Zootaxa A rapid international journal for animal taxonomists

Issue emailed to me from Jeff Oliver, working with David Maddison:

I am setting up an instance of Scratchpads host on my local machine, and I have a couple of questions. Following some fun setting up the apache / tomcat / solr configuration, I have a Scratchpads site up and running. However, there are many notices and some warnings and errors that occur during site configuration and site use. I thought I'd ask if there is any more information regarding how to setup a (local) host for Scratchpads. Specifically:

1. Which branch from the git repository should I be checking out? I have tried master and entity_stable, but found no real difference between the two (same notices / errors).

2. In addition to changing the Apache solr URL to my instance of solr, are there other settings that will need to be changed within Scratchpads once the site is created?

3. There are many modules considered out of date and at least six have security updates available. Is Scratchpads development using these older versions, or should I make the recommended updates?

Thanks in advance for any information.

Cheers,

Jeff

Currently when searching for taxonomic terms, with Taxonomy button selected, through the search field only one result is returned even when more than one homonyms are present in the same classification or in different classifications.

We should ensure that all homonyms are returned as results

If there's a validation error when saving taxonomy editor form, button is below the bottom of the screen so isn't clickable

When editing an image that was added inside a page (with button "add media"). Alignment to the left or right of the text seems possible (right click on the image, click on "image properties" and specify left/right alignment) but after saving the edited page, the alignment is not kept. The same happens with all three internet explorer programs that I tested (Firefox, Chrome and Explorer). Is there a way to solve this problem?
Thank you very much
Gontran Sonet

When I go to image-> add and drag and drop an image into the upload tab of the media browser in IE 9.0.8112, the image opens up in a page for viewing, rather than being listed for uploading.

Is it possible to change the number of page summaries in the main block of the frontpage.
I think that it will be possible to keep the default frontpage on our s2.bebol.myspecies.org site by presenting page summaries in the main block instead of images. Unfortunately, there are currently 5 pages presented in this main block and spacing between each page is too large. For a better layout (allowing an alignment with the welcome message), is it possible to change the number of page summaries presented on the front page and to reduce the spacing between them?
Thank you

Information taken from Google Doc - Portal Feedback Specification

A new comments extension to DwC-A would be developed to feed subsequent comments back to the portal (in practice all comments on all content will be in this file). As an example (derived from http://www.openannotation.org/spec/core/)

RowType http://www.w3.org/ns/oa#Annotation

Fields:

http://www.w3.org/ns/oa#hasTarget the identifier of the object being commented on - here you could merge the uri and inreplyto parameters such that, if the target is another annotation, the comment is in reply to the target, and if the target is not, it is a direct comment about that object. It might be useful to have a column with the type of object that the target is (e.g. dwc:Taxon / gbif:Image / gbif:Reference / oa:Annotation) http://www.w3.org/ns/oa#hasBody the comment itself

Pensoft have changed their format, so we need to update our code.

When the module is first enabled, the CKEditor profile is not associated with the Publication HTML format, and this needs to be done manually.

when accessing to the site using Google Chrome, there is a small icon on the top of each page, on the left side of the title of the site 'belgian network for DNA barcoding'. Is it possible to remove this and how?
Thank you

When accessing the site 's2.bebol.myspecies.info' with google chrome, there is a small icon on the top of each page, on the left of the title of the site 'Belgian network for DNA barcoding'. Is it possible to remove this? How?
Thank you very much

We have an issue with the labelling of images in our Pleistocene bryozoan Scratchpad (http://pleistocenekokemushi.myspecies.info/). This concerns instances where we describe a species using the qualifiers 'cf.' or 'aff.' but wish to include images (figures and text) of the original species description as media files. When we add the taxonomic names to these images they are of course automatically captioned with 'cf.' or 'aff.', but this is incorrect as they represent the species itself. Is there a way of getting round this problem?

Thanks for your help in this matter.

I have found that any image I have tried to edit that has a location is impossible to edit, either in slickgrid or editing the image metadata directly. To edit any image with a location, I have had to delete the location and move it into the comments before saving the image. So, location data is currently not useful to us at all for images (cyperaceae.e-monocot.org).

When an editor logs in to amend a species account, or other taxonomy record they receive 'Access Denied'

Checked on http://urostylididae.myspecies.info

On SP1 sites with forums the migrated SP2 version has forums but on the tools page they are not shown as "on".

Some images behave differently than others. Now this still applies to the two images "picture-10.jpg" and "picture-22.jpg" uploaded by the scratchpads team. When I click on them in the media gallery, a small window opens saying "image 1 of 2". From here, it is not possible to edit these images, because the cogwheel (the editing symbol) vanishes when the cursor comes closer.

I edited these images from content \ image. In some other images this helped (originally there were six behaving like this), and the image behaved normally afterwards. Here, however, it didn't change anything.

And if I try to delete such an image, it says: "This file is currently in use and may cause problems if deleted." How is it possible to delete a file without causing problems?

Can I change the sequence in which the information appears on the taxon pages?

Example: Under the newly added species Nectandra ovatocautata (http://s2.lauraceae.myspecies.info/taxonomy/term/18307#), the sequence of the headings now is Family - Genus - Species - Usage - Reference - Additional type data - Reference for current status - Original type data.

I would prefer a slightly different sequence: Family - Genus - Species - Reference - Usage - Reference for current status - Original type data - Additional type data.

Would that be possible?

When I click on "Literature", it still says "Either no literature content has been added to this site, or it has not yet been indexed. Indexing can take up to one hour, so please check back later" - months after the site has been migrated.

However, the literature data are there (somewhere). When I added a new taxonomic name (Nectandra ovatocautata), it was possible to select one of the references.

When I tried to edit another taxonomic name, I noted that the literature citations appearing in the dropdown list are obviously based on a string contained in the title of the article. Wouldn't it make more sense to have them based on the author?

The URL where I tried this is http://s2.lauraceae.myspecies.info/category/lauraceae/lauraceae/acrodiclidium#overlay=admin/structure/taxonomy/lauraceae_taxonomy//10523%3Fdestination%3Dtaxonomy/term/10523

I just noticed that when you delete a media gallery, all images related to that gallery are also deleted. Not sure that is the intent, though it sort of makes sense. However someone may want to reuse those images in another gallery?
I tested this locally and on the solanaceae site on quartz

Simon and I tried to enable the Publication Module on the eMoncoot Dioscoreaceae site (http://dioscoreaceae.e-monocot.org/)

We experience a number of issues:

• When I tried to enable it, it failed on enabling a dependency (relations) and I could no longer access the Modules menu
• After Simon tried to enable it there were no obvious problems until I created a "pensoft" content type where there were missing entry fields

We should test the module on other sites (Scratchpads and eMonocot) prior to the Pensoft meeting (3rd April 2013)