Inspire installation from sources

About Inspire source code repository

Inspire uses Git as its source code management system. The official source code repository is hosted alongside the standard Invenio source code repository and can be browsed via a git repo web interface. For example, you can subscribe to an RSS feed there in order to follow recent Inspire source code changes.

The main repository is named inspire and it is an "overlay" repository containing customization of templates and formats to change the "look and feel" as well as functionality of the Inspire site.

An additional repository called invenio-inspire-ops is the operational repository for the Inspire production servers. It contains modifications and addition to the Invenio core modules that does not fit into the normal Inspire overlay repository.

How to obtain Inspire sources

How to obtain Inspire-specific sources:

   $ git clone http://invenio-software.org/repo/inspire

How to obtain Inspire-operations sources:

   $ git clone http://invenio-software.org/repo/invenio-inspire-ops

How to install Inspire test site

INSPIRE sources are to be installed after the Invenio sources. You can customize some things in config-local.mk, for example on Debian GNU/Linux, the standard apache user is www-data:

   $ cat config-local.mk
   INSTALL = install -g www-data -m 775

(Replace www-data with your own if you have configured it so.)

Any required Python packages can be installed by running the following command inside the root inspire source folder:

  $ pip install -r requirements.txt

To install a small INSPIRE demo site from scratch, you can use:

  • `inspire-recreate-demo-site' helper devscript, see instructions at [https://github.com/tiborsimko/inspire-devscripts#installation]
or
  • alternatively, you can follow the steps below one-by-one.

Step-by-step guide

This is a step-by-step guide to install Inspire sources including demo records.

1. If you do not already have Invenio installed, build a clean (no test records) Invenio demo site from Invenio git sources, following the InspireInvenioInstallation guide, such as:

      $ git clone http://invenio-software.org/repo/invenio
      $ cd invenio

      $ aclocal-1.9
      $ automake-1.9 -a
      $ autoconf

      $ ./configure
      $ make
      $ make install

      $ inveniocfg --create-tables \
                          --create-demo-site \
                          --yes-i-know

Or, if you already have an Invenio demo site up and running, then just clean away its demo records:

      $ inveniocfg --drop-demo-site \
                          --create-demo-site \
                          --yes-i-know

2. For Inspire you need to modify the standard invenio-local.conf to activate some special options.

    $ cat /opt/invenio/etc/invenio-local.conf
    [Invenio]
    ### BEGIN-customize-me
    CFG_SITE_URL = http://localhost
    CFG_SITE_SECURE_URL = https://localhost
    CFG_SITE_SUPPORT_EMAIL = root@localhost
    CFG_SITE_ADMIN_EMAIL = root@localhost
    CFG_WEBALERT_ALERT_ENGINE_EMAIL = root@localhost
    CFG_WEBCOMMENT_ALERT_ENGINE_EMAIL = root@localhost
    CFG_WEBCOMMENT_DEFAULT_MODERATOR = root@localhost
    CFG_WEBALERT_ALERT_ENGINE_EMAIL = root@localhost
    CFG_BIBAUTHORID_AUTHOR_TICKET_ADMIN_EMAIL = root@localhost
    #CFG_DATABASE_HOST = localhost
    #CFG_DATABASE_PORT = 3306
    #CFG_DATABASE_NAME = cdsinvenio
    #CFG_DATABASE_USER = cdsinvenio
    #CFG_DATABASE_PASS = my123p$ss
    #CFG_BIBDOCFILE_USE_XSENDFILE = 1
    ### END-customize-me
    CFG_SITE_LANG = en
    CFG_SITE_LANGS = bg,ca,de,el,en,es,fr,hr,it,ja,no,pl,pt,ru,sk,sv,zh_CN,zh_TW
    CFG_SITE_NAME = HEP
    CFG_SITE_NAME_INTL_en = HEP
    CFG_SITE_NAME_INTL_fr = HEP
    CFG_SITE_NAME_INTL_de = HEP
    CFG_SITE_NAME_INTL_es = HEP
    CFG_SITE_NAME_INTL_ca = HEP
    CFG_SITE_NAME_INTL_pt = HEP
    CFG_SITE_NAME_INTL_it = HEP
    CFG_SITE_NAME_INTL_ru = HEP
    CFG_SITE_NAME_INTL_sk = HEP
    CFG_SITE_NAME_INTL_cs = HEP
    CFG_SITE_NAME_INTL_no = HEP
    CFG_SITE_NAME_INTL_sv = HEP
    CFG_SITE_NAME_INTL_el = HEP
    CFG_SITE_NAME_INTL_uk = HEP
    CFG_SITE_NAME_INTL_ja = HEP
    CFG_SITE_NAME_INTL_pl = HEP
    CFG_SITE_NAME_INTL_bg = HEP
    CFG_SITE_NAME_INTL_hr = HEP
    CFG_SITE_NAME_INTL_zh_CN = HEP
    CFG_SITE_NAME_INTL_zh_TW = HEP
    CFG_BIBINDEX_FULLTEXT_INDEX_LOCAL_FILES_ONLY = 1
    CFG_WEBSTYLE_TEMPLATE_SKIN = inspire
    CFG_WEBSEARCH_INSTANT_BROWSE = 0
    CFG_WEBSEARCH_SPLIT_BY_COLLECTION = 0
    CFG_INSPIRE_SITE = 1
    CFG_ACCESS_CONTROL_LEVEL_ACCOUNTS = 5
    CFG_WEBCOMMENT_ALLOW_COMMENTS = 0
    CFG_WEBCOMMENT_ALLOW_REVIEWS = 0
    CFG_WEBCOMMENT_ALLOW_SHORT_REVIEWS = 0
    CFG_WEBSEARCH_DEF_RECORDS_IN_GROUPS = 25
    CFG_WEBSEARCH_NB_RECORDS_TO_SORT = 5000
    CFG_WEBSEARCH_USE_MATHJAX_FOR_FORMATS = hb,hd
    CFG_WEBSUBMIT_FILESYSTEM_BIBDOC_GROUP_LIMIT = 20000
    CFG_BIBUPLOAD_FFT_ALLOWED_LOCAL_PATHS = /tmp,/afs/cern.ch/project/inspire
    CFG_WEBSEARCH_FULLTEXT_SNIPPETS = 5
    CFG_WEBSEARCH_FULLTEXT_SNIPPETS_WORDS = 10
    CFG_WEBSEARCH_FIELDS_CONVERT = {'eprint':'reportnumber','bb':'reportnumber',
                                'bbn':'reportnumber','bull':'reportnumber',
                                'r':'reportnumber','rn':'reportnumber',
                                'cn':'collaboration','a':'author',
                                'au':'author','name':'author',
                                'ea':'exactauthor','exp':'experiment',
                                'expno':'experiment','sd':'experiment',
                                'se':'experiment','j':'journal',
                                'kw':'keyword', 'keywords':'keyword',
                                'k':'keyword', 'au':'author', 'ti':'title',
                                't':'title', 'irn':'970__a',
                                'institution':'affiliation',
                                'inst':'affiliation', 'affil':'affiliation',
                                'aff':'affiliation', 'af':'affiliation',
                                'topic':'695__a','tp':'695__a','dk':'695__a',
                                'date':'year','d':'year','date-added':'datecreated',
                                'da':'datecreated','dadd':'datecreated',
                                'date-updated':'datemodified','dupd':'datemodified',
                                'du':'datemodified','vol':'volume',}
    CFG_BIBRANK_SHOW_DOWNLOAD_GRAPHS_CLIENT_IP_DISTRIBUTION = 0
    CFG_BIBRANK_SHOW_DOWNLOAD_GRAPHS = 0
    CFG_BIBRANK_SHOW_DOWNLOAD_STATS = 0
    CFG_BIBINDEX_AUTHOR_WORD_INDEX_EXCLUDE_FIRST_NAMES = True
    CFG_WEBSEARCH_SEARCH_CACHE_SIZE = 0
    CFG_WEBSTYLE_HTTP_STATUS_ALERT_LIST = 400,5*,41*
    CFG_WEBSEARCH_SYNONYM_KBRS = {
    'journal': ['JOURNALS', 'leading_to_comma'],
    'collection': ['COLLECTION', 'exact'],
    'subject': ['SUBJECT', 'exact'],
    }
    CFG_BIBEDIT_QUEUE_CHECK_METHOD = regexp
    CFG_WEBSEARCH_SPIRES_SYNTAX = 9
    CFG_PLOTEXTRACTOR_SOURCE_BASE_URL = http://export.arxiv.org/
    CFG_SELFCITES_USE_BIBAUTHORID = 1
    CFG_SELFCITES_PRECOMPUTE_FRIENDS = 0
    CFG_WEBSEARCH_DISPLAY_NEAREST_TERMS = 0
    #CFG_REFEXTRACT_TICKET_QUEUE = Inspire-References
    #CFG_REFEXTRACT_KBS_OVERRIDE = {'journals': 'kb:docextract-journals'}
    CFG_BIBUPLOAD_STRONG_TAGS = 999,084
    CFG_BIBFORMAT_DISABLE_I18N_FOR_CACHED_FORMATS = ha,hb,hs,hx,hdref
    CFG_WEBAUTHORPROFILE_USE_BIBAUTHORID = 1
    CFG_BIBDOCFILE_ENABLE_BIBDOCFSINFO_CACHE = 1
    CFG_WEBSEARCH_CITESUMMARY_SELFCITES_THRESHOLD = 0
    CFG_BASE_URL =
    CFG_BIBDOCFILE_DOCUMENT_FILE_MANAGER_DOCTYPES = [('INSPIRE-PUBLIC', 'INSPIRE-PUBLIC'),
                                                 ('arXiv', 'arXiv'),
                                                 ('Springer','Springer'),
                                                 ('JHEP','JHEP'),
                                                 ('Hindawi','Hindawi'),
                                                 ('APS','APS'),
                                                 ('Plot','Plot'),
                                                 ('PlotMisc', 'PlotMisc'),
                                                 ('Supplementary Material','Supplementary Material'),
                                                 ('Data','Data')]
    CFG_BIBFORMAT_CACHED_FORMATS =

Remember to update the configuration:

      $ inveniocfg --update-all

3. Apply Inspire-specific code and templates from Inspire sources:

      $ cd ..
      $ git clone http://invenio-software.org/repo/inspire
      $ cd inspire
      $ vim config.mk ## verify that PREFIX matches the above --prefix and that INSTALL is correct
      $ make install

4. Apply INSPIRE specific DB configurations and content.

      $ make install-dbchanges

If you are prompted for a username, type admin. To avoid typing this you can add the global environmental variable in your .bashrc:

      $ export CFG_INSPIRE_BIBTASK_USER=admin

5. Load test records from SPIRES:

      $ make load-demo-records
      $ bibsched ## run any waiting bibupload tasks
      $ bibindex -u admin -s5m ## index records
      $ bibrank -u admin -s5m ## rank records -- needed e.g. for citations
      $ webcoll -u admin -s5m ## regenerate search collection cache

How to run reference extraction without installing Invenio

If you want to run the reference extraction script without having to do the full Invenio installation, you can follow these steps:

    ## Download Git sources of Invenio:
    $ git clone http://invenio-software.org/repo/invenio

    ## Download a test article:
    $ wget -O /tmp/z.pdf http://doc.cern.ch/archive/electronic/hep-th/0101/0101001.pdf

    ## You have to go to the refextract folder in order to run it in a standalone mode:
    $ cd invenio/modules/bibedit/lib

    ## Run refextract with a fake record ID of 123 (say):
    $ python ./refextract.py 123:/tmp/z.pdf
    <?xml version="1.0" encoding="UTF-8"?>
    <collection xmlns="http://www.loc.gov/MARC21/slim">
    <record>
       <controlfield tag="001">123</controlfield>
       <datafield tag="999" ind1="C" ind2="5">
          <subfield code="o">[1]</subfield>
       </datafield>
       <datafield tag="999" ind1="C" ind2="5">
          <subfield code="m">T. Banks, W. Fischler, S. Shenker, L. Susskind "M Theory Ann. Sci. a Matrix Model a Conjecture,"</subfield>
          <subfield code="s">Phys. Rev., D 55 (1997) 5112</subfield>
          <subfield code="r">hep-th/9610043</subfield>
       </datafield>
        [...]

Note that running refextract in a standalone mode means that there is no checking of the location of required tools such as pdftotext. This location is hardcoded in the beginning of the refextract.py script.

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Topic revision: r20 - 2013-06-12 - JanLavik
 
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