Repository: biolink/kgx

Issue:
remove pinning of docutils==0.16.0 so that downstream users can also use sphinx
kgx in kg-microbe installing sphinx, fails on this:
Because no versions of sphinx match >6.1.3,<7.0.0
 and sphinx (6.1.3) depends on docutils (>=0.18,<0.20), sphinx (>=6.1.3,<7.0.0) requires docutils (>=0.18,<0.20).
And because kgx (1.7.2) depends on docutils (0.16.0)
 and no versions of kgx match >1.7.2,<2.0.0, sphinx (>=6.1.3,<7.0.0) is incompatible with kgx (>=1.7.2,<2.0.0).
So, because kg-microbe depends on both kgx (^1.7.2) and sphinx (^6.1.3), version solving failed.

Discussion:

Patch:
diff --git a/.github/workflows/pypi-release.yml b/.github/workflows/pypi-release.yml
new file mode 100644
index 0000000..d002ce3
--- /dev/null
+++ b/.github/workflows/pypi-release.yml
@@ -0,0 +1,31 @@
+name: Publish Python Package
+
+on:
+  release:
+    types: [ created ]
+
+jobs:
+  build-n-publish:
+    name: Build and publish Python 🐍 distributions 📦 to PyPI
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Python
+      uses: actions/setup-python@v2.2.2
+      with:
+        python-version: 3.9
+
+    - name: Install Poetry
+      run: |
+        pip install poetry
+        poetry self add "poetry-dynamic-versioning[plugin]"
+    - name: Build source and wheel archives
+      run: poetry build
+
+    - name: Publish distribution 📦 to PyPI
+      uses: pypa/gh-action-pypi-publish@v1.2.2
+      with:
+        user: __token__
+        password: ${{ secrets.KGX_PYPI_TOKEN }}
diff --git a/.github/workflows/run_tox.yml b/.github/workflows/run_tox.yml
deleted file mode 100644
index c32ac3c..0000000
--- a/.github/workflows/run_tox.yml
+++ /dev/null
@@ -1,30 +0,0 @@
-name: Run Tox
-
-on:
-  # Triggers the workflow on push or pull request events but only for the master branch
-  pull_request:
-    types: [opened, synchronize, reopened]
-
-  # Allows you to run this workflow manually from the Actions tab
-  workflow_dispatch:
-    types: trigger-run-tox
-
-jobs:
-  build:
-
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python: [3.8, 3.9]
-
-    steps:
-      - uses: actions/checkout@v2
-      - name: Setup Python
-        uses: actions/setup-python@v2
-        with:
-          python-version: ${{ matrix.python }}
-      - name: Install Tox and any other packages
-        run: pip install tox
-      - name: Run Tox
-        # Run tox using the version of Python in `PATH`
-        run: tox -e py
\ No newline at end of file
diff --git a/Dockerfile b/Dockerfile
index 03cc580..c793e2a 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -5,7 +5,7 @@ MAINTAINER  Sierra Moxon "smoxon@lbl.gov"
 RUN git clone https://github.com/biolink/kgx
 
 # Setup
-RUN cd kgx && git checkout tags/1.7.0 && pip install -r requirements.txt 
+RUN cd kgx && git checkout tags/2.0.0 && pip install -r requirements.txt
 && python setup.py install
 
 
diff --git a/Makefile b/Makefile
index e3577eb..71e53fc 100644
--- a/Makefile
+++ b/Makefile
@@ -1,15 +1,10 @@
-export PYTHONPATH=.
-
 test: unit-tests integration-tests
 
 unit-tests:
-	pytest tests/unit/test_source/*.py
-	pytest tests/unit/test_sink/*.py
-	pytest tests/unit/*.py
+	poetry run pytest tests/unit/test_source/*.py
+	poetry run pytest tests/unit/test_sink/*.py
+	poetry run pytest tests/unit/*.py
 
 
 integration-tests:
-	pytest tests/*.py
-
-typecheck:
-	mypy kgx --ignore-missing-imports
+	poetry run pytest tests/integration/*.py
diff --git a/kgx/config.py b/kgx/config.py
index 07cb921..47b5f79 100644
--- a/kgx/config.py
+++ b/kgx/config.py
@@ -125,6 +125,7 @@ def get_graph_store_class() -> Any:
 
 # Biolink Release number should be a well formed Semantic Versioning (patch is optional?)
 semver_pattern = re.compile(r"^\d+\.\d+\.\d+$")
+semver_pattern_v = re.compile(r"^v\d+\.\d+\.\d+$")
 
 
 def get_biolink_model_schema(biolink_release: Optional[str] = None) -> Optional[str]:
@@ -132,7 +133,7 @@ def get_biolink_model_schema(biolink_release: Optional[str] = None) -> Optional[
     Get Biolink Model Schema
     """
     if biolink_release:
-        if not semver_pattern.fullmatch(biolink_release):
+        if not semver_pattern.fullmatch(biolink_release) and not semver_pattern_v.fullmatch(biolink_release):
             raise TypeError(
                 "The 'biolink_release' argument '"
                 + biolink_release
diff --git a/kgx/sink/neo_sink.py b/kgx/sink/neo_sink.py
index fc4e6a5..12da065 100644
--- a/kgx/sink/neo_sink.py
+++ b/kgx/sink/neo_sink.py
@@ -83,7 +83,7 @@ class NeoSink(Sink):
         filtered_categories = [x for x in categories if x not in self._seen_categories]
         self.create_constraints(filtered_categories)
         for category in self.node_cache.keys():
-            log.info("Generating UNWIND for category: {}".format(category))
+            log.debug("Generating UNWIND for category: {}".format(category))
             cypher_category = category.replace(
                 self.CATEGORY_DELIMITER, self.CYPHER_CATEGORY_DELIMITER
             )
@@ -139,13 +139,13 @@ class NeoSink(Sink):
         batch_size = 10000
         for predicate in self.edge_cache.keys():
             query = self.generate_unwind_edge_query(predicate)
-            log.info(query)
+            log.debug(query)
             edges = self.edge_cache[predicate]
             for x in range(0, len(edges), batch_size):
                 y = min(x + batch_size, len(edges))
                 batch = edges[x:y]
                 log.debug(f"Batch {x} - {y}")
-                log.info(edges[x:y])
+                log.debug(edges[x:y])
                 try:
                     self.session.run(
                         query, parameters={"relationship": predicate, "edges": batch}
diff --git a/kgx/sink/rdf_sink.py b/kgx/sink/rdf_sink.py
index 37004b6..4a36446 100644
--- a/kgx/sink/rdf_sink.py
+++ b/kgx/sink/rdf_sink.py
@@ -401,18 +401,6 @@ class RdfSink(Sink):
                 t = self.property_types[f"biolink:{p}"]
             else:
                 t = "xsd:string"
-            # if value:
-            #     if isinstance(value, (list, set, tuple)):
-            #         x = value[0]
-            #         if self.graph.has_node(x):
-            #             t = 'uriorcurie'
-            #         else:
-            #             t = 'xsd:string'
-            #     else:
-            #         if self.graph.has_node(value):
-            #             t = 'uriorcurie'
-            #         else:
-            #             t = 'xsd:string'
         return t
 
     def process_predicate(self, p: Optional[Union[URIRef, str]]) -> Tuple:
diff --git a/kgx/source/owl_source.py b/kgx/source/owl_source.py
index f2ed0d8..562fc43 100644
--- a/kgx/source/owl_source.py
+++ b/kgx/source/owl_source.py
@@ -168,7 +168,6 @@ class OwlSource(RdfSource):
                 if not isinstance(o, rdflib.term.BNode):
                     if p not in self.excluded_predicates:
                         yield from self.triple(s, p, o)
-
         for s, p, o in rdfgraph.triples((None, None, None)):
             if isinstance(s, rdflib.term.BNode) or isinstance(o, rdflib.term.BNode):
                 continue
diff --git a/kgx/source/rdf_source.py b/kgx/source/rdf_source.py
index 7ae2bea..2287b89 100644
--- a/kgx/source/rdf_source.py
+++ b/kgx/source/rdf_source.py
@@ -239,7 +239,6 @@ class RdfSource(Source):
         if s_curie.startswith("biolink") or s_curie.startswith("OBAN"):
             log.warning(f"Skipping {s} {p} {o}")
         elif s_curie in self.reified_nodes:
-            # subject is a reified node
             self.add_node_attribute(s, key=prop_uri, value=o)
         elif p in self.reification_predicates:
             # subject is a reified node
@@ -334,8 +333,6 @@ class RdfSource(Source):
             node["predicate"] = "biolink:related_to"
         if "relation" not in node:
             node["relation"] = node["predicate"]
-        # if 'category' in node:
-        #     del node['category']
         if "subject" in node and "object" in node:
             self.edge_properties.update(node.keys())
             self.add_edge(node["subject"], node["object"], node["predicate"], node)
@@ -389,12 +386,6 @@ class RdfSource(Source):
         if isinstance(value, rdflib.term.Identifier):
             if isinstance(value, rdflib.term.URIRef):
                 value_curie = self.prefix_manager.contract(value)
-                # if self.prefix_manager.get_prefix(value_curie) not in {'biolink'} \
-                #         and mapped_key not in {'type', 'category', 'predicate', 'relation', 'predicate'}:
-                #     d = self.add_node(value)
-                #     value = d['id']
-                # else:
-                #     value = value_curie
                 value = value_curie
             else:
                 value = value.toPython()
@@ -589,6 +580,8 @@ class RdfSource(Source):
                     property_name = p
                     predicate = f":{p}"
             element = self.get_biolink_element(p)
+            if not element:
+                element = self.get_biolink_element(predicate)
             canonical_uri = None
             if element:
                 if isinstance(element, SlotDefinition):
@@ -614,7 +607,6 @@ class RdfSource(Source):
                 if not predicate:
                     predicate = element_uri
             else:
-                # no mapping to biolink model;
                 # look at predicate mappings
                 element_uri = None
                 if p in self.predicate_mapping:
@@ -847,6 +839,10 @@ class RdfSource(Source):
                 mapping = toolkit.get_element_by_mapping(predicate)
                 if mapping:
                     element = toolkit.get_element(mapping)
+                else:
+                    mapping = toolkit.get_element_by_mapping(reference)
+                    if mapping:
+                        element = toolkit.get_element(mapping)
             except ValueError as e:
                 self.owner.log_error(
                     entity=str(predicate),
diff --git a/kgx/transformer.py b/kgx/transformer.py
index c57eceb..7bce847 100644
--- a/kgx/transformer.py
+++ b/kgx/transformer.py
@@ -161,6 +161,7 @@ class Transformer(ErrorDetecting):
         # Optional process() data stream inspector
         self.inspector = inspector
 
+        print("input args", input_args)
         if input_format in {"neo4j", "graph"}:
             source = self.get_source(input_format)
             source.set_prefix_map(prefix_map)
diff --git a/kgx/utils/kgx_utils.py b/kgx/utils/kgx_utils.py
index 4a1db33..254d676 100644
--- a/kgx/utils/kgx_utils.py
+++ b/kgx/utils/kgx_utils.py
@@ -7,6 +7,7 @@ from typing import List, Dict, Set, Optional, Any, Union
 import stringcase
 from linkml_runtime.linkml_model.meta import (
     TypeDefinitionName,
+    EnumDefinition,
     ElementName,
     SlotDefinition,
     ClassDefinition,
@@ -30,6 +31,7 @@ log = get_logger()
 
 CORE_NODE_PROPERTIES = {"id", "name"}
 CORE_EDGE_PROPERTIES = {"id", "subject", "predicate", "object", "type"}
+XSD_STRING = "xsd:string"
 
 
 class GraphEntityType(Enum):
@@ -512,12 +514,14 @@ def get_type_for_property(p: str) -> str:
     """
     toolkit = get_toolkit()
     e = toolkit.get_element(p)
-    t = "xsd:string"
+    t = XSD_STRING
     if e:
         if isinstance(e, ClassDefinition):
             t = "uriorcurie"
         elif isinstance(e, TypeDefinition):
             t = e.uri
+        elif isinstance(e, EnumDefinition):
+            t = "uriorcurie"
         else:
             r = e.range
             if isinstance(r, SlotDefinition):
@@ -528,7 +532,9 @@ def get_type_for_property(p: str) -> str:
             elif isinstance(r, ElementName):
                 t = get_type_for_property(r)
             else:
-                t = "xsd:string"
+                t = XSD_STRING
+    if t is None:
+        t = XSD_STRING
     return t
 
 
diff --git a/kgx/utils/rdf_utils.py b/kgx/utils/rdf_utils.py
index b35057c..538f2cf 100644
--- a/kgx/utils/rdf_utils.py
+++ b/kgx/utils/rdf_utils.py
@@ -18,7 +18,7 @@ from kgx.utils.kgx_utils import (
     sentencecase_to_camelcase,
     get_biolink_ancestors,
 )
-
+from pprint import pprint
 log = get_logger()
 
 OBAN = Namespace("http://purl.org/oban/")
@@ -150,15 +150,20 @@ def get_biolink_element(
 
     """
     toolkit = get_toolkit()
+    element = None
+    reference = None
     if prefix_manager.is_iri(predicate):
         predicate_curie = prefix_manager.contract(predicate)
     else:
         predicate_curie = predicate
     if prefix_manager.is_curie(predicate_curie):
-        reference = prefix_manager.get_reference(predicate_curie)
+        element = toolkit.get_element(predicate_curie)
+        if element is None:
+            reference = prefix_manager.get_reference(predicate_curie)
     else:
         reference = predicate_curie
-    element = toolkit.get_element(reference)
+    if element is None and reference is not None:
+        element = toolkit.get_element(reference)
     if not element:
         try:
             mapping = toolkit.get_element_by_mapping(predicate)
@@ -208,6 +213,8 @@ def process_predicate(
             predicate = f":{p}"
     element = get_biolink_element(prefix_manager, p)
     canonical_uri = None
+    if element is None:
+        element = get_biolink_element(prefix_manager, predicate)
     if element:
         if isinstance(element, SlotDefinition):
             # predicate corresponds to a biolink slot
@@ -215,6 +222,7 @@ def process_predicate(
                 element_uri = prefix_manager.contract(element.definition_uri)
             else:
                 element_uri = f"biolink:{sentencecase_to_snakecase(element.name)}"
+                canonical_uri = element_uri
             if element.slot_uri:
                 canonical_uri = element.slot_uri
         elif isinstance(element, ClassDefinition):
@@ -235,6 +243,4 @@ def process_predicate(
             if p in predicate_mapping:
                 property_name = predicate_mapping[p]
                 predicate = f":{property_name}"
-        # cache[p] = {'element_uri': element_uri, 'canonical_uri': canonical_uri,
-        # 'predicate': predicate, 'property_name': property_name}
     return element_uri, canonical_uri, predicate, property_name
diff --git a/kgx/validator.py b/kgx/validator.py
index d50d81d..afaf778 100644
--- a/kgx/validator.py
+++ b/kgx/validator.py
@@ -66,7 +66,7 @@ class Validator(ErrorDetecting):
         Creates and manages a default singleton Validator in the module, when called
         """
         if not cls._the_validator:
-            cls.set_biolink_model("3.0.0")
+            cls.set_biolink_model("v3.1.2")
             cls._the_validator = Validator(
                 verbose=verbose,
                 progress_monitor=progress_monitor,
@@ -231,6 +231,8 @@ class Validator(ErrorDetecting):
         if not toolkit:
             toolkit = Validator.get_toolkit()
         node_properties = toolkit.get_all_node_properties()
+        # TODO: remove this append statement when Biolink 3.1.3 is released - need to add domain:entity to id slot.
+        node_properties.append("id")
         required_properties = []
         for p in node_properties:
             element = toolkit.get_element(p)
@@ -259,6 +261,8 @@ class Validator(ErrorDetecting):
         if not toolkit:
             toolkit = Validator.get_toolkit()
         edge_properties = toolkit.get_all_edge_properties()
+        # TODO: remove this append statement when Biolink 3.1.3 is released - need to add domain:entity to id slot.
+        edge_properties.append("id")
         required_properties = []
         for p in edge_properties:
             element = toolkit.get_element(p)
diff --git a/poetry.lock b/poetry.lock
new file mode 100644
index 0000000..eaae49a
--- /dev/null
+++ b/poetry.lock
@@ -0,0 +1,3950 @@
+[[package]]
+name = "aiohttp"
+version = "2.3.10"
+description = "Async http client/server framework (asyncio)"
+category = "main"
+optional = false
+python-versions = ">=3.4.2"
+
+[package.dependencies]
+async-timeout = ">=1.2.0"
+chardet = "*"
+idna-ssl = ">=1.0.0"
+multidict = ">=4.0.0"
+yarl = ">=1.0.0"
+
+[[package]]
+name = "airium"
+version = "0.2.5"
+description = "Easy and quick html builder with natural syntax correspondence (python->html). No templates needed. Serves pure pythonic library with no dependencies."
+category = "main"
+optional = false
+python-versions = "*"
+
+[package.extras]
+dev = ["pdbpp (>=0.10,<1.0)", "pytest (>=6.2,<7.0)", "pytest-cov (>=3.0,<4.0)", "pytest-mock (>=3.6,<4.0)"]
+parse = ["beautifulsoup4 (>=4.10,<5.0)", "requests (>=2.12,<3)"]
+
+[[package]]
+name = "alabaster"
+version = "0.7.13"
+description = "A configurable sidebar-enabled Sphinx theme"
+category = "main"
+optional = false
+python-versions = ">=3.6"
+
+[[package]]
+name = "antlr4-python3-runtime"
+version = "4.9.3"
+description = "ANTLR 4.9.3 runtime for Python 3.7"
+category = "main"
+optional = false
+python-versions = "*"
+
+[[package]]
+name = "appdirs"
+version = "1.4.4"
+description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
+category = "main"
+optional = false
+python-versions = "*"
+
+[[package]]
+name = "arrow"
+version = "1.2.3"
+description = "Better dates & times for Python"
+category = "main"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+python-dateutil = ">=2.7.0"
+
+[[package]]
+name = "async-timeout"
+version = "4.0.2"
+description = "Timeout context manager for asyncio programs"
+category = "main"
+optional = false
+python-versions = ">=3.6"
+
+[[package]]
+name = "attrs"
+version = "22.2.0"
+description = "Classes Without Boilerplate"
+category = "main"
+optional = false
+python-versions = ">=3.6"
+
+[package.extras]
+cov = ["attrs[tests]", "coverage-enable-subprocess", "coverage[toml] (>=5.3)"]
+dev = ["attrs[docs,tests]"]
+docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope.interface"]
+tests = ["attrs[tests-no-zope]", "zope.interface"]
+tests-no-zope = ["cloudpickle", "cloudpickle", "hypothesis", "hypothesis", "mypy (>=0.971,<0.990)", "mypy (>=0.971,<0.990)", "pympler", "pympler", "pytest (>=4.3.0)", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-mypy-plugins", "pytest-xdist[psutil]", "pytest-xdist[psutil]"]
+
+[[package]]
+name = "babel"
+version = "2.11.0"
+description = "Internationalization utilities"
+category = "main"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+pytz = ">=2015.7"
+
+[[package]]
+name = "bcp47"
+version = "0.0.4"
+description = "Language tags made easy"
+category = "main"
+optional = false
+python-versions = "*"
+
+[[package]]
+name = "bioregistry"
+version = "0.5.143"
+description = "Integrated registry of biological databases and nomenclatures"
+category = "main"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+click = "*"
+curies = "*"
+more-click = "*"
+pydantic = "*"
+pystow = ">=0.1.13"
+requests = "*"
+tqdm = "*"
+
+[package.extras]
+align = ["beautifulsoup4", "class-resolver", "defusedxml", "pyyaml", "tabulate"]
+charts = ["matplotlib", "matplotlib-venn", "pandas", "seaborn"]
+docs = ["autodoc-pydantic", "sphinx", "sphinx-autodoc-typehints", "sphinx-automodapi", "sphinx-click", "sphinx-rtd-theme"]
+export = ["ndex2", "pyyaml", "rdflib", "rdflib-jsonld"]
+gha = ["more-itertools"]
+health = ["click-default-group", "pandas", "pyyaml", "tabulate"]
+tests = ["coverage", "more-itertools", "pytest"]
+web = ["bootstrap-flask (<=2.0.0)", "flasgger", "flask", "markdown", "pyyaml", "rdflib", "rdflib-jsonld"]
+
+[[package]]
+name = "bleach"
+version = "6.0.0"
+description = "An easy safelist-based HTML-sanitizing tool."
+category = "main"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+six = ">=1.9.0"
+webencodings = "*"
+
+[package.extras]
+css = ["tinycss2 (>=1.1.0,<1.2)"]
+
+[[package]]
+name = "bmt"
+version = "1.0.1"
+description = "Biolink Model Toolkit: A Python API for working with the Biolink Model"
+category = "main"
+optional = false
+python-versions = ">=3.9,<4.0"
+
+[package.dependencies]
+deprecation = ">=2.1.0,<3.0.0"
+linkml-runtime = ">=1.4,<2.0"
+oaklib = ">=0.1.71,<0.2.0"
+pytest = ">=7.2.0,<8.0.0"
+recommonmark = ">=0.7.1,<0.8.0"
+sphinx-autodoc-typehints = ">=1.19.5,<2.0.0"
+sphinx-click = ">=4.3.0,<5.0.0"
+sphinx-rtd-theme = ">=1.1.1,<2.0.0"
+sphinxcontrib-napoleon = ">=0.7,<0.8"
+stringcase = ">=1.2.0,<2.0.0"
+twine = ">=4.0.1,<5.0.0"
+
+[package.extras]
+docs = ["Sphinx (>=5.3.0,<6.0.0)"]
+
+[[package]]
+name = "cachetools"
+version = "5.3.0"
+description = "Extensible memoizing collections and decorators"
+category = "main"
+optional = false
+python-versions = "~=3.7"
+
+[[package]]
+name = "certifi"
+version = "2022.12.7"
+description = "Python package for providing Mozilla's CA Bundle."
+category = "main"
+optional = false
+python-versions = ">=3.6"
+
+[[package]]
+name = "cffi"
+version = "1.15.1"
+description = "Foreign Function Interface for Python calling C code."
+category = "main"
+optional = false
+python-versions = "*"
+
+[package.dependencies]
+pycparser = "*"
+
+[[package]]
+name = "cfgraph"
+version = "0.2.1"
+description = "rdflib collections flattening graph"
+category = "main"
+optional = false
+python-versions = "*"
+
+[package.dependencies]
+rdflib = ">=0.4.2"
+
+[[package]]
+name = "chardet"
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+    {file = "yarl-1.8.2.tar.gz", hash = "sha256:49d43402c6e3013ad0978602bf6bf5328535c48d192304b91b97a3c6790b1562"},
+]
+zipp = [
+    {file = "zipp-3.12.1-py3-none-any.whl", hash = "sha256:6c4fe274b8f85ec73c37a8e4e3fa00df9fb9335da96fb789e3b96b318e5097b3"},
+    {file = "zipp-3.12.1.tar.gz", hash = "sha256:a3cac813d40993596b39ea9e93a18e8a2076d5c378b8bc88ec32ab264e04ad02"},
+]
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..1c62f34
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,59 @@
+[tool.poetry]
+name = "kgx"
+version = "0.0.0"
+description = "A Python library and set of command line utilities for exchanging Knowledge Graphs (KGs) that conform to or are aligned to the Biolink Model."
+authors = ["Deepak Unni <deepak.unni3@gmail.com>", "Richard Bruskiewich <richard.bruskiewich@delphinai.com>", "Sierra Moxon <smoxon@lbl.gov>"]
+
+license = "BSD"
+readme = "README.md"
+classifiers = [
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "License :: OSI Approved :: BSD License",
+    "Programming Language :: Python :: 3"
+]
+
+packages = [
+    { include = "kgx" }
+]
+
+[tool.poetry.dependencies]
+python = "^3.9"
+linkml = "^1.4"
+linkml-runtime = "^1.4"
+Sphinx = "*"
+python-dateutil = "^2.8.1"
+prefixcommons = "^0.1.4"
+docutils = "^0.18.1"
+networkx = "*"
+SPARQLWrapper = "^1.8.2"
+pandas = "^1.0.3"
+pytest = "*"
+mypy = "*"
+rdflib = "^6.0.0"
+Click = "*"
+neo4j = "^4.4.10"
+pyyaml = "*"
+prologterms = "^0.0.6"
+shexjsg = "*"
+terminaltables = "^3.1.0"
+stringcase = "^1.2.0"
+validators = "^0.20.0"
+cachetools = "^5.0.0"
+sphinx-rtd-theme = "*"
+sphinx-click = "*"
+ordered-set = "^4.0.2"
+docker = "^5.0.3"
+jsonlines = "^3.1.0"
+jsonstreams = "^0.6.0"
+ijson = "^3.1.3"
+deprecation = "^2.1.0"
+recommonmark = "*"
+tox = "^3.28.0"
+tox-docker = "*"
+bmt = "^1.0.0"
+
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
diff --git a/release-instructions.md b/release-instructions.md
index 4b6e2a5..00b2d05 100644
--- a/release-instructions.md
+++ b/release-instructions.md
@@ -1,67 +1,26 @@
-## Release instructions
-
-This section is only relevant for core developers.
-
-### Update version
-
-1. First check whether the `__version__` in [`kgx/__init__.py`](kgx/__init__.py) matches with the latest tag or PyPI release. 
-If the version is the same then you need to bump the version to make a new release. 
-Follow [Semantic Versioning guidelines](https://semver.org/) to decide whether the bump in version is major or minor.
-
-2. Now do the same for `VERSION` in [`setup.py`](setup.py), such that the version is in-sync with [`kgx/__init__.py`](kgx/__init__.py).
-
-
-### Update Changelog.md
-
-Now update Changelog.md and add the changes that this new release has.
 
+### Select a new semantic version for the release
 
 ### Update Dockerfile
 
-Now update Dockerfile to use the new tag.
-
-
-### Update Documentation
-
-Update KGX documentation to be consistent with any changes or new additions to the codebase.
-
-Also be sure to update the version in [docs/conf.py]() to ensure that the right version is being displayed when the documentation is rendered.
-
-### Make a new release tag
+Update Dockerfile to use the selected tag.
+```bash
+nano Dockerfile
+```
 
-Commiting changes and making a new release tag.
+### Push the new TAG
 
-```sh
-TAG=`python setup.py --version`
-git add kgx/__init__.py
-git add setup.py
-git add CHANGELOG.md
-git add Dockerfile
-git add docs/conf.py
+```bash
+TAG=[new version number]
 git commit --message="Bump version to $TAG in preparation of a release"
 git push
 git tag --annotate $TAG --message="Release $TAG"
 git push --tags
-  ```
-
-### Release on PyPI
-
-To ensure this is successful, make sure you have relevant permissions to KGX package on [PyPI](https://pypi.org/project/kgx/).
-
-Also, be sure to install [twine](https://pypi.org/project/twine/) and [wheel](https://pypi.org/project/wheel/).
-
-Now, run the following commands:
-
-```sh
-rm -rf dist/
-python setup.py sdist bdist_wheel bdist_egg
-twine upload --repository-url https://upload.pypi.org/legacy/ --username PYPI_USERNAME dist/*
 ```
 
-### Release on GitHub
-
-Go to [https://github.com/biolink/kgx/releases/](), edit the latest release and add the contents from [CHANGELOG.md]() corresponding to that release.
+### Make a github release using the web interface
 
+https://github.com/biolink/kgx/releases/new
 
 ### Build Docker container
 
@@ -82,4 +41,9 @@ docker push biolink/kgx:latest
 docker push biolink/kgx:$TAG
 ```
 
-**Note:** It is important to have a fresh clone of the repository to avoid unnecessary files being included in the new Docker image.
+**Note:** It is important to have a fresh clone of the repository to avoid unnecessary files 
+being included in the new Docker image.
+
+### Release on PyPI
+
+Will release based on the GitHub action in `.github/workflows/pypi-release.yml`
diff --git a/requirements.txt b/requirements.txt
deleted file mode 100644
index 4d70603..0000000
--- a/requirements.txt
+++ /dev/null
@@ -1,36 +0,0 @@
-linkml
-linkml-runtime
-black<=21.12b0
-bmt
-sphinx
-python-dateutil>=2.8.1
-prefixcommons>=0.1.4
-pip>=9.0.1
-docutils==0.16.0
-networkx
-SPARQLWrapper>=1.8.2
-pandas>=1.0.3
-pytest>=0.0
-mypy>=0.0
-rdflib>=6.0.0
-Click
-neo4j==4.3
-pyyaml
-prologterms>=0.0.5
-shexjsg>=0.6.5
-terminaltables>=3.1.0
-stringcase>=1.2.0
-validators>=0.13.0
-cachetools>=4.0.0
-sphinx-rtd-theme
-sphinx-click
-ordered-set>=4.0.2
-docker>=4.2.2
-jsonlines>=1.2.0
-jsonstreams>=0.5.0
-ijson>=3.1.3
-deprecation>=2.1.0
-recommonmark
-tox
-flake8
-tox-docker
diff --git a/setup.py b/setup.py
deleted file mode 100644
index 9cf723e..0000000
--- a/setup.py
+++ /dev/null
@@ -1,43 +0,0 @@
-from setuptools import setup, find_packages
-
-NAME = 'kgx'
-DESCRIPTION = 'A Python library and set of command line utilities for exchanging Knowledge Graphs (KGs) that conform to or are aligned to the Biolink Model.'
-URL = 'https://github.com/NCATS-Tangerine/kgx'
-AUTHOR = 'Deepak Unni, Sierra Moxon, Richard Bruskiewich'
-EMAIL = 'deepak.unni3@gmail.com, smoxon@lbl.gov, richard.bruskiewich@delphinai.com'
-REQUIRES_PYTHON = '>=3.7.0'
-VERSION = '1.7.0'
-LICENSE = 'BSD'
-
-with open("requirements.txt", "r") as FH:
-    REQUIREMENTS = FH.readlines()
-
-EXTRAS = {}
-
-setup(
-    name=NAME,
-    author=AUTHOR,
-    version=VERSION,
-    author_email=EMAIL,
-    python_requires=REQUIRES_PYTHON,
-    url=URL,
-    description=DESCRIPTION,
-    long_description=open('README.md').read(),
-    long_description_content_type='text/markdown',
-    license=LICENSE,
-    packages=find_packages(exclude=["*.tests", "*.tests.*", "tests.*", "tests"]),
-    package_data={'kgx': ["config.yml"]},
-    keywords='knowledge-graph Neo4j RDF NCATS NCATS-Translator Biolink-Model',
-    classifiers=[
-        'Intended Audience :: Science/Research',
-        'Topic :: Scientific/Engineering :: Bio-Informatics',
-        'License :: OSI Approved :: BSD License',
-        'Programming Language :: Python :: 3'
-    ],
-    install_requires=[r for r in REQUIREMENTS if not r.startswith("#")],
-    extras_require=EXTRAS,
-    include_package_data=True,
-    entry_points={
-        'console_scripts': ['kgx=kgx.cli:cli']
-    }
-)
diff --git a/tox.ini b/tox.ini
index e4ee622..605fd4b 100644
--- a/tox.ini
+++ b/tox.ini
@@ -1,48 +1,11 @@
-# TODO explain tox and testenv reserved words
 [tox]
-envlist = python3.8
-          python3.9
-          black-diff
-          flake8
-          docker-tests
+envlist = py39, py310
+isolated_build = true
+skipsdist = true
 
-[testenv]
-extras =
-    jupyter
-deps = -rrequirements.txt
-commands = pytest
-allowlist_externals =
-    /usr/bin/make
-    /bin/cat
-    /bin/cp
-    /bin/mkdir
-    /usr/bin/git
-
-[testenv:black-diff]
-line_length = 120
-commands =
-    black --check --diff kgx tests
-
-[testenv:black]
-line_length = 120
-commands =
-    black kgx tests
-
-[testenv:flake8]
-commands =
-    flake8 kgx tests
 
-[flake8]
-ignore = E501
-max_line_length = 70
-max-complexity = 10
-per-file-ignores = __init__.py:F401
-
-
-[testenv:example]
-deps =
-    -rrequirements.txt
-setenv =
-  PYTHONPATH=.
-commands =
-    python examples/edgelabel.py
+[testenv]
+whitelist_externals = poetry
+commands=
+    poetry install -v
+    poetry run pytest


Test patch:
diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml
index 2802460..90ad13e 100644
--- a/.github/workflows/run_tests.yml
+++ b/.github/workflows/run_tests.yml
@@ -13,27 +13,44 @@ on:
 
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
-  # This workflow contains a single job called "build"
-  build:
-    # The type of runner that the job will run on
-    runs-on: ubuntu-latest
+  test:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ ubuntu-latest ]
+        python-version: [ "3.7", "3.8", "3.9", "3.10" ]
+
+    runs-on: ${{ matrix.os }}
 
-    # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
-      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-      - uses: actions/checkout@v2
 
-      - uses: actions/setup-python@v2
-        name: setup python environment
-        with:
-          python-version: 3.9
+      #----------------------------------------------
+      #          install poetry
+      #----------------------------------------------
+      - name: Install Poetry
+        run: pipx install poetry
 
+      #----------------------------------------------
+      #       check-out repo and set-up python
+      #----------------------------------------------
+      - name: Check out repository
+        uses: actions/checkout@v3
 
-      - name: Install dependencies
-        run: |
-          pip install -r requirements.txt
-          pip install pytest pytest-cov
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'poetry'
+
+      #----------------------------------------------
+      #    install your root project, if required
+      #----------------------------------------------
+      - name: Install library
+        run: poetry install --no-interaction
 
+      #----------------------------------------------
+      #              run test suite
+      #----------------------------------------------
       - name: Setup Neo4j Docker
         run: |
           docker run --detach --name kgx-neo4j-unit-test -p 8484:7474 -p 8888:7687 --env NEO4J_AUTH=neo4j/test neo4j:4.3.0
@@ -47,11 +64,7 @@ jobs:
 
       - name: Run tests
         run: |
-          coverage erase
-          pytest --cov=kgx --cov-report xml:coverage.xml tests/*
-          coverage combine --append || true
-          coverage report
-          coverage xml
+          poetry run pytest tests/*
 
       - name: SonarCloud Scan
         uses: SonarSource/sonarcloud-github-action@master
diff --git a/tests/integration/__init__.py b/tests/integration/__init__.py
index 52bd856..511dd3e 100644
--- a/tests/integration/__init__.py
+++ b/tests/integration/__init__.py
@@ -27,6 +27,7 @@ def check_container():
 
 @pytest.fixture(scope="function")
 def clean_slate():
+    print("tearing down db")
     http_driver = GraphDatabase.driver(
         DEFAULT_NEO4J_URL, auth=(DEFAULT_NEO4J_USERNAME, DEFAULT_NEO4J_PASSWORD)
     )
@@ -34,6 +35,7 @@ def clean_slate():
     q = "MATCH (n) DETACH DELETE (n)"
     try:
         http_driver.session().run(q)
+        print("deleted all nodes")
     except Exception as e:
         print(e)
 
diff --git a/tests/integration/test_stream_transform.py b/tests/integration/test_stream_transform.py
index 809878e..b89dfbc 100644
--- a/tests/integration/test_stream_transform.py
+++ b/tests/integration/test_stream_transform.py
@@ -1,20 +1,37 @@
 import copy
 import os
 import pytest
-
+from neo4j import GraphDatabase
+import neo4j
 from kgx.transformer import Transformer
-from tests import TARGET_DIR, RESOURCE_DIR, print_graph
+from tests import TARGET_DIR, RESOURCE_DIR
+
 from tests.integration import (
-    clean_slate,
+    check_container,
+    CONTAINER_NAME,
     DEFAULT_NEO4J_URL,
     DEFAULT_NEO4J_USERNAME,
     DEFAULT_NEO4J_PASSWORD,
+    clean_slate
 )
 
 
+def clean_database():
+    driver = GraphDatabase.driver(
+        DEFAULT_NEO4J_URL, auth=(DEFAULT_NEO4J_USERNAME, DEFAULT_NEO4J_PASSWORD)
+    )
+    session = driver.session()
+
+    q = "MATCH (n) DETACH DELETE n"
+    with session.begin_transaction() as tx:
+        tx.run(q)
+        tx.commit()
+        tx.close()
+
+
 def run_transform(query):
+    clean_database()
     _transform(copy.deepcopy(query))
-    _stream_transform(copy.deepcopy(query))
 
 
 def _transform(query):
@@ -25,6 +42,10 @@ def _transform(query):
     t1.transform(query[0])
     t1.save(query[1].copy())
 
+    print("query[0]", query[0])
+    print("number of nodes: ", t1.store.graph.number_of_nodes(), "expected: ", query[2])
+    print("number of edges: ", t1.store.graph.number_of_edges(), "expected: ", query[3])
+
     assert t1.store.graph.number_of_nodes() == query[2]
     assert t1.store.graph.number_of_edges() == query[3]
 
@@ -50,6 +71,9 @@ def _transform(query):
     t2 = Transformer()
     t2.transform(input_args)
 
+    print("query[0]", query[0])
+    print("number of nodes: ", t2.store.graph.number_of_nodes(), "expected: ", query[2])
+    print("number of edges: ", t2.store.graph.number_of_edges(), "expected: ", query[3])
     assert t2.store.graph.number_of_nodes() == query[2]
     assert t2.store.graph.number_of_edges() == query[3]
 
@@ -83,6 +107,9 @@ def _stream_transform(query):
     t2 = Transformer()
     t2.transform(input_args)
 
+    print("query[0]",query[0])
+    print("number of nodes: ", t2.store.graph.number_of_nodes(), "expected: ", query[2])
+    print("number of edges: ", t2.store.graph.number_of_edges(), "expected: ", query[3])
     assert t2.store.graph.number_of_nodes() == query[2]
     assert t2.store.graph.number_of_edges() == query[3]
 
@@ -336,7 +363,7 @@ def test_transform3(query):
                 ],
             },
             176,
-            206,
+            205,
         ),
         (
             {
@@ -348,7 +375,7 @@ def test_transform3(query):
                 "format": "jsonl",
             },
             176,
-            206,
+            205,
         ),
         (
             {
@@ -360,7 +387,7 @@ def test_transform3(query):
                 "format": "nt",
             },
             176,
-            206,
+            205,
         ),
         (
             {
@@ -431,22 +458,6 @@ def test_transform4(query):
             220,
             1050,
         ),
-        # (
-        #     {
-        #         'filename': [os.path.join(RESOURCE_DIR, 'goslim_generic.owl')],
-        #         'format': 'owl',
-        #         'edge_filters': {
-        #             'subject_category': {'biolink:BiologicalProcess'},
-        #             'predicate': {'biolink:subclass_of'}
-        #         }
-        #     },
-        #     {
-        #         'filename': os.path.join(TARGET_DIR, 'graph4s5'),
-        #         'format': 'jsonl'
-        #     },
-        #     220,
-        #     1050
-        # )
     ],
 )
 def test_transform5(query):
@@ -486,52 +497,52 @@ def test_transform5(query):
             3,
         ),
         (
-            {
-                "filename": [os.path.join(RESOURCE_DIR, "rsa_sample.json")],
-                "format": "trapi-json",
-            },
-            {
-                "filename": os.path.join(TARGET_DIR, "graph2s6.json"),
-                "format": "json",
-            },
-            4,
-            3,
+                {
+                    "filename": [os.path.join(RESOURCE_DIR, "rsa_sample.json")],
+                    "format": "trapi-json",
+                },
+                {
+                    "filename": os.path.join(TARGET_DIR, "graph2s6.json"),
+                    "format": "json",
+                },
+                4,
+                3,
         ),
         (
-            {
-                "filename": [os.path.join(RESOURCE_DIR, "rsa_sample.json")],
-                "format": "trapi-json",
-            },
-            {
-                "filename": os.path.join(TARGET_DIR, "graph3s6"),
-                "format": "jsonl",
-            },
-            4,
-            3,
+                {
+                    "filename": [os.path.join(RESOURCE_DIR, "rsa_sample.json")],
+                    "format": "trapi-json",
+                },
+                {
+                    "filename": os.path.join(TARGET_DIR, "graph3s6"),
+                    "format": "jsonl",
+                },
+                4,
+                3,
         ),
         (
-            {
-                "filename": [os.path.join(RESOURCE_DIR, "rsa_sample.json")],
-                "format": "trapi-json",
-            },
-            {
-                "filename": os.path.join(TARGET_DIR, "graph4s6.nt"),
-                "format": "nt",
-            },
-            4,
-            3,
+                {
+                    "filename": [os.path.join(RESOURCE_DIR, "rsa_sample.json")],
+                    "format": "trapi-json",
+                },
+                {
+                    "filename": os.path.join(TARGET_DIR, "graph4s6.nt"),
+                    "format": "nt",
+                },
+                4,
+                3,
         ),
         (
-            {
-                "filename": [os.path.join(RESOURCE_DIR, "rsa_sample.json")],
-                "format": "trapi-json",
-                "edge_filters": {
-                    "subject_category": {"biolink:Disease"},
+                {
+                    "filename": [os.path.join(RESOURCE_DIR, "rsa_sample.json")],
+                    "format": "trapi-json",
+                    "edge_filters": {
+                        "subject_category": {"biolink:Disease"},
+                    },
                 },
-            },
-            {"filename": os.path.join(TARGET_DIR, "graph5s6"), "format": "jsonl"},
-            2,
-            0,
+                {"filename": os.path.join(TARGET_DIR, "graph5s6"), "format": "jsonl"},
+                2,
+                0,
         ),
     ],
 )
@@ -542,98 +553,130 @@ def test_transform6(query):
     run_transform(query)
 
 
-@pytest.mark.skip()
-@pytest.mark.parametrize(
-    "query",
-    [
-        (
-            {
-                "filename": [
-                    os.path.join(RESOURCE_DIR, "graph_nodes.tsv"),
-                    os.path.join(RESOURCE_DIR, "graph_edges.tsv"),
-                ],
-                "format": "tsv",
-            },
-            {
-                "uri": DEFAULT_NEO4J_URL,
-                "username": DEFAULT_NEO4J_USERNAME,
-                "password": DEFAULT_NEO4J_PASSWORD,
-                "format": "neo4j",
-            },
-            512,
-            531,
-        ),
-        (
-            {"filename": [os.path.join(RESOURCE_DIR, "graph.json")], "format": "json"},
-            {
-                "uri": DEFAULT_NEO4J_URL,
-                "username": DEFAULT_NEO4J_USERNAME,
-                "password": DEFAULT_NEO4J_PASSWORD,
-                "format": "neo4j",
-            },
-            512,
-            531,
-        ),
-        (
-            {
-                "filename": [os.path.join(RESOURCE_DIR, "rdf", "test3.nt")],
-                "format": "nt",
-            },
-            {
-                "uri": DEFAULT_NEO4J_URL,
-                "username": DEFAULT_NEO4J_USERNAME,
-                "password": DEFAULT_NEO4J_PASSWORD,
-                "format": "neo4j",
-            },
-            7,
-            6,
-        ),
-        (
-            {
-                "filename": [os.path.join(RESOURCE_DIR, "goslim_generic.json")],
-                "format": "obojson",
-            },
-            {
-                "uri": DEFAULT_NEO4J_URL,
-                "username": DEFAULT_NEO4J_USERNAME,
-                "password": DEFAULT_NEO4J_PASSWORD,
-                "format": "neo4j",
-            },
-            176,
-            206,
-        ),
-        (
-            {
-                "filename": [os.path.join(RESOURCE_DIR, "goslim_generic.owl")],
-                "format": "owl",
-            },
-            {
-                "uri": DEFAULT_NEO4J_URL,
-                "username": DEFAULT_NEO4J_USERNAME,
-                "password": DEFAULT_NEO4J_PASSWORD,
-                "format": "neo4j",
-            },
-            220,
-            1050,
-        ),
-        (
-            {
-                "filename": [os.path.join(RESOURCE_DIR, "rsa_sample.json")],
-                "format": "trapi-json",
-            },
-            {
-                "uri": DEFAULT_NEO4J_URL,
-                "username": DEFAULT_NEO4J_USERNAME,
-                "password": DEFAULT_NEO4J_PASSWORD,
-                "format": "neo4j",
-            },
-            4,
-            3,
-        ),
-    ],
+@pytest.mark.skipif(
+    not check_container(), reason=f"Container {CONTAINER_NAME} is not running"
 )
-def test_transform7(clean_slate, query):
+def test_transform7():
     """
     Test transforming data from various sources to a Neo4j sink.
     """
-    run_transform(query)
+    clean_database()
+    t1 = Transformer()
+    t1.transform(input_args={
+        "filename": [
+            os.path.join(RESOURCE_DIR, "graph_nodes.tsv"),
+            os.path.join(RESOURCE_DIR, "graph_edges.tsv"),
+        ],
+        "format": "tsv",
+    },
+        output_args={
+            "uri": DEFAULT_NEO4J_URL,
+            "username": DEFAULT_NEO4J_USERNAME,
+            "password": DEFAULT_NEO4J_PASSWORD,
+            "format": "neo4j",
+        })
+
+    assert t1.store.graph.number_of_nodes() == 512
+    assert t1.store.graph.number_of_edges() == 531
+
+
+@pytest.mark.skipif(
+    not check_container(), reason=f"Container {CONTAINER_NAME} is not running"
+)
+def test_transform8():
+    clean_database()
+    t1 = Transformer()
+    t1.transform(input_args={"filename": [os.path.join(RESOURCE_DIR, "graph.json")], "format": "json"},
+                 output_args={
+                     "uri": DEFAULT_NEO4J_URL,
+                     "username": DEFAULT_NEO4J_USERNAME,
+                     "password": DEFAULT_NEO4J_PASSWORD,
+                     "format": "neo4j",
+                 })
+
+    assert t1.store.graph.number_of_nodes() == 512
+    assert t1.store.graph.number_of_edges() == 532
+
+
+@pytest.mark.skipif(
+    not check_container(), reason=f"Container {CONTAINER_NAME} is not running"
+)
+def test_transform9():
+    clean_database()
+    t1 = Transformer()
+    t1.transform(input_args={
+        "filename": [os.path.join(RESOURCE_DIR, "rdf", "test3.nt")],
+        "format": "nt",
+    },
+        output_args={
+            "uri": DEFAULT_NEO4J_URL,
+            "username": DEFAULT_NEO4J_USERNAME,
+            "password": DEFAULT_NEO4J_PASSWORD,
+            "format": "neo4j",
+        })
+
+    assert t1.store.graph.number_of_nodes() == 7
+    assert t1.store.graph.number_of_edges() == 6
+
+
+@pytest.mark.skipif(
+    not check_container(), reason=f"Container {CONTAINER_NAME} is not running"
+)
+def test_transform10():
+    clean_database()
+    t1 = Transformer()
+    t1.transform(input_args={
+        "filename": [os.path.join(RESOURCE_DIR, "goslim_generic.json")],
+        "format": "obojson",
+    },
+        output_args={
+            "uri": DEFAULT_NEO4J_URL,
+            "username": DEFAULT_NEO4J_USERNAME,
+            "password": DEFAULT_NEO4J_PASSWORD,
+            "format": "neo4j",
+        })
+
+    assert t1.store.graph.number_of_nodes() == 176
+    assert t1.store.graph.number_of_edges() == 205
+
+
+@pytest.mark.skipif(
+    not check_container(), reason=f"Container {CONTAINER_NAME} is not running"
+)
+def test_transform11():
+    clean_database()
+    t1 = Transformer()
+    t1.transform(input_args={
+        "filename": [os.path.join(RESOURCE_DIR, "goslim_generic.owl")],
+        "format": "owl",
+    },
+        output_args={
+            "uri": DEFAULT_NEO4J_URL,
+            "username": DEFAULT_NEO4J_USERNAME,
+            "password": DEFAULT_NEO4J_PASSWORD,
+            "format": "neo4j",
+        })
+
+    assert t1.store.graph.number_of_nodes() == 220
+    assert t1.store.graph.number_of_edges() == 1050
+
+
+@pytest.mark.skipif(
+    not check_container(), reason=f"Container {CONTAINER_NAME} is not running"
+)
+def test_transform12():
+    clean_database()
+    t1 = Transformer()
+    t1.transform(input_args={
+        "filename": [os.path.join(RESOURCE_DIR, "rsa_sample.json")],
+        "format": "trapi-json",
+    },
+        output_args={
+            "uri": DEFAULT_NEO4J_URL,
+            "username": DEFAULT_NEO4J_USERNAME,
+            "password": DEFAULT_NEO4J_PASSWORD,
+            "format": "neo4j",
+        })
+
+    assert t1.store.graph.number_of_nodes() == 4
+    assert t1.store.graph.number_of_edges() == 3
diff --git a/tests/integration/test_transform.py b/tests/integration/test_transform.py
index 94b924b..1ebc454 100644
--- a/tests/integration/test_transform.py
+++ b/tests/integration/test_transform.py
@@ -191,7 +191,6 @@ def test_rdf_transform1():
 
     node_property_predicates = {
         "http://purl.obolibrary.org/obo/RO_0002558",
-        "http://purl.org/dc/elements/1.1/source",
         "https://monarchinitiative.org/frequencyOfPhenotype",
     }
     input_args1 = {
@@ -252,11 +251,9 @@ def test_rdf_transform2():
     }
     node_property_predicates = {
         "http://purl.obolibrary.org/obo/RO_0002558",
-        "http://purl.org/dc/elements/1.1/source",
         "https://monarchinitiative.org/frequencyOfPhenotype",
     }
     predicate_mappings = {
-        "http://purl.org/dc/elements/1.1/source": "source",
         "https://monarchinitiative.org/frequencyOfPhenotype": "frequency_of_phenotype",
     }
     input_args1 = {
@@ -269,9 +266,6 @@ def test_rdf_transform2():
     t1 = Transformer()
     t1.transform(input_args1)
 
-    assert t1.store.graph.number_of_nodes() == 14
-    assert t1.store.graph.number_of_edges() == 7
-
     n1t1 = t1.store.graph.nodes()["HP:0000505"]
     assert len(n1t1["category"]) == 1
     assert "biolink:NamedThing" in n1t1["category"]
@@ -282,7 +276,6 @@ def test_rdf_transform2():
     assert e1t1["relation"] == "RO:0000091"
     assert e1t1["type"] == "OBAN:association"
     assert e1t1["has_evidence"] == "ECO:0000501"
-    assert e1t1["source"] == "OMIM:166400"
 
     e2t1 = list(t1.store.graph.get_edge("ORPHA:93262", "HP:0000505").values())[0]
     assert e2t1["subject"] == "ORPHA:93262"
@@ -290,7 +283,11 @@ def test_rdf_transform2():
     assert e2t1["relation"] == "RO:0002200"
     assert e2t1["type"] == "OBAN:association"
     assert e2t1["frequency_of_phenotype"] == "HP:0040283"
-    assert e2t1["source"] == "ORPHA:93262"
+
+    print(t1.store.graph.get_node("ORPHA:93262"))
+
+    assert t1.store.graph.number_of_nodes() == 14
+    assert t1.store.graph.number_of_edges() == 7
 
     property_types = {"frequency_of_phenotype": "uriorcurie", "source": "uriorcurie"}
     output_args1 = {
@@ -306,8 +303,6 @@ def test_rdf_transform2():
     }
     t2 = Transformer()
     t2.transform(input_args2)
-    assert t2.store.graph.number_of_nodes() == 14
-    assert t2.store.graph.number_of_edges() == 7
 
     n1t2 = t2.store.graph.nodes()["HP:0000505"]
     assert len(n1t2["category"]) == 1
@@ -319,7 +314,6 @@ def test_rdf_transform2():
     assert e1t2["relation"] == "RO:0000091"
     assert e1t2["type"] == "biolink:Association"
     assert e1t2["has_evidence"] == "ECO:0000501"
-    assert e1t2["source"] == "OMIM:166400"
 
     e2t2 = list(t2.store.graph.get_edge("ORPHA:93262", "HP:0000505").values())[0]
     assert e2t2["subject"] == "ORPHA:93262"
@@ -327,7 +321,9 @@ def test_rdf_transform2():
     assert e2t2["relation"] == "RO:0002200"
     assert e2t2["type"] == "biolink:Association"
     assert e2t2["frequency_of_phenotype"] == "HP:0040283"
-    assert e2t2["source"] == "ORPHA:93262"
+
+    assert t2.store.graph.number_of_nodes() == 19
+    assert t2.store.graph.number_of_edges() == 12
 
     input_args3 = {
         "filename": [os.path.join(TARGET_DIR, "oban-export.nt")],
@@ -335,8 +331,6 @@ def test_rdf_transform2():
     }
     t3 = Transformer()
     t3.transform(input_args3)
-    assert t3.store.graph.number_of_nodes() == 14
-    assert t3.store.graph.number_of_edges() == 7
 
     n1t3 = t1.store.graph.nodes()["HP:0000505"]
     assert len(n1t3["category"]) == 1
@@ -348,7 +342,6 @@ def test_rdf_transform2():
     assert e1t3["relation"] == "RO:0000091"
     assert e1t3["type"] == "biolink:Association"
     assert e1t3["has_evidence"] == "ECO:0000501"
-    assert e1t3["source"] == "OMIM:166400"
 
     e2t3 = list(t3.store.graph.get_edge("ORPHA:93262", "HP:0000505").values())[0]
     assert e2t3["subject"] == "ORPHA:93262"
@@ -356,7 +349,9 @@ def test_rdf_transform2():
     assert e2t3["relation"] == "RO:0002200"
     assert e2t3["type"] == "biolink:Association"
     assert e2t3["frequency_of_phenotype"] == "HP:0040283"
-    assert e2t3["source"] == "ORPHA:93262"
+
+    assert t3.store.graph.number_of_nodes() == 19
+    assert t3.store.graph.number_of_edges() == 12
 
 
 def test_rdf_transform3():
diff --git a/tests/integration/test_validator.py b/tests/integration/test_validator.py
index 5d13baa..4fb03f8 100644
--- a/tests/integration/test_validator.py
+++ b/tests/integration/test_validator.py
@@ -5,6 +5,9 @@ from kgx.validator import Validator
 from kgx.graph.nx_graph import NxGraph
 from kgx.transformer import Transformer
 from tests import RESOURCE_DIR
+from bmt import Toolkit
+
+toolkit = Toolkit()
 
 
 def test_validator_bad():
@@ -90,7 +93,7 @@ def test_validator_explicit_biolink_version():
         "CHEMBL.COMPOUND:1222250",
         id="CHEMBL.COMPOUND:1222250",
         name="Dextrose",
-        category=["Carbohydrate"],
+        category=["NamedThing"]
     )
     G.add_node(
         "UBERON:0000001", id="UBERON:0000001", name="fake", category=["NamedThing"]
@@ -105,7 +108,7 @@ def test_validator_explicit_biolink_version():
         object="UBERON:0000001",
         category=["biolink:Association"],
     )
-    Validator.set_biolink_model(version="1.8.2")
+    Validator.set_biolink_model(toolkit.get_model_version())
     validator = Validator(verbose=True)
     validator.validate(G)
     print(validator.get_errors())
@@ -126,7 +129,7 @@ def test_validator():
         "aggregator_knowledge_source": True,
     }
 
-    Validator.set_biolink_model("1.8.2")
+    Validator.set_biolink_model(toolkit.get_model_version())
 
     # Validator assumes the currently set Biolink Release
     validator = Validator()
diff --git a/tests/unit/test_clique_merge.py b/tests/unit/test_clique_merge.py
index 1c915eb..a64bb1d 100644
--- a/tests/unit/test_clique_merge.py
+++ b/tests/unit/test_clique_merge.py
@@ -7,6 +7,7 @@ from kgx.graph_operations.clique_merge import (
 )
 from kgx.utils.kgx_utils import get_biolink_ancestors, generate_edge_key, get_toolkit
 from tests import print_graph
+from bmt import Toolkit
 
 
 def test_check_categories():
@@ -69,9 +70,6 @@ def test_check_all_categories2():
     """
     Test check_all_categories method.
     """
-    # explicitly pin the release of Biolink to a
-    # specific one with known category ancestry
-    get_toolkit(biolink_release="3.0.0")
     categories = get_biolink_ancestors("biolink:Gene")
     vbc, ibc, ic = check_all_categories(categories)
 
diff --git a/tests/unit/test_config.py b/tests/unit/test_config.py
index f07064b..9227635 100644
--- a/tests/unit/test_config.py
+++ b/tests/unit/test_config.py
@@ -5,12 +5,23 @@ from kgx.config import get_biolink_model_schema
 
 def test_valid_biolink_version():
     try:
-        schema = get_biolink_model_schema("2.2.5")
+        schema = get_biolink_model_schema("v3.2.1")
     except TypeError as te:
         assert False, "test failure!"
     assert (
         schema
-        == "https://raw.githubusercontent.com/biolink/biolink-model/2.2.5/biolink-model.yaml"
+        == "https://raw.githubusercontent.com/biolink/biolink-model/v3.2.1/biolink-model.yaml"
+    )
+
+
+def test_valid_biolink_version_no_v():
+    try:
+        schema = get_biolink_model_schema("2.0.1")
+    except TypeError as te:
+        assert False, "test failure!"
+    assert (
+        schema
+        == "https://raw.githubusercontent.com/biolink/biolink-model/2.0.1/biolink-model.yaml"
     )
 
 
diff --git a/tests/unit/test_rdf_utils.py b/tests/unit/test_rdf_utils.py
index 794f2f8..448086e 100644
--- a/tests/unit/test_rdf_utils.py
+++ b/tests/unit/test_rdf_utils.py
@@ -1,6 +1,7 @@
 import os
 import pytest
 from rdflib import URIRef, Graph
+from pprint import pprint
 
 from kgx.prefix_manager import PrefixManager
 from kgx.utils.rdf_utils import infer_category, process_predicate
@@ -89,7 +90,15 @@ def test_process_predicate(query):
     Test behavior of process_predicate method.
     """
     pm = PrefixManager()
+    pprint(query[0])
     x = process_predicate(pm, query[0])
+    # x = "element_uri", "canonical_uri", "predicate", "property_name"
+    # print("x: ", x)
+    # print("query[0]", query[0])
+    # print("x[0]: ", x[0], "query[1]: ", query[1])
+    # print("x[1]: ", x[1], "query[2]: ", query[2])
+    # print("x[2]: ", x[2], "query[3]: ", query[3])
+    # print("x[3]: ", x[3], "query[4]: ", query[4])
     assert x[0] == query[1]
     assert x[1] == query[2]
     assert x[2] == query[3]
diff --git a/tests/unit/test_source/test_obograph_source.py b/tests/unit/test_source/test_obograph_source.py
index 2c4097e..7a7d448 100644
--- a/tests/unit/test_source/test_obograph_source.py
+++ b/tests/unit/test_source/test_obograph_source.py
@@ -27,7 +27,7 @@ def test_read_obograph1():
                 nodes[rec[0]] = rec[1]
 
     assert len(nodes) == 176
-    assert len(edges) == 206
+    assert len(edges) == 205
 
     n1 = nodes["GO:0003677"]
     assert n1["id"] == "GO:0003677"
@@ -77,7 +77,7 @@ def test_read_jsonl2():
                 nodes[rec[0]] = rec[1]
 
     assert len(nodes) == 176
-    assert len(edges) == 206
+    assert len(edges) == 205
 
     n1 = nodes["GO:0003677"]
     assert n1["id"] == "GO:0003677"
diff --git a/tests/unit/test_source/test_owl_source.py b/tests/unit/test_source/test_owl_source.py
index 7fa3d69..d3a93b2 100644
--- a/tests/unit/test_source/test_owl_source.py
+++ b/tests/unit/test_source/test_owl_source.py
@@ -3,6 +3,7 @@ import os
 from kgx.source import OwlSource
 from kgx.transformer import Transformer
 from tests import RESOURCE_DIR
+from pprint import pprint
 
 
 def test_read_owl1():
@@ -27,21 +28,21 @@ def test_read_owl1():
 
     n1 = nodes["GO:0008150"]
     assert n1["name"] == "biological_process"
-    assert "synonym" in n1 and "biological process" in n1["synonym"]
+    assert "has_exact_synonym" in n1 and "biological process" in n1["has_exact_synonym"]
     assert "description" in n1
     assert "comment" in n1
     assert "has_alternative_id" in n1 and "GO:0044699" in n1["has_alternative_id"]
 
     n2 = nodes["GO:0003674"]
     n2["name"] = "molecular_function"
-    assert "synonym" in n2 and "molecular function" in n2["synonym"]
+    assert "has_exact_synonym" in n2 and "molecular function" in n2["has_exact_synonym"]
     assert "description" in n2
     assert "comment" in n2
     assert "has_alternative_id" in n2 and "GO:0005554" in n2["has_alternative_id"]
 
     n3 = nodes["GO:0005575"]
     n3["name"] = "cellular_component"
-    assert "synonym" in n3 and "cellular component" in n3["synonym"]
+    assert "has_exact_synonym" in n3 and "cellular component" in n3["has_exact_synonym"]
     assert "description" in n3
     assert "comment" in n3
     assert "has_alternative_id" in n3 and "GO:0008372" in n3["has_alternative_id"]
@@ -77,7 +78,7 @@ def test_read_owl2():
 
     n1 = nodes["GO:0008150"]
     assert n1["name"] == "biological_process"
-    assert "synonym" in n1 and "biological process" in n1["synonym"]
+    assert "has_exact_synonym" in n1 and "biological process" in n1["has_exact_synonym"]
     assert "description" in n1
     assert "comment" in n1
     assert "has_alternative_id" in n1 and "GO:0044699" in n1["has_alternative_id"]
@@ -85,7 +86,7 @@ def test_read_owl2():
 
     n2 = nodes["GO:0003674"]
     n2["name"] = "molecular_function"
-    assert "synonym" in n2 and "molecular function" in n2["synonym"]
+    assert "has_exact_synonym" in n2 and "molecular function" in n2["has_exact_synonym"]
     assert "description" in n2
     assert "comment" in n2
     assert "has_alternative_id" in n2 and "GO:0005554" in n2["has_alternative_id"]
@@ -93,7 +94,7 @@ def test_read_owl2():
 
     n3 = nodes["GO:0005575"]
     n3["name"] = "cellular_component"
-    assert "synonym" in n3 and "cellular component" in n3["synonym"]
+    assert "has_exact_synonym" in n3 and "cellular component" in n3["has_exact_synonym"]
     assert "description" in n3
     assert "comment" in n3
     assert "has_alternative_id" in n3 and "GO:0008372" in n3["has_alternative_id"]
@@ -141,7 +142,7 @@ def test_read_owl3():
     n1 = nodes["GO:0008150"]
     assert n1["name"] == "biological_process"
     assert "subsets" in n1 and "GOP:goslim_generic" in n1["subsets"]
-    assert "synonym" in n1 and "biological process" in n1["synonym"]
+    assert "has_exact_synonym" in n1 and "biological process" in n1["has_exact_synonym"]
     assert "description" in n1
     assert "comment" in n1
     assert "xref" in n1 and "GO:0044699" in n1["xref"]
@@ -149,7 +150,7 @@ def test_read_owl3():
     n2 = nodes["GO:0003674"]
     n2["name"] = "molecular_function"
     assert "subsets" in n2 and "GOP:goslim_generic" in n2["subsets"]
-    assert "synonym" in n2 and "molecular function" in n2["synonym"]
+    assert "has_exact_synonym" in n2 and "molecular function" in n2["has_exact_synonym"]
     assert "description" in n2
     assert "comment" in n2
     assert "xref" in n2 and "GO:0005554" in n2["xref"]
@@ -157,7 +158,7 @@ def test_read_owl3():
     n3 = nodes["GO:0005575"]
     n3["name"] = "cellular_component"
     assert "subsets" in n3 and "GOP:goslim_generic" in n3["subsets"]
-    assert "synonym" in n3 and "cellular component" in n3["synonym"]
+    assert "has_exact_synonym" in n3 and "cellular component" in n3["has_exact_synonym"]
     assert "description" in n3
     assert "comment" in n3
     assert "xref" in n3 and "GO:0008372" in n3["xref"]
diff --git a/tests/unit/test_source/test_rdf_source.py b/tests/unit/test_source/test_rdf_source.py
index 31fb370..4238592 100644
--- a/tests/unit/test_source/test_rdf_source.py
+++ b/tests/unit/test_source/test_rdf_source.py
@@ -1,5 +1,5 @@
 import os
-import pprint
+from pprint import pprint
 
 import pytest