Merge pull request #7 from NYU-CI/paco_update

prep release 1.0.0 on PyPi

.gitignore

@@ -1,13 +1,23 @@
+# RichContext configuration -- do not commit these
 rc.cfg
 chromedriver
 chromedriver.exe
 
-.ipynb_checkpoints
+# Python compiled modules
+*.pyc
+__pycache__
+
+# Setuptools distribution folder
+/dist/
+/build/
+
+# Python egg metadata, regenerated from source files by setuptools
+/*.egg-info
+/*.egg
+
+# Jupyter notebooks
+.ipynb_checkpoints/
+
+# editor junk
 .DS_Store
 **~
-
-dist
-build
-__pycache__
-*.pyc
-*.egg-info

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2019 The Coleridge Initiative @NYU
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

MANIFEST.in

@@ -0,0 +1,5 @@
+include LICENSE
+include README.md
+include changelog.txt
+include example.py
+include rc_template.cfg

README.md

@@ -1,21 +1,46 @@
-# RCApi
+# richcontext.scholapi
 
-API integrations for federating metadata lookup across multiple
-scholarly infrastructure providers.
+[Rich Context](https://coleridgeinitiative.org/richcontext)
+API integrations for federating metadata discovery and exchange across
+multiple scholarly infrastructure providers.
 
-For the development of the Rich Context knowledge graph this library
-is used to identify:
+Development of the Rich Context knowledge graph uses this library to:
 
-  * dataset links to research
-  * locating open access publications
-  * reconciling author profiles
-  * reconciling keyword mesh
+  * identify dataset links to research publications
+  * locate open access publications
+  * reconcile author profiles
+  * reconcile keyword mesh
+
+This library has been guided by collaborative work on community
+building and metadata exchange to improve Scholarly Infrastructure,
+held at the *2019 Rich Context Workshop*.
 
 
 ## Installation
 
-Copy the configuration file template `rc_template.cfg` to `rc.cfg`
-then populate it with your credentials.
+Prerequisites:
+
+- [Python 3.x](https://www.python.org/downloads/)
+- [Beautiful Soup](https://www.crummy.com/software/BeautifulSoup/bs4/doc/)
+- [Dimensions CLI](https://github.com/digital-science/dimcli)
+- [Requests](https://2.python-requests.org/en/master/)
+- [Selenium](https://github.com/SeleniumHQ/selenium/)
+
+To install from [PyPi](https://pypi.python.org/pypi/richcontext.scholapi):
+
+```
+pip install richcontext.scholapi
+```
+
+If you install directly from this Git repo, be sure to install the 
+dependencies as well:
+
+```
+pip install -r requirements.txt
+```
+
+Then copy the configuration file template `rc_template.cfg` to `rc.cfg`
+and populate it with your credentials.
 
 NB: be careful not to commit the `rc.cfg` file in Git since it
 contains sensitive data such as passwords.
@@ -33,6 +58,27 @@ Download the [Chrome webdriver](https://chromedriver.chromium.org/downloads)
 to enable use of Selenium.
 
 
+## Usage
+
+```
+from richcontext import scholapi as rc_scholapi
+import pprint
+
+# initialize the federated API access
+schol = rc_scholapi.ScholInfraAPI(config_file="rc.cfg", logger=None)
+
+# search parameters for example publications
+title = "Deal or no deal? The prevalence and nutritional quality of price promotions among U.S. food and beverage purchases."
+
+# run it...
+meta = schol.openaire.title_search(title)
+
+# report results
+pprint.pprint(meta)
+print("\ntime: {:.3f} ms - {}".format(schol.openaire.elapsed_time, schol.openaire.name))
+```
+
+
 ## API Integrations
 
 APIs used to retrieve metadata:
@@ -62,28 +108,29 @@ The State of OA: A large-scale analysis of the prevalence and impact of Open Acc
 To run unit tests for the APIs which do not require credentials:
 
 ```
-python test.py
+python test/test.py
 ```
 
 To run unit tests for all of the APIs:
 
 ```
-python full_test.py
+python test/full_test.py
 ```
 
 
 ## To Do
 
-
- * Dimensions datasets
+ * Dimensions API for dataset metadata
+ * scrape metadata from web pages PMC/Pubmed, NIH, etc.
  * SSRN
- * Springer (https://github.com/srand525/search_springer/blob/master/SpringerFetch.py)
  * https://paperswithcode.com/?ref=semscholar
-=======
-#### To Do
-##### Add Apis:
-* PMC/Pubmed
-* RePEc
-* Springer (https://github.com/srand525/search_springer/blob/master/SpringerFetch.py)
-* https://paperswithcode.com/?ref=semscholar
+ * Springer <https://github.com/srand525/search_springer/blob/master/SpringerFetch.py>
+
+
+## Kudos
 
+Contributors:
+[@ceteri](https://github.com/ceteri), 
+[@srand525](https://github.com/srand525), 
+plus many thanks for the inspiring *2019 Rich Context Workshop* notes by 
+[@metasj](https://github.com/metasj).

changelog.txt

@@ -0,0 +1,11 @@
+# `richcontext.scholapi` changelog
+
+## 1.0.0
+
+2019-11-23
+
+### Initial
+
+  * first release on PyPi
+  * supports `title_search()` and `publication_lookup()` using several discovery APIs for Scholarly Infrastructure
+  * aligned with Community session goals from 2019 Rich Context Workshop (notes by Sameul Klein)

setup.py

@@ -0,0 +1,40 @@
+from setuptools import setup, find_namespace_packages
+
+with open("README.md", "r") as fh:
+    long_description = fh.read()
+
+setup(
+    name="richcontext-scholapi",
+    version="1.0.0",
+    author="Coleridge Initiative",
+    author_email="[email protected]",
+    description="Rich Context API integrations for federating metadata discovery and exchange across multiple scholarly infrastructure providers",
+    long_description=long_description,
+    long_description_content_type="text/markdown",
+    url="https://github.com/NYU-CI/RCApi",
+    packages=find_namespace_packages(include=['richcontext.*']),
+    classifiers=[
+        "Programming Language :: Python :: 3",
+        "License :: OSI Approved :: MIT License",
+        "Operating System :: OS Independent",
+        "Development Status :: 4 - Beta",
+        "Intended Audience :: Developers",
+        "Intended Audience :: Education",
+        "Intended Audience :: Information Technology",
+        "Intended Audience :: Science/Research",
+        "Topic :: Scientific/Engineering :: Artificial Intelligence",
+        "Topic :: Scientific/Engineering :: Human Machine Interfaces",
+        "Topic :: Scientific/Engineering :: Information Analysis",
+    ],
+    python_requires=">=3.5",
+    install_requires=[
+        "beautifulsoup4",
+        "dimcli",
+        "requests",
+        "selenium",
+    ],
+    keywords="DOI, RePEc, Rich Context, discovery, federated API, federated metadata, knowledge graph, metadata API, metadata exchange, metadata, persistent identifiers, research publication ontology, research publications, scholarly infrastructure, scholarly metadata, scholarly publishing",
+    license="MIT",
+    include_package_data=True,
+    zip_safe=False
+)