Recap – shortcodes and people data

This post is a recap for a question that comes up quite often about adding information from either PURE (research@st-andrews) or Symbiosis (School) databases to WordPress sites. I’m going to try to give a summary here, and link to other posts with more detailed information.

The basic idea here is to use ‘shortcodes’ on pages of a synergy wordpress site to pull in information from these data sources.  The shortcodes are instructions added to the page in [square brackets] that are interpreted by WordPress. The particular shortcodes required use a plug-in that I wrote to access various databases and do helpful things with the results.

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Complete group People page in one line!

Extending my work on pulling data into WordPress using short codes, I’ve made an entire ‘People’ page which can be displayed by typing just one short code into the page content area, an example is

[SDS_SYMBIOSIS  piid='dp1' data="researchGroupAccordion" uid="*" ]

where piid = the ID of the Principle Investigator (PI).  In this instance the PI is Dave Paterson (dp1), whose the group is called SERG.

If the PI has entered his research group into the School database, the above single line will make a complete research group ‘People’ page in WordPress entirely using data (and images) from School and PURE data.

See demo page.

It looks like SERG (whose site is in prep) will be the first to use this ‘live’.

Biologists: If you are authoring here at present, and want to see if your PI has entered their research group yet, visit the PI index, and click the ‘School’ link beside their name.  If there is a list like the one near the bottom right of this page, they’ve entered the group.  If not, ask your PI if they can do this, or send details of the list to me.

Research Group Lists – more content for less work

Combining research group lists from the School database, with the facilities I made earlier to allow data from School and Pure databases to be used, it is possible to populate a research group website with ‘people’ pages by making only two very short pages.

An example of this is shown below, for Dave Paterson, who had already made a list of his research group in the School database.

From a WordPress author’s point of view, the entire resource – the index, and all of the content for the people, required just two pages, and four short codes.  All content existed already in School of Pure databases.  Not bad…

Try example research group list, and researcher profile pages.

How to for PIs

Using data from databases on your WordPress site…

I’ve been working to implement shortcodes which allow you to use data already stored on people in either our School database (called Symbiosis) or in the PURE database (aka research@st-andrews) to your WordPress research group site.

Mr Steve Smart
Shortcodes are simple codes enclosed in square brackets that you can type in your posts or pages which WordPress will convert into content when the post or page is viewed.  I’ve made some new codes that you can use.  For example, this code:

[SDS_SYMBIOSIS uid="sds" data="image" format="right"]

makes my image from the School database appear on the right of the page… (OK – I have even less hair now – time I put a new picture there, I know…)

You can find out more and see the full list of shortcodes on this post

 

Use data from databases on your WordPress site…

I’ve been working to implement shortcodes which allow you to use data already stored on people in either our School database (called Symbiosis) or in the PURE database (aka research@st-andrews) to your WordPress research group site.

Mr Steve Smart
Shortcodes are simple codes enclosed in square brackets that you can type in your posts or pages which WordPress will convert into content when the post or page is viewed.  I’ve made some new codes that you can use.  For example, this code:

Mr Steve Smart

makes my image from the School database appear on the right of the page… (OK – I have even less hair now – time I put a new picture there, I know…)

I’ve made shortcodes which allow you to place information stored in Symbiosis (School) and Pure (research@st-andrews) on your research group pages or posts, or even to quickly make a complete staff profile page.  For example, here is a sample page which includes information from both databases, as well as text typed in WordPress. The entire page was made with only the following typed in WordPress:

Prof Anne Magurran:
Professor

This page illustrates the combination of information straight
from WordPress – like this paragraph – and from the Symbiosis
(School) database, and from Pure (research@st-andrews)…

I am an ecologist investigating biological diversity. My goal is to quantify the patterns, and understand the processes, linked to change in ecological communities over space and time, and to use this research to protect and manage natural capital.

 



Royal Society Wolfson Research Merit Award

ERC Advanced Grant

Deputy Convenor Biology Panel Hong Kong RAE 2014

Board of Reviewing Editors, Science

Fellow of the Royal Society of Edinburgh
Beverton Medal (FSBI) 2006

Research Group:

Dr Amy Deacon

Dr Hideyasu Shimadzu

Ms Faye Moyes

Ms Morelia Camacho-Cervantes

Mr Al Reeve

Ms Alessanda Rocha Kortz

Funded collaborations:

University of the West Indies, Trinidad
Mamiraua Sustainable Development Institute, Brazil

source: symbiosis


Recent Publications:

Recent publications


5  (of 163 published available) for aem1. (source: University of St Andrews PURE)
Please click title of any item for full details.


Ecology Letters
vol.Early View 
(Article)
A balance of winners and losers in the Anthropocene
Maria Dornelas, Nicholas J. Gotelli, Hideyasu Shimadzu, Faye Helen Moyes, Anne Magurran, Brian J. McGill 
Keywords: Anthropogenic, Biodiversity, Colonisation, Extinction, Population change
2019 (1)
Journal of Fish Biology
vol.94 pp.96-102
(Article)

Ecography
vol.Early View 
(Article)
2018 (24/7)
Global Ecology and Biogeography
vol.27 pp.760-786
(Article)
BioTIME
Maria Dornelas, Laura H. Antão, Faye Helen Moyes, Amanda E. Bates, Anne Magurran, DuÅ¡an Adam, Asem A. Akhmetzhanova, Ward Appeltans, José Manuel Arcos, Narayanan Ayyappan, Gal Badihi, Andrew H. Baird, Tiago Egydio Barreto, Claus Bässler, Alecia Bellgrove, Jonathan Belmaker, Lisandro Benedetti-cecchi, Brian J. Bett, Anne D. Bjorkman, Magdalena Błażewicz, Shane A. Blowes, Christopher P. Bloch, Timothy C. Bonebrake, Susan Boyd, Matt Bradford, Andrew J. Brooks, James H. Brown, Helge Bruelheide, Phaedra Budy, Fernando Carvalho, Edward Castañeda-moya, Chaolun Allen Chen, John F. Chamblee, Tory J. Chase, Laura Siegwart Collier, Sharon K. Collinge, Richard Condit, Elisabeth J. Cooper, J. Hans C. Cornelissen, Unai Cotano, Shannan Kyle Crow, Gabriella Damasceno, Claire H. Davies, Robert A. Davis, Frank P. Day, Steven Degraer, Tim S. Doherty, Timothy E. Dunn, Giselda Durigan, J. Emmett Duffy, Dor Edelist, Graham J. Edgar, Robin Elahi, Sarah C. Elmendorf, Anders Enemar, S. K. Morgan Ernest, Rubén Escribano, Marc Estiarte, Brian S. Evans, Tung-yung Fan, Fabiano Turini Farah, Luiz Loureiro Fernandes, Fábio Z. Farneda, Alessandra Fidelis, Robert Fitt, Anna Maria Fosaa, Geraldo Antonio Daher Correa Franco, Grace E. Frank, William R. Fraser, Hernando García, Roberto Cazzolla Gatti, Or Givan, Elizabeth Gorgone-barbosa, William A. Gould, Corinna Gries, Gary D. Grossman, Julio R. Gutierréz, Stephen Hale, Mark E. Harmon, John Harte, Gary Haskins, Donald L. Henshaw, Luise Hermanutz, Pamela Hidalgo, Pedro Higuchi, Andrew Hoey, Gert Van Hoey, Annika Hofgaard, Kristen Holeck, Robert D. Hollister, Richard Holmes, Mia Hoogenboom, Chih-hao Hsieh, Stephen P. Hubbell, Falk Huettmann, Christine L. Huffard, Allen H. Hurlbert, Natália Macedo Ivanauskas, David Janík, Ute Jandt, Anna Jażdżewska, Tore Johannessen, Jill Johnstone, Julia Jones, Jungwon Kang, Tasrif Kartawijaya, Erin C. Keeley, Douglas A. Kelt, Rebecca Jane Kinnear, Kari Klanderud, Halvor Knutsen, Christopher C. Koenig, Alessandra R. Kortz, Kamil Král, Linda A. Kuhnz, Chao-yang Kuo, David J. Kushner, Claire Laguionie-marchais, Lesley T. Lancaster, Cheol Min Lee, Jonathan S. Lefcheck, Esther Lévesque, David Lightfoot, Francisco Lloret, John D. Lloyd, Adrià López-baucells, Maite Louzao, Joshua S. Madin, Borgþór Magnússon, Shahar Malamud, Iain McCombe Matthews, Kent P. Mcfarland, Brian Mcgill, Diane Mcknight, William O. Mclarney, Jason Meador, Peter L. Meserve, Daniel J. Metcalfe, Christoph F. J. Meyer, Anders Michelsen, Nataliya Milchakova, Tom Moens, Even Moland, Jon Moore, Carolina Mathias Moreira, Jörg Müller, Grace Murphy, Isla H. Myers-smith, Randall W. Myster, Andrew Naumov, Francis Neat, James A. Nelson, Michael Paul Nelson, Stephen F. Newton, Natalia Norden, Jeffrey C. Oliver, Esben M. Olsen, Vladimir G. Onipchenko, Krzysztof Pabis, Robert J. Pabst, Alain Paquette, Sinta Pardede, David Maxwell Paterson, Raphaël Pélissier, Josep Peñuelas, Alejandro Pérez-matus, Oscar Pizarro, Francesco Pomati, Eric Post, Herbert H. T. Prins, John C. Priscu, Pieter Provoost, Kathleen L. Prudic, Erkki Pulliainen, B. R. Ramesh, Andrew Rassweiler, Jose Eduardo Rebelo, Daniel C. Reed, Peter B. Reich, Suzanne M. Remillard, Anthony J. Richardson, J. Paul Richardson, Itai Van Rijn, Ricardo Rocha, Victor H. Rivera-monroy, Christian Rixen, Kevin P. Robinson, Ricardo Ribeiro Rodrigues, Denise De Cerqueira Rossa-feres, Lars Rudstam, Henry Ruhl, Catalina S. Ruz, Erica M. Sampaio, Nancy Rybicki, Andrew Rypel, Sofia Sal, Beatriz Salgado, Flavio A. M. Santos, Ana Paula Savassi-coutinho, Sara Scanga, Jochen Schmidt, Robert Schooley, Fakhrizal Setiawan, Kwang-tsao Shao, Gaius R. Shaver, Sally Sherman, Thomas W. Sherry, Jacek Siciński, Ana Carolina Da Silva, Fernando Rodrigues Da Silva, Fabio L. Silveira, Jasper Slingsby, Tracey Smart, Sara J. Snell, Nadejda A. Soudzilovskaia, Gabriel B. G. Souza, Flaviana Maluf Souza, Vinícius Castro Souza, Christopher D. Stallings, Rowan Stanforth, Emily H. Stanley, José Mauro Sterza, Maarten Stevens, Rick Stuart-smith, Yzel Rondon Suarez, Sarah Supp, Jorge Yoshio Tamashiro, Sukmaraharja Tarigan, Gary P. Thiede, Simon Thorn, Anne Tolvanen, Maria Teresa Zugliani Toniato, Ørjan Totland, Robert R. Twilley, Gediminas Vaitkus, Nelson Valdivia, Martha Isabel Vallejo, Thomas J. Valone, Carl Van Colen, Jan Vanaverbeke, Fabio Venturoli, Hans M. Verheye, Marcelo Vianna, Rui P. Vieira, Tomáš VrÅ¡ka, Con Quang Vu, Lien Van Vu, Robert B. Waide, Conor Waldock, Dave Watts, Sara Webb, Tomasz Wesołowski, Ethan P. White, Claire E. Widdicombe, Dustin Wilgers, Richard Williams, Stefan B. Williams, Mark Williamson, Michael R. Willig, Trevor J. Willis, Sonja Wipf, Kerry D. Woods, Eric J. Woehler, Michael L. Zettler 
Keywords: Biodiversity, Global, Spatial, Species richness, Temporal, Turnover
2018 (20/2)
Proceedings of the National Academy of Sciences of the United States of America
vol.115 pp.1843-1847
(Article)
Divergent biodiversity change within ecosystems
Anne Magurran, Amy Elizabeth Deacon, Faye Helen Moyes, Hideyasu Shimadzu, Maria Dornelas, Dawn Phillip, Indar Ramnarine 
Keywords: Biodiversity change, Tropical ecology, Freshwater, Temporal turnover, Community-level regulation

The general form for these shortcodes is:  [SHORTCODE data=”value” uid=”value“]

Below is a summary of available codes, all of these use the parameter uid=”abc” where abc is a St Andrews user-id to indicate the person for whom information should be shown.  An additional parameter – format – which is optional, and controls placement of the content is described below the table.

SHORTCODE data="value" output
SDS_SYMBIOSIS fullname title preferred-firstname surname
SDS_SYMBIOSIS jobTitle job title
SDS_SYMBIOSIS title name and job title e.g. Dr John Smith: Lecturer
SDS_SYMBIOSIS contactDetails name; full postal address with postcode; phone; fax; email (clickable); room number
SDS_SYMBIOSIS image staff portrait image
SDS_SYMBIOSIS bioLink link to a staff profile on the School of Biology website
SDS_SYMBIOSIS edit link to editing page (requires password) – non-administartive users may only edit their own content
SDS_SYMBIOSIS generalText the main text block used on School pages
SDS_SYMBIOSIS relatedSites related sites list derived from personal site link (if any) and group memberships (each link opens to new window)
SDS_SYMBIOSIS relatedSitesWithPure as related sites list with link to research@st-andrews profile included
SDS_PURE publications publications list – Formatting not perfect at present but links do work. Default is five publications – for more add an additional parameter such as number="10" with the required value.  A parameter uid="dp1" indicates an individual user ID – or a parameter orgid="SOI" may be used in order to access publications relating to an organisational unit defined in PURE.  Our plug-in 'knows' and will translate correctly a limited number of codes – eg medicine / biology / SOI / SMRU… or the correct values may be input in the shortcode (eg orgid="40SCBIOL" for biology).  Contact rpo@st-andrews.ac.uk for more details about organisational IDs.
SDS_PURE overview overview text from Pure/research@st-andrews
SDS_PURE link a link to the user's profile page in research@st-andrews
SDS_SYMBIOSIS full a complete profile page combining most of the above elements. Default is five publications – for more add an additional parameter such as number="10" with the required value.
SDS_SYMBIOSIS sidebar a right-justified sidebar with image; name; address; contact details; room number; related sites; link to school page; link to content edit page
SDS_SYMBIOSIS sidebarWithPure as sidebar with link to research@st-andrews profile included
SDS_SYMBIOSIS
body Pure overview; School general text; Pure publications. Default is five publications – for more add an additional parameter such as number="10" with the required value.
SDS_SYMBIOSIS
researchGroupMembers requires uid="*" and piid="someone". Optional format="right" title="List Title".  The uid parameter is not used.  The piid is the St Andrews user-id of the research group PI.  Data entered in the PI's record in SYMBIOSIS defines members of his/her research group.   Produces a linking list of people in the PI's group.  Demo
SDS_SYMBIOSIS
researchGroupAccordion used to produce a profile of all researchers in a research group.  Requires parameters: uid="*" and piid="someone".  The uid parameter is not used.  The piid is the St Andrews user-id of the research group PI.  Data entered in the PI's record in SYMBIOSIS defines members of his/her research group.  Data from both SYMBIOSIS and PURE is used to create a complete accordion of the group with images.  Individual members expand to reveal detailed profiles.  More & Demo
SDS_SYMBIOSIS groupList used to make a list of any people defined as a group in symbiosis.  Requires a parameter groupcode="IBANS".  An optional parameter is jobcat which may be used to refine a list based on job category.  A comma separated list of jobcat values may also be entered.  Individual members expand to reveal details as defined in a site page called profile (the profile page may use a customised combination of other codes above).  Valid jobcat codes are: academic; administrative; research; technical; postgraduate student. The following parameters may also be set to "yes" with various effects: suppress_school; suppress_shorttext; suppress_roleshorttext; suppress_room; suppress_tel; listLinkToPure. The attribute style may be used with CSS codes to style the output list.
SDS_SYMBIOSIS grouplistImages As groupList but includes a portrait image of each person if one is on file (symbiosis). Example output
SDS_SYMBIOSIS grouplistImages_recursive As grouplistImages but looks for research groups of people who are in the group list and adds found research group members to the group list. Jobcat filters applied to the grouplist are also applied to the research group lists. Example output

As I mentioned you can optionally add a format parameter, which has the following results in most instances (‘headspace’ only is available for the shortcodes full, sidebar, body)

format="value" effect
newline add a line break after the content
right make the content be in a right aligned block
left make the content be in a left aligned block
headspace add a line break above the content