- #166: Add new custom IDS method :meth:`icat.client.Client.restoreData`.
- #165: Fix missing documentation on the environment injected by :class:`icat.ingest.IngestReader` into the input as changed in 1.5.0.
- #160, #161, #163: Add class attributes to :class:`icat.ingest.IngestReader` to make some prescribed values in the transformation to ICAT data file format configurable.
- #155, #156: Add an option to disable parsing of command line arguments in :class:`icat.config.Config`.
- #157: :mod:`icat.ingest` now considered stable.
- #143, #144: Make it easier to configure XSLT files to use for processing the input in custom versions of :class:`icat.ingest.IngestReader`.
- #148, #149: Inject an additional element with environment information into the input data in :class:`icat.ingest.IngestReader`.
- #146, #147, #151: Better error handling in :class:`icat.ingest.IngestReader`.
#144: Drop class attribute :attr:`icat.ingest.IngestReader.XSLT_name` in favour of :attr:`icat.ingest.IngestReader.XSLT_Map`.
Note that :mod:`icat.ingest` has been declared experimental for now.
- #125, #140: Add support to link datasets with samples in :mod:`icat.ingest`.
- #122, #133: Allow referencing related objects by reference key in object references in XML ICAT data file format.
#138, #139: Fix the input that :mod:`icat.ingest` generates on the fly to be valid according to the ICAT data file schema. This also affects the input that the module accepts: the order of subelements of data need to be changed such that datasetTechnique comes before datasetInstrument.
Note that :mod:`icat.ingest` has been declared experimental for now.
- #131, #135: Fix :meth:`icat.ids.IDSClient.getApiVersion` to yield correct results for ids.server 2.0.0 and newer.
- #132, #136: Fix a spurious :exc:`AttributeError` on cleanup after connecting to an invalid url.
- #130, #137: Review test suite.
- #113, #123: Add module :mod:`icat.ingest`.
- #124: Add an optional keyword argument keepInstRel to :meth:`icat.entity.Entity.truncateRelations`.
- #126, #127: Update outdated documentation.
- #112, #118: Extend icatdata XSD adding extra attributes to reference objects.
- #111, #121: Change the type of :attr:`icat.client.Client.Register` to :class:`weakref.WeakValueDictionary`, fixing a memory leak.
- #119, #120: Remove _config attribute from :class:`icat.config.Configuration`.
- #115, #116: Fix the test suite to work if either PyYAML or lxml is not available.
- #128: Return an empty list from :func:`icat.dump_queries.getDataPublicationQueries` when talking to an ICAT server older than 5.0.
- #117: Fixed deprecation warnings from upcoming Python 3.12.
- #129: Review the build of the documentation at Read the Docs.
- #73, #106: Add support for the ICAT schema 5.0 extensions.
- #102, #104: Make the obj argument to :meth:`icat.client.Client.new` case insensitive.
- #77, #103: Add a keyword argument preset to allow directly passing configuration values to the constructor of class :class:`icat.config.Config`.
- #66, #75: Add pathlib support: methods that take a file name argument also accept a :class:`pathlib.Path` object. Internal representation of file system paths are changed to use :class:`pathlib.Path` where appropriate. The predefined configuarion variable configFile now supports tilde expansion. Note incompatible changes below.
- #74: :class:`icat.ids.DataSelection` also accepts DataCollection as argument.
- The order and arrangement of data objects in the dump file created by :ref:`icatdump` has been changed. In some cases, older versions of :ref:`icatingest` will fail to read dump files written by new versions of :ref:`icatdump`.
- As a consequence of switching to pathlib for file system paths some
return values and variables are now :class:`pathlib.Path` objects
rather then :class:`str`. This affects:
- the return value of :func:`icat.config.cfgpath`,
- the predefined configuarion variable configFile,
- the module variable :data:`icat.config.cfgdirs`.
- Drop support for Python 2 and Python 3.3.
- Drop keyword argument attribute and method :meth:`icat.query.Query.setAttribute` from class :class:`icat.query.Query`, deprecated in 0.18.0.
- Drop module :mod:`icat.cgi`, deprecated in 0.13.0.
- Drop module :mod:`icat.icatcheck` and exception :exc:`icat.exception.GenealogyError`, deprecated in 0.17.0.
- Drop methods :meth:`icat.ids.IDSClient.resetPrepared`, :meth:`icat.ids.IDSClient.getPreparedDatafileIds`, :meth:`icat.ids.IDSClient.getPreparedData`, :meth:`icat.ids.IDSClient.getPreparedDataUrl`, :meth:`icat.client.Client.getPreparedData`, and :meth:`icat.client.Client.getPreparedDataUrl`, deprecated in 0.17.0.
- Drop the predefined configuration variable configDir, deprecated in 0.13.0.
- Drop helper function :func:`icat.exception.stripCause`, deprecated in 0.14.0.
- Deprecate :data:`icat.config.defaultsection`. Use the new preset keyword argument to :class:`icat.config.Config` instead.
- #98, #105: Review build tool chain. Add a helper class :class:`icat.helper.Version`.
- #101: Fix tests failing with PyYAML 6.0.
- Some (more) example scripts now require ICAT 4.4.0 or newer.
- #100: Add read only attributes :attr:`icat.query.Query.select_clause`, :attr:`icat.query.Query.join_clause`, :attr:`icat.query.Query.where_clause`, :attr:`icat.query.Query.order_clause`, :attr:`icat.query.Query.include_clause`, and :attr:`icat.query.Query.limit_clause` to access the respective clauses of the query string.
- #96: Fix failing build of the documentation at Read the Docs.
- #86, #89: allow SQL functions to be used on the attributes in the arguments to :meth:`icat.query.Query.setOrder` and :meth:`icat.query.Query.addConditions`.
- #94: the implementation of #89 changed the internal data structures in :attr:`icat.query.Query.conditions` and :attr:`icat.query.Query.order`. These attributes are considered internal and are deliberately not documented, so one could argue that this is not an incompatible change. But the changes also have an impact on the return value of :meth:`icat.query.Query.__repr__` such that it is not suitable to recreate the query object.
- #90, #91, #95: :attr:`icat.query.Query.join_specs` was not taken into account in :meth:`icat.query.Query.copy` and :meth:`icat.query.Query.__repr__`.
- #85: add an argument join_specs to the constructor of class :class:`icat.query.Query` and a corresponding method :meth:`icat.query.Query.setJoinSpecs` to override the join specification to be used in the created query for selected related objects.
- #83, #84: enable ordering on one to many relationships in class :class:`icat.query.Query`.
- #84: Add warning classes :exc:`icat.exception.QueryOneToManyOrderWarning` and :exc:`icat.exception.QueryWarning`, the latter being a common base class for warnings emitted during creation of a query.
- #82: Change the search result in the case of multiple fields from list to tuple.
- #76, #81: work around an issue in icat.server using DISTINCT in search queries for multiple fields.
- #76, #78: add client side support for searching for multiple fields introduced in icat.server 4.11.0. Add support for building the corresponding queries in the in class :class:`icat.query.Query`.
- Since :class:`icat.query.Query` now also accepts a list of attribute names rather then only a single one, the corresponding keyword argument attribute has been renamed to attributes (in the plural). Accordingly, the method :meth:`icat.query.Query.setAttribute` has been renamed to :meth:`icat.query.Query.setAttributes`. The old names are retained as aliases, but are deprecated.
- #79: fix an encoding issue in :attr:`icat.client.Client.apiversion`, only relevant with Python 2.
- #80: add :exc:`TypeError` as additional ancestor of :exc:`icat.exception.EntityTypeError`.
- #65: Add support for the extended IDS API calls :meth:`icat.ids.IDSClient.getSize` and :meth:`icat.ids.IDSClient.getStatus` accepting a preparedId as introduced in ids.server 1.11.0. Also extend the methods :meth:`icat.ids.IDSClient.reset`, :meth:`icat.ids.IDSClient.getDatafileIds`, :meth:`icat.ids.IDSClient.getData`, :meth:`icat.ids.IDSClient.getDataUrl`, :meth:`icat.client.Client.getData`, and :meth:`icat.client.Client.getDataUrl` to accept a preparedId in the place of a data selection.
- #63: Set a default path in the URL for ICAT and IDS respectively.
- Drop support for ICAT 4.2.*, deprecated in 0.13.0.
- #61, #64: Review :mod:`icat.entities`. The entity classes from the ICAT schema are now dynamically created based on the information gathered with the :meth:`icat.client.Client.getEntityInfo` ICAT API call. Code that relied on the internals of :mod:`icat.entities` such as the class hierarchy or that referenced any of the entity classes directly will need to be revisited. Note that common python-icat programs don't need to do any of that. So it is assumed that most existing programs are not concerned.
- Deprecate :meth:`icat.ids.IDSClient.resetPrepared`, :meth:`icat.ids.IDSClient.getPreparedDatafileIds`, :meth:`icat.ids.IDSClient.getPreparedData`, :meth:`icat.ids.IDSClient.getPreparedDataUrl`, :meth:`icat.client.Client.getPreparedData`, and :meth:`icat.client.Client.getPreparedDataUrl`. Call the corresponding methods without Prepared in the name with the same arguments instead.
- Deprecate support for Python 2 and Python 3.3.
- Deprecate module :mod:`icat.icatcheck`. This module was not intended to be used in python-icat programs anyway.
- #68: :ref:`wipeicat` enters an infinite loop if Datafiles are missing from IDS storage.
- #19, #69: Review documentation and add tutorial.
- #62: Minor fixes in the error handling in setup.py.
- Fix icatdata-4.10.xsd: :attr:`Study.endDate` was erroneously not marked as optional.
- #70: Fix several errors in the tests.
- #58: Use specific test data for different ICAT versions.
- #67, #71, #72: document the option to use suds-community instead of suds-jurko.
- Do not include the documentation in the source distribution. Rely on the online documentation (see link in the README.rst) instead.
- #59: Add support for sub-commands in :mod:`icat.config`.
- Drop support for Python 2.6.
- #60: Fix bad coding style dealing with function parameters.
- Use :mod:`setuptools_scm` to manage the version number.
- Issue #56: :ref:`icatdump` fails to include :attr:`Shift.instrument`.
- Issue #57: :meth:`icat.client.Client.searchChunked` still susceptible to LIMIT clause bug in icat.server (Issue icatproject/icat.server#128).
- Call :func:`yaml.safe_load` rather then :func:`yaml.load`, fixing a deprecation warning from PyYAML 5.1.
- #53: Add support for ICAT 4.10.0 including schema changes in that version.
- Require pytest 3.1.0 or newer to run the test suite. Note that this pytest version in turn requires Python 2.6, 2.7, or 3.3 and newer.
- Drop support for Python 3.1 and 3.2. There is no known issue with these Python versions in python-icat (so far). But since we can't test this any more, see above, we drop the claim to support them.
- #49: Module icat.eval is outdated.
- #50, #52: Fix DeprecationWarnings.
- #51: Fix a compatibility issue with pytest 4.1.0 in the tests.
- #54: Fix a UnicodeDecodeError in the tests.
- Add a hook to control internal diverting of :attr:`sys.err` in the :mod:`icat.config` module. This is intentionally not documented as it goes deeply into the internals of this module and most users will probably not need it.
- Fix a misleading error message if the IDS server returns an error for the Write API call.
- #45: Add support for the IDS Write API call introduced in ids.server 1.9.0.
- #46, #47: Add a :meth:`ìcat.client.Client.autoRefresh` method. The scripts :ref:`icatdump` and :ref:`icatingest` call this method periodically to prevent the session from expiring.
- #48: Add support for an ordering direction qualifier in class :class:`icat.query.Query`.
- #44: Add method :meth:`icat.entity.Entity.as_dict`.
- #40: Add method :meth:`icat.client.Client.clone`.
Deprecate function :func:`icat.exception.stripCause`.
This was an internal helper function not really meant to be part of the API. The functionality has been moved in a base class of the exception hierarchy.
- Add the :meth:`icat.ids.IDSClient.version` API call introduced in ids.server 1.8.0.
- #41: Incomprehensible error messages with Python 3.
- #43: :meth:`icat.client.Client.logout` should silently ignore :exc:`icat.exception.ICATSessionError`.
- Minor changes in the error handling. Add new exception :exc:`icat.exception.EntityTypeError`.
- Documentation fixes.
- #38: There should be a way to access the kwargs used to create the client in config.
#11: Support discovery of info about available ICAT authenticators.
If supported by the ICAT server (icat.server 4.9.0 and newer), the :mod:`icat.config` module queries the server for information on available authenticators and the credential keys they require for login. The configuration variables for these keys are then adapted accordingly. Note incompatible changes below.
Review :ref:`wipeicat`. This was an example script, but is now promoted to be a regular utility script that gets installed.
#32: Add support for using aggregate functions in class :class:`icat.query.Query`.
#30: Add a predefined config variable type :func:`icat.config.cfgpath`.
#31: Add a flag to add the default variables to the :class:`icat.config.Config` constructor (default: True).
:class:`icat.dumpfile_xml.XMLDumpFileReader` also accepts a XML tree object as input.
Verify support for ICAT 4.9.0. Add new ICAT API method :meth:`icat.client.Client.getVersion`.
As a consequence of the discovery of available authenticators, the workflow during configuration need to be changed. Until now, the beginning of a typical python-icat program would look like:
config = icat.config.Config() # Optionally, add custom configuration variables: # config.add_variable(...) conf = config.getconfig() client = icat.Client(conf.url, **conf.client_kwargs)
E.g. first the configuration variables are set up, then the configuration is applied and finally the :class:`icat.client.Client` object is created using the configuration values. With the discovery of authenticators, the :class:`icat.config.Config` object itself needs a working :class:`icat.client.Client` object in order to connect to the ICAT server and query the authenticator info. The :class:`icat.client.Client` object will now be created in the :class:`icat.config.Config` constructor and returned along with the configuration values by :meth:`icat.config.Config.getconfig`. You will need to replace the code from above by:
config = icat.config.Config() # Optionally, add custom configuration variables: # config.add_variable(...) client, conf = config.getconfig()
The derived configuration variable client_kwargs that was used to pass additional arguments from the configuration to the Client constructor is no longer needed and has been removed.
The optional argument args has been moved from the :meth:`icat.config.Config.getconfig` call to the :class:`icat.config.Config` constructor, retaining the same semantics. E.g. you must change in your code:
config = icat.config.Config() conf = config.getconfig(args) client = icat.Client(conf.url, **conf.client_kwargs)
to:
config = icat.config.Config(args) client, conf = config.getconfig()
Deprecate support for ICAT 4.2.*.
Note that already now significant parts of python-icat require features from ICAT 4.3 such as the JPQL like query language. The only workaround is to upgrade your icat.server.
Deprecate module :mod:`icat.cgi`.
It is assumed that this has never actually been used in production. For web applications it is recommended to use the Python Web Server Gateway Interface (WSGI) rather then CGI.
Deprecate the predefined configuration variable configDir.
The main use case for this variable was to be substituted in the default value for the path of an additional configuration file. The typical usage was the definition of a configuration variable like:
config = icat.config.Config() config.add_variable('extracfg', ("--extracfg",), dict(help="Extra config file"), default="%(configDir)s/extra.xml", subst=True)This set the default path for the extra config file to the same directory the main configuration file was found in. Using the new config variable type :func:`icat.config.cfgpath` you can replace this by:
config = icat.config.Config() config.add_variable('extracfg', ("--extracfg",), dict(help="Extra config file"), default="extra.xml", type=icat.config.cfgpath)This will search the extra config file in all the default config directories, regardless where the main configuration file was found.
The fixes for #35 and #36 require some changes in the semantics in the f and the mode argument to :func:`icat.dumpfile.open_dumpfile`. Most users will probably not notice the difference.
- Changed the default for the :class:`icat.config.Config` constructor
argument ids from :const:`False` to
"optional". - Improved :meth:`icat.client.Client.searchChunked`. This version is not susceptible to Issue icatproject/icat.server#128 anymore.
- Move the management of dependencies of tests into a separate package pytest-dependency that is distributed independently.
- #34: :exc:`TypeError` in the :class:`icat.client.Client` constructor if setting the sslContext keyword argument.
- #35: :exc:`io.UnsupportedOperation` is raised if :func:`icat.dumpfile.open_dumpfile` is called with an in-memory stream.
- #36: :class:`icat.dumpfile.DumpFileReader` and :class:`icat.dumpfile.DumpFileWriter` must not close file.
- #37: :exc:`TypeError` is raised when writing a YAML dumpfile to :class:`io.StringIO`.
- Verify support for ICAT 4.8.0 and IDS 1.7.0.
- Add methods :meth:`icat.ids.IDSClient.reset` and :meth:`icat.ids.IDSClient.resetPrepared`.
- #28: Add support for searching for attributes in class :class:`icat.query.Query`.
- Sort objects in :ref:`icatdump` before writing them to the dump file. This keeps the order independent from the collation used in the ICAT database backend.
- #2: for Python 3.6 (expected to be released in Dec 2016) and newer, use the support for chunked transfer encoding in the standard lib. Keep our own implementation in module :mod:`icat.chunkedhttp` only for compatibility with older Python versions.
- Improved the example script :ref:`wipeicat`.
- Add an example script dumprules.py.
- Add missing schema definition for the ICAT XML data file format for ICAT 4.7.
- Fix an :exc:`AttributeError` during error handling.
- #12, #23: add support for ICAT 4.7.0 and IDS 1.6.0. ICAT 4.7.0 had some small schema changes that have been taken into account.
- Remove the autoget argument from :meth:`icat.entity.Entity.getUniqueKey`. Deprecated since 0.9.0.
- #21: configuration variable promptPass is ignored when set in the configuration file.
- #18: Documentation: missing stuff in the module index.
- #20: add test on compatibility with icat.server.
- #24, #25: test failures caused by different timezone settings of the test server.
- Use a separate module distutils_pytest to run the tests from setup.py.
- :mod:`icat.icatcheck`: move checking of exceptions into a separate method :meth:`icat.icatcheck.ICATChecker.checkExceptions`. Do not report exceptions defined in the client, but not found in the schema.
- Many fixes in the example script :ref:`wipeicat`.
- Fix a missing import in the icatexport.py example script.
- Somewhat clearer error messages for some special cases of :exc:`icat.exception.SearchAssertionError`.
- Change license to Apache 2.0.
- Add a method :meth:`icat.entity.Entity.copy`.
- Implement setting an INCLUDE 1 clause equivalent in class :class:`icat.query.Query`.
- Add an optional argument includes to :meth:`icat.client.Client.searchMatching`.
- Add a hook for a custom method to validate entity objects before creating them at the ICAT server.
- Add support for ids.server 1.5.0:
- Add :meth:`icat.ids.IDSClient.getDatafileIds` and :meth:`icat.ids.IDSClient.getPreparedDatafileIds` calls.
- :meth:`icat.ids.IDSClient.getStatus` allows sessionId to be None.
- Add new exception class :exc:`icat.exception.ICATNotImplementedError` that is supposed to be raised by the upcoming version 4.6.0 of icat.server.
- #13: :meth:`icat.client.Client.searchChunked` raises exception if the query contains a percent character.
- #15: :ref:`icatdump` raises :exc:`icat.exception.DataConsistencyError` for DataCollectionParameter.
- #14: :meth:`icat.entity.Entity.__sortkey__` may raise :exc:`RuntimeError` "maximum recursion depth exceeded".
- Allow a :class:`icat.ids.DataSelection` to be created from (almost) any Iterator, not just a :class:`Sequence`. Store the object ids in :class:`icat.ids.DataSelection` internally in a :class:`set` rather then a :class:`list`.
- Add optional arguments objindex to :meth:`icat.dumpfile.DumpFileReader.getobjs` and keyindex to :meth:`icat.dumpfile.DumpFileWriter.writedata` to allow the caller to control these internal indices.
- Add optional argument chunksize to :meth:`icat.dumpfile.DumpFileWriter.writedata`.
- The constructor of class :class:`icat.query.Query` checks the version of the ICAT server and raises an error if too old.
- The :meth:`icat.ids.IDSClient.getIcatUrl` call checks the version of the IDS server.
- Some changes in the test suite, add more tests.
#4: Extend :ref:`icatrestore <icatingest>` to become a generic ingestion tool.
Rename :ref:`icatrestore <icatingest>` to :ref:`icatingest`.
Allow referencing of objects by attribute rather then by unique key in the input file for :ref:`icatingest` (only in the XML backend).
Allow adding references to already existing objects in the input file for :ref:`icatingest` (only in the XML backend).
Change the name of the root element in the input file for :ref:`icatingest` (and the output of :ref:`icatdump`) from icatdump to icatdata (only in the XML backend).
Implement upload of Datafiles to IDS rather then only creating the ICAT object from :ref:`icatingest`.
Implement handling of duplicates in :ref:`icatingest`. The same options (THROW, IGNORE, CHECK, and OVERWRITE) as in the import call in the ICAT restful interface are supported.
#1: add a test suite.
#3: use Sphinx to generate the API documentation.
Add method :meth:`icat.client.Client.searchMatching`.
Add the :meth:`icat.ids.IDSClient.getIcatUrl` call introduced with IDS 1.4.0.
- The Lucene calls that have been removed in ICAT 4.5.0 are also removed from the client.
- Deprecate the use of the autoget argument in :meth:`icat.entity.Entity.getUniqueKey`.
- #6: :class:`icat.query.Query`: adding a condition on a meta attribute fails.
- #10: client.putData: IDSInternalError is raised if datafile.datafileCreateTime is set.
- Ignore import errors from the backend modules in :ref:`icatingest` and :ref:`icatdump`. This means one can use the scripts also if the prerequisites for some backends are not fulfilled, only the concerned backends are not available then.
- #5, compatibility with ICAT 4.5: entity ids are not guaranteed to be unique among all entities, but only for entities of the same type.
- #5, compatibility with ICAT 4.5: :meth:`icat.client.Client.getEntityInfo` also lists createId, createTime, modId, and modTime as attributes. This need to be taken into account in :mod:`icat.icatcheck`.
- The last fix in 0.8.0 on the string representation operator :meth:`icat.query.Query.__str__` was not complete, the operator still had unwanted side effects.
- Fix a bug in the handling of errors raised from the ICAT or the IDS server. This bug affected only Python 3.
- Add proper type checking and conversion for setting an attribute that corresponds to a one to many relationship in class :class:`icat.entity.Entity`. Accept any iterable of entities as value.
- #9: :ref:`icatingest` with duplicate=CHECK may fail when attributes are not strings. Note that this bug was only present in an alpha version, but not in any earlier release version.
- Source repository moved to Git. This gives rise to a few tiny changes. To name the most visible ones: python2_6.patch is now auto generated by comparing two source branches and must be applied with -p1 instead of -p0, the format of the icat module variable :attr:`icat.__revision__` has changed.
- Review default exports of modules. Mark some helper functions as internal.
Enable verification of the SSL server certificate in HTTPS connections. Add a new configuration variable checkCert to control this. It is set to :const:`True` by default.
Note that this requires either Python 2.7.9 or 3.2 or newer. With older Python version, this configuration option has no effect.
Add type conversion of configuration variables.
Add substituting the values of configuration variables in other variables.
Add another derived configuration variable configDir.
Default search path for the configuration file: add an appropriate path on Windows, add
/etc/icatand~/.config/icatto the path if not on Windows.Add icatexport.py and icatimport.py example scripts that use the corresponding calls to the ICAT RESTful interface to dump and restore the ICAT content.
The constructor of :exc:`icat.exception.ICATError` and the :func:`icat.exception.translateError` function are now able to construct exceptions based on a dict such as those returned by the ICAT RESTful interface in case of an error.
Unified handling of errors raised from the ICAT and the IDS server.
As a consequence of the unified handling of errors, the exception class hierarchy has been reviewed, with a somewhat more clear separation of exceptions raised by other libraries, exceptions raised by the server, and exceptions raised by python-icat respectively.
If you put assumptions on the exception hierarchy in your code, this might need a review. In particular, :exc:`icat.exception.IDSResponseError` is not derived from :exc:`icat.exception.IDSError` any more. :exc:`icat.exception.IDSServerError` has been removed.
I.e., replace all references to :exc:`icat.exception.IDSServerError` by :exc:`icat.exception.IDSError` in your code. Furthermore, if you catch :exc:`icat.exception.IDSError` in your code with the intention to catch both, errors from the IDS server and :exc:`icat.exception.IDSResponseError` in one branch, replace:
try: # ... except IDSError: # ...by
try: # ... except (IDSError, IDSResponseError): # ...
- The :class:`icat.query.Query` class now checks the attributes referenced in conditions and includes for validity.
- Fix a regression introduced with version 0.7.0 that caused non-ASCII characters in queries not to work.
- Fix :exc:`icat.exception.ICATError` and :exc:`icat.exception.IDSError` to gracefully deal with non-ASCII characters in error messages. Add a common abstract base class :exc:`icat.exception.ICATException` that cares about this.
- Fix: the string representation operator :meth:`icat.query.Query.__str__` should not modify the query object.
- Cosmetic improvement in the formal representation operator :meth:`icat.query.Query.__repr__`.
Add a module :mod:`icat.query` with a class :class:`icat.query.Query` that can be used to build ICAT search expressions. Instances of the class may be used in place of search expression strings where appropriate.
Numerous examples on how to use this new class can be found in querytest.py in the examples.
Add a class method :meth:`icat.entity.Entity.getNaturalOrder` that returns a list of attributes suitable to be used in an ORDER BY clause in an ICAT search expression.
Add a class method :meth:`icat.entity.Entity.getAttrInfo` that queries the EntityInfo from the ICAT server and extracts the information on an attribute.
Add a method :meth:`icat.client.Client.getEntityClass` that returns the :class:`icat.entity.Entity` subclass corresponding to a name.
Add a warning class :exc:`icat.exception.QueryNullableOrderWarning`.
Add an optional argument username to the :meth:`icat.ids.IDSClient.getLink` method.
Add support for ICAT 4.4.0: add new :class:`icat.entity.Entity` type InvestigationGroup, role has been added to the constraint in InvestigationUser.
Add new API method :meth:`icat.ids.IDSClient.getApiVersion` that will be introduced with the upcoming version 1.3.0 of IDS. This method may also be called with older IDS servers: if it is not available because the server does not support it yet, the server version is guessed from visible features in the API.
:class:`icat.ids.IDSClient` checks the API version on init.
Add new API methods :meth:`icat.ids.IDSClient.isReadOnly`, :meth:`icat.ids.IDSClient.isTwoLevel`, :meth:`icat.ids.IDSClient.getLink`, and :meth:`icat.ids.IDSClient.getSize` introduced with IDS 1.2.0.
Add no_proxy support. The proxy configuration variables, http_proxy, https_proxy, and no_proxy are set in the environment. [Suggested by Alistair Mills]
Rework the dump file backend API for :ref:`icatdump` and :ref:`icatrestore <icatingest>`. As a result, writing custom dump or restore scripts is much cleaner and easier now.
This may cause compatibility issues for users who either wrote their own dump file backend or for users who wrote custom dump or restore scripts, using the XML or YAML backends. In the first case, compare the old XML and YAML backends with the new versions and you'll easily see what needs to get adapted. In the latter case, have a look into the new versions of :ref:`icatdump` and :ref:`icatrestore <icatingest>` to see how to use the new backend API.
Add method :meth:`icat.client.Client.searchChunked`.
Add method :meth:`icat.entity.Entity.getAttrType`.
Move the group argument to method :meth:`icat.client.Client.createRules` to the last position and make it optional, having default :const:`None`.
In the client code, replace:
client.createRules(group, crudFlags, what)
by
client.createRules(crudFlags, what, group)
The :meth:`icat.client.Client.putData` method returns the new Datafile object created by IDS rather then only its id.
If you depend on the old behavior in the client code, replace:
dfid = client.putData(file, datafile)
by
df = client.putData(file, datafile) dfid = df.id
The :meth:`icat.client.Client.searchText` and :meth:`icat.client.Client.luceneSearch` client method have been deprecated. They are destined to be dropped from the ICAT server or at least changed in version 4.5.0 and might get removed from python-icat in a future release as well.
The methods now emit a deprecation warning when called. Note however that Python by default ignores deprecation warnings, so you won't see this unless you switch them on.
Fixed overly strict type checking in the constructor arguments of :class:`icat.ids.DataSelection` and as a consequence also in the arguments of the ICAT client methods :meth:`icat.client.Client.getData`, :meth:`icat.client.Client.getDataUrl`, :meth:`icat.client.Client.prepareData`, and :meth:`icat.client.Client.deleteData`: now, any :class:`Sequence` of entity objects will be accepted, in particular an :class:`icat.entity.EntityList`.
Change :meth:`icat.ids.IDSClient.archive` and :meth:`icat.ids.IDSClient.restore` to not to return anything. While formally, this might be considered an incompatible change, these methods never returned anything meaningful in the past.
Slightly modified the == and != operator for :class:`icat.entity.Entity`. Add a :meth:`icat.entity.Entity.__hash__` method. The latter means that you will more likely get what you expect when you create a set of :class:`icat.entity.Entity` objects or use them as keys in a dict.
The module :mod:`icat.eval` now only does its work (parsing command line arguments and connecting to an ICAT server) when called from the Python command line. When imported as a regular module, it will essentially do nothing. This avoids errors to occur when imported.
setup.py raises an error with Python 2.6 if python2_6.patch has not been applied.
Add missing MANIFEST.in in the source distribution.
Remove the work around the Suds datetime value bug (setting the environment variable TZ to
UTC) from :mod:`icat`. Instead, document it along with other known issues in the README.Minor fixes in the sorting of entity objects.
Add an optional argument args to :meth:`icat.config.Config.getconfig`. If set to a list of strings, it replaces :attr:`sys.argv`. Mainly useful for testing.
Add comparison operators to class :class:`icat.listproxy.ListProxy`.
Add a module :mod:`icat.eval` that is intended to be run using the
-mcommand line switch to Python. It allows to evaluate Python expressions within an ICAT session as one liners directly from the command line, as for example:# get all Dataset ids $ python -m icat.eval -e 'client.search("Dataset.id")' -s root [102284L, 102288L, 102289L, 102293L]Fix an issue in the error handling in the IDS client that caused an :exc:`urllib2.HTTPError` to be raised instead of an :exc:`icat.exception.IDSServerError` in the case of an error from the IDS server and thus the loss of all details about the error reported in the reply from the server.
Add specific exception classes for the different error codes raised by the IDS server.
Fix compatibility issue with Python 3.3 that caused the HTTP method to be set to :const:`None` in some IDS methods, which in turn caused an internal server error to be raised in the IDS server.
Fix compatibility issues with Python 3.4: some methods have been removed from class :class:`urllib.request.Request` which caused an :exc:`AttributeError` in the :class:`icat.ids.IDSClient`.
Fix: failed to connect to an ICAT server if it advertises a version number having a trailing "-SNAPSHOT" in :meth:`icat.client.Client.getApiVersion`. For compatibility, a trailing "-SNAPSHOT" will be replaced by "a1" in the client.apiversion attribute.
Suppress misleading context information introduced with Python 3 (PEP 3134) from the traceback in some error messages. Unfortunately, the fix only works for Python 3.3 and newer.
Make example files compatible across Python versions without modifications, such as running 2to3 on them.
Integrate an IDS client in the ICAT client.
Improved :ref:`icatdump` and :ref:`icatrestore <icatingest>`:
- Changed the logical structure of the dump file format which significantly simplified the scripts. Note that old dump files are not compatible with the new versions.
- Add support for XML dump files. A XML Schema Definition for the dump file format is provided in the doc directory.
The scripts are now considered to be legitimate tools (though still alpha) rather then mere examples. Consequently, they will be installed into the bin directory.
Implicitly set a one to many relation to an empty list if it is accessed but not present in an :class:`icat.entity.Entity` object rather then raising an :exc:`AttributeError`. See ICAT Issue 112.
Allow setting one to many relationship attributes and deletion of attributes in :class:`icat.entity.Entity`. Add method :meth:`icat.entity.Entity.truncateRelations`. Truncate dummy relations set by the factory in newly created entity objects.
Cache the result from :meth:`icat.client.Client.getEntityInfo` in the client.
Add a method :meth:`icat.entity.Entity.__sortkey__` that return a key that when used as a sorting key in :meth:`list.sort` allows any list of entity objects to have a well defined order. Sorting is based on the Constraint attributes. Add a class variable :attr:`icat.entity.Entity.SortAttrs` that overrides this and will be set as a fall back for those entity classes that do not have a suitable Constraint.
- Add support for the jurko fork of Suds and for Python 3.
- Add a new method :meth:`icat.client.Client.searchUniqueKey`.
- Add an optional argument keyindex to method :meth:`icat.entity.Entity.getUniqueKey` that is used as a cache of previously generated keys. Remove the argument addbean. It had been documented as for internal use only, so this is not considered an incompatible change.
- Add a new exception :exc:`icat.exception.DataConsistencyError`. Raise this in :meth:`icat.entity.Entity.getUniqueKey` if a relation that is required in a constraint is not set.
- Rename :exc:`icat.exception.SearchResultError` to :exc:`icat.exception.SearchAssertionError`. SearchResultError was a misnomer here, as this exception class is very specific to :meth:`icat.client.Client.assertedSearch`. Add a new generic exception class :exc:`icat.exception.SearchResultError` and derive :exc:`icat.exception.SearchAssertionError` from it. This way, the change should not create any compatibility problems in client programs.
- Add a check in :mod:`icat.icatcheck` that the :exc:`icat.exception.ICATError` subclasses are in sync with icatExceptionType as defined in the schema.
- Bugfix: The code dealing with exceptions raised by the ICAT server did require all attributes in IcatException sent by the server to be set, although some of these attributes are marked as optional in the schema.
- Do not delete the Suds cache directory in :meth:`icat.client.Client.cleanup`.
- Installation: python-icat requires Python 2.6 or newer. Raise an error if setup.py is run by a too old Python version.
- Move some internal routines in a separate module :mod:`icat.helper`.
- Greatly improved example scripts :ref:`icatdump` and :ref:`icatrestore <icatingest>`.
Add support for ICAT 4.3.1. (Compatibility with ICAT 4.3.2 has also been tested but did not require any changes.)
Implement alias names for entity attributes. This facilitates compatibility of client programs to different ICAT versions. E.g. a client program may use rule.grouping regardless of the ICAT version, for ICAT 4.2.* this is aliased to rule.group.
Add a method :meth:`icat.client.Client.assertedSearch`.
Add a method :meth:`icat.entity.Entity.getUniqueKey`.
Add entity methods :meth:`Group.getUsers` and :meth:`Instrument.getInstrumentScientists`.
WARNING, incompatible change!
Changed entity methods :meth:`Instrument.addInstrumentScientist` and :meth:`Investigation.addInvestigationUser` to not to create the respective user any more, but rather expect a list of existing users as argument. Renamed :meth:`Group.addUser`, :meth:`Instrument.addInstrumentScientist`, and :meth:`Investigation.addInvestigationUser` to :meth:`addUsers`, :meth:`addInstrumentScientists`, and :meth:`addInvestigationUsers` (note the plural "s") respectively.
In the client code, replace:
pi = investigation.addInvestigationUser(uid, fullName=userName, search=True, role="Principal Investigator")by
pi = client.createUser(uid, fullName=userName, search=True) investigation.addInvestigationUsers([pi], role="Principal Investigator")
Work around a bug in the way SUDS deals with datetime values: set the local time zone to
UTC.Add example scripts :ref:`icatdump` and :ref:`icatrestore <icatingest>`.
Rework internals of :mod:`icat.config`.
Bugfix: :class:`icat.config.Config` required a password to be set even if prompt for password was requested.
Add support for configuration via environment variables.
Add support of HTTP proxy settings. [Suggested by Alistair Mills]
WARNING, incompatible change! The configuration read by :mod:`icat.config` is not stored as attributes on the :class:`icat.config.Config` object itself, but rather :meth:`icat.config.Config.getconfig` returns an object with these attributes set. This keeps the configuration values cleanly separated from the attributes of the :class:`icat.config.Config` object.
In the client code, replace:
conf = icat.config.Config() conf.getconfig()
by
config = icat.config.Config() conf = config.getconfig()
Move :exc:`ConfigError` from :mod:`icat.config` to :mod:`icat.exception`.
Move :exc:`GenealogyError` from :mod:`icat.icatcheck` to :mod:`icat.exception`.
Review export of symbols. Most client programs should only need to import :mod:`icat` and :mod:`icat.config`.
- Initial version