https://github.com/scilifelabdatacentre/publications
A web-based publications reference database system.
https://github.com/scilifelabdatacentre/publications
Last synced: 3 months ago
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A web-based publications reference database system.
- Host: GitHub
- URL: https://github.com/scilifelabdatacentre/publications
- Owner: ScilifelabDataCentre
- License: mit
- Created: 2017-03-14T15:55:25.000Z (about 8 years ago)
- Default Branch: master
- Last Pushed: 2024-05-03T21:17:19.000Z (12 months ago)
- Last Synced: 2024-05-03T22:28:55.384Z (12 months ago)
- Language: Python
- Homepage:
- Size: 65 MB
- Stars: 10
- Watchers: 3
- Forks: 3
- Open Issues: 12
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
Publications
============
A web-based publications reference database system.
- [Features](#features)
- [Important changes](#important-changes)
- [Implementation](#implementation)
- [Installation](#installation)
- [Command-line interface](#command-line-interface)
- [Example instances](#example-instances)
Features
--------
- All publication reference data is visible to all. No login is
required for viewing.
- Publication references can be added by fetching data from:
- [PubMed](https://www.ncbi.nlm.nih.gov/pubmed)
using the PubMed identifier (PMID).
- [Crossref](https://www.crossref.org/)
using the Digital Object Identifier (DOI).
- Publication references can be added manually.
- A powerful subset selection expression evaluator, to produce a wide
range of publication subsets from the data. New in version 6.0.
- Curator accounts for adding and editing the publication entries can
be created by the admin of the instance.
- All curators can edit every publication reference. There is a log
for each publication, so it is possible to see who did what when.
- Publication references can be labeled. The labels can be used to
indicate e.g. research group, facility or some other classification.
A label can have a qualifier, e.g. to denote if the publication was
due to facility service or to a collaboration.
- A curator can use only the labels that she has been assigned by the
admin.
- There is a blacklist registry based on the PMID and/or DOI of
publications. When a publication is blacklisted, it will not be
fetched when using PMID, DOI or automatic scripts. This is to avoid
adding publications that have already been determined to be
irrelevant.
- Researcher entity, which can be associated with a publication.
This is done automatically if the PubMed or Crossref data specifies
ORCID for a publication author. New in version 4.0.
- Allow setting a flag 'Open Access' for a publication. New in version 4.0.
- The publications data can be extracted in JSON, CSV, XLSX and TXT formats.
- API to ask the server to fetch publications from PubMed or Crossref.
See [its README](https://github.com/pekrau/Publications/tree/master/publications/api).
Important changes
-----------------
- Since version 8.0, Python 3.9 or later is required.
- Since version 8.0, the main file to be executed is called `main.py` rather
than `app_publications.py`. The Docker file has been changed accordingly.
- Since version 6.4, the GitHub wiki has been discontinued. Installation
information is available below, and other information is available
in the web app interface.
- Since version 6.3, the directory containing site-specific data
(e.g. `settings.yaml`, `static` directory for favicon and logo image files)
has been moved from `Publications/publications/site` to `Publications/site`.
The installation procedure has changed accordingly.
- Since version 6.0, the Python module
[CouchDB2](https://pypi.org/project/CouchDB2/) is used instead of
[CouchDB](https://pypi.org/project/CouchDB/). Upgrade your packages
according to the `requirements.txt`.
Implementation
--------------
This system requires Python 3.6 or higher.
### Front-end (via CDN's)
- [Bootstrap 3](https://getbootstrap.com/docs/3.4/)
- [jQuery](https://jquery.com/)
- [jQuery UI](https://jqueryui.com/)
- [DataTables](https://datatables.net/)
### Back-end (installed on server)
- [Python 3.6](https://www.python.org/)
- [tornado](http://www.tornadoweb.org/en/stable/)
- [CouchDB server](http://couchdb.apache.org/)
- [CouchDB2](https://pypi.python.org/pypi/CouchDB2/)
(changed from [CouchDB 1.2](https://pypi.org/project/CouchDB/)
in version 6.0)
- [pyyaml](https://pypi.python.org/pypi/PyYAML)
- [requests](http://docs.python-requests.org/en/master/)
Installation
------------
0. NOTE: tornado is difficult (even impossible?) to set up on Windows
systems, so Linux is strongly recommended.
1. Ensure that you have Python 3.9 or higher.
2. Your Python environment must include the Publications directory in
its path, e.g.:
```
$ cd wherever/Publications
$ export PYTHONPATH=$PWd
```
3. Install the required Python modules (see `Publications/requirements.txt`)
4. Ensure that you have the CouchDB server installed and running.
5. Create the database publications in the CouchDB server using its
own interface. Ensure that the database allows read/write access
for the CouchDB server account of your choice. Record the CouchDB
server account name and password for the `settings.yaml` file (see below).
6. Copy the directory `Publications/site_template` and all its contents to
`Publications/site`. The latter directory contains files that can or
should be modified for your site.
7. Edit your settings file `Publications/site/settings.yaml`.
In particular, set the CouchDB connection, site name, etc.
8. The Publications CouchDB database must be initialized using the CLI.
This also tests that the CouchDB variables in the `settings.yaml`
file are correct.
```
$ python cli.py initialize
```
9. Create an admin account using the CLI. This admin account is needed to
create other accounts (admin or curator) in the web interface.
```
$ python cli.py admin
```
10. Set up the tornado web server to start on boot, using the port
number you have defined in the `settings.yaml` file. You need to figure
this out yourself.
11. Set a proxy from your outward-facing web server (Apache, nginx, or
whatever your site supports) for the tornado server. You need to figure
this out yourself.
Command-line interface
----------------------
There is a command-line interface (CLI) for admin work on the machine
the system is running on. See its help texts. The top-level help text is:
```
$ python cli.py --help
Usage: cli.py [OPTIONS] COMMAND [ARGS]...
Options:
-s, --settings TEXT Name of settings YAML file.
--log Enable logging output.
--help Show this message and exit.
Commands:
add-label Add a label to a set of publications.
admin Create a user account having the admin role.
counts Output counts of database entities.
curator Create a user account having the curator role.
dump Dump all data in the database to a .tar.gz dump file.
fetch Fetch publications given a file containing PMIDs...
find-pmid Find the PMID for the publications in the CSV file.
initialize Initialize the database, which must exist; load all...
password Set the password for the given account.
remove-label Remove a label from a set of publications.
select Select a subset of publications and output to a file.
show Display the JSON for the single item in the database.
undump Load a Publications database .tar.gz dump file.
update-crossref Use Crossref to update the publications in the CSV file.
update-pubmed Use PubMed to update the publications in the CSV file.
xrefs Output all xrefs as CSV data to the given file.
```
Example instances
-----------------
- [SciLifeLab Infrastructure Units Publications](https://publications.scilifelab.se/)
which keeps track of the publications to which the infrastructure
units of SciLifeLab have contributed. This was the need that the
system was designed for.
- [Covid-19 Publications](https://publications-covid19.scilifelab.se/)
for publications with contributions from Swedish research.