BibEdit Admin Guide


1. Overview
2. Edit records via Web interface
       2.1. Keyboard shortcuts
3. Edit multiple records via Web interface
       3.1. Multi-Record Editor user guide
4. Edit records via command line
5. Delete records via command line
6. Delete all records
7. Access record history

1. Overview

BibEdit enables you to directly manipulate bibliographic data, edit a single record, do global replacements, and other cataloguing tasks.

2. Edit records via Web interface

To edit records via the web interface, please go to BibEdit Editor. This interface will let you add, change or delete fields in a record.

If you want to change several records at once, you can use the batch command-line techniques described below or the Multi-Record Editor.

Please note that 8564 tags pointing to fulltext files managed by Invenio can't be manipulated via BibEdit. In order to modify them please use the FFT tags through BibUpload or the bibdocfile command line tool.

2.1 Keyboard shortcuts on BibEdit

Basic record actions

Shortcut Definition Action
g Select Go to the record selection field
Ctrl+Right Next Go to next record (in search results).
Ctrl+Left Previous Go to previous record (in search results).
Shift+n New record Opens the new record dialog.
Shift+s Submit Submit the record.
Shift+c Cancel Cancel editing of the record.
Shift+l Clone Clone the record.
Shift+t Tags Toggle MARC/human tags.
a Add field Add a new, empty field.
s Open first field Opens first field for editing.
Del Delete selected Deletes all selected fields.

Focused (clicked) subfield or field

Shortcut Definition Action
Ctrl+Up Move up Move focused subfield up.
Ctrl+Down Move down Move focused subfield down.

Input field/form

Shortcut Definition Action
Esc Cancel Cancel edition of subfield
Ctrl+* Jump next Jump to next marc field
Ctrl+/ Jump previous Jump to previous marc field

Display modes

Shortcut Definition Action
Ctrl+Shift+r References Display only references
Ctrl+Shift+a Authors Display only authors
Ctrl+Shift+o Others Display only other fields
Ctrl+Shift+d All Display all fields

Other functionality

Shortcut Definition Action
Ctrl+Shift+z Undo Undo last action.
Ctrl+Shift+y Redo Redo last action.
Shift+p Open PDF Open attached PDF

3. Edit multiple records via web interface

The purpose of the Multi-Record Editor Web interface is to allow cataloguers to easily edit more than one record in one go.

The Multi-Record Editor allows cataloguers to easily look up various records in the system in order to find record sets upon which to operate, and then to allow some easy replacement procedures on these records in one go, e.g. a substring substitution of some field value in some field tags.

3.1 Multi-Record Editor user guide

While working with the Multi-Record Editor, the first step is to filter the set of records that are going to be modified.

In order to do that, three options are available in the interface:

        Search criteria:    [         ]
        Filter collection:  [         ]
        Output tags:        [         ]

After clicking the Search button, the set of records that will be affected by the changes will be visible at the bottom of the interface. It is possible to specify whether to visualize them in MARC format or in HTML Brief format.

The next step is to specify the desired changes to be made on the records. When defining a new field action, the field tag and its indicators (if necessary) have to be specified and one of the three actions (Add field, Delete field, Update field) selected.

    [ tag ][ind1][ind2]     [Select action[V]]

After that, as many actions on subfields as needed can be defined. The subfield tag has to be specified and one action (Add subfield, Delete subfield, Replace full content, Replace substring) selected. Depending on the field action selected some actions for subfields will not be available.

The difference between Replace full content and Replace substring resides in that the former deletes all the content present in a subfield and writes the specified value on it whereas the latter looks for a string and substitutes it by a new string.

All subfield actions have the Apply only to specific field instances option. This is useful, for example, in cases where there are multiple authors (700__ tags) and we do not want to act in all of them.

In that case one could add the condition that only fields where the tag $a is equal to Ellis A. should be modified.

    700__   Update Field
            [u] [Replace full content]
                [Ellis J.]
            when other subfield [u] is equal to [Ellis A.]

Every subfield action defined has to be saved using the correspondent button before applying the changes.

Once all the actions for fields and subfields have been specified the modifications can be previewed using the corresponding button.

Finally, when clicking on the Apply changes button all modifications will be sent to the server and will be visible after some time.

4. Edit records via command line

The idea is to download record in XML MARC format, edit it by using any editor, and upload the changes back. Note that you can edit any number of records at the same time: for example, you can download all records written by Qllis, J, open the file in your favourite text editor, and change globally the author name to the proper form Ellis, J.

You therefore continue as follows:

  1. Download the record in XML MARC. For example, download record ID 1234:
             $ wget -O z.xml ''
    or download latest 5,000 public documents written by Qllis, J:
             $ wget -O z.xml ''
    Note also that you can access history of records as covered in a access record history section below.

  2. Edit the metadata as necessary:
             $ emacs z.xml
  3. Upload changes back:
             $ bibupload -r z.xml
  4. See the progress of the treatment of the file via BibSched:
             $ bibsched
    If you do not want to wait for the next wake-up time of indexing and formatting daemons, launch them manually now:
             $ bibindex
             $ bibreformat
             $ webcoll
    and watch the progress via bibsched.

After which the record(s) should be fully modified and formatted and all indexes and collections updated, as necessary.

5. Delete records via command line

Once a record has been uploaded, we prefer not to *destroy* it fully anymore (i.e. to wipe it out and to reuse its record ID for another record) for a variety of reasons. For example, some users may have put this record already into their baskets in the meantime, or the record might have already been announced by alert emails to the external world, or the OAI harvestors might have harvested it already, etc. We usually prefer only to *mark* records as deleted, so that our record IDs are ensured to stay permanent.

Thus said, the canonical way to delete the record #1234 in Invenio v0.1.x development branch is to download its XML MARC:

       $ wget -O z.xml ''
and to mark it as deleted by adding the indicator ``DELETED'' into the MARC 980 $$c tag:
       $ emacs z.xml
        <datafield tag="980" ind1=" " ind2=" ">
          <subfield code="a">PREPRINT</subfield>
          <subfield code="c">DELETED</subfield>
and upload thusly modified record in the `replace' mode:
       $ bibupload -r z.xml
and watch the progress via bibsched, as mentioned in the section 3.

This procedure will remove the record from the collection cache so that the record won't be findable anymore. In addition, if the users try to access this record via direct URL such as distributed by the alert engine (record/1234) or via their baskets, they will see a message ``This record has been deleted''. Please note though that the original MARCXML of the record stays kept in the database, for example you can access it by:

   $ python -c "from zlib import decompress; \\
                from invenio.dbquery import run_sql; \\
                print decompress(run_sql('SELECT value FROM bibfmt \\
                WHERE id_bibrec=1234 AND format=\'xm\'')[0][0])"

In some cases you may want to hide the record from the searches, but to leave it accessible via direct URLs or via baskets. In this case the best it to alter its collection tag (980) to some non-existent collection, for example:

   $ wget -O z.xml 'http:://localhost/record/1234?of=xm'
   $ perl -pi -e 's,ARTICLE,HIDDENARTICLE,g' z.xml
   $ bibupload -r z.xml
This will make the record non-existent as far as the search engine is concerned, because it won't belong to any existing collection, but the record will exist ``on its own'' and the users knowing its recID will be able to access it.

P.S. Note that the ``bibXXx'' tables will keep having entries for the deleted records. These entries are to be cleaned from time to time by the BibEdit garbage collector. This GC isn't part of Invenio yet; moreover in the future we plan to abolish all the bibXXx tables, so that this won't be necessary anymore.

6. Delete all records

If you want to wipe out all the existing bibliographic content of your site, for example to start uploading the documents from scratch again, you can launch:

       $ /opt/invenio/bin/dbexec < /opt/invenio/src/invenio-0.90/modules/miscutil/sql/tabbibclean.sql
       $ rm -rf /opt/invenio/var/data/files/*
       $ /opt/invenio/bin/webcoll
       $ /opt/invenio/bin/bibindex --reindex
Note that you may also want to delete the fulltext files and the submission counters in /opt/invenio/var/data subdirectories, if you use WebSubmit.

7. Access record history

Every revision of the metadata of a record is stored in the "history" table containing all previous MARCXML master formats of the record. You can access them via the bibedit command line utility.

To list previous revisions of record ID 1:

     $ /opt/invenio/bin/bibedit --list-revisions 1

To get MARCXML of the revision 1.20080318172536 (record ID 1, revision date 2008-03-18 17:25:36):

     $/opt/invenio/bin/bibedit --get-revision 1.20080318172536 | head -5
       <controlfield tag="001">1</controlfield>
       <datafield tag="037" ind1=" " ind2=" ">
         <subfield code="a">CERN-EX-0106015</subfield>

To compare the differences between the two last revisions:

     $ /opt/invenio/bin/bibedit --diff-revisions 1.20080318172536 1.20080319193118
     --- 1.20080318172536
     +++ 1.20080319193118
     @@ -4,7 +4,7 @@
          <subfield code="a">CERN-EX-0106015</subfield>
        <datafield tag="100" ind1=" " ind2=" ">
     -    <subfield code="a">Photolab</subfield>
     +    <subfield code="a">Photolab SOME TEST EDIT HERE</subfield>
        <datafield tag="245" ind1=" " ind2=" ">
          <subfield code="a">ALEPH experiment: Candidate of Higgs boson production</subfield>
     @@ -26,7 +26,7 @@
        <datafield tag="650" ind1="1" ind2="7">
          <subfield code="2">SzGeCERN</subfield>
     -    <subfield code="a">Experiments and Tracks</subfield>
     +    <subfield code="a">Experiments and Tracks SOME TEST EDIT THERE</subfield>
        <datafield tag="653" ind1="1" ind2=" ">
          <subfield code="a">LEP</subfield>