feature request #6203
open
Implement unplaced and excluded in dataportal
Added by Andreas Müller over 7 years ago.
Updated about 5 years ago.
Estimated time:
(Total: 0:00 h)
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.
- Priority changed from New to Highest
- Description updated (diff)
- Priority changed from Highest to New
- Priority changed from New to Highest
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.
- 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.
- Target version changed from Release 4.4 to Release 4.5
- 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.
- Copied to task #6221: mention the unplaced and excluded states in the taxon page added
- Description updated (diff)
- Description updated (diff)
- Priority changed from New to Highest
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.
- Target version changed from Release 4.5 to Release 4.6
- Target version changed from Release 4.6 to Release 4.7
- Target version changed from Release 4.7 to Release 4.8
- Target version changed from Release 4.8 to Release 4.9
- Target version changed from Release 4.9 to Release 4.10
- Target version changed from Release 4.10 to Release 4.11
- Target version changed from Release 4.11 to Release 4.12
- Target version changed from Release 4.12 to Release 4.13
- 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.
- Target version changed from Release 4.13 to Release 4.14
- Target version changed from Release 4.14 to Release 5.0
- Severity changed from normal to major
- Description updated (diff)
- Description updated (diff)
- Target version changed from Release 5.0 to Release 5.1
- Target version changed from Release 5.1 to Release 5.2
- Target version changed from Release 5.2 to Release 5.3
- Target version changed from Release 5.3 to Release 5.4
- Target version changed from Release 5.4 to Release 5.5
- Target version changed from Release 5.5 to Release 5.6
- Target version changed from Release 5.6 to Reviewed Next Major Release
- Related to bug #9741: cdm_dataportal_shortname_of truncates uninomial with not abbreviated author strings and causes other odds added
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