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A rapid international journal for animal taxonomists

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Bug #4155 (Completed - Requires Review): Image gallery ghosts

Scratchpads issue queue - Tue, 2014-06-17 13:47

After deleting a series of image galleries I see what I think may be some 'ghosts' of these galleries in the Gallery section of the left sidebar. These are only four digit numbers that lead to an odd error when I click on them.
Cheers, Lukas

Bug #4153 (Active): Specimen names have changed

Scratchpads issue queue - Tue, 2014-06-17 12:35

Hi all,
it would seem that the v2 scratchpads now render the specimen names with a hyphen/minus (i.e. "-") between the Institution code, Collection code and Catalogue number, which is problematic because I have already published specimens without these hyphens (Schärer et al. 2011, PNAS). These hyphens now mean that a search of these original specimen names (e.g. MTP LS 144) will not find the current specimens (i.e. MTP - LS - 144) anymore on the scratchpads.
Please fix this immediately, or at least make the hyphens optional. You really can't just change stuff like that. Moreover, the specimen names are rendered as MTP - LS - 144 on the page (i.e. with spaces) and as MTP-LS-144 in the URLs.
Cheers, Lukas

Bug #4152 (Active): Change in pages layout after resolution of bug 4151

Scratchpads issue queue - Mon, 2014-06-16 11:30

Following the successful resolution of bug 4151, the layout of my pages has changed. Previously, the taxon tree appeared on the left side and the other elements of a particular page (type) on the right. Now, the taxon tree takes up the entire screen width meaning that one has to scroll down through the whole of that to get to the rest of the page content, which likewise takes up the full screen width. This occurs on all tabs except "distribution", where the Taxon Tree simply fails to open, being replaced by the rotating "loading in progress" icon. The columns on the home page have also disappeared, the elements now appearing sequentially top to bottom.

Can I please have my layout back the way it was?

Bug #4149 (Active): Update example on twitter help page to one that returns results.

Scratchpads issue queue - Tue, 2014-06-10 09:40

Hi team, I was just trying out the twitter functionality, but couldn't get it to work on my site. http://threatenedplants.myspecies.info/content/twitter
I tried to follow the help pages here: http://help.scratchpads.eu/index.php?title=Special%3ASearch&search=twitter&go=Go
Thanks! Steve

Bug #4148 (Active): Updating imported classification- content doesn't detach from old nodes

Scratchpads issue queue - Mon, 2014-06-09 17:50

Hello again! In the spirit of users who would like to occasionally synchronize their Scratchpad classification with eg: WoRMS, I have been testing methods to switch out an old classification for an updated one, on a Scratchpad with existing content. For files content (eg: images, video) attached to taxa, the following works except for one problem. Possibly that problem should be fixed, or possibly I should use another method.

Create new Taxonomy
import provider classification into new taxonomy
delete old Taxonomy
download file_importer_image template. search/replace "|" in the [Taxonomic name (Name)] column and upload new template.

This worked fine in that it attached the content to names in the new Taxonomy. However, the content was also still attached to nodes (now nameless) from the deleted taxonomy. These nodes were listed in the file_importer_image template by their TID, and I was hoping that deleting them in there would detach the content from the dead nodes, but that seems not to have worked.

If that's a bug and can be fixed, great, we probably have a method for manually syncing a Scratchpad to a major provider classification with a few fairly brief chores. Of course, this only works if the content has something in the [Taxonomic name (Name)] field, and assuming those names all appear in the new classification. The latter assumption is probably reasonable to make the responsibility of the Scratchpadian wishing to update the classification. Also, I have not tested this kind of method on taxon description or biblio objects (the latter auto-attached by taxonomic keyword)

If there's a different method that I should be using, that's cool too.

Bug #4147 (Active): CAPTCHA session reuse attack detected

Scratchpads issue queue - Mon, 2014-06-09 15:28

Hi there,

I had a user complain today that she couldn'tupload pics on this link: http://phasmid-study-group.org/content/report-uk-phasmid-sightings because she kept getting the attached error emssage. She reported:

"I have three photos so first I tried to upload a single zipped file but it failed because of size (2.1 vs 1.9 MB limit) so then I tried loading the three separately. The first would upload but when I hit the second to upload I would get the “attack” message. My only suspicion is that I work in Ireland on a computer network that’s based in Germany so perhaps your site was a bit suspicious of the mixed ips or something"

She was not logged in at the time.

Please can you see what caused this? It seems to work ok for me (not logged in), but obviously we need to be aware what the cause is.

Many thanks

Bug #4146 (Active): Request for a "goto" button in Taxon Description listing

Scratchpads issue queue - Mon, 2014-06-09 11:26

When we go to the "Taxon Description" listing, at the bottom of the page there are a number of page options in the bottom left corner and "Next" and "Last" buttons on the right.
It would be a great efficiency aid to able to nominate a page number to go to. Please could this be added?

Bug #4145 (Active): Problem with native taxon description grid view

Scratchpads issue queue - Sun, 2014-06-08 08:03

Dear Team,

The grid option for taxon description here http://doryctinaekey.myspecies.info/#overlay-context=&overlay=admin/content
doesn't run the native slickgrid but one of my block test (a customised view)

Please will it be possible to have the original slickgrid view on the content page for Taxon description?

Thank you for your help.

Bug #4144 (Active): Cannot create a new Scratchpad

Scratchpads issue queue - Fri, 2014-06-06 18:29

When I received my new Scratchpad welcome email (pasted below) and selected the one time login link, the page I was taken to had a login button, which I selected. I was redirected to the Scratchpads homepage.

Dear Jen Hammock,


Your new Scratchpad "EOL Students" has been created for you.

You can now login to EOL Students by clicking on this link or copying it into
your browser:


This is a one-time login, so it can be used only once.

Once you have logged in, you will need to set your password by visiting:


If you experience any problems help is available on the Scratchpad help wiki
[1] and by using the "Issues..." tab once logged into your Scratchpad.

The Scratchpad Team

[1] http://help.scratchpads.eu/


Bug #4143 (Active): Column for author in text import

Scratchpads issue queue - Thu, 2014-06-05 23:41

For excel import template of taxon descriptions, could we have a column for Author, please?This will be super important for migrating LifeDesks. Author appears to be an overwritable text field now in the taxon description edit form, there's just no place for it in the template.

Bug #4142 (Active): In Excel classification import, parent child relationship isn't detected unle...

Scratchpads issue queue - Thu, 2014-06-05 21:08

In the excel template for classification import, any children that appear above their parents in the list are placed at the root of the classification. Got around the problem on http://eolhotlist.myspecies.info/ (biota) by ordering names by rank, but I'm expecting to have the same problem on other new Scratchpads whose classifications don't have ranks. Help!

Bug #4141 (Active): Line breaks in Cyperaceae Description file

Scratchpads issue queue - Thu, 2014-06-05 10:19

Numerous rows are broken over several lines (e.g. line194-197) which means that the file cannot be parsed correctly.

Bug #4140 (Active): "access denied" in Taxonomy and many other pages

Scratchpads issue queue - Thu, 2014-06-05 07:30

The "access denied" stays also when I'm logged in.

Bug #4137 (Active): Taxonomic name not updated with specimen/observation import

Scratchpads issue queue - Thu, 2014-05-29 21:22

I would like to use the Excel import to update taxonomic information for Specimen/Observation records. I have filled in the Taxonomic Name (GUID) column and deleted values in the Taxonomic Name (TID) column. However, when I import the excel file, I receive the message "There are no new nodes". While this statement is correct (I did not add any additional specimens), the taxonomic information was not altered. Should it be possible to update field values in this manner? If not, is the only bulk update option to download the import file, delete all the specimen/observation nodes, then re-import the updated any information? This seems undesireable, as media links might be broken when specimens are deleted...

Bug #4136 (Active): Column width not retained

Scratchpads issue queue - Thu, 2014-05-29 15:53

Column width when changed by user is not retained, in the view mode or in the edit mode when the matrix is refreshed or reloaded.

Feature #4135 (Active): Visualise uncertainty of occurrence records

Scratchpads issue queue - Wed, 2014-05-28 18:23

Many specimen record geographical coordinates are entered with relevant uncertainty levels. This is captured in the corresponding field in the specimen/observation content type.

It would be great if we could visualise this uncertainty as a circle around the specimen point using the google.maps.Circle function.

Bug #4134 (Active): wrong placement of new taxa in taxonomy

Scratchpads issue queue - Tue, 2014-05-27 16:12

Dear team,

I have added three new taxa on my taxonomy but they appear just under the firts term.
I have tried to place them manually at their right place (txaonomic terms are ordered alphabetically) but they returns each time to their wrong place when I view them in user view.
The three wrongly placed terms are ficobolus, plesiopsenobolus, and sabinita in taxonomy of Doryctinae

Please could you fix that?
Is it possible to have a tool allowing an alphabetical sorting of the main term of a taxonomy ? This could be helpfull.

Thank youfor your help!

Feature #4133 (Active): Investigate use of the ChEBI ontology in Scratchpads

Scratchpads issue queue - Tue, 2014-05-27 15:55

As part of the development of the NHM Hypericum site (http://hypericum.myspecies.info) we are trying to establish the best way to use a standardised way of registering chemical compounds.

The chEBI database and ontology of Chemical Entities of Biological Interest seems to provide a very good way of capturing chemical data in a Scratchpad.

Please investigate the best way of integrating this dataset (maybe in the context of the vocabulary integration module?)



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