Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Refactor finding ids #105

Merged
merged 28 commits into from
Jan 25, 2021
Merged

Refactor finding ids #105

merged 28 commits into from
Jan 25, 2021

Conversation

bredelings
Copy link
Contributor

@bredelings bredelings commented Dec 2, 2020 •
edited
Loading

This addresses issues raised in #84

The patches are in three groups:

  1. Add tests
  2. Add functionality
  3. Fix functionality (and tests)

This might seem a bit odd because it was actually written in the order 2, 1, 3.

@bredelings
Add test for handling id 'asdf'.
9fff18e
@bredelings
Add test for ids that are too big.
e889957
@bredelings
Add test for id that is not in OTT.
1827c6a
@bredelings
Use more readable / operator instead of join_paths( )
c1fa0b0
@bredelings
Also use / in tools/meson.build
146ca9c
@bredelings
Add a test for a pruned ottid.
4dc0ef5
@bredelings
Add a test for a broken taxon.
00bf765
@bredelings
Add a test for multiple issues happening at once.
350c2ae
@bredelings
Construct NameToSynth object in parallel with node_lookup_t.
402354d
@bredelings
Give NameToSynth the same interface as node_lookup_t
9c8eccd
@bredelings
Replace node_lookup_t with NameToSynth
c3c7d02
@bredelings
Factor out find_node_by_ottid_str( ).
1d205a7
@bredelings
Factor out find_node_by_valid_ottid( ).
cae212d
@bredelings
Use the right ott_id for InvalidID{}.
b1e6ff4
@bredelings
Fix finding mrca of broken taxa.
6445950
@bredelings
Factor out find_node_by_mrca_str( ).
f774f47
@bredelings
Reformat find_nodes_for_id_strings( ).
49bf9db
@bredelings
Clean up attributes on NameToSynth
9f912f0
@bredelings
Use NameToSynth attributes to determine broken / pruned / invalid .
51ee5d3
@bredelings
Factor out node-finding routines into their own file.
24d8897
@bredelings
Add interface for filtering.
3362c21
@bredelings
The actually regex match command should NOT be inside the assert!
7ceb347
@bredelings
Don't loop infinitely waiting for pidfile to vanish.
4d8f642
@bredelings
Don't write experimental "filtered" property, just "unknown" property.
4e2359c
@bredelings
Fix test for ottX where X is too long.
69b5da7
@bredelings
Check expected.json even if the status code is wrong.
b1efa7f
@bredelings
Write both messages.
bdd5900
@bredelings
Update test.
f1fa7d8
@mtholder mtholder merged commit 73405aa into development Jan 25, 2021
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@mtholder mtholder Awaiting requested review from mtholder

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@bredelings @mtholder