From 245fc7f23c66de8a458e8ad3e63c9f0b11affbd8 Mon Sep 17 00:00:00 2001
From: Rok Roskar <rok.roskar@sdsc.ethz.ch>
Date: Tue, 22 Sep 2020 14:56:21 +0200
Subject: [PATCH 1/5] feat: initial support for neo4j

---
 calamus/backends/__init__.py |  31 +++++++++++
 calamus/backends/neo4j.py    | 103 +++++++++++++++++++++++++++++++++++
 calamus/fields.py            |   7 ++-
 calamus/schema.py            |   5 +-
 4 files changed, 144 insertions(+), 2 deletions(-)
 create mode 100644 calamus/backends/__init__.py
 create mode 100644 calamus/backends/neo4j.py

diff --git a/calamus/backends/__init__.py b/calamus/backends/__init__.py
new file mode 100644
index 0000000..3ba8447
--- /dev/null
+++ b/calamus/backends/__init__.py
@@ -0,0 +1,31 @@
+# -*- coding: utf-8 -*-
+#
+# Copyright 2017-2020- Swiss Data Science Center (SDSC)
+# A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
+# Eidgenössische Technische Hochschule Zürich (ETHZ).
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""Calamus db backends."""
+
+class CalamusDbBackend:
+    def __init__(self, **config):
+        """Initialize provided the backend config."""
+        return NotImplementedError
+
+    def commit(self, entity, schema):
+        """Commit an object to the db using the schema."""
+        raise NotImplementedError
+
+    def fetch_by_id(self, identifier, schema):
+        """Fetch an entity by identifier from the db."""
+        raise NotImplementedError
diff --git a/calamus/backends/neo4j.py b/calamus/backends/neo4j.py
new file mode 100644
index 0000000..e503488
--- /dev/null
+++ b/calamus/backends/neo4j.py
@@ -0,0 +1,103 @@
+# -*- coding: utf-8 -*-
+#
+# Copyright 2020- Swiss Data Science Center (SDSC)
+# A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
+# Eidgenössische Technische Hochschule Zürich (ETHZ).
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""Neo4J connection utils."""
+import json
+import requests
+
+from urllib.parse import quote
+
+import py2neo
+from py2neo import Graph
+from py2neo.database.work import ClientError
+
+from . import CalamusDbBackend
+
+
+class CalamusNeo4JBackend(CalamusDbBackend):
+    """Neo4J backend for Calamus."""
+
+    def __init__(self, auth={"user": "neo4j", "pass": "test"}, host="localhost", bolt_port=7687, http_port=7474):
+        self.auth = auth
+        self.bolt_url = f"bolt://{auth['user']}:{auth['pass']}@{host}:{bolt_port}"
+        self.http_url = f"http://{auth['user']}:{auth['pass']}@{host}:{http_port}"
+
+        self.graph = None
+
+    def initialize(self):
+        """Initialize the Neo4J graph."""
+        # TODO: provide options for adding extra configs
+        self.graph = Graph(self.bolt_url)
+        try:
+            # initialize the config
+            self.graph.call.n10s.graphconfig.init({"handleVocabUris": "KEEP"})
+
+            # set URI constraint
+            res = self.graph.run(
+                """
+            CREATE CONSTRAINT n10s_unique_uri ON (r:Resource)
+            ASSERT r.uri IS UNIQUE;
+            """
+            )
+        # TODO: handle the client error in a more specific way
+        except ClientError:
+            pass
+
+        ## Comment: seems like setting prefixes is maybe not something we'd want to do
+        # initialize prefixes
+        #     g.call.n10s.nsprefixes.add("prov", "http://www.w3.org/ns/prov#")
+        #     g.call.n10s.nsprefixes.add("renku", "https://swissdatasciencecenter.github.io/renku-ontology#")
+        #     g.call.n10s.nsprefixes.add("wfprov", "http://purl.org/wf4ever/wfprov#")
+        return self.graph
+
+    def commit(self, entity, schema):
+        """Commit an object to Neo4J using the schema."""
+        # TODO: use automatic schema retrieval
+        # schema = _model_registry[entity.__class__]
+        if not self.graph:
+            raise RuntimeError("The graph must first be initialized.")
+
+        res = self.graph.run(
+            "call n10s.rdf.import.inline('{jsonld}', \"JSON-LD\")".format(jsonld=schema().dumps(entity))
+        )
+        return res
+
+    def fetch_by_id(self, identifier):
+        """Fetch an entity by id from Neo4J using the provided schema."""
+        if not self.graph:
+            raise RuntimeError("The graph must first be initialized.")
+
+        # cypher = f"""
+        # MATCH path=((n {{uri: "{identifier}"}}) -[*1..]-> ()) RETURN path
+        # """
+
+        cypher = f"""
+        MATCH path=((n {{uri: "{identifier}"}}) -[*0..1]-> ()) RETURN path
+        """
+
+        payload = {"cypher": cypher, "format": "JSON-LD"}
+
+        data = requests.post(
+            f"{self.http_url}/rdf/neo4j/cypher", data=json.dumps(payload), auth=tuple(self.auth.values())
+        ).json()
+
+        # grab just the data we asked for - depending on the node, we might have a @graph or just
+        # data for the single node
+        if data and '@graph' in data:
+            data = [x for x in data.get('@graph') if x.get('@id') == identifier].pop()
+
+        return data
diff --git a/calamus/fields.py b/calamus/fields.py
index bd1839a..f9eaab2 100644
--- a/calamus/fields.py
+++ b/calamus/fields.py
@@ -342,6 +342,7 @@ def schema(self):
                         dump_only=self._nested_normalized_option("dump_only"),
                         lazy=self.root.lazy,
                         flattened=self.root.flattened,
+                        session=self.root.session,
                         _visited=self.root._visited,
                         _top_level=False,
                     )
@@ -449,7 +450,11 @@ def _load(self, value, data, partial=None, many=False):
 
     def _dereference_single_id(self, value, attr, **kwargs):
         """Dereference a single id."""
-        data = kwargs["_all_objects"].get(value, None)
+        session = kwargs.get("session")
+        if session:
+            data = session.fetch_by_id(value)
+        else:
+            data = kwargs["_all_objects"].get(value, None)
         if not data:
             raise ValueError("Couldn't dereference id {id}".format(id=value))
 
diff --git a/calamus/schema.py b/calamus/schema.py
index 01b537f..53b93ab 100644
--- a/calamus/schema.py
+++ b/calamus/schema.py
@@ -123,6 +123,7 @@ def __init__(
         unknown=None,
         flattened=False,
         lazy=False,
+        session=None,
         _all_objects=None,
         _visited=None,
         _top_level=True,
@@ -139,7 +140,8 @@ def __init__(
             unknown=unknown,
         )
 
-        self.flattened = flattened
+        self.session = session
+        self.flattened = flattened | (session is not None)
         self.lazy = lazy
         self._top_level = _top_level
         self._all_objects = _all_objects
@@ -326,6 +328,7 @@ def _deserialize(
                 d_kwargs["_all_objects"] = self._all_objects
                 d_kwargs["flattened"] = self.flattened
                 d_kwargs["lazy"] = self.lazy
+                d_kwargs["session"] = self.session
                 getter = lambda val: field_obj.deserialize(val, field_name, data, **d_kwargs)
                 value = self._call_and_store(
                     getter_func=getter, data=raw_value, field_name=field_name, error_store=error_store, index=index,

From e3abd31e6fce2d429fb22e4e80d3646377d8c316 Mon Sep 17 00:00:00 2001
From: Rok Roskar <rok.roskar@sdsc.ethz.ch>
Date: Tue, 22 Sep 2020 15:44:03 +0200
Subject: [PATCH 2/5] chore: deal with dependencies

---
 calamus/backends/__init__.py |   1 +
 calamus/backends/neo4j.py    |  23 +-
 poetry.lock                  | 417 +++++++++++++++++++++++++++++------
 pyproject.toml               |   3 +
 4 files changed, 364 insertions(+), 80 deletions(-)

diff --git a/calamus/backends/__init__.py b/calamus/backends/__init__.py
index 3ba8447..60a1faa 100644
--- a/calamus/backends/__init__.py
+++ b/calamus/backends/__init__.py
@@ -17,6 +17,7 @@
 # limitations under the License.
 """Calamus db backends."""
 
+
 class CalamusDbBackend:
     def __init__(self, **config):
         """Initialize provided the backend config."""
diff --git a/calamus/backends/neo4j.py b/calamus/backends/neo4j.py
index e503488..3ab9b4c 100644
--- a/calamus/backends/neo4j.py
+++ b/calamus/backends/neo4j.py
@@ -17,13 +17,20 @@
 # limitations under the License.
 """Neo4J connection utils."""
 import json
-import requests
+
+try:
+    import requests
+except ImportError:
+    pass
 
 from urllib.parse import quote
 
-import py2neo
-from py2neo import Graph
-from py2neo.database.work import ClientError
+try:
+    import py2neo
+    from py2neo import Graph
+    from py2neo.database.work import ClientError
+except ImportError:
+    pass
 
 from . import CalamusDbBackend
 
@@ -81,10 +88,6 @@ def fetch_by_id(self, identifier):
         if not self.graph:
             raise RuntimeError("The graph must first be initialized.")
 
-        # cypher = f"""
-        # MATCH path=((n {{uri: "{identifier}"}}) -[*1..]-> ()) RETURN path
-        # """
-
         cypher = f"""
         MATCH path=((n {{uri: "{identifier}"}}) -[*0..1]-> ()) RETURN path
         """
@@ -97,7 +100,7 @@ def fetch_by_id(self, identifier):
 
         # grab just the data we asked for - depending on the node, we might have a @graph or just
         # data for the single node
-        if data and '@graph' in data:
-            data = [x for x in data.get('@graph') if x.get('@id') == identifier].pop()
+        if data and "@graph" in data:
+            data = [x for x in data.get("@graph") if x.get("@id") == identifier].pop()
 
         return data
diff --git a/poetry.lock b/poetry.lock
index d16064b..70f5f74 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -29,13 +29,13 @@ description = "Classes Without Boilerplate"
 name = "attrs"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "19.3.0"
+version = "20.2.0"
 
 [package.extras]
-azure-pipelines = ["coverage", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface", "pytest-azurepipelines"]
-dev = ["coverage", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface", "sphinx", "pre-commit"]
-docs = ["sphinx", "zope.interface"]
-tests = ["coverage", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface"]
+dev = ["coverage (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface", "sphinx", "sphinx-rtd-theme", "pre-commit"]
+docs = ["sphinx", "sphinx-rtd-theme", "zope.interface"]
+tests = ["coverage (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface"]
+tests_no_zope = ["coverage (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six"]
 
 [[package]]
 category = "main"
@@ -84,13 +84,24 @@ optional = true
 python-versions = "*"
 version = "2020.6.20"
 
+[[package]]
+category = "main"
+description = "Foreign Function Interface for Python calling C code."
+name = "cffi"
+optional = true
+python-versions = "*"
+version = "1.14.3"
+
+[package.dependencies]
+pycparser = "*"
+
 [[package]]
 category = "dev"
 description = "Validate configuration and produce human readable error messages."
 name = "cfgv"
 optional = false
 python-versions = ">=3.6.1"
-version = "3.1.0"
+version = "3.2.0"
 
 [[package]]
 category = "main"
@@ -117,6 +128,25 @@ optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 version = "0.4.3"
 
+[[package]]
+category = "main"
+description = "cryptography is a package which provides cryptographic recipes and primitives to Python developers."
+name = "cryptography"
+optional = true
+python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*"
+version = "3.1"
+
+[package.dependencies]
+cffi = ">=1.8,<1.11.3 || >1.11.3"
+six = ">=1.4.1"
+
+[package.extras]
+docs = ["sphinx (>=1.6.5,<1.8.0 || >1.8.0,<3.1.0 || >3.1.0,<3.1.1 || >3.1.1)", "sphinx-rtd-theme"]
+docstest = ["doc8", "pyenchant (>=1.6.11)", "twine (>=1.12.0)", "sphinxcontrib-spelling (>=4.0.1)"]
+pep8test = ["black", "flake8", "flake8-import-order", "pep8-naming"]
+ssh = ["bcrypt (>=3.1.5)"]
+test = ["pytest (>=3.6.0,<3.9.0 || >3.9.0,<3.9.1 || >3.9.1,<3.9.2 || >3.9.2)", "pretend", "iso8601", "pytz", "hypothesis (>=1.11.4,<3.79.2 || >3.79.2)"]
+
 [[package]]
 category = "dev"
 description = "Distribution utilities"
@@ -125,6 +155,24 @@ optional = false
 python-versions = "*"
 version = "0.3.1"
 
+[[package]]
+category = "main"
+description = "A Python library for the Docker Engine API."
+name = "docker"
+optional = true
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+version = "4.3.1"
+
+[package.dependencies]
+pywin32 = "227"
+requests = ">=2.14.2,<2.18.0 || >2.18.0"
+six = ">=1.4.0"
+websocket-client = ">=0.32.0"
+
+[package.extras]
+ssh = ["paramiko (>=2.4.2)"]
+tls = ["pyOpenSSL (>=17.5.0)", "cryptography (>=1.3.4)", "idna (>=2.0.0)"]
+
 [[package]]
 category = "main"
 description = "Docutils -- Python Documentation Utilities"
@@ -133,6 +181,17 @@ optional = true
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 version = "0.16"
 
+[[package]]
+category = "main"
+description = "English language utility library for Python"
+name = "english"
+optional = true
+python-versions = "*"
+version = "2020.7.0"
+
+[package.dependencies]
+six = "*"
+
 [[package]]
 category = "dev"
 description = "A platform independent file lock."
@@ -172,7 +231,7 @@ description = "File identification library for Python"
 name = "identify"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,>=2.7"
-version = "1.4.24"
+version = "1.5.4"
 
 [package.extras]
 license = ["editdistance"]
@@ -194,7 +253,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 version = "1.2.0"
 
 [[package]]
-category = "dev"
+category = "main"
 description = "Read metadata from Python packages"
 marker = "python_version < \"3.8\""
 name = "importlib-metadata"
@@ -245,8 +304,8 @@ category = "main"
 description = "A fast and thorough lazy object proxy."
 name = "lazy-object-proxy"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "1.5.0"
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+version = "1.5.1"
 
 [[package]]
 category = "main"
@@ -276,11 +335,11 @@ description = "A lightweight library for converting complex datatypes to and fro
 name = "marshmallow"
 optional = false
 python-versions = ">=3.5"
-version = "3.7.0"
+version = "3.8.0"
 
 [package.extras]
 dev = ["pytest", "pytz", "simplejson", "mypy (0.782)", "flake8 (3.8.3)", "flake8-bugbear (20.1.4)", "pre-commit (>=2.4,<3.0)", "tox"]
-docs = ["sphinx (3.1.2)", "sphinx-issues (1.2.0)", "alabaster (0.7.12)", "sphinx-version-warning (1.1.2)", "autodocsumm (0.1.13)"]
+docs = ["sphinx (3.2.1)", "sphinx-issues (1.2.0)", "alabaster (0.7.12)", "sphinx-version-warning (1.1.2)", "autodocsumm (0.2.0)"]
 lint = ["mypy (0.782)", "flake8 (3.8.3)", "flake8-bugbear (20.1.4)", "pre-commit (>=2.4,<3.0)"]
 tests = ["pytest", "pytz", "simplejson"]
 
@@ -292,13 +351,33 @@ optional = false
 python-versions = "*"
 version = "0.6.1"
 
+[[package]]
+category = "main"
+description = "An implementation of time.monotonic() for Python 2 & < 3.3"
+name = "monotonic"
+optional = true
+python-versions = "*"
+version = "1.5"
+
 [[package]]
 category = "dev"
 description = "More routines for operating on iterables, beyond itertools"
 name = "more-itertools"
 optional = false
 python-versions = ">=3.5"
-version = "8.4.0"
+version = "8.5.0"
+
+[[package]]
+category = "main"
+description = "Nanosecond resolution temporal types"
+name = "neotime"
+optional = true
+python-versions = "*"
+version = "1.7.4"
+
+[package.dependencies]
+pytz = "*"
+six = "*"
 
 [[package]]
 category = "dev"
@@ -306,7 +385,7 @@ description = "Node.js virtual environment builder"
 name = "nodeenv"
 optional = false
 python-versions = "*"
-version = "1.4.0"
+version = "1.5.0"
 
 [[package]]
 category = "main"
@@ -320,6 +399,17 @@ version = "20.4"
 pyparsing = ">=2.0.2"
 six = "*"
 
+[[package]]
+category = "main"
+description = "ANSI escape code library for Python"
+name = "pansi"
+optional = true
+python-versions = "*"
+version = "2020.7.3"
+
+[package.dependencies]
+six = "*"
+
 [[package]]
 category = "dev"
 description = "Utility library for gitignore style pattern matching of file paths."
@@ -350,7 +440,7 @@ description = "A framework for managing and maintaining multi-language pre-commi
 name = "pre-commit"
 optional = false
 python-versions = ">=3.6.1"
-version = "2.6.0"
+version = "2.7.1"
 
 [package.dependencies]
 cfgv = ">=2.0.0"
@@ -368,6 +458,18 @@ version = "*"
 python = "<3.7"
 version = "*"
 
+[[package]]
+category = "main"
+description = "Library for building powerful interactive command lines in Python"
+name = "prompt-toolkit"
+optional = true
+python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
+version = "2.0.10"
+
+[package.dependencies]
+six = ">=1.9.0"
+wcwidth = "*"
+
 [[package]]
 category = "dev"
 description = "library with cross-python path, ini-parsing, io, code, log facilities"
@@ -376,6 +478,29 @@ optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 version = "1.9.0"
 
+[[package]]
+category = "main"
+description = "Python client library and toolkit for Neo4j"
+name = "py2neo"
+optional = true
+python-versions = "*"
+version = "2020.0.0"
+
+[package.dependencies]
+certifi = "*"
+cryptography = "*"
+docker = "*"
+english = "*"
+monotonic = "*"
+neotime = ">=1.7.4,<1.8.0"
+packaging = "*"
+pansi = ">=2020.7.3"
+prompt-toolkit = ">=2.0.7,<2.1.0"
+pygments = ">=2.0.0"
+pytz = "*"
+six = ">=1.15.0"
+urllib3 = "*"
+
 [[package]]
 category = "dev"
 description = "Python style guide checker"
@@ -384,6 +509,14 @@ optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 version = "2.6.0"
 
+[[package]]
+category = "main"
+description = "C parser in Python"
+name = "pycparser"
+optional = true
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+version = "2.20"
+
 [[package]]
 category = "main"
 description = "Python bindings for the Enchant spellchecking system"
@@ -406,7 +539,7 @@ description = "Pygments is a syntax highlighting package written in Python."
 name = "pygments"
 optional = true
 python-versions = ">=3.5"
-version = "2.6.1"
+version = "2.7.1"
 
 [[package]]
 category = "main"
@@ -414,7 +547,7 @@ description = "Python implementation of the JSON-LD API"
 name = "pyld"
 optional = false
 python-versions = "*"
-version = "2.0.2"
+version = "2.0.3"
 
 [package.dependencies]
 cachetools = "*"
@@ -467,7 +600,7 @@ description = "A pytest plugin to enable format checking with black"
 name = "pytest-black"
 optional = false
 python-versions = ">=2.7"
-version = "0.3.10"
+version = "0.3.11"
 
 [package.dependencies]
 pytest = ">=3.5.0"
@@ -485,6 +618,15 @@ optional = true
 python-versions = "*"
 version = "2020.1"
 
+[[package]]
+category = "main"
+description = "Python for Window Extensions"
+marker = "sys_platform == \"win32\""
+name = "pywin32"
+optional = true
+python-versions = "*"
+version = "227"
+
 [[package]]
 category = "dev"
 description = "YAML parser and emitter for Python"
@@ -541,7 +683,7 @@ description = "Python documentation generator"
 name = "sphinx"
 optional = true
 python-versions = ">=3.5"
-version = "3.1.2"
+version = "3.2.1"
 
 [package.dependencies]
 Jinja2 = ">=2.3"
@@ -655,13 +797,18 @@ description = "Sphinx spelling extension"
 name = "sphinxcontrib-spelling"
 optional = true
 python-versions = ">=3.5"
-version = "5.1.2"
+version = "5.4.0"
 
 [package.dependencies]
 PyEnchant = ">=3.1.1"
 Sphinx = ">=3.0.0"
 
+[package.dependencies.importlib-metadata]
+python = "<3.8"
+version = ">=1.7.0"
+
 [package.extras]
+docs = ["reno"]
 linter = ["flake8 (3.8.2)"]
 test = ["pytest", "pytest-cov", "fixtures (>=3.0.0)", "coverage (>=4.0,<4.4 || >4.4)"]
 
@@ -687,7 +834,7 @@ description = "HTTP library with thread-safe connection pooling, file post, and
 name = "urllib3"
 optional = true
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, <4"
-version = "1.25.9"
+version = "1.25.10"
 
 [package.extras]
 brotli = ["brotlipy (>=0.6.0)"]
@@ -700,7 +847,7 @@ description = "Virtual Python Environment builder"
 name = "virtualenv"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,>=2.7"
-version = "20.0.27"
+version = "20.0.31"
 
 [package.dependencies]
 appdirs = ">=1.4.3,<2"
@@ -717,11 +864,11 @@ python = "<3.7"
 version = ">=1.0"
 
 [package.extras]
-docs = ["sphinx (>=3)", "sphinx-argparse (>=0.2.5)", "sphinx-rtd-theme (>=0.4.3)", "towncrier (>=19.9.0rc1)", "proselint (>=0.10.2)"]
-testing = ["pytest (>=4)", "coverage (>=5)", "coverage-enable-subprocess (>=1)", "pytest-xdist (>=1.31.0)", "pytest-mock (>=2)", "pytest-env (>=0.6.2)", "pytest-randomly (>=1)", "pytest-timeout (>=1)", "pytest-freezegun (>=0.4.1)", "flaky (>=3)", "packaging (>=20.0)", "xonsh (>=0.9.16)"]
+docs = ["proselint (>=0.10.2)", "sphinx (>=3)", "sphinx-argparse (>=0.2.5)", "sphinx-rtd-theme (>=0.4.3)", "towncrier (>=19.9.0rc1)"]
+testing = ["coverage (>=5)", "coverage-enable-subprocess (>=1)", "flaky (>=3)", "pytest (>=4)", "pytest-env (>=0.6.2)", "pytest-freezegun (>=0.4.1)", "pytest-mock (>=2)", "pytest-randomly (>=1)", "pytest-timeout (>=1)", "pytest-xdist (>=1.31.0)", "packaging (>=20.0)", "xonsh (>=0.9.16)"]
 
 [[package]]
-category = "dev"
+category = "main"
 description = "Measures the displayed width of unicode strings in a terminal"
 name = "wcwidth"
 optional = false
@@ -729,7 +876,18 @@ python-versions = "*"
 version = "0.2.5"
 
 [[package]]
-category = "dev"
+category = "main"
+description = "WebSocket client for Python. hybi13 is supported."
+name = "websocket-client"
+optional = true
+python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+version = "0.57.0"
+
+[package.dependencies]
+six = "*"
+
+[[package]]
+category = "main"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 marker = "python_version < \"3.8\""
 name = "zipp"
@@ -743,9 +901,11 @@ testing = ["jaraco.itertools", "func-timeout"]
 
 [extras]
 docs = ["sphinx", "sphinx-rtd-theme", "sphinxcontrib-spelling"]
+neo4j = ["py2neo", "requests"]
 
 [metadata]
-content-hash = "f009ca29f15c4b0b388ea4ad5d081015016c4b6c4e99e1fde78491cd6f1653de"
+content-hash = "25eab4f841cfa33b01a2ee443e7e6b805aedba5f21ada3bc7d28a2521c358688"
+lock-version = "1.0"
 python-versions = "^3.6.1"
 
 [metadata.files]
@@ -762,8 +922,8 @@ atomicwrites = [
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+    {file = "attrs-20.2.0.tar.gz", hash = "sha256:26b54ddbbb9ee1d34d5d3668dd37d6cf74990ab23c828c2888dccdceee395594"},
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@@ -781,9 +941,47 @@ certifi = [
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 ]
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+]
 cfgv = [
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@@ -797,14 +995,46 @@ colorama = [
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 ]
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 docutils = [
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@@ -817,8 +1047,8 @@ frozendict = [
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+    {file = "pywin32-227-cp36-cp36m-win_amd64.whl", hash = "sha256:9b31e009564fb95db160f154e2aa195ed66bcc4c058ed72850d047141b36f3a2"},
+    {file = "pywin32-227-cp37-cp37m-win32.whl", hash = "sha256:47a3c7551376a865dd8d095a98deba954a98f326c6fe3c72d8726ca6e6b15507"},
+    {file = "pywin32-227-cp37-cp37m-win_amd64.whl", hash = "sha256:31f88a89139cb2adc40f8f0e65ee56a8c585f629974f9e07622ba80199057511"},
+    {file = "pywin32-227-cp38-cp38-win32.whl", hash = "sha256:7f18199fbf29ca99dff10e1f09451582ae9e372a892ff03a28528a24d55875bc"},
+    {file = "pywin32-227-cp38-cp38-win_amd64.whl", hash = "sha256:7c1ae32c489dc012930787f06244426f8356e129184a02c25aef163917ce158e"},
+    {file = "pywin32-227-cp39-cp39-win32.whl", hash = "sha256:c054c52ba46e7eb6b7d7dfae4dbd987a1bb48ee86debe3f245a2884ece46e295"},
+    {file = "pywin32-227-cp39-cp39-win_amd64.whl", hash = "sha256:f27cec5e7f588c3d1051651830ecc00294f90728d19c3bf6916e6dba93ea357c"},
+]
 pyyaml = [
     {file = "PyYAML-5.3.1-cp27-cp27m-win32.whl", hash = "sha256:74809a57b329d6cc0fdccee6318f44b9b8649961fa73144a98735b0aaf029f1f"},
     {file = "PyYAML-5.3.1-cp27-cp27m-win_amd64.whl", hash = "sha256:240097ff019d7c70a4922b6869d8a86407758333f02203e0fc6ff79c5dcede76"},
@@ -1048,8 +1321,8 @@ snowballstemmer = [
     {file = "snowballstemmer-2.0.0.tar.gz", hash = "sha256:df3bac3df4c2c01363f3dd2cfa78cce2840a79b9f1c2d2de9ce8d31683992f52"},
 ]
 sphinx = [
-    {file = "Sphinx-3.1.2-py3-none-any.whl", hash = "sha256:97dbf2e31fc5684bb805104b8ad34434ed70e6c588f6896991b2fdfd2bef8c00"},
-    {file = "Sphinx-3.1.2.tar.gz", hash = "sha256:b9daeb9b39aa1ffefc2809b43604109825300300b987a24f45976c001ba1a8fd"},
+    {file = "Sphinx-3.2.1-py3-none-any.whl", hash = "sha256:ce6fd7ff5b215af39e2fcd44d4a321f6694b4530b6f2b2109b64d120773faea0"},
+    {file = "Sphinx-3.2.1.tar.gz", hash = "sha256:321d6d9b16fa381a5306e5a0b76cd48ffbc588e6340059a729c6fdd66087e0e8"},
 ]
 sphinx-rtd-theme = [
     {file = "sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl", hash = "sha256:00cf895504a7895ee433807c62094cf1e95f065843bf3acd17037c3e9a2becd4"},
@@ -1080,8 +1353,8 @@ sphinxcontrib-serializinghtml = [
     {file = "sphinxcontrib_serializinghtml-1.1.4-py2.py3-none-any.whl", hash = "sha256:f242a81d423f59617a8e5cf16f5d4d74e28ee9a66f9e5b637a18082991db5a9a"},
 ]
 sphinxcontrib-spelling = [
-    {file = "sphinxcontrib-spelling-5.1.2.tar.gz", hash = "sha256:7f220647f1d9270bd90f0a42146b75a03c51a60184ced6584a9e5ef8f385b5a1"},
-    {file = "sphinxcontrib_spelling-5.1.2-py3-none-any.whl", hash = "sha256:4c17bc16cdb08a50b430245dfe351d6e5b61b5e86aa5432956f0e4ab41dabc41"},
+    {file = "sphinxcontrib-spelling-5.4.0.tar.gz", hash = "sha256:3e832c2b863f0f71df04a98e5976cf4da005ee6e9c03be41b3618d95a5fbfeb4"},
+    {file = "sphinxcontrib_spelling-5.4.0-py3-none-any.whl", hash = "sha256:bc076508b66d78c079889be367423fdaceeb6c14d137e05eb013cf14627a921b"},
 ]
 toml = [
     {file = "toml-0.10.1-py2.py3-none-any.whl", hash = "sha256:bda89d5935c2eac546d648028b9901107a595863cb36bae0c73ac804a9b4ce88"},
@@ -1111,17 +1384,21 @@ typed-ast = [
     {file = "typed_ast-1.4.1.tar.gz", hash = "sha256:8c8aaad94455178e3187ab22c8b01a3837f8ee50e09cf31f1ba129eb293ec30b"},
 ]
 urllib3 = [
-    {file = "urllib3-1.25.9-py2.py3-none-any.whl", hash = "sha256:88206b0eb87e6d677d424843ac5209e3fb9d0190d0ee169599165ec25e9d9115"},
-    {file = "urllib3-1.25.9.tar.gz", hash = "sha256:3018294ebefce6572a474f0604c2021e33b3fd8006ecd11d62107a5d2a963527"},
+    {file = "urllib3-1.25.10-py2.py3-none-any.whl", hash = "sha256:e7983572181f5e1522d9c98453462384ee92a0be7fac5f1413a1e35c56cc0461"},
+    {file = "urllib3-1.25.10.tar.gz", hash = "sha256:91056c15fa70756691db97756772bb1eb9678fa585d9184f24534b100dc60f4a"},
 ]
 virtualenv = [
-    {file = "virtualenv-20.0.27-py2.py3-none-any.whl", hash = "sha256:c51f1ba727d1614ce8fd62457748b469fbedfdab2c7e5dd480c9ae3fbe1233f1"},
-    {file = "virtualenv-20.0.27.tar.gz", hash = "sha256:26cdd725a57fef4c7c22060dba4647ebd8ca377e30d1c1cf547b30a0b79c43b4"},
+    {file = "virtualenv-20.0.31-py2.py3-none-any.whl", hash = "sha256:e0305af10299a7fb0d69393d8f04cb2965dda9351140d11ac8db4e5e3970451b"},
+    {file = "virtualenv-20.0.31.tar.gz", hash = "sha256:43add625c53c596d38f971a465553f6318decc39d98512bc100fa1b1e839c8dc"},
 ]
 wcwidth = [
     {file = "wcwidth-0.2.5-py2.py3-none-any.whl", hash = "sha256:beb4802a9cebb9144e99086eff703a642a13d6a0052920003a230f3294bbe784"},
     {file = "wcwidth-0.2.5.tar.gz", hash = "sha256:c4d647b99872929fdb7bdcaa4fbe7f01413ed3d98077df798530e5b04f116c83"},
 ]
+websocket-client = [
+    {file = "websocket_client-0.57.0-py2.py3-none-any.whl", hash = "sha256:0fc45c961324d79c781bab301359d5a1b00b13ad1b10415a4780229ef71a5549"},
+    {file = "websocket_client-0.57.0.tar.gz", hash = "sha256:d735b91d6d1692a6a181f2a8c9e0238e5f6373356f561bb9dc4c7af36f452010"},
+]
 zipp = [
     {file = "zipp-3.1.0-py3-none-any.whl", hash = "sha256:aa36550ff0c0b7ef7fa639055d797116ee891440eac1a56f378e2d3179e0320b"},
     {file = "zipp-3.1.0.tar.gz", hash = "sha256:c599e4d75c98f6798c509911d08a22e6c021d074469042177c8c86fb92eefd96"},
diff --git a/pyproject.toml b/pyproject.toml
index 03846cf..421aac9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -46,6 +46,8 @@ sphinx = {version = "^3.0.3", optional = true}
 sphinx-rtd-theme = {version = "^0.4.3", optional = true}
 sphinxcontrib-spelling = {version = "^5.0.0", optional = true}
 lazy-object-proxy = "^1.4.3"
+py2neo = {version = "^2020.0.0", extras = ["neo4j"], optional = true}
+requests = {version = "^2.24.0", extras = ["neo4j"], optional = true}
 
 [tool.poetry.dev-dependencies]
 pytest = "^5.2"
@@ -56,6 +58,7 @@ pytest-black = "^0.3.9"
 
 [tool.poetry.extras]
 docs = ["sphinx", "sphinx-rtd-theme", "sphinxcontrib-spelling"]
+neo4j = ["py2neo", "requests"]
 
 [tool.black]
 line-length = 120

From cd096b3a196a95b98ea34dd7b42a70d818c1b172 Mon Sep 17 00:00:00 2001
From: RenkuBot <renku@datascience.ch>
Date: Tue, 22 Sep 2020 14:00:46 +0000
Subject: [PATCH 3/5] chore: automatically update setup.py

---
 setup.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 46aedcc..73400c5 100644
--- a/setup.py
+++ b/setup.py
@@ -43,7 +43,7 @@
         "Programming Language :: Python :: 3.8",
         "Development Status :: 4 - Beta",
     ],
-    packages=["calamus"],
+    packages=["calamus", "calamus.backends"],
     package_dir={"": "."},
     package_data={},
     install_requires=["lazy-object-proxy==1.*,>=1.4.3", "marshmallow==3.*,>=3.5.1", "pyld==2.*,>=2.0.2"],
@@ -56,5 +56,6 @@
             "pytest-black==0.*,>=0.3.9",
         ],
         "docs": ["sphinx==3.*,>=3.0.3", "sphinx-rtd-theme==0.*,>=0.4.3", "sphinxcontrib-spelling==5.*,>=5.0.0"],
+        "neo4j": ["py2neo[neo4j]==2020.*,>=2020.0.0", "requests[neo4j]==2.*,>=2.24.0"],
     },
 )

From 6fbedecfb4688353a8c389ae33192fc01d768e6d Mon Sep 17 00:00:00 2001
From: Rok Roskar <rok.roskar@sdsc.ethz.ch>
Date: Tue, 22 Sep 2020 16:16:45 +0200
Subject: [PATCH 4/5] chore: remove renku-specific prefixes

---
 calamus/backends/neo4j.py | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/calamus/backends/neo4j.py b/calamus/backends/neo4j.py
index 3ab9b4c..218af69 100644
--- a/calamus/backends/neo4j.py
+++ b/calamus/backends/neo4j.py
@@ -64,11 +64,10 @@ def initialize(self):
         except ClientError:
             pass
 
-        ## Comment: seems like setting prefixes is maybe not something we'd want to do
-        # initialize prefixes
-        #     g.call.n10s.nsprefixes.add("prov", "http://www.w3.org/ns/prov#")
-        #     g.call.n10s.nsprefixes.add("renku", "https://swissdatasciencecenter.github.io/renku-ontology#")
-        #     g.call.n10s.nsprefixes.add("wfprov", "http://purl.org/wf4ever/wfprov#")
+        # TODO: provide options for initializing prefixes
+        # for prefix, prefix_uri in prefixes:
+        #     g.call.n10s.nsprefixes.add(f"{prefix}", f"{prefix_uri}")
+
         return self.graph
 
     def commit(self, entity, schema):

From cdf0ac13599fadea6b0c7dba3d38f68060c1f104 Mon Sep 17 00:00:00 2001
From: Rok Roskar <rok.roskar@sdsc.ethz.ch>
Date: Tue, 2 Mar 2021 15:18:22 +0100
Subject: [PATCH 5/5] feat: dereference objects as needed

---
 calamus/backends/neo4j.py | 21 +++++++++++++--------
 calamus/fields.py         | 13 +++++++++----
 2 files changed, 22 insertions(+), 12 deletions(-)

diff --git a/calamus/backends/neo4j.py b/calamus/backends/neo4j.py
index 218af69..f67af3a 100644
--- a/calamus/backends/neo4j.py
+++ b/calamus/backends/neo4j.py
@@ -17,6 +17,7 @@
 # limitations under the License.
 """Neo4J connection utils."""
 import json
+import time
 
 try:
     import requests
@@ -88,18 +89,22 @@ def fetch_by_id(self, identifier):
             raise RuntimeError("The graph must first be initialized.")
 
         cypher = f"""
-        MATCH path=((n {{uri: "{identifier}"}}) -[*0..1]-> ()) RETURN path
+        MATCH path=((n:Resource {{uri: "{identifier}"}}) -[*0..1]-> ()) RETURN path
         """
 
         payload = {"cypher": cypher, "format": "JSON-LD"}
 
-        data = requests.post(
+        print(cypher)
+        timein = time.time()
+        res = requests.post(
             f"{self.http_url}/rdf/neo4j/cypher", data=json.dumps(payload), auth=tuple(self.auth.values())
-        ).json()
-
-        # grab just the data we asked for - depending on the node, we might have a @graph or just
-        # data for the single node
-        if data and "@graph" in data:
-            data = [x for x in data.get("@graph") if x.get("@id") == identifier].pop()
+        )
+        print(f"time: {time.time()-timein}")
+        data = res.json()
 
+        if data is not None:
+            data = data.get("@graph", data)
         return data
+
+    def query(self, data, schema):
+        """Construct a query based on the data and the schema."""
diff --git a/calamus/fields.py b/calamus/fields.py
index f9eaab2..c3da9e5 100644
--- a/calamus/fields.py
+++ b/calamus/fields.py
@@ -37,7 +37,7 @@
 
 @total_ordering
 class IRIReference(object):
-    """ Represent an IRI in a namespace.
+    """Represent an IRI in a namespace.
 
     Args:
         namespace (Namespace): The ``Namespace`` this IRI is part of.
@@ -451,10 +451,15 @@ def _load(self, value, data, partial=None, many=False):
     def _dereference_single_id(self, value, attr, **kwargs):
         """Dereference a single id."""
         session = kwargs.get("session")
-        if session:
-            data = session.fetch_by_id(value)
-        else:
+
+        data = None
+
+        if kwargs["_all_objects"] is not None:
             data = kwargs["_all_objects"].get(value, None)
+
+        if not data and session:
+            data = session.fetch_by_id(value)
+
         if not data:
             raise ValueError("Couldn't dereference id {id}".format(id=value))