Adding agroportal implementation.

Added ability to dynamically make sqlite from owl. Added query datamodel. Various documentation. Added LOV implementation
INCATools · May 10, 2022 · 379acdb · 379acdb
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diff --git a/Makefile b/Makefile
@@ -51,3 +51,6 @@ stage-docs:
 
 tests/input/%.db: tests/input/%.owl
 	$(RUN) semsql make $@
+
+bin/runoak:
+	echo `poetry run which runoak` '"$$0"' > $@ && chmod +x $@
diff --git a/docs/best-practice.rst b/docs/best-practice.rst
@@ -69,4 +69,13 @@ The :ref:`.chunk` utility function will chunk iterator calls into sizeable amoun
 
 This is slightly more boilerplate code, and may not be necessary for an in-memory implementation like Pronto. However, this
 pattern could have considerable advantages for result sets that are potentially large. Even if the external server is
-slow to return results, users will see batches or results rather than waiting on the external server to produce *all* results.
+slow to return results, users will see batches or results rather than waiting on the external server to produce *all* results.
+
+Command Line
+------------
+
+If you are extending the CLI module or writing a Python application that uses OAK:
+
+- Use click
+- Follow CLIG guidelines
+- Ensure that there are tests for the command line using test_click
diff --git a/docs/faq.rst b/docs/faq.rst
@@ -32,10 +32,23 @@ Using OAK with...
 Bioportal
     todo
 
+OLS
+    todo
+
+Command Line
+------------
+
+What do the codes "i" and "p" mean?
+    Many commands take a :code:`--predicates` option, the value is a comma separated list of CURIEs.
+    You can use "i" as a shortcut for is_a and "p" as a shortcut for part_of
+
 Troubleshooting
 ---------------
 
 ... Why do I get a "Error: No such option: -i" message
     The :code:`--input` or :code:`-i` option must come *before* the subcommand name. This is because
     the input option is one of the few options that are shared across *all* subcommands.
-    For example, you should write :code:`runoak -i my-ont.owl lexmatch -o results.sssom.tsv`
+    For example, you should write :code:`runoak -i my-ont.owl lexmatch -o results.sssom.tsv`
+
+... How do I get a bioportal API key
+    TODO
diff --git a/docs/glossary.rst b/docs/glossary.rst
@@ -25,7 +25,7 @@ Glossary
     An |Ontology element| that formally represents something that can be instantiated. For example, the class "heart"
 
    Mapping
-    See SSSOM
+    See :ref:`SSSOM`
 
    Graph
     Formally...

diff --git a/docs/howtos/perform-lexical-matching.rst b/docs/howtos/perform-lexical-matching.rst
@@ -0,0 +1 @@
+TODO
diff --git a/docs/howtos/roll-up-annotations-to-a-subset.rst b/docs/howtos/roll-up-annotations-to-a-subset.rst
diff --git a/docs/howtos/visualize-ontology-subgraphs.rst b/docs/howtos/visualize-ontology-subgraphs.rst
diff --git a/docs/interfaces/validator.rst b/docs/interfaces/validator.rst
@@ -1,6 +1,23 @@
 Validator Interface
 --------------------
 
+.. warning ::
+
+   Currently the main validator methods are only implemented for :ref:`SqlDatabaseImplementation`
+
+The validate method is configured using a *metadata schema*. The default one used is:
+
+- `Ontology Metadata <https://incatools.github.io/ontology-access-kit/datamodels/ontology-metadata/index.html>`_
+
+This is specified using LinkML which provides an expressive way to state constraints on metadata elements,
+such as :ref:`AnnotationProperty` assertions in ontologies. For example, this schema states that definition
+is *recommended* (not required), and that it is single-valued.
+
+Different projects may wish to configure this - it is possible to pass in a different or modified schema
+
+For more details see `this howto guide <https://incatools.github.io/ontology-access-kit/howtos/validate-an-obo-ontology>`_
+
+
 .. currentmodule:: oaklib.interfaces.validator_interface
 
 .. autoclass:: ValidatorInterface