scopus/README.txt

README scopus
Ak, 27.3.2017

Get information from Scopus database.

This queries work only with access to Scopus (e.g. from KIT LAN)
Scopus service is not public vailable.


Content
info		Documentation, website, etc

readme.txt	This file
my_scopus.py	List of scopus author ids
ak_scopus.py	Functions to access scopus
ak_wordpress.py Functions to creates Wordpress posts + comments
scopus-get-publications.py Script to query Scopus

test-scopus.py	Application with some functions to get publication entries
		Prints a list with some formatting
test-scopus2.py Example from one of the website, only one query


Usage: 
1. Go to Scopus and retrieve the scopus author ids for the scientists in your group.
Define the ids in my_scopus.py and group them.

2. Select one of more author groups in scopus-get-publications.py (main part at
the end of the file). Check definition of database and wordpress installation.

3. Execute scopus-get-publications.py.
python -W ignore scopus-get-publications.py

Note: The -W ignore flag might be necessary if the INSERT IGNORE causes warnings.

Example run:
ufo:~/scopus # python -W ignore scopus-get-publications.py 

***********************************************
**** scopus-get-publications / 2017-03-27 *****
***********************************************

=== Update of publications for the author group: Computing
Total number of publications: 54
=== Update of publications for the author group: X-ray Imaging
Total number of publications: 39
=== Update of publications for the author group: Electronics
Total number of publications: 132
=== Update of publications for the author group: Morphology
Total number of publications: 21

=== Create posts for newly registered publication in scopus
Nothing new found

=== Update citatation of all publication in the database
Total number of publications is 281

=== Create comments for newly registered citations in scopus
Number of new citations is 0

Summary: (see also logfile /root/scopus/scopus-publications.log) 
Date       = 2017-03-27 21:28:36.002624
NPubs      = 281
NNewPubs   = 0
NCites     = 4699
NNewCites  = 0
Runtime    = 0:00:11.496362


Further enhancements

Todo:
- Reprocessing of all post, if the format has changed 
E.g. add button 
with Email to author or a new category has been added
- Query only the latest citations for each publications not all.
- Store JSON-Data of all publications
- Get bibliographic information for display at the web page of a reseach group 
like UFO or may be also later for the DTS program.
- Handle wrong publications in scopus for author with same name
- Automatically include reports and student thesis by
bibtex definition and upload on a server!?
-> Would have the nice effect, that all student work is organized systematically!!!



Structure of the database

Both tables keep the reference to the publications in Scopus and the 
Wordpress ids. With this information, reprocessing is possible (but not
implemented now).


Table publocations:

MariaDB [scopus]> describe publications;
+--------------+--------------+------+-----+---------+----------------+
| Field        | Type         | Null | Key | Default | Extra          |
+--------------+--------------+------+-----+---------+----------------+
| id           | int(11)      | NO   | PRI | NULL    | auto_increment |
| scopusid     | varchar(255) | YES  | UNI | NULL    |                |
| wpid         | int(11)      | YES  |     | NULL    |                |
| citedbycount | int(11)      | YES  |     | NULL    |                |
| citesloaded  | int(11)      | YES  |     | NULL    |                |
| categories   | varchar(255) | YES  |     | NULL    |                |
| doi          | varchar(255) | YES  |     | NULL    |                |
| title        | varchar(255) | YES  |     | NULL    |                |
| abstract     | text         | YES  |     | NULL    |                |
| bibtex       | text         | YES  |     | NULL    |                |
| ts           | datetime     | YES  |     | NULL    |                |
| scopusdata   | text         | YES  |     | NULL    |                |
| eid          | varchar(255) | YES  |     | NULL    |                |
+--------------+--------------+------+-----+---------+----------------+

Table citations:

MariaDB [scopus]> describe citations;
+--------------+--------------+------+-----+---------+----------------+
| Field        | Type         | Null | Key | Default | Extra          |
+--------------+--------------+------+-----+---------+----------------+
| id           | int(11)      | NO   | PRI | NULL    | auto_increment |
| scopusid     | varchar(255) | YES  |     | NULL    |                |
| eid          | varchar(255) | YES  |     | NULL    |                |
| wpid         | int(11)      | YES  | MUL | NULL    |                |
| wpcommentid  | int(11)      | YES  |     | NULL    |                |
| citedbycount | int(11)      | YES  |     | NULL    |                |
| citesloaded  | int(11)      | YES  |     | NULL    |                |
| categories   | varchar(255) | YES  |     | NULL    |                |
| doi          | varchar(255) | YES  |     | NULL    |                |
| scopusdata   | text         | YES  |     | NULL    |                |
| title        | varchar(255) | YES  |     | NULL    |                |
| abstract     | text         | YES  |     | NULL    |                |
| bibtex       | text         | YES  |     | NULL    |                |
| ts           | datetime     | YES  |     | NULL    |                |
+--------------+--------------+------+-----+---------+----------------+



Setup of scopus database in mysql 

create database scopus;

CREATE USER 'scopus@localhost';
grant all on scopus.* to 'scopus'@'localhost' identified by '$scopus$';

# create tables
mysql -u scopus -p scopus < create_scopus.sql



Publications in Scopus:

Sometime (unfortunately quite often) a author id in Scopus is not unique but 
identifies several researchers with the same name. E.g. Michele Caselle (3 persons)
Matthias Balzer (2).

This case is currently handled manually by deleting all publications from the unknown
authors. Might be possible to implement also a black list??


Sample data from Scopus:
{
    "abstracts-retrieval-response": {
        "authors": {
            "author": [
                {
                    "@_fa": "true",
                    "@auid": "15076530600",
                    "@seq": "1",
                    "affiliation": {
                        "@href": "http://api.elsevier.com/content/affiliation/affiliation_id/60102538",
                        "@id": "60102538"
                    },
                    "author-url": "http://api.elsevier.com/content/author/author_id/15076530600",
                    "ce:given-name": "Suren",
                    "ce:indexed-name": "Chilingaryan S.",
                    "ce:initials": "S.",
                    "ce:surname": "Chilingaryan",
                    "preferred-name": {
                        "ce:given-name": "Suren",
                        "ce:indexed-name": "Chilingaryan S.",
                        "ce:initials": "S.",
                        "ce:surname": "Chilingaryan"
                    }
                },
                {
                    "@_fa": "true",
                    "@auid": "35313939900",
                    "@seq": "2",
                    "affiliation": {
                        "@href": "http://api.elsevier.com/content/affiliation/affiliation_id/60102538",
                        "@id": "60102538"
                    },
                    "author-url": "http://api.elsevier.com/content/author/author_id/35313939900",
                    "ce:given-name": "Andreas",
                    "ce:indexed-name": "Kopmann A.",
                    "ce:initials": "A.",
                    "ce:surname": "Kopmann",
                    "preferred-name": {
                        "ce:given-name": "Andreas",
                        "ce:indexed-name": "Kopmann A.",
                        "ce:initials": "A.",
                        "ce:surname": "Kopmann"
                    }
                },
                {
                    "@_fa": "true",
                    "@auid": "56001075000",
                    "@seq": "3",
                    "affiliation": {
                        "@href": "http://api.elsevier.com/content/affiliation/affiliation_id/60032633",
                        "@id": "60032633"
                    },
                    "author-url": "http://api.elsevier.com/content/author/author_id/56001075000",
                    "ce:given-name": "Alessandro",
                    "ce:indexed-name": "Mirone A.",
                    "ce:initials": "A.",
                    "ce:surname": "Mirone",
                    "preferred-name": {
                        "ce:given-name": "Alessandro",
                        "ce:indexed-name": "Mirone A.",
                        "ce:initials": "A.",
                        "ce:surname": "Mirone"
                    }
                },
                {
                    "@_fa": "true",
                    "@auid": "35277157300",
                    "@seq": "4",
                    "affiliation": {
                        "@href": "http://api.elsevier.com/content/affiliation/affiliation_id/60102538",
                        "@id": "60102538"
                    },
                    "author-url": "http://api.elsevier.com/content/author/author_id/35277157300",
                    "ce:given-name": "Tomy",
                    "ce:indexed-name": "Dos Santos Rolo T.",
                    "ce:initials": "T.",
                    "ce:surname": "Dos Santos Rolo",
                    "preferred-name": {
                        "ce:given-name": "Tomy",
                        "ce:indexed-name": "Dos Santos Rolo T.",
                        "ce:initials": "T.",
                        "ce:surname": "Dos Santos Rolo"
                    }
                },
                {
                    "@_fa": "true",
                    "@auid": "35303862100",
                    "@seq": "5",
                    "affiliation": {
                        "@href": "http://api.elsevier.com/content/affiliation/affiliation_id/60102538",
                        "@id": "60102538"
                    },
                    "author-url": "http://api.elsevier.com/content/author/author_id/35303862100",
                    "ce:given-name": "Matthias",
                    "ce:indexed-name": "Vogelgesang M.",
                    "ce:initials": "M.",
                    "ce:surname": "Vogelgesang",
                    "preferred-name": {
                        "ce:given-name": "Matthias",
                        "ce:indexed-name": "Vogelgesang M.",
                        "ce:initials": "M.",
                        "ce:surname": "Vogelgesang"
                    }
                }
            ]
        },
        "coredata": {
            "citedby-count": "0",
            "dc:description": "X-ray tomography has been proven to be a valuable tool for understanding internal, otherwise invisible, mechanisms in biology and other fields. Recent advances in digital detector technology enabled investigation of dynamic processes in 3D with a temporal resolution down to the milliseconds range. Unfortunately it requires computationally intensive recon- struction algorithms with long post-processing times. We have optimized the reconstruction software employed at the micro-tomography beamlines at KIT and ESRF. Using a 4 stage pipelined architecture and the computational power of modern graphic cards, we were able to reduce the processing time by a factor 75 with a single server. The time required to reconstruct a typical 3D image is reduced down to several seconds only and online visualization is possible for the first time.Copyright is held by the author/owner(s).",
            "dc:identifier": "SCOPUS_ID:84859045029",
            "dc:title": "Poster: A GPU-based architecture for real-time data assessment at synchrotron experiments",
            "link": [
                {
                    "@_fa": "true",
                    "@href": "http://api.elsevier.com/content/abstract/scopus_id/84859045029",
                    "@rel": "self"
                }
            ],
            "prism:aggregationType": "Conference Proceeding",
            "prism:coverDate": "2011-12-01",
            "prism:doi": "10.1145/2148600.2148624",
            "prism:pageRange": "51-52",
            "prism:publicationName": "SC'11 - Proceedings of the 2011 High Performance Computing Networking, Storage and Analysis Companion, Co-located with SC'11",
            "prism:url": "http://api.elsevier.com/content/abstract/scopus_id/84859045029"
        }
    }
}



Installation of python, mysql et al:

pip install python-wordpress-xmlrpc

Konfiguration Webserver (muss man wohl nach jeder Installation neu machen!!!)

/etc/apache2/httpd.conf:
LoadModule userdir_module libexec/apache2/mod_userdir.so
LoadModule php5_module libexec/apache2/libphp5.so
Include /private/etc/apache2/extra/httpd-userdir.conf

/etc/apache2/extra/httpd-userdir.conf:
Include /private/etc/apache2/users/*.conf

/etc/php.ini:
pdo_mysql.default_socket= /tmp/mysql.sock
mysql.default_socket = /tmp/mysql.sock
mysqli.default_socket = /tmp/mysql.sock


sh-3.2# apachectl restart


Install website:

Create archive with wp dublicator

Save scopus database

mysqldump -u scopus -p scopus > scopus-170322.sql


Create database on remote system

mysql:
CREATE USER 'scopus'@'localhost' IDENTIFIED BY '$scopus$';
GRANT ALL PRIVILEGES ON scopus.* TO 'scopus'@'localhost';

CREATE DATABASE scopus;

mysql -u scopus -p scopus < scopus-170322.sql


Create database wp_ufo2;

CREATE USER ‘ufo’@‘localhost' IDENTIFIED BY '$ipepdv$';
GRANT ALL PRIVILEGES ON wp_ufo2.* TO ‘ufo’@‘localhost';

CREATE DATABASE wp_ufo2;


Import WP archive:
mkdir ufo2
chown -R wwwrun:www ufo2

http://ufo.kit.edu/ufo2/installer.php


Error: PHP module ZipArchive is missing 
Manual extraction is available in the advanced options !!!


Installation Scopus-Scripts:

pip install requests
pip install python-wordpress-xmlrpc
pip install pymysql

Check configurations:
scopus-get-piblications.py
ak_wordpress.py