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Bug #3767 (Completed - Requires Review): Permissions issue with some pages

Scratchpads issue queue - Mon, 2014-01-06 11:48

Some pages in http://s2.grassworld.myspecies.info are not accessible by anonymous users although they are set as public

Other pages are accessible

Bug #3766 (Active): Taxonomy tagging

Scratchpads issue queue - Fri, 2014-01-03 18:43

I am trying to set up tagging, but i am not sure it is working properly. I can see that it searches for species and adds the species to a chosen field. My problem is what happens next, i.e. The text gets added to a field but i had hoped this would be a ling to the species taxon page - should this be the case? If so what steps do i need to set this up.

To recap - when a block of text includes a listed taxon, i would like an automatic link to the page for that taxon, and if possible a reverse link to the node from the taxon page.

I have tried many different field combos but cant get this to work. any help would be very much appreciated - we aim to go live in january.

Bug #3764 (Active): DOI lookup broken when creating a biblio

Scratchpads issue queue - Fri, 2014-01-03 16:36

Every DOI I enter in the DOI Lookup field returns this error msg:

HTTP error: 400 when trying to contact crossref.org for XML input

Task #3763 (Active): Ciliate guide

Scratchpads issue queue - Fri, 2014-01-03 14:02

Alan writes

Ciliate guide. I believe there is some generic scratchpad development project going on and, when this is completed, the ciliate guide can be transferred to a web format. Presumably Katherine will then be able to do this with a simple mouse-click (yes?).

Dave responds

I doubt that it will be so simple. The generic development is called the 'character project' and is a necessary precursor to key building. Basically the character project will allow the construction and maintenance of a table (matrix) of species vs characters. From such a matrix, a key should be straightforward. We will need some mechanism to select taxa other than nomenclatural (e.g. a key to Vorticella), specifically a key to sewage ciliates. That should be straightforward by creating a character in the matrix for 'habitat' that has nested states (freshwater/marine, and within freshwater, sewage, stream, lake etc.).

What I was trying to achieve here is the ability to bind additional taxa into the key as they are discovered without having to re-write the key each time.

Task #3762 (Postponed): Species name list editing rights

Scratchpads issue queue - Fri, 2014-01-03 14:00

Alan asks

Is the file on the scratchpad? I could not find it after a quick look but I recall you said it was not there the day or two before you departed. As I recall, the main job for Katherine to set up a system whereby various levels of editing rights can be granted to whoever those that need them. And that the person who carries out the editing can be given credit in the form of a name-check on the appropriate page. Was that pretty much it? Anything else?

Dave replies
No, not yet. I need to write a couple of small scripts to tidy up some issues (a few duplicate entries, minor formatting discrepancies, and some missing species names). I've been focussed on the reprints in available moments. Tidying up the species list is next up.

For clarity, the species list that I'll upload is a simple trawl of the web species lists. The Scratchpads taxonomic editor can be used to declare individual names as 'valid' (the validity field is empty at upload), or 'invalid', with the reason, such as 'synonym of ...' etc.. That's what we're expecting editors to do. They can also upload pictures, descriptions etc..

Setting editing rights is straightforward and is a question of allocating users to roles (Katherine will know exactly what this means). The key is for you (with John, Weibo and Denis) to decide who is allowed what rights and who can grant and withdraw them (this is a long-term administrative task).

For example, lets say Jun Gong is granted editing rights and undertakes to review the genus Nassula. Somewhere on the genus page, it should say that Jun is the taxonomist whose opinion is represented in the visible list of valid species.

It may be that we can automate this by aggregating the 'last modifier' for the species in the genus. Would editors be happy with that? The date of review would also be important, so needs to be obvious.

After that we need to go for a round of beta testing and see the reactions of the core team.

Task #3761 (Active): Finishing up ciliates

Scratchpads issue queue - Fri, 2014-01-03 13:58

Work with Alan Warren to finish up Dave Roberts ciliate site

Task #3755 (Active): Add Collector (GUID) to specimens import template

Scratchpads issue queue - Fri, 2014-01-03 11:32

When I import my specimens, I first import all the collectors as people with a unique feeds GUID as there may be multiple people with the same name.

I would like to be able to refer to that person GUID when I then import my specimens.

Therefore a new column, Collector (GUID) is required in the import_into_specimenobservations template which allows a feeds GUID to be used to refer to a user

Bug #3753 (Active): Classifications links

Scratchpads issue queue - Sun, 2013-12-29 14:29

I inadvertently deleted "Anopheles classification" and two or its subordinate pages ("Subgenus Anopheles" and "Subgenus Nyssorhynchus" from Classifications of the main menu, and created new pages for these. I was able to link the "Anopheles classification" so that it shows when Classifications is selected, but instead of being displayed as the first item in the list, Aedini classification is displayed. When I clink on Anopheles classification, the page appears but Subgenus Anopheles,Subgenus Cellia and Subgenus Nyssorhynchus do not appear below Anopheles Classification in the drop-down menu (note that these should appear below Anopheles classification in the same manner that the subgenera of Culex appears in the list when Culex classification is chosen). Furthermore, if I go to content, page, view and click on "Subgenus Cellia" [http://mosquito-taxonomic-inventory.info/subgenus-ltemgtcellialtemgt#overlay-context=], when the page comes up, the Classifications menu appears in its complete form. I obviously messed up the links for the various pages that should appear under Classifications on the main menu. I shall be grateful if this could be resolved as I have not been able to correct this. Thanks.


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