From 1c48bafa9a7b9c65be9b451b9fdae717491fc162 Mon Sep 17 00:00:00 2001 From: Mark Watts Date: Mon, 29 May 2023 18:56:39 -0500 Subject: [PATCH 1/5] fixing a couple of tests --- examples/add_reference.py | 21 ++++++++++++++++++--- tests/EvidenceTest.py | 5 ++++- 2 files changed, 22 insertions(+), 4 deletions(-) diff --git a/examples/add_reference.py b/examples/add_reference.py index 3cf334d9..6fdfe61e 100644 --- a/examples/add_reference.py +++ b/examples/add_reference.py @@ -10,7 +10,8 @@ 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 @@ -18,13 +19,18 @@ # 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() diff --git a/tests/EvidenceTest.py b/tests/EvidenceTest.py index 5cb47dc8..4024b153 100644 --- a/tests/EvidenceTest.py +++ b/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) From 0ecc5b936573897d02f56902b2216b16a2edf52c Mon Sep 17 00:00:00 2001 From: Mark Watts Date: Thu, 1 Jun 2023 23:59:29 -0500 Subject: [PATCH 2/5] Correcting context for data context declaration in README - The supports query constrains to contexts, but the evidence context lacked the rdf:type statement for the data context --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index fcd63300..e1945b58 100644 --- a/README.md +++ b/README.md @@ -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") From f5d55309b8059dc7fed8898dcafa8ffba34f61b2 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Mon, 24 Jun 2024 18:48:52 +0100 Subject: [PATCH 3/5] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index e1945b58..4720c5d3 100644 --- a/README.md +++ b/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 ====== pyow_in_overview From a1d3f3ff9cb726a7e148381cceb4e17e49456224 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Mon, 22 Jul 2024 14:07:54 -0300 Subject: [PATCH 4/5] Update scheduled-dev-build.yml --- .github/workflows/scheduled-dev-build.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/scheduled-dev-build.yml b/.github/workflows/scheduled-dev-build.yml index 7048b87b..20889a3f 100644 --- a/.github/workflows/scheduled-dev-build.yml +++ b/.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: From 16a9199b803c26119f2d227395da1ccf608d6ad9 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Mon, 22 Jul 2024 14:11:33 -0300 Subject: [PATCH 5/5] Update scheduled-master-build.yml --- .github/workflows/scheduled-master-build.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/scheduled-master-build.yml b/.github/workflows/scheduled-master-build.yml index f7087e9b..d70e2a38 100644 --- a/.github/workflows/scheduled-master-build.yml +++ b/.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: