Latest dev to test branch

.github/workflows/scheduled-dev-build.yml

@@ -2,7 +2,7 @@ name: Build develop
 
 on:
   schedule:
-    - cron:  '39 4,10,16,22 * * *'
+    - cron:  '39 12 10,23 * *'
 
 jobs:
   test:

.github/workflows/scheduled-master-build.yml

@@ -2,7 +2,7 @@ name: Build master
 
 on:
   schedule:
-    - cron:  '13 2 * * *'
+    - cron:  '13 2 10,23 * *'
 
 jobs:
   test:

README.md

@@ -2,7 +2,7 @@
 [![Docs](https://readthedocs.org/projects/owmeta/badge/?version=latest)](https://owmeta.readthedocs.io/en/latest)
 [![Coverage Status](https://coveralls.io/repos/github/openworm/owmeta/badge.svg?branch=dev)](https://coveralls.io/github/openworm/owmeta?branch=dev)
 
-owmeta
+owmeta 
 ======
 <img width="1207" alt="pyow_in_overview" src="openworm-overview.png">
 
@@ -170,7 +170,7 @@ data and models to corresponding articles from peer-reviewed literature:
 >>> evctx = conn(Context)(ident='http://example.org/evidence/context')
 
 # Make a context for defining domain knowledge
->>> dctx = conn(Context)(ident='http://example.org/data/context')
+>>> dctx = evctx(Context)(ident='http://example.org/data/context')
 >>> doc = evctx(Document)(key="Sulston83", author='Sulston et al.', date='1983')
 >>> e = evctx(Evidence)(key="Sulston83", reference=doc)
 >>> avdl = dctx(Neuron)(name="AVDL")

examples/add_reference.py

@@ -10,21 +10,27 @@
 
 import owmeta_core as P
 from owmeta_core.data import Data
-from owmeta_core.context import Context
+from owmeta_core.dataobject import DataObject
+from owmeta_core.context import Context, IMPORTS_CONTEXT_KEY
 
 from owmeta.evidence import Evidence
 from owmeta.neuron import Neuron
 from owmeta.document import Document
 
 # Create dummy database configuration.
 d = Data()
+d[IMPORTS_CONTEXT_KEY] = 'http://example.org/imports'
 
 # Connect to database with dummy configuration
 conn = P.connect(conf=d)
 conn.mapper.add_class(Evidence)
 conn.mapper.add_class(Document)
-ctx = conn(Context)(ident='http://example.org/data')
 evctx = conn(Context)(ident='http://example.org/meta')
+ctx = evctx(Context)(ident='http://example.org/data')
+
+# Add the Context RDF class to the mapper -- normally you'd get these from the
+# openworm/owmeta-core bundle as a dependency
+conn.mapper.add_class(type(ctx.rdf_object))
 
 # Create a new Neuron object to work with
 n = ctx(Neuron)(name='AVAL')
@@ -46,9 +52,18 @@
 ctx.save_context()
 evctx.save_context()
 
+evctx.add_import(Document.definition_context)
+evctx.save_imports()
+
+# Add a couple contexts to the store so we can resolve needed types. normally you'd get
+# these from the openworm/owmeta-core bundle as a dependency, so they don't have to be
+# added to the database again.
+Document.definition_context.save_context(conn.rdf)
+DataObject.definition_context.save_context(conn.rdf)
+
 # What does my evidence object contain?
 for e_i in evctx.stored(Evidence)().load():
     print(e_i.reference(), e_i.supports())
 
 # Disconnect from the database.
-P.disconnect(conn)
+conn.disconnect()

tests/EvidenceTest.py

@@ -4,6 +4,7 @@
 
 from owmeta_core.dataobject import DataObject
 from owmeta_core.configure import Configurable
+from owmeta_core.context import Context
 
 from owmeta.evidence import Evidence
 
@@ -14,6 +15,7 @@
 except ImportError:
     from mock import patch
 
+import rdflib
 
 class EvidenceTest(_DataTest):
     ctx_classes = (Evidence,)
@@ -32,7 +34,8 @@ def test_asserts(self):
         Asserting something should allow us to get it back.
         """
         e = self.ctx.Evidence(key='WBPaper00044600')
-        r = DataObject(key="context_data_object")
+        ctx = self.context(Context)(rdflib.URIRef('https://example.org/context'))
+        r = ctx.rdf_object
         e.supports(r)
         s = list(e.supports.get())
         self.assertIn(r, s)