virtool virtool-cli issues

virtool / virtool-cli

A command line interface for working with Virtool data

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issues

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Schema and sequence patching

#166 sygao opened 3 months ago
0
Add OTU schema features

#165 sygao closed 3 months ago
1
Streamline `Molecule`

#164 sygao closed 3 months ago
1
CLI-48: Add handling for rare boolean qualifiers

#163 sygao closed 4 months ago
2
refactor: rename `EventIndex` module

#162 igboyes closed 4 months ago
1
refactor: simplify event index

#161 igboyes closed 4 months ago
1
Snapshotter cleanup 1

#160 igboyes closed 4 months ago
2
Minor NCBI Refactor (RuntimeError, test move)

#159 sygao closed 4 months ago
1
Add Snapshots/Read Model

#158 sygao closed 4 months ago
1
Skip recurring ESpell issue

#157 sygao closed 4 months ago
0
Refactor lower-level `EventSourcedRepo` functionality into `EventStore`

#156 sygao closed 4 months ago
1
Refactor lower-level `EventSourcedRepo` functionality into `EventIndex` and `EventStore`

#155 sygao closed 4 months ago
0
Convenience features for resources: OTUs, isolates and sequences

#154 sygao closed 4 months ago
1
Performance enhancements, util refactor and and clean up tests

#153 sygao closed 5 months ago
2
feat: `virtool ref snapshot`

#152 sygao closed 5 months ago
0
CLI-52, CLI-54: Add and update commands, private indexing storage for `OTU` and `Isolate`

#151 sygao closed 5 months ago
2
Fix for event indexing bug & minor utility functions/properties

#150 sygao closed 6 months ago
1
Exlude accessions with an event

#149 igboyes closed 6 months ago
1
Remove some unused functions

#148 igboyes closed 6 months ago
1
Partial CLI-57: EventIndexCache

#147 sygao closed 6 months ago
3
feat: add legacy repository validation

#146 igboyes closed 6 months ago
1
test: consolidate fixtures

#145 igboyes closed 6 months ago
1
Simplify models

#144 igboyes closed 6 months ago
1
fix: set entrez credentials on app load

#143 igboyes closed 6 months ago
0
CLI-53: Remove `virtool ref update uncache` command

#142 sygao closed 7 months ago
2
.cache/nuccore -> .cache/genbank

#141 sygao closed 7 months ago
2
CLI-44: Change cache directory name from nuccore -> genbank

#140 sygao closed 7 months ago
1
CLI-51: Change isolate naming

#139 sygao closed 7 months ago
2
Remove `check`

#138 igboyes closed 7 months ago
1
CLI-47: Handle `molecule` at the OTU level

#137 sygao closed 7 months ago
2
`NCBIGenbank` field updates; basic isolate extraction sample

#136 sygao closed 7 months ago
1
ci: update .deepsource.toml

#135 igboyes closed 6 months ago
0
NCBIGenbank modifications

#134 sygao closed 7 months ago
1
Add `NCBITaxonomyOtherNames` to handle data from the OtherNames field

#133 sygao closed 7 months ago
1
More event sourcing

#132 igboyes closed 7 months ago
1
More event sourcing

#131 igboyes closed 7 months ago
0
Change `abbreviation` to `acronym`

#130 igboyes closed 7 months ago
0
Remove all async functionality from NCBIClient

#129 sygao closed 7 months ago
0
Sync only

#128 sygao closed 7 months ago
0
Basic event sourcing

#127 igboyes closed 7 months ago
0
Fix: Only sets Entrez credentials if non-empty input is provided

#126 sygao closed 7 months ago
0
ci: update .deepsource.toml

#125 igboyes closed 7 months ago
0
Change most `nuccore` naming to `genbank`

#124 sygao closed 7 months ago
0
Simplify client

#123 sygao closed 7 months ago
2
Removed `cache_results` options from fetch methods

#122 sygao closed 7 months ago
0
Move parsing functionality to `ncbi.model.NCBITaxonomy`

#121 sygao closed 7 months ago
2
EXTERNAL: Gate NCBI-dependent CI tests behind internal pull request

#120 sygao closed 7 months ago
0
Gate NCBI-dependent CI tests

#119 sygao closed 7 months ago
1
Trying out environment ci

#118 sygao closed 7 months ago
0
Taxonomy record parser; New manual test workflow

#117 sygao closed 7 months ago
1