feat: warn when standalone ref and tree ref don't match exactly #1474
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Following conversation in #1455 (comment) Let's add a warning if the reference sequence provided any of the possible ways (fasta in dataset files, through CLI argument, Web URL param, or Web "Customization" interface) does not exactly match (as in string comparison) the `.root_sequence.nuc` in Auspice JSON. The warning message is the following. Please suggest improvements (paste a full quote into reply message or feel free to modify in the code). <details> <summary>Click to expand</summary> > Nextclade detected that reference sequence provided does not exactly match reference (root) sequence in Auspice JSON. > > This could be due to one of the reasons: > > - Nextclade dataset author provided reference sequence and reference tree that are incompatible > - The reference tree has been constructed incorrectly > - The reference sequence provided using `--input-ref` CLI argument is not compatible with the reference tree in the dataset > - The reference tree provided using `--input-tree` CLI argument is not compatible with the reference sequence in the dataset > - The reference sequence provided using `&input-ref` parameter in Nextclade Web URL is not compatible with the reference tree in the dataset > - The reference tree provided using `&input-tree` parameter in Nextclade Web URL is not compatible with the reference sequence in the dataset > > This warning signals that there is a potential for failures if the mismatch is not intended. </details>
|
The latest updates on your projects. Learn more about Vercel for Git ↗︎
|
|
Should the warning also explain why the match is important and perhaps link the docs? It's kinda getting long. Not sure if the enumeration of all of the cases is also important here. It's basically a list of ways of how you can get ref and tree into the program. |
ivan-aksamentov
added a commit
to nextstrain/nextclade_data
that referenced
this pull request
Jun 4, 2024
This is the same check as in nextstrain/nextclade#1474, but during dataset indexing, to catch it earlier for datasets we control.
|
Added the same check during index rebuild in the data repo for our own datasets: nextstrain/nextclade_data#206 |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Following conversation in #1455 (comment)
Let's add a warning if the reference sequence provided any of the possible ways (fasta in dataset files, through CLI argument, Web URL param, or Web "Customization" interface) does not exactly match (as in string comparison) the
.root_sequence.nucin Auspice JSON.The warning is emitted:
The warning message is the following. Please suggest improvements (paste a full quote into reply message or feel free to modify in the code).
Click to expand