Merge pull request #18 from INCATools/sssom-mappings

Adding aggregayor interface

docs/implementations/aggregator.rst

@@ -0,0 +1,16 @@
+Aggregator Implementation
+==================
+
+.. warning ::
+
+   Highly incomplete!
+
+This wraps any number of other implementations, multiplexing queries and aggregating results, treating
+as if it were a single unified endpoints
+
+Code
+----
+
+.. currentmodule:: oaklib.implementations.aggregator.aggregator_implementation
+
+.. autoclass:: AggregatorImplementation

docs/implementations/bioportal.rst

@@ -16,4 +16,3 @@ Code
 .. currentmodule:: oaklib.implementations.bioportal.bioportal_implementation
 
 .. autoclass:: BioportalImplementation
-    :members: create

docs/implementations/index.rst

@@ -22,6 +22,7 @@ The most mature implementations are:
    obofiles
    sqldb
    robot
+   funowl
    skos
    ols
    bioportal
@@ -30,4 +31,6 @@ The most mature implementations are:
    ontobee
    ols
    bioportal
+   kgx
+   aggregator
 

docs/implementations/obofiles.rst

@@ -15,4 +15,3 @@ Code
 .. currentmodule:: oaklib.implementations.pronto.pronto_implementation
 
 .. autoclass:: ProntoImplementation
-    :members: create

docs/implementations/ols.rst

@@ -3,14 +3,13 @@ Ontology Lookup Service (OLS) Endpoint
 
 .. warning ::
 
-   not yet implemented!
+   very partially implemented!
 
-When implemented this will also provide implementation of the mapping interface via OxO
+Also provides interface to OxO
 
 Code
 ----
 
 .. currentmodule:: oaklib.implementations.ols.ols_implementation
 
 .. autoclass:: OlsImplementation
-    :members: create

docs/implementations/ontobee.rst

@@ -14,4 +14,3 @@ Code
 .. currentmodule:: oaklib.implementations.ontobee.ontobee_implementation
 
 .. autoclass:: OntobeeImplementation
-    :members: create

docs/implementations/owlery.rst

@@ -11,4 +11,3 @@ Code
 .. currentmodule:: oaklib.implementations.owlery.owlery_implementation
 
 .. autoclass:: OwleryImplementation
-    :members: create

docs/implementations/sparql.rst

@@ -5,4 +5,4 @@ Sparql Endpoint
 .. currentmodule:: oaklib.implementations.sparql.sparql_implementation
 
 .. autoclass:: SparqlImplementation
-    :members: create
+

docs/implementations/ubergraph.rst

@@ -21,7 +21,6 @@ Code
 .. currentmodule:: oaklib.implementations.ubergraph.ubergraph_implementation
 
 .. autoclass:: UbergraphImplementation
-    :members: create
 
 .. autoclass:: RelationGraphEnum
 

docs/index.rst

@@ -11,10 +11,12 @@ Ontology Access Kit (OAK) Documentation
    :caption: Contents:
 
    introduction
+   intro/index
    architecture
    interfaces/index
    implementations/index
    cli
+   selectors
    datamodels/index
    utilities
    notebooks

docs/interfaces/mapping-provider.rst

@@ -0,0 +1,7 @@
+Mapping Provider
+==============
+
+.. currentmodule:: oaklib.interfaces.mapping_provider_interface
+
+.. autoclass:: MappingProviderInterface
+    :members:

docs/selectors.rst

@@ -0,0 +1,121 @@
+.. _selectors:
+
+Ontology Implementation Selectors
+=================
+
+In the command line interface and in Python code, *descriptors* can be used as a shorthand way to refer to either a local or remote ontology, plus
+a method for parsing/querying it. The OntologyResource that is returned can be used
+to instantiate an implementation. The descriptors can also be used in the :ref:`cli`
+
+Syntax
+-----
+
+A descriptor is EITHER:
+
+ - prefixed with a *scheme* OR
+ - is a *path (in which case the scheme is inferred)
+
+Examples
+-----
+
+Examples of scheme-less descriptors, implicit implementation:
+
+- :code:`tests/input/go-nucleus.obo` - local obo format file loaded with pronto
+- :code:`tests/input/go-nucleus.json` - local obojson format file loaded with pronto
+- :code:`tests/input/go-nucleus.owl` - local OWL rdf/xml format file (loaded with pronto at the moment may change)
+- :code:`tests/input/go-nucleus.db` - local sqlite3 db loaded with SqlImplementation
+- :code:`http://purl.obolibrary.org/obo/pato.obo` - NOT IMPLEMENTED; download locally for now
+- :code:`http://purl.obolibrary.org/obo/pato.owl` - NOT IMPLEMENTED; download locally for now
+
+Examples of explicit schemes:
+
+- :code:`pronto:tests/input/go-nucleus.obo` - local obo format file loaded with pronto
+- :code:`pronto:tests/input/go-nucleus.json` - local obojson format file loaded with pronto
+- :code:`pronto:tests/input/go-nucleus.owl` - local OWL rdf/xml format file (loaded with pronto at the moment may change)
+- :code:`pronto:tests/input/go-nucleus.db` - local sqlite3 db loaded with SqlImplementation
+- :code:`prontolib:pato.obo` - remote obo format file loaded from OBO Library with pronto
+- :code:`prontolib:pato.owl` - remote owl format file loaded from OBO Library with pronto
+- :code:`bioportal:` all of bioportal
+- :code:`bioportal:pato` pato in bioportal (NOT IMPLEMENTED)
+- :code:`ontobee:` all of ontobee
+- :code:`ontobee:pato` pato in ontobee (NOT IMPLEMENTED)
+- :code:`ols:` all of OLS
+- :code:`ols:pato` pato in OLS (NOT IMPLEMENTED)
+- :code:`ubergraph:` all of OLS
+- :code:`ubergraph:pato` pato in ubergraph (NOT IMPLEMENTED)
+
+See :ref:`cli` for more examples
+
+Schemes
+-------
+
+pronto
+^^^^
+
+Implementation: :ref:`ProntoImplementation`
+
+The slug is a path to a file on disk. Must be in obo or owl or json
+
+prontolib
+^^^^
+
+Implementation: :ref:`ProntoImplementation`
+
+The slug is the name of the resource on obo, e.g. pato.obo, cl.owl
+
+sqlite
+^^^^
+
+Implementation: :ref:`SqlImplementation`
+
+The slug is the path to the sqlite .db file on local disk
+
+obosqlite
+^^^^
+
+Implementation: :ref:`SqlImplementation`
+
+The slug is the name of the ontology, e.g 'hp', 'uberon'
+
+TODO: download from s3
+
+ontobee
+^^^^
+
+Implementation: :ref:`OntobeeImplementation`
+
+Currently the slug is ignored
+
+ols
+^^^^
+
+Implementation: :ref:`OlsImplementation`
+
+Currently the slug is ignored
+
+bioportal
+^^^^
+
+Implementation: :ref:`BioportalImplementation`
+
+Currently the slug is ignored
+
+funowl
+^^^^
+
+Implementation: :ref:`OwlImplementation`
+
+NOT IMPLEMENTED YET
+
+owlery
+^^^^
+
+Implementation: :ref:`OwleryImplementation`
+
+NOT IMPLEMENTED YET
+
+Functions
+----
+
+.. automodule:: oaklib.selector
+    :members:

docs/utilities.rst

@@ -6,10 +6,15 @@ Where possible, this library uses simple standalone python functions organized i
 Note: some of these may involve iterated calls on a remote backend, these are candidates for
 being turned into :ref:`interfaces`.
 
+.. currentmodule:: oaklib
+   :toctree: src
+
+   selector
+
 .. currentmodule:: oaklib.utilities
 
 .. autosummary::
-   :toctree: DIRNAME
+   :toctree: src
 
    obograph_utils
    graph.relationship_walker

src/oaklib/__init__.py

@@ -9,3 +9,6 @@
 
 """
 __version__ = '0.1.0'
+
+from oaklib.interfaces import BasicOntologyInterface
+