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DokuWiki plugins

There are DokuWiki plugins for research & education which I developed. All plugins are under GPL2 license, so feel free to use them in your DokuWiki.

Dokuwiki Official

Scientific plugins

DokuWiki plugins for bioscience and biotechnology.

General plugins

tabinclude_plugin

Tabinclude plugin

This DokuWiki plugin creates a tab-control for selected wiki pages. By clicking a tab, an DokuWiki page appears on the site using AJAX.

Example

{{tabinclude>start,*chem_plugin,pubmed_plugin|Plugin for PubMed}}

  • Symplus Wiki
  • Chem plugin
  • Plugin for PubMed
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Symplus Wiki

This wiki contains information about source codes for DokuWiki plugin.

  • PubMed plugin
  • PubChem Plugin
  • Chem plugin
  • PDB plugin

PubMed plugin

This is a plugin for DokuWiki that retrieves the information from PubMed widh PMID. The plugin stores NCBI ESummary XML file in /data/media/ncbi_esummary directory.

Functions

{{pubmed>[Command]:[PubMed ID]}}

Command item function
short link Show a short pubmed link from NCBI Structure database
long link Show a detailed pubmed link from NCBI Structure database
summaryXML xml Show a XML summary data from the NCBI database using Entrez Utilities
clear_summary - Clear cached XML files in /data/media/ncbi_esummary
remove_dir - Clear cached files and remove cache directory

Examples

short

{{pubmed>short:9039911}}
Wilmut Iet al.Nature385p810-3(1997 Feb 27)

long

{{pubmed>long:9039911}}
Viable offspring derived from fetal and adult mammalian cells.
Wilmut I, Schnieke AE, McWhir J, Kind AJ, Campbell KH
Nature385p810-3(1997 Feb 27)

summaryXML

{{pubmed>summaryXML:9039911}}

<?xml version="1.0" encoding="UTF-8" ?>
<!DOCTYPE eSummaryResult PUBLIC "-//NLM//DTD esummary v1 20041029//EN" "https://eutils.ncbi.nlm.nih.gov/eutils/dtd/20041029/esummary-v1.dtd">
<eSummaryResult>
<DocSum>
	<Id>9039911</Id>
	<Item Name="PubDate" Type="Date">1997 Feb 27</Item>
	<Item Name="EPubDate" Type="Date"></Item>
	<Item Name="Source" Type="String">Nature</Item>
	<Item Name="AuthorList" Type="List">
		<Item Name="Author" Type="String">Wilmut I</Item>
		<Item Name="Author" Type="String">Schnieke AE</Item>
		<Item Name="Author" Type="String">McWhir J</Item>
		<Item Name="Author" Type="String">Kind AJ</Item>
		<Item Name="Author" Type="String">Campbell KH</Item>
	</Item>
	<Item Name="LastAuthor" Type="String">Campbell KH</Item>
	<Item Name="Title" Type="String">Viable offspring derived from fetal and adult mammalian cells.</Item>
	<Item Name="Volume" Type="String">385</Item>
	<Item Name="Issue" Type="String">6619</Item>
	<Item Name="Pages" Type="String">810-3</Item>
	<Item Name="LangList" Type="List">
		<Item Name="Lang" Type="String">English</Item>
	</Item>
	<Item Name="NlmUniqueID" Type="String">0410462</Item>
	<Item Name="ISSN" Type="String">0028-0836</Item>
	<Item Name="ESSN" Type="String">1476-4687</Item>
	<Item Name="PubTypeList" Type="List">
		<Item Name="PubType" Type="String">Journal Article</Item>
	</Item>
	<Item Name="RecordStatus" Type="String">PubMed - indexed for MEDLINE</Item>
	<Item Name="PubStatus" Type="String">ppublish</Item>
	<Item Name="ArticleIds" Type="List">
		<Item Name="pubmed" Type="String">9039911</Item>
		<Item Name="doi" Type="String">10.1038/385810a0</Item>
		<Item Name="eid" Type="String">9039911</Item>
		<Item Name="rid" Type="String">9039911</Item>
	</Item>
	<Item Name="DOI" Type="String">10.1038/385810a0</Item>
	<Item Name="History" Type="List">
		<Item Name="pubmed" Type="Date">1997/02/27 00:00</Item>
		<Item Name="medline" Type="Date">1997/02/27 00:01</Item>
		<Item Name="entrez" Type="Date">1997/02/27 00:00</Item>
	</Item>
	<Item Name="References" Type="List">
		<Item Name="Comment in" Type="String">Nature. 1997 Mar 13;386(6621):119. PMID: 9062180</Item>
		<Item Name="Comment in" Type="String">Nature. 1997 Apr 3;386(6624):431. PMID: 9087390</Item>
		<Item Name="Comment in" Type="String">Nature. 2006 Apr 27;440(7088):1112. PMID: 16641972</Item>
		<Item Name="Comment in" Type="String">Nature. 1997 Jun 19;387(6635):754. PMID: 9194550</Item>
		<Item Name="Comment in" Type="String">Nature. 1997 Feb 27;385(6619):753. PMID: 9039891</Item>
		<Item Name="Comment in" Type="String">Nature. 1997 Mar 6;386(6620):12. PMID: 9052771</Item>
		<Item Name="Comment in" Type="String">Nature. 1997 Apr 3;386(6624):431. PMID: 9087392</Item>
		<Item Name="Erratum in" Type="String">Nature 1997 Mar 13;386(6621):200</Item>
	</Item>
	<Item Name="HasAbstract" Type="Integer">1</Item>
	<Item Name="PmcRefCount" Type="Integer">460</Item>
	<Item Name="FullJournalName" Type="String">Nature</Item>
	<Item Name="ELocationID" Type="String"></Item>
	<Item Name="SO" Type="String">1997 Feb 27;385(6619):810-3</Item>
</DocSum>

</eSummaryResult>

When you want to create a link, use [[pubmed>9039911]]. → 9039911

History

  • 2016.10.24
    • URLs in code were changed to https according to changes in Web API of NCBI database.
  • 2008.3.22
  • 2008.3.7
    • Bug fix of incorrect permission of cache files
  • 2008.2.26
    • Cache ESummary XML file in /data/media/ncbi_esummary directory
  • 2007.12.08
    • Fix around directory creation & ACL
    • Append an icon image

Installation

Recent version of DokuWiki has Extention manager that can download and install plugin automatically. Use the manager.

In very old dokuwiki

  1. Install bio plugin and cache plugin if not installed.
  2. Download pubmed.zip and extract.
  3. Upload the folder to /lib/plugins/ directory.

Syntax

You can specify tab pages separated by comma to show.

{{tabinclude>page1,page2,page3, ...}}

Initial page

Initial page just after loading is the first page as default (page1 in the previous example). Also, the initial page can be defined prefix '*'. The following example will show page2 at first.

{{tabinclude>page1,*page2,page3,..}}

Tab name

As default, title in tabs are first heading of the page. If it is not found, ID would be shown. You can also set the specific title in tabs by splitting with '|' (pipe). It is like standard DokuWiki syntax to define a title of link.

{{tabinclude>page1|Top page,page2|Second page,page3,..}}

Appearance

The latest version is independent of jQuery tab UI. Colors of text and background in tab control is compliant with each template's colors written in style.ini. You can use almost templates without destroying look & feel. You can customize the lib/tpl/xxx/style.ini file for entire style. For example, if you change __text__ color for both contents and the tab control. Further detailed styles are defined in lib/plugins/tabinclude/style.css.

The tab control showed good appearance with the following popular templates. :)

  • dokuwiki/default
  • monobook
  • arctic
  • arctic-mbo
  • roundbox
  • vector

Installation & setting

You can install this plugin with standard method in Admin→Manage Plugins. If you want to install manually, rename extracted zip folder to 'tabinclude' to place in lib/plugins/ directory.

History

  • 2013-02-05
    • Tab control become independent on jQuery UI.
    • Rewritten script.js converting from tw-sack to jQuery.
    • CSS is compliant to each templates' color.
    • localized to Japanese
  • 2013-01-27
    • Supported only recent version using jQuery UI. (Angua, Adolla Belle)
  • 2008-10-13
    • Vulnerability for XSS was fixed.
    • ODT export has been supported.

Links

Translations of this page:
tabinclude_plugin.txt · Last modified: 2016/10/30 17:24 by swadmin