Opened 5 years ago

Last modified 10 months ago

#774 _started enhancement

allow custom node-IDs during tree-import

Reported by: westram Owned by: westram
Priority: major Milestone: wishlist
Component: Library (DB) Version: SVN
Keywords: Cc: jgerken@…

Description (last modified by westram)

Need a possibility to import trees that use alternative IDs at leafs, e.g. 'acc' and/or 'start'/'stop' positions etc.

Possible implementation:

  • provide importer with 2 ACI expressions:
    • 1st expression creates a unique ID from every leaf ID found in imported tree
      • if not specified ⇒ use ID as found in tree
    • 2nd expression creates a unique ID from every species existing in the DB
      • if not specified ⇒ use 'name' field as ID
  • test that all IDs generated by one expression are unique! (or bail out)
  • map leafs of imported tree to species
    1. wherever both generated IDs match or (alternatively)
    2. one ID is contained in other ID.
  • create zombies and warn on mismatch.

The method described above can be applied

  • to all leaf labels of imported tree or
  • to all zombie labels of any existing tree.

Notes:

  • allow to define ACI expressions via tree import GUI
  • allow to specify ACI expressions via arb_read_tree CLI

Example ACI (2nd expression) to generate IDs:

readdb("acc");".";readdb("start");".";readdb("stop")|merge

Related:

  • allow to specify an explicit ACI in tree-exporter
    • use as alternative to NDS-label
    • these ACIs are identical to 2nd expression for import above
      ⇒ use same config manager?

Change History (6)

comment:1 Changed 4 years ago by westram

  • [16866] provides a workaround
    • synchronize IDs in original database & save
    • run script to generate special IDs (e.g. from field "full_name")
    • import tree
    • again synchronize IDs
    • export tree to file
    • quit database without saving
    • reload prev. saved database and import tree from file

comment:2 Changed 4 years ago by westram

  • Milestone set to proposals

comment:3 Changed 4 years ago by westram

  • Milestone changed from proposals to wishlist

comment:4 Changed 11 months ago by westram

  • Owner changed from devel to westram
  • Status changed from new to _started

comment:5 Changed 10 months ago by westram

  • Description modified (diff)

comment:6 Changed 10 months ago by westram

  • Description modified (diff)
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