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feature request #6203

open

Implement unplaced and excluded in dataportal

Added by Andreas Müller about 6 years ago. Updated almost 4 years ago.

Status:
New
Priority:
Priority13
Category:
cdm-dataportal
Start date:
Due date:
% Done:

0%

Estimated time:
(Total: 0:00 h)
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 1 (1 open0 closed)

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

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Related issues

Related to EDIT - feature request #6547: Implement excluded and unplaced in taxon navigatorClosedKatja Luther

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Related to EDIT - bug #9741: cdm_dataportal_shortname_of truncates uninomial with not abbreviated author strings and causes other oddsNewAndreas Kohlbecker

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Precedes EDIT - feature request #3925: Unplaced and excluded to TaxonNodeClosedAndreas Müller

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Copied to EDIT - task #6221: mention the unplaced and excluded states in the taxon pageNewAndreas Kohlbecker

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Actions #1

Updated by Andreas Müller about 6 years ago

Actions #2

Updated by Andreas Müller about 6 years ago

  • Priority changed from New to Highest
Actions #3

Updated by Andreas Kohlbecker about 6 years ago

  • Description updated (diff)
  • Priority changed from Highest to New
Actions #4

Updated by Andreas Kohlbecker about 6 years ago

  • Priority changed from New to Highest
Actions #5

Updated by Andreas Kohlbecker about 6 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.

Actions #6

Updated by Andreas Müller about 6 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.

Actions #7

Updated by Andreas Müller about 6 years ago

  • Target version changed from Release 4.4 to Release 4.5
Actions #8

Updated by Andreas Kohlbecker about 6 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.

Actions #9

Updated by Andreas Kohlbecker about 6 years ago

  • Copied to task #6221: mention the unplaced and excluded states in the taxon page added
Actions #10

Updated by Andreas Kohlbecker about 6 years ago

  • Description updated (diff)
Actions #11

Updated by Andreas Müller about 6 years ago

  • Description updated (diff)
  • Priority changed from New to Highest
Actions #12

Updated by Katja Luther about 6 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.

Actions #13

Updated by Andreas Müller about 6 years ago

  • Target version changed from Release 4.5 to Release 4.6
Actions #14

Updated by Andreas Kohlbecker almost 6 years ago

  • Target version changed from Release 4.6 to Release 4.7
Actions #15

Updated by Andreas Müller almost 6 years ago

Actions #16

Updated by Andreas Müller over 5 years ago

  • Target version changed from Release 4.7 to Release 4.8
Actions #17

Updated by Andreas Müller over 5 years ago

  • Target version changed from Release 4.8 to Release 4.9
Actions #18

Updated by Andreas Müller over 5 years ago

  • Target version changed from Release 4.9 to Release 4.10
Actions #19

Updated by Andreas Müller over 5 years ago

  • Target version changed from Release 4.10 to Release 4.11
Actions #20

Updated by Andreas Müller about 5 years ago

  • Target version changed from Release 4.11 to Release 4.12
Actions #21

Updated by Andreas Müller about 5 years ago

  • Target version changed from Release 4.12 to Release 4.13
Actions #22

Updated by Katja Luther about 5 years 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.

Actions #23

Updated by Andreas Müller about 5 years ago

  • Target version changed from Release 4.13 to Release 4.14
Actions #24

Updated by Andreas Müller almost 5 years ago

  • Target version changed from Release 4.14 to Release 5.0
Actions #25

Updated by Andreas Kohlbecker almost 5 years ago

  • Severity changed from normal to major
Actions #26

Updated by Andreas Kohlbecker almost 5 years ago

  • Description updated (diff)
Actions #27

Updated by Andreas Müller almost 5 years ago

  • Description updated (diff)
Actions #28

Updated by Andreas Kohlbecker over 4 years ago

  • Target version changed from Release 5.0 to Release 5.1
Actions #29

Updated by Andreas Müller over 4 years ago

  • Target version changed from Release 5.1 to Release 5.2
Actions #30

Updated by Andreas Kohlbecker over 4 years ago

  • Target version changed from Release 5.2 to Release 5.3
Actions #31

Updated by Andreas Kohlbecker over 4 years ago

  • Target version changed from Release 5.3 to Release 5.4
Actions #32

Updated by Andreas Kohlbecker over 4 years ago

  • Target version changed from Release 5.4 to Release 5.5
Actions #33

Updated by Andreas Kohlbecker about 4 years ago

  • Target version changed from Release 5.5 to Release 5.6
Actions #34

Updated by Andreas Kohlbecker almost 4 years ago

  • Target version changed from Release 5.6 to Reviewed Next Major Release
Actions #35

Updated by Andreas Müller over 1 year ago

  • Related to bug #9741: cdm_dataportal_shortname_of truncates uninomial with not abbreviated author strings and causes other odds added
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