Academic Tracker
================
.. image:: https://img.shields.io/pypi/v/academic_tracker.svg
:target: https://pypi.org/project/academic_tracker
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.. image:: https://img.shields.io/pypi/pyversions/academic_tracker.svg
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.. image:: https://github.com/MoseleyBioinformaticsLab/academic_tracker/actions/workflows/build.yml/badge.svg
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.. image:: https://img.shields.io/badge/DOI-10.1371%2Fjournal.pone.0277834-blue.svg
:target: https://doi.org/10.1371/journal.pone.0277834
:alt: Citation link
.. image:: https://img.shields.io/github/stars/MoseleyBioinformaticsLab/academic_tracker.svg?style=social&label=Star
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|
Academic Tracker was created to automate the process of making sure that federally
funded publications get listed on PubMed and that the grant funding source for
them is cited.
Academic Tracker is a command line tool to search PubMed, ORCID, Google Scholar,
and Crossref for publications. The program can either be given a list of authors
to look for publications for, or references/citations to publications themselves.
The program will then will look for publications on the aforementioned sources
and return what relevant information is available from those sources.
The primary use case is to give the program a list of authors to find publications
for. From this list of publications it can then be determined which ones need
further action to be in compliance.
A secondary use case for finding author's publications is to create a report of
the collaborators they have worked with, and can be done by specifying the creation
of that report in the configuration file. Details on reports are in the `documentation <https://moseleybioinformaticslab.github.io/academic_tracker/reporting.html>`__.
The other primary use case is to give the program a list of publication references
to find information for.
Links
~~~~~
* Academic Tracker @ GitHub_
* Academic Tracker @ PyPI_
* Documentation @ Pages_
Installation
~~~~~~~~~~~~
The Academic Tracker package runs under Python 3.8+. Use pip_ to install.
Starting with Python 3.4, pip_ is included by default. Be sure to use the latest
version of pip as older versions are known to have issues grabbing all dependencies.
Academic Tracker relies on sendmail to send emails, so if you need to use that
feature be sure sendmail is installed and in PATH.
Install on Linux, Mac OS X
--------------------------
.. code:: bash
python3 -m pip install academic-tracker
Install on Windows
------------------
.. code:: bash
py -3 -m pip install academic-tracker
Upgrade on Linux, Mac OS X
--------------------------
.. code:: bash
python3 -m pip install academic-tracker --upgrade
Upgrade on Windows
------------------
.. code:: bash
py -3 -m pip install academic-tracker --upgrade
Quickstart
~~~~~~~~~~
Academic Tracker has several commands and options. The simplest most common use
case is simply:
.. code:: bash
academic_tracker author_search config_file.json
Example config files can be downloaded from the `example_configs <https://github.com/MoseleyBioinformaticsLab/academic_tracker>`_
directory of the GitHub_.
Academic Tracker's behavior can be quite complex though, so it is highly encouraged
to read the `guide <https://moseleybioinformaticslab.github.io/academic_tracker/guide.html>`_
and `tutorial <https://moseleybioinformaticslab.github.io/academic_tracker/tutorial.html>`_.
Creating The Configuration JSON
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
A configuration JSON file is required to run Academic Tracker, but initially creating
it the first time can be burdensome. Unfortunately, there is no easy solution for
this. It is encouraged to read the configuration JSON section in `jsonschema <https://moseleybioinformaticslab.github.io/academic_tracker/jsonschema.html>`_
and use the example there to create it initially. The add_authors command can help
with building the Authors section if you already have a csv file with author
information. A good tool to help track down pesky JSON syntax errors is `here <https://csvjson.com/json_validator>`__.
There are also examples in the `example_configs <https://github.com/MoseleyBioinformaticsLab/academic_tracker/tree/main/example_configs>`__
directory of the GitHub repo. There are also more examples in the supplemental
material of the paper https://doi.org/10.6084/m9.figshare.19412165.
Registering With ORCID
~~~~~~~~~~~~~~~~~~~~~~
In order to have this program search ORCID you must register with ORCID and obtain
a key and secret. Details on how to do that are `here <https://info.orcid.org/documentation/integration-guide/registering-a-public-api-client/>`__.
If you do not want to do that then the --no_ORCID option can be used to skip searching
ORCID, or don't include the ORCID_search section in the config file.
Mac OS Note
~~~~~~~~~~~
When you try to run the program on Mac OS you may get an SSL error.
certificate verify failed: unable to get local issuer certificate
This is due to a change in Mac OS and Python. To fix it go to to your Python
folder in Applications and run the Install Certificates.command shell command
in the /Applications/Python 3.x folder. This should fix the issue.
Email Sending Note
~~~~~~~~~~~~~~~~~~
Academic Tracker uses sendmail to send emails, so any system it is going to be
used on needs to have sendmail installed and the path in PATH. If you try to
send emails without this the program will display a warning. This can be avoided
by using the --test option though. The --test option blocks email sending. Email
sending can also be avoided by leaving the from_email attribute out of the report
sections of the configuration JSON file.
How Authors Are Identified
~~~~~~~~~~~~~~~~~~~~~~~~~~
When searching by authors it is necessary to confirm that the author given to
Academic Tracker matches the author returned in the query. In general this matching
is done by matching the first and last names and at least one affiliation given
for the author in the configuration JSON file. Note that affiliations can change
over time as authors move, so they may need many affiliations to accurately match
them to their publications depending on how far back you want to search in time.
How Publications Are Matched
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
When searching by publications it is necessary to confirm that the publication
in the given reference matches the publication returned in the query. This is done
by either matching the DOIs, PMIDs, or the title and at least one author. Titles
are fuzzy matched using fuzzywuzzy which is why at least one author must also be
matched. Author's are matched using last name and at least one affiliation.
Troubleshooting Errors
~~~~~~~~~~~~~~~~~~~~~~
If you experience errors when running Academic Tracker the first thing to do is
simply try again. Since Academic Tracker is communicating with multiple web sources
it is not uncommon for a problem to occur with one of these sources. It might also
be a good idea to wait several hours or the next day to try again if there is a communication
issue with a particular source. You can also use the various "--no_Source" options
for whatever source is causing an error. For example, if Crossref keeps having 504
HTTP errors you can run with the --no_Crossref option. If the issue persists across
multiple runs then try upgrading Academic Tracker's dependencies with
"pip install --upgrade dependency_name". The list of dependencies is in the `guide <https://moseleybioinformaticslab.github.io/academic_tracker/guide.html>`_.
License
~~~~~~~
This package is distributed under the BSD `license <https://moseleybioinformaticslab.github.io/academic_tracker/license.html>`__.
.. _GitHub: https://github.com/MoseleyBioinformaticsLab/academic_tracker
.. _Pages: https://moseleybioinformaticslab.github.io/academic_tracker/
.. _PyPI: https://pypi.org/project/academic_tracker
.. _pip: https://pip.pypa.io
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"description": "Academic Tracker\r\n================\r\n\r\n.. image:: https://img.shields.io/pypi/v/academic_tracker.svg\r\n :target: https://pypi.org/project/academic_tracker\r\n :alt: Current library version\r\n\r\n.. image:: https://img.shields.io/pypi/pyversions/academic_tracker.svg\r\n :target: https://pypi.org/project/academic_tracker\r\n :alt: Supported Python versions\r\n\r\n.. image:: https://github.com/MoseleyBioinformaticsLab/academic_tracker/actions/workflows/build.yml/badge.svg\r\n :target: https://github.com/MoseleyBioinformaticsLab/academic_tracker/actions/workflows/build.yml\r\n :alt: Build status\r\n\r\n.. image:: https://codecov.io/gh/MoseleyBioinformaticsLab/academic_tracker/branch/main/graphs/badge.svg?branch=main\r\n :target: https://codecov.io/gh/MoseleyBioinformaticsLab/academic_tracker\r\n :alt: Code coverage information\r\n\r\n.. image:: https://img.shields.io/badge/DOI-10.1371%2Fjournal.pone.0277834-blue.svg\r\n :target: https://doi.org/10.1371/journal.pone.0277834\r\n :alt: Citation link\r\n\r\n.. image:: https://img.shields.io/github/stars/MoseleyBioinformaticsLab/academic_tracker.svg?style=social&label=Star\r\n :target: https://github.com/MoseleyBioinformaticsLab/academic_tracker\r\n :alt: GitHub project\r\n\r\n|\r\n\r\nAcademic Tracker was created to automate the process of making sure that federally \r\nfunded publications get listed on PubMed and that the grant funding source for \r\nthem is cited. \r\n\r\nAcademic Tracker is a command line tool to search PubMed, ORCID, Google Scholar, \r\nand Crossref for publications. The program can either be given a list of authors \r\nto look for publications for, or references/citations to publications themselves. \r\nThe program will then will look for publications on the aforementioned sources \r\nand return what relevant information is available from those sources.\r\n\r\nThe primary use case is to give the program a list of authors to find publications \r\nfor. From this list of publications it can then be determined which ones need \r\nfurther action to be in compliance.\r\n\r\nA secondary use case for finding author's publications is to create a report of \r\nthe collaborators they have worked with, and can be done by specifying the creation \r\nof that report in the configuration file. Details on reports are in the `documentation <https://moseleybioinformaticslab.github.io/academic_tracker/reporting.html>`__.\r\n\r\nThe other primary use case is to give the program a list of publication references \r\nto find information for.\r\n\r\nLinks\r\n~~~~~\r\n\r\n * Academic Tracker @ GitHub_\r\n * Academic Tracker @ PyPI_\r\n * Documentation @ Pages_\r\n\r\n\r\nInstallation\r\n~~~~~~~~~~~~\r\nThe Academic Tracker package runs under Python 3.8+. Use pip_ to install.\r\nStarting with Python 3.4, pip_ is included by default. Be sure to use the latest \r\nversion of pip as older versions are known to have issues grabbing all dependencies. \r\nAcademic Tracker relies on sendmail to send emails, so if you need to use that \r\nfeature be sure sendmail is installed and in PATH.\r\n\r\n\r\nInstall on Linux, Mac OS X\r\n--------------------------\r\n\r\n.. code:: bash\r\n\r\n python3 -m pip install academic-tracker\r\n\r\n\r\nInstall on Windows\r\n------------------\r\n\r\n.. code:: bash\r\n\r\n py -3 -m pip install academic-tracker\r\n \r\n\r\nUpgrade on Linux, Mac OS X\r\n--------------------------\r\n\r\n.. code:: bash\r\n\r\n python3 -m pip install academic-tracker --upgrade\r\n \r\n\r\nUpgrade on Windows\r\n------------------\r\n\r\n.. code:: bash\r\n\r\n py -3 -m pip install academic-tracker --upgrade\r\n\r\n\r\n\r\nQuickstart\r\n~~~~~~~~~~\r\nAcademic Tracker has several commands and options. The simplest most common use \r\ncase is simply:\r\n\r\n.. code:: bash\r\n \r\n academic_tracker author_search config_file.json\r\n \r\nExample config files can be downloaded from the `example_configs <https://github.com/MoseleyBioinformaticsLab/academic_tracker>`_ \r\ndirectory of the GitHub_.\r\n\r\nAcademic Tracker's behavior can be quite complex though, so it is highly encouraged \r\nto read the `guide <https://moseleybioinformaticslab.github.io/academic_tracker/guide.html>`_ \r\nand `tutorial <https://moseleybioinformaticslab.github.io/academic_tracker/tutorial.html>`_.\r\n\r\n\r\nCreating The Configuration JSON\r\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\r\nA configuration JSON file is required to run Academic Tracker, but initially creating \r\nit the first time can be burdensome. Unfortunately, there is no easy solution for \r\nthis. It is encouraged to read the configuration JSON section in `jsonschema <https://moseleybioinformaticslab.github.io/academic_tracker/jsonschema.html>`_ \r\nand use the example there to create it initially. The add_authors command can help \r\nwith building the Authors section if you already have a csv file with author \r\ninformation. A good tool to help track down pesky JSON syntax errors is `here <https://csvjson.com/json_validator>`__. \r\nThere are also examples in the `example_configs <https://github.com/MoseleyBioinformaticsLab/academic_tracker/tree/main/example_configs>`__ \r\ndirectory of the GitHub repo. There are also more examples in the supplemental \r\nmaterial of the paper https://doi.org/10.6084/m9.figshare.19412165.\r\n\r\n\r\nRegistering With ORCID\r\n~~~~~~~~~~~~~~~~~~~~~~\r\nIn order to have this program search ORCID you must register with ORCID and obtain \r\na key and secret. Details on how to do that are `here <https://info.orcid.org/documentation/integration-guide/registering-a-public-api-client/>`__. \r\nIf you do not want to do that then the --no_ORCID option can be used to skip searching \r\nORCID, or don't include the ORCID_search section in the config file.\r\n\r\n \r\nMac OS Note\r\n~~~~~~~~~~~\r\nWhen you try to run the program on Mac OS you may get an SSL error.\r\n\r\n certificate verify failed: unable to get local issuer certificate\r\n \r\nThis is due to a change in Mac OS and Python. To fix it go to to your Python \r\nfolder in Applications and run the Install Certificates.command shell command \r\nin the /Applications/Python 3.x folder. This should fix the issue.\r\n\r\n\r\nEmail Sending Note\r\n~~~~~~~~~~~~~~~~~~\r\nAcademic Tracker uses sendmail to send emails, so any system it is going to be \r\nused on needs to have sendmail installed and the path in PATH. If you try to \r\nsend emails without this the program will display a warning. This can be avoided \r\nby using the --test option though. The --test option blocks email sending. Email \r\nsending can also be avoided by leaving the from_email attribute out of the report \r\nsections of the configuration JSON file.\r\n\r\n\r\nHow Authors Are Identified\r\n~~~~~~~~~~~~~~~~~~~~~~~~~~\r\nWhen searching by authors it is necessary to confirm that the author given to \r\nAcademic Tracker matches the author returned in the query. In general this matching \r\nis done by matching the first and last names and at least one affiliation given \r\nfor the author in the configuration JSON file. 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