You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Academic Tracker was created to automate the process of making sure that NIH
30
+
Academic Tracker was created to automate the process of making sure that federally
39
31
funded publications get listed on PubMed and that the grant funding source for
40
32
them is cited.
41
33
@@ -47,24 +39,30 @@ and return what relevant information is available from those sources.
47
39
48
40
The primary use case is to give the program a list of authors to find publications
49
41
for. From this list of publications it can then be determined which ones need
50
-
further action to be in compliance with NIH.
42
+
further action to be in compliance.
51
43
44
+
A secondary use case for finding author's publications is to create a report of
45
+
the collaborators they have worked with, and can be done by specifying the creation
46
+
of that report in the configuration file. Details on reports are in the `documentation <https://moseleybioinformaticslab.github.io/academic_tracker/reporting.html>`__.
52
47
48
+
The other primary use case is to give the program a list of publication references
49
+
to find information for.
53
50
54
51
Links
55
52
~~~~~
56
53
57
54
* Academic Tracker @ GitHub_
58
55
* Academic Tracker @ PyPI_
59
-
* Documentation @ ReadTheDocs_
56
+
* Documentation @ Pages_
60
57
61
58
62
59
Installation
63
60
~~~~~~~~~~~~
64
-
The Academic Tracker package runs under Python 3.7+. Use pip_ to install.
65
-
Starting with Python 3.4, pip_ is included by default. Academic Tracker relies
66
-
on sendmail which is built into Linux to send emails, so it is only available for
67
-
use there.
61
+
The Academic Tracker package runs under Python 3.8+. Use pip_ to install.
62
+
Starting with Python 3.4, pip_ is included by default. Be sure to use the latest
63
+
version of pip as older versions are known to have issues grabbing all dependencies.
64
+
Academic Tracker relies on sendmail to send emails, so if you need to use that
65
+
feature be sure sendmail is installed and in PATH.
68
66
69
67
70
68
Install on Linux, Mac OS X
@@ -75,14 +73,28 @@ Install on Linux, Mac OS X
75
73
python3 -m pip install academic_tracker
76
74
77
75
76
+
Install on Windows
77
+
------------------
78
78
79
+
.. code:: bash
80
+
81
+
py -3 -m pip install academic_tracker
82
+
79
83
80
84
Upgrade on Linux, Mac OS X
81
85
--------------------------
82
86
83
87
.. code:: bash
84
88
85
89
python3 -m pip install academic_tracker --upgrade
90
+
91
+
92
+
Upgrade on Windows
93
+
------------------
94
+
95
+
.. code:: bash
96
+
97
+
py -3 -m pip install academic_tracker --upgrade
86
98
87
99
88
100
@@ -94,30 +106,34 @@ case is simply:
94
106
.. code:: bash
95
107
96
108
academic_tracker author_search config_file.json
97
-
109
+
98
110
Example config files can be downloaded from the `example_configs <https://github.com/MoseleyBioinformaticsLab/academic_tracker>`_
99
111
directory of the GitHub_.
100
112
101
113
Academic Tracker's behavior can be quite complex though, so it is highly encouraged
102
-
to read the :doc:`guide` and :doc:`tutorial`.
114
+
to read the `guide <https://moseleybioinformaticslab.github.io/academic_tracker/guide.html>`_
115
+
and `tutorial <https://moseleybioinformaticslab.github.io/academic_tracker/tutorial.html>`_.
103
116
104
117
105
118
Creating The Configuration JSON
106
119
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
107
120
A configuration JSON file is required to run Academic Tracker, but initially creating
108
121
it the first time can be burdensome. Unfortunately, there is no easy solution for
109
-
this. It is encouraged to read the configuration JSON section in :doc:`jsonschema`
122
+
this. It is encouraged to read the configuration JSON section in `jsonschema<https://moseleybioinformaticslab.github.io/academic_tracker/jsonschema.html>`_
110
123
and use the example there to create it initially. The add_authors command can help
111
124
with building the Authors section if you already have a csv file with author
112
-
information. A good tool to help track down pesky JSON syntax errors is `here <https://csvjson.com/json_validator>`_.
125
+
information. A good tool to help track down pesky JSON syntax errors is `here <https://csvjson.com/json_validator>`__.
126
+
There are also examples in the `example_configs <https://github.com/MoseleyBioinformaticsLab/academic_tracker/tree/main/example_configs>`__
127
+
directory of the GitHub repo. There are also more example in the supplemental
128
+
material of the paper https://doi.org/10.6084/m9.figshare.19412165.
113
129
114
130
115
131
Registering With ORCID
116
132
~~~~~~~~~~~~~~~~~~~~~~
117
133
In order to have this program search ORCID you must register with ORCID and obtain
118
-
a key and secret. Details on how to do that are `here <https://info.orcid.org/documentation/integration-guide/registering-a-public-api-client/>`_.
134
+
a key and secret. Details on how to do that are `here <https://info.orcid.org/documentation/integration-guide/registering-a-public-api-client/>`__.
119
135
If you do not want to do that then the --no_ORCID option can be used to skip searching
120
-
ORCID.
136
+
ORCID, or don't include the ORCID_search section in the config file.
121
137
122
138
123
139
Mac OS Note
@@ -127,17 +143,16 @@ When you try to run the program on Mac OS you may get an SSL error.
127
143
certificate verify failed: unable to get local issuer certificate
128
144
129
145
This is due to a change in Mac OS and Python. To fix it go to to your Python
130
-
folder in Applications and run the Install Certificates.command shell command.
131
-
This should fix the issue.
146
+
folder in Applications and run the Install Certificates.command shell command
147
+
in the /Applications/Python 3.x folder. This should fix the issue.
132
148
133
149
134
150
Email Sending Note
135
151
~~~~~~~~~~~~~~~~~~
136
152
Academic Tracker uses sendmail to send emails, so any system it is going to be
137
-
used on needs to have sendmail installed in /usr/sbin/sendmail. If you try to
138
-
send emails without this the program will error. This can be avoided by using
139
-
the --test option though. The --test option blocks email sending so the program
140
-
can be ran just fine on systems without sendmail if that option is used. Email
153
+
used on needs to have sendmail installed and the path in PATH. If you try to
154
+
send emails without this the program will display a warning. This can be avoided
155
+
by using the --test option though. The --test option blocks email sending. Email
141
156
sending can also be avoided by leaving the from_email attribute out of the report
142
157
sections of the configuration JSON file.
143
158
@@ -176,11 +191,10 @@ multiple runs then try upgrading Academic Tracker's dependencies with
176
191
177
192
License
178
193
~~~~~~~
179
-
This package is distributed under the BSD_ `license`.
194
+
This package is distributed under the BSD `license<https://moseleybioinformaticslab.github.io/academic_tracker/license.html>`__.
0 commit comments