Add caching specification to file to ensure readability of distributed files #242
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@@ Coverage Diff @@
## dev #242 +/- ##
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- Coverage 56.06% 55.2% -0.87%
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Files 56 56
Lines 5105 5355 +250
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+ Hits 2862 2956 +94
- Misses 2243 2399 +156
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…d files NWB files contain a currently freeform area in ``/general/specifications`` for storing specifications. To ease use of the specification data it is now possible to: * Assign a neurodata_type to ``/general/specifications`` and create a custom ``NWBContainer`` class to manage specifications. * Create a new neurodata_type to be stored in ``/general/specifications`` to structure the storage of namespace and associated specification files rather than requiring that specs be stored in a single dataset * Automatically write all specs used by (or registered with) PyNWB to the NWB file when a file is written. This will help ensure that the spec for all objects are always stored in the file. * Add ability to use use specifications (including custom extensions) from the HDF5 directly on read. We possibly need an option here to allow the user decide whether to use specs from the HDF5 file or the specs currently registered with PyNWB. See #44, #108 More specifically, this commit adds: * class for loading namespace * class for writing namespace * tooling to ``h5tools`` for caching spec to file * getter for ``FORMIO`` source * return of registered types to ``SpecCatalog.auto_register`` * tracking of type sources in ``NamespaceCatalog`` * class for building specification files to ``NamespaceBuilder`` * requirement that spec files be in the same directory as namespace file * getters for ``NamespaceCatalog`` to ``BuildManager`` * tracking of overridden specs * ability to read/write specs to/from HDF5 file * reference-to-reference write * roundtrip test for caching spec to hdf5 file * add roundtrip test for caching spec This commit also implements the following changes: * make dataset fill methods classmethods * make ``Spec`` and ``Namespace`` catalogs maintain specs and namespaces with OrderedDict * require parent spec be passed in, rather than parent spec nam * import ``SpecNamespace`` to ``h5tools`` * fix bug when showing default strings in signature * allow string to be passed into ``BaseStorageSpec`` when extending * refactor caching of spec * import HDF5 spec reader/writer classes to package-level * use ``unittest2`` instead of ``unittest`` for ``integration.test_io`` * import spec reader/writer abstract classes to ``form.spec`` subpackage * deploy spec caching feature
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dorukozturk
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NWB files contain a currently freeform area in
/general/specificationsfor storingspecifications. To ease use of the specification data it is now possible to:
Assign a neurodata_type to
/general/specificationsand create a customNWBContainerclass to manage specifications.
Create a new neurodata_type to be stored in
/general/specificationsto structure thestorage of namespace and associated specification files rather than requiring that specs
be stored in a single dataset
Automatically write all specs used by (or registered with) PyNWB to the NWB file when a
file is written. This will help ensure that the spec for all objects are always stored
in the file.
Add ability to use use specifications (including custom extensions) from the HDF5 directly
on read. We possibly need an option here to allow the user decide whether to use specs from
the HDF5 file or the specs currently registered with PyNWB.
See #44, #108
More specifically, this commit adds:
h5toolsfor caching spec to fileFORMIOsourceSpecCatalog.auto_registerNamespaceCatalogNamespaceBuilderNamespaceCatalogtoBuildManagerThis commit also implements the following changes:
SpecandNamespacecatalogs maintain specs and namespaces with OrderedDictSpecNamespacetoh5toolsBaseStorageSpecwhen extendingunittest2instead ofunittestforintegration.test_ioform.specsubpackage