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Merge pull request #549 from dimitri-yatsenko/master
Add documentation of transactions
2 parents 5a17452 + 29d8853 commit 24f1978

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‎datajoint/declare.py

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@@ -271,10 +271,10 @@ def compile_attribute(line, in_key, foreign_key_sql):
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match['default'] = ''
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match = {k: v.strip() for k, v in match.items()}
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match['nullable'] = match['default'].lower() == 'null'
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acceptable_datatype_pattern = r'^(time|date|year|enum|(var)?char|float|real|double|decimal|numeric|' \
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r'(tiny|small|medium|big)?int|bool|' \
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r'(tiny|small|medium|long)?blob|external|attach)'
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if re.match(acceptable_datatype_pattern, match['type'], re.I) is None:
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accepted_datatype = r'time|date|year|enum|(var)?char|float|real|double|decimal|numeric|' \
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r'(tiny|small|medium|big)?int|bool|' \
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r'(tiny|small|medium|long)?blob|external|attach'
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if re.match(accepted_datatype, match['type'], re.I) is None:
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raise DataJointError('DataJoint does not support datatype "{type}"'.format(**match))
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literals = ['CURRENT_TIMESTAMP'] # not to be enclosed in quotes

‎docs-parts/computation/01-autopopulate_lang1.rst

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img = (test.Image & key).fetch1['image']
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key['filtered_image'] = myfilter(img)
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self.insert(key)
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The ``make`` method receives one argument: the dict ``key`` containing the primary key value of an element of :ref:`key source <keysource>` to be worked on.

‎docs-parts/intro/Releases_lang1.rst

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0.11.1 -- Nov 15, 2018
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----------------------
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* Fix ordering of attributes in proj (#483 and #516)
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* Prohibit direct insert into auto-populated tables (#511)
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0.11.0 -- Oct 25, 2018
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----------------------
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* Full support of dependencies with renamed attributes using projection syntax (#300, #345, #436, #506, #507)
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* Rename internal class and module names to comply with terminology in documentation (#494, #500)
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* Full support of secondary indexes (#498, 500)
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* ERD no longer shows numbers in nodes corresponding to derived dependencies (#478, #500)
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* Full support of unique and nullable dependencies (#254, #301, #493, #495, #500)
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* Improve memory management in ``populate`` (#461, #486)
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* Fix query errors and redundancies (#456, #463, #482)
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0.10.1 -- Aug 28, 2018
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-----------------------
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* Fix ERD Tooltip message (#431)
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* Networkx 2.0 support (#443)
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* Fix insert from query with skip_duplicates=True (#451)
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* Sped up queries (#458)
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* Bugfix in restriction of the form (A & B) * B (#463)
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* Improved error messages (#466)
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0.10.0 -- Jan 10, 2018
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----------------------
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* Deletes are more efficient (#424)
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* ERD shows table definition on tooltip hover in Jupyter (#422)
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* S3 external storage
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* Garbage collection for external sorage
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* Most operators and methods of tables can be invoked as class methods rather than instance methods (#407)
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* The schema decorator object no longer requires locals() to specify the context
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* Compatibility with pymysql 0.8.0+
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* More efficient loading of dependencies (#403)
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0.9.0 -- Nov 17, 2017
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---------------------
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* Made graphviz installation optional
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* Implement file-based external storage
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* Implement union operator +
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* Implement file-based external storage
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0.8.0 -- Jul 26, 2017
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---------------------
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Documentation and tutorials available at https://docs.datajoint.io and https://tutorials.datajoint.io
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* improved the ERD graphics and features using the graphviz libraries (#207, #333)
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* improved password handling logic (#322, #321)
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* the use of the ``contents`` property to populate tables now only works in ``dj.Lookup`` classes (#310).
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* allow suppressing the display of size of query results through the ``show_tuple_count`` configuration option (#309)
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* implemented renamed foreign keys to spec (#333)
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* added the ``limit`` keyword argument to populate (#329)
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* reduced the number of displayed messages (#308)
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* added ``size_on_disk`` property for dj.Schema() objects (#323)
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* job keys are entered in the jobs table (#316, #243)
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* simplified the ``fetch`` and ``fetch1`` syntax, deprecating the ``fetch[...]`` syntax (#319)
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* the jobs tables now store the connection ids to allow identifying abandoned jobs (#288, #317)
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0.5.0 (#298) -- Mar 8, 2017
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---------------------------
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* All fetched integers are now 64-bit long and all fetched floats are double precision.
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* Added ``dj.create_virtual_module``
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0.4.10 (#286) -- Feb 6, 2017
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----------------------------
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* Removed Vagrant and Readthedocs support
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* Explicit saving of configuration (issue #284)
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0.4.9 (#285) -- Feb 2, 2017
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---------------------------
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* Fixed setup.py for pip install
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0.4.7 (#281) -- Jan 24, 2017
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----------------------------
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* Fixed issues related to order of attributes in projection.
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0.4.6 (#277) -- Dec 22, 2016
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----------------------------
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* Proper handling of interruptions during populate
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0.4.5 (#274) -- Dec 20, 2016
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----------------------------
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* Populate reports how many keys remain to be populated at the start.
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0.4.3 (#271) -- Dec 6, 2016
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----------------------------
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* Fixed aggregation issues (#270)
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* datajoint no longer attempts to connect to server at import time
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* dropped support of view (reversed #257)
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* more elegant handling of insufficient privileges (#268)
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0.4.2 (#267) -- Dec 6, 2016
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----------------------------
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* improved table appearance in Jupyter
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0.4.1 (#266) -- Oct 28, 2016
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----------------------------
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* bugfix for very long error messages
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0.3.9 -- Sep 27, 2016
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---------------------
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* Added support for datatype ``YEAR``
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* Fixed issues with ``dj.U`` and the ``aggr`` operator (#246, #247)
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0.3.8 -- Aug 2, 2016
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---------------------
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* added the ``_update`` method in ``base_relation``. It allows updating values in existing tuples.
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* bugfix in reading values of type double. Previously it was cast as float32.
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0.3.7 -- Jul 31, 2016
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----------------------
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* added parameter ``ignore_extra_fields`` in ``insert``
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* ``insert(..., skip_duplicates=True)`` now relies on ``SELECT IGNORE``. Previously it explicitly checked if tuple already exists.
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* table previews now include blob attributes displaying the string <BLOB>
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0.3.6 -- Jul 30, 2016
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----------------------
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* bugfix in ``schema.spawn_missing_classes``. Previously, spawned part classes would not show in ERDs.
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* dj.key now causes fetch to return as a list of dicts. Previously it was a recarray.
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0.3.5
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-----
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* ``dj.set_password()`` now asks for user confirmation before changing the password.
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* fixed issue #228
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0.3.4
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-----
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* Added method the ``ERD.add_parts`` method, which adds the part tables of all tables currently in the ERD.
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* ``ERD() + arg`` and ``ERD() - arg`` can now accept relation classes as arg.
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0.3.3
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-----
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* Suppressed warnings (redirected them to logging). Previoiusly, scipy would throw warnings in ERD, for example.
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* Added ERD.from_sequence as a shortcut to combining the ERDs of multiple sources
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* ERD() no longer text the context argument.
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* ERD.draw() now takes an optional context argument. By default uses the caller's locals.
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0.3.2
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-----
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* Fixed issue #223: ``insert`` can insert relations without fetching.
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* ERD() now takes the ``context`` argument, which specifies in which context to look for classes. The default is taken from the argument (schema or relation).
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* ERD.draw() no longer has the ``prefix`` argument: class names are shown as found in the context.

‎docs-parts/intro/empty.txt

Whitespace-only changes.

‎docs-parts/manipulation/3-Transactions_lang1.rst

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Transactions are formed using the ``transaction`` property of the connection object.
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The connection object may be obtained from any table object.
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The ``transaction`` property can then be used as a context manager in Python's ``with`` statement.
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For example, the following code inserts matching entries for the master table ``Session`` and its part table ``Session.Experimenter``.
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.. code-block:: python
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# get the connection object
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connection = Session.connection
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# insert Session and Session.Experimenter entries in a transaction
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with connection.transaction:
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key = {'subject_id': animal_id, 'session_time': session_time}
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Session.insert1({**key, 'brain_region':region, 'cortical_layer':layer})
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Session.Experimenter.insert1({**key, 'experimenter': username})
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Here, to external observers, both inserts will take effect together upon exiting from the ``with`` block or will not have any effect at all.
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For example, if the second insert fails due to an error, the first insert will be rolled back.
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