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Andreas Kopmann 336dfe22a6 Added Python dummmy app 2 years ago
doc bfd1f56e7b Started to generate documentation of the scripts with Python docstrings and Sphinx 5 years ago
etc 2162fb6fde Update of group members 2 years ago
log 2162fb6fde Update of group members 2 years ago
.gitignore bb759cd515 Removed swp files from repository 4 years ago
README.md 85a1f4e17f Merge branch 'master' of https://fuzzy.fzk.de/gogs/kopmann/scopus 2 years ago
ak_scopus.py b804481a8c Added filter for collaboration papers with too many authors 4 years ago
ak_wordpress.py 1d335367ec Fix configuration to use now slugs instead of real dispalyed names 4 years ago
app.py 336dfe22a6 Added Python dummmy app 2 years ago
config.py.sample d04208d108 Fixed author id of Michele Caselle 5 years ago
create_scopus.sql e58e305e1d Initial version 5 years ago
requirements.txt 336dfe22a6 Added Python dummmy app 2 years ago
rm-scopusid.py b804481a8c Added filter for collaboration papers with too many authors 4 years ago
scopus-rawdata.png a6274973e7 Added a web script to dump a full dataset for a publication 4 years ago
scopus-rawdata.py a6274973e7 Added a web script to dump a full dataset for a publication 4 years ago
scopus-update-database.py 0fa61ce682 Excluded the disabled publication already in SQL query 5 years ago
scopus_get_publications.py 331c932c71 Move counting of publication from update_citations to update_publications 4 years ago
test-citations.py 5c98017e3c Updated log of the UFO site 4 years ago
test-citations2.py 5c98017e3c Updated log of the UFO site 4 years ago
test-scopus.py b804481a8c Added filter for collaboration papers with too many authors 4 years ago
test-scopus2.py 5730f8a3fb Added Webers Scopus IDs and started affiliation splitting 5 years ago
test-wp.py b804481a8c Added filter for collaboration papers with too many authors 4 years ago
test-wp2.py 5196b16ef9 Changed configuration to match the new category names in Wordpress 4 years ago
update.sh 338ce23a2a Merged conflict and generalized update script 4 years ago

README.md

README scopus

Ak, 23.5.2017

Get information on publications of work groups from Elsevier's Scopus database for usage in websites. For each publication a post on a Wordpress CMS is created. Citations are mapped to Wordpress comments. The get-publication script is intended to run on a regualr basis (e.g. by cron).

Note: All scopus scripts run only with valid access to the Scopus database (e.g. from KIT LAN). The Scopus service is not public available.

Version history

Todo:

  • Add script to list all affiliations for one of the authors
  • Change author defintion to author id+ affiliation id If a author has been in two places, add a second author with the same id the other affilitation
  • Generate a sensible API documentation; Add a basic user documentation along with the API description
  • Add maintenance scripts, that check consittence of Scopus data and cache database; update of post categories; warning in case of inconsistencies
  • Add configuration for all IPE scientists (and setup IPE publication website)

Version 1.3, 23.5.17 (ak):

  • generated python inline documentation

Version 1.2, 24.4.17 (ak):

  • move complete configuration of author lists to config file
  • removed old list of Scopus author keys in my_scopus.py
  • added Philipp Lösel to the author list
  • added config management in etc
  • added log file

Version 1.1, 12.4.17 (ak):

  • added a second script to synchronize publication database and posts in wordpress
  • pushed repository to IPE GIT server
  • using markup for documentation
  • added configration file to become site indepandant

Version 1.0, 8.3.17 (ak):

  • initial version of a single script without any options It runs in 4 phases: get publiations for individual author groups, create posts, get all citations, create comments.
  • used with the test installation at the UFO server in March 2017

Content

readme.md       This file
config.py       Site dependant configuration file (in GIT as config.py.sample)
scopus-rawdata.py 		Display the complete dataset for a publication in Scopus
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
scopus-update-database.py   Synchronize database and available Wordpress posts

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
test-wp.py	Test script for access to the wordpress API	
test-wp2.py 	Test script for wordpress - only query, no modification

etc		Configuration files of different installations
info            Documentation, website, etc (not in GIT)
log		Log file use scopus-publications-<hostname>.log 

Usage

  1. Go to Scopus and retrieve the scopus author ids for the scientists in your group. Define the ids in etc/config-.py and group them.

  2. Create a symbolic link

    ln -s etc/config-<hostname>.py  config.py
    
  3. Select one of more author groups and define the list sc_workgroups in config.py Check the definition of database and wordpress installation.

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

  5. 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
    

    Dump datasets

    Use the Python script scopus-rawdata.py to get the full dataset of a certain publication. The script is intended for usage in a web browser. Most browsers have pulgins to print formated JSON output.

    Example:

    http://localhost/~kopmann/scopus/scopus-rawdata.py?85042753214
    

    Scrennshot

    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!? This would have the nice effect, that all student work is organized systematically!!!

    • keywords

    Configuration

    For each site database, access to wordpress and the author profiles need to be configured in config.py.

    For the UFO webpage the configuration looks like diplayed below. In the first part the access to the database is configured. The database is used as a cache to keep track which publications are already available in Wordpress.

    In the second block the access to the Wordpress server is given. The specified user (e.g. called scopus) need to have editor permissions in order to submit new posts and to suggest keywords.

    For the access to scopus a key is required.

    The main part of the configuration is dedicated to author identification and grouping of authors. At first variables for each author are defined. If a author is registered with more than one Scopus ID also these IDs should be added.

    Finally in the variable sc_workgroups a named list of all groups of authors that should be considered is defined. The name of the groups need to be defined in Wordpress as categories. The slug name of the category in wordpress is used in the configuration file as identification of the author group.

    Config.py:

    """ Scopus script's configration
        
        *A Kopmann, 12.4.17*
    
    Configuration for the active setup at ufo.kit.edu
    
    """
    
    # Local publication database
    
    db_host = 'localhost'
    db_user = 'scopus'
    db_pw = '$scopus$'
    db_name = 'scopus'
    
    
    # Access to Wordpress installation
    
    wp_api_url = "https://ufo.kit.edu/dis/xmlrpc.php"
    """ Access to the Wordpress installation """
    wp_user = "scopus"
    wp_password = "$scopus$"
    
    
    # Reporting
    
    log_file = "/root/scopus/log/scopus-publications-ufo-kit-edu.log"
    """ Logfile name for reporting """
    
    
    # Scopus query definition
    
    MY_API_KEY = "14d431d052c2caf5e9c4b1ab7de7463d"
    """ Scopus access key (Andreas Kopmann) """
    DTS_API_KEY = "f2b35fe46478f22f3c14cf53f73d4f93"
    
    # Scopus author IDs
    
    # KIT, PDV
    ak = "35313939900"
    ak2 = "57193311016"
    csa = "15076530600"
    matthiasVogelgesang = "35303862100"
    timoDritschler = "56473578500"
    andreiShkarin = "56950893700"
    nicholasTanJerome = "57200247965"
    tillBergmann = "35308595100"
    armenBeglarian = "55343303900"
    petraRohr = "40561503300"
    norbertKunka = "35276889200"
    horstDemattio = "6506285395"
    
    # KIT, EPS
    micheleCaselle = "57194376511"
    mc2 = "57194376512"
    urosStevanovic = "55557712600"
    lorenzoRota = "56473442500"
    matthiasBalzer = "35519411500"
    
    # KIT, IPE
    marcWeber = "56654729000"
    mw2 = "56603987800"
    mw3 = "7404138824"
    
    # KIT, IPE
    marcWeber = "56654729000"
    mw2 = "56603987800"
    mw3 = "7404138824"
    
    # KIT, IPS
    tomyRolo = "56118820400"
    tr2 = "35194644400"
    tr3 = "35277157300"
    tomasFarago = "56655045700"
    alexyErshof = "56441809800"
    romanShkarin = "56951331000"
    tiloBaumbach = "7003270957"
    thomasVandekamp = "46761453500"
    danielHaenschke = "55532222200"
    
    # TUD
    michaelHeethoff = "55979397800"
    sebastianSchmelzle = "34768986100"
    
    # UHD, has been combined with another person in Munich !!!
    philipLoesel = "57203423658"
    
    # Others (e.g. for black list)
    ashotChiligarian = "7004126133"
    hansBluemer = "7006284555"
    matthiasKleifegs = "6602072426"
    
    # Definition of workgroups for automatic Scopus publication retrieval
    
    sc_start = 2010
    sc_citations = False
    sc_keywords = True
    sc_max_authors = 25
    
    
    ufo_pdv = [ak, ak2, csa, matthiasVogelgesang, timoDritschler ]
    ufo_eps = [matthiasBalzer, lorenzoRota, micheleCaselle, mc2 ]
    ufo_ips = [tomyRolo, tr2, tr3, tomasFarago, danielHaenschke]
    ufo_apps = [thomasVandekamp]
    ufo_alg = [philipLoesel]
    
    sc_workgroups = [
    {'name':'computing','authors':ufo_pdv},
    {'name':'electronics','authors':ufo_eps},
    {'name':'x-ray-imaging','authors':ufo_ips},
    {'name':'morphology','authors':ufo_apps},
    {'name':'algorithms','authors':ufo_alg}
    ]
    """ Definition of the workgroups
        
        Each workgroup is defined by a list of Scopus ID's and the
        name of the category to be used in Wordpress. The category
        for a new workgroup has to be created in Wordpress before
        adding publications
        """
    
    
    

    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 publications:

    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"
            }
        }
    }
    

    Keywords in Scopus

    There are two types of keywords known in Scopus. Not all datasets have both fields. Most of them have the index terms (field: idxterms) that seem to be selected by Scopus. Many have additional keywords given by the author (field authkeywords.

    Often author keywords are used as index term. Index term always start with a capital letter, while author keywords are less systematic. Somtimes author keywords are very long, with brackets and semicolon.

    The question is how to use this keywords. Are there some that apprear in more than one article. This one might be used to find similar articles in Wordpress later!?

    Should I take both keywords, or should I use the index terms, although I don't know where they come from? Does it make sense to modify the keywords once there are in Wordpress???

    Für wordpress macht es wahrscheinlich Sinn die Keywords auf zwei bis drei Wörter zu beschränken und die anderen einfach weg zu lassen, da sie doch nicht zweimal auftreten werden!

    ipekopmann2:scopus kopmann$ python test-scopus.py 
    ==> Index terms:
    Drying at ambient conditions
    High complexity
    Line of Sight
    On-line analysis
    Parallel computing architecture
    Particle image velocimetries
    Polymer Coating
    Thin polymer films
    !!! Error encoding title of publication !!!
    Cavadini P., Weinhold H., Tonsmann M., Chilingaryan S., Kopmann A., Lewkowicz A., Miao C., Scharfer P., Schabel W.: Investigation of the flow structure in thin polymer films using 3D µPTV enhanced by GPU, Experiments in Fluids, 59, 4 (2018-04-01) 61, doi:10.1007/s00348-017-2482-z (cited 0 times).
    
    Chilingarian A., Chilingaryan S., Karapetyan T., Kozliner L., Khanikyants Y., Hovsepyan G., Pokhsraryan D., Soghomonyan S.: On the initiation of lightning in thunderclouds, Scientific Reports, 7, 1 (2017-12-01) 1371, doi:10.1038/s41598-017-01288-0 (cited 3 times).
    
    ==> Index terms:
    Free space propagation
    High speed imaging
    Parallelizations
    simulation
    Xray imaging
    ==> Keywords:
    coherence
    free-space propagation
    high-speed imaging
    parallelization
    simulation
    synchrotron radiation
    X-ray imaging
    Farago T., Mikulik P., Ershov A., Vogelgesang M., Hanschke D., Baumbach T.: Syris: A flexible and efficient framework for X-ray imaging experiments simulation, Journal of Synchrotron Radiation, 24, 6 (2017-11-01) 1283-1295, doi:10.1107/S1600577517012255 (cited 0 times).
    
    ==> Index terms:
    Direct communications
    High quality reconstruction
    High speed computing
    High-performance computing resources
    Online data processing
    Reconstruction algorithms
    Regularization methods
    Spatial and temporal resolutions
    Kopmann A., Chilingaryan S., Vogelgesang M., Dritschler T., Shkarin A., Shkarin R., Dos Santos Rolo T., Farago T., Van De Kamp T., Balzer M., Caselle M., Weber M., Baumbach T.: UFO - A scalable platform for high-speed synchrotron X-ray imaging, 2016 IEEE Nuclear Science Symposium, Medical Imaging Conference and Room-Temperature Semiconductor Detector Workshop, NSS/MIC/RTSD 2016, 2017-January (2017-10-16) 8069895, doi:10.1109/NSSMIC.2016.8069895 (cited 0 times).
    
    ==> Index terms:
    Computing (architecture, farms, GRID for recording, storage, archiving, and distribution of data)
    Data processing methods
    Dedicated hardware
    Floating point operations
    Hardware and software
    Hough Transformation
    Large Hadron collider LHC
    Modified algorithms
    ==> Keywords:
    Computing (architecture, farms, GRID for recording, storage, archiving, and distribution of data)
    Trigger algorithms; Data processing methods
    Trigger concepts and systems (hardware and software)
    Mohr H., Dritschler T., Ardila L.E., Balzer M., Caselle M., Chilingaryan S., Kopmann A., Rota L., Schuh T., Vogelgesang M., Weber M.: Evaluation of GPUs as a level-1 track trigger for the High-Luminosity LHC, Journal of Instrumentation, 12, 4 (2017-04-21) C04019, doi:10.1088/1748-0221/12/04/C04019 (cited 0 times).
    
    ==> Index terms:
    Advanced mezzanine cards
    Board support packages
    Commercial components
    Component based approach
    Detector control systems
    Front end electronics
    Parallel-computing environment
    Research and development
    ==> Keywords:
    Data acquisition concepts
    Detector control systems (detector and experiment monitoring and slow-control systems, architecture, hardware, algorithms, databases)
    Image reconstruction in medical imaging
    Software architectures (event data models, frameworks and databases)
    Kaever P., Balzer M., Kopmann A., Zimmer M., Rongen H.: The Common Data Acquisition Platform in the Helmholtz Association, Journal of Instrumentation, 12, 4 (2017-04-03) C04004, doi:10.1088/1748-0221/12/04/C04004 (cited 0 times).
    
    ==> Index terms:
    Computing nodes
    Direct communications
    Event building
    Future generations
    Hardware and software
    High-level triggers
    Internal memory
    Trigger systems
    ==> Keywords:
    Data acquisition concepts
    Trigger concepts and systems (hardware and software)
    Caselle M., Perez L.E.A., Balzer M., Dritschler T., Kopmann A., Mohr H., Rota L., Vogelgesang M., Weber M.: A high-speed DAQ framework for future high-level trigger and event building clusters, Journal of Instrumentation, 12, 3 (2017-03-06) C03015, doi:10.1088/1748-0221/12/03/C03015 (cited 1 times).
    
    ==> Index terms:
    Accelerator physics
    Coherent synchrotron radiation
    Data acquisition system
    Electronic detectors
    High repetition rate
    Radiation accelerators
    Sampling accuracies
    Terahertz detectors
    ==> Keywords:
    Data acquisition concepts
    Electronic detector readout concepts (solid-state)
    Instrumentation for synchrotron radiation accelerators
    Caselle M., Perez L.E.A., Balzer M., Kopmann A., Rota L., Weber M., Brosi M., Steinmann J., Brundermann E., Muller A.-S.: KAPTURE-2. A picosecond sampling system for individual THz pulses with high repetition rate, Journal of Instrumentation, 12, 1 (2017-01-16) C01040, doi:10.1088/1748-0221/12/01/C01040 (cited 0 times).
    
    ==> Index terms:
    Conventional approach
    Micro-tomography
    Phase contrasts
    Photosynthetic activity
    Physiological activity
    Picea Abies (L.) Karst
    Spruce
    Tracheid
    ==> Keywords:
    Absorption contrast
    Microtomography
    Phase contrast
    Spruce
    Synchrotron radiation
    Tracheid
    Wood
    !!! Error encoding title of publication !!!
    Lautner S., Lenz C., Hammel J., Moosmann J., Kuhn M., Caselle M., Vogelgesang M., Kopmann A., Beckmann F.: Using SRμCT to define water transport capacity in Picea abies, Proceedings of SPIE - The International Society for Optical Engineering, 10391 (2017-01-01) 1039118, doi:10.1117/12.2287221 (cited 3 times).
    
    ==> Index terms:
    Data catalog
    Insect head
    Interactive interfaces
    Scientific data
    Semi-automatic segmentation
    Synchrotron x rays
    Visual data
    Web visualization
    ==> Keywords:
    3D web visualization
    Cooperative data analysis
    Data catalog
    Insect head
    Interactive interfaces
    Semi-automatic segmentation
    Synchrotron X-ray micro computed tomography
    Virtual Reality for scientific data
    Visual data browsing
    Web portal for scientific data
    !!! Error encoding title of publication !!!
    Schmelzle S., Heethoff M., Heuveline V., Losel P., Becker J., Beckmann F., Schluenzen F., Hammel J.U., Kopmann A., Mexner W., Vogelgesang M., Jerome N.T., Betz O., Beutel R., Wipfler B., Blanke A., Harzsch S., Hornig M., Baumbach T., Van De Kamp T.: The NOVA project: Maximizing beam time efficiency through synergistic analyses of SRμCT data, Proceedings of SPIE - The International Society for Optical Engineering, 10391 (2017-01-01) 103910P, doi:10.1117/12.2275959 (cited 0 times).
    
    ==> Index terms:
    Astroparticle physics
    DAQ system
    Dark matter
    Data acquisition system
    Direct search
    Germaniums (Ge)
    High-rate channels
    Underground laboratory
    Bergmann T., Balzer M., Bormann D., Chilingaryan S.A., Eitel K., Kleifges M., Kopmann A., Kozlov V., Menshikov A., Siebenborn B., Tcherniakhovski D., Vogelgesang M., Weber M.: A scalable DAQ system with high-rate channels and FPGA- and GPU-Trigger for the dark matter experiment EDELWEISS-III, 2015 IEEE Nuclear Science Symposium and Medical Imaging Conference, NSS/MIC 2015 (2016-10-03) 7581841, doi:10.1109/NSSMIC.2015.7581841 (cited 2 times).
    
    ==> Index terms:
    Computational power
    Digital electronic circuits
    Direct memory access
    Direct memory transfers
    Hardware and software
    High performance computing
    High-performance computing applications
    Intrinsic parallelisms
    ==> Keywords:
    Data acquisition concepts
    Digital electronic circuits
    Trigger concepts and systems (hardware and software)
    Rota L., Vogelgesang M., Perez L.E.A., Caselle M., Chilingaryan S., Dritschler T., Zilio N., Kopmann A., Balzer M., Weber M.: A high-throughput readout architecture based on PCI-Express Gen3 and DirectGMA technology, Journal of Instrumentation, 11, 2 (2016-02-12) P02007, doi:10.1088/1748-0221/11/02/P02007 (cited 5 times).
    
    ==> Index terms:
    Data acquisition system
    Experiment platforms
    GPU computing
    High-throughput data
    OpenCL
    Programmable hardware
    Real-time operation
    Synchrotron beamlines
    ==> Keywords:
    Data acquisition
    data processing
    FPGA
    FPGA-GPU communication
    GPU computing
    OpenCL
    Vogelgesang M., Rota L., Perez L.E.A., Caselle M., Chilingaryan S., Kopmann A.: High-throughput data acquisition and processing for real-time X-ray imaging, Proceedings of SPIE - The International Society for Optical Engineering, 9967 (2016-01-01) 996715, doi:10.1117/12.2237611 (cited 0 times).
    
    Ametova E., Ferrucci M., Chilingaryan S., McCarthy M., Dewulf W.: Uncertainty quantification in dimensional measurements by computed tomography due to uncertainty in data acquisition geometrical parameters, Proceedings - ASPE 2016 Annual Meeting (2016-01-01) 287-292 (cited 0 times).
    
    ==> Index terms:
    Architecture-based
    Building blockes
    Efficient construction
    High-level control systems
    Laminography
    Real time images
    Realtime processing
    Synchrotron radiation facility
    High-throughput data
    Work-flow systems
    ==> Keywords:
    control
    laminography
    tomography
    Vogelgesang M., Farago T., Morgeneyer T.F., Helfen L., Dos Santos Rolo T., Myagotin A., Baumbach T.: Real-time image-content-based beamline control for smart 4D X-ray imaging, Journal of Synchrotron Radiation, 23 (2016-01-01) 1254-1263, doi:10.1107/S1600577516010195 (cited 6 times).
    
    ==> Index terms:
    Armenia
    Energy spectra
    Energy thresholds
    Enhancements
    Ground
    Solar cosmic rays
    ==> Keywords:
    Atmospheric electricity
    Enhancements
    Ground
    Particle detectors
    Thunderstorm
    Chilingarian A., Chilingaryan S., Hovsepyan G.: Calibration of particle detectors for secondary cosmic rays using gamma-ray beams from thunderclouds, Astroparticle Physics, 69 (2015-09-01) 37-43, doi:10.1016/j.astropartphys.2015.03.011 (cited 3 times).
    
    ==> Keywords:
    atmospheric electricity
    radiation in atmosphere
    Chilingarian A., Chilingaryan S., Reymers A.: Atmospheric discharges and particle fluxes, Journal of Geophysical Research A: Space Physics, 120, 7 (2015-07-01) 5845-5853, doi:10.1002/2015JA021259 (cited 2 times).
    
    ==> Index terms:
    Data throughput
    Direct memory access
    High-speed data
    PCI Express
    Readout Electronics
    ==> Keywords:
    Data Acquisition
    direct memory access
    FPGA
    high data throughput
    high speed data streaming applications
    PCI express
    readout electronics
    Rota L., Caselle M., Chilingaryan S., Kopmann A., Weber M.: A PCIe DMA Architecture for Multi-Gigabyte per Second Data Transmission, IEEE Transactions on Nuclear Science, 62, 3 (2015-06-01) 972-976, doi:10.1109/TNS.2015.2426877 (cited 9 times).
    
    ==> Index terms:
    CMOS image sensor
    Complementary metal-oxide-semiconductor sensor (CMOS)
    Data acquisition system
    Embedded processing
    Material science
    Smart cameras
    Synchrotron radiation facility
    Temporal evolution
    ==> Keywords:
    CMOS image sensors
    control systems
    data processing
    FPGAs
    smart cameras
    Stevanovic U., Caselle M., Cecilia A., Chilingaryan S., Farago T., Gasilov S., Herth A., Kopmann A., Vogelgesang M., Balzer M., Baumbach T., Weber M.: A control system and streaming DAQ platform with image-based trigger for X-ray imaging, IEEE Transactions on Nuclear Science, 62, 3 (2015-06-01) 911-918, doi:10.1109/TNS.2015.2425911 (cited 2 times).
    
    ==> Index terms:
    Coherent synchrotron radiation
    Continuous sampling
    Data throughput
    Intrinsic response
    Peak amplitude
    Synchrotron light source
    Terahertz pulse
    Thin film detectors
    Caselle M., Brosi M., Chilingaryan S., Dritschler T., Judin V., Kopmann A., Mueller A.-S., Raasch J., Smale N.J., Steinmann J., Vogelgesang M., Wuensch S., Siegel M., Weber M.: An ultra-fast digitizer with picosecond sampling time for Coherent Synchrotron Radiation, 2014 19th IEEE-NPSS Real Time Conference, RT 2014 - Conference Records (2015-04-28) 7097535, doi:10.1109/RTC.2014.7097535 (cited 2 times).
    

    Installation of tools

    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
    

    Run the installer:

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

    Installation Scopus-Scripts:

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

    Check configurations:

    scopus-get-piblications.py
    ak_wordpress.py
    

    Limitations

    Sometimes there are errors in the database. This case required manual intervention.

    Eamples of error that have been observed:

    • The cover date is quite far in the future. In this case the post do not appear on the website but are marked as scheduled. The date of publication should be looked up at the journal page and corrected manually.
    • Some authors are listed with more than one id. In this case the merge of author ids should be requested. The second author id cann be added the the author list.
    • In rare case (scientists with common names) several persons share the same id. Splitting of accounts should be requested. Wrong publications need to be deleted manually.
    • Publications that are out of topic can't be excluded automatically
    • Reprocessing of categories is currently not foreseen
    • It is not clear how to deal with scientists that leave a group. When should the name be excluded. It migth be desirable to check for authors and their affiliation.