Allow annotation stores to include/depend on other annotation stores (stand-off STAM JSON files)

[proycon]

Currently an annotation store in STAM JSON can reference annotation datasets
and resources in separate stand-off files. What is not yet possible, however,
is to reference annotations defined in other STAM JSON annotation stores.

This use-case was raised in #21 by @tenzin3, see the lead up discussion there.

In such a case, an annotation in store_a.store.stam.json makes reference (via
an annotation selector) to an annotation defined in store_b.store.stam.json.
That is currently not possible. I do think it is a fair use case and more
flexibility in using stand-off files fits nicely with STAM's stand-off
philosophy.

This issue proposes to expand the STAM model to allow this:

• The @include mechanism in STAM JSON would be extended to allow including
  other annotation stores. In effect, an annotation store can then depend
  on on another by importing it, these includes are executed before loading any of its own annotations.
  Recursive includes would be allowed (allowing more complex dependency chains),
  but cyclic includes would be explicitly forbidden! Includes may (and are in fact encouraged to) reference the same
  stand-off resources and annotation data sets.

Possible syntax for this:

{
    "@type":"AnnotationStore",
    "@include": [ "store_b.stam.store.json", "store_c.stam.store.json" ],
    ...
}

• On the implementation-side, when loaded into memory there is still always one
  AnnotationStore instance to work with at any given time. This would
  however serialize to multiple files. This requires some extra bookkeeping
  to be implemented, as for each annotation we need to know to what
  annotation store it should go. The implementation might define
  'substores' and keep map filenames to lists of annotation handles.
  This new bookkeeping would at the same time make splitting stores easier
  than it is in the currently implementation (where splitting is basically a fairly expensive deletion action).
  Merging and splitting becomes more reversible.

[proycon]

@tenzin3 @ngawangtrinley This has now been implemented (in stam-rust 0.15.0, stam-tools 0.8.0, stam-python 0.9.0). The @include mechanism is extended to allow including other annotation stores as dependencies. The STAM JSON specification here explains how this works.

The implementation should still be considered a bit experimental though, as it hasn't yet been thoroughly tested in real use cases like yours, so it's possible that some bugs may still surface or that some more API methods are desired.

When creating multiple annotation stores that have dependencies, it is recommended to first create the dependencies independently, and then later include them from the 'superstore' using this new method: https://stam-python.readthedocs.io/en/latest/autoapi/stam/index.html#stam.AnnotationStore.add_substore .

[tenzin3]

@proycon. Thank you for implementing this feature so quickly. We will test this out and get back to you if we are facing any issues .