latest odML version.
When cloning a Section or a Property by default the id of any object is changed
to a new UUID. The cloning methods now feature a new keep_id attribute. If set to
True, the cloned object and any cloned children retain their original id. This
is meant to create exact copies of Section-Property trees in different documents.
When a document is saved, a new validation check makes sure, that a document contains only unique UUIDs this is required due to the introduction of creating clones with identical ids.
pyyaml was version fixed on 3.13 to circumvent introduced breaking changes in the library. See #291, #292, #296, #298.docopt was added to support console scriptsVersionConverter XML parser. See #288, #296.XMLParser that when reading a single string value from csv which contains commata, it now remains a single value and is not split up at each comma. See #295, #296.XMLParser any leading or trailing whitespaces are removed from any string values when it is written to csv. Along the same lines, multiple values that are saved to file via the VersionConverter do not contain leading whitespaces any longer. See #296.unicode has been introduced to all Parsers and Converters to avoid encoding errors with Python 2 and Python 3. See #297.Section and Property SmartListSmartList.sort(). By default Document and Section child lists will retain the order in which child elements were added, but now a sort by name can be manually triggered. See #290.SmartList comparison magic methods to partially address #265. The introduction of the RDF backend led to an issue when comparing odML entities. The used RDF library rdflib does not respect child order upon loading of a file, odML entities with children can not be compared without sorting the child elements. The added magic methods sort child elements by name before comparison without changing the actual order of the child elements. This only addresses the issue for Section and Property child lists, but does not solve the problem for the order of Property.values. See #290._origin_file_name is added to the Document entity. When an odML document is loaded from file, this attribute is now set with the file name from whence the document was loaded. See #297.Seq is now used instead of Bag to store odml.Property values to respect the order of values. See #292.rdflib currently does not support proper Seq behaviour with RDF li items, for now the index of the value items will be manually written as RDF properties, which rdflib supports when reading an RDF file. See #292._origin_file_name, the value is exported as odml:hasFileName. See #297.xml is now the default ODMLWriter format when writing a document to RDF since the XML format of RDF is still the format with the broadest acceptance. See #297.odmltordf convenience console script has been added to convert multiple odML files to the RDF format from any odML format or version. See #298.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.
base._baseobj class, leaving BaseObject as the root odML class.doc.Document class, leaving BaseDocument as the only odML Document class.section.Section class, leaving BaseSection as the only odML Section class.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.reorder method is moved from the base to the Section class. See #267.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.__setitem__ method of a PropertyValue attributes uncertainty, unit, dtype and reference have been moved to
Property and now apply to all values of the Property.value list.Value attributes filename, encoder and checksum have been removed.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 functionality has been removed.XMLReader.fromFile() and .fromString() have been renamed to .from_file() and .from_string() respectively.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.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.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.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.new_id() method to Document, Section and Property which generates
and sets a new valid id for any entity. See #262.None or ""."false", "f", 0, False, "true", "t", 1 or True
will now raise a ValueError. See #224base.Sectionable.extend method for child Sections and Properties. See #237.base.Sectionable.insert and .append methods. Only proper
BaseSections with a unique name can be added to the Section child list of a
Sectionable.append method to
mirror Property append functionality and since extend now serves this need.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.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.reference and definition from the "source" Section if they
were None in the "destination" Section. See #273.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.Section or a Property is cloned, a new id is set for the clone and of any
cloned children. See #259.Document.append since
Document.extend should be used to add multiple new Sections to a Document.Section.extend method.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.Property init. See #253.http://portal.g-node.org/odml/terminologies/v1.1/terminologies.xml.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.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/.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.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.tools.jsonparser file which is no longer required due to the classes in
tools.odmlparser and tools.dict_parser.tools.FormatConverter class which enables batch conversion of one odML
format into another.tools.VersionConverter class which enables conversion of pre-v1.4 odML files
into valid v1.4 odML.
VersionConverter converts XML, JSON and YAML based odML files of odML file
version 1.0 to odML file version 1.1.Document, Section and Property are exported. Any
non supported attribute will produce a warning message, the content will be
discarded.Value object to its parent Property value list.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.filename attribute content of a Value is moved to the value_origin
attribute of its parent Property.repository or link is updated from v1.0 to their
v1.1 counterparts if available.VersionConverter object provides a .conversion_log list attribute to access all
info and warning messages after a conversion has taken place. See #234.False as well as F are now properly converted to bool values in both
Python 2 and 3. See #222.XMLParser.Document now properly uses the dtypes date setter on init. See #249.None boolean and datetime related values. See #245.id when comparing odML entities for equality. See #260.Property is cloned, the parent of the clone is now properly set to None.AttributeError on get_path() when a Property has no parent. See #256.AttributeError on get_merged_equivalent() when a Property
has no parent. See #257.Property.append(), if the dtype was not set. See #266.Property.append() exits on empty values but accepts 0 and False.Property.uncertainty to None if an empty string is passed to it.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.Property.parent = None bugs in remove() and insert() methods.ODMLParser class. See #199.BaseSection or BaseDocument for isinstance checks throughout
base instead of a mixture of BaseSection and Section.info.py.Version, Format version, Contact,
Homepage, Author, PyPI Classifiers, Copyright.setup.py. The license text interfered with the PyPI
process in a way, that the description was not displayed on PyPI.json or yaml files; #191.json or yaml files when Section.repository, Section.link or Section.include are present; #194.backend argument that specifies the parser or writer.
Can be one of XML, JSON, or YAML.