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Academic Tracker was created to automate the process of making sure that federally
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Academic Tracker was created to automate the process of making sure that NIH
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funded publications get listed on PubMed and that the grant funding source for
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them is cited.
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@@ -39,30 +47,24 @@ and return what relevant information is available from those sources.
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The primary use case is to give the program a list of authors to find publications
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for. From this list of publications it can then be determined which ones need
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further action to be in compliance.
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further action to be in compliance with NIH.
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A secondary use case for finding author's publications is to create a report of
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the collaborators they have worked with, and can be done by specifying the creation
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of that report in the configuration file. Details on reports are in the `documentation <https://moseleybioinformaticslab.github.io/academic_tracker/reporting.html>`__.
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The other primary use case is to give the program a list of publication references
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to find information for.
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Links
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~~~~~
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* Academic Tracker @ GitHub_
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* Academic Tracker @ PyPI_
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* Documentation @ Pages_
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* Documentation @ ReadTheDocs_
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Installation
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~~~~~~~~~~~~
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The Academic Tracker package runs under Python 3.8+. Use pip_ to install.
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Starting with Python 3.4, pip_ is included by default. Be sure to use the latest
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version of pip as older versions are known to have issues grabbing all dependencies.
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Academic Tracker relies on sendmail to send emails, so if you need to use that
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feature be sure sendmail is installed and in PATH.
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The Academic Tracker package runs under Python 3.7+. Use pip_ to install.
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Starting with Python 3.4, pip_ is included by default. Academic Tracker relies
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on sendmail which is built into Linux to send emails, so it is only available for
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use there.
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Install on Linux, Mac OS X
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python3 -m pip install academic_tracker
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Install on Windows
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------------------
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.. code:: bash
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py -3 -m pip install academic_tracker
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Upgrade on Linux, Mac OS X
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--------------------------
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.. code:: bash
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python3 -m pip install academic_tracker --upgrade
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Upgrade on Windows
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------------------
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.. code:: bash
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py -3 -m pip install academic_tracker --upgrade
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academic_tracker author_search config_file.json
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Example config files can be downloaded from the `example_configs <https://github.com/MoseleyBioinformaticsLab/academic_tracker>`_
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directory of the GitHub_.
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Academic Tracker's behavior can be quite complex though, so it is highly encouraged
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to read the `guide <https://moseleybioinformaticslab.github.io/academic_tracker/guide.html>`_
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and `tutorial <https://moseleybioinformaticslab.github.io/academic_tracker/tutorial.html>`_.
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to read the :doc:`guide` and :doc:`tutorial`.
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Creating The Configuration JSON
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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A configuration JSON file is required to run Academic Tracker, but initially creating
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it the first time can be burdensome. Unfortunately, there is no easy solution for
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this. It is encouraged to read the configuration JSON section in `jsonschema<https://moseleybioinformaticslab.github.io/academic_tracker/jsonschema.html>`_
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this. It is encouraged to read the configuration JSON section in :doc:`jsonschema`
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and use the example there to create it initially. The add_authors command can help
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with building the Authors section if you already have a csv file with author
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information. A good tool to help track down pesky JSON syntax errors is `here <https://csvjson.com/json_validator>`__.
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There are also examples in the `example_configs <https://github.com/MoseleyBioinformaticsLab/academic_tracker/tree/main/example_configs>`__
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directory of the GitHub repo. There are also more example in the supplemental
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material of the paper https://doi.org/10.6084/m9.figshare.19412165.
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information. A good tool to help track down pesky JSON syntax errors is `here <https://csvjson.com/json_validator>`_.
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Registering With ORCID
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~~~~~~~~~~~~~~~~~~~~~~
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In order to have this program search ORCID you must register with ORCID and obtain
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a key and secret. Details on how to do that are `here <https://info.orcid.org/documentation/integration-guide/registering-a-public-api-client/>`__.
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a key and secret. Details on how to do that are `here <https://info.orcid.org/documentation/integration-guide/registering-a-public-api-client/>`_.
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If you do not want to do that then the --no_ORCID option can be used to skip searching
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ORCID, or don't include the ORCID_search section in the config file.
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ORCID.
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Mac OS Note
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certificate verify failed: unable to get local issuer certificate
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This is due to a change in Mac OS and Python. To fix it go to to your Python
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folder in Applications and run the Install Certificates.command shell command
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in the /Applications/Python 3.x folder. This should fix the issue.
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folder in Applications and run the Install Certificates.command shell command.
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This should fix the issue.
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Email Sending Note
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~~~~~~~~~~~~~~~~~~
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Academic Tracker uses sendmail to send emails, so any system it is going to be
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used on needs to have sendmail installed and the path in PATH. If you try to
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send emails without this the program will display a warning. This can be avoided
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by using the --test option though. The --test option blocks email sending. Email
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used on needs to have sendmail installed in /usr/sbin/sendmail. If you try to
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send emails without this the program will error. This can be avoided by using
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the --test option though. The --test option blocks email sending so the program
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can be ran just fine on systems without sendmail if that option is used. Email
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sending can also be avoided by leaving the from_email attribute out of the report
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sections of the configuration JSON file.
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@@ -173,12 +161,26 @@ are fuzzy matched using fuzzywuzzy which is why at least one author must also be
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matched. Author's are matched using last name and at least one affiliation.
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Troubleshooting Errors
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~~~~~~~~~~~~~~~~~~~~~~
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If you experience errors when running Academic Tracker the first thing to do is
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simply try again. Since Academic Tracker is communicating with multiple web sources
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it is not uncommon for a problem to occur with one of these sources. It might also
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be a good idea to wait several hours or the next day to try again if there is a communication
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issue with a particular source. You can also use the various "--no_Source" options
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for whatever source is causing an error. For example, if Crossref keeps having 504
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HTTP errors you can run with the --no_Crossref option. If the issue persists across
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multiple runs then try upgrading Academic Tracker's dependencies with
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"pip install --upgrade dependency_name". The list of dependencies is in the `guide <https://moseleybioinformaticslab.github.io/academic_tracker/guide.html>`_.
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License
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~~~~~~~
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This package is distributed under the BSD `license<https://moseleybioinformaticslab.github.io/academic_tracker/license.html>`__.
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This package is distributed under the BSD_ `license`.
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@@ -16,3 +16,4 @@ Add PMCID and grants to pymed package.
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Add expanded search to orcid package or look for more up to date package to use. Expanded search was added to ORCID's API with 3.0 release. orcid package appears to be 2.0 only.
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Add capability to get the citations each paper cites.
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