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scratchpads2's Introduction

Scratchpads 2.x

Overview

Scratchpads are an online virtual research environment for biodiversity, allowing anyone to share their data and create their own research networks.

Sites can focus on specific taxonomic groups, or the biodiversity of a biogeographic region, or indeed any aspect of natural history. Scratchpads are also suitable for societies or for managing and presenting projects. Key features of Scratchpads (see also Scratchpads feature list) include: tools to manage biological classifications, bibliography management, media (images, video and audio), rich taxon pages (with structured descriptions, specimen records, and distribution data), and character matrices.

Scratchpads support various ways of communicating with site members and visitors such as blogs, forums, newsletters and a commenting system.

For more information about what scratchpads are, see http://scratchpads.org

User Support

We offer extensive support to users of the Scratchpads, whether using an NHM maintained Scratchpad, or a local one.

Please raise an issue on Github, or using the "Issues..." tab which is visible when logged in to a Scratchpad (and will post your issue to the Github issue queue).

Hosted Scratchpads

Scratchpads are hosted at the Natural History Museum London, and offered freely to any scientist that completes an online registration form.

Running your own Scratchpad

We recommend running Scratchpads in production using Docker.

Requirements:

Usage:

To get a production Scratchpad running on Ubuntu:

  • Install Docker CE and Docker Compose

  • clone the Scratchpads project or download a release >= 2.9.2 from Github

  • Copy .env.template to .env and set environment values (MYSQL credentials etc.,))

  • Run daemonized docker compose:

    docker-compose -f docker-compose.yml -f docker-compose.production.yml up -d

To turn off warnings

/admin/config/development/logging

Set error messages to display to 'None'.

Developing Scratchpads

If you want to help develop Scratchpads please don't hesitate to get in touch! You can raise an issue on the Github issue queue, or contact the development team at the Natural History Museum [email protected].

We recommend developing Scratchpads with DDEV, a defacto community standard for local developer setup.

DDEV

Requirements:

Usage:

A DDEV config file is included with Scratchpads. To start the DDEV Scratchpad enviornment, run:

ddev start

After start up, you will need to:

  • Run install.php to start the installation process (make sure you choose the "Scratchpad 2" profile)
  • Change the SOLR SERVER URL (admin/config/search/apachesolr/settings/solr/edit) to http://127.0.0.1:18983

Notes:

To access the SQL database, use ddev mysql

For more information, please see our development wiki

Docker

Requirements:

Usage:

  • Copy .env.template to .env and set environment values
  • Run docker-sync start
  • Run docker-compose up -d apache mysql solr (excludes varnish service - only for production, not supported on local).

After start up, you will need to:

  • Go to localhost:8080/install.php to start the installation process (make sure you choose the "Scratchpad 2" profile)
  • This repo will be mounted inside the docker, so you will be able to see any changes in real time (-ish)

More info:

Please see our development wiki.

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scratchpads2's Issues

Publication: taxon description fields don’t show up in the view

Description:

Taxon description fields usually do not show up in the view. You have to do the following to make them appear: When you are on the 'Sections' tab you need to click on 'Edit term fields' and save even if you don't change anything. You should then see all the selected fields underneath the taxon description header. You will need to do this for each taxon. This needs to be changed. The fields should show up without having to edit them.

Taxon description fields sequence

Description:

The sequence of the fields in the taxon description view seems completely random and differs from the ‘Edit’ view. It should be the same. Having said this, the sequence in the ‘Edit’ view should also be changed with the fields we can expect most of our users to use in a more prominent position. It is really annoying to search through all these fields for the ones you need.
Fields that have been used on the Scratchpads so far are: Distribution, Morphology, Diagnostic Description, General Description, Biology, Size, Ecology, Association, Conservation status and Look alikes.

Image matrix editor not saving taxonomic names and not selecting several fields

Description:

I can sometimes select several fields at http://milichiidae.info/matrix-editor/image, but when I wanted to save changes in the classification field I first got a warning about some duplicate maps and then it looked like the images were updated, but the the classification field hasn’t been updated. Actually if I refresh my browser I see that the taxonomic name was only added in one of the fields I selected. When I select multiple ‘Notes’ fields and edit them, it works. Selecting several fields is a bit funny now, with several rows getting blue and I can’t see any more which fields I selected.
Now any changes in the classification don't save any more and I can't select several fields.

Image gallery tagging lost

Publication: create author bug

Description:

When I create an author I get the “This user already has a content profile of this type. You can only create one profile per user” message. I remember there was some way to fix this, but others don’t know this. So as long as this bug is not fixed there should be a message popping up with an explanation of what you have to do.

Multiple image upload improvement suggestions

Description:

  • It might not be intended this way, but I expected to be able to click on the plus icon next to the ‘Select files’ at the top.
  • The way my mouse changes when hovering over the upload screen is confusing. I get an arrow over the just mentioned plus icon, but the ‘I’ when over ‘Select files and the light grey bar underneath. I get the ‘I’ when hovering over ‘Add files’ though it should be the hand sign. When I hover over ‘Start upload’ I have the arrow and the font changes to grey regardless of when there are files to upload or not.
  • I think the way the screen looks at the moment people might easily forget to click on the ‘Start upload’ button and instead directly click on ‘Edit uploaded images’ because it is so prominent. To avoid this it might be good to enlarge the ‘Add files’ and ‘Start upload’ buttons.

Taxon pages: Improve panel sorting

Description:

  • after sorting and closing the panel, the new sort order should be immediately visible
  • there should be an option to move images to an area where they are not shown in the panel
  • there should be the option to show none of the images
  • I can choose to show 20 images, but only 10 images are shown in the sort view, so I have no option to sort the next 10.
  • If I have more than 10 (20) images I need to have an option to select from all of the images tagged with this term

Character project: Improvements

Description:

For controlled character states the viewer should be able to see the name of the character in addition to the text of the respective character state when hovering over the number.

When entering a character the user should be able to see the description of this character. This is useful for example for the definition of ratios or measurements.

Publication: edit publication/bibliography bug

Description:

When I ‘Edit publication image’, same happens as with authors, I don’t see an image, just part of a red x and when I save, I see no thumbnail, though I do get the warning that I should save.
For the bibliography the references show up when I edit, but when I save I don’t see them any more. Only when I then save the tab again, I see them.

Matrix editor: filter bugs

Description:

When I filter for ‘Title’ first and then change the fields, the ‘Title’ filter is removed, which it shouldn’t. It only works the other way round. Same for ‘Author’.
I tried to find out whether I can filter for two different titles and entered “Car & tui”. No images could be found, so the ‘&’ sign wasn’t a good idea. However, now I am stuck. My matrix is gone and clicking on ‘Advanced filters’ has no effect. I should be able to extend the filters again to change my search. Also, is there an option to search for several title words?

Matrix editor - make node links target="_blank"

Description:

Assuming that people only click on one of the node links, e.g. for the publication or the specimen, to check these data, I think it would be good if clicking on these links would open a new tab or small window and not lead away from the matrix editor.

'Last edited by Username' note

Description:

I have the ‘submitted by Username on date’ text at the top of each node. However, I actually think it much more useful for my users to know when this node was last updated, not when it was generated. So I would like to have a ‘last edited by Username on date’ text in addition.

Publication bugs

Description:

When I ‘Edit publication author’ I don’t see the user name, just part of a red x. I can click on this x and get a “[nid:1]” in the authors box, but when I save there is no author. Since there are no other users on the sandbox I guess I shouldn’t be able to click anything but a link to ‘Create author’

Taxonomic Editor: allow multi-select for tagging, e.g. from 'none' to 'species'

Description:

When the classification of a group is imported from a plain text-file, all entries are untagged. Tagging them with 'genus' or 'species' is laborious (and rather tedious). Multi-selection + tagging would be a great improvement.

NB: subgenera and subspecies are currently not supported; I think that is an omission... [Bram Breure]

Single image upload for multiple images

Description:

I think we have to discuss the option to upload multiple images as single image in a Scratchpad meeting. Currently only one node is generated which shows all the images. In the gallery the images are shown separately but link to the one node. In my opinion, if you upload multiple images via the single image upload (which I like), you should generate separate nodes for each images with the same metadata like we used to have in Drupal 5. The title of additional images should get a sequence number. After I have saved I should get a page with thumbnails of all images and the option to matrix edit the images.

Nexus controlled character export

  • Original ID: 1568
  • Added by Irina Brake
  • Scratchpads URL: null

Description:

Export of Nexus DNA characters seems to work. However, when I export Nexus controlled characters, I get an export of the DNA characters with the '?' and '-' missing. At least those are the only characters I see in Winclada and TNT had problems with the file, too.

Change sandbox email

Description:

Please remove the scratchpads email from the sandbox, so that the team members don’t all get messages when someone plays around with groups.

Country maps for genera aggregating species data

Description:

It would be nice when I have country maps for all the species in a genus to then be able to automatically generate a map for the genus which shows the distribution of the genus. When I hover over a country with the mouse a list of all the species occurring in this country should pop up. The same could be possible for all higher taxa, not just genera.

Matrix editor should show more fields

Description:

The matrix editor for the various content types should always have all fields available under the 'Advanced filters', and show only a selection as default.
For taxon description the default selection should be Distribution, Morphology, Diagnostic Description, General Description.
For the biblio matrix editor there should be a note referring to the option to edit authors and keywords under the biblio settings. The biblio default selection should include journals, for example.

Classification: Create checklists

  • Original ID: 1552
  • Added by Irina Brake
  • Scratchpads URL: null

Description:

Generate species lists from the taxonomy. If possible combine with specimen module and/or country maps to produce species lists from certain countries/regions

Image upload: Library gallery as default

Description:

All uploaded images should by default go into the 'Library' gallery, so that they are visible when clicking on 'Image' in the Content menu. For old sites all images that are not currently attached to an image gallery should be moved to the 'Library' gallery. However, before this is done it must be sure that these sites were not affected by the bug which removed the gallery tagging.

Matrix editor: improvements

Description:

http://sandbox.scratchpads.eu/matrix-editor/image. I can click on a row header, e.g. ‘Image galleries’ but nothing happens. The headers look to be clickable, so something should happen. For example add a sentence below the matrix like “To edit content select one or more fields within a column (Ctrl+click on PC, Cmd+click on Mac) and edit the content in the field that appears below the matrix. Then click on the ‘Save changes’ button”.

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