Opened 4 years ago
Last modified 2 years ago
#832 _started task
emphasize group name conventions
Reported by: | westram | Owned by: | westram |
---|---|---|---|
Priority: | major | Milestone: | |
Component: | ARB_NTREE | Version: | SVN |
Keywords: | Cc: |
Description (last modified by westram)
The following conventions for names of taxonomic groups are/shallBe used in arb databases.
Some characters are problematic
character | problem | implemented behavior |
---|---|---|
|
used for groups combining multiple taxonomic ranks | warn-on-write since [19278] |
| used when a taxon is "spread" across the . In that case the taxonname may occur in an enumerated flavour like
| warn-on-write since [19278] |
|
used by taxonomy() ACI-command. | warn-on-write since [17110] |
| used in "tax…" entries to separate groups | warn-on-write since [19278] |
|
used as prefix for keeled groups | error-on-write since [17110] |
Needed fixes:
- extend ACI command taxonomy to accept a 3rd parameter to specify the separator to use, e.g. taxonomy(100,";")
- predefined ACIs for generating tax entries shall
- use new taxonomy parameter to directly create ';'-separated tax-entries
- translate _ → ;
- remove enumerated suffixes
- review parts of arb which auto-generate group names
- make sure their defaults follow the above conventions:
- group name modifications performed by Move groups.. (see also predefined config "report2name")
group names generated by Cluster detectionfixed by [19283]- group names generated/assumed by predefined configs in Search taxonomic groups
do not notify about violation of group naming convention for each of e.g. 100 generated groups.implemented with [19277].
Instead collect all and maybe show the first three warnings or so.
- make sure their defaults follow the above conventions:
- implement #833 (generate taxonomic groups from tax…-entries)
Change History (11)
comment:1 Changed 4 years ago by westram
- Description modified (diff)
comment:2 Changed 4 years ago by westram
- Description modified (diff)
comment:3 Changed 4 years ago by westram
- Description modified (diff)
comment:4 Changed 4 years ago by westram
- Description modified (diff)
comment:5 Changed 2 years ago by westram
- Owner changed from devel to westram
- Priority changed from normal to major
- Status changed from new to _started
comment:6 Changed 2 years ago by westram
- Description modified (diff)
comment:7 Changed 2 years ago by westram
- Description modified (diff)
comment:8 Changed 2 years ago by westram
- Description modified (diff)
comment:9 Changed 2 years ago by westram
comment:10 Changed 2 years ago by westram
- Description modified (diff)
comment:11 Changed 2 years ago by westram
- Description modified (diff)
arb now complains about "unwanted" group names using the following messages: