refbase - User contributions [en]

Sharing records

2023-11-22T20:57:02Z

WikiSysop: Hide section edit links

This document describes how to share records & bibliographies among different users and answers sharing-related questions.

== Benefits of sharing your bibliographic records with other users ==

refbase was developed to allow different users to share the same pool of bibliographic records. By collaboratively working on the same bibliographic dataset, members of a research group can work more efficiently since it means less work for each individual group member. A shared reference database will also help everyone in the group to stay on top of the most recent literature. In addition, it allows you to build shared bibliographies and fulltext repositories for particular research topics, groups or authors.

== How can I share a record with others? ==

By default, a record is "owned" by the person who added or imported it. For each record, the name of the record's owner is listed at the beginning of the ''location'' field which is shown in details view (but can also be displayed in list view using the [[Display Options]] form).

You can "subscribe" to an existing record (that's owned by somebody else) using these steps:

* Login to your refbase database.
* Find the record you'd like to add to your own library of records.
* Click the 'edit record' link (the little "pencil" icon) that's displayed next to your record.
* At the very bottom of the displayed editing form, choose ''''add''' my name & email address' from the drop-down menu.
* Click the 'Save Changes' button.

<div class="right-sidebar">[[image:SubscribeToRecord.jpg|thumb|How to add a record to your library]]</div>

This will add the record to your own library, and the record will be returned when clicking the 'My Refs' link on any search results page. Note that your name will also be appended to the contents of that record's ''location'' field, which tells other users that this record belongs to your personal library of records.

== Can everybody view & edit my own records? ==

Yes and no. refbase works similar to a [http://en.wikipedia.org/wiki/Wiki wiki] where every (logged-in) user is allowed to view & edit the common fields of every database record. This is done to encourage collaboration and generally helps to improve the quality of your records ([[Editing records|more info]]). However, the admin is able to globally disallow editing for particular users and future versions may allow for record-specific access control (see [[#Future plans|below]]).

It's also worth noting that every user has a list of private fields (we call them user-specific fields) which are marked with a yellow background color. Since each user will only be able to view & edit his own user-specific fields, you can rest assured that your input within these "yellow" fields will be kept private.

== How can I browse bibliographies of other users? ==

Want to see all records in the library of a particular user? This can be done by searching the ''location'' field for that user's name (or parts of it). The ''location'' field is availabe in [[Advanced Search]] as well as the [[Search within Results]] form that's displayed on any search results page. So, one way of displaying another user's entire library would be to click the 'Show All' link in the page header, then searching the ''location'' field for that user's name using the 'Search within Results' form. (see [[#Future plans|below]] for future plans regarding the browsing of other user's bibliographies)

As always, you can use the 'Search within Results' and 'Display Options' forms to further narrow down your search results and customize its display. If you've found some interesting records, you may want to subscribe to them (see [[#How can I share a record with others?|above]]) or add them to your personal groups. Also note that you can easily [[Recall My Query|save any search result set]] (including its current display settings) using the 'save' link in the page header. Results of any saved query can be easily recalled via the 'Recall My Query' form on the main page.

== How can I track literature on my research topic or from a particular author? ==

refbase offers several methods to discover newly added records that match a particular topic or author:

=== Links on main page ===

You can always checkout recently added records via any of the relevant links on the main page (added: today | yesterday | last 7 days | since last login), then use the 'Search within Results' functionality to find records that interest you. See below for more fine-tuned and/or automatic ways to stay on track with recent database additions.

=== Email notifications ===

The database admin can setup a mailing list for the purpose of refbase notifications. If you're subscribed to such a mailing list, refbase will let you know via email whenever a new record is added to the database. The email will contain the main bibliographic info of the newly added record as well as a direct link to its full record details in the database. A screenshot of such an email notification is available [http://refbase.sourceforge.net/features/EmailAnnouncement.html here]. Most current email clients will allow you to filter the refbase email notifications for particular topics or authors.

=== Saved queries ===

If you'd only like to see records matching a particular topic or author, you could perform a query for your desired search term(s), sort results by creation date and save the query using the 'save query' feature. Choosing again your saved query (via the 'Recall My Query' form on the main page) will always display all records matching your saved search terms, with newly added records being listed at the top of your search results list. An example for this method is given [[Recall My Query|here]].

=== Custom RSS feeds ===

refbase can generate RSS feeds from your searches. This allows you to use your RSS newsreader to track newly added records matching a certain topic or author. To do so, simply perform a query for your desired search term(s), then subscribe to the RSS feed that's available via the 'RSS' link in the page header above the search results list. ([[RSS features|more info]])

== How can I build shared bibliographies for particular research topics, groups or authors? ==

refbase allows you to construct links to automatically updating bibliographies of particular topics, groups or authors. These links can be included in your web pages, and users could subscribe to any of your shared bibliographies via RSS feeds. The feature is described in more detail (and with many examples) [[Linking to records#Displaying records of a particular author|here]] and [[Auto-updating author/group bibliographies|here]].

== Future plans ==

We plan to open up the refbase group (aka tagging) mechanism so that groups can be made public, group-specific or private. This will enable users to share their groups with each other and establish a common categorization system. In addition, we'd like to implement a simple note taking system where multiple notes/comments could be attached to a particular record and which could also be made public, group-specific or private. ([[Planned feature additions#Sharing|more info]])

Future versions of refbase may also allow record owners to set fine-grained access control on record level. This would enable the record owner (or the admin) to specify who'll be permitted to view or edit a particular record (see our planned feature "[[Planned feature additions#Record-specific permissions|record-specific permissions]]").

With regard to browsing of other user's bibliographies, we have started to develop a generic "browse" feature which will make it easy to browse your refbase database by particular field values (such as authors, keywords, users, etc). This would give you easy access to the bibliographies of all database users directly from the main page.

[[Category:Usage]]
__NOEDITSECTION__

Sharing records

2023-11-22T20:54:46Z

WikiSysop: Original page content from 04-Mar-2007

Deleting records

2023-11-22T20:33:46Z

WikiSysop: Minor tweaks to wording

In order to delete a record please click the little pencil (edit) icon that's available in any list view next to a record. Then press the "Delete Record" button at the bottom of the edit page.

The admin user is allowed to delete any records. A user, who is not logged in as admin, can remove an entry if all of the following conditions are met:

* user is logged in
* user is the owner/creator of this record (i.e., the user is the first one listed in the ''location'' field)
* nobody else is subscribed to this record (i.e., no other users are listed within the ''location'' field)
* user has permission to delete records (which is [[User permissions|set by the admin]])

When deleting a record, the information previously stored in the ''refs'' table of the database is not deleted but moved to the ''deleted'' table which obscures it from the web application. This allows an admin to recover accidentally deleted files. However, so far no interface has been made to do this.

== Batch Deletion of Records ==

In the current version of refbase, there is no way to do a batch deletion of entries from within the web interface.
However, the admin can execute an [[Batch SQL modifications|appropriate MySQL command]] (via ''sql_search.php'') to remove many records at once.

PLEASE NOTE: In both cases, the uploaded and linked files (e.g. .pdf's) will not be deleted. So the admin has to remove any related files manually.

[[Category:Usage]]
__NOEDITSECTION__

Deleting records

2023-11-22T20:25:02Z

WikiSysop: Hide section edit links

In order to delete a record please click the little pencil (edit) icon that's available in any list view next to a record. Then press the "Delete Record" button at the bottom of the edit page.

The admin user is allowed to delete any records. A user, who is not logged in as admin, can remove an entry if all of the following conditions are met:

* user is logged in
* user is the owner/creator of this record (i.e., the user is the first one listed in the ''location'' field)
* nobody else is subscribed to this record (i.e., no other users are listed within the ''location'' field)
* user has permission to delete records (which is [[User permissions|set by the admin]])

When deleting a record, the information previously stored in the ''refs'' table of the database is not deleted but moved to the ''deleted'' table which obscures it from the web application. This allows an admin to recover accidentally deleted files (though, currently, no interface had been made to do this).

== Batch Deletion of Records ==

In the current version of refbase, there is no way to do a batch deletion of entries from within the web interface.
However, the admin can execute an [[Batch SQL modifications|appropriate MySQL command]] (via ''sql_search.php'') to remove many records at once.

PLEASE NOTE: in both cases, the uploaded and linked files (e.g. .pdf's) will not be deleted. So the admin should do this manually.

[[Category:Usage]]
__NOEDITSECTION__

Deleting records

2023-11-22T20:24:45Z

WikiSysop: Original page content from 05-May-2008

In order to delete a record please click the little pencil (edit) icon that's available in any list view next to a record. Then press the "Delete Record" button at the bottom of the edit page.

The admin user is allowed to delete any records. A user, who is not logged in as admin, can remove an entry if all of the following conditions are met:

* user is logged in
* user is the owner/creator of this record (i.e., the user is the first one listed in the ''location'' field)
* nobody else is subscribed to this record (i.e., no other users are listed within the ''location'' field)
* user has permission to delete records (which is [[User permissions|set by the admin]])

When deleting a record, the information previously stored in the ''refs'' table of the database is not deleted but moved to the ''deleted'' table which obscures it from the web application. This allows an admin to recover accidentally deleted files (though, currently, no interface had been made to do this).

== Batch Deletion of Records ==

In the current version of refbase, there is no way to do a batch deletion of entries from within the web interface.
However, the admin can execute an [[Batch SQL modifications|appropriate MySQL command]] (via ''sql_search.php'') to remove many records at once.

PLEASE NOTE: in both cases, the uploaded and linked files (e.g. .pdf's) will not be deleted. So the admin should do this manually.

[[Category:Usage]]

Adding records

2023-11-20T17:49:32Z

WikiSysop: Moves a sentence to the next section

== General requirement for adding records ==

* By default, one has to be logged in to edit a record. This default can be changed by the admin.

== General description of the ''Add Record'' page ==

Open the ''Add record'' page by clicking the link at the top of every page.

* The ''Add record'' page has several input fields, which are grouped. Groups are indicated by color coding:
# Grey fields:
#* e.g. ''author'', ''title'', ''year'' and ''publication''
#* these are mandatory fields, which are necessary for correct citation of references
# White fields:
#* e.g. ''abstract'', ''keywords'' and ''ISBN''
#* these are facultative fields, which are not necessary for correct citation
#* however, filling these fields will be beneficial for your database users, e.g. when searching abstracts
# Yellow fields:
#* e.g. ''marked'', ''user keys'' and ''related''
#* these fields are facultative fields, which are '''only visible for the logged in user'''
#* this allows a personalization of a common used references

== Filling the fields ==

Hints for filling the fields should be displayed when moving the mouse over a field. More information is given below and at the definition page for the [[Table refs|''refs'']] MySQL table.

=== Mandatory fields (grey fields) ===

==== Author ====

The author(s) of the publication.
* Separate multiple authors by a semicolon (<code>;</code>)
* Separate surname and forename(s) ( or forename initials) by a comma (<code>,</code>)
* No space character between forename initials

Note that you should decide whether you'd like to use fully written forenames or initials and apply this rule to all of your database records. When citing records, correct sorting of records is only possible if ''all'' cited records have either fully written forenames or just initials.

Example:

Granskog,MA; Virkanen, J

==== is Editor ====

'''Yes''' if author is editor.
* Mark this field if persons entered in the ''author'' field are actually editors of the publication.
* Only relevant for books (type "''book whole''").

==== Title ====

The title of the publication.
* No dot at the end.
* Species or ship name(s) can be set in ''italics'' by surrounding the name(s) with underscores.
* Wrapping superscript letters with <code>[super:...]</code> will cause them to appear above the normal text baseline.
* Wrapping subscript letters with <code>[sub:...]</code> will cause them to appear below the normal text baseline.

Examples:

Feeding of _Sprattus sprattus_ in the Baltic Sea
Decomposition of [super:14]C-labelled glucose
Factors controlling CaCO[sub:2] dissolution in the Weddell Sea

==== Type ====

Defines the type of the publication.
* Simply select an item from the drop-down list.
* Note that the publication type will influence the visibility of related files (e.g. .pdf files). By default, for publications of type "''Thesis''", attached files are also visible for not-logged in users.

==== Year ====

The year of the publication.
* Enter years in four-digit style.

Example:

2003

==== Publication ====

The complete name of the publication.
* Insert here the complete name of the Journal (if type ''Journal Article'') or book (if type ''Book Chapter'').
* Abbreviated jounal names should be entered in the "''Abbrev Jounal''" field.

Examples:

Canadian Journal of Fisheries and Aquatic Sciences
The northern North Atlantic: A changing environment

==== Abbrev Journal ====

The abbreviated name of the publication.
* For a list of journal names and its abbreviations, see e.g. [https://images.webofknowledge.com/images/help/WOS/A_abrvjt.html Web of Science] or [https://ftp.ncbi.nih.gov/pubmed/J_Medline.txt PubMed].

Example:

Can J Fish Aquat Sci

==== Volume ====

The volume of the publication.

Example:

245

==== Issue ====

The issue of a publication within a volume.
* Often, a ''Volume'' of a journal consists of several issues.
* An ''Issue'' is a single booklet and is labelled by a number.

Examples:

3
C2

==== Pages ====

Defines which pages of the publication are covered by the reference.
* Enter a '''range of pages''', when using types "''Journal Article''" and "''Book Chapter''".
* Enter the '''total number of pages''' including "''pp''" (without any dots) when using types "''Book Whole''" and "''Manuscript''".

Examples:

12 ''-> article has only one page''
35-42 ''-> article or book chapter starts at page 35 and ends at page 42''
620 pp ''-> book has 620 pages in total''

=== Facultative fields (white fields) ===

==== Corporate Author ====

The institution or society associated with the author.
* Usually the institution under which the author published his/her work.
* For Diploma or Phd theses, this would be the name of the university/department.

Example:

Leibniz-Institute for Marine Sciences at the University of Kiel

==== Thesis ====

The type of a thesis.
* If the publication is a thesis, this field defines the type of academic degree.

Examples:

diploma thesis
Ph.D.thesis
Doctoral thesis
Habilitation thesis

==== Adress ====

The address and/or contact information of the author(s).
* Any info on how to contact the corresponding author(s) (often the first author of the paper), e.g. postal address of author institution, email address etc.).

Example:

Granskog: Department of Geophysics, P.O. Box 64, FIN-00014 University of Helsinki, Finland, Email: mats@iki.fi;
Meiners: Institute for Polar Ecology, University of Kiel, Wischhofstrasse 1-3, D-24148 Kiel, Germany

==== Keywords ====

The keywords given by the author.
* Contains keywords, as given in the article.
* Your personal keywords can be entered under "[[Adding_records#User Keys|User Keys]]".
* Multiple keywords should be separated by a semicolon (<code>;</code>).

Examples:

Baltic Sea; hydroacoustic; Sprat; Herring; GAM

==== Abstract ====

The abstract of this publication (if any) as given by the author.

==== Publisher ====

=== User fields (yellow fields) ===

==== User Keys ====

==== Marked & Selected ====

* Both fields can be used to permanently "mark" (or "select") records so that one can easily come back to these records later on. It's up to you how you use these fields.
* The "selected" field is meant to indicate your "selected publications". This can be used to easily gather all publications of a particular author that shall be included on the institute's web site. Here's an example:

[http://polaris.ipoe.uni-kiel.de/refs/show.php?author=piepenburg,%20d&userID=4&selected=yes&submit=Cite&showRows=100&citeOrder=year&headerMsg=Publications%20of%20**Dieter%20Piepenburg**: Publications of Dieter Piepenburg]

: In the above URL, note the use of the <code>&selected=yes</code> bit. I.e. the above URL displays all selected records that were authored by "D. Piepenburg" in Citation view (grouped by publication year), and adds a header message above the results list.

: For more info, please see how to setup dynamically updating [[Auto-updating_author/group_bibliographies|author (or group) bibliographies]].

[[Category:Usage]]
__NOEDITSECTION__

Adding records

2023-11-20T17:46:18Z

WikiSysop: Adds field info for the "Marked" & "Selected" fields

== General requirement for adding records ==

* By default, one has to be logged in to edit a record. This default can be changed by the admin.
* Open the ''Add record'' page by clicking the link at the top of every page.

== General description of the ''Add Record'' page ==

* The ''Add record'' page has several input fields, which are grouped. Groups are indicated by color coding:
# Grey fields:
#* e.g. ''author'', ''title'', ''year'' and ''publication''
#* these are mandatory fields, which are necessary for correct citation of references
# White fields:
#* e.g. ''abstract'', ''keywords'' and ''ISBN''
#* these are facultative fields, which are not necessary for correct citation
#* however, filling these fields will be beneficial for your database users, e.g. when searching abstracts
# Yellow fields:
#* e.g. ''marked'', ''user keys'' and ''related''
#* these fields are facultative fields, which are '''only visible for the logged in user'''
#* this allows a personalization of a common used references

== Filling the fields ==

Hints for filling the fields should be displayed when moving the mouse over a field. More information is given below and at the definition page for the [[Table refs|''refs'']] MySQL table.

=== Mandatory fields (grey fields) ===

==== Author ====

The author(s) of the publication.
* Separate multiple authors by a semicolon (<code>;</code>)
* Separate surname and forename(s) ( or forename initials) by a comma (<code>,</code>)
* No space character between forename initials

Note that you should decide whether you'd like to use fully written forenames or initials and apply this rule to all of your database records. When citing records, correct sorting of records is only possible if ''all'' cited records have either fully written forenames or just initials.

Example:

Granskog,MA; Virkanen, J

==== is Editor ====

'''Yes''' if author is editor.
* Mark this field if persons entered in the ''author'' field are actually editors of the publication.
* Only relevant for books (type "''book whole''").

==== Title ====

The title of the publication.
* No dot at the end.
* Species or ship name(s) can be set in ''italics'' by surrounding the name(s) with underscores.
* Wrapping superscript letters with <code>[super:...]</code> will cause them to appear above the normal text baseline.
* Wrapping subscript letters with <code>[sub:...]</code> will cause them to appear below the normal text baseline.

Examples:

Feeding of _Sprattus sprattus_ in the Baltic Sea
Decomposition of [super:14]C-labelled glucose
Factors controlling CaCO[sub:2] dissolution in the Weddell Sea

==== Type ====

Defines the type of the publication.
* Simply select an item from the drop-down list.
* Note that the publication type will influence the visibility of related files (e.g. .pdf files). By default, for publications of type "''Thesis''", attached files are also visible for not-logged in users.

==== Year ====

The year of the publication.
* Enter years in four-digit style.

Example:

2003

==== Publication ====

The complete name of the publication.
* Insert here the complete name of the Journal (if type ''Journal Article'') or book (if type ''Book Chapter'').
* Abbreviated jounal names should be entered in the "''Abbrev Jounal''" field.

Examples:

Canadian Journal of Fisheries and Aquatic Sciences
The northern North Atlantic: A changing environment

==== Abbrev Journal ====

The abbreviated name of the publication.
* For a list of journal names and its abbreviations, see e.g. [https://images.webofknowledge.com/images/help/WOS/A_abrvjt.html Web of Science] or [https://ftp.ncbi.nih.gov/pubmed/J_Medline.txt PubMed].

Example:

Can J Fish Aquat Sci

==== Volume ====

The volume of the publication.

Example:

245

==== Issue ====

The issue of a publication within a volume.
* Often, a ''Volume'' of a journal consists of several issues.
* An ''Issue'' is a single booklet and is labelled by a number.

Examples:

3
C2

==== Pages ====

Defines which pages of the publication are covered by the reference.
* Enter a '''range of pages''', when using types "''Journal Article''" and "''Book Chapter''".
* Enter the '''total number of pages''' including "''pp''" (without any dots) when using types "''Book Whole''" and "''Manuscript''".

Examples:

12 ''-> article has only one page''
35-42 ''-> article or book chapter starts at page 35 and ends at page 42''
620 pp ''-> book has 620 pages in total''

=== Facultative fields (white fields) ===

==== Corporate Author ====

The institution or society associated with the author.
* Usually the institution under which the author published his/her work.
* For Diploma or Phd theses, this would be the name of the university/department.

Example:

Leibniz-Institute for Marine Sciences at the University of Kiel

==== Thesis ====

The type of a thesis.
* If the publication is a thesis, this field defines the type of academic degree.

Examples:

diploma thesis
Ph.D.thesis
Doctoral thesis
Habilitation thesis

==== Adress ====

The address and/or contact information of the author(s).
* Any info on how to contact the corresponding author(s) (often the first author of the paper), e.g. postal address of author institution, email address etc.).

Example:

Granskog: Department of Geophysics, P.O. Box 64, FIN-00014 University of Helsinki, Finland, Email: mats@iki.fi;
Meiners: Institute for Polar Ecology, University of Kiel, Wischhofstrasse 1-3, D-24148 Kiel, Germany

==== Keywords ====

The keywords given by the author.
* Contains keywords, as given in the article.
* Your personal keywords can be entered under "[[Adding_records#User Keys|User Keys]]".
* Multiple keywords should be separated by a semicolon (<code>;</code>).

Examples:

Baltic Sea; hydroacoustic; Sprat; Herring; GAM

==== Abstract ====

The abstract of this publication (if any) as given by the author.

==== Publisher ====

=== User fields (yellow fields) ===

==== User Keys ====

==== Marked & Selected ====

* Both fields can be used to permanently "mark" (or "select") records so that one can easily come back to these records later on. It's up to you how you use these fields.
* The "selected" field is meant to indicate your "selected publications". This can be used to easily gather all publications of a particular author that shall be included on the institute's web site. Here's an example:

[http://polaris.ipoe.uni-kiel.de/refs/show.php?author=piepenburg,%20d&userID=4&selected=yes&submit=Cite&showRows=100&citeOrder=year&headerMsg=Publications%20of%20**Dieter%20Piepenburg**: Publications of Dieter Piepenburg]

: In the above URL, note the use of the <code>&selected=yes</code> bit. I.e. the above URL displays all selected records that were authored by "D. Piepenburg" in Citation view (grouped by publication year), and adds a header message above the results list.

: For more info, please see how to setup dynamically updating [[Auto-updating_author/group_bibliographies|author (or group) bibliographies]].

[[Category:Usage]]
__NOEDITSECTION__

Adding records

2023-11-20T17:27:30Z

WikiSysop: Fix internal link

Adding records

2023-11-20T17:26:24Z

WikiSysop: Updates formatting & case, removes outdated info and fixes some typos

== General requirement for adding records ==

* By default, one has to be logged in to edit a record. This default can be changed by the admin.
* Open the ''Add record'' page by clicking the link at the top of every page.

== General description of the ''Add Record'' page ==

* The ''Add record'' page has several input fields, which are grouped. Groups are indicated by color coding:
# Grey fields:
#* e.g. ''author'', ''title'', ''year'' and ''publication''
#* these are mandatory fields, which are necessary for correct citation of references
# White fields:
#* e.g. ''abstract'', ''keywords'' and ''ISBN''
#* these are facultative fields, which are not necessary for correct citation
#* however, filling these fields will be beneficial for your database users, e.g. when searching abstracts
# Yellow fields:
#* e.g. ''marked'', ''user keys'' and ''related''
#* these fields are facultative fields, which are '''only visible for the logged in user'''
#* this allows a personalization of a common used references

== Filling the fields ==

Hints for filling the fields should be displayed when moving the mouse over a field. More information is given below and at the definition page for the [[Table refs|''refs'']] MySQL table.

=== Mandatory fields (grey fields) ===

==== Author ====

The author(s) of the publication.
* Separate multiple authors by a semicolon (<code>;</code>)
* Separate surname and forename(s) ( or forename initials) by a comma (<code>,</code>)
* No space character between forename initials

Note that you should decide whether you'd like to use fully written forenames or initials and apply this rule to all of your database records. When citing records, correct sorting of records is only possible if ''all'' cited records have either fully written forenames or just initials.

Example:

Granskog,MA; Virkanen, J

==== is Editor ====

'''Yes''' if author is editor.
* Mark this field if persons entered in the ''author'' field are actually editors of the publication.
* Only relevant for books (type "''book whole''").

==== Title ====

The title of the publication.
* No dot at the end.
* Species or ship name(s) can be set in ''italics'' by surrounding the name(s) with underscores.
* Wrapping superscript letters with <code>[super:...]</code> will cause them to appear above the normal text baseline.
* Wrapping subscript letters with <code>[sub:...]</code> will cause them to appear below the normal text baseline.

Examples:

Feeding of _Sprattus sprattus_ in the Baltic Sea
Decomposition of [super:14]C-labelled glucose
Factors controlling CaCO[sub:2] dissolution in the Weddell Sea

==== Type ====

Defines the type of the publication.
* Simply select an item from the drop-down list.
* Note that the publication type will influence the visibility of related files (e.g. .pdf files). By default, for publications of type "''Thesis''", attached files are also visible for not-logged in users.

==== Year ====

The year of the publication.
* Enter years in four-digit style.

Example:

2003

==== Publication ====

The complete name of the publication.
* Insert here the complete name of the Journal (if type ''Journal Article'') or book (if type ''Book Chapter'').
* Abbreviated jounal names should be entered in the "''Abbrev Jounal''" field.

Examples:

Canadian Journal of Fisheries and Aquatic Sciences
The northern North Atlantic: A changing environment

==== Abbrev Journal ====

The abbreviated name of the publication.
* For a list of journal names and its abbreviations, see e.g. [https://images.webofknowledge.com/images/help/WOS/A_abrvjt.html Web of Science] or [https://ftp.ncbi.nih.gov/pubmed/J_Medline.txt PubMed].

Example:

Can J Fish Aquat Sci

==== Volume ====

The volume of the publication.

Example:

245

==== Issue ====

The issue of a publication within a volume.
* Often, a ''Volume'' of a journal consists of several issues.
* An ''Issue'' is a single booklet and is labelled by a number.

Examples:

3
C2

==== Pages ====

Defines which pages of the publication are covered by the reference.
* Enter a '''range of pages''', when using types "''Journal Article''" and "''Book Chapter''".
* Enter the '''total number of pages''' including "''pp''" (without any dots) when using types "''Book Whole''" and "''Manuscript''".

Examples:

12 ''-> article has only one page''
35-42 ''-> article or book chapter starts at page 35 and ends at page 42''
620 pp ''-> book has 620 pages in total''

=== Facultative fields (white fields) ===

==== Corporate Author ====

The institution or society associated with the author.
* Usually the institution under which the author published his/her work.
* For Diploma or Phd theses, this would be the name of the university/department.

Example:

Leibniz-Institute for Marine Sciences at the University of Kiel

==== Thesis ====

The type of a thesis.
* If the publication is a thesis, this field defines the type of academic degree.

Examples:

diploma thesis
Ph.D.thesis
Doctoral thesis
Habilitation thesis

==== Adress ====

The address and/or contact information of the author(s).
* Any info on how to contact the corresponding author(s) (often the first author of the paper), e.g. postal address of author institution, email address etc.).

Example:

Granskog: Department of Geophysics, P.O. Box 64, FIN-00014 University of Helsinki, Finland, Email: mats@iki.fi;
Meiners: Institute for Polar Ecology, University of Kiel, Wischhofstrasse 1-3, D-24148 Kiel, Germany

==== Keywords ====

The keywords given by the author.
* Contains keywords, as given in the article.
* Your personal keywords can be entered under "[[Adding Records#User Keys|User Keys]]".
* Multiple keywords should be separated by a semicolon (<code>;</code>).

Examples:

Baltic Sea; hydroacoustic; Sprat; Herring; GAM

==== Abstract ====

The abstract of this publication (if any) as given by the author.

==== Publisher ====

=== User fields (yellow fields) ===

==== User Keys ====

[[Category:Usage]]
__NOEDITSECTION__

Configuring refbase

2023-11-20T17:09:56Z

WikiSysop: Remove "todo comments" about configuring different publication & thesis types

This document presents some tips how to configure your refbase installation:

The refbase admin has a variety of options to configure or customize refbase. Some of them are listed in this article. If you don't find the desired option, please refer to file ''initialize/ini.inc.php'' within your refbase installation. This configuration file contains many global settings which are not accessible via the refbase web interface:

* initial database settings (database name, admin email, database URL, character set, etc)
* default user settings when a new user is created
* visibility of files (e.g., .pdf files)
* important settings for file upload (file renaming, directory creation, etc)
* appearance of links within refbase
* server settings for link resolvers (OpenURL, ISBN)
* rich text formatting (e.g., greek letters, italic or superscript/subscript text)

The configuration file ''initialize/ini.inc.php'' is well commented, therefore you will find much more information in this file.

Below you can find answers to some frequently asked questions about configuring refbase.

== How can I change the logo? ==

You can change the main logo image that's displayed in the refbase page header by setting variable <code>$logoImageURL</code> in ''initialize/ini.inc.php'' to the path of your logo file. In addition, please be sure to set the variables <code>$logoImageWidth</code> and <code>$logoImageHeight</code> to the dimensions of your logo. You may also be interested to specify your own paths for the smaller logos (<code>$logoSmallImageURL</code> and <code>$faviconImageURL</code>).

== How can I setup refbase so that users can register themselves? ==

By default, only the admin is allowed to setup new user accounts. Here's how to setup your refbase installation such that users can automatically register themselves:

In ''initialize/ini.inc.php'' set the <code>$addNewUsers</code> variable to "everyone". Then, provide a link on the main page to ''user_details.php'' where users can use the provided form to register themselves.

Just set the <code>$addNewUsers</code> variable back to "admin" if you want to prevent other users from messing with your users table.

== How can I change the default number of records shown? ==

You can change the default number of records that is returned by any (web, RSS or SRU) query by changing the value of the <code>$defaultNumberOfRecords</code> variable in ''initialize/ini.inc.php''.

== How can I change the default language? ==

You can change the language that's displayed by default in file ''intialize/ini.inc.php'' within your refbase root directory. Search for this paragraph:

// The default language selection, can be overwritten by userdefined language
$defaultLanguage = "de"; // e.g. "en", "de" or "fr"

and set the value of the <code>$defaultLanguage</code> variable to either "en" (English), "de" (German) or "fr" (French). In case of problems, please check that your desired default language is enabled within MySQL table ''languages''.

Note that logged-in database users can switch to another language. This can be done by clicking the ''Options'' link when logged in.

== How can I make some PDFs available to all users? ==

Ususally, access to PDFs should only be made available to logged-in users. This is controlled by variable <code>$fileVisibility</code> in ''initialize/ini.inc.php''. However, often one wants to make a few PDFs available to all users. Variable <code>$fileVisibilityException</code> (also in ''initialize/ini.inc.php'') can be used to specify a condition where attached files will be displayed to ''all'' users, no matter whether they're logged in or not.

By default, refbase will publicly display files for all records where the ''thesis'' field in table ''refs'' is not empty, i.e. if a thesis type has been specified for the record:

$fileVisibilityException = array("thesis", "/.+/");

If, instead, you'd like to allow public access to PDFs for arbitrary records, a common approach would be to put some unique string into one of the fields from table ''refs'', and use this field & identifier string in variable <code>$fileVisibilityException</code>.†As an example, for all records where the attached PDF should be displayed publicly, you could add the string "author copyright" to the ''notes'' field. Then use the following pattern:

$fileVisibilityException = array("notes", "/author copyright/");

As another example, if you'd like to offer public access to all PDFs that where authored by a member of your institution, you could make use of the ''contribution_id'' field ([[Auto-updating_author/group_bibliographies#Institutional_or_group_bibliographies|more info]]), and specify this field and your institutional abbreviation in variable <code>$fileVisibilityException</code>. If your institutional abbreviation is, say, "NUCAPT", you'd use this pattern:

$fileVisibilityException = array("contribution_id", "/NUCAPT/");

== How can I change options & permissions for everyone who's not logged in? ==

=== Setting options via the web interface ===

When logged in as admin, you can set options and access permissions for everyone who's not logged in by calling the script ''user_options.php'' with the <code>userID=0</code> parameter:

user_options.php?userID=0

For all permissions that are set to off, the relevant interface elements will be hidden from the refbase GUI.

Note that some of the available user permissions require a user being logged in. I.e., enabling these options for anyone who isn't logged in won't have any effect. Following user permissions require a login:

* Add records
* Edit records
* Delete records
* File upload
* User groups
* User queries
* Import
* Batch import
* Modify options

If you want to allow users who are not logged in to query the refbase database via the [[Search/Retrieve web services|SRU search/retrieve webservice]], then either the ''Export'' or the ''Batch export'' user permission needs to be enabled. This will allow export of XML records via ''sru.php'' but won't allow a user who isn't logged in to export records via the web interface.

=== Setting options within ''ini.inc.php'' ===

If you like to change the permission to see/download files (e.g., .pdf files), you (the admin) can find the appropriate option in file ''initialize/ini.inc.php''. The relevant variable is called <code>$fileVisibility</code>. You are able to allow file download for everyone, logged-in users only, or on a user-specific basis.

Additionally, you can set exceptions to this rule in variable <code>$fileVisibilityException</code>, which enables you to always allow download access to files that meet a particular criterion. A typical usage example would be to always grant download access to theses or papers that were written by members of your own institution.

For more details, please refer to the comments in ''ini.inc.php''.

== How can I change the default citation style? ==

You can use variable <code>$defaultCiteStyle</code> in file ''initialize/ini.in.php'' to change the citation style that's displayed by default in the web interface (Citation view) as well as for export of formatted citation lists to RTF, PDF, LaTeX, etc. The given style name must have a matching entry in the ''styles'' table of your refbase MySQL database.

Note that the admin can enable or disable particular citation styles individually for each user. And if desired, logged-in users can deselect some of the enabled styles in their user-specific options.

== How can I change the names & order of citation styles? ==

=== Changing the names of citation styles ===

Here's how to change the names of citation styles displayed in the "Cite using style" drop-down (in the form below the query results list): Currently, you have to directly edit the ''styles'' MySQL table. E.g., to change the display name of the "Polar Biol" citation style to "Default" execute the following MySQL command from within your SQL command line interpreter:

UPDATE styles SET style_name = "Default" WHERE style_name = "Polar Biol";

Note that you must also change the corresponding names for the variables <code>$defaultCiteStyle</code> and <code>$defaultUserStyles</code> in ''initialize/ini.inc.php''.

=== Changing the order of citation styles ===

Similar to the above, you can edit the ''styles'' MySQL table to change the order of citation styles displayed in the "Cite using style" drop-down menu. If, for example, you want to switch the order of the first two citation styles, execute the two commands below:

UPDATE styles SET order_by = "2" WHERE style_id = 1;
UPDATE styles SET order_by = "1" WHERE style_id = 2;

Note: this example assumes that you have table entries with style_id's of 1 and 2, otherwise adopt or use something like:

UPDATE styles SET order_by = "...(whatever)..." WHERE style_name = "...(whatever)..."

The ''order_by'' field is of type <code>varchar(25)</code>, i.e., you can also use more fine grained values (such as "1a", "1b", etc).

== How can I add or disable a particular citation style? ==

=== Adding a citation style ===

Currently, citation styles are written as a PHP function, so you'll need to know a bit of PHP to add your own style. The PHP function that outputs records in citation format is called <code>citeRecord()</code>. For each citation style, there's a separate file with a dedictated version of this function. These citation style files are located within the ''cite'' sub-directory of your refbase root directory.

To build your own style, you may want to have a look at the existing citation style files and [[#How to create a new citation style|modify]] one of them to suit your needs.

After you've created your own citation style, copy it into the ''cite'' sub-directory of your refbase root directory. Then, in order to add your citation style file to the "Cite using style" drop-down, execute the following MySQL command from within your SQL command line interpreter:

INSERT INTO styles VALUES (NULL, 'STYLENAME', 'true', 'STYLEFILE', '1', '1');

In the above MySQL command, replace <code>STYLENAME</code> with the actual name of your citation style. This name will appear in the "Cite using style" drop-down. Similarly, <code>STYLEFILE</code> must be replaced with the file name of your citation style file, prefixed with "styles/" (example: "styles/MyStyleFile.php"). In addition, you can change the first number ('1') in the above command to change the position at which your style name will be displayed in the drop-down. To see all available styles and confirm that your style has been successfully added to the ''styles'' MySQL table, execute this command:

SELECT * FROM styles;

Now, login as admin via the refbase web interface, click on "Manage Users" and activate your new style (using the "edit options" link) for all those users who shall see this style. If you've enabled/disabled any citation styles for the admin user, you'll have to logout and login again in order to see your changes.

=== Disabling a citation style ===

You can globally disable existing styles by setting the ''style_enabled'' field to "false". E.g., if you want to disable the "Polar Biol" citation style, execute:

UPDATE styles SET style_enabled = "false" WHERE style_name = "Polar Biol";

=== How to create a new citation style ===

Before we start this section, a comment in advance:

To improve refbase: If you have created a new citation style, we would be interested to offer this style for all refbase users. If possible, please
* post this new .php file to [[refbase:Community_Portal|the community]].
* include the journal title for you built the style with their website.

This section should contain information/hints for non-php professionals

==== Adapting existing work ====

Before investing energy in creating a new style, it is wise to check the [https://sourceforge.net/p/refbase/code/HEAD/tree/ refbase subversion repository] for new styles that are under development but not yet included in the project release. Be aware that styles obtained from the [https://sourceforge.net/p/refbase/code/HEAD/tree/branches/bleeding-edge/cite/styles/ bleeding edge branch] are not necessarily in working condition, and even if they appear to work, may be unfit for a production environment.

== How can I add a new interface language? ==

In order to add a new language (locale) to refbase, you need to perform these steps:

* Within the refbase ''locales/'' directory, copy one of the existing subdirectories and rename it to the [http://www.loc.gov/standards/iso639-2/php/code_list.php two-letter code] of the language you'd like to add (e.g. "es" in case of Spanish).
* Within your new subdirectory, translate all lines in file ''common.inc'' into your language, and save a copy of this file with encoding "Unicode (UTF-8, no BOM)" to ''common_utf8.inc''.
* Issue following MySQL command via ''sql_search.php'' when logged into refbase as admin:

INSERT INTO languages VALUES (NULL, 'LANGCODE', 'true', '4');

In the above MySQL command, replace <code>LANGCODE</code> with the two-letter code of your language, e.g. "es" for Spanish. In addition, you can change the last number ("4" in the above example) to alter the position at which your language name will be displayed in the language drop-down.

The new language option should now appear within the language drop-down in the refbase user options.

To see all currently available languages and to confirm that your language has been successfully added to the ''languages'' MySQL table, execute this command from within your MySQL command line interpreter (after you've selected the refbase MySQL database):

SELECT * FROM languages;

Please note that in refbase-0.9.0, not the entire interface is available for localization. We plan to finish internationalization until version 1.0.

If you've translated the refbase interface strings in ''common.inc'' into your own language, please [[refbase:Community_Portal|send us]] this file so that we can include it with a future release of refbase.

[[Category:Configuration]]
__NOEDITSECTION__

Adding records

2023-11-20T15:56:54Z

WikiSysop: Hide section edit links

== General requirement for adding records ==

*as default, one has to be logged in to edit an record. This default can be changed from the admin
*the ''add record''-page has to be opened. This can be easily done at with the link at the header of every page
*some browsers (e.g. firefox) have problems with pasting in text with line breaks. So please remove line breaks before pasting the text in these cases.

== General description of the ''Add Record'' page ==

*you will see several input-fields, which are grouped. Groups are indicated by color-coding (colors may vary with used browser, used stylesheets etc.)
#grey fields:
#*such as ''author'', ''title'', ''year'' and ''publication''
#*these are mandatory fields, which are necessary for correct citation of references
#white fields:
#*such as ''abstract'', ''keywords'' and ''ISBN''
#*these are facultative fields, which are not necessary for correct citation
#*but these fields will give a additional benifit to your database, for searching abstracts etc.
#yellow fields:
#*such as ''marked'', ''user keys'' and ''related''
#*these fields are facultative fields, which are '''only visible for the logged in user'''
#*this allows a personalization of a common used references

== Filling the fields ==

Hints for filling the fields should be displayed when moving the mouse over a field. More information is given below and at the definition page for the [[Table refs|''refs'']] MySQL table.

=== Mandatory fields (grey fields) ===

==== Author ====

the author(s) of the publication
*several authors separated by semicolon (;)
*surname and '''forename(s)''' or forename-initials separated by comma (,)
*no points and no space character between forename-initials

Note that you should decide whether you'd like to use fully written fornames or initials and apply this rule to all of your database records. When citing records, correct sorting of records is only possible if ''all'' cited records have either fully written forenames or just initials.

example: Granskog,MA; Virkanen, J

==== is Editor ====

'''Yes''' if author is Editor
*please activate, if persons, entered in ''author''-field are editors of the publication
*only relevant for books (Type: "''book whole''")

==== Title ====

the title of the publication
*no dot at the end
*species-names can be set as '''italic''' by surrounding by underscore
*use "[super:...]" to impose words
*use "[sub:...]" to lower words
examples:
Feeding of _Sprattus sprattus_ in the Baltic Sea
Decomposition of [super:14]C-labelled glucose
Factors controlling CaCO[sub:2] dissolution in the Weddell Sea

==== Type ====

defines the type of the publication
*simply select an item from drop-down-list
*'''this entry is used for defining the citation style of the publication'''. Therefore selection should be made carfully
*this entry defines visibility of related files (e.g. .pdf). As default, for publications of Type="''Thesis''" the files are visible for not logged in users, as well
*see [[Configuring refbase|configuration of refbase]] to learn how to add/remove entries in the list

==== Year ====

the year of the publication
*enter in four-digit-style
example: 2003

==== Publication ====

complete name of publication
*insert here the complete (!) name of the Journal (if Type=''Journal Article'') or of the book (if Type=''Book Chapter'')
*abbreviated Jounal-names has to be entered in the field "''Abbrev Jounal''"
*'''a list of journal-names and -abbreviations (related to aquatic sciences) can be found by open ''journals.php'' in the root directory of the refbase URL'''
examples:
Canadian Journal of Fisheries and Aquatic Sciences
The northern North Atlantic: A changing environment

==== Abbrev Journal ====

the abbreviated name of the publication
*enter the abbreviated journal-name without dots
*'''a list of journal-names and -abbreviations (related to aquatic sciences) can be found by open ''journals.php'' in the root directory of the refbase URL'''
example:
Can J Fish Aquat Sci

==== Volume ====

the volume of the publication
example: 245

==== Issue ====

the issue of a publication within a volume
*often a ''Volume'' of a journal consist of several issues
*the single booklet is called ''Issue'' and is labelled by a number
examples: 3 ''or'' C2

==== Pages ====

defines which pages of the publication are covered with the reference
*enter '''range of pages''', when using Types "''Journal Articles''" and "''Book Chapter''"
*enter '''total number of pages''' including "''pp''" (without dot) when using Types"''Book Whole''" and "''Manuscript''"
examples:
12 (article has only one page)
35-42 (article or book chapter starts at page 35 and ends at page 42)
620 pp (book has 620 pages in total)

=== Facultative fields (white fields) ===

==== Corporate Author ====

the institution or society to which so the author is associated
*defines the institution under which the author published his work
*for Diploma- or Phd-thesis this would be the name of the university/department
example: Leibniz-Institute for Marine Sciences at the University of Kiel

==== Thesis ====

the type of a thesis
*if the publication is a thesis, this field defines the type of academic degree
*see [[Configuring refbase|configuration of refbase]] to learn how to add/remove entries in the list
examples: diploma thesis, Ph.D.thesis, Doctoral thesis, Habilitation thesis

==== Adress ====

the adress of the authors
*contains contact informations, how to contact the authors (in most cases the first author) of the paper (e.g. postal adress, Fax, email et.)
example:
Granskog: Department of Geophysics, P.O. Box 64, FIN-00014
University of Helsinki, Finland, Email: mats@iki.fi;
Meiners: Institute for Polar Ecology, University of Kiel,
Wischhofstrasse 1-3, D-24148 Kiel, Germany

==== Keywords ====

the keywords given by the author
*contains keywords, as given in the article
*your personal keywords can be entered under [[Adding Records#User Keys|User Keys]]
*multiple items should be seperated by semicolon (";")
examples:
Baltic Sea; hydroacoustic; Sprat; Herring; GAM

==== Abstract ====

the abstract for this publication (if any)as given by the author
*some browsers (e.g. firefox) have problems with pasting in text with line breaks. So please remove line breaks before pasting the text in these cases.

==== Publisher ====

=== User fields (yellow fields) ===

==== User Keys ====

[[Category:Usage]]
__NOEDITSECTION__

Adding records

2023-11-20T15:56:00Z

WikiSysop: Original page content from 20-Mar-2012

Editing records

2023-11-20T15:38:43Z

WikiSysop: Update external links

== General notes about editing ==

We strongly believe in the '''[http://en.wikipedia.org/wiki/Wiki wiki] approach of collaboration''' where every (logged-in) user is allowed to edit every database record. Normally, this tremendeously helps to improve the quality of your records since everybody can easily make corrections and/or additions. Actually, we have never heard of any serious misuse of this feature.

Of course, there may be some valid concerns among your users about data persistence. When discussing this issue with your users, it's worth pointing out these things:

* While the basic bibliographic data of a record are shared among users (and can be edited by every user), every user has in fact private, i.e., '''user-specific fields''' that nobody else can view. These are the "yellow" fields at the bottom of each entry when viewed in details view. People can put their private keys and notes there without having to fear that somebody else will read them.

* refbase allows users to setup (and subscribe to) custom '''RSS feeds''' that '''track''' any '''changes''' made to records that belong to their own library.

* It should be relatively easy to setup a cron job on your '''server''' that '''backups''' the refbase database at regular intervals, say, every night. An example for a backup script is given [[Backup_the_database|here]].

: This ensures that you can retrieve a previous version of a particular record in case some malicious user did something bad. And with a rigorous backup strategy on the server, this setup may already be much safer than most people's own literature database on their local machine.

* It's also worth pointing out that every user can '''install refbase locally''' – provided the user has a webserver installed. But with projects such as [https://www.apachefriends.org/ XAMPP], this has become very easy.

: The backup dump file that you get from the [[Backup_the_database#mysqldump|mysqldump]] utility can be used as base data file when installing refbase. This means, that users could grab a recent backup copy of your refbase database from your server (if you allow them to do so) and install it locally on their machine for convenient '''offline access'''. The same method can be used to update a local copy of a refbase database with updated data from the server's master database.

[[Category:Usage]]
__NOEDITSECTION__

Editing records

2023-11-20T15:37:29Z

WikiSysop: Hide section edit links

== General notes about editing ==

We strongly believe in the '''[http://en.wikipedia.org/wiki/Wiki wiki] approach of collaboration''' where every (logged-in) user is allowed to edit every database record. Normally, this tremendeously helps to improve the quality of your records since everybody can easily make corrections and/or additions. Actually, we have never heard of any serious misuse of this feature.

Of course, there may be some valid concerns among your users about data persistence. When discussing this issue with your users, it's worth pointing out these things:

* While the basic bibliographic data of a record are shared among users (and can be edited by every user), every user has in fact private, i.e., '''user-specific fields''' that nobody else can view. These are the "yellow" fields at the bottom of each entry when viewed in details view. People can put their private keys and notes there without having to fear that somebody else will read them.

* refbase allows users to setup (and subscribe to) custom '''RSS feeds''' that '''track''' any '''changes''' made to records that belong to their own library.

* It should be relatively easy to setup a cron job on your '''server''' that '''backups''' the refbase database at regular intervals, say, every night. An example for a backup script is given [[Backup_the_database|here]].

: This ensures that you can retrieve a previous version of a particular record in case some malicious user did something bad. And with a rigorous backup strategy on the server, this setup may already be much safer than most people's own literature database on their local machine.

* It's also worth pointing out that every user can '''install refbase locally''' – provided the user has a webserver installed. But with projects such as [http://www.xampp.org/ XAMPP], this has become very easy.

: The backup dump file that you get from the [[Backup_the_database#mysqldump|mysqldump]] utility can be used as base data file when installing refbase. This means, that users could grab a recent backup copy of your refbase database from your server (if you allow them to do so) and install it locally on their machine for convenient '''offline access'''. The same method can be used to update a local copy of a refbase database with updated data from the server's master database.

[[Category:Usage]]
__NOEDITSECTION__

Editing records

2023-11-20T15:36:54Z

WikiSysop: Original page content from 23-Oct-2006

== General notes about editing ==

We strongly believe in the '''[http://en.wikipedia.org/wiki/Wiki wiki] approach of collaboration''' where every (logged-in) user is allowed to edit every database record. Normally, this tremendeously helps to improve the quality of your records since everybody can easily make corrections and/or additions. Actually, we have never heard of any serious misuse of this feature.

Of course, there may be some valid concerns among your users about data persistence. When discussing this issue with your users, it's worth pointing out these things:

* While the basic bibliographic data of a record are shared among users (and can be edited by every user), every user has in fact private, i.e., '''user-specific fields''' that nobody else can view. These are the "yellow" fields at the bottom of each entry when viewed in details view. People can put their private keys and notes there without having to fear that somebody else will read them.

* refbase allows users to setup (and subscribe to) custom '''RSS feeds''' that '''track''' any '''changes''' made to records that belong to their own library.

* It should be relatively easy to setup a cron job on your '''server''' that '''backups''' the refbase database at regular intervals, say, every night. An example for a backup script is given [[Backup_the_database|here]].

: This ensures that you can retrieve a previous version of a particular record in case some malicious user did something bad. And with a rigorous backup strategy on the server, this setup may already be much safer than most people's own literature database on their local machine.

* It's also worth pointing out that every user can '''install refbase locally''' – provided the user has a webserver installed. But with projects such as [http://www.xampp.org/ XAMPP], this has become very easy.

: The backup dump file that you get from the [[Backup_the_database#mysqldump|mysqldump]] utility can be used as base data file when installing refbase. This means, that users could grab a recent backup copy of your refbase database from your server (if you allow them to do so) and install it locally on their machine for convenient '''offline access'''. The same method can be used to update a local copy of a refbase database with updated data from the server's master database.

[[Category:Usage]]

Searching

2023-11-20T15:20:43Z

WikiSysop: Update external links (TODO: appropriate replacements for https://refbase.ipoe.uni-kiel.de links)

This page explains how to use the refbase search facilities:

== Search options ==

=== Basic search ===

* [[Quick Search]]

=== Search pages ===

* [[Simple Search]]
* [[Advanced Search]]
* [[SQL Search]]
* [[Library Search]]

=== Refine your search results ===

* [[Search within Results]]
* [[SQL Search]]

=== Directly jump to particular records ===

* [[Display Details]]

=== User-specific search options ===

* [[Show My Refs]]
* [[Show My Group]]
* [[Recall My Query]]
* [[Display Details]]

== Search syntax ==

=== Basic queries ===

When searching, refbase performs a "contains" search by default. This means that refbase will return all records where the searched field contains the specified search string. As an example, searching the ''title'' field for:

[https://refbase.ipoe.uni-kiel.de/refs/show.php?title=arctic arctic]

will return records where the ''title'' field contains "Arctic", "Antarctic", "Antarctica", "Antarcticque" "subarctic", etc.

This "contains" search is the standard search behaviour in simple search forms such as the [[Quick Search]] or [[Search within Results]] forms. It is also used in all other search forms if "contains" or "does not contain" is selected in the drop-down that specifies the search mode.

If your search string consists of several words, refbase will return all records where the searched field literally contains the given string of words. E.g., if you searched in the ''title'' field for:

[https://refbase.ipoe.uni-kiel.de/refs/show.php?title=sea%20ice%20thickness sea ice thickness]

then refbase will return any records whose title exactly contains the string "sea ice thickness". This means that you don't need to enclose a string with quotation marks to force an exact match (as is the case for various online search engines such as Google). When searching a refbase database, quotation marks are treated as regular characters and have no special meaning.

Now, what if you wanted to search a database field for the occurrence of two words which are not necessarily next to each other? In refbase, the easiest way of searching for something like "contains <code>xxx</code> AND contains <code>yyy</code>" is to simply start your search with the first search term (<code>xxx</code>), then use the [[Search within Results]] form above the search results list to search for the second search term (<code>yyy</code>). Using this method, you can quickly perform complex searches on multiple fields (and using multiple search terms) without the need of figuring out the correct search pattern in advance.

When searching for two (or more) authors of a particular paper, you often know the order in which the two authors occur. In this case you can make use of the <code>.+</code> metacharacter sequence which matches any string of characters (more on metacharacters below). As an example, you can use:

[https://refbase.ipoe.uni-kiel.de/refs/show.php?author=Cota%2E%2BSmith&without=dups Cota.+Smith]

to find all records where the ''author'' field contains "Cota" followed by "Smith".

=== Using metacharacters to form complex queries ===

By default, refbase allows you to use metacharacters to describe a more complex search pattern. The deployed search syntax is called [http://en.wikipedia.org/wiki/Regular_expressions regular expressions] (often abbreviated as regexp or regex) which comes in many flavors. refbase supports MySQL regular expressions via use of the MySQL <code>REGEXP</code> (or <code>RLIKE</code>) syntax. The MySQL website offers an introduction on [https://dev.mysql.com/doc/refman/8.0/en/pattern-matching.html pattern matching] and provides more information about the [https://dev.mysql.com/doc/refman/8.0/en/regexp.html <code>REGEXP</code> syntax] for regular expressions. See the examples section below for some simple usage examples.

While regular expressions provide a powerful syntax for searching they may be somewhat difficult to write and daunting if you're new to the concept of regular expressions. There are various [https://www.google.com/search?q=regular+expressions+tutorial tutorials on regular expressions] on the net that can help you getting started. A nice [http://linuxclass.heinz.cmu.edu/doc/regex.html basic introduction to regular expressions] ([https://solaris-8.tripod.com/regexp.pdf PDF version]) was written by Stephen Ramsay.

=== Search examples ===

Below are some basic examples that will show you how to use MySQL regular expressions with refbase. The given links are all working examples which you can try out.

If you want to find all records where a particular person is the ''first'' author of the publication, you can prefix the person's name with a caret sign (<code>^</code>). For example, searching the ''author'' field for:

[https://refbase.ipoe.uni-kiel.de/refs/show.php?author=^Ackley, ^Ackley,]

will find all records whose first author name is "Ackley". If you want to restrict the list of returned results further to only those records where a particular person is the publication's ''only'' author (i.e., has no co-authors), you may append the dollar sign (<code>$</code>) at the end of the author's full name and initials. For example, searching for:

[https://refbase.ipoe.uni-kiel.de/refs/show.php?author=^Ackley,%20SF$ ^Ackley, SF$]

will only find those records whose author field exactly (and only) contains the string "Ackley, SF".

Often you want to search for a particular author but you're faced with the problem that the author's name is written differently in different database records. This is often the case for authors whose names contain accented characters or umlauts. You can find all instances of an author's name by using the dot metacharacter (<code>.</code>) which matches every character but the newline character. As an example, to find records where the ''author'' field contains "Gómez" as well as "Gomez", you may use:

[https://refbase.ipoe.uni-kiel.de/refs/show.php?author=G.mez G.mez]

Since the dot metacharacter does not only match the characters "o" and "ó" but also other characters, this search would also find authors whose name is e.g. "Gimez". To avoid this, you can specify the allowed characters explicitly by enclosing them with square brackets:

[https://refbase.ipoe.uni-kiel.de/refs/show.php?author=G%5Bo%F3%5Dmez G[oó]mez]

This will only find records whose ''author'' field contains either "Gomez" or "Gómez". In the above example, the square brackets denote a so-called character class, which you can also use to specify a range of characters. The following example will find all records where the year field contains years between 2002 and 2006:

[https://refbase.ipoe.uni-kiel.de/refs/show.php?year=200%5B2-6%5D 200[2-6]]

You can also use a negated character class by prefixing your list of characters within the square brackets with a caret sign (<code>^</code>) – which effectively matches every character that is ''not'' given within your character class. This may come in handy if you want to find an author whose name may contain more than one variable character. For example, searching for:

[https://refbase.ipoe.uni-kiel.de/refs/show.php?author=L%5B^%20%5D%2Bnne L[^ ]+nne]

will find entries where the ''author'' field contains "Lonne", "Lönne", "Lønne" but also "Loenne". In this example, the negated character class <code>[^ ]</code> matches any single character that is not a space. The plus sign (<code>+</code>) is a quantifier that allows the pattern before this quantifier to match more than once, thus matching also cases such as "Loenne". However, the above search pattern will also match author names such as "Gallienne" or "Delzenne" which may be not what you want. Again, you can specify the allowed characters more explicitly to circumvent this problem:

[https://refbase.ipoe.uni-kiel.de/refs/show.php?author=L(%5Bo%F6%F8%5D%7Coe)nne L([oöø]|oe)nne]

In this example we're using grouping parentheses (<code>(...)</code>) in combination with the alternation metacharacter (i.e. the pipe character: <code>|</code>) which allows to match either the part within the enclosing parentheses that's left from the pipe character or the one that's right to it. In our example, the left part within the parentheses (i.e. the character class <code>[oöø]</code>) will match author names such as "Lonne", "Lönne" and "Lønne" but not "Loenne". The right part within the parentheses (<code>oe</code>) causes "Loenne" to be matched as well.

The dot metacharacter (<code>.</code>) or it's repeated form (<code>.+</code>) can be also used to find all records where the searched field isn't empty. Here's an example for the ''author'' field:

[https://refbase.ipoe.uni-kiel.de/refs/show.php?author=%2E%2B .+]

Speaking of quantifiers, you can use the question mark (<code>?</code>) which indicates that the single character (or search pattern) before the question mark is optional. This is useful when you want to search for multiple variants of a particular keyword, for example:

[https://refbase.ipoe.uni-kiel.de/refs/show.php?keywords=pha%3Feopigment&submit=Display pha?eopigment]

will find records whose ''keywords'' field contains either "phaeopigment" or "pheopigment". You can also append a question mark to a multi-character string that's enclosed by parentheses to indicate that this string is optional. For example, searching the ''title'' field for:

[https://refbase.ipoe.uni-kiel.de/refs/show.php?title=bio(geo)%3Fchemistry bio(geo)?chemistry]

will find records whose title contains either "biogeochemistry" or "biochemistry".

[[refbase:Community_portal|Let us know]] if you've got further questions regarding the refbase search facilities.

[[Category:Usage]]
__NOEDITSECTION__

Searching

2023-11-20T14:47:18Z

WikiSysop: Hide section edit links

This page explains how to use the refbase search facilities:

== Search options ==

=== Basic search ===

* [[Quick Search]]

=== Search pages ===

* [[Simple Search]]
* [[Advanced Search]]
* [[SQL Search]]
* [[Library Search]]

=== Refine your search results ===

* [[Search within Results]]
* [[SQL Search]]

=== Directly jump to particular records ===

* [[Display Details]]

=== User-specific search options ===

* [[Show My Refs]]
* [[Show My Group]]
* [[Recall My Query]]
* [[Display Details]]

== Search syntax ==

=== Basic queries ===

When searching, refbase performs a "contains" search by default. This means that refbase will return all records where the searched field contains the specified search string. As an example, searching the ''title'' field for:

[https://refbase.ipoe.uni-kiel.de/refs/show.php?title=arctic arctic]

will return records where the ''title'' field contains "Arctic", "Antarctic", "Antarctica", "Antarcticque" "subarctic", etc.

This "contains" search is the standard search behaviour in simple search forms such as the [[Quick Search]] or [[Search within Results]] forms. It is also used in all other search forms if "contains" or "does not contain" is selected in the drop-down that specifies the search mode.

If your search string consists of several words, refbase will return all records where the searched field literally contains the given string of words. E.g., if you searched in the ''title'' field for:

[https://refbase.ipoe.uni-kiel.de/refs/show.php?title=sea%20ice%20thickness sea ice thickness]

then refbase will return any records whose title exactly contains the string "sea ice thickness". This means that you don't need to enclose a string with quotation marks to force an exact match (as is the case for various online search engines such as Google). When searching a refbase database, quotation marks are treated as regular characters and have no special meaning.

Now, what if you wanted to search a database field for the occurrence of two words which are not necessarily next to each other? In refbase, the easiest way of searching for something like "contains <code>xxx</code> AND contains <code>yyy</code>" is to simply start your search with the first search term (<code>xxx</code>), then use the [[Search within Results]] form above the search results list to search for the second search term (<code>yyy</code>). Using this method, you can quickly perform complex searches on multiple fields (and using multiple search terms) without the need of figuring out the correct search pattern in advance.

When searching for two (or more) authors of a particular paper, you often know the order in which the two authors occur. In this case you can make use of the <code>.+</code> metacharacter sequence which matches any string of characters (more on metacharacters below). As an example, you can use:

[https://refbase.ipoe.uni-kiel.de/refs/show.php?author=Cota%2E%2BSmith&without=dups Cota.+Smith]

to find all records where the ''author'' field contains "Cota" followed by "Smith".

=== Using metacharacters to form complex queries ===

By default, refbase allows you to use metacharacters to describe a more complex search pattern. The deployed search syntax is called [http://en.wikipedia.org/wiki/Regular_expressions regular expressions] (often abbreviated as regexp or regex) which comes in many flavors. refbase supports MySQL regular expressions via use of the MySQL <code>REGEXP</code> (or <code>RLIKE</code>) syntax. The MySQL website offers an introduction on [http://dev.mysql.com/doc/refman/5.0/en/pattern-matching.html pattern matching] and provides more information about the [http://dev.mysql.com/doc/refman/5.0/en/regexp.html <code>REGEXP</code> syntax] for regular expressions. See the examples section below for some simple usage examples.

While regular expressions provide a powerful syntax for searching they may be somewhat difficult to write and daunting if you're new to the concept of regular expressions. There are various [http://directory.google.com/Top/Computers/Programming/Languages/Regular_Expressions/FAQs,_Help,_and_Tutorials/ tutorials on regular expressions] on the net that can help you getting started. A nice [http://etext.lib.virginia.edu/helpsheets/regex.html basic introduction to regular expressions] was written by Stephen Ramsay. A listing of regex-related links is available at http://grep.extracts.de/.

=== Search examples ===

Below are some basic examples that will show you how to use MySQL regular expressions with refbase. The given links are all working examples which you can try out.

If you want to find all records where a particular person is the ''first'' author of the publication, you can prefix the person's name with a caret sign (<code>^</code>). For example, searching the ''author'' field for:

[https://refbase.ipoe.uni-kiel.de/refs/show.php?author=^Ackley, ^Ackley,]

will find all records whose first author name is "Ackley". If you want to restrict the list of returned results further to only those records where a particular person is the publication's ''only'' author (i.e., has no co-authors), you may append the dollar sign (<code>$</code>) at the end of the author's full name and initials. For example, searching for:

[https://refbase.ipoe.uni-kiel.de/refs/show.php?author=^Ackley,%20SF$ ^Ackley, SF$]

will only find those records whose author field exactly (and only) contains the string "Ackley, SF".

Often you want to search for a particular author but you're faced with the problem that the author's name is written differently in different database records. This is often the case for authors whose names contain accented characters or umlauts. You can find all instances of an author's name by using the dot metacharacter (<code>.</code>) which matches every character but the newline character. As an example, to find records where the ''author'' field contains "Gómez" as well as "Gomez", you may use:

[https://refbase.ipoe.uni-kiel.de/refs/show.php?author=G.mez G.mez]

Since the dot metacharacter does not only match the characters "o" and "ó" but also other characters, this search would also find authors whose name is e.g. "Gimez". To avoid this, you can specify the allowed characters explicitly by enclosing them with square brackets:

[https://refbase.ipoe.uni-kiel.de/refs/show.php?author=G%5Bo%F3%5Dmez G[oó]mez]

This will only find records whose ''author'' field contains either "Gomez" or "Gómez". In the above example, the square brackets denote a so-called character class, which you can also use to specify a range of characters. The following example will find all records where the year field contains years between 2002 and 2006:

[https://refbase.ipoe.uni-kiel.de/refs/show.php?year=200%5B2-6%5D 200[2-6]]

You can also use a negated character class by prefixing your list of characters within the square brackets with a caret sign (<code>^</code>) – which effectively matches every character that is ''not'' given within your character class. This may come in handy if you want to find an author whose name may contain more than one variable character. For example, searching for:

[https://refbase.ipoe.uni-kiel.de/refs/show.php?author=L%5B^%20%5D%2Bnne L[^ ]+nne]

will find entries where the ''author'' field contains "Lonne", "Lönne", "Lønne" but also "Loenne". In this example, the negated character class <code>[^ ]</code> matches any single character that is not a space. The plus sign (<code>+</code>) is a quantifier that allows the pattern before this quantifier to match more than once, thus matching also cases such as "Loenne". However, the above search pattern will also match author names such as "Gallienne" or "Delzenne" which may be not what you want. Again, you can specify the allowed characters more explicitly to circumvent this problem:

[https://refbase.ipoe.uni-kiel.de/refs/show.php?author=L(%5Bo%F6%F8%5D%7Coe)nne L([oöø]|oe)nne]

In this example we're using grouping parentheses (<code>(...)</code>) in combination with the alternation metacharacter (i.e. the pipe character: <code>|</code>) which allows to match either the part within the enclosing parentheses that's left from the pipe character or the one that's right to it. In our example, the left part within the parentheses (i.e. the character class <code>[oöø]</code>) will match author names such as "Lonne", "Lönne" and "Lønne" but not "Loenne". The right part within the parentheses (<code>oe</code>) causes "Loenne" to be matched as well.

The dot metacharacter (<code>.</code>) or it's repeated form (<code>.+</code>) can be also used to find all records where the searched field isn't empty. Here's an example for the ''author'' field:

[https://refbase.ipoe.uni-kiel.de/refs/show.php?author=%2E%2B .+]

Speaking of quantifiers, you can use the question mark (<code>?</code>) which indicates that the single character (or search pattern) before the question mark is optional. This is useful when you want to search for multiple variants of a particular keyword, for example:

[https://refbase.ipoe.uni-kiel.de/refs/show.php?keywords=pha%3Feopigment&submit=Display pha?eopigment]

will find records whose ''keywords'' field contains either "phaeopigment" or "pheopigment". You can also append a question mark to a multi-character string that's enclosed by parentheses to indicate that this string is optional. For example, searching the ''title'' field for:

[https://refbase.ipoe.uni-kiel.de/refs/show.php?title=bio(geo)%3Fchemistry bio(geo)?chemistry]

will find records whose title contains either "biogeochemistry" or "biochemistry".

[http://sourceforge.net/forum/forum.php?forum_id=218758 Let us know], if you've got further questions regarding the refbase search facilities.

[[Category:Usage]]
__NOEDITSECTION__

Searching

2023-11-20T14:45:39Z

WikiSysop: Original page content from 19-Mar-2012

This page explains how to use the refbase search facilities:

== Search options ==

=== Basic search ===

* [[Quick Search]]

=== Search pages ===

* [[Simple Search]]
* [[Advanced Search]]
* [[SQL Search]]
* [[Library Search]]

=== Refine your search results ===

* [[Search within Results]]
* [[SQL Search]]

=== Directly jump to particular records ===

* [[Display Details]]

=== User-specific search options ===

* [[Show My Refs]]
* [[Show My Group]]
* [[Recall My Query]]
* [[Display Details]]

== Search syntax ==

=== Basic queries ===

When searching, refbase performs a "contains" search by default. This means that refbase will return all records where the searched field contains the specified search string. As an example, searching the ''title'' field for:

[https://refbase.ipoe.uni-kiel.de/refs/show.php?title=arctic arctic]

will return records where the ''title'' field contains "Arctic", "Antarctic", "Antarctica", "Antarcticque" "subarctic", etc.

This "contains" search is the standard search behaviour in simple search forms such as the [[Quick Search]] or [[Search within Results]] forms. It is also used in all other search forms if "contains" or "does not contain" is selected in the drop-down that specifies the search mode.

If your search string consists of several words, refbase will return all records where the searched field literally contains the given string of words. E.g., if you searched in the ''title'' field for:

[https://refbase.ipoe.uni-kiel.de/refs/show.php?title=sea%20ice%20thickness sea ice thickness]

then refbase will return any records whose title exactly contains the string "sea ice thickness". This means that you don't need to enclose a string with quotation marks to force an exact match (as is the case for various online search engines such as Google). When searching a refbase database, quotation marks are treated as regular characters and have no special meaning.

Now, what if you wanted to search a database field for the occurrence of two words which are not necessarily next to each other? In refbase, the easiest way of searching for something like "contains <code>xxx</code> AND contains <code>yyy</code>" is to simply start your search with the first search term (<code>xxx</code>), then use the [[Search within Results]] form above the search results list to search for the second search term (<code>yyy</code>). Using this method, you can quickly perform complex searches on multiple fields (and using multiple search terms) without the need of figuring out the correct search pattern in advance.

When searching for two (or more) authors of a particular paper, you often know the order in which the two authors occur. In this case you can make use of the <code>.+</code> metacharacter sequence which matches any string of characters (more on metacharacters below). As an example, you can use:

[https://refbase.ipoe.uni-kiel.de/refs/show.php?author=Cota%2E%2BSmith&without=dups Cota.+Smith]

to find all records where the ''author'' field contains "Cota" followed by "Smith".

=== Using metacharacters to form complex queries ===

By default, refbase allows you to use metacharacters to describe a more complex search pattern. The deployed search syntax is called [http://en.wikipedia.org/wiki/Regular_expressions regular expressions] (often abbreviated as regexp or regex) which comes in many flavors. refbase supports MySQL regular expressions via use of the MySQL <code>REGEXP</code> (or <code>RLIKE</code>) syntax. The MySQL website offers an introduction on [http://dev.mysql.com/doc/refman/5.0/en/pattern-matching.html pattern matching] and provides more information about the [http://dev.mysql.com/doc/refman/5.0/en/regexp.html <code>REGEXP</code> syntax] for regular expressions. See the examples section below for some simple usage examples.

While regular expressions provide a powerful syntax for searching they may be somewhat difficult to write and daunting if you're new to the concept of regular expressions. There are various [http://directory.google.com/Top/Computers/Programming/Languages/Regular_Expressions/FAQs,_Help,_and_Tutorials/ tutorials on regular expressions] on the net that can help you getting started. A nice [http://etext.lib.virginia.edu/helpsheets/regex.html basic introduction to regular expressions] was written by Stephen Ramsay. A listing of regex-related links is available at http://grep.extracts.de/.

=== Search examples ===

Below are some basic examples that will show you how to use MySQL regular expressions with refbase. The given links are all working examples which you can try out.

If you want to find all records where a particular person is the ''first'' author of the publication, you can prefix the person's name with a caret sign (<code>^</code>). For example, searching the ''author'' field for:

[https://refbase.ipoe.uni-kiel.de/refs/show.php?author=^Ackley, ^Ackley,]

will find all records whose first author name is "Ackley". If you want to restrict the list of returned results further to only those records where a particular person is the publication's ''only'' author (i.e., has no co-authors), you may append the dollar sign (<code>$</code>) at the end of the author's full name and initials. For example, searching for:

[https://refbase.ipoe.uni-kiel.de/refs/show.php?author=^Ackley,%20SF$ ^Ackley, SF$]

will only find those records whose author field exactly (and only) contains the string "Ackley, SF".

Often you want to search for a particular author but you're faced with the problem that the author's name is written differently in different database records. This is often the case for authors whose names contain accented characters or umlauts. You can find all instances of an author's name by using the dot metacharacter (<code>.</code>) which matches every character but the newline character. As an example, to find records where the ''author'' field contains "Gómez" as well as "Gomez", you may use:

[https://refbase.ipoe.uni-kiel.de/refs/show.php?author=G.mez G.mez]

Since the dot metacharacter does not only match the characters "o" and "ó" but also other characters, this search would also find authors whose name is e.g. "Gimez". To avoid this, you can specify the allowed characters explicitly by enclosing them with square brackets:

[https://refbase.ipoe.uni-kiel.de/refs/show.php?author=G%5Bo%F3%5Dmez G[oó]mez]

This will only find records whose ''author'' field contains either "Gomez" or "Gómez". In the above example, the square brackets denote a so-called character class, which you can also use to specify a range of characters. The following example will find all records where the year field contains years between 2002 and 2006:

[https://refbase.ipoe.uni-kiel.de/refs/show.php?year=200%5B2-6%5D 200[2-6]]

You can also use a negated character class by prefixing your list of characters within the square brackets with a caret sign (<code>^</code>) – which effectively matches every character that is ''not'' given within your character class. This may come in handy if you want to find an author whose name may contain more than one variable character. For example, searching for:

[https://refbase.ipoe.uni-kiel.de/refs/show.php?author=L%5B^%20%5D%2Bnne L[^ ]+nne]

will find entries where the ''author'' field contains "Lonne", "Lönne", "Lønne" but also "Loenne". In this example, the negated character class <code>[^ ]</code> matches any single character that is not a space. The plus sign (<code>+</code>) is a quantifier that allows the pattern before this quantifier to match more than once, thus matching also cases such as "Loenne". However, the above search pattern will also match author names such as "Gallienne" or "Delzenne" which may be not what you want. Again, you can specify the allowed characters more explicitly to circumvent this problem:

[https://refbase.ipoe.uni-kiel.de/refs/show.php?author=L(%5Bo%F6%F8%5D%7Coe)nne L([oöø]|oe)nne]

In this example we're using grouping parentheses (<code>(...)</code>) in combination with the alternation metacharacter (i.e. the pipe character: <code>|</code>) which allows to match either the part within the enclosing parentheses that's left from the pipe character or the one that's right to it. In our example, the left part within the parentheses (i.e. the character class <code>[oöø]</code>) will match author names such as "Lonne", "Lönne" and "Lønne" but not "Loenne". The right part within the parentheses (<code>oe</code>) causes "Loenne" to be matched as well.

The dot metacharacter (<code>.</code>) or it's repeated form (<code>.+</code>) can be also used to find all records where the searched field isn't empty. Here's an example for the ''author'' field:

[https://refbase.ipoe.uni-kiel.de/refs/show.php?author=%2E%2B .+]

Speaking of quantifiers, you can use the question mark (<code>?</code>) which indicates that the single character (or search pattern) before the question mark is optional. This is useful when you want to search for multiple variants of a particular keyword, for example:

[https://refbase.ipoe.uni-kiel.de/refs/show.php?keywords=pha%3Feopigment&submit=Display pha?eopigment]

will find records whose ''keywords'' field contains either "phaeopigment" or "pheopigment". You can also append a question mark to a multi-character string that's enclosed by parentheses to indicate that this string is optional. For example, searching the ''title'' field for:

[https://refbase.ipoe.uni-kiel.de/refs/show.php?title=bio(geo)%3Fchemistry bio(geo)?chemistry]

will find records whose title contains either "biogeochemistry" or "biochemistry".

[http://sourceforge.net/forum/forum.php?forum_id=218758 Let us know], if you've got further questions regarding the refbase search facilities.

[[Category:Usage]]

Interface FAQ

2023-11-19T16:47:45Z

WikiSysop: Hide section edit links

This page lists some frequently asked questions about the refbase interface:

== Where can I change the citation style? ==

You can change the citation style in the "Display Options" form when you're in Citation view. Here's how to do it:

# Perform your search as usual.
# Above the list of your search results, click on the "Citations" link (it's on the right-hand side of the screen). This will display your search results in Citation view.
# Now click the "Search & Display Options" link (it's also above the list of search results, on the left-hand side of the screen). This will display some forms that let you refine your query or change the display of results.
# Choose your preferred citation style from the "Style" dropdown menu in the "Display Options" form, then click the "Show" button that's next to the dropdown menu.

Your chosen citation style should now get used for all citation output on the web interface as well as for export of formatted citation lists to RTF, PDF, LaTeX, etc. See also the next FAQ entry.

== Can I specify my own default citation style? ==

While the database admin can choose a global default style ([[Configuring_refbase#How_can_I_change_the_default_citation_style.3F|more info]]), there currently isn't an option to choose the default citation style individually for each user. However, as long as you stay in the search results list, your selected citation style will be honoured — even when switching between views, using any of the search & display options, or when performing new searches via the Quick Search form (at the top right corner of the screen).

== How can I delete records? ==

The [[Deleting records]] pages describes how to remove record entries from the database, and explains how to achieve batch deletions.

[[Category:Usage]]
__NOEDITSECTION__

Interface FAQ

2023-11-19T16:47:05Z

WikiSysop: Original page content from 19-Dec-2008

Library Search

2023-11-19T16:24:50Z

WikiSysop: Remove excessive whitespace

The "library search" is a special one-click search, offered directly at the start page and in the footer of every page. The refbase admin can configure which subset of the database the "library search" uses.

== Changing the library search ==

This chapter is solely relavant for the refbase admin

=== Definition of what this search is searching for ===

The <code>library_search.php</code> script will search within a subset of your refbase database. Searches via this library search form will be restricted to the condition given in variable <code>$librarySearchPattern</code> in file <code>initialize/ini.inc.php</code>.

There you will find this explanation:

<blockquote>
Define what will be searched by <code>library_search.php</code>: refbase offers a "Library Search" feature that provides a separate search page for searching an institution's library. All searches performed thru this search form will be restricted to records that match the specified condition. First param must be a valid field name from table <code>refs</code>, second param the conditional expression (specified as MySQL extended regular expression -> see note at the end of this file). Of course, you could also use this feature to restrict searches thru <code>library_search.php</code> by _any_ other condition. E.g., with <code>location</code> as the first parameter and your own login email address as the second parameter, any "library" search would be restricted to your personal literature data set.
</blockquote>

If, for example, items of your institute's library are also catalogued in your refbase database, then you could use the library search feature to only search items in your institute's library.

At the Institute for Polarecology Kiel, we add items of our local library to our refbase database using a dedicated refbase account (named "Library Admin" or the like). We've then set variable <code>$librarySearchPattern</code> in <code>ini.inc.php</code> to:

$librarySearchPattern = array("location", "library"); // e.g. <code>array("location", "IPÖ Library")</code>

This will restrict searches via <code>library_search.php</code> to records that contain the word "Library" within the <code>location</code> field. Thus search results will only show items from our institute's library. The search results list will also display additional/different fields by default, such as the <code>call_number</code> field (which contains the unique library identifier for the item).

You could, instead, search results to items that contain a particular author, publication, keyword, contribution_id, etc. As an example, consider that you've tagged a particular subset of your database records with the word "Students Reading List" in the <code>keywords</code> field. Then you could use this setup:

$librarySearchPattern = array("keywords", "Students Reading List");

to restrict searches via <code>library_search.php</code> to records that contain the keyword "Students Reading List".

=== Changing the name of "library search" ===

Since the name of the standard-link <code>library search</code> is sometimes confusing (especially, if you define your own query), you can change this in one of two ways. Both involve modifying refbase files which will be overwritten on upgrades.

==== Customized localization ====

"Library" and "Search" are defined in the language-file <code>locales/common.inc</code>. You can modify "Library" to make it more descriptive.

==== Alternative: customize index.php ====

* Open <code>index.php</code> of your refbase installation.

Search for this line:

<pre>
<li><a href="library_search.php"><?php echo $loc["Library"]; ?> <?php echo $loc["Search"]; ?>
</pre>

and replace this

<pre>
?php echo $loc["Library"]; ?> <?php echo $loc["Search"]; ?
</pre>

part of the line with your desired link name.

* Open the <code>includes/footer.inc.php</code> file and search for <code>library</code>

you have to change the <code>title</code>-parameter and the link name.

For these changes, you may either use static names (which will remove the localization of refbase for your users) or define new localized variables.

== Hiding the link ==

An alternative to customizing the search is to remove it completely. One can safely comment out or remove the lines in <code>index.php</code> and <code>includes/footer.inc.php</code>.

__NOEDITSECTION__

Library Search

2023-11-19T16:23:56Z

WikiSysop: Hide section edit links

Library Search

2023-11-19T16:21:18Z

WikiSysop: Better wikitext approximation of the original page content

Library Search

2023-11-19T16:05:12Z

WikiSysop: Rough version of the original page content (recovered from https://web.archive.org/web/20160427032455/http://www.refbase.net/index.php/Library_Search)

The "library search," is a special one-click search, offered directly at the start page and in the footer of every page. The refbase admin can configure which subset of the database the "library search" uses.

== Changing the library search ==

This chapter is solely relavant for the refbase admin

=== Definition of what this search is searching for ===

The 'library_search.php' script will search within a subset of your refbase database. Searches via this library search form will be restricted to the condition given in variable '$librarySearchPattern' in file 'initialize/ini.inc.php'.

There you will find this explanation:

> Define what will be searched by "library_search.php": refbase offers a "Library Search" feature that provides a separate search page for searching an institution's library. All searches performed thru this search form will be restricted to records that match the specified condition. First param must be a valid field name from table 'refs', second param the conditional expression (specified as MySQL extended regular expression -> see note at the end of this file). Of course, you could also use this feature to restrict searches thru "library_search.php" by _any_ other condition. E.g., with "location" as the first parameter and your own login email address as the second parameter, any "library" search would be restricted to your personal literature data set.

If, for example, items of your institute's library are also catalogued in your refbase database, then you could use the library search feature to only search items in your institute's library.

At the Institute for Polarecology Kiel, we add items of our local library to our refbase database using a dedicated refbase account (named "Library Admin" or the like). We've then set variable '$librarySearchPattern' in 'ini.inc.php' to:

$librarySearchPattern = array("location", "library"); // e.g. 'array("location", "IPÖ Library")'

This will restrict searches via 'library_search.php' to records that contain the word "Library" within the 'location' field. Thus search results will only show items from our institute's library. The search results list will also display additional/different fields by default, such as the 'call_number' field (which contains the unique library identifier for the item).

You could, instead, search results to items that contain a particular author, publication, keyword, contribution_id, etc. As an example, consider that you've tagged a particular subset of your database records with the word "Students Reading List" in the 'keywords' field. Then you could use this setup:

$librarySearchPattern = array("keywords", "Students Reading List");

to restrict searches via 'library_search.php' to records that contain the keyword "Students Reading List".

=== Changing the name of "library search" ===

Since the name of the standard-link 'library search' is sometimes confusing (especially, if you define your own query), you can change this in one of two ways. Both involve modifying refbase files which will be overwritten on upgrades.

==== Customized localization ====

"Library" and "Search" are defined in the language-file 'locales/common.inc'. You can modify "Library" to make it more descriptive.

==== Alternative: customize index.php ====

1. Open 'index.php' of your refbase installation.
Search for this line:

<li><a href="library_search.php"><?php echo $loc["Library"]; ?> <?php echo $loc["Search"]; ?>

and replace this

?php echo $loc["Library"]; ?> <?php echo $loc["Search"]; ?

part of the line with your desired link name.

2. Open the 'includes/footer.inc.php' file and search for 'library'

you have to change the 'title'-parameter and the link name.

For these changes, you may either use static names (which will remove the localization of refbase for your users) or define new localized variables.

== Hiding the link ==

An alternative to customizing the search is to remove it completely. One can safely comment out or remove the lines in 'index.php' and 'includes/footer.inc.php'.

Recall My Query

2023-11-19T15:44:15Z

WikiSysop: Hide section edit links

refbase offers to save any of your queries for easy later retrieval. In addition, refbase will store the following display options with your query:

* name (and order) of displayed fields
* number of records displayed per page
* sort order of records
* if links and/or SQL query are displayed
* view type (i.e., web view or print view)

This means that you can use the 'save query' functionality to save custom views.

== Example 1 ==

Say, you regularly find yourself scanning the abstracts within your own literature. To save a custom view for that purpose, perform the following steps:

* Login and click on the 'My Refs' link in the upper right corner. This will show all records belonging to your own literature data set.
* Adopt the column view to fit your needs, i.e., use the 'Display Options' form to hide, say, the ''publication'', ''volume'' and ''pages'' fields and show the ''abstract'' field instead. You may also want to increase the number of records being displayed per page.
* Now click the 'save' link in the header line that says "x-x of xxx records found matching your query (save | RSS)".
* You'll see a form containing your current query. If you want, you can further refine your query or any display options here (like suppressing the 'Links' column or choosing 'Print' view for display). If you're done, give your query a meaningful name and click the 'Add Query' button.

You can now always access your saved query from the drop down of the 'Recall My Query' form on the main page. Note that the items in the drop down are sorted by history of usage, i.e., most recently chosen queries will be always at the top of the list.

The forms in the header of your search results list (i.e., 'Show My Group', 'Search within Results' and 'Display Options') will respect your current view settings. By this, you can perform a search within your own literature or display a different group but still have, say, the ''abstract'' field displayed instead of the default set of columns.

== Example 2 ==

Another use of the 'save query' feature might be the quick access to hidden fields (or fields not shown in the drop down menus) that you would otherwise need to type in manually using the SQL search form.

As an example, refbase offers hidden fields that store information about when a record was created/modified and who did create/modify the record. To save a custom query/view that displays modification info for all records that were edited today, perform the following steps:

* Click the 'save' link in the header line of any search results page or call the ''query_manager.php'' script directly using the URL field of your browser.
* Select the displayed SQL query and replace it with this one:
SELECT author, title, year, location, modified_by, modified_date, modified_time FROM refs WHERE modified_date = CURDATE() ORDER BY modified_date DESC, modified_time DESC
* Adopt the display options as desired, name your query (e.g., 'Edited Today') and click the 'Add Query' button.

Selecting this query (from the drop down of the 'Recall My Query' form on the main page) will give you an instant overview of who edited what during the day.

[[Category:Usage]]
__NOEDITSECTION__

Recall My Query

2023-11-19T15:41:51Z

WikiSysop: Original page content from 05-Jan-2007

Interface

2023-11-19T15:31:29Z

WikiSysop: Original page content from 07-Feb-2006

Use the links below to learn more about the refbase interface:

* [[Main page]]:
** [[Show My Refs]]
** [[Quick Search]]
** [[Browse My Refs]]
** [[Show My Group]]
** [[Recall My Query]]

* Search pages:
** [[Simple Search]]
** [[Advanced Search]]
** [[SQL Search]]
** [[Library Search]]

* Views:
** [[List View]]
** [[Details View]]
** [[Print View]]
** [[Browse View]]
** [[Citation View]]
** [[Export View]]

* Forms on results pages:
** [[Show My Group]]
** [[Search within Results]]
** [[Display Options]]
** [[Display full Entries]]
** [[Cite]]
** [[Add or Remove Group]]
** [[Export]]

* Special Pages:
** [[Display Details]]
** [[Extract Citations]]

[[Category:Usage]]

Planned feature additions

2023-11-07T13:08:07Z

WikiSysop: Fix incorrect display of accented characters & umlauts

This page lists planned feature additions:

'''Important''': Please note that the items listed below are simply suggestions for improving refbase and that we cannot (and don't want to) speculate on whether or when any of the listed features will be added to refbase.

== General ==

=== Resource types ===

Goal: Increase number of supported resource types.

Priority: 6

Status: added types Abstract, Conference Article, Conference Volume, Magazine Article, Manual, Miscellaneous, Newspaper Article, Report, Patent, Software

Progress: 50%

Description: refbase should allow users to choose from a variety of additional resource types including conference proceeding, patent, report, newspaper article, computer program, etc. All these types should invoke appropriate output on citation. In addition, the admin should be allowed to add additional resource types and users should be able to disable any unused types.

=== Migrate to more common libraries ===

Goal: To work under a larger number of configurations & to depend on only well-maintained code.

Priority: 3

Status: not started

Progress: 0%

Description: We should consider migrating away from the ActiveLink XML library, as it isn't maintained. refbase should also be able to use MySQLi.

== Installation and updates ==

=== Redirect from ''index.php'' to ''install.php'' or ''update.php'' ===

Goal: refbase should direct to ''install.php'' or ''update.php'' as needed.

Priority: 6

Status: not started

Progress: 0%

Description: If the database doesn't exist, refbase should direct to ''install.php''. A version number or date for refbase could be stored in the database. If it is older than a version variable in ''index.php'', ''index.php'' could redirect to the update script.

=== Improvements to ''install.php'' ===

Goal: The ''install.php'' script should verify required server settings and provide more options for installation on different server setups.

Priority: 6

Status: not started

Progress: 0%

Description: 1) ''install.php'' should check required server settings prior to installation, and report possible problems in advance. 2) ''install.php'' should allow for installation into an existing database by providing an option for a table prefix that will be used for the refbase MySQL tables (currently, this can only be done by editing some configuration files). 3) To allow for web-based installation on shared hosts, ''install.php'' could offer an option to use an existing MySQL user (instead of setting up its own MySQL user which requires a MySQL admin user & password). 4) ''install.php'' should provide an option to omit the sample data, i.e. install with a blank database.

=== Allow editing of configuration scripts through a web interface ===

Goal: Offer a web interface to the settings provided in ''ini.inc.php'', ''db.inc.php' and other config files.

Priority: 3

Status: not started

Progress: 0%

Description: Upon installation or update, refbase could list the settings in the various configuration files that are now manually edited & allow users to make changes with the web interface.

== Searching ==

=== Search for duplicates ===

Goal: Offer the user means for handling duplicate database entries.

Priority: 4

Status: in development

Progress: 40%

Description: The database should offer means to easily spot duplicate entries and mark particular records as original (or duplicate) entry. Search features should allow users to exclude duplicate entries from the results list. It would be preferable if a smart dup detection mechanism such as phonetic matching could be used. See the [http://dev.mysql.com/doc/refman/4.1/en/string-functions.html MySQL string functions] <code>SOUNDEX</code> and <code>SOUNDS LIKE</code>.

=== ''OR'' search capabilities ===

Goal: Allow ''OR'' searches via the GUI.

Priority: 3

Status: not started

Progress: 0%

Description: When searching via one of the dedicated search pages, users should be able to specify whether a search on multiple fields will invoke an ''AND'' or an ''OR'' query (currently, entering search terms in multiple fields will always connect search terms with ''AND''). In addition, the "Search within Results" query form should allow users to expand the current result set, i.e. add found results to the existing list of results.

=== Simple handling of accented characters or umlauts ===

Goal: Allow naive users to search for accented characters by using the unaccented character and vice-versa.

Priority: 3

Status: not started

Progress: 0%

Description: If a search query contains no accents, it might be desirable to automatically search for commonly accented characters (especially in the Quick and Simple searches). If a user enters 'Jon', refbase could search for 'J[oóöø]n'. Similarly, it might be desirable to search for unaccented characters if a query contains an accent. If a user entered in 'Jón', refbase might search instead for 'J[oó]n'. Naturally, there should be a mechanism for "advanced users" to have exact searches (perhaps by requiring a pre or post fix for more precise handling of (un)accented search strings.

=== Cross-site searches ===

Goal: Allow users to search and display results from other databases.

Priority: 2

Status: not started

Progress: 0%

Description: refbase should allow for cross-site searches both through other installations of refbase as well as through other bibliographic databases of the [http://bibliophile.sourceforge.net/ Bibliophile initiative]. Support for web service protocols such as [[Search/Retrieve_web_services|SRU]] and [[#OpenSearch support|OpenSearch]] will ease communication between different applications.

== Adding/Editing of records ==

=== Import ===

Goal: Offer direct data import from MODS XML.

Priority: 6

Status: not started

Progress: 0%

Description: refbase currently offers a number of native import scripts, as well as scripts which use [[Bibutils]] to convert formats to something which refbase can read. Long-term plans are to provide native import capabilities for [http://www.loc.gov/standards/mods/ MODS XML]. [[Importing records]] describes the import functionality available in refbase and future plans on import.

=== Direct import via arXiv ID ===

Goal: Use arXiv API to directly fetch and import records & PDFs from arXiv.org.

Priority: 5

Status: import from arXiv.org has been fully implemented, though some aspects (such as parsing of the "Journal Ref" string) might need some further testing and fine-tuning

Progress: 95%

Description: refbase allows to directly fetch and import records from [http://www.pubmed.gov PubMed.gov] via their PubMed ID. A similar feature should be added for the [http://www.arxiv.org/ arXiv.org] e-Print archive. The [http://export.arxiv.org/api_help/docs/user-manual.html arXiv API] allows for HTTP GET queries by arXiv ID and returns OpenSearch Atom feeds with basic metadata (title, author(s), publication date, abstract, and journal info if given) and any URLs (HTML, PDF, DOI) associated with an article. refbase should parse the OpenSearch response and add new database records for each feed entry. Ideally, associated PDFs would be fetched as well and stored with the record.

=== Record-type specific forms ===

Goal: Simplify manual data input by providing record-type specific forms.

Priority: 2

Status: not started

Progress: 0%

Description: Record-type specific forms would guide a user by only showing those fields that are required for a particular record-type (like journal articles, book chapters or whole books). Record-type specific forms might not be necessary if the current "Add/Edit Record" form would be able to dynamically indicate required fields for a given record-type.

=== Input validation ===

Goal: refbase should dynamically validate input in the "Add/Edit Record" form.

Priority: 4

Status: not started

Progress: 0%

Description: refbase should provide on-the-fly validation of data while a user inputs or edits data in the "Add/Edit Record" form. This would help users to ensure correct formatting for fields that require a specific string formatting (such as the ''author'' field). Dynamic form input validation may be best realized using [http://en.wikipedia.org/wiki/AJAX AJAX] style methods.

=== Auto-filling of fields ===

Goal: refbase should auto-fill fields if possible.

Priority: 4

Status: not started

Progress: 0%

Description: refbase should be able to auto-fill empty fields based on information available in other fields and/or tables. This is especially useful if a flat database design is maintained. A typical application would be the auto-filling of journal-related fields (e.g. ''publisher'', ''place'', ''abbrev_journal'', ''language'' or ''summary_language'') from a journal database if the journal name (or ISSN) can be uniquely matched. If no journal info is available in the refbase journal database, a public service such as http://journalseek.net/ could be used for information retrieval and the fetched journal data could be automatically added to refbase's own journal database. Similarly, refbase could use web services from CrossRef (see [http://hublog.hubmed.org/archives/001624.html HubLog post] and links therein), WorldCat ([http://xissn.worldcat.org/xissnadmin/index.htm xISSN] & [http://www.worldcat.org/affiliate/webservices/xisbn/app.jsp xISBN]) or LibraryThing ([http://www.librarything.com/thingology/2006/06/introducing-thingisbn_14.php thingISBN]) to supplement record metadata.

=== Auto-completion of field input ===

Goal: refbase should auto-complete user input in the "Add/Edit Record" form.

Priority: 4

Status: auto-completion has been fully implemented for the "Add/Edit Record" form and search suggestions are provided in some of the search forms (but they're not yet available in the "Advanced Search" and "Library Search" forms)

Progress: 95%

Description: It would be helpful if refbase would offer auto-completion features for fields of the "Add/Edit Record" form. This would allow users to start typing a string, then choose from a list of matching values (such as authors, keywords or journal names) that already exist in the database. Ideally, such a feature would not interfere with browser-specific auto-completion features and would be platform/browser agnostic. One way of implementing this would be a pop-up window where a generic database value browser would be combined with "Search within Results" functionality, and selected values would be written/appended to the field that's currently selected in the "Add/Edit Record" form.

=== Multiple files per record ===

Goal: refbase should allow users to upload multiple files per record.

Priority: 5

Status: not started

Progress: 0%

Description: Currently, refbase allows to upload one file per record. It would be useful if multiple files could be attached to a given record. This would allow users to upload different representations, variants or versions of the same publication. Besides the final PDF, users could then attach a Powerpoint presentation or an audio file of an associated talk (though, in a strictly hierarchical design, talks or posters may warrant different but related records). Other use cases could be the upload of supplementary material or different manuscript revisions during collaborative preparation of an article, or the upload of a publicly available Open Access version (such as preprints or postprints). Upon upload, users should be able to specify file info (such as file type, language or a description) and access permissions individually for each file.

=== Multiple URLs per record ===

Goal: refbase should allow users to specify multiple URLs per record.

Priority: 5

Status: not started

Progress: 0%

Description: Currently, refbase allows to specify one URL per record. It would be useful if multiple URLs could be added to a given record. While the primary URL could point to the publication's entry at the publisher site, additional URLs could point to, say, further info/news about the publication, any supplementary material, or related discussion located elsewhere. As is true for multiple files, some options to categorize and/or describe the given URLs as well as individual access permissions might be useful.

=== Support foreign record identifiers ===

Goal: refbase should support record identifiers from foreign repositories (e.g. from [http://www.pubmed.gov PubMed.gov] or [http://www.arxiv.org/ arXiv.org]) explicitly, and auto-generate links back to these repositories.

Priority: 5

Status: not started

Progress: 0%

Description: Upon import, refbase currently puts foreign record identifiers (such as IDs from arXiv, ISI Web of Science, PubMed, or SciFinder) into the ''notes'' field. It would be nice, however, if these record identifiers would be stored in some dedicated field(s). This would allow refbase to auto-generate links back to the corresponding record entries at the foreign repositories.

== Sharing ==

=== Public groups (tags) ===

Goal: Allow users to collectively share and categorize groups of records.

Priority: 6

Status: not started

Progress: 0%

Description: We plan to open up the refbase group (aka tagging) mechanism so that groups can be made public, group-specific or private. This will enable users to share their groups with each other and establish a common categorization system.

=== User comments ===

Goal: Allow users to comment on particular records and exchange their thoughts with others.

Priority: 3

Status: not started

Progress: 0%

Description: We imagine a comment system where multiple comments would be allowed for a particular record and where comments could be made public, group-specific or private. Comments could be searched and displayed similar to (and in combination with) bibliographic references. Here's an ASCII mockup of how we envision such a system:

+-------------------------------------------------------------------+
| |
| Cota GF, Horne EPW (1989) Physical control of Arctic ice algal |
| production. Mar Ecol Prog Ser 52(2):111-121 |
| |
| Matthias Steffens | This is an essential article that provides |
| ***** | a good dataset on environmental control of |
| 2005-04-27 23:33 | primary production in polar areas. |
| |
+-------------------------------------------------------------------+
| |
| Mock T (2002) In situ primary production in young Antarctic sea |
| ice. Hydrobiologia 470(1-3):127-132 |
| |
| Matthias Steffens | Given the inaccessibility of the location |
| *** | it's valuable data nonetheless. In situ |
| 2004-12-18 16:05 | measurements are still very rare. |
| |
| Paul Miller | I didn't get the point of this article. |
| * | IMHO, it's based on a weak dataset and |
| 2004-12-03 12:19 | the conclusions are fuzzy. |
| |
| Matthias Steffens | Did anybody read this one? I'd appreciate |
| | your opinions on the used method and |
| 2004-12-01 11:22 | how this relates to existing methods. |
| |
+-------------------------------------------------------------------+

According to the above visualization, comments would print below the reference they are referring to. The reference would be displayed as a citation. Multiple citations with multiple comments could be displayed and you could search within results as usual. Note the stars which indicate the users rating. Users could edit/delete their own comments and decide who'll be able to see them (everyone, certain group(s) or private).

=== Better integration with desktop reference managers ===

Goal: Provide means for easy download of records to desktop reference managers, and for direct record upload to a refbase database.

Priority: 5

Status: for [http://www.sonnysoftware.com/ Bookends], "Upload to refbase" functionality has been added

Progress: 5%

Description: refbase should integrate with desktop reference managers (such as [http://bibdesk.sourceforge.net/ BibDesk], [http://www.sonnysoftware.com/ Bookends], [http://jabref.sourceforge.net/ JabRef], [http://mekentosj.com/papers/ Papers] or [http://www.zotero.org/ Zotero]) so that records stored in a refbase database can be easily retrieved from within these applications. Zotero can already extract bibliographic metadata from refbase's web pages via [[COinS]] or [[unAPI service|unAPI]], and something similar could work for other apps that feature web views. In addition, it would be desirable if users could search an online refbase database from within their desktop reference managers. The refbase search & retrieve webservices offer standardized APIs for this, such as the [[Search/Retrieve_web_services|SRU/W webservice]] or [[#OpenSearch support|OpenSearch]] in conjunction with the existing [[unAPI service]]. Finally, it would be also useful if users of desktop reference managers could upload (and eventually synch) records to a refbase server directly from within their desktop application. In case of Zotero, "upload to refbase" functionality could be developed via an [http://dev.zotero.org/docs/sample_utility Zotero utility].

== Webservices ==

=== OpenSearch support ===

Goal: Allow OpenSearch clients to query refbase and return found results in OpenSearch response format.

Priority: 6

Status: OpenSearch support has been implemented with support for auto-discovery, multiple response formats (HTML, Atom, RSS, SRW_DC XML, SRW_MODS XML), simple CQL searches and support for search suggestions (returned in JSON or HTML); a better CQL parser would be desirable

Progress: 95%

Description: Similar to the refbase [[Search/Retrieve_web_services|SRU/W webservice]], refbase should support an [[OpenSearch service|OpenSearch]] webservice. OpenSearch capable clients would be able to [http://www.opensearch.org/Specifications/OpenSearch/1.1#OpenSearch_Query_element query] a refbase database and retrieve search results in an OpenSearch [http://www.opensearch.org/Specifications/OpenSearch/1.1#OpenSearch_response_elements response format], e.g. RSS 2.0 or Atom 1.0, plus the OpenSearch response extensions. This would also allow to integrate several refbase servers (or other OpenSearch capable servers) via [[Planned_feature_additions#Cross-site_searches|cross-site searches]]. When implemented, refbase should support auto-discovery to allow for [http://developer.mozilla.org/en/docs/Creating_OpenSearch_plugins_for_Firefox search plugins]. Eventual support for JSON for fetching of search suggestions would be nice.

=== API ===

Goal: Provide an API that allows clients to query a refbase database, retrieve results in a structured format and modify any database information.

Priority: 5

Status: not started

Progress: 0%

Description: Opposed to pure search/retrieve webservices (such as [[Search/Retrieve_web_services|SRU/W]] and [[OpenSearch service|OpenSearch]]), a [http://en.wikipedia.org/wiki/Representational_State_Transfer RESTful] API should also allow clients to send requests that ''alter'' the database, i.e. add, edit or delete records, meta-data or users. This will allow for easy integration with third-party tools and enable the development of alternative interfaces to a refbase database. It would be desirable to support an existing framework such as Google's [http://code.google.com/apis/gdata/index.html GData], [http://www.ukoln.ac.uk/repositories/digirep/index/SWORD SWORD] (Simple Web-service Offering Repository Deposit), or the [http://www.loc.gov/standards/sru/record-update/ Record Update service] that is proposed by the SRU community.

=== OAI Protocol for Metadata Harvesting ===

Goal: Provide (yet another) standard way for software to retrieve information from refbase. Eventually provide a mechanism for retrieval from arxiv/dspace/eprints, and other software which is targeted at larger institutions.

Priority: 5

Status: implemented support for the simple/unqualified Dublin Core (OAI_DC) XML format which is a prerequisite for OAI-PMH

Progress: 10%

Description: [http://www.openarchives.org/OAI/openarchivesprotocol.html The Open Archives Initiative Protocol for Metadata Harvesting], which is implemented by [http://software.eprints.org/ EPrints] and [http://www.dspace.org/ DSpace] uses Dublin Core XML over HTTP. This is harvested by google and yahoo and others.

== Citation support ==

=== Increase number of available citation styles ===

Goal: Add most commonly used citation styles and generally increase the number of available styles.

Priority: 6

Status: added styles: AMA, APA, Chicago, Harvard (3 variants), MLA, Vancouver

Progress: 75%

Description: By default, refbase should include at least the most universal styles (i.e. APA, MLA, Chicago, Harvard, Turabian, CB, CGOS, CBE, AMA). Besides that, it would be nice to increase the list of available citation styles substantially.

=== User-customizable citation styles ===

Goal: Allow users to create custom citation styles, preferably via the use of a plugin structure.

Priority: 4

Status: not started

Progress: 0%

Description: Currently, citation styles are defined as PHP functions which is very powerful but not very user friendly. We plan to enhance the cite feature by adding support for other (more general) citation formats. We'd like to integrate refbase with other solutions which offer users an easier way of adding or editing any citation styles. Projects such as Mark Grimshaw's [http://sourceforge.net/project/showfiles.php?group_id=113285&package_id=150961 OSBib] or [http://xbiblio.sourceforge.net/ xbiblio] developed by Bruce D'Arcus come to mind. Some implementation of CSL (backed by Bruce and used by Zotero) would be nice.

== Export ==

== Access permissions ==

=== Record-specific permissions ===

Goal: Offer fine-grained access control on record-level.

Priority: 6

Status: not started

Progress: 0%

Description: The creator (or the admin) of a record should be able to specify who will be allowed to view a particular record. For each record, an authorized user should be able to set the record visibility to everyone, private or to particular groups of database users. Separate access control settings should be provided for file downloads and edits.

== Metadata and Microformats ==

=== Embedded RDF ===

Goal: Embed citation metadata in HTML pages as machine-readable RDF which may be processed by clients.

Priority: 5

Status: not started

Progress: 0%

Description: [http://en.wikipedia.org/wiki/Resource_Description_Framework RDF] is less supported than [[COinS]], but is a useful alternative that has some advantages (such as multiple author support). This will allow client-side tools (such as [http://www.zotero.org/ Zotero]) to more easily use the data provided by refbase.

=== Other microformats? ===

Goal: Other formats may be useful as well

Priority: 1

Status: not started

Progress: 0%

Description: [http://microformats.org/wiki/citation Other citation microformats] and a [http://microformats.org/wiki/search-results-example search results microformat] might eventually be useful. It seems like COinS is the most useful at this point in time, though.

=== Wikipedia citations & other UnAPI goodness ===

Goal: Make it easy for WP contributors to use refbase deployments to add articles

Priority:

Status: not started

Progress: 0%

Description: WP's citation templates are pretty straightforward clips of text, a'la:
<nowiki>{{cite journal | author = Greiner C, Oppenheimer SM, Dunand DC | title = High strength, low stiffness, porous NiTi with superelastic properties. | journal = Acta Biomater | volume = 1 | issue = 6 | pages = 705-16 | year = 2005 | id = PMID 16701851}}</nowiki>
[http://www.hubmed.org/ Hubmed] has a good example of UnAPIed Wikipedia citation generation. They also have del.icio.us bookmarking (I guess we could add less obtrusive citeulike/connotea/etc. links this way).

[[Category:General]]
__NOEDITSECTION__

Installation-Troubleshooting

2023-11-07T13:02:53Z

WikiSysop: Fix incorrect display of accented characters & umlauts

This document presents solutions & tips for installation-related problems, and for things that don't seem to be working correctly after installation.

Other issues are discussed on the generic [[Troubleshooting]] page.

If you experience any problems while installing refbase, please read this chapter before [[refbase:Community_portal|contacting us]].

== Preparations before contacting us ==

In few cases, the refbase installation shows an unwanted behaviour. This may be caused by special settings of your server setup.

'''Important''': Please check following settings and REPORT THEM when [[refbase:Community_portal|contacting us]]. This information will help us a lot to figure out what might be wrong:

* Which version of refbase do you use?
* Which platform are you using?
* Do you use a particular package such as XAMPP?
* Which versions of Apache, MySQL and PHP are you running?
* Can you execute other PHP web applications just fine? I.e., is it only refbase that is causing you trouble?
* Can you access MySQL correctly, from the command line as well as from web administration tools such as phpMyAdmin?
* Do you experience the same error/problem using a different browser or computer?
* Do you know about special config settings within your ''httpd.conf'', ''php.ini'' or ''my.cnf'' configuration files?
* Compare your ''php.ini'' with the list of [[Required_PHP-INI_Settings|required ''php.ini'' settings]] and report any differences.
* Regarding ''php.ini'' settings, especially verify that <code>safe_mode</code> is OFF for installation. If you can't change this setting, you may need to perform a [[Manual installation|manual installation]].
* Have a look at your server's error log and report anything that may be connected with refbase.
* Please make sure that PHP error reporting is enabled and report any error messages displayed in your browser. To enable error reporting, set the following variables in your ''php.ini'' file:
error_reporting = E_ALL
display_errors = On

=== General tips ===

Please ensure that you have checked the following:

* If you're using an older refbase version, you may want to [[Updating_refbase|update]] to the newest version and see if this cures your problems.
* If you receive errors when using refbase (e.g., when adding or importing data), please try the same procedure in our [[Refbase_users|demo databases]] to check, whether this problem is specific to your own installation/data or whether it's a general issue.
* Make sure that you've restarted your web server to apply any changes you've made to your ''php.ini'' file.
* Some installations come with multiple ''php.ini'' copies at different locations. To make sure that you're dealing with the correct ''php.ini'' file, checkout the output of the <code>phpinfo()</code> function, it will tell you the location of the active ''php.ini'' file ([[Required_PHP-INI_Settings|more info]]). The returned status info may contain other useful information and it may help to send us the output via private mail.
* If your package manager separates php-mysql from the main php-package (eg. Fedora) make sure to install both. Otherwise every request to refbase will give an empty white page.
* Make sure that the refbase scripts have correct permission settings so that they can be accessed by your server.

== Known problems and possible solutions ==

=== Fail to login ===

If you have problems to log in with your newly created user account after installing refbase, please refer to [[Creating the first user]].

=== Upload of large files fails ===

If you're able to upload files of small file size but experience errors when attempting to upload large files, checkout the variables <code>post_max_size</code> and <code>upload_max_filesize</code> in your active ''php.ini'' file. The values given for <code>post_max_size</code> and <code>upload_max_filesize</code> must be larger than the maximum file size you'd like to be able to upload (see also [[Required_PHP-INI_Settings|required ''php.ini'' settings]]).

=== Upload of files under XAMPP doesn't work ===

In some versions of [https://www.apachefriends.org/ XAMPP] the default temporary folder for uploads, as defined in ''php.ini'', is wrong:

upload_tmp_dir = ".;c:\apachefriends\xampp\tmp"

correct would be:

upload_tmp_dir = "c:\apachefriends\xampp\tmp"

=== Renaming of uploaded files does not work under XAMPP ===

In some versions of [https://www.apachefriends.org/ XAMPP] the needed PHP function <code>iconv</code> is disabled. To fix this, open the ''php.ini'' file of your XAMPP distribution, search for <code>iconv</code> and enable the function by deleting the heading comment sign (').

=== Export of records results in a blank page ===

At present, the '''ADS''', '''BibTeX''', '''EndNote''', '''ISI''', '''RIS''' and '''Word XML''' export formats require a correctly configured Bibutils while any of the other XML formats (e.g. MODS XML or ODF XML) do '''not''' depend on Bibutils. If the latter are working while the former are not, most likely the issue pertains to your [[Bibutils]] install.

You can check that the Bibutils path was correctly configured by viewing the contents of the ''depends'' table. The <code>depends_path</code> for the <code>bibutils</code> record should '''not''' be <code>NULL</code> as seen below:

<pre>
mysql> SELECT * FROM depends;

+------------+------------------+-----------------+--------------+
| depends_id | depends_external | depends_enabled | depends_path |
+------------+------------------+-----------------+--------------+
| 1 | refbase | true | NULL |
| 2 | bibutils | true | NULL |
+------------+------------------+-----------------+--------------+
</pre>

In addition, please note that:

* the path to the Bibutils programs given in table ''depends'' must end with a slash
* permissions must be set correctly so that the Bibutils programs can be executed by Apache/PHP
* if <code>safe_mode</code> is set to On in your active ''php.ini'' file, then you'll need to put the Bibutils programs within the directory that's specified in <code>safe_mode_exec_dir</code>
* the PHP temp/session directory must be accessible & writable by Apache/PHP/Bibutils
* if you're on a hosted service, your Internet Service Provider may have given you a specific temp directory path which you may need to set explicitly in variable <code>$sessionTempDir</code> in file ''initialize/ini.inc.php''

=== Some exports fail in refbase-0.8.0 on some win32 servers ===

Some WAMP stacks fail to execute Bibutils. A workaround is to upgrade to refbase-0.9.0 or greater.

=== Upload of files results in error message ===

If you're using refbase-0.9.0 and you're getting following error message when adding (or editing) a record that includes a file
for upload:

Warning: preg_replace() [function.preg-replace]: Unknown modifier '\' in
.../refbase-0.9.0/includes/include.inc.php on line 3631

Warning: preg_replace() [function.preg-replace]: Unknown modifier '\' in
.../refbase-0.9.0/includes/include.inc.php on line 3634

then you may want to upgrade to refbase-0.9.5 or greater. Alternatively, you can apply a simple patch manually:

Please open file ''modify.php'' in your refbase root directory, goto line 1100 and replace this code:

$dirNamingScheme = trimTextPattern($dirNamingScheme, "[/\\]+", true, true);

with this:

$dirNamingScheme = trimTextPattern($dirNamingScheme, "[\/\\\\]+", true, true);

=== Import of records results in an error message ===

If you're trying to import records into your refbase database and you're getting an error message such as this one:

There were validation errors regarding the data you entered

then you might want check whether your record format is supported by refbase and whether its syntax is correct. Please see our [[Importing records|import]] page for more information and links to example records for all supported formats.

If you're sure that your record format is supported but you still get an error message, please try to import your records at one of our [[Refbase_users|demo databases]]. If this throws up the same error message, then refbase probably has problems recognizing your record format. In that case, we'd appreciate if you'd [[refbase:Community_portal|send us]] your problematic records so that we can look into the problem.

If, however, your records import fine in our demo database, then this hints at a problem with your local refbase installation. Note that import of records in BibTeX, Copac, Endnote (tagged text or XML), PubMed XML, SciFinder or MODS XML format requires [[Bibutils]] being installed on your server. If you think that you've correctly installed Bibutils on your server and still can't get import of the above mentioned formats to work, please [[refbase:Community_portal|let us know]] and we'll try to help.

=== Undefined iconv() despite --with-iconv ===

This problem was experienced on a FreeBSD web host, and has also been reported as a [http://ca.php.net/manual/en/function.iconv.php#47428 FreeBSD issue] in the user comments at php.net, which suggests the resolution (which worked for me) to add the following block of code to the application before iconv() is called:

<pre>
if (!function_exists('iconv') && function_exists('libiconv')) {
function iconv($input_encoding, $output_encoding, $string) {
return libiconv($input_encoding, $output_encoding, $string);
}
}
</pre>

=== Problems with special characters ===

See below for some troubleshooting guidance if you have problems getting higher ASCII characters (such as accented characters or umlauts) displayed correctly in refbase, or if you cannot correctly enter or search for higher ASCII chars in the refbase web interface. Encoding problems can be really tricky since many factors interact with each other, and encoding settings can differ greatly among different systems and versions.

==== Server settings ====

First of all, you should make sure that your MySQL server's character set and collation settings are setup correctly and consistently. For more information and instructions, please see parts 'a)' and 'b)' in section [[Troubleshooting#MySQL_migration_and_character_set_problems|MySQL migration and character set problems]].

If you'd like to use refbase with UTF-8 encoding, then you'll need MySQL version 4.1.x or greater. However, in our experience, MySQL 4.1.x seems to have problems with some Unicode characters, so if possible you should use refbase in conjunction with MySQL 5.x.

It might be also worth checking your web server's configuration file (e.g., in case of the Apache web server: ''httpd.conf'' or ''apache2.conf''). On Ubuntu, for example, some users managed to cure their encoding issues by (un)commenting (or altering) following config setting in Apache 2:

AddDefaultCharset ISO-8859-1

==== Settings in refbase ====

When installing refbase via ''install.php'', make sure that you've chosen the desired default character set (latin1 or utf8). Be aware that if you've tried to install refbase multiple times using the same MySQL database name (in ''initialize/db.inc.php'') but with different settings as default character set, you must drop (i.e. delete) the database before installing it again with a different character encoding.

You can check the encoding of your MySQL database by issuing following command from within your MySQL command line interpreter:

SHOW CREATE DATABASE ''DATABASE_NAME'';

In the above command, replace <code>''DATABASE_NAME''</code> with the actual name of your refbase MySQL database.

If you've chosen "utf8" upon installation, then you have to make sure that variable <code>$contentTypeCharset</code> in file ''initialize/ini.inc.php'' is set to "UTF-8". And if you're using higher ASCII chars in any variable values in file ''ini.inc.php'', you should also re-save that file with encoding "Unicode (UTF-8, no BOM)".

If you've set variable <code>$contentTypeCharset</code> to "UTF-8", you could now access refbase in your web browser and verify that the head of the HTML source states the correct encoding:

<meta http-equiv="content-type" content="text/html; charset=UTF-8">

In case of a latin1-based refbase installation, the contents of the <code>charset</code> attribute should read "ISO-8859-1".

In order to test if refbase has been setup correctly, you should now add or edit a record via the refbase web interface and enter some special characters (such as áéíàèì or åæøöäü etc). Then, checkout again the added/edited record and verify that your entered characters display correctly. In addition, use refbase to search for these special characters and verify that your added/edited record is listed among the search results.

So, in summary, if you can 1) successfully enter special characters in refbase, 2) have them displayed correctly after saving your edits '''and''' 3) successfully search for these newly entered characters, then refbase has been set up correctly. However, if one of these actions (enter/display/search) does not work as expected, then you've still got problems.

==== Browser settings ====

If you're still experiencing problems, it's always a ''very'' good idea to try out another browser (or another browser on another platform). Also, try to manually set the encoding of your browser page to either "Unicode (UTF-8)" or "Western (ISO-8859-1)". In Firefox, this can be done via the "View > Character Encoding" menu. After you've set the encoding explicitly, please see if you can now enter/display/search for higher ASCII chars successfully.

Speaking of browser settings, you can often set a default character encoding within the browser's preferences which might be also worth checking out.

==== Import and file encodings ====

Finally, note that when importing data into refbase, you have to make sure that the character encoding of your bibliographic data file matches the character encoding of your refbase database. If this is causing you any trouble, copying and pasting the data into the refbase import form may actually work better. With regard to import, you should also ensure that you're using a recent version of [[Bibutils]] since some earlier versions of Bibutils had issues with character set support.

If you still can't get rid of your encoding issues, please [[refbase:Community_portal|let us know]] and we'll see what we can do.

[[Category:Installation]]
[[Category:Troubleshooting]]
__NOEDITSECTION__

Troubleshooting

2023-11-07T12:55:51Z

WikiSysop: Update external links

This document lists common problems and presents possible solutions.

For problems regarding the installation process or things that don't seem to be working correctly after installation, please see [[Installation-Troubleshooting]].

For tips on how to get records from other reference managers or online services into refbase, please see [[Integration with other reference managers]] or [[Integration with online services]], respectively.

== MySQL migration and character set problems ==

To migrate your refbase installation from one computer to another,
you need to be very careful about the character sets and MySQL versions you're using. Otherwise you will end up with garbled and strange characters when viewing what was once nice accented characters or "umlauts" (like norwegian å, æ, ø, or the german ä, ö, ü or swedish ø).

'''a)''' To solve the problem, you need to first check that the character sets used on the two database installations are the same. Use either [http://www.phpmyadmin.net/ phpMyAdmin] or the MySQL command line interpreter.

'''phpMyAdmin'''

* login and click on "Show MySQL system variables"

* then check for these variables:

------------------------------------------------------------------
Varaible: Session: Global:
------------------------------------------------------------------
...
character set client utf8 latin1
character set connection utf8 latin1
character set database latin1 latin1
character set results utf8 latin1
character set server latin1 latin1
character set system utf8 utf8
...
collation connection utf8_general_ci latin1_general_ci
collation database latin1_general_ci latin1_general_ci
collation server latin1_general_ci latin1_general_ci
...
------------------------------------------------------------------

'''MySQL'''

Enter the MySQL command line interpreter, select your refbase MySQL database, and execute following commands:

mysql> SHOW VARIABLES LIKE '%character%';
mysql> SHOW VARIABLES LIKE '%collation%';

Another possibility is to issue following command from the command line shell:

mysqladmin variables | grep "character\|collation"

'''b)''' If you see discrepancies between the two database installations with respect to these variables, it is better that they coincide. This can be done by adding two lines to the "[mysqld]" section of the MySQL config file (''my.cnf'') and restarting your MySQL server. Here's an example for a latin1-based database:

------------------------------------------
...
[mysqld]
#init-connect = 'SET NAMES latin1'
#init-connect = 'SET CHARACTER SET latin1'
character-set-server = latin1
collation-server = latin1_general_ci
...
------------------------------------------

Note that for some MySQL systems/versions, some variable names seem to use underscores instead of hyphens. As an example, using MySQL 4.1.11 on Mac OS X 10.4, the following settings are recognized in the MySQL config file for latin1 (ISO-8859-1):

[mysqld]
character_set_server = latin1
collation_server = latin1_general_ci

or, in case of UTF-8:

[mysqld]
character_set_server = utf8
collation_server = utf8_general_ci

'''c)''' Next you need to "properly" dump the data from your original database, which can be achieved by use of the [https://dev.mysql.com/doc/refman/8.0/en/mysqldump.html mysqldump] command line program. The regular mysqldump statement (without any flags) may not work correctly, because mysqldump will, by default, output data using the UTF-8 character set. So, if you're using a different character set (such as latin1), you must specify the <code>--default-character-set=WHAT_YOU_FIND_UNDER_character_set_server_ABOVE</code> flag. And if you use an older MySQL version you may also need to use the <code>--compatible</code> flag. Example: assuming your refbase ''latin1''-based database is named ''refbase'' and with ''root'' being the authorized user, your mysqldump statement would read:

$ mysqldump refbase -u root -p --opt --default-character-set=latin1 > refbase.sql

If you no longer have access to the old database for making this kind of dump, you may try to directly convert the old dump's character set with the iconv command line program. Here we convert the file ''dump.sql'' from UTF-8 to latin1 (ISO-8859-1) and write the data into a new file named ''iso_dump.sql'':

$ iconv -f UTF-8 -t ISO-8859-1 dump.sql -o iso_dump.sql

'''d)''' You may want to test the new data by loading your MySQL dump file into a separate refbase database. To do so, perform these steps:

* Duplicate your refbase scripts to another directory (e.g. named "refbase_test") within your web directory.

* Copy your MySQL dump file into this new "refbase_test" directory (let's assume the dump file is named "refbase.sql").

* Within this new refbase folder, edit the ''$databaseName'' variable in file ''initialize/db.ini.php'' so that it has a name that does NOT collide with any existing MySQL database names (this is very important!).

* Access your "refbase_test" directory via the browser and point it to ''install.php''.

* On the install form, enter for "Path to the database structure file" the name of your MySQL dump file (the file from step 2, e.g. "refbase.sql").

* Edit the other fields to suit your server setup and check that the chosen default character set matches the charset of your MySQL dump file, then click the "Install" button.

The above steps can be also used to quickly setup a local read-only copy of your refbase database, e.g. on a personal laptop that is meant to be used in places without internet access.

[[Category:Troubleshooting]]
__NOEDITSECTION__

Troubleshooting

2023-11-07T12:55:12Z

WikiSysop: Hide section edit links

This document lists common problems and presents possible solutions.

For problems regarding the installation process or things that don't seem to be working correctly after installation, please see [[Installation-Troubleshooting]].

For tips on how to get records from other reference managers or online services into refbase, please see [[Integration with other reference managers]] or [[Integration with online services]], respectively.

== MySQL migration and character set problems ==

To migrate your refbase installation from one computer to another,
you need to be very careful about the character sets and MySQL versions you're using. Otherwise you will end up with garbled and strange characters when viewing what was once nice accented characters or "umlauts" (like norwegian å, æ, ø, or the german ä, ö, ü or swedish ø).

'''a)''' To solve the problem, you need to first check that the character sets used on the two database installations are the same. Use either [http://www.phpmyadmin.net/ phpMyAdmin] or the MySQL command line interpreter.

'''phpMyAdmin'''

* login and click on "Show MySQL system variables"

* then check for these variables:

------------------------------------------------------------------
Varaible: Session: Global:
------------------------------------------------------------------
...
character set client utf8 latin1
character set connection utf8 latin1
character set database latin1 latin1
character set results utf8 latin1
character set server latin1 latin1
character set system utf8 utf8
...
collation connection utf8_general_ci latin1_general_ci
collation database latin1_general_ci latin1_general_ci
collation server latin1_general_ci latin1_general_ci
...
------------------------------------------------------------------

'''MySQL'''

Enter the MySQL command line interpreter, select your refbase MySQL database, and execute following commands:

mysql> SHOW VARIABLES LIKE '%character%';
mysql> SHOW VARIABLES LIKE '%collation%';

Another possibility is to issue following command from the command line shell:

mysqladmin variables | grep "character\|collation"

'''b)''' If you see discrepancies between the two database installations with respect to these variables, it is better that they coincide. This can be done by adding two lines to the "[mysqld]" section of the MySQL config file (''my.cnf'') and restarting your MySQL server. Here's an example for a latin1-based database:

------------------------------------------
...
[mysqld]
#init-connect = 'SET NAMES latin1'
#init-connect = 'SET CHARACTER SET latin1'
character-set-server = latin1
collation-server = latin1_general_ci
...
------------------------------------------

Note that for some MySQL systems/versions, some variable names seem to use underscores instead of hyphens. As an example, using MySQL 4.1.11 on Mac OS X 10.4, the following settings are recognized in the MySQL config file for latin1 (ISO-8859-1):

[mysqld]
character_set_server = latin1
collation_server = latin1_general_ci

or, in case of UTF-8:

[mysqld]
character_set_server = utf8
collation_server = utf8_general_ci

'''c)''' Next you need to "properly" dump the data from your original database, which can be achieved by use of the [http://dev.mysql.com/doc/refman/5.0/en/mysqldump.html mysqldump] command line program. The regular mysqldump statement (without any flags) may not work correctly, because mysqldump will, by default, output data using the UTF-8 character set. So, if you're using a different character set (such as latin1), you must specify the <code>--default-character-set=WHAT_YOU_FIND_UNDER_character_set_server_ABOVE</code> flag. And if you use an older MySQL version you may also need to use the <code>--compatible</code> flag. Example: assuming your refbase ''latin1''-based database is named ''refbase'' and with ''root'' being the authorized user, your mysqldump statement would read:

$ mysqldump refbase -u root -p --opt --default-character-set=latin1 > refbase.sql

If you no longer have access to the old database for making this kind of dump, you may try to directly convert the old dump's character set with the iconv command line program. Here we convert the file ''dump.sql'' from UTF-8 to latin1 (ISO-8859-1) and write the data into a new file named ''iso_dump.sql'':

$ iconv -f UTF-8 -t ISO-8859-1 dump.sql -o iso_dump.sql

'''d)''' You may want to test the new data by loading your MySQL dump file into a separate refbase database. To do so, perform these steps:

* Duplicate your refbase scripts to another directory (e.g. named "refbase_test") within your web directory.

* Copy your MySQL dump file into this new "refbase_test" directory (let's assume the dump file is named "refbase.sql").

* Within this new refbase folder, edit the ''$databaseName'' variable in file ''initialize/db.ini.php'' so that it has a name that does NOT collide with any existing MySQL database names (this is very important!).

* Access your "refbase_test" directory via the browser and point it to ''install.php''.

* On the install form, enter for "Path to the database structure file" the name of your MySQL dump file (the file from step 2, e.g. "refbase.sql").

* Edit the other fields to suit your server setup and check that the chosen default character set matches the charset of your MySQL dump file, then click the "Install" button.

The above steps can be also used to quickly setup a local read-only copy of your refbase database, e.g. on a personal laptop that is meant to be used in places without internet access.

[[Category:Troubleshooting]]
__NOEDITSECTION__

Troubleshooting

2023-11-07T12:52:51Z

WikiSysop: Original page content from 18-Jul-2007

This document lists common problems and presents possible solutions.

For problems regarding the installation process or things that don't seem to be working correctly after installation, please see [[Installation-Troubleshooting]].

For tips on how to get records from other reference managers or online services into refbase, please see [[Integration with other reference managers]] or [[Integration with online services]], respectively.

== MySQL migration and character set problems ==

To migrate your refbase installation from one computer to another,
you need to be very careful about the character sets and MySQL versions you're using. Otherwise you will end up with garbled and strange characters when viewing what was once nice accented characters or "umlauts" (like norwegian å, æ, ø, or the german ä, ö, ü or swedish ø).

'''a)''' To solve the problem, you need to first check that the character sets used on the two database installations are the same. Use either [http://www.phpmyadmin.net/ phpMyAdmin] or the MySQL command line interpreter.

'''phpMyAdmin'''

* login and click on "Show MySQL system variables"

* then check for these variables:

------------------------------------------------------------------
Varaible: Session: Global:
------------------------------------------------------------------
...
character set client utf8 latin1
character set connection utf8 latin1
character set database latin1 latin1
character set results utf8 latin1
character set server latin1 latin1
character set system utf8 utf8
...
collation connection utf8_general_ci latin1_general_ci
collation database latin1_general_ci latin1_general_ci
collation server latin1_general_ci latin1_general_ci
...
------------------------------------------------------------------

'''MySQL'''

Enter the MySQL command line interpreter, select your refbase MySQL database, and execute following commands:

mysql> SHOW VARIABLES LIKE '%character%';
mysql> SHOW VARIABLES LIKE '%collation%';

Another possibility is to issue following command from the command line shell:

mysqladmin variables | grep "character\|collation"

'''b)''' If you see discrepancies between the two database installations with respect to these variables, it is better that they coincide. This can be done by adding two lines to the "[mysqld]" section of the MySQL config file (''my.cnf'') and restarting your MySQL server. Here's an example for a latin1-based database:

------------------------------------------
...
[mysqld]
#init-connect = 'SET NAMES latin1'
#init-connect = 'SET CHARACTER SET latin1'
character-set-server = latin1
collation-server = latin1_general_ci
...
------------------------------------------

Note that for some MySQL systems/versions, some variable names seem to use underscores instead of hyphens. As an example, using MySQL 4.1.11 on Mac OS X 10.4, the following settings are recognized in the MySQL config file for latin1 (ISO-8859-1):

[mysqld]
character_set_server = latin1
collation_server = latin1_general_ci

or, in case of UTF-8:

[mysqld]
character_set_server = utf8
collation_server = utf8_general_ci

'''c)''' Next you need to "properly" dump the data from your original database, which can be achieved by use of the [http://dev.mysql.com/doc/refman/5.0/en/mysqldump.html mysqldump] command line program. The regular mysqldump statement (without any flags) may not work correctly, because mysqldump will, by default, output data using the UTF-8 character set. So, if you're using a different character set (such as latin1), you must specify the <code>--default-character-set=WHAT_YOU_FIND_UNDER_character_set_server_ABOVE</code> flag. And if you use an older MySQL version you may also need to use the <code>--compatible</code> flag. Example: assuming your refbase ''latin1''-based database is named ''refbase'' and with ''root'' being the authorized user, your mysqldump statement would read:

$ mysqldump refbase -u root -p --opt --default-character-set=latin1 > refbase.sql

If you no longer have access to the old database for making this kind of dump, you may try to directly convert the old dump's character set with the iconv command line program. Here we convert the file ''dump.sql'' from UTF-8 to latin1 (ISO-8859-1) and write the data into a new file named ''iso_dump.sql'':

$ iconv -f UTF-8 -t ISO-8859-1 dump.sql -o iso_dump.sql

'''d)''' You may want to test the new data by loading your MySQL dump file into a separate refbase database. To do so, perform these steps:

* Duplicate your refbase scripts to another directory (e.g. named "refbase_test") within your web directory.

* Copy your MySQL dump file into this new "refbase_test" directory (let's assume the dump file is named "refbase.sql").

* Within this new refbase folder, edit the ''$databaseName'' variable in file ''initialize/db.ini.php'' so that it has a name that does NOT collide with any existing MySQL database names (this is very important!).

* Access your "refbase_test" directory via the browser and point it to ''install.php''.

* On the install form, enter for "Path to the database structure file" the name of your MySQL dump file (the file from step 2, e.g. "refbase.sql").

* Edit the other fields to suit your server setup and check that the chosen default character set matches the charset of your MySQL dump file, then click the "Install" button.

The above steps can be also used to quickly setup a local read-only copy of your refbase database, e.g. on a personal laptop that is meant to be used in places without internet access.

[[Category:Troubleshooting]]

Configuring refbase

2023-11-07T12:43:03Z

WikiSysop: Update external links

This document presents some tips how to configure your refbase installation:

The refbase admin has a variety of options to configure or customize refbase. Some of them are listed in this article. If you don't find the desired option, please refer to file ''initialize/ini.inc.php'' within your refbase installation. This configuration file contains many global settings which are not accessible via the refbase web interface:

* initial database settings (database name, admin email, database URL, character set, etc)
* default user settings when a new user is created
* visibility of files (e.g., .pdf files)
* important settings for file upload (file renaming, directory creation, etc)
* appearance of links within refbase
* server settings for link resolvers (OpenURL, ISBN)
* rich text formatting (e.g., greek letters, italic or superscript/subscript text)

The configuration file ''initialize/ini.inc.php'' is well commented, therefore you will find much more information in this file.

Below you can find answers to some frequently asked questions about configuring refbase.

== How can I change the logo? ==

You can change the main logo image that's displayed in the refbase page header by setting variable <code>$logoImageURL</code> in ''initialize/ini.inc.php'' to the path of your logo file. In addition, please be sure to set the variables <code>$logoImageWidth</code> and <code>$logoImageHeight</code> to the dimensions of your logo. You may also be interested to specify your own paths for the smaller logos (<code>$logoSmallImageURL</code> and <code>$faviconImageURL</code>).

== How can I setup refbase so that users can register themselves? ==

By default, only the admin is allowed to setup new user accounts. Here's how to setup your refbase installation such that users can automatically register themselves:

In ''initialize/ini.inc.php'' set the <code>$addNewUsers</code> variable to "everyone". Then, provide a link on the main page to ''user_details.php'' where users can use the provided form to register themselves.

Just set the <code>$addNewUsers</code> variable back to "admin" if you want to prevent other users from messing with your users table.

== How can I change the default number of records shown? ==

You can change the default number of records that is returned by any (web, RSS or SRU) query by changing the value of the <code>$defaultNumberOfRecords</code> variable in ''initialize/ini.inc.php''.

== How can I change the default language? ==

You can change the language that's displayed by default in file ''intialize/ini.inc.php'' within your refbase root directory. Search for this paragraph:

// The default language selection, can be overwritten by userdefined language
$defaultLanguage = "de"; // e.g. "en", "de" or "fr"

and set the value of the <code>$defaultLanguage</code> variable to either "en" (English), "de" (German) or "fr" (French). In case of problems, please check that your desired default language is enabled within MySQL table ''languages''.

Note that logged-in database users can switch to another language. This can be done by clicking the ''Options'' link when logged in.

== How can I make some PDFs available to all users? ==

Ususally, access to PDFs should only be made available to logged-in users. This is controlled by variable <code>$fileVisibility</code> in ''initialize/ini.inc.php''. However, often one wants to make a few PDFs available to all users. Variable <code>$fileVisibilityException</code> (also in ''initialize/ini.inc.php'') can be used to specify a condition where attached files will be displayed to ''all'' users, no matter whether they're logged in or not.

By default, refbase will publicly display files for all records where the ''thesis'' field in table ''refs'' is not empty, i.e. if a thesis type has been specified for the record:

$fileVisibilityException = array("thesis", "/.+/");

If, instead, you'd like to allow public access to PDFs for arbitrary records, a common approach would be to put some unique string into one of the fields from table ''refs'', and use this field & identifier string in variable <code>$fileVisibilityException</code>.†As an example, for all records where the attached PDF should be displayed publicly, you could add the string "author copyright" to the ''notes'' field. Then use the following pattern:

$fileVisibilityException = array("notes", "/author copyright/");

As another example, if you'd like to offer public access to all PDFs that where authored by a member of your institution, you could make use of the ''contribution_id'' field ([[Auto-updating_author/group_bibliographies#Institutional_or_group_bibliographies|more info]]), and specify this field and your institutional abbreviation in variable <code>$fileVisibilityException</code>. If your institutional abbreviation is, say, "NUCAPT", you'd use this pattern:

$fileVisibilityException = array("contribution_id", "/NUCAPT/");

== How can I change options & permissions for everyone who's not logged in? ==

=== Setting options via the web interface ===

When logged in as admin, you can set options and access permissions for everyone who's not logged in by calling the script ''user_options.php'' with the <code>userID=0</code> parameter:

user_options.php?userID=0

For all permissions that are set to off, the relevant interface elements will be hidden from the refbase GUI.

Note that some of the available user permissions require a user being logged in. I.e., enabling these options for anyone who isn't logged in won't have any effect. Following user permissions require a login:

* Add records
* Edit records
* Delete records
* File upload
* User groups
* User queries
* Import
* Batch import
* Modify options

If you want to allow users who are not logged in to query the refbase database via the [[Search/Retrieve web services|SRU search/retrieve webservice]], then either the ''Export'' or the ''Batch export'' user permission needs to be enabled. This will allow export of XML records via ''sru.php'' but won't allow a user who isn't logged in to export records via the web interface.

=== Setting options within ''ini.inc.php'' ===

If you like to change the permission to see/download files (e.g., .pdf files), you (the admin) can find the appropriate option in file ''initialize/ini.inc.php''. The relevant variable is called <code>$fileVisibility</code>. You are able to allow file download for everyone, logged-in users only, or on a user-specific basis.

Additionally, you can set exceptions to this rule in variable <code>$fileVisibilityException</code>, which enables you to always allow download access to files that meet a particular criterion. A typical usage example would be to always grant download access to theses or papers that were written by members of your own institution.

For more details, please refer to the comments in ''ini.inc.php''.

== How can I change the default citation style? ==

You can use variable <code>$defaultCiteStyle</code> in file ''initialize/ini.in.php'' to change the citation style that's displayed by default in the web interface (Citation view) as well as for export of formatted citation lists to RTF, PDF, LaTeX, etc. The given style name must have a matching entry in the ''styles'' table of your refbase MySQL database.

Note that the admin can enable or disable particular citation styles individually for each user. And if desired, logged-in users can deselect some of the enabled styles in their user-specific options.

== How can I change the names & order of citation styles? ==

=== Changing the names of citation styles ===

Here's how to change the names of citation styles displayed in the "Cite using style" drop-down (in the form below the query results list): Currently, you have to directly edit the ''styles'' MySQL table. E.g., to change the display name of the "Polar Biol" citation style to "Default" execute the following MySQL command from within your SQL command line interpreter:

UPDATE styles SET style_name = "Default" WHERE style_name = "Polar Biol";

Note that you must also change the corresponding names for the variables <code>$defaultCiteStyle</code> and <code>$defaultUserStyles</code> in ''initialize/ini.inc.php''.

=== Changing the order of citation styles ===

Similar to the above, you can edit the ''styles'' MySQL table to change the order of citation styles displayed in the "Cite using style" drop-down menu. If, for example, you want to switch the order of the first two citation styles, execute the two commands below:

UPDATE styles SET order_by = "2" WHERE style_id = 1;
UPDATE styles SET order_by = "1" WHERE style_id = 2;

Note: this example assumes that you have table entries with style_id's of 1 and 2, otherwise adopt or use something like:

UPDATE styles SET order_by = "...(whatever)..." WHERE style_name = "...(whatever)..."

The ''order_by'' field is of type <code>varchar(25)</code>, i.e., you can also use more fine grained values (such as "1a", "1b", etc).

== How can I add or disable a particular citation style? ==

=== Adding a citation style ===

Currently, citation styles are written as a PHP function, so you'll need to know a bit of PHP to add your own style. The PHP function that outputs records in citation format is called <code>citeRecord()</code>. For each citation style, there's a separate file with a dedictated version of this function. These citation style files are located within the ''cite'' sub-directory of your refbase root directory.

To build your own style, you may want to have a look at the existing citation style files and [[#How to create a new citation style|modify]] one of them to suit your needs.

After you've created your own citation style, copy it into the ''cite'' sub-directory of your refbase root directory. Then, in order to add your citation style file to the "Cite using style" drop-down, execute the following MySQL command from within your SQL command line interpreter:

INSERT INTO styles VALUES (NULL, 'STYLENAME', 'true', 'STYLEFILE', '1', '1');

In the above MySQL command, replace <code>STYLENAME</code> with the actual name of your citation style. This name will appear in the "Cite using style" drop-down. Similarly, <code>STYLEFILE</code> must be replaced with the file name of your citation style file, prefixed with "styles/" (example: "styles/MyStyleFile.php"). In addition, you can change the first number ('1') in the above command to change the position at which your style name will be displayed in the drop-down. To see all available styles and confirm that your style has been successfully added to the ''styles'' MySQL table, execute this command:

SELECT * FROM styles;

Now, login as admin via the refbase web interface, click on "Manage Users" and activate your new style (using the "edit options" link) for all those users who shall see this style. If you've enabled/disabled any citation styles for the admin user, you'll have to logout and login again in order to see your changes.

=== Disabling a citation style ===

You can globally disable existing styles by setting the ''style_enabled'' field to "false". E.g., if you want to disable the "Polar Biol" citation style, execute:

UPDATE styles SET style_enabled = "false" WHERE style_name = "Polar Biol";

=== How to create a new citation style ===

Before we start this section, a comment in advance:

To improve refbase: If you have created a new citation style, we would be interested to offer this style for all refbase users. If possible, please
* post this new .php file to [[refbase:Community_Portal|the community]].
* include the journal title for you built the style with their website.

This section should contain information/hints for non-php professionals

==== Adapting existing work ====

Before investing energy in creating a new style, it is wise to check the [https://sourceforge.net/p/refbase/code/HEAD/tree/ refbase subversion repository] for new styles that are under development but not yet included in the project release. Be aware that styles obtained from the [https://sourceforge.net/p/refbase/code/HEAD/tree/branches/bleeding-edge/cite/styles/ bleeding edge branch] are not necessarily in working condition, and even if they appear to work, may be unfit for a production environment.

----
Todo-list:
*A link is set from [[Adding Records]]-page: how to configure different Types of publication and different Types of Thesis
**in the database
**in view options

== How can I add a new interface language? ==

In order to add a new language (locale) to refbase, you need to perform these steps:

* Within the refbase ''locales/'' directory, copy one of the existing subdirectories and rename it to the [http://www.loc.gov/standards/iso639-2/php/code_list.php two-letter code] of the language you'd like to add (e.g. "es" in case of Spanish).
* Within your new subdirectory, translate all lines in file ''common.inc'' into your language, and save a copy of this file with encoding "Unicode (UTF-8, no BOM)" to ''common_utf8.inc''.
* Issue following MySQL command via ''sql_search.php'' when logged into refbase as admin:

INSERT INTO languages VALUES (NULL, 'LANGCODE', 'true', '4');

In the above MySQL command, replace <code>LANGCODE</code> with the two-letter code of your language, e.g. "es" for Spanish. In addition, you can change the last number ("4" in the above example) to alter the position at which your language name will be displayed in the language drop-down.

The new language option should now appear within the language drop-down in the refbase user options.

To see all currently available languages and to confirm that your language has been successfully added to the ''languages'' MySQL table, execute this command from within your MySQL command line interpreter (after you've selected the refbase MySQL database):

SELECT * FROM languages;

Please note that in refbase-0.9.0, not the entire interface is available for localization. We plan to finish internationalization until version 1.0.

If you've translated the refbase interface strings in ''common.inc'' into your own language, please [[refbase:Community_Portal|send us]] this file so that we can include it with a future release of refbase.

[[Category:Configuration]]
__NOEDITSECTION__

MediaWiki:Common.css

2023-11-06T23:25:50Z

WikiSysop: Make subheadings appear less bold

/* CSS placed here will be applied to all skins */

.branding-box {
font-weight: bold;
}

h1 {
text-align: center;
padding-top: 15px;
color: #990000;
}

h3, h4 {
font-weight: 500;
}

.mw-headline {
color: #990000;
}

pre+h2 {
margin-top: 22px;
}

ul+h2 {
margin-top: 22px;
}

pre+h3 {
margin-top: 35px;
}

ul+h3 {
margin-top: 29px;
}

pre+h4 {
margin-top: 23px;
}

ul+h4 {
margin-top: 16px;
}

.minerva__tab-container {
display: none;
}

.page-actions-menu {
display: none;
}

#content {
border-top: 2px solid #990000;
}

.minerva-footer {
color: #F0F0F0;
background-color: #073970;
}

.footer-content:before{
content: url('https://wiki.refbase.net/skins/common/images/refbase_icon.svg');
}

.last-modified-bar {
border-bottom: 3px solid #990000;
background-color: #EAECF0;
}

#footer-places {
margin-bottom: 15px;
}

#footer-places a:link {
color: #CCCCCC;
}

#footer-places a:visited {
color: #AAAAAA;
}

#refbase-badge {
font-weight: normal;
font-family: luxi serif, georgia, times new roman, times, serif;
font-size: 220%;
color: #990000;
background: none;
}

html>body #refbase-badge {
/* hidden from IE */
margin: -8pt;
}

#refbase-badge:before{
content: url('https://wiki.refbase.net/skins/common/images/refbase_icon_small.png');
position: absolute;
top: -36px;
left: 0;
}

MediaWiki:Common.css

2023-11-06T23:18:16Z

WikiSysop: More accurate vertical space in front of headings that are preceded by a "pre" or "ul" tag

/* CSS placed here will be applied to all skins */

.branding-box {
font-weight: bold;
}

h1 {
text-align: center;
padding-top: 15px;
color: #990000;
}

.mw-headline {
color: #990000;
}

pre+h2 {
margin-top: 22px;
}

ul+h2 {
margin-top: 22px;
}

pre+h3 {
margin-top: 35px;
}

ul+h3 {
margin-top: 29px;
}

pre+h4 {
margin-top: 23px;
}

ul+h4 {
margin-top: 16px;
}

.minerva__tab-container {
display: none;
}

.page-actions-menu {
display: none;
}

#content {
border-top: 2px solid #990000;
}

.minerva-footer {
color: #F0F0F0;
background-color: #073970;
}

.footer-content:before{
content: url('https://wiki.refbase.net/skins/common/images/refbase_icon.svg');
}

.last-modified-bar {
border-bottom: 3px solid #990000;
background-color: #EAECF0;
}

#footer-places {
margin-bottom: 15px;
}

#footer-places a:link {
color: #CCCCCC;
}

#footer-places a:visited {
color: #AAAAAA;
}

#refbase-badge {
font-weight: normal;
font-family: luxi serif, georgia, times new roman, times, serif;
font-size: 220%;
color: #990000;
background: none;
}

html>body #refbase-badge {
/* hidden from IE */
margin: -8pt;
}

#refbase-badge:before{
content: url('https://wiki.refbase.net/skins/common/images/refbase_icon_small.png');
position: absolute;
top: -36px;
left: 0;
}

MediaWiki:Common.css

2023-11-06T22:55:00Z

WikiSysop: Also add missing vertical space in front of headings that are preceded by a "ul" tag

/* CSS placed here will be applied to all skins */

.branding-box {
font-weight: bold;
}

h1 {
text-align: center;
padding-top: 15px;
color: #990000;
}

.mw-headline {
color: #990000;
}

pre+h2, pre+h3, ul+h2, ul+h3 {
margin-top: 22px;
}

.minerva__tab-container {
display: none;
}

.page-actions-menu {
display: none;
}

#content {
border-top: 2px solid #990000;
}

.minerva-footer {
color: #F0F0F0;
background-color: #073970;
}

.footer-content:before{
content: url('https://wiki.refbase.net/skins/common/images/refbase_icon.svg');
}

.last-modified-bar {
border-bottom: 3px solid #990000;
background-color: #EAECF0;
}

#footer-places {
margin-bottom: 15px;
}

#footer-places a:link {
color: #CCCCCC;
}

#footer-places a:visited {
color: #AAAAAA;
}

#refbase-badge {
font-weight: normal;
font-family: luxi serif, georgia, times new roman, times, serif;
font-size: 220%;
color: #990000;
background: none;
}

html>body #refbase-badge {
/* hidden from IE */
margin: -8pt;
}

#refbase-badge:before{
content: url('https://wiki.refbase.net/skins/common/images/refbase_icon_small.png');
position: absolute;
top: -36px;
left: 0;
}

MediaWiki:Common.css

2023-11-06T22:50:57Z

WikiSysop: Add missing vertical space in front of headings that are preceded by a "pre" tag

/* CSS placed here will be applied to all skins */

.branding-box {
font-weight: bold;
}

h1 {
text-align: center;
padding-top: 15px;
color: #990000;
}

.mw-headline {
color: #990000;
}

pre+h2, pre+h3 {
margin-top: 22px;
}

.minerva__tab-container {
display: none;
}

.page-actions-menu {
display: none;
}

#content {
border-top: 2px solid #990000;
}

.minerva-footer {
color: #F0F0F0;
background-color: #073970;
}

.footer-content:before{
content: url('https://wiki.refbase.net/skins/common/images/refbase_icon.svg');
}

.last-modified-bar {
border-bottom: 3px solid #990000;
background-color: #EAECF0;
}

#footer-places {
margin-bottom: 15px;
}

#footer-places a:link {
color: #CCCCCC;
}

#footer-places a:visited {
color: #AAAAAA;
}

#refbase-badge {
font-weight: normal;
font-family: luxi serif, georgia, times new roman, times, serif;
font-size: 220%;
color: #990000;
background: none;
}

html>body #refbase-badge {
/* hidden from IE */
margin: -8pt;
}

#refbase-badge:before{
content: url('https://wiki.refbase.net/skins/common/images/refbase_icon_small.png');
position: absolute;
top: -36px;
left: 0;
}

Configuring refbase

2023-11-06T22:24:16Z

WikiSysop: Hide section edit links

This document presents some tips how to configure your refbase installation:

The refbase admin has a variety of options to configure or customize refbase. Some of them are listed in this article. If you don't find the desired option, please refer to file ''initialize/ini.inc.php'' within your refbase installation. This configuration file contains many global settings which are not accessible via the refbase web interface:

* initial database settings (database name, admin email, database URL, character set, etc)
* default user settings when a new user is created
* visibility of files (e.g., .pdf files)
* important settings for file upload (file renaming, directory creation, etc)
* appearance of links within refbase
* server settings for link resolvers (OpenURL, ISBN)
* rich text formatting (e.g., greek letters, italic or superscript/subscript text)

The configuration file ''initialize/ini.inc.php'' is well commented, therefore you will find much more information in this file.

Below you can find answers to some frequently asked questions about configuring refbase.

== How can I change the logo? ==

You can change the main logo image that's displayed in the refbase page header by setting variable <code>$logoImageURL</code> in ''initialize/ini.inc.php'' to the path of your logo file. In addition, please be sure to set the variables <code>$logoImageWidth</code> and <code>$logoImageHeight</code> to the dimensions of your logo. You may also be interested to specify your own paths for the smaller logos (<code>$logoSmallImageURL</code> and <code>$faviconImageURL</code>).

== How can I setup refbase so that users can register themselves? ==

By default, only the admin is allowed to setup new user accounts. Here's how to setup your refbase installation such that users can automatically register themselves:

In ''initialize/ini.inc.php'' set the <code>$addNewUsers</code> variable to "everyone". Then, provide a link on the main page to ''user_details.php'' where users can use the provided form to register themselves.

Just set the <code>$addNewUsers</code> variable back to "admin" if you want to prevent other users from messing with your users table.

== How can I change the default number of records shown? ==

You can change the default number of records that is returned by any (web, RSS or SRU) query by changing the value of the <code>$defaultNumberOfRecords</code> variable in ''initialize/ini.inc.php''.

== How can I change the default language? ==

You can change the language that's displayed by default in file ''intialize/ini.inc.php'' within your refbase root directory. Search for this paragraph:

// The default language selection, can be overwritten by userdefined language
$defaultLanguage = "de"; // e.g. "en", "de" or "fr"

and set the value of the <code>$defaultLanguage</code> variable to either "en" (English), "de" (German) or "fr" (French). In case of problems, please check that your desired default language is enabled within MySQL table ''languages''.

Note that logged-in database users can switch to another language. This can be done by clicking the ''Options'' link when logged in.

== How can I make some PDFs available to all users? ==

Ususally, access to PDFs should only be made available to logged-in users. This is controlled by variable <code>$fileVisibility</code> in ''initialize/ini.inc.php''. However, often one wants to make a few PDFs available to all users. Variable <code>$fileVisibilityException</code> (also in ''initialize/ini.inc.php'') can be used to specify a condition where attached files will be displayed to ''all'' users, no matter whether they're logged in or not.

By default, refbase will publicly display files for all records where the ''thesis'' field in table ''refs'' is not empty, i.e. if a thesis type has been specified for the record:

$fileVisibilityException = array("thesis", "/.+/");

If, instead, you'd like to allow public access to PDFs for arbitrary records, a common approach would be to put some unique string into one of the fields from table ''refs'', and use this field & identifier string in variable <code>$fileVisibilityException</code>.†As an example, for all records where the attached PDF should be displayed publicly, you could add the string "author copyright" to the ''notes'' field. Then use the following pattern:

$fileVisibilityException = array("notes", "/author copyright/");

As another example, if you'd like to offer public access to all PDFs that where authored by a member of your institution, you could make use of the ''contribution_id'' field ([[Auto-updating_author/group_bibliographies#Institutional_or_group_bibliographies|more info]]), and specify this field and your institutional abbreviation in variable <code>$fileVisibilityException</code>. If your institutional abbreviation is, say, "NUCAPT", you'd use this pattern:

$fileVisibilityException = array("contribution_id", "/NUCAPT/");

== How can I change options & permissions for everyone who's not logged in? ==

=== Setting options via the web interface ===

When logged in as admin, you can set options and access permissions for everyone who's not logged in by calling the script ''user_options.php'' with the <code>userID=0</code> parameter:

user_options.php?userID=0

For all permissions that are set to off, the relevant interface elements will be hidden from the refbase GUI.

Note that some of the available user permissions require a user being logged in. I.e., enabling these options for anyone who isn't logged in won't have any effect. Following user permissions require a login:

* Add records
* Edit records
* Delete records
* File upload
* User groups
* User queries
* Import
* Batch import
* Modify options

If you want to allow users who are not logged in to query the refbase database via the [[Search/Retrieve web services|SRU search/retrieve webservice]], then either the ''Export'' or the ''Batch export'' user permission needs to be enabled. This will allow export of XML records via ''sru.php'' but won't allow a user who isn't logged in to export records via the web interface.

=== Setting options within ''ini.inc.php'' ===

If you like to change the permission to see/download files (e.g., .pdf files), you (the admin) can find the appropriate option in file ''initialize/ini.inc.php''. The relevant variable is called <code>$fileVisibility</code>. You are able to allow file download for everyone, logged-in users only, or on a user-specific basis.

Additionally, you can set exceptions to this rule in variable <code>$fileVisibilityException</code>, which enables you to always allow download access to files that meet a particular criterion. A typical usage example would be to always grant download access to theses or papers that were written by members of your own institution.

For more details, please refer to the comments in ''ini.inc.php''.

== How can I change the default citation style? ==

You can use variable <code>$defaultCiteStyle</code> in file ''initialize/ini.in.php'' to change the citation style that's displayed by default in the web interface (Citation view) as well as for export of formatted citation lists to RTF, PDF, LaTeX, etc. The given style name must have a matching entry in the ''styles'' table of your refbase MySQL database.

Note that the admin can enable or disable particular citation styles individually for each user. And if desired, logged-in users can deselect some of the enabled styles in their user-specific options.

== How can I change the names & order of citation styles? ==

=== Changing the names of citation styles ===

Here's how to change the names of citation styles displayed in the "Cite using style" drop-down (in the form below the query results list): Currently, you have to directly edit the ''styles'' MySQL table. E.g., to change the display name of the "Polar Biol" citation style to "Default" execute the following MySQL command from within your SQL command line interpreter:

UPDATE styles SET style_name = "Default" WHERE style_name = "Polar Biol";

Note that you must also change the corresponding names for the variables <code>$defaultCiteStyle</code> and <code>$defaultUserStyles</code> in ''initialize/ini.inc.php''.

=== Changing the order of citation styles ===

Similar to the above, you can edit the ''styles'' MySQL table to change the order of citation styles displayed in the "Cite using style" drop-down menu. If, for example, you want to switch the order of the first two citation styles, execute the two commands below:

UPDATE styles SET order_by = "2" WHERE style_id = 1;
UPDATE styles SET order_by = "1" WHERE style_id = 2;

Note: this example assumes that you have table entries with style_id's of 1 and 2, otherwise adopt or use something like:

UPDATE styles SET order_by = "...(whatever)..." WHERE style_name = "...(whatever)..."

The ''order_by'' field is of type <code>varchar(25)</code>, i.e., you can also use more fine grained values (such as "1a", "1b", etc).

== How can I add or disable a particular citation style? ==

=== Adding a citation style ===

Currently, citation styles are written as a PHP function, so you'll need to know a bit of PHP to add your own style. The PHP function that outputs records in citation format is called <code>citeRecord()</code>. For each citation style, there's a separate file with a dedictated version of this function. These citation style files are located within the ''cite'' sub-directory of your refbase root directory.

To build your own style, you may want to have a look at the existing citation style files and [[#How to create a new citation style|modify]] one of them to suit your needs.

After you've created your own citation style, copy it into the ''cite'' sub-directory of your refbase root directory. Then, in order to add your citation style file to the "Cite using style" drop-down, execute the following MySQL command from within your SQL command line interpreter:

INSERT INTO styles VALUES (NULL, 'STYLENAME', 'true', 'STYLEFILE', '1', '1');

In the above MySQL command, replace <code>STYLENAME</code> with the actual name of your citation style. This name will appear in the "Cite using style" drop-down. Similarly, <code>STYLEFILE</code> must be replaced with the file name of your citation style file, prefixed with "styles/" (example: "styles/MyStyleFile.php"). In addition, you can change the first number ('1') in the above command to change the position at which your style name will be displayed in the drop-down. To see all available styles and confirm that your style has been successfully added to the ''styles'' MySQL table, execute this command:

SELECT * FROM styles;

Now, login as admin via the refbase web interface, click on "Manage Users" and activate your new style (using the "edit options" link) for all those users who shall see this style. If you've enabled/disabled any citation styles for the admin user, you'll have to logout and login again in order to see your changes.

=== Disabling a citation style ===

You can globally disable existing styles by setting the ''style_enabled'' field to "false". E.g., if you want to disable the "Polar Biol" citation style, execute:

UPDATE styles SET style_enabled = "false" WHERE style_name = "Polar Biol";

=== How to create a new citation style ===

Before we start this section, a comment in advance:

To improve refbase: If you have created a new citation style, we would be interested to offer this style for all refbase users. If possible, please
* post this new .php file to [[refbase:Community_Portal|the community]].
* include the journal title for you built the style with their website.

This section should contain information/hints for non-php professionals

==== Adapting existing work ====

Before investing energy in creating a new style, it is wise to check the [http://refbase.svn.sourceforge.net/viewvc/refbase/ refbase subversion repository] for new styles that are under development but not yet included in the project release. Be aware that styles obtained from the [http://refbase.svn.sourceforge.net/viewvc/refbase/branches/bleeding-edge/cite/styles/ bleeding edge branch] are not necessarily in working condition, and even if they appear to work, may be unfit for a production environment.

----
Todo-list:
*A link is set from [[Adding Records]]-page: how to configure different Types of publication and different Types of Thesis
**in the database
**in view options

== How can I add a new interface language? ==

In order to add a new language (locale) to refbase, you need to perform these steps:

* Within the refbase ''locales/'' directory, copy one of the existing subdirectories and rename it to the [http://www.loc.gov/standards/iso639-2/php/code_list.php two-letter code] of the language you'd like to add (e.g. "es" in case of Spanish).
* Within your new subdirectory, translate all lines in file ''common.inc'' into your language, and save a copy of this file with encoding "Unicode (UTF-8, no BOM)" to ''common_utf8.inc''.
* Issue following MySQL command via ''sql_search.php'' when logged into refbase as admin:

INSERT INTO languages VALUES (NULL, 'LANGCODE', 'true', '4');

In the above MySQL command, replace <code>LANGCODE</code> with the two-letter code of your language, e.g. "es" for Spanish. In addition, you can change the last number ("4" in the above example) to alter the position at which your language name will be displayed in the language drop-down.

The new language option should now appear within the language drop-down in the refbase user options.

To see all currently available languages and to confirm that your language has been successfully added to the ''languages'' MySQL table, execute this command from within your MySQL command line interpreter (after you've selected the refbase MySQL database):

SELECT * FROM languages;

Please note that in refbase-0.9.0, not the entire interface is available for localization. We plan to finish internationalization until version 1.0.

If you've translated the refbase interface strings in ''common.inc'' into your own language, please [[refbase:Community_Portal|send us]] this file so that we can include it with a future release of refbase.

[[Category:Configuration]]
__NOEDITSECTION__

Configuring refbase

2023-11-06T22:23:39Z

WikiSysop: Original page content from 09-Dec-2008

This document presents some tips how to configure your refbase installation:

The refbase admin has a variety of options to configure or customize refbase. Some of them are listed in this article. If you don't find the desired option, please refer to file ''initialize/ini.inc.php'' within your refbase installation. This configuration file contains many global settings which are not accessible via the refbase web interface:

* initial database settings (database name, admin email, database URL, character set, etc)
* default user settings when a new user is created
* visibility of files (e.g., .pdf files)
* important settings for file upload (file renaming, directory creation, etc)
* appearance of links within refbase
* server settings for link resolvers (OpenURL, ISBN)
* rich text formatting (e.g., greek letters, italic or superscript/subscript text)

The configuration file ''initialize/ini.inc.php'' is well commented, therefore you will find much more information in this file.

Below you can find answers to some frequently asked questions about configuring refbase.

== How can I change the logo? ==

You can change the main logo image that's displayed in the refbase page header by setting variable <code>$logoImageURL</code> in ''initialize/ini.inc.php'' to the path of your logo file. In addition, please be sure to set the variables <code>$logoImageWidth</code> and <code>$logoImageHeight</code> to the dimensions of your logo. You may also be interested to specify your own paths for the smaller logos (<code>$logoSmallImageURL</code> and <code>$faviconImageURL</code>).

== How can I setup refbase so that users can register themselves? ==

By default, only the admin is allowed to setup new user accounts. Here's how to setup your refbase installation such that users can automatically register themselves:

In ''initialize/ini.inc.php'' set the <code>$addNewUsers</code> variable to "everyone". Then, provide a link on the main page to ''user_details.php'' where users can use the provided form to register themselves.

Just set the <code>$addNewUsers</code> variable back to "admin" if you want to prevent other users from messing with your users table.

== How can I change the default number of records shown? ==

You can change the default number of records that is returned by any (web, RSS or SRU) query by changing the value of the <code>$defaultNumberOfRecords</code> variable in ''initialize/ini.inc.php''.

== How can I change the default language? ==

You can change the language that's displayed by default in file ''intialize/ini.inc.php'' within your refbase root directory. Search for this paragraph:

// The default language selection, can be overwritten by userdefined language
$defaultLanguage = "de"; // e.g. "en", "de" or "fr"

and set the value of the <code>$defaultLanguage</code> variable to either "en" (English), "de" (German) or "fr" (French). In case of problems, please check that your desired default language is enabled within MySQL table ''languages''.

Note that logged-in database users can switch to another language. This can be done by clicking the ''Options'' link when logged in.

== How can I make some PDFs available to all users? ==

Ususally, access to PDFs should only be made available to logged-in users. This is controlled by variable <code>$fileVisibility</code> in ''initialize/ini.inc.php''. However, often one wants to make a few PDFs available to all users. Variable <code>$fileVisibilityException</code> (also in ''initialize/ini.inc.php'') can be used to specify a condition where attached files will be displayed to ''all'' users, no matter whether they're logged in or not.

By default, refbase will publicly display files for all records where the ''thesis'' field in table ''refs'' is not empty, i.e. if a thesis type has been specified for the record:

$fileVisibilityException = array("thesis", "/.+/");

If, instead, you'd like to allow public access to PDFs for arbitrary records, a common approach would be to put some unique string into one of the fields from table ''refs'', and use this field & identifier string in variable <code>$fileVisibilityException</code>.†As an example, for all records where the attached PDF should be displayed publicly, you could add the string "author copyright" to the ''notes'' field. Then use the following pattern:

$fileVisibilityException = array("notes", "/author copyright/");

As another example, if you'd like to offer public access to all PDFs that where authored by a member of your institution, you could make use of the ''contribution_id'' field ([[Auto-updating_author/group_bibliographies#Institutional_or_group_bibliographies|more info]]), and specify this field and your institutional abbreviation in variable <code>$fileVisibilityException</code>. If your institutional abbreviation is, say, "NUCAPT", you'd use this pattern:

$fileVisibilityException = array("contribution_id", "/NUCAPT/");

== How can I change options & permissions for everyone who's not logged in? ==

=== Setting options via the web interface ===

When logged in as admin, you can set options and access permissions for everyone who's not logged in by calling the script ''user_options.php'' with the <code>userID=0</code> parameter:

user_options.php?userID=0

For all permissions that are set to off, the relevant interface elements will be hidden from the refbase GUI.

Note that some of the available user permissions require a user being logged in. I.e., enabling these options for anyone who isn't logged in won't have any effect. Following user permissions require a login:

* Add records
* Edit records
* Delete records
* File upload
* User groups
* User queries
* Import
* Batch import
* Modify options

If you want to allow users who are not logged in to query the refbase database via the [[Search/Retrieve web services|SRU search/retrieve webservice]], then either the ''Export'' or the ''Batch export'' user permission needs to be enabled. This will allow export of XML records via ''sru.php'' but won't allow a user who isn't logged in to export records via the web interface.

=== Setting options within ''ini.inc.php'' ===

If you like to change the permission to see/download files (e.g., .pdf files), you (the admin) can find the appropriate option in file ''initialize/ini.inc.php''. The relevant variable is called <code>$fileVisibility</code>. You are able to allow file download for everyone, logged-in users only, or on a user-specific basis.

Additionally, you can set exceptions to this rule in variable <code>$fileVisibilityException</code>, which enables you to always allow download access to files that meet a particular criterion. A typical usage example would be to always grant download access to theses or papers that were written by members of your own institution.

For more details, please refer to the comments in ''ini.inc.php''.

== How can I change the default citation style? ==

You can use variable <code>$defaultCiteStyle</code> in file ''initialize/ini.in.php'' to change the citation style that's displayed by default in the web interface (Citation view) as well as for export of formatted citation lists to RTF, PDF, LaTeX, etc. The given style name must have a matching entry in the ''styles'' table of your refbase MySQL database.

Note that the admin can enable or disable particular citation styles individually for each user. And if desired, logged-in users can deselect some of the enabled styles in their user-specific options.

== How can I change the names & order of citation styles? ==

=== Changing the names of citation styles ===

Here's how to change the names of citation styles displayed in the "Cite using style" drop-down (in the form below the query results list): Currently, you have to directly edit the ''styles'' MySQL table. E.g., to change the display name of the "Polar Biol" citation style to "Default" execute the following MySQL command from within your SQL command line interpreter:

UPDATE styles SET style_name = "Default" WHERE style_name = "Polar Biol";

Note that you must also change the corresponding names for the variables <code>$defaultCiteStyle</code> and <code>$defaultUserStyles</code> in ''initialize/ini.inc.php''.

=== Changing the order of citation styles ===

Similar to the above, you can edit the ''styles'' MySQL table to change the order of citation styles displayed in the "Cite using style" drop-down menu. If, for example, you want to switch the order of the first two citation styles, execute the two commands below:

UPDATE styles SET order_by = "2" WHERE style_id = 1;
UPDATE styles SET order_by = "1" WHERE style_id = 2;

Note: this example assumes that you have table entries with style_id's of 1 and 2, otherwise adopt or use something like:

UPDATE styles SET order_by = "...(whatever)..." WHERE style_name = "...(whatever)..."

The ''order_by'' field is of type <code>varchar(25)</code>, i.e., you can also use more fine grained values (such as "1a", "1b", etc).

== How can I add or disable a particular citation style? ==

=== Adding a citation style ===

Currently, citation styles are written as a PHP function, so you'll need to know a bit of PHP to add your own style. The PHP function that outputs records in citation format is called <code>citeRecord()</code>. For each citation style, there's a separate file with a dedictated version of this function. These citation style files are located within the ''cite'' sub-directory of your refbase root directory.

To build your own style, you may want to have a look at the existing citation style files and [[#How to create a new citation style|modify]] one of them to suit your needs.

After you've created your own citation style, copy it into the ''cite'' sub-directory of your refbase root directory. Then, in order to add your citation style file to the "Cite using style" drop-down, execute the following MySQL command from within your SQL command line interpreter:

INSERT INTO styles VALUES (NULL, 'STYLENAME', 'true', 'STYLEFILE', '1', '1');

In the above MySQL command, replace <code>STYLENAME</code> with the actual name of your citation style. This name will appear in the "Cite using style" drop-down. Similarly, <code>STYLEFILE</code> must be replaced with the file name of your citation style file, prefixed with "styles/" (example: "styles/MyStyleFile.php"). In addition, you can change the first number ('1') in the above command to change the position at which your style name will be displayed in the drop-down. To see all available styles and confirm that your style has been successfully added to the ''styles'' MySQL table, execute this command:

SELECT * FROM styles;

Now, login as admin via the refbase web interface, click on "Manage Users" and activate your new style (using the "edit options" link) for all those users who shall see this style. If you've enabled/disabled any citation styles for the admin user, you'll have to logout and login again in order to see your changes.

=== Disabling a citation style ===

You can globally disable existing styles by setting the ''style_enabled'' field to "false". E.g., if you want to disable the "Polar Biol" citation style, execute:

UPDATE styles SET style_enabled = "false" WHERE style_name = "Polar Biol";

=== How to create a new citation style ===

Before we start this section, a comment in advance:

To improve refbase: If you have created a new citation style, we would be interested to offer this style for all refbase users. If possible, please
* post this new .php file to [[refbase:Community_Portal|the community]].
* include the journal title for you built the style with their website.

This section should contain information/hints for non-php professionals

==== Adapting existing work ====

Before investing energy in creating a new style, it is wise to check the [http://refbase.svn.sourceforge.net/viewvc/refbase/ refbase subversion repository] for new styles that are under development but not yet included in the project release. Be aware that styles obtained from the [http://refbase.svn.sourceforge.net/viewvc/refbase/branches/bleeding-edge/cite/styles/ bleeding edge branch] are not necessarily in working condition, and even if they appear to work, may be unfit for a production environment.

----
Todo-list:
*A link is set from [[Adding Records]]-page: how to configure different Types of publication and different Types of Thesis
**in the database
**in view options

== How can I add a new interface language? ==

In order to add a new language (locale) to refbase, you need to perform these steps:

* Within the refbase ''locales/'' directory, copy one of the existing subdirectories and rename it to the [http://www.loc.gov/standards/iso639-2/php/code_list.php two-letter code] of the language you'd like to add (e.g. "es" in case of Spanish).
* Within your new subdirectory, translate all lines in file ''common.inc'' into your language, and save a copy of this file with encoding "Unicode (UTF-8, no BOM)" to ''common_utf8.inc''.
* Issue following MySQL command via ''sql_search.php'' when logged into refbase as admin:

INSERT INTO languages VALUES (NULL, 'LANGCODE', 'true', '4');

In the above MySQL command, replace <code>LANGCODE</code> with the two-letter code of your language, e.g. "es" for Spanish. In addition, you can change the last number ("4" in the above example) to alter the position at which your language name will be displayed in the language drop-down.

The new language option should now appear within the language drop-down in the refbase user options.

To see all currently available languages and to confirm that your language has been successfully added to the ''languages'' MySQL table, execute this command from within your MySQL command line interpreter (after you've selected the refbase MySQL database):

SELECT * FROM languages;

Please note that in refbase-0.9.0, not the entire interface is available for localization. We plan to finish internationalization until version 1.0.

If you've translated the refbase interface strings in ''common.inc'' into your own language, please [[refbase:Community_Portal|send us]] this file so that we can include it with a future release of refbase.

[[Category:Configuration]]

Roadmap

2023-11-06T22:18:33Z

WikiSysop: Hide section edit links

This is a rough roadmap of feature additions and bug fixes for our upcoming releases.

== Post refbase-0.9.5 ==

* Discussion
** Coding style
** HTML layout (templates/skins, CSS styling)
** Reference types
** Citation formatting
** Ways to improve build/release cycle
** How to further modularize the code to allow for other RDBMS, custom database schemes and a plugin mechanism
** Prioritize [[Planned_feature_additions|planned features]]
* Fix referrer-related bugs

[[Category:General]]
__NOEDITSECTION__

Roadmap

2023-11-06T22:18:10Z

WikiSysop: Original page content from 20-Nov-2008

The 'next release' question

2023-11-06T22:13:18Z

WikiSysop: Update link to refbase Feature Requests forum

Often, the question arises: ''When do you release the next version of refbase?''

It is not easy to give an answer to that question. Unfortunately, we cannot (and don't want to) announce exact release dates. Experience shows that these dates are almost never met and it only leads to user frustration. We understand that it may seem equally frustrating that there is no info at all. But this is as good as we can do.

Nevertheless, refbase is under constant development. The most recent fixes & additions are available in our [[SVN_version|SVN repository]].

We encourage you to leave your ideas for future enhancements at the [[Feature request]] page in the wiki or in our [https://sourceforge.net/p/refbase/discussion/351913/ Feature Requests forum].

[[Category:General]]

The 'next release' question

2023-11-06T22:11:53Z

WikiSysop: Original page content from 09-Dec-2006

Often, the question arises: ''When do you release the next version of refbase?''

It is not easy to give an answer to that question. Unfortunately, we cannot (and don't want to) announce exact release dates. Experience shows that these dates are almost never met and it only leads to user frustration. We understand that it may seem equally frustrating that there is no info at all. But this is as good as we can do.

Nevertheless, refbase is under constant development. The most recent fixes & additions are available in our [[SVN_version|SVN repository]].

We encourage you to leave your ideas for future enhancements at the [[Feature request]] page in the wiki or in our [http://sourceforge.net/forum/forum.php?forum_id=351913 Feature Requests forum].

[[Category:General]]

Release notes

2023-11-06T21:56:46Z

WikiSysop: Hide section edit links

This document lists the major additions, changes and fixes since the release of refbase-0.9.0. See also the 'NEWS' file that comes with the refbase package.

== refbase-0.9.5 ==

=== Feature additions ===

==== Import/Add Records ====

* Added support for resource types Abstract, Conference Article, Conference Volume, Magazine Article, Manual, Miscellaneous, Newspaper Article, Patent, Report, Software

* Added import capabilities from SciFinder and Endnote XML

* refbase now supports direct import from [http://arxiv.org/ arXiv.org] & [http://crossref.org/ CrossRef.org]: enter one or more arXiv IDs, DOIs or OpenURLs, and refbase will fetch & import the corresponding record metadata

* Added support for direct upload of references from [http://www.sonnysoftware.com/ Bookends]

==== Export/Citation ====

* Added support for new export formats: ADS, Atom XML, ISI Web of Science, OAI_DC XML, SRW_DC XML, and Word XML

* Added new citation styles: AMA, APA, Chicago, Harvard (3 variants), MLA, and Vancouver

* refbase can now output citations in LaTeX bibliography (.bbl) format

* It is now possible to cite, group, or export ALL found records (instead of only the selected records)

* When outputting citations as PDF, US letter is now supported as page format

* Headers can now be added to cite formats via the <code>headerMsg</code> URL parameter

* Links to corresponding files are now included in the export data if the export format and user permissions allow so

==== Search/Display ====

* refbase sports a refined interface:
** Revamped the refbase main page: all forms are now styled via CSS, and citations of the most recent publications are now dynamically included upon page load
** Redesigned the page footer & header as well as the forms on the results pages
** The "Quick Search" form is now always available in the page header
** refbase now makes use of the [http://www.prototypejs.org/ Prototype] & [http://script.aculo.us/ script.aculo.us] JavaScript frameworks to offer auto-completions (or search suggestions) for text entered by the user in text entry fields of the refbase interface
** Forms on search results pages can now be hidden (and if enabled by the admin, a sliding effect is now used when a user toggles the display of these forms)
** Search results can be browsed & searched in three different views: List view, Citations, and Details
** Additional record info (keywords, abstract, etc) and links to cite/export the record can now be displayed underneath each citation

* refbase now supports [[OpenSearch service|OpenSearch]] which allows clients to search refbase and retrieve results in a standardized manner; as an example, this enables Firefox 3 & IE 8 users to search refbase directly from their browser's toolbar, and the browsers can now offer search suggestions for search terms entered in the browser's search box

* Initial support for searching & managing of duplicate records

* For the current session, refbase now offers a query history with links to any previous search results

* The ''show.php'' API now allows to include results from a refbase server into other web pages; this makes it possible to [[Integrating_refbase_into_your_web_site|dynamically include results]] from a refbase database into static HTML pages (using an <code>iframe</code> or AJAX-style JavaScript)

* Added a "main fields" search option to the "Quick Search" form which allows to search all of the main fields at once; the list of "main fields" can be specified globally as well as individually for each user

* The default number of records per page can now be specified globally as well as individually for each user

* Added initial support for output to mobile devices (<code>viewType=Mobile</code>)

* Many more minor enhancements

==== Localization ====

* Added initial support for spanish and [[Chinese_localization_package|chinese]] localizations

==== Command Line Clients ====

* The [[Command_line_clients|'refbase' command line client]] now supports the new export formats ''atom'', ''isi'', ''oai_dc'', ''srw_dc'' and ''word'' as well as <code>--view=Mobile</code> and <code>--order=creation-date</code>

* [[Command_line_clients|'refbase' command line client]]: added options <code>-A|--append</code> and <code>-B|--update</code> which let you append found records to a local BibTeX or MODS/SRW XML file (if they don't yet exist in that file), and update existing records in that file if their modification date on the server is more recent; by default, a backup file is created before adding or changing anything in the local file

* [[Command_line_clients|'refbase' command line client]]: added <code>-E|--extract</code> option which extracts citation IDs from a file and retrieves matching records from refbase (supported file types: .aux, .bbl, .bib, .enw, .ris, .tex, and (MODS|SRW|Endnote) .xml)

==== Miscellaneous ====

* Added a [http://www.mediawiki.org/wiki/Extension:Refbase refbase extension for MediaWiki] which allows to place a serial number within <code><refbase>...</refbase></code> markup tags; metadata for the reference is retrieved from refbase and marked-up according to a MediaWiki citation template

* Added support for the [http://www.sitemaps.org sitemaps.org] protocol which allows for better indexing by search engines

* The refbase [[UnAPI_service|unAPI service]] now supports the new export formats ''atom'', ''oai_dc'' and ''srw_dc''

* Many more minor enhancements

=== Changes ===

* Introduced measures to better prevent cross-site scripting (XSS) attacks

* For security reasons, HTML tags are now stripped from the <code>headerMsg</code> URL parameter; string formatting can now be done using the refbase markup syntax

* Improved support for PHP installations running with <code>safe_mode=On</code>

* By default, export of data via the refbase GUI is now enabled for anonymous users

* The citation output options (previously located in the results footer) have been moved to the Display Options form of the results header in Citation view

* refbase now remembers many more search & display options while navigating or refining the results list

* Changed the HTTP transfer method in most forms from POST to GET; this helps to avoid warnings about re-sending POST data in some browsers (such as Firefox)

* We now use a ''show.php'' URL for the "show details" link in the search results list since it is much shorter and easier to bookmark as a permanent link

* When linking to particular records via ''show.php'', one can now use consecutive serial number ranges as values of the <code>records</code> parameter; examples: ''show.php?records=123-131'' or ''show.php?records=123-141,145,147,150-152''

* When viewing/outputting citations, the list of citations can now be sorted by record creation date (use <code>citeOrder=creation-date</code> in ''show.php'' URLs); this allows to sort records such that newly added/edited records get listed top of the list

* Redesigned the page footer to make it fit on one line (and thus less heavy)

* Added many CSS attributes (id/class names) to HTML output where appropriate; this allows to easier refine the CSS styling of the refbase interface

* The admin can now define any of the supported views (List view, Citations, Details) as the default view

* For each view, the admin can now define whether the results header & footer should be displayed open or closed by default, or whether they should be entirely hidden from the interface

* The admin can now customize the list of fields that are displayed by default in List & Details view; similarly, the list of fields that are available in dropdown menus of the results header can also be customized

* The admin can now define ''accesskey'' values which allow for keyboard navigation of the main parts of the refbase interface

* The <code>$databaseBaseURL</code> in ''ini.inc.php'' is now auto-generated by default

* The refbase logo image files have been updated to the new refbase logo, and the logo URL path & dimensions can now be customized easily via ''ini.inc.php''

* The session/temp dir path can now be specified explicitly in ''ini.inc.php''; this allows you to define a custom directory path that's used on your server to save session data and to write any temporary files

* The ''edition'' field now accepts string values

* After any add, edit, or delete action, refbase now includes a link to the last multi-record search result list in the feedback header message if the previous query resulted in a single record; together with other changes, this obviates ''receipt.php''

* By default, the SRU formats ''SRW_DC XML'' and ''SRW_MODS XML'' are now transformed to HTML via XSL stylesheets

* Authenticated users can now use ''opensearch.php'' or ''sru.php'' to query any of their user-specific fields

* For OpenSearch & SRU searches, the ''keywords'' field will now be queried by default if no context set & index name is given ("cql.serverChoice")

* Renamed the [[Bibutils]] ''xml2word'' command line tool to ''xml2wordbib'' according to the name changes in Bibutils v3.40; note that if you're using a Bibutils version prior to Bibutils v3.40, you must revert this change in file ''export/bibutils/export_xml2word.php''

* Underline fontshape markup is now supported in various import and citation formats as well as in refbase markup (use: <code>__underlined text__</code>)

* When importing multiple records, ALL records are now imported by default

* Improved UTF-8 handling on import so that e.g. a best-effort conversion is done for UTF-8 data which are imported into a latin1-based database

* When importing (or exporting) RIS records, the type of thesis (such as "Masters thesis" or "Ph.D. thesis") is now taken from (or exported to) the ''U1'' field (as is supported by Bibutils v3.35 or greater);

* Upon import, if the given URL actually is a DOI prefixed with [http://dx.doi.org/ http://dx.doi.org/], we'll extract the DOI and move it to the ''doi'' field

* Import of user-specific fields into the "Add record" form is now possible

* We now generate (or honour existing) cite keys/IDs for the import data, and copy them to the user's ''cite_key'' field; the uniqueness of cite keys is ensured among all imported records as well as the user's existing records

* Improved recognition of PubMed resource types

* For the "Extract citations" functionality, we now check whether the extracted serial numbers and cite keys exist in the database and report any missing record identifiers

* Changed or merged some localization strings to allow for better translations to languages such as Spanish or Chinese

* Refined layout of ''user_receipt.php''

* The [[Command_line_clients#.27refbase_import.27_command_line_client|'refbase_import' command line client]] now supports common output options from the 'refbase' CLI client; this allows to instruct the refbase server to return all imported records in any of the supported export or citation formats & styles

* Many more minor changes

=== Bug fixes ===

* Fixed bug that prevented correct directory creation/renaming and/or file upload on some platforms

* Fixed <code>preg_match()</code> compilation errors when importing BibTeX records into a refbase UTF-8 database

* When importing PubMed MEDLINE source data, we now extract author information from the ''AU'' field if the ''FAU'' field is not available

* We now convert Endnote XML text style markup into appropriate refbase markup

* Upon RIS import, we now make sure that HTML encoded source data (such as <code>&auml;</code>, <code>&#xF6;</code> or <code>&#233;</code>) get decoded before import

* Records of unrecognized resource type were omitted upon citation output; fixed

* When outputting to LaTeX or RIS, curly brackets are now escaped to avoid incorrect output

* Fixed an issue were it wasn't possible to correctly import (or cite) records which contained non-ASCII characters in author's given names

* Worked around an error in Internet Explorer when importing single records via the web interface

* Fixed an error when exporting data to ODF XML and when the user-specific fields were missing from the SQL query

* Fixed referrer-related problems that could cause unexpected behaviour and incorrect warning/error messages; however note that working simultaneously in different browser windows or tabs can still cause some unexpected results

* Worked around PREG compilation errors on some UTF8-based systems

* For theses, the corporate author (i.e. the corporate body granting the degree) is now labeled correctly in MODS XML output; as a result, the degree grantor is now recognized correctly by Bibutils and copied to the BibTeX ''school'' field

* Many more minor bug fixes

[[Category:General]]
__NOEDITSECTION__

Release notes

2023-11-06T21:56:15Z

WikiSysop: Original page content from 23-Nov-2008

Creating the first user

2023-11-05T22:37:57Z

WikiSysop: Make the first list into an ordered list

After your (hopefully) successfull installation of refbase, you should create your own admin account.

Please, make sure that you exactly follow the steps outlined on the welcome page after successful installation. These steps are:

# Goto the main refbase page (''Home'')
# Login with email address = ''user@refbase.net'' and password = ''start''
#: (make sure that the top right corner of your screen says: "You're logged in as Admin (''user@refbase.net''), if not see [[#Troubleshooting| Troubleshooting]] below)
# Click on ''Add User'' and enter the name, institutional abbreviation, email address and password of the admin user
# Open the file ''initialize/ini.inc.php'' in a text editor and change the value of the ''$adminLoginEmail'' variable to the email address you've specified for the admin user
# Log out, then login again using the email address and password of your newly created admin account

Especially note that you must set the value of the ''$adminLoginEmail'' variable in file ''initialize/ini.inc.php'' to the email address of your newly created admin user (step 4.).

== Troubleshooting ==

When being logged in as admin, you should see a red "Admin" label in front of your email address at the top right corner of the screen. An example screenshot is given [[Manual_installation#2.5_Setup_your_own_admin_user|here]]. If this is not the case for you, the following tips may help you to get things working properly.

You won't be able to login as admin using email address = ''user@refbase.net'' and password = ''start'' if you've already changed the value of the ''$adminLoginEmail'' variable ''before'' attempting to login for the first time. This variable must only be changed ''after'' you've created your own admin user.

Also, please make sure that:

* your PHP installation supports sessions
* <code>session.use_cookies</code> is set to ON in your [[Required_PHP-INI_Settings#How_to_locate_your_active_php.ini_file|active ''php.ini'' file]]
* you have cookies enabled in your browser
* you've instructed your browser to accept cookies from your refbase site

[[Category:Installation]]
__NOEDITSECTION__

Creating the first user

2023-11-05T22:30:22Z

WikiSysop: Hide section edit links

After your (hopefully) successfull installation of refbase, you should create your own admin account.

Please, make sure that you exactly follow the steps outlined on the welcome page after successful installation. These steps are:

* Goto the main refbase page (''Home'')
* Login with email address = ''user@refbase.net'' and password = ''start''
: (make sure that the top right corner of your screen says: "You're logged in as Admin (''user@refbase.net''), if not see [[#Troubleshooting| Troubleshooting]] below)
* Click on ''Add User'' and enter the name, institutional abbreviation, email address and password of the admin user
* Open the file ''initialize/ini.inc.php'' in a text editor and change the value of the ''$adminLoginEmail'' variable to the email address you've specified for the admin user
* Log out, then login again using the email address and password of your newly created admin account

Especially note that you must set the value of the ''$adminLoginEmail'' variable in file ''initialize/ini.inc.php'' to the email address of your newly created admin user (step 4.).

== Troubleshooting ==

When being logged in as admin, you should see a red "Admin" label in front of your email address at the top right corner of the screen. An example screenshot is given [[Manual_installation#2.5_Setup_your_own_admin_user|here]]. If this is not the case for you, the following tips may help you to get things working properly.

You won't be able to login as admin using email address = ''user@refbase.net'' and password = ''start'' if you've already changed the value of the ''$adminLoginEmail'' variable ''before'' attempting to login for the first time. This variable must only be changed ''after'' you've created your own admin user.

Also, please make sure that:

* your PHP installation supports sessions
* <code>session.use_cookies</code> is set to ON in your [[Required_PHP-INI_Settings#How_to_locate_your_active_php.ini_file|active ''php.ini'' file]]
* you have cookies enabled in your browser
* you've instructed your browser to accept cookies from your refbase site

[[Category:Installation]]
__NOEDITSECTION__

Creating the first user

2023-11-05T22:29:36Z

WikiSysop: Original page content from 09-Feb-2009

After your (hopefully) successfull installation of refbase, you should create your own admin account.

Please, make sure that you exactly follow the steps outlined on the welcome page after successful installation. These steps are:

* Goto the main refbase page (''Home'')
* Login with email address = ''user@refbase.net'' and password = ''start''
: (make sure that the top right corner of your screen says: "You're logged in as Admin (''user@refbase.net''), if not see [[#Troubleshooting| Troubleshooting]] below)
* Click on ''Add User'' and enter the name, institutional abbreviation, email address and password of the admin user
* Open the file ''initialize/ini.inc.php'' in a text editor and change the value of the ''$adminLoginEmail'' variable to the email address you've specified for the admin user
* Log out, then login again using the email address and password of your newly created admin account

Especially note that you must set the value of the ''$adminLoginEmail'' variable in file ''initialize/ini.inc.php'' to the email address of your newly created admin user (step 4.).

== Troubleshooting ==

When being logged in as admin, you should see a red "Admin" label in front of your email address at the top right corner of the screen. An example screenshot is given [[Manual_installation#2.5_Setup_your_own_admin_user|here]]. If this is not the case for you, the following tips may help you to get things working properly.

You won't be able to login as admin using email address = ''user@refbase.net'' and password = ''start'' if you've already changed the value of the ''$adminLoginEmail'' variable ''before'' attempting to login for the first time. This variable must only be changed ''after'' you've created your own admin user.

Also, please make sure that:

* your PHP installation supports sessions
* <code>session.use_cookies</code> is set to ON in your [[Required_PHP-INI_Settings#How_to_locate_your_active_php.ini_file|active ''php.ini'' file]]
* you have cookies enabled in your browser
* you've instructed your browser to accept cookies from your refbase site

[[Category:Installation]]

Installation-Troubleshooting

2023-11-05T22:27:31Z

WikiSysop: Fixed some typos

This document presents solutions & tips for installation-related problems, and for things that don't seem to be working correctly after installation.

Other issues are discussed on the generic [[Troubleshooting]] page.

If you experience any problems while installing refbase, please read this chapter before [[refbase:Community_portal|contacting us]].

== Preparations before contacting us ==

In few cases, the refbase installation shows an unwanted behaviour. This may be caused by special settings of your server setup.

'''Important''': Please check following settings and REPORT THEM when [[refbase:Community_portal|contacting us]]. This information will help us a lot to figure out what might be wrong:

* Which version of refbase do you use?
* Which platform are you using?
* Do you use a particular package such as XAMPP?
* Which versions of Apache, MySQL and PHP are you running?
* Can you execute other PHP web applications just fine? I.e., is it only refbase that is causing you trouble?
* Can you access MySQL correctly, from the command line as well as from web administration tools such as phpMyAdmin?
* Do you experience the same error/problem using a different browser or computer?
* Do you know about special config settings within your ''httpd.conf'', ''php.ini'' or ''my.cnf'' configuration files?
* Compare your ''php.ini'' with the list of [[Required_PHP-INI_Settings|required ''php.ini'' settings]] and report any differences.
* Regarding ''php.ini'' settings, especially verify that <code>safe_mode</code> is OFF for installation. If you can't change this setting, you may need to perform a [[Manual installation|manual installation]].
* Have a look at your server's error log and report anything that may be connected with refbase.
* Please make sure that PHP error reporting is enabled and report any error messages displayed in your browser. To enable error reporting, set the following variables in your ''php.ini'' file:
error_reporting = E_ALL
display_errors = On

=== General tips ===

Please ensure that you have checked the following:

* If you're using an older refbase version, you may want to [[Updating_refbase|update]] to the newest version and see if this cures your problems.
* If you receive errors when using refbase (e.g., when adding or importing data), please try the same procedure in our [[Refbase_users|demo databases]] to check, whether this problem is specific to your own installation/data or whether it's a general issue.
* Make sure that you've restarted your web server to apply any changes you've made to your ''php.ini'' file.
* Some installations come with multiple ''php.ini'' copies at different locations. To make sure that you're dealing with the correct ''php.ini'' file, checkout the output of the <code>phpinfo()</code> function, it will tell you the location of the active ''php.ini'' file ([[Required_PHP-INI_Settings|more info]]). The returned status info may contain other useful information and it may help to send us the output via private mail.
* If your package manager separates php-mysql from the main php-package (eg. Fedora) make sure to install both. Otherwise every request to refbase will give an empty white page.
* Make sure that the refbase scripts have correct permission settings so that they can be accessed by your server.

== Known problems and possible solutions ==

=== Fail to login ===

If you have problems to log in with your newly created user account after installing refbase, please refer to [[Creating the first user]].

=== Upload of large files fails ===

If you're able to upload files of small file size but experience errors when attempting to upload large files, checkout the variables <code>post_max_size</code> and <code>upload_max_filesize</code> in your active ''php.ini'' file. The values given for <code>post_max_size</code> and <code>upload_max_filesize</code> must be larger than the maximum file size you'd like to be able to upload (see also [[Required_PHP-INI_Settings|required ''php.ini'' settings]]).

=== Upload of files under XAMPP doesn't work ===

In some versions of [https://www.apachefriends.org/ XAMPP] the default temporary folder for uploads, as defined in ''php.ini'', is wrong:

upload_tmp_dir = ".;c:\apachefriends\xampp\tmp"

correct would be:

upload_tmp_dir = "c:\apachefriends\xampp\tmp"

=== Renaming of uploaded files does not work under XAMPP ===

In some versions of [https://www.apachefriends.org/ XAMPP] the needed PHP function <code>iconv</code> is disabled. To fix this, open the ''php.ini'' file of your XAMPP distribution, search for <code>iconv</code> and enable the function by deleting the heading comment sign (').

=== Export of records results in a blank page ===

At present, the '''ADS''', '''BibTeX''', '''EndNote''', '''ISI''', '''RIS''' and '''Word XML''' export formats require a correctly configured Bibutils while any of the other XML formats (e.g. MODS XML or ODF XML) do '''not''' depend on Bibutils. If the latter are working while the former are not, most likely the issue pertains to your [[Bibutils]] install.

You can check that the Bibutils path was correctly configured by viewing the contents of the ''depends'' table. The <code>depends_path</code> for the <code>bibutils</code> record should '''not''' be <code>NULL</code> as seen below:

<pre>
mysql> SELECT * FROM depends;

+------------+------------------+-----------------+--------------+
| depends_id | depends_external | depends_enabled | depends_path |
+------------+------------------+-----------------+--------------+
| 1 | refbase | true | NULL |
| 2 | bibutils | true | NULL |
+------------+------------------+-----------------+--------------+
</pre>

In addition, please note that:

* the path to the Bibutils programs given in table ''depends'' must end with a slash
* permissions must be set correctly so that the Bibutils programs can be executed by Apache/PHP
* if <code>safe_mode</code> is set to On in your active ''php.ini'' file, then you'll need to put the Bibutils programs within the directory that's specified in <code>safe_mode_exec_dir</code>
* the PHP temp/session directory must be accessible & writable by Apache/PHP/Bibutils
* if you're on a hosted service, your Internet Service Provider may have given you a specific temp directory path which you may need to set explicitly in variable <code>$sessionTempDir</code> in file ''initialize/ini.inc.php''

=== Some exports fail in refbase-0.8.0 on some win32 servers ===

Some WAMP stacks fail to execute Bibutils. A workaround is to upgrade to refbase-0.9.0 or greater.

=== Upload of files results in error message ===

If you're using refbase-0.9.0 and you're getting following error message when adding (or editing) a record that includes a file
for upload:

Warning: preg_replace() [function.preg-replace]: Unknown modifier '\' in
.../refbase-0.9.0/includes/include.inc.php on line 3631

Warning: preg_replace() [function.preg-replace]: Unknown modifier '\' in
.../refbase-0.9.0/includes/include.inc.php on line 3634

then you may want to upgrade to refbase-0.9.5 or greater. Alternatively, you can apply a simple patch manually:

Please open file ''modify.php'' in your refbase root directory, goto line 1100 and replace this code:

$dirNamingScheme = trimTextPattern($dirNamingScheme, "[/\\]+", true, true);

with this:

$dirNamingScheme = trimTextPattern($dirNamingScheme, "[\/\\\\]+", true, true);

=== Import of records results in an error message ===

If you're trying to import records into your refbase database and you're getting an error message such as this one:

There were validation errors regarding the data you entered

then you might want check whether your record format is supported by refbase and whether its syntax is correct. Please see our [[Importing records|import]] page for more information and links to example records for all supported formats.

If you're sure that your record format is supported but you still get an error message, please try to import your records at one of our [[Refbase_users|demo databases]]. If this throws up the same error message, then refbase probably has problems recognizing your record format. In that case, we'd appreciate if you'd [[refbase:Community_portal|send us]] your problematic records so that we can look into the problem.

If, however, your records import fine in our demo database, then this hints at a problem with your local refbase installation. Note that import of records in BibTeX, Copac, Endnote (tagged text or XML), PubMed XML, SciFinder or MODS XML format requires [[Bibutils]] being installed on your server. If you think that you've correctly installed Bibutils on your server and still can't get import of the above mentioned formats to work, please [[refbase:Community_portal|let us know]] and we'll try to help.

=== Undefined iconv() despite --with-iconv ===

This problem was experienced on a FreeBSD web host, and has also been reported as a [http://ca.php.net/manual/en/function.iconv.php#47428 FreeBSD issue] in the user comments at php.net, which suggests the resolution (which worked for me) to add the following block of code to the application before iconv() is called:

<pre>
if (!function_exists('iconv') && function_exists('libiconv')) {
function iconv($input_encoding, $output_encoding, $string) {
return libiconv($input_encoding, $output_encoding, $string);
}
}
</pre>

=== Problems with special characters ===

See below for some troubleshooting guidance if you have problems getting higher ASCII characters (such as accented characters or umlauts) displayed correctly in refbase, or if you cannot correctly enter or search for higher ASCII chars in the refbase web interface. Encoding problems can be really tricky since many factors interact with each other, and encoding settings can differ greatly among different systems and versions.

==== Server settings ====

First of all, you should make sure that your MySQL server's character set and collation settings are setup correctly and consistently. For more information and instructions, please see parts 'a)' and 'b)' in section [[Troubleshooting#MySQL_migration_and_character_set_problems|MySQL migration and character set problems]].

If you'd like to use refbase with UTF-8 encoding, then you'll need MySQL version 4.1.x or greater. However, in our experience, MySQL 4.1.x seems to have problems with some Unicode characters, so if possible you should use refbase in conjunction with MySQL 5.x.

It might be also worth checking your web server's configuration file (e.g., in case of the Apache web server: ''httpd.conf'' or ''apache2.conf''). On Ubuntu, for example, some users managed to cure their encoding issues by (un)commenting (or altering) following config setting in Apache 2:

AddDefaultCharset ISO-8859-1

==== Settings in refbase ====

When installing refbase via ''install.php'', make sure that you've chosen the desired default character set (latin1 or utf8). Be aware that if you've tried to install refbase multiple times using the same MySQL database name (in ''initialize/db.inc.php'') but with different settings as default character set, you must drop (i.e. delete) the database before installing it again with a different character encoding.

You can check the encoding of your MySQL database by issuing following command from within your MySQL command line interpreter:

SHOW CREATE DATABASE ''DATABASE_NAME'';

In the above command, replace <code>''DATABASE_NAME''</code> with the actual name of your refbase MySQL database.

If you've chosen "utf8" upon installation, then you have to make sure that variable <code>$contentTypeCharset</code> in file ''initialize/ini.inc.php'' is set to "UTF-8". And if you're using higher ASCII chars in any variable values in file ''ini.inc.php'', you should also re-save that file with encoding "Unicode (UTF-8, no BOM)".

If you've set variable <code>$contentTypeCharset</code> to "UTF-8", you could now access refbase in your web browser and verify that the head of the HTML source states the correct encoding:

<meta http-equiv="content-type" content="text/html; charset=UTF-8">

In case of a latin1-based refbase installation, the contents of the <code>charset</code> attribute should read "ISO-8859-1".

In order to test if refbase has been setup correctly, you should now add or edit a record via the refbase web interface and enter some special characters (such as ·ÈÌ‡ËÏ or ÂÊ¯ˆ‰¸ etc). Then, checkout again the added/edited record and verify that your entered characters display correctly. In addition, use refbase to search for these special characters and verify that your added/edited record is listed among the search results.

So, in summary, if you can 1) successfully enter special characters in refbase, 2) have them displayed correctly after saving your edits '''and''' 3) successfully search for these newly entered characters, then refbase has been set up correctly. However, if one of these actions (enter/display/search) does not work as expected, then you've still got problems.

==== Browser settings ====

If you're still experiencing problems, it's always a ''very'' good idea to try out another browser (or another browser on another platform). Also, try to manually set the encoding of your browser page to either "Unicode (UTF-8)" or "Western (ISO-8859-1)". In Firefox, this can be done via the "View > Character Encoding" menu. After you've set the encoding explicitly, please see if you can now enter/display/search for higher ASCII chars successfully.

Speaking of browser settings, you can often set a default character encoding within the browser's preferences which might be also worth checking out.

==== Import and file encodings ====

Finally, note that when importing data into refbase, you have to make sure that the character encoding of your bibliographic data file matches the character encoding of your refbase database. If this is causing you any trouble, copying and pasting the data into the refbase import form may actually work better. With regard to import, you should also ensure that you're using a recent version of [[Bibutils]] since some earlier versions of Bibutils had issues with character set support.

If you still can't get rid of your encoding issues, please [[refbase:Community_portal|let us know]] and we'll see what we can do.

[[Category:Installation]]
[[Category:Troubleshooting]]
__NOEDITSECTION__

Installation-Troubleshooting

2023-11-05T22:16:46Z

WikiSysop: Update external links

This document presents solutions & tips for installation-related problems, and for things that don't seem to be working correctly after installation.

Other issues are discussed on the generic [[Troubleshooting]] page.

If you experience any problems while installing refbase, please read this chapter before [[refbase:Community_portal|contacting us]].

== Preparations before contacting us ==

In few cases, the refbase installation shows an unwanted behaviour. This may be caused by special settings of your server setup.

'''Important''': Please check following settings and REPORT THEM when [[refbase:Community_portal|contacting us]]. This information will help us a lot to figure out what might be wrong:

* Which version of refbase do you use?
* Which platform are you using?
* Do you use a particular package such as XAMPP?
* Which versions of Apache, MySQL and PHP are you running?
* Can you execute other PHP web applications just fine? I.e., is it only refbase that is causing you trouble?
* Can you access MySQL correctly, from the command line as well as from web administration tools such as phpMyAdmin?
* Do you experience the same error/problem using a different browser or computer?
* Do you know about special config settings within your ''httpd.conf'', ''php.ini'' or ''my.cnf'' configuration files?
* Compare your ''php.ini'' with the list of [[Required_PHP-INI_Settings|required ''php.ini'' settings]] and report any differences.
* Regarding ''php.ini'' settings, especially verify that <code>safe_mode</code> is OFF for installation. If you can't change this setting, you may need to perform a [[Manual installation|manual installation]].
* Have a look at your server's error log and report anything that may be connected with refbase.
* Please make sure that PHP error reporting is enabled and report any error messages displayed in your browser. To enable error reporting, set the following variables in your ''php.ini'' file:
error_reporting = E_ALL
display_errors = On

=== General tips ===

Please ensure that you have checked the following:

* If you're using an older refbase version, you may want to [[Updating_refbase|update]] to the newest version and see if this cures your problems.
* If you receive errors when using refbase (e.g., when adding or importing data), please try the same procedure in our [[Refbase_users|demo databases]] to check, whether this problem is specific to your own installation/data or whether it's a general issue.
* Make sure that you've restarted your web server to apply any changes you've made to your ''php.ini'' file.
* Some installations come with multiple ''php.ini'' copies at different locations. To make sure that you're dealing with the correct ''php.ini'' file, checkout the output of the <code>phpinfo()</code> function, it will tell you the location of the active ''php.ini'' file ([[Required_PHP-INI_Settings|more info]]). The returned status info may contain other useful information and it may help to send us the output via private mail.
* If your package manager separates php-mysql from the main php-package (eg. Fedora) make sure to install both. Otherwise every request to refbase will give an empty white page.
* Make sure that the refbase scripts have correct permission settings so that they can be accessed by your server.

== Known problems and possible solutions ==

=== Fail to login ===

If you have problems to log in with your newly created user account after installing refbase, please refer to [[Creating the first user]].

=== Upload of large files fails ===

If you're able to upload files of small file size but experience errors when attempting to upload large files, checkout the variables <code>post_max_size</code> and <code>upload_max_filesize</code> in your active ''php.ini'' file. The values given for <code>post_max_size</code> and <code>upload_max_filesize</code> must be larger than the maximum file size you'd like to be able to upload (see also [[Required_PHP-INI_Settings|required ''php.ini'' settings]]).

=== Upload of files under XAMPP doesn't work ===

In some versions of [https://www.apachefriends.org/ XAMPP] the default temporary folder for uploads, as defined in ''php.ini'', is wrong:

upload_tmp_dir = ".;c:\apachefriends\xampp\tmp"

correct would be:

upload_tmp_dir = "c:\apachefriends\xampp\tmp"

=== Renaming of uploaded files does not work under XAMPP ===

In some versions of [https://www.apachefriends.org/ XAMPP] the needed PHP function <code>iconv</code> is disabled. To fix this, open the ''php.ini'' file of your XAMPP distribution, search for <code>iconv</code> and enable the function by deleting the heading comment sign (').

=== Export of records results in a blank page ===

At present, the '''ADS''', '''BibTeX''', '''EndNote''', '''ISI''', '''RIS''' and '''Word XML''' export formats require a correctly configured Bibutils while any of the other XML formats (e.g. MODS XML or ODF XML) do '''not''' depend on Bibutils. If the latter are working while the former are not, most likely the issue pertains to your [[Bibutils]] install.

You can check that the Bibutils path was correctly configured by viewing the contents of the ''depends'' table. The <code>depends_path</code> for the <code>bibutils</code> record should '''not''' be <code>NULL</code> as seen below:

<pre>
mysql> SELECT * FROM depends;

+------------+------------------+-----------------+--------------+
| depends_id | depends_external | depends_enabled | depends_path |
+------------+------------------+-----------------+--------------+
| 1 | refbase | true | NULL |
| 2 | bibutils | true | NULL |
+------------+------------------+-----------------+--------------+
</pre>

In addition, please note that:

* the path to the Bibutils programs given in table ''depends'' must end with a slash
* permissions must be set correctly so that the Bibutils programs can be executed by Apache/PHP
* if <code>safe_mode</code> is set to On in your active ''php.ini'' file, then you'll need to put the Bibutils programs within the directory that's specified in <code>safe_mode_exec_dir</code>
* the PHP temp/session directory must be accessible & writable by Apache/PHP/Bibutils
* if you're on a hosted service, your Internet Service Provider may have given you a specific temp directory path which you may need to set explicitly in variable <code>$sessionTempDir</code> in file ''initialize/ini.inc.php''

=== Some exports fail in refbase-0.8.0 on some win32 servers ===

Some WAMP stacks fail to execute Bibutils. A workaround is to upgrade to refbase-0.9.0 or greater.

=== Upload of files results in error message ===

If you're using refbase-0.9.0 and you're getting following error message when adding (or editing) a record that includes a file
for upload:

Warning: preg_replace() [function.preg-replace]: Unknown modifier '\' in
.../refbase-0.9.0/includes/include.inc.php on line 3631

Warning: preg_replace() [function.preg-replace]: Unknown modifier '\' in
.../refbase-0.9.0/includes/include.inc.php on line 3634

then you may want to upgrade to refbase-0.9.5 or greater. Alternatively, you can apply a simple patch manually:

Please open file ''modify.php'' in your refbase root directory, goto line 1100 and replace this code:

$dirNamingScheme = trimTextPattern($dirNamingScheme, "[/\\]+", true, true);

with this:

$dirNamingScheme = trimTextPattern($dirNamingScheme, "[\/\\\\]+", true, true);

=== Import of records results in an error message ===

If you're trying to import records into your refbase database and you're getting an error message such as this one:

There were validation errors regarding the data you entered

then you might want check whether your record format is supported by refbase and whether its syntax is correct. Please see our [[Importing records|import]] page for more information and links to example records for all supported formats.

If you're sure that your record format is supported but you still get an error message, please try to import your records at one of our [[Refbase_users|demo databases]]. If this throws up the same error message, then refbase probably has problems recognizing your record format. In that case, we'd appreciate if you'd [[refbase:Community_portal|send us]] your problematic records so that we can look into the problem.

If, however, your records import fine in our demo database, then this hints at a problem with your local refbase installation. Note that import of records in BibTeX, Copac, Endnote (tagged text or XML), PubMed XML, SciFinder or MODS XML format requires [[Bibutils]] being installed on your server. If you think that you've correctly installed Bibutils on your server and still can't get import of the above mentioned formats to work, please [[refbase:Community_portal|let us know]] and we'll try to help.

=== Undefined iconv() despite --with-iconv ===

This problem was experience on a FreeBSD web host, and has also been reported as a [http://ca.php.net/manual/en/function.iconv.php#47428 FreeBSD issue] in the user comments at php.net, which suggests the resolution (which worked for me) to add the following block of code to the application before iconv() is called:

<pre>
if (!function_exists('iconv') && function_exists('libiconv')) {
function iconv($input_encoding, $output_encoding, $string) {
return libiconv($input_encoding, $output_encoding, $string);
}
}
</pre>

=== Problems with special characters ===

See below for some troubleshooting guidance if you have problems getting higher ASCII characters (such as accented characters or umlauts) displayed correctly in refbase, or if you cannot correctly enter or search for higher ASCII chars in the refbase web interface. Encoding problems can be really tricky since many factors interact with each other, and encoding settings can differ greatly among different systems and versions.

==== Server settings ====

First of all, you should make sure that your MySQL server's character set and collation settings are setup correctly and consistently. For more information and instructions, please see parts 'a)' and 'b)' in section [[Troubleshooting#MySQL_migration_and_character_set_problems|MySQL migration and character set problems]].

If you'd like to use refbase with UTF-8 encoding, then you'll need MySQL version 4.1.x or greater. However, in our experience, MySQL 4.1.x seems to have problems with some Unicode characters, so if possible you should use refbase in conjunction with MySQL 5.x.

It might be also worth checking your web server's configuration file (e.g., in case of the Apache web server: ''httpd.conf'' or ''apache2.conf''). On Ubuntu, for example, some users managed to cure their encoding issues by (un)commenting (or altering) following config setting in Apache 2:

AddDefaultCharset ISO-8859-1

==== Settings in refbase ====

When installing refbase via ''install.php'', make sure that you've chosen the desired default character set (latin1 or utf8). Be aware that if you've tried to install refbase multiple times using the same MySQL database name (in ''initialize/db.inc.php'') but with different settings as default character set, you must drop (i.e. delete) the database before installing it again with a different character encoding.

You can check the encoding of your MySQL database by issuing following command from within your MySQL command line interpreter:

SHOW CREATE DATABASE ''DATABASE_NAME'';

In the above command, replace <code>''DATABASE_NAME''</code> with the actual name of your refbase MySQL database.

If you've choosen "utf8" upon installation, then you have to make sure that variable <code>$contentTypeCharset</code> in file ''initialize/ini.inc.php'' is set to "UTF-8". And if you're using higher ASCII chars in any variable values in file ''ini.inc.php'', you should also re-save that file with encoding "Unicode (UTF-8, no BOM)".

If you've set variable <code>$contentTypeCharset</code> to "UTF-8", you could now access refbase in your web browser and verify that the head of the HTML source states the correct encoding:

<meta http-equiv="content-type" content="text/html; charset=UTF-8">

In case of a latin1-based refbase installation, the contents of the <code>charset</code> attribute should read "ISO-8859-1".

In order to test if refbase has been setup correctly, you should now add or edit a record via the refbase web interface and enter some special characters (such as ·ÈÌ‡ËÏ or ÂÊ¯ˆ‰¸ etc). Then, checkout again the added/edited record and verify that your entered characters display correctly. In addition, use refbase to search for these special characters and verify that your added/edited record is listed among the search results.

So, in summary, if you can 1) successfully enter special characters in refbase, 2) have them displayed correctly after saving your edits '''and''' 3) successfully search for these newly entered characters, then refbase has been set up correctly. However, if one of these actions (enter/display/search) does not work as expected, then you've still got problems.

==== Browser settings ====

If you're still experiencing problems, it's always a ''very'' good idea to try out another browser (or another browser on another platform). Also, try to manually set the encoding of your browser page to either "Unicode (UTF-8)" or "Western (ISO-8859-1)". In Firefox, this can be done via the "View > Character Encoding" menu. After you've set the encoding explicitly, please see if you can now enter/display/search for higher ASCII chars successfully.

Speaking of browser settings, you can often set a default character encoding within the browser's preferences which might be also worth checking out.

==== Import and file encodings ====

Finally, note that when importing data into refbase, you have to make sure that the character encoding of your bibliographic data file matches the character encoding of your refbase database. If this is causing you any trouble, copying and pasting the data into the refbase import form may actually work better. With regard to import, you should also ensure that you're using a recent version of [[Bibutils]] since some earlier versions of Bibutils had issues with character set support.

If you still can't get rid of your encoding issues, please [[refbase:Community_portal|let us know]] and we'll see what we can do.

[[Category:Installation]]
[[Category:Troubleshooting]]
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