Open jameshadfield opened 3 weeks ago
I can reproduce locally by changing the dataset via one of the dropdowns that is not the last one, e.g. changing from http://localhost:4000/flu/seasonal/h1n1pdm/ha/12y to na via sidebar triggers the warning.
This bug is only observed when using the Auspice server (i.e. not within nextstrain.org). Steps to reproduce:
nextstrain remote download nextstrain.org/seasonal-flu/h3n2/ha/2y
nextstrain remote download nextstrain.org/seasonal-flu/h3n2/na/2y
nextstrain remote download nextstrain.org/seasonal-flu/h3n2/ha/3y
TypeError: rawJSON.pivots is undefined
Notes from a briefly looking into this (have to jump to other things now):
In the above example, we use an incomplete URL to fetch the tip frequencies:
this.apiCalls.tipFrequencies = /charon/getDataset?prefix=seasonal-flu/h3n2/na&type=tip-frequencies
(note the missing "2y" from the path). The auspice server redirects to /charon/getDataset?prefix=/seasonal-flu/h3n2/na/2y
and thus returns the main dataset JSON. Because this is a valid JSON, we don't have a fetch error and end up with a frequencies parsing error.
There seem to be two potential solutions: have the server redirect and respect the type
query (I presume this is what nextstrain.org does, must check), or redesign how we formulate the api calls (addresses) for sidecars.
The server behaves the same way for root-sequence & measurements URLs, so these should also be tested.
Nextstrain org redirect flow:
/charon/getDataset?prefix=seasonal-flu/h3n2/na&type=tip-frequencies
is a 307 to /charon/getDataset?prefix=seasonal-flu/h3n2/na/2y&type=tip-frequencies
Auspice (localhost) is:
/charon/getDataset?prefix=seasonal-flu/h3n2/na&type=tip-frequencies
is a 302 to charon/getDataset?prefix=/seasonal-flu/h3n2/na/2y
When changing between two datasets via the sidebar dropdown UI, each with a tip frequencies sidecar, we saw someone get a warning banner indicating a failure to normalise frequencies and the sidebar option is not available. The relevant code for the sidebar is:
https://github.com/nextstrain/auspice/blob/de94b72e155e7d386f1c82509727b422f0c6f99d/src/components/controls/frequency-normalization.js#L22-L32
and
checkIfNormalizableFromRawData
seems to always returntrue
(!)https://github.com/nextstrain/auspice/blob/de94b72e155e7d386f1c82509727b422f0c6f99d/src/util/processFrequencies.js#L62-L63
implying a race condition around
this.props.frequencies.loaded && this.props.tree.loaded
.Reloading the page works as expected.
I don't have any reproducible datasets (have asked for them), and note that changing https://nextstrain.org/seasonal-flu/h3n2/ha/3y to 2y (via sidebar) works as expected. Perhaps it's dataset specific (hard to understand after skimming the relevant code) or using an old version of auspice (normalisation checking was removed in https://github.com/nextstrain/auspice/commit/7b9495b107517008ef5d1dca7466e83f3db2984a in 2001)