catalogueoflife/checklistbank

UI for checklistbank.org

Catalogue of Life — ChecklistBank UI

The Catalogue of Life ChecklistBank is an environment to place taxonomic and nomenclatural information from different sources in different formats into a consistent data model exposed with a rich API.

The UI allows public exploring of all data in ChecklistBank. It is also a tool for assembling taxonomic checklists from multiple sources for authorized users. Source checklists can be imported in several formats and quality checks are applied during import. ChecklistBank includes tools for duplicate detection and allows for editorial decisions to be recorded and applied repeatedly when syncronising data from sources to an assembled checklist.

Prerequisites

node >= 14

The ChecklistBank UI is build with React using UI components from Ant design.

Available Scripts

This project was bootstrapped with Create React App. In the project directory, you can run:

node writeEnums.js

Fetch all enums and write them as json files to src/enumeration

npm install

To install the package.json dependencies.

npm start

Runs the app in the development mode.
Open http://localhost:3000 to view it in the browser.

The page will reload if you make edits.
You will also see any lint errors in the console.

npm test

Launches the test runner in the interactive watch mode.
See the section about running tests for more information.

npm run build

Builds the app for production to the build folder.
It correctly bundles React in production mode and optimizes the build for the best performance.

The build is minified and the filenames include the hashes.
Your app is ready to be deployed!

checklistbank's Issues

Action buttons in table

Actions:

• Block name
• Change status (Accepted name, Ambiguous synonym, Misapplied name, Prov accepted name, synonym)
• No action

Show dataset import metrics

Show import metrics for a dataset on a new tab.
Maybe as the home tab even instead of the metadata?

Show on dataset page if import is currently running

Show a warning on all dataset scoped pages if an import is currently running to alarm users that data is changing and results might be inconsistent

Search names by ID, name or issue

Species estimates

Possibility to add species estimates to nodes in the MC

Direct link to data file in GitHub

Is not always present, but show when available

organize issues by issue group

All issues are organized to either be general or specific for some kind of entity, e.g. names, taxa, references, etc.

It would be good to show issues on the dataset issue tab by these groups.
Needs to be exposed via http://api.col.plus/vocab/issue

See https://github.com/Sp2000/colplus-backend/blob/master/colplus-api/src/main/java/org/col/api/vocab/Issue.java#L401

Trees break if there a hundreds of roots.

If a dataset is a flat list of e.g. families, prompt the user to choose which roots to show (rather than showing all by default and breking the UI)

Show Col Assembly menu item only to EDITORs

All assembly, add dataset and import pages should not be visible to normal users.
Only show those item to users with role editor.

Drag n drop between nodes in the classification explorer

Show issues on Taxon and Names

... coming in via the verbatim record currently

Add species estimate directly in the tree node

Display if dataset has been updated from source after last edition of CoL

“Is new?” [values: 0=untouched, 1=new in a year cycle, 2=updated in a year cycle] (A flag for new and updated databases in a year cycle)

Cancel create new sector button visibility inconsistent

Implement rules for Drag n drop between nodes in MC

Species can not be moved
You cant move downwards

Ability to delete currently applied decision

Design simple landing page

There should be a Clearinghouse landing page when fist visiting the site.
Ideas to show:

• short paragraph what the site is about
• key numbers with links (num datasets, num names index names, num taxa/names in CoL draft)
• latest dataset(s) added and imported

Show current mappings in MC tree

Depends on CatalogueOfLife/backend#162

Error if no running imports

Cannot read property 'concat' of undefined

Show verbatim record

verbatim record and its issues

Edit a name of a node, both in GSDs and MC

Modify MC

Add child
Del child
Change name lookup via names index

Add comment to name

less navigation menus?

we have a top n side menu, tabs and a breadcrumb which often show very much the same. Can we reduce this without sacrifycing functionality? maybe we can reserve the sidebar for actions, stats or faved items?

About page

There should be an about page describing the purpose of the site in more detail.

Sector comparison view

Visualizing changes between different sector sync attempts should assist the editorial work a lot. The API is providing two ways of comparing different versions of a sector:

TextTree
A indented, simple text tree representation including synonyms for the entire sector is part of the SyncImport metrics we generate for every sync attempt. The API offers a diff service between any two successful attempts which can be rendered as a markdown table. We can easily change the representation or even allow to ask for different formats (e.g UnifiedDiff, Markdown, Html)

http://api-dev.col.plus/assembly/3/sync/210/treediff?attempts=7..9

NameIndeIds
Also the complete set of NameIndexIds for all names is included.
The API will offer a diff between any 2 attempts which could be visualised in a simple (potentially large) table.

http://api-dev.col.plus/assembly/3/sync/210/namesdiff?attempts=7..9

Add recent imports tab

would be nice to also know about the last successful imports

more compact record view

I prefer if you do not have to scroll. can we present details data in a more compact view?

Show verbatim data differently

Verbatim data is a different kind of representation and I think it would be better to show it more in a code style like json:

{
  "acef:AcceptedTaxonID" : "Fis-33634",
  "acef:AuthorString" : "Borodin, 1897",
  "acef:Sp2000NameStatus" : "synonym",
}

http://test.col.plus/dataset/1010/name/Fis-115182

Discuss how to best show synonyms

Synonyms need to expose their status and accordingTo in case of misapplied names. Status is missing from the Synonymy object currently.

And heterotypic synonyms might better not be labeled as such. Its a catch all. Only homotypic synonyms are clearly homotypic and should be shown as such.

Checkbox in table for multiple name selection to apply decisions

Filter datasets by catalogue

Allow dataset table to only show datasets for the scrutinized or provisional cat.

@yroskov Maybe rename the rendered value to "pCat" and "sCat" or "CoL" and "prov CoL"

Search in tree through names index

Table view of names

Upload dataset or source logo

A logo image for a dataset or ColSource should be hosted in the Clearinghouse.
This can be done either by pointing to an external image URL via the dataset metadata OR by manually uploading an image. Logo upload endpoint to be done:

CatalogueOfLife/backend#172
CatalogueOfLife/backend#152

Allow NameUsage search

search by name, author, issue & rank at least initially

create dataset issue tab

for more space in showing issues in a table

Show homotypic names and name relations on name page

We should not show "Homotypic Name Id", but instead list all homotypic names via the call:
/dataset/{dkey}/name/{id}/synonyms

Also show the publication and all name relations:
/dataset/{dkey}/name/{id}/relations
/dataset/{dkey}/name/{id}/publishedIn

show taxon/name link URL

A plain name, taxon or synonym can have a link property that takes a URL to its "homepage" in the original source. Show that link on a taxon/synonym/bare names page

Allow manual upload of archives

to quickly test new archives. This should only be possible if the dataset is of origin UPLOADED.

Manage imports

List currently running and queued imports.
Allow to cancel running or queued imports and schedule new ones

Allow manual update of all logos

apart from pulling a single logo during an import this triggers an update of all dataset logos from their configured URL can be manually triggered by calling: http://api.col.plus/admin/logo-update

Show username in menu when logged in

Show/hide shadowed nodes

Rename "Management Classification" menu

Maybe a better name would be "CoL Working Draft", "CoL Assembly" or just "CoL Draft"?

Draft preview button

Split view Management classification / GSD

Browse Management classification side by side with a chosen GSD, with opportunity to drag nodes from the GSD onto the management classification.

Sector attachment

Col Source form - input from @yroskov

Please rearrange them as I present below:

• [Please add field] “Source ID” (A unique ID assigned to the dataset by the CoL software).
• “Title” to “Full Name” (Full title of Source Database, as it is supplied by the custodian)
• “Alias” to “Short Name” (Abbreviated or shortened memorable name of Source Database intended for easy use in day-to-day communications, as supplied by the custodian)
• “Version” (Number or code, plus date, where Month and Year are obligatory) provided by the custodian; style specified by the CoL editor and custodian of Source Database)
• “Released” to “Release Date” (Original date (Year-Month-Date) of issue of the version for the Catalogue of Life).
• “Authors and editor” to “Authors/Editors” (Name(s) of Source Database editor or author; as specified by the custodian).
• “Coverage” to “Taxonomic Coverage” (Higher taxa, which represent taxonomic position of sector(s) covered by the database in the classification). This field should be filled automatically after database sectors attached in the Tree.
• “Group” to “English name of the group” (English name of the taxon covered by the Source Database).
• “Description” to “Abstract” (Standardised short database description (text of 80-90 words) for use in the Catalogue of Life and supporting materials, such as the booklet published with the Annual Checklist).
• Organization (Name of the Organisation that hosts the Source Database).
• Home Page (Internet address of the project/resource website).
• “Citation” to “Bibliographic Citation”. This field should be filled by the software. Bibliographic citation should be generated from Authors/Editors, Year of the product, GSD name “as displayed”, “Version” and selected CoL metadata.

Please add fields:

• “Is new?” [values: 0=untouched, 1=new in a year cycle, 2=updated in a year cycle] (A flag for new and updated databases in a year cycle)
• “Coverage” [values: Global, Regional] (Geographic coverage of the Source Database for the taxon)
• “Completeness” [values: 1 to 100%] (Percentage of completeness of species list of the taxon provided by the Source Database)
• “Checklist Confidence” [values: 1, 2, 3, 4, 5] (Quality of taxonomic checklist with values 1 to 5; quality is stated by the custodian in agreement with CoL editor. Confidence indicators are described at http://www.catalogueoflife.org/col/info/databases).
• “Editor’s comments” [this field is new; it was not implemented in old structure. Perhaps later it should be extended into number of fields with management information].

Customise columns

Default settings based on issue types
User defined, save in localStorage, maybe persist to GBIF user later