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feature request #6203

Implement unplaced and excluded in dataportal

Added by Andreas Müller almost 3 years ago. Updated 6 months ago.

Status:
New
Priority:
Priority13
Category:
cdm-dataportal
Start date:
02/10/2017
Due date:
% Done:

0%

Severity:
major

Description

The unplaced and excluded flags have been moved from Taxon to TaxonNode (#3925). This should be taken in account in dataportal code. DONE

Unplaced taxon nodes should be put to an incertis sedis node in the tree. Excluded nodes should be put to an excluded node in the tree.

I don't know if this already happened for the flag in Taxon class. NOPE!

Also we should mention the state somehow on the taxon page. --> see #6221

see cdm_daaportal.module#cdm_dataportal_shortname_of() DONE

At least for phycobank a special configuration options are needed in the portal:

  • [ ] virtual classification nodes for unplaced and excluded taxa ( default = true, description = "Unplaced taxa are shown at the end of the classification. If this option is activated unplaced taxa will be put into the virtual classification node incertis sedis, excluded taxa in the virtual node excluded. If this option is inactive the taxa flagged as unplaced or excluded are shown as separately ordered set at the end of the siblings list with first unplaced then excluded taxa and internally ordered by rank and alphabet.

Subtasks

bug #6414: use short name for excluded, unplaced taxa when the genus of the parent taxa is differentNewAndreas Kohlbecker


Related issues

Related to Edit - feature request #6547: Implement excluded and unplaced in taxon navigator Closed 03/30/2017
Precedes Edit - feature request #3925: Unplaced and excluded to TaxonNode Closed 02/13/2017 02/13/2017
Copied to Edit - task #6221: mention the unplaced and excluded states in the taxon page New 11/25/2016

Associated revisions

Revision a0e3ae5c (diff)
Added by Andreas Kohlbecker over 2 years ago

ref #6203 checked return types of classification services and updated documentation

History

#1 Updated by Andreas Müller almost 3 years ago

#2 Updated by Andreas Müller almost 3 years ago

  • Priority changed from New to Highest

#3 Updated by Andreas Kohlbecker almost 3 years ago

  • Description updated (diff)
  • Priority changed from Highest to New

#4 Updated by Andreas Kohlbecker almost 3 years ago

  • Priority changed from New to Highest

#5 Updated by Andreas Kohlbecker over 2 years ago

Unplaced taxon nodes should be put to an incertis sedis node in the tree. Excluded nodes should be put to an excluded node in the tree.

I am not sure if this is only a task for the dataportal. I rather would see this as a feature for the cdmlib.

#6 Updated by Andreas Müller over 2 years ago

  • Assignee changed from Andreas Kohlbecker to Katja Luther

Katja, could you have a look on this.

We definetely need to move the unplaced and excluded (in this order) taxa to the end in the according cdmlib method.

It needs to be discussed if we already want to create explicit nodes in the result. This may make sense for the dataportal but as these nodes are volatile they better should be created by the application itself that shows the data (they can easily be created).

Is the TaxEditor navigator using the same cdmlib method here? Maybe we need to discuss the same issue for the TaxEditor.

#7 Updated by Andreas Müller over 2 years ago

  • Target version changed from Release 4.4 to Release 4.5

#8 Updated by Andreas Kohlbecker over 2 years ago

  • Tracker changed from bug to feature request
  • Priority changed from Highest to New

unplaced and excluded are handled correctly in the portal at least in the sense that the model change is not causing any problems in the portal. So this issue is not a bug report but a feature request. I am resetting the priority to 'new' since we still need to decide on the priority.

#9 Updated by Andreas Kohlbecker over 2 years ago

  • Copied to task #6221: mention the unplaced and excluded states in the taxon page added

#10 Updated by Andreas Kohlbecker over 2 years ago

  • Description updated (diff)

#11 Updated by Andreas Müller over 2 years ago

  • Description updated (diff)
  • Priority changed from New to Highest

#12 Updated by Katja Luther over 2 years ago

In the navigator of the editor the nodes are loaded step by step. Therefore it is difficult to move all excluded and unplaced taxonnodes in corresponding nodes in the tree on the editor side. These nodes would be filled while the user opens parents with excluded or unplaced children.
So I think for the editor the only solution is to create two nodes excluded and incertis sedis and move the excluded and unplaced nodes to these nodes.

#13 Updated by Andreas Müller over 2 years ago

  • Target version changed from Release 4.5 to Release 4.6

#14 Updated by Andreas Kohlbecker over 2 years ago

  • Target version changed from Release 4.6 to Release 4.7

#15 Updated by Andreas Müller over 2 years ago

#16 Updated by Andreas Müller over 2 years ago

  • Target version changed from Release 4.7 to Release 4.8

#17 Updated by Andreas Müller about 2 years ago

  • Target version changed from Release 4.8 to Release 4.9

#18 Updated by Andreas Müller about 2 years ago

  • Target version changed from Release 4.9 to Release 4.10

#19 Updated by Andreas Müller almost 2 years ago

  • Target version changed from Release 4.10 to Release 4.11

#20 Updated by Andreas Müller almost 2 years ago

  • Target version changed from Release 4.11 to Release 4.12

#21 Updated by Andreas Müller over 1 year ago

  • Target version changed from Release 4.12 to Release 4.13

#22 Updated by Katja Luther over 1 year ago

  • Assignee changed from Katja Luther to Andreas Kohlbecker

Katja Luther wrote:

In the navigator of the editor the nodes are loaded step by step. Therefore it is difficult to move all excluded and unplaced taxonnodes in corresponding nodes in the tree on the editor side. These nodes would be filled while the user opens parents with excluded or unplaced children.
So I think for the editor the only solution is to create two nodes excluded and incertis sedis and move the excluded and unplaced nodes to these nodes.

But they are not put to an extra node, did they? I had a look for the caryophyllales DB and there the excluded/unplaced taxa are still under their parent node.

#23 Updated by Andreas Müller over 1 year ago

  • Target version changed from Release 4.13 to Release 4.14

#24 Updated by Andreas Müller over 1 year ago

  • Target version changed from Release 4.14 to Release 5.0

#25 Updated by Andreas Kohlbecker over 1 year ago

  • Severity changed from normal to major

#26 Updated by Andreas Kohlbecker over 1 year ago

  • Description updated (diff)

#27 Updated by Andreas Müller over 1 year ago

  • Description updated (diff)

#28 Updated by Andreas Kohlbecker over 1 year ago

  • Target version changed from Release 5.0 to Release 5.1

#29 Updated by Andreas Müller about 1 year ago

  • Target version changed from Release 5.1 to Release 5.2

#30 Updated by Andreas Kohlbecker about 1 year ago

  • Target version changed from Release 5.2 to Release 5.3

#31 Updated by Andreas Kohlbecker 12 months ago

  • Target version changed from Release 5.3 to Release 5.4

#32 Updated by Andreas Kohlbecker 10 months ago

  • Target version changed from Release 5.4 to Release 5.5

#33 Updated by Andreas Kohlbecker 7 months ago

  • Target version changed from Release 5.5 to Release 5.6

#34 Updated by Andreas Kohlbecker 6 months ago

  • Target version changed from Release 5.6 to Reviewed Next Major Release

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