Repository: mirandrom/PyS2

Issue:
add logging
**Is your feature request related to a problem? Please describe.**
Currently, if a response contains an error status code, information about the paperId/authorId is printed. This doesn't work well when trying to perform large amounts of requests over an extended period of time. 

**Describe the solution you'd like**
Use logging

**Describe alternatives you've considered**
NA

**Additional context**
NA


Discussion:

Patch:
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 339202e..a68bc3e 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -27,11 +27,6 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         python -m pip install .[test]
-        python -m pip install pytest-cov
-    - name: Run pytest with coverage
-      run: pytest --cov=s2 tests/
-    - name: Run pytest and upload coverage to Codecov
-      uses: codecov/codecov-action@v1
-      with:
-        token: ${{ secrets.CODECOV_TOKEN }}
-        fail_ci_if_error: true
+    - name: Test with pytest
+      run: |
+        pytest
diff --git a/README.md b/README.md
index 56610b7..191e80e 100644
--- a/README.md
+++ b/README.md
@@ -3,7 +3,6 @@
 [![Latest PyS2 Version](https://img.shields.io/pypi/v/pys2.svg)](https://pypi.python.org/pypi/pys2)
 [![License](https://img.shields.io/github/license/mirandrom/pys2.svg)](https://pypi.python.org/pypi/pys2)
 [![CI](https://github.com/mirandrom/pys2/actions/workflows/ci.yml/badge.svg)](https://github.com/mirandrom/pys2/actions?query=branch%3Amaster)
-[![codecov](https://codecov.io/gh/mirandrom/PyS2/branch/master/graph/badge.svg?token=4GTVZ5P6S2)](https://codecov.io/gh/mirandrom/PyS2)
 [![ReadTheDocs](https://readthedocs.org/projects/pys2/badge/?version=latest)](https://pys2.readthedocs.io/)
 
 
diff --git a/doc/code_overview/api.rst b/doc/api_reference/api.rst
similarity index 67%
rename from doc/code_overview/api.rst
rename to doc/api_reference/api.rst
index 9193ef6..1ddec14 100644
--- a/doc/code_overview/api.rst
+++ b/doc/api_reference/api.rst
@@ -1,6 +1,5 @@
-API Endpoints
-=============
-
+s2.api
+================================================================================
 PyS2 uses :meth:`requests.Session.get` to query Semantic Scholar API
 endpoints. Functionality for `Data Partners
 <https://pages.semanticscholar.org/data-partners>`_,
@@ -10,5 +9,5 @@ or :class:`.models.S2Author` classes are included.
 .. toctree::
     :maxdepth: 2
 
-    api/get_paper
-    api/get_author
\ No newline at end of file
+.. include:: api/get_paper.rst
+.. include:: api/get_author.rst
\ No newline at end of file
diff --git a/doc/api_reference/api/get_author.rst b/doc/api_reference/api/get_author.rst
new file mode 100644
index 0000000..8c397cf
--- /dev/null
+++ b/doc/api_reference/api/get_author.rst
@@ -0,0 +1,4 @@
+get_author
+--------------------------------------------------------------------------------
+
+.. autofunction:: s2.api.get_author
\ No newline at end of file
diff --git a/doc/api_reference/api/get_paper.rst b/doc/api_reference/api/get_paper.rst
new file mode 100644
index 0000000..3c444ea
--- /dev/null
+++ b/doc/api_reference/api/get_paper.rst
@@ -0,0 +1,5 @@
+get_paper
+--------------------------------------------------------------------------------
+
+.. autofunction:: s2.api.get_paper
+
diff --git a/doc/api_reference/db.rst b/doc/api_reference/db.rst
new file mode 100644
index 0000000..988d663
--- /dev/null
+++ b/doc/api_reference/db.rst
@@ -0,0 +1,14 @@
+.. _s2.db:
+
+s2.db
+================================================================================
+
+PyS2 allows you to store and retrieve :class:`S2Paper` and :class:`S2Author`
+objects via arbitrary :class:`MutableMapping` classes. For an example, see
+:any:`saving_with_db`.
+
+.. toctree::
+    :maxdepth: 2
+
+.. include:: db/json_paper.rst
+.. include:: db/json_author.rst
diff --git a/doc/api_reference/db/json_author.rst b/doc/api_reference/db/json_author.rst
new file mode 100644
index 0000000..4f65a40
--- /dev/null
+++ b/doc/api_reference/db/json_author.rst
@@ -0,0 +1,6 @@
+JsonS2AuthorDB
+--------------------------------------------------------------------------------
+
+.. autoclass:: s2.db.json.JsonS2AuthorDB
+
+
diff --git a/doc/api_reference/db/json_paper.rst b/doc/api_reference/db/json_paper.rst
new file mode 100644
index 0000000..c9750d0
--- /dev/null
+++ b/doc/api_reference/db/json_paper.rst
@@ -0,0 +1,6 @@
+JsonS2PaperDB
+--------------------------------------------------------------------------------
+
+.. autoclass:: s2.db.json.JsonS2PaperDB
+
+
diff --git a/doc/code_overview/models.rst b/doc/api_reference/models.rst
similarity index 59%
rename from doc/code_overview/models.rst
rename to doc/api_reference/models.rst
index 2c6573e..6d9547f 100644
--- a/doc/code_overview/models.rst
+++ b/doc/api_reference/models.rst
@@ -1,5 +1,5 @@
-S2 Models
-==========================
+s2.models
+================================================================================
 PyS2 uses `pydantic <https://pydantic-docs.helpmanual.io/>`_.
 to convert the JSON objects returned by the Semantic Scholar API into
 self-documenting python classes with built-in data validation.
@@ -7,5 +7,5 @@ self-documenting python classes with built-in data validation.
 .. toctree::
     :maxdepth: 2
 
-    models/S2Paper
-    models/S2Author
\ No newline at end of file
+.. include:: models/s2paper.rst
+.. include:: models/s2author.rst
diff --git a/doc/code_overview/models/note_attributes.txt b/doc/api_reference/models/note_attributes.txt
similarity index 100%
rename from doc/code_overview/models/note_attributes.txt
rename to doc/api_reference/models/note_attributes.txt
diff --git a/doc/api_reference/models/s2author.rst b/doc/api_reference/models/s2author.rst
new file mode 100644
index 0000000..345f78d
--- /dev/null
+++ b/doc/api_reference/models/s2author.rst
@@ -0,0 +1,8 @@
+S2Author
+--------------------------------------------------------------------------------
+
+.. autoclass:: s2.models.S2Author
+
+.. autoclass:: s2.models.S2AuthorPaper
+
+.. include:: /api_reference/models/note_attributes.txt
diff --git a/doc/code_overview/models/S2Paper.rst b/doc/api_reference/models/s2paper.rst
similarity index 53%
rename from doc/code_overview/models/S2Paper.rst
rename to doc/api_reference/models/s2paper.rst
index 9d4c81c..14c9488 100644
--- a/doc/code_overview/models/S2Paper.rst
+++ b/doc/api_reference/models/s2paper.rst
@@ -1,5 +1,5 @@
 S2Paper
-=======
+--------------------------------------------------------------------------------
 
 .. autoclass:: s2.models.S2Paper
 
@@ -9,4 +9,4 @@ S2Paper
 
 .. autoclass:: s2.models.S2Topic
 
-.. include:: note_attributes.txt
+.. include:: /api_reference/models/note_attributes.txt
diff --git a/doc/getting_started/quick_start.rst b/doc/getting_started/quick_start.rst
index 52b3c28..7885211 100644
--- a/doc/getting_started/quick_start.rst
+++ b/doc/getting_started/quick_start.rst
@@ -65,6 +65,12 @@ Using a custom :class:`requests.Session`
     session.headers = {'x-api-key': API_KEY}
     paper = s2.api.get_paper(paperId=pid, session=session)
 
+.. note::
+
+    Passing an API key through the ``api_key`` argument will
+    temporarily overwrite a key stored in ``session`` for that request.
+    However, the ``session`` object itself will remain unchanged.
+
 The same approaches can be used for the :func:`.api.get_author` function
 covered below.
 
@@ -136,3 +142,74 @@ published *h* papers that have each been cited at least *h* times.
             break
 
 Which gives us an *h*-index 12 for Bill Gates!
+
+.. _saving_with_db:
+
+Saving and Working Locally with :any:`s2.db`
+--------------------------------------------------------------------------------
+The :any:`s2.db` API makes it easy to save and retrieve your :class:`.S2Paper`
+and :class:`.S2Author` objects through a dict-like interface.
+
+.. code-block:: python
+
+    from s2.db.json import JsonS2PaperDB, JsonS2AuthorDB
+
+    # path of directory where S2Papers will be saved as jsons
+    s2paper_json_dir = "pdb"
+
+    # if the directory does not exist, it is created
+    # otherwise, previously saved S2Papers become accessible
+    pdb = JsonS2PaperDB(s2paper_json_dir)
+
+    # lets save Bill's papers from the previous example
+    for p in papers:
+        pdb[p.paperId] = p
+
+    # now lets delete pdb and recover Bill's papers
+    del pdb
+    pdb = JsonS2PaperDB(s2paper_json_dir)
+    for p in papers:
+        p2 = pdb[p.paperId]
+        assert p2 == p
+
+    # we can do the same for S2Author objects
+    adb = JsonS2AuthorDB("adb")
+    adb[author.authorId] = author
+
+    # note that setting a value requires the key to be equal to the
+    # S2 identifier of the object, but this behaviour can be disabled
+    adb = JsonS2AuthorDB("adb", enforce_id=False)
+    adb["billy"] = author
+
+
+.. _saving_unknown:
+
+Saving Objects without S2 Identifiers
+--------------------------------------------------------------------------------
+Sometimes, a :class:`.S2Reference` object may not have a ``paperId`` value if
+you are using ``include_unknown_references=True``.
+In this case, you still may want to save it (e.g. to attempt recovering it
+via different methods at a later date). To do this, you can cast it to
+:class:`.S2Paper` and create a unique placeholder id
+
+.. code-block:: python
+
+    from s2.db.json import JsonS2PaperDB, JsonS2AuthorDB
+
+    # note that enforce_id=False is not necessary
+    pdb = JsonS2PaperDB("pdb")
+
+    # lets hunt ourselves an unknown reference from Bill's paper
+    paper = s2.api.get_paper(
+        "bdfa1a62c964f19b5ce000d7812ba9f66456a4a4",
+         params=dict(include_unknown_references=True),
+    )
+    for r in paper.references:
+        if not r.paperId:
+            break
+
+    # create a 40-char key from the hashed content and a signpost prefix
+    hash = hashlib.md5(r.json().encode("utf-8")).hexdigest()
+    placeholder_id = f"unknown_{hash}"
+    pdb[placeholder_id] = S2Paper(**r.dict())
+
diff --git a/doc/index.rst b/doc/index.rst
index d231c76..b26d2c7 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -4,7 +4,7 @@ S2py
 PyS2's documentation is organized into the following sections:
 
 - :ref:`getting_started`
-- :ref:`code_overview`
+- :ref:`api_reference`
 - :ref:`package_info`
 
 .. _getting_started:
@@ -16,14 +16,15 @@ PyS2's documentation is organized into the following sections:
     getting_started/installation
     getting_started/quick_start
 
-.. _code_overview:
+.. _api_reference:
 
 .. toctree::
     :maxdepth: 1
-    :caption: Code Overview
+    :caption: API Reference
 
-    code_overview/models
-    code_overview/api
+    api_reference/models
+    api_reference/api
+    api_reference/db
 
 .. _package_info:
 
diff --git a/s2/__init__.py b/s2/__init__.py
index 6d1c9df..039c552 100644
--- a/s2/__init__.py
+++ b/s2/__init__.py
@@ -1,4 +1,19 @@
-__version__ = "1.0.2"
+__version__ = "1.1.0"
 
-from s2 import api
-from s2 import models
+import logging
+from s2 import api, models
+
+
+def _setup_logger():
+    logger = logging.getLogger(__name__)
+    handler = logging.StreamHandler()
+    handler.setFormatter(
+        logging.Formatter(
+            "%(asctime)s\t%(levelname)s %(filename)s:%(lineno)s -- %(message)s"
+        ))
+    logger.addHandler(handler)
+    logger.setLevel(logging.INFO)
+    logger.propagate = False
+
+
+_setup_logger()
diff --git a/s2/api.py b/s2/api.py
index f3df050..219ebeb 100644
--- a/s2/api.py
+++ b/s2/api.py
@@ -1,11 +1,15 @@
 import requests
 import time
 from s2.models import S2Paper, S2Author
+import logging
 from typing import Optional, Union, Dict, Tuple
+import copy
 
 API_URL = "https://api.semanticscholar.org/v1"
 PARTNER_URL = "https://partner.semanticscholar.org/v1"
 
+logger = logging.getLogger('s2')
+
 
 def build_url(
         api_id: str,
@@ -19,15 +23,20 @@ def build_url(
 def build_session(
         session: Optional[requests.Session] = None,
         api_key: Optional[str] = None,
-) -> Tuple[requests.Session, str]:
-    """ Build session and reconcile passing of api key via arg or via session"""
+) -> requests.Session:
+    """ Build session and reconcile passing of api key via arg or via session
+
+    If an api key is included in the session headers, and passed through the
+    `api_key` arg, then the value in the session headers will be overwritten
+    temporarily for this request.
+    """
+    if api_key and session:
+        session = copy.deepcopy(session)
     if session is None:
         session = requests.Session()
     if api_key:
         session.headers['x-api-key'] = api_key
-    else:
-        api_key = session.headers.get('x-api-key', None)
-    return session, api_key
+    return session
 
 
 def get_paper(
@@ -59,11 +68,12 @@ def get_paper(
             * Corpus ID : ``CorpusID:37220927``
         api_key  (:obj:`str`, optional):
             A `Data Partners <https://pages.semanticscholar.org/data-partners>`_
-            API key.
+            API key. Overwrites API key passed through ``session``.
             Defaults to ``None``
         session (:obj:`requests.Session`, optional):
-            A :class:`requests.Session` object, can be used to store API key
-            (see :any:`using_an_api_key`).
+            A :class:`requests.Session` object, can be used to store an API key
+            (see :any:`using_an_api_key`). Note that ``api_key`` will overwrite
+            this value if it is provided.
             Defaults to ``None``
         return_json (:obj:`bool`, optional):
             Return original json from get request
@@ -86,10 +96,11 @@ def get_paper(
 
     Returns:
         :class:`dict` or :class:`~s2.models.S2Paper`:
-        A :class:`~s2.models.S2Paper` or `dict` object describing the paper
+        A :class:`~s2.models.S2Paper` or ``dict`` object describing the paper
     """
-    session, api_key = build_session(session, api_key)
-    url = build_url(paperId, endpoint='paper', partner=bool(api_key))
+    session = build_session(session, api_key)
+    partner = 'x-api-key' in session.headers
+    url = build_url(paperId, endpoint='paper', partner=partner)
     r = session.get(url, **kwargs)
 
     if r.ok:
@@ -99,14 +110,14 @@ def get_paper(
             return S2Paper(**r.json())
     # I found I was getting 403 Forbidden errors when exceeding rate limits
     elif r.status_code in [429, 403] and retries > 0:
-        print(f"Error {r.status_code} on paper {paperId}: "
-              f" sleeping for {wait} seconds"
-              f" with {retries} attempts remaining.")
+        logger.warning(f"Error {r.status_code} on paper {paperId}: "
+                       f" sleeping for {wait} seconds"
+                       f" with {retries} attempts remaining.")
         time.sleep(wait)
         return get_paper(paperId, api_key, session, return_json,
                          retries-1, wait, **kwargs)
     else:
-        print(f"Error {r.status_code} on paper {paperId}")
+        logger.error(f"Error {r.status_code} on paper {paperId}")
         r.raise_for_status()
 
 
@@ -128,11 +139,12 @@ def get_author(
             Semantic Scholar author identifier.
         api_key  (:obj:`str`, optional):
             A `Data Partners <https://pages.semanticscholar.org/data-partners>`_
-            API key.
+            API key. Temporarily overwrites API key passed through ``session``.
             Defaults to ``None``
         session (:obj:`requests.Session`, optional):
-            A :class:`requests.Session` object, can be used to store API key
-            (see :any:`using_an_api_key`).
+            A :class:`requests.Session` object, can be used to store an API key
+            (see :any:`using_an_api_key`). Note that ``api_key`` will overwrite
+            this value temporarily if it is provided.
             Defaults to ``None``
         return_json (:obj:`bool`, optional):
             Return original json from get request
@@ -153,10 +165,11 @@ def get_author(
 
     Returns:
         :class:`dict` or :class:`~s2.models.S2Author`:
-        A :class:`~s2.models.S2Author` or `dict` object describing the author
+        A :class:`~s2.models.S2Author` or ``dict`` object describing the author
     """
-    session, api_key = build_session(session, api_key)
-    url = build_url(authorId, endpoint='author', partner=bool(api_key))
+    session = build_session(session, api_key)
+    partner = 'x-api-key' in session.headers
+    url = build_url(authorId, endpoint='author', partner=partner)
     r = session.get(url, **kwargs)
 
     if r.ok:
@@ -166,12 +179,12 @@ def get_author(
             return S2Author(**r.json())
     # I found I was getting 403 Forbidden errors when exceeding rate limits
     elif r.status_code in [429, 403] and retries > 0:
-        print(f"Error {r.status_code} on author {authorId}: "
-              f" sleeping for {wait} seconds"
-              f" with {retries} attempts remaining.")
+        logger.warning(f"Error {r.status_code} on author {authorId}: "
+                       f" sleeping for {wait} seconds"
+                       f" with {retries} attempts remaining.")
         time.sleep(wait)
         return get_author(authorId, api_key, session, return_json,
                           retries-1, wait, **kwargs)
     else:
-        print(f"Error {r.status_code} on author {authorId}")
+        logger.error(f"Error {r.status_code} on author {authorId}")
         r.raise_for_status()
diff --git a/s2/db/__init__.py b/s2/db/__init__.py
new file mode 100644
index 0000000..c8812d4
--- /dev/null
+++ b/s2/db/__init__.py
@@ -0,0 +1,1 @@
+from .json import JsonS2PaperDB, JsonS2AuthorDB
\ No newline at end of file
diff --git a/s2/db/json.py b/s2/db/json.py
new file mode 100644
index 0000000..07e3565
--- /dev/null
+++ b/s2/db/json.py
@@ -0,0 +1,202 @@
+from s2.models import S2Paper, S2Author
+from _collections_abc import MutableMapping
+from pathlib import Path
+import json
+
+import logging
+logger = logging.getLogger("s2")
+
+from typing import Iterator, Union
+
+PaperId = str
+AuthorId = str
+
+
+# TODO: look into yapic.json/ujson/orjson for fast encoding/decoding
+# TODO: get rid of duplicate code for S2Paper/S2Author, either through:
+#       (1) class inheritance (not sure how to properly handle typing
+#           without reduplicating every method anyways)
+#       (2) a single interface with e.g. paper/author kwarg passed e.g.
+#           at class instantiation (once again not sure how to handle
+#           typing, and it doesn't feel very user-friendy)
+#       whatever gets implemented should be consistent with the s2.api interface
+
+
+class JsonS2PaperDB(MutableMapping):
+    """Dict-like interface to store S2Papers as jsons and retrieve as S2Papers
+
+    Note:
+        Types are enforced, so keys must be valid PaperIds and values must
+        be instances of :class:`.S2Paper`.
+
+    Args:
+        json_dir (str or :class:`~pathlib.Path`):
+            Directory where papers are saved as jsons. If directory does not
+            exist, it will be created and populated with jsons as values are
+            set in the object. For example:
+
+            .. code-block:: python
+
+                pdb = JsonS2PaperDB("db")
+                paper = s2.api.get_paper(k)
+                pdb[k] = paper
+
+            will first create a directory ``db``, then a file ``db/{k}.json``
+            containing the :class:`S2Paper` that was passed,
+            in a json-serialized format.
+
+            Similarly, removing items from the object (e.g. ``pdb.pop(k)``)
+            will delete the corresponding json file.
+
+        enforce_id (`bool`, optional):
+            Enforce that a key be equal to the ``paperId`` field of the
+            :class:`.S2Paper` object (if it exists; for handling unknown
+            references without a ``paperId`` value, see :any:`saving_unknown`).
+
+    Attributes:
+        paperIds (`set` of `str`):
+            In-memory lookup of existing keys, updated whenever a key is
+            added or removed. Will likely be updated to something less scrappy.
+    """
+    def __init__(self, json_dir: Union[str, Path], enforce_id: bool = True):
+        self.json_dir = Path(json_dir)
+        self.json_dir.mkdir(exist_ok=True, parents=True)
+        self.enforce_id = enforce_id
+        self.paperIds = set([f.stem for f in self.json_dir.glob("*.json")])
+
+    def _check_key_type(self, k: PaperId):
+        if type(k) is not str:
+            raise TypeError(f"{type(k)} instead of str")
+
+    def _check_val_type(self, v: S2Paper):
+        if type(v) is not S2Paper:
+            raise TypeError(f"{type(v)} instead of S2Paper")
+
+    def _check_file_exists(self, f: Path):
+        if not f.exists():
+            raise KeyError(f.stem)
+
+    def _check_key_value(self, k: PaperId, v: S2Paper):
+        if v.paperId and v.paperId != k:
+            raise KeyError(f"Provided key {k} for S2Paper with id {v.paperId}")
+
+    def __contains__(self, k: PaperId) -> bool:
+        return k in self.paperIds
+
+    def __delitem__(self, k: PaperId) -> None:
+        self._check_key_type(k)
+        f = (self.json_dir / f"{k}.json")
+        self._check_file_exists(f)
+        self.paperIds.remove(k)
+        f.unlink()
+
+    def __getitem__(self, k: PaperId) -> S2Paper:
+        self._check_key_type(k)
+        f = (self.json_dir / f"{k}.json")
+        self._check_file_exists(f)
+        return S2Paper(**json.loads(f.read_text()))
+
+    def __len__(self) -> int:
+        return len(self.paperIds)
+
+    def __iter__(self) -> Iterator[PaperId]:
+        return self.paperIds.__iter__()
+
+    def __setitem__(self, k: PaperId, v: S2Paper) -> None:
+        self._check_key_type(k)
+        self._check_val_type(v)
+        if self.enforce_id:
+            self._check_key_value(k, v)
+        f = (self.json_dir / f"{k}.json")
+        f.write_text(v.json())
+        self.paperIds.add(k)
+
+
+class JsonS2AuthorDB(MutableMapping):
+    """Dict-like interface to store S2Authors as jsons and retrieve as S2Authors
+
+    Note:
+        Types are enforced, so keys must be valid AuthorIds and values must
+        be instances of :class:`.S2Author`.
+
+    Args:
+        json_dir (str or :class:`~pathlib.Path`):
+            Directory where authors are saved as jsons. If directory does not
+            exist, it will be created and populated with jsons as values are
+            set in the object. For example:
+
+            .. code-block:: python
+
+                adb = JsonS2AuthorDB("db")
+                author = s2.api.get_author(k)
+                adb[k] = author
+
+            will first create a directory ``db``, then a file ``db/{k}.json``
+            containing the class:`.S2Author` that was passed,
+            in a json-serialized format.
+
+            Similarly, removing items from the object (e.g. ``pdb.pop(k)``)
+            will delete the corresponding json file.
+
+        enforce_id (`bool`, optional):
+            Enforce that a key be equal to the ``authorId`` field of the
+            :class:`.S2Author` object (if it exists; for handling unknown
+            authors without an ``authorId`` value, see :any:`saving_unknown`).
+
+    Attributes:
+        authorIds (`set` of `str`):
+            In-memory lookup of existing keys, updated whenever a key is
+            added or removed. Will likely be updated to something less scrappy.
+    """
+    def __init__(self, json_dir: Union[str, Path], enforce_id: bool = True):
+        self.json_dir = Path(json_dir)
+        self.json_dir.mkdir(exist_ok=True, parents=True)
+        self.enforce_id = enforce_id
+        self.authorIds = set([f.stem for f in self.json_dir.glob("*.json")])
+
+    def _check_key_type(self, k: AuthorId):
+        if type(k) is not str:
+            raise TypeError(f"{type(k)} instead of str")
+
+    def _check_val_type(self, v: S2Author):
+        if type(v) is not S2Author:
+            raise TypeError(f"{type(v)} instead of S2Author")
+
+    def _check_file_exists(self, f: Path):
+        if not f.exists():
+            raise KeyError(f.stem)
+
+    def _check_key_value(self, k: AuthorId, v: S2Author):
+        if v.authorId and v.authorId != k:
+            raise KeyError(f"Provided key {k} for S2Author with id {v.authorId}")
+
+    def __contains__(self, k: AuthorId) -> bool:
+        return k in self.authorIds
+
+    def __delitem__(self, k: AuthorId) -> None:
+        self._check_key_type(k)
+        f = (self.json_dir / f"{k}.json")
+        self._check_file_exists(f)
+        self.authorIds.remove(k)
+        f.unlink()
+
+    def __getitem__(self, k: AuthorId) -> S2Author:
+        self._check_key_type(k)
+        f = (self.json_dir / f"{k}.json")
+        self._check_file_exists(f)
+        return S2Author(**json.loads(f.read_text()))
+
+    def __len__(self) -> int:
+        return len(self.authorIds)
+
+    def __iter__(self) -> Iterator[PaperId]:
+        return self.authorIds.__iter__()
+
+    def __setitem__(self, k: PaperId, v: S2Author) -> None:
+        self._check_key_type(k)
+        self._check_val_type(v)
+        if self.enforce_id:
+            self._check_key_value(k, v)
+        f = (self.json_dir / f"{k}.json")
+        f.write_text(v.json())
+        self.authorIds.add(k)
\ No newline at end of file
diff --git a/s2/models.py b/s2/models.py
index 9c148d8..6886c9d 100644
--- a/s2/models.py
+++ b/s2/models.py
@@ -1,6 +1,9 @@
 from pydantic import BaseModel
 from typing import List, Optional
 
+# TODO: add data validators for consistent handling of empty types
+#       see https://github.com/samuelcolvin/pydantic/discussions/2611#discussion-3300585
+
 
 class S2Topic(BaseModel):
     """
@@ -135,8 +138,8 @@ class S2Paper(BaseModel):
     doi: Optional[str]
     fieldsOfStudy: Optional[List[str]]
     influentialCitationCount: Optional[int]
-    is_open_access: bool
-    is_publisher_licensed: bool
+    is_open_access: Optional[bool]
+    is_publisher_licensed: Optional[bool]
     paperId: Optional[str]
     references: Optional[List[S2Reference]]
     title: Optional[str]


Test patch:
diff --git a/tests/context.py b/tests/context.py
index 50f04ac..243ba0e 100644
--- a/tests/context.py
+++ b/tests/context.py
@@ -3,4 +3,5 @@ import sys
 sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))
 
 import s2
-from s2 import api, models
\ No newline at end of file
+from s2 import api, models
+from s2.db.json import JsonS2PaperDB, JsonS2AuthorDB
\ No newline at end of file
diff --git a/tests/db/__init__.py b/tests/db/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/tests/db/test_json.py b/tests/db/test_json.py
new file mode 100644
index 0000000..d2aaf5e
--- /dev/null
+++ b/tests/db/test_json.py
@@ -0,0 +1,107 @@
+from pathlib import Path
+from unittest import TestCase
+import pytest
+from ..context import JsonS2PaperDB, JsonS2AuthorDB
+
+
+def rm_tree(pth: Path):
+    """ Utility for removing directory recursively"""
+    pth = Path(pth)
+    if pth.exists():
+        for child in pth.glob('*'):
+            if child.is_file():
+                child.unlink()
+            else:
+                rm_tree(child)
+        pth.rmdir()
+
+
+class TestJson(TestCase):
+    def setUp(self):
+        fixtures = Path("tests/fixtures/db/json")
+        self.pdb_path = fixtures / "s2papers"
+        self.pdb_path_tmp = fixtures / "s2papers_tmp"
+        self.adb_path = fixtures / "s2authors"
+        self.adb_path_tmp = fixtures / "s2authors_tmp"
+        assert self.pdb_path.exists()
+        assert self.adb_path.exists()
+        assert not self.pdb_path_tmp.exists()
+        assert not self.adb_path_tmp.exists()
+        self.addCleanup(lambda: rm_tree(self.pdb_path_tmp))
+        self.addCleanup(lambda: rm_tree(self.adb_path_tmp))
+
+    def test_pdb(self):
+        # create new pdb (paper database)
+        pdb_tmp = JsonS2PaperDB(self.pdb_path_tmp)
+        assert pdb_tmp.json_dir.exists()
+
+        # load existing db and check values; testing contains and len methods
+        pdb = JsonS2PaperDB(self.pdb_path)
+        assert "a04fc380c61040c7ffa21375bf2a0c9d30b674a4" in pdb
+        assert "bdfa1a62c964f19b5ce000d7812ba9f66456a4a4" in pdb
+        assert "c656a68a2bf155fa1a8ef4dd38a0af2cac3911da" in pdb
+        assert len(pdb) == 3
+
+        # copy values into temp pdb; testing iter, set, and get methods
+        for k,v in pdb.items():
+            pdb_tmp[k] = v
+        for k in pdb_tmp.keys():
+            assert pdb[k] == pdb_tmp[k]
+
+        # delete key and check for keyerrors
+        p = pdb_tmp.pop(k)
+        with pytest.raises(KeyError):
+            _ = pdb_tmp[k]
+
+        # enforce_id behavior
+        with pytest.raises(KeyError):
+            wrong_key = k[:-1]
+            pdb_tmp[wrong_key] = p
+
+        # check for type errors
+        p = pdb[k]
+        for invalid_value in [k, 0, None, p.dict(), p.json()]:
+            with pytest.raises(TypeError):
+                pdb_tmp[k] = invalid_value
+        for invalid_key in [0, None]:
+            with pytest.raises(TypeError):
+                _ = pdb_tmp[invalid_key]
+
+    def test_adb(self):
+        # create new adb (author database)
+        assert not self.adb_path_tmp.exists()
+        adb_tmp = JsonS2AuthorDB(self.adb_path_tmp)
+        assert adb_tmp.json_dir.exists()
+
+        # load existing db and check values; testing contains and len methods
+        assert self.adb_path.exists()
+        adb = JsonS2AuthorDB(self.adb_path)
+        assert "80806115" in adb
+        assert "144794037" in adb
+        assert "2051526200" in adb
+        assert len(adb) == 3
+
+        # copy values into temp pdb; testing iter, set, and get methods
+        for k,v in adb.items():
+            adb_tmp[k] = v
+        for k in adb_tmp.keys():
+            assert adb[k] == adb_tmp[k]
+
+        # delete key and check for keyerrors
+        a = adb_tmp.pop(k)
+        with pytest.raises(KeyError):
+            _ = adb_tmp[k]
+
+        # enforce_id behavior
+        with pytest.raises(KeyError):
+            wrong_key = k[:-1]
+            adb_tmp[wrong_key] = a
+
+        # check for type errors
+        a = adb[k]
+        for invalid_value in [k, 0, None, a.dict(), a.json()]:
+            with pytest.raises(TypeError):
+                adb_tmp[k] = invalid_value
+        for invalid_key in [0, None]:
+            with pytest.raises(TypeError):
+                _ = adb_tmp[invalid_key]
\ No newline at end of file
diff --git a/tests/fixtures/db/json/s2authors/144794037.json b/tests/fixtures/db/json/s2authors/144794037.json
new file mode 100644
index 0000000..dfb66bf
--- /dev/null
+++ b/tests/fixtures/db/json/s2authors/144794037.json
@@ -0,0 +1,1 @@
+{"aliases": ["B Gates", "Billy J. Gates", "Bill Gates"], "authorId": "144794037", "influentialCitationCount": 49, "name": "B. Gates", "papers": [{"paperId": "a04fc380c61040c7ffa21375bf2a0c9d30b674a4", "title": "What Will Be: How the New World of Information Will Change Our Lives", "url": "https://www.semanticscholar.org/paper/a04fc380c61040c7ffa21375bf2a0c9d30b674a4", "year": 1997}, {"paperId": "bdfa1a62c964f19b5ce000d7812ba9f66456a4a4", "title": "Responding to Covid-19 - A Once-in-a-Century Pandemic?", "url": "https://www.semanticscholar.org/paper/bdfa1a62c964f19b5ce000d7812ba9f66456a4a4", "year": 2020}, {"paperId": "c656a68a2bf155fa1a8ef4dd38a0af2cac3911da", "title": "A robot in every home.", "url": "https://www.semanticscholar.org/paper/c656a68a2bf155fa1a8ef4dd38a0af2cac3911da", "year": 2007}, {"paperId": "4c27d9bfc56d3fa57d4d865348a6ae8b2b0e0373", "title": "The next epidemic--lessons from Ebola.", "url": "https://www.semanticscholar.org/paper/4c27d9bfc56d3fa57d4d865348a6ae8b2b0e0373", "year": 2015}, {"paperId": "9089886ca890e5597656b7d0e9d1a6d695a88a9f", "title": "Business @ the Speed of Thought", "url": "https://www.semanticscholar.org/paper/9089886ca890e5597656b7d0e9d1a6d695a88a9f", "year": 1999}, {"paperId": "a4de012becd2340515ed2c374e29b80b6d44018f", "title": "Business @ the Speed of Thought: Succeeding in the Digital Economy", "url": "https://www.semanticscholar.org/paper/a4de012becd2340515ed2c374e29b80b6d44018f", "year": 2000}, {"paperId": "25824366ed235d4ca679f0fddffa5992a6476490", "title": "2012 Annual Letter From Bill Gates", "url": "https://www.semanticscholar.org/paper/25824366ed235d4ca679f0fddffa5992a6476490", "year": 2012}, {"paperId": "6257f6fbfa97ca5106857a40e2d260e93d59f43b", "title": "Business at the Speed of Thought: Using a Digital Nervous System", "url": "https://www.semanticscholar.org/paper/6257f6fbfa97ca5106857a40e2d260e93d59f43b", "year": 1998}, {"paperId": "a71eeac39ce91689ceb08537c7b1f2639d03e5ce", "title": "Linked Up for Learning.", "url": "https://www.semanticscholar.org/paper/a71eeac39ce91689ceb08537c7b1f2639d03e5ce", "year": 1996}, {"paperId": "77d0cff6b41b548af608127689584efd53e95765", "title": "Meeting Students Where They Are", "url": "https://www.semanticscholar.org/paper/77d0cff6b41b548af608127689584efd53e95765", "year": 2016}, {"paperId": "1dee97358fdf1f075aa768bfa75d65d730e3fcd7", "title": "A robot in every home.", "url": "https://www.semanticscholar.org/paper/1dee97358fdf1f075aa768bfa75d65d730e3fcd7", "year": 2007}, {"paperId": "9c8ef724e143a76e339d571f4c0ccc30ba2619ec", "title": "Innovation for Pandemics.", "url": "https://www.semanticscholar.org/paper/9c8ef724e143a76e339d571f4c0ccc30ba2619ec", "year": 2018}, {"paperId": "1d6ac5513fab83696e7d42a7d8576b360c814d63", "title": "Strengthening American Competitiveness for the 21st Century", "url": "https://www.semanticscholar.org/paper/1d6ac5513fab83696e7d42a7d8576b360c814d63", "year": 2008}, {"paperId": "073102fa8e6b9b75f88caa4be822d157dd9bbddc", "title": "Gates, W., (2000). Business @ the Speed of Thought.", "url": "https://www.semanticscholar.org/paper/073102fa8e6b9b75f88caa4be822d157dd9bbddc", "year": 2003}, {"paperId": "6eddd20ce0bbf54a8338be17eb722386352dda44", "title": "An interview with Bill and Melinda Gates", "url": "https://www.semanticscholar.org/paper/6eddd20ce0bbf54a8338be17eb722386352dda44", "year": 2013}, {"paperId": "17ba04a3c3763728b6ed1ceaaffeee0aa0a68d6a", "title": "Bill Gates Speaks: Wisdom from the World's Greatest Entrepreneur", "url": "https://www.semanticscholar.org/paper/17ba04a3c3763728b6ed1ceaaffeee0aa0a68d6a", "year": 1998}, {"paperId": "6dbbd916ff48d13f9bd05a50bef95f8ec827dafa", "title": "Life As We Know It", "url": "https://www.semanticscholar.org/paper/6dbbd916ff48d13f9bd05a50bef95f8ec827dafa", "year": 2016}, {"paperId": "2dd5ffc09e8b13ae2d0f58ba53f153092ff4feb5", "title": "Computers in Schools, Today and Tomorrow", "url": "https://www.semanticscholar.org/paper/2dd5ffc09e8b13ae2d0f58ba53f153092ff4feb5", "year": 1988}, {"paperId": "43cf41d2e4ee267999a2cc09c1ac7467fc9d5435", "title": "A Basic Guide for Curious Minds", "url": "https://www.semanticscholar.org/paper/43cf41d2e4ee267999a2cc09c1ac7467fc9d5435", "year": 2015}, {"paperId": "8ff49bca6a9332862de1ec7d42d9b16df4393fe4", "title": "Saving the world is within our grasp.", "url": "https://www.semanticscholar.org/paper/8ff49bca6a9332862de1ec7d42d9b16df4393fe4", "year": 2007}, {"paperId": "ea4632d118239969ea04da098ffb2ce87330fa27", "title": "Business @ The Speed of Though: Menggunakan Sistem Saraf Digital", "url": "https://www.semanticscholar.org/paper/ea4632d118239969ea04da098ffb2ce87330fa27", "year": 2009}, {"paperId": "e5af1912ef329b0438b1b522d53153d051ead3f7", "title": "Beyond macro processing", "url": "https://www.semanticscholar.org/paper/e5af1912ef329b0438b1b522d53153d051ead3f7", "year": 1987}, {"paperId": "c8a126e1c71fa9507b89d1944673842f65f2e5bd", "title": "The Energy Research Imperative", "url": "https://www.semanticscholar.org/paper/c8a126e1c71fa9507b89d1944673842f65f2e5bd", "year": 2011}, {"paperId": "d77eec76046b8ab506f1cb2b8545787ea66c4b19", "title": "America\u2019s Secret Weapon", "url": "https://www.semanticscholar.org/paper/d77eec76046b8ab506f1cb2b8545787ea66c4b19", "year": 2016}, {"paperId": "899af3cddffef4aeddeaae0fa7dbb31d7f6cd46e", "title": "More Momentum for Clean Energy", "url": "https://www.semanticscholar.org/paper/899af3cddffef4aeddeaae0fa7dbb31d7f6cd46e", "year": 2016}, {"paperId": "591b76a0cce68d7e2c8111be051c399463a4a92b", "title": "The Road Ahead: Completely Revised and Up-to-Date", "url": "https://www.semanticscholar.org/paper/591b76a0cce68d7e2c8111be051c399463a4a92b", "year": 1995}, {"paperId": "3282eb0aae92b5f9e83d3ef3b4d978f82a72f287", "title": "Microsoft and object-oriented programming: or, \u201cRealizing objects in commercial platforms\u201d", "url": "https://www.semanticscholar.org/paper/3282eb0aae92b5f9e83d3ef3b4d978f82a72f287", "year": 1992}, {"paperId": "7c35df5019f6c41ea8ceef2f14cf93fc24e14a22", "title": "Bill Gates on Education and the Web. Enter \"Generation I.\".", "url": "https://www.semanticscholar.org/paper/7c35df5019f6c41ea8ceef2f14cf93fc24e14a22", "year": 2000}, {"paperId": "9c8155404f2bca56a403813530a09a5c64ae32e2", "title": "Why I Would Raise Chickens", "url": "https://www.semanticscholar.org/paper/9c8155404f2bca56a403813530a09a5c64ae32e2", "year": 2016}, {"paperId": "553fc7a3d222b2adb045e454c629f80e986631f9", "title": "Update: What Ever Happened to the Machine That Turns Feces Into Water?", "url": "https://www.semanticscholar.org/paper/553fc7a3d222b2adb045e454c629f80e986631f9", "year": 2015}, {"paperId": "5f933abc6b6153e5095c651464ff96d5c34853ac", "title": "Wealth and Our Commonwealth: Why America Should Tax Accumulated Fortunes", "url": "https://www.semanticscholar.org/paper/5f933abc6b6153e5095c651464ff96d5c34853ac", "year": 2003}, {"paperId": "47dabe29b7b0fa2509bd2f48889ea97fc6839700", "title": "The way we give.", "url": "https://www.semanticscholar.org/paper/47dabe29b7b0fa2509bd2f48889ea97fc6839700", "year": 2007}, {"paperId": "f6588e54d4c57520b2a7d97c9b8dc939aedde744", "title": "Bloot will tell us everything", "url": "https://www.semanticscholar.org/paper/f6588e54d4c57520b2a7d97c9b8dc939aedde744", "year": 2018}, {"paperId": "db5414958d4ff4d9e567572dda376b345857b0c8", "title": "Un mundo feliz = A happy world", "url": "https://www.semanticscholar.org/paper/db5414958d4ff4d9e567572dda376b345857b0c8", "year": 2006}, {"paperId": "1e9fa6d53b2d2e835e834bf7ab9b483caa3b065a", "title": "Microsoft CD-ROM yearbook", "url": "https://www.semanticscholar.org/paper/1e9fa6d53b2d2e835e834bf7ab9b483caa3b065a", "year": 1989}, {"paperId": "01fdbdd5149465b5ea81b8f9d2897406e5d4f237", "title": "Address at Harvard: Commencement, July 7, 2007", "url": "https://www.semanticscholar.org/paper/01fdbdd5149465b5ea81b8f9d2897406e5d4f237", "year": 2007}, {"paperId": "1e3dd63e15813abc9d26f48e9ff2bf1805b111b1", "title": "Investing in Research, SIGMOD Conference 1998 Keynote Speech, Video", "url": "https://www.semanticscholar.org/paper/1e3dd63e15813abc9d26f48e9ff2bf1805b111b1", "year": 1999}, {"paperId": "c3b89d50083d005e71148d41005844c184d58a00", "title": "The Road Ahead", "url": "https://www.semanticscholar.org/paper/c3b89d50083d005e71148d41005844c184d58a00", "year": 1960}, {"paperId": "a1c8d303ff24add72ac263d9c9f8668b1855c8f7", "title": "Will Frankenfood feed the world?", "url": "https://www.semanticscholar.org/paper/a1c8d303ff24add72ac263d9c9f8668b1855c8f7", "year": 2000}, {"paperId": "f99ba26c3871b0517fad14697c8b55217d8830df", "title": "The 25th birthday of BASIC", "url": "https://www.semanticscholar.org/paper/f99ba26c3871b0517fad14697c8b55217d8830df", "year": 1989}, {"paperId": "4e4d9b12545d04cba82a90ca54ee083e42093e6b", "title": "Immunizing the world.", "url": "https://www.semanticscholar.org/paper/4e4d9b12545d04cba82a90ca54ee083e42093e6b", "year": 2000}, {"paperId": "36fa99b75737bacdfb4435013388b1b3ad4c972c", "title": "Newsmaker interview. Bill and Melinda Gates talk science. 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\ No newline at end of file
diff --git a/tests/test_api.py b/tests/test_api.py
index 46558bc..5af9df0 100644
--- a/tests/test_api.py
+++ b/tests/test_api.py
@@ -80,28 +80,24 @@ class TestApi(TestCase):
 
     def test_build_session(self):
         # default no session and no api key
-        session, api_key = api.build_session(None, None)
+        session = api.build_session(None, None)
         assert 'x-api-key' not in session.headers
-        assert api_key is None
         # custom session and no api key
-        session, api_key = api.build_session(Session(), None)
+        session = api.build_session(Session(), None)
         assert 'x-api-key' not in session.headers
-        assert api_key is None
         # custom session and arg api key
         arg_api_key = '123'
-        session, api_key = api.build_session(Session(), arg_api_key)
+        session = api.build_session(Session(), arg_api_key)
         assert session.headers['x-api-key'] == arg_api_key
-        assert api_key == arg_api_key
         # custom session and session api key
         session = Session()
         session_api_key = '456'
         session.headers['x-api-key'] = session_api_key
-        session, api_key = api.build_session(session, None)
+        session = api.build_session(session, None)
         assert session.headers['x-api-key'] == session_api_key
-        assert api_key == session_api_key
         # custom session and session+arg api key (allow overriding)
-        session = Session()
-        session.headers['x-api-key'] = session_api_key
-        session, api_key = api.build_session(session, arg_api_key)
+        custom_session = Session()
+        custom_session.headers['x-api-key'] = session_api_key
+        session = api.build_session(session, arg_api_key)
         assert session.headers['x-api-key'] == arg_api_key
-        assert api_key == arg_api_key
+        assert custom_session.headers['x-api-key'] == session_api_key