Merge speed update with new connectome & data integrity tests #262
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- Set skipIfNewer option to true in loadData for ExampleRunnerTest - PEP-8 formatting in a couple files
- Split off Property into its own module - Moved old dataObject into v0 subpackage (split into two modules) - Restored ExampleRunnerTest
- Partially adapted Neuron's special properties to work with graphObject querier
- Added SimpleProperty::defined_values and replaced calls to SimpleProperty::values in identifier() definitions for consistent resoulution of identifiers generated from values - Altered DataIntegrity test to test worm.db in project root - Several `autopep8' formatting adjustments - Made use of __future__.print_function in test.py is anticipation of Python 3 compat (#66)
- Removed Property values from Property identifier calculation. Greatly improves the speed of graph serialization - Replaced list type of values with internal sub-class of list type - Fixed up insert_worm.py - Use a single worm and single network object and save only once - Renamed upload_* methods to add_* to reflect behavior - Removed do-nothing type Relationship as parent of connection.Connection - Redirected tests.DataIntegrityTest to actually load data into the database under test
- Added expectedFailure to a SimpleProperty test to reflect changed behavior, and modified another to match its description
- Allowed ObjectProperties to accept SimpleProperty objects
- Corrected EvidenceTest tests
- Minor code cleanup
- Changed channel_name to name - Restored subfamily attribute doc
Conflicts: PyOpenWorm/__init__.py setup.py tests/DataIntegrityTest.py tests/test.py
- Moved infer() before serialization in insert_worm.py - Reset the Neuron __str__ method to just the neuron name - Went back to generating the connection identifier on-demand - Reset the SimpleProperty __repr__ to show its values - Un-pinned the yarom dependency to v0.7.0 - Set the skipIfNewer option in DataIntegrityTest back to False - Fixed undefined names in expected_failures in DataIntegrityTest
- Moved DataIntegrityTest test database deletion back to teardown
- Removed data loading from ExampleRunnerTest
Changes to some neuron names and associated URLs AVFL/R -> AVFL + AVFR DB1/3 -> DB1 DB3/1 -> DB3 Added "1" to indicate AVM is a neuron
Update connectome tsv sheet from google sheets
- was mis-named test_diff_value_same_id_not_empty Conflicts: PyOpenWorm/simpleProperty.py
- Removed expected failure from DocumentationTest
Conflicts: OpenWormData/scripts/insert_worm.py tests/DataIntegrityTest.py tests/DataTestTemplate.py tests/GraphDBInit.py
- Removed duplicate tests in DataIntegrityTest.py - Added URIs to the acceptable keys for Evidence - Removed the print-out of the config in gap_junctions.py
Merging latest changes from mwatts15 into experimental branch
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For the neuron count being off, at least one problem is that Connection objects are being initialized with strings for the pre and post cell, but these default to Neuron objects rather than whatever kind of cell is supposed to be involved. |
- Reduced repetition in upload_connections() in insert_worm.py
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Merge speed update with new connectome & data integrity tests
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This is an attempt to merge the contents of pull requests #213 #252 and #258.
Merging the new connectome and data integrity tests resulted in performance that made the system unusable. The updates by @mwatts15 in #213 improve the situation.
Currently there are failing tests related to certain values not working appropriately. Also, most of the data integrity tests are currently skipped due to performance that is still too slow :-/
If we can at least get the values correct, we can integrate and then look at the performance issue separately.
cc: @ahrasheed @signija @travs