Allow "minimal" augur export

[trvrb]

Currently, it's way harder than it should be to just get a simple auspice JSON from a Newick tree + CSV metadata. I propose to allow augur export to not require --node-data and also to not require --auspice-config. Currently, this is the Zika export:

augur export \
--tree results/tree.nwk
--metadata results/metadata.tsv \
--node-data results/branch_lengths.json results/traits.json \
--auspice-config config/auspice_config.json \ 
--output-tree auspice/zika_tree.json \ 
--output-meta auspice/zika_meta.json

This should work (dropping --auspice-config), but does not:

augur export \
--tree results/tree.nwk \
--metadata results/metadata.tsv \
--node-data results/branch_lengths.json results/traits.json \
--output-tree auspice/zika_tree.json \
--output-meta auspice/zika_meta.json

Augur runs, but the resulting meta.json is not auspice compatible.

This should also work (dropping --node-data), but does not:

augur export \
--tree results/tree.nwk \
--metadata results/metadata.tsv \
--output-tree auspice/zika_tree.json \
--output-meta auspice/zika_meta.json

Augur complains that --node-data is required.

[huddlej]

This issue still isn't completely resolved after the augur v6 upgrade. Although users can omit metadata from the augur export v2 command, augur still prints "ERROR: read_metadata called without a filename". The corresponding code in augur/utils.py needs to be updated to output a warning instead.

Also, at least one node data JSON is required by augur export v2. The updated version of Trevor's simplest export would now be:

augur export v2 \
--tree results/tree.nwk \
--metadata results/metadata.tsv \
--output auspice/zika.json

To allow this, the following sections need to be updated in augur/export_v2.py:

• --node-data should not be required and should accept zero or more arguments
• parse_node_data_and_metadata needs to accept a node data value of None or receive an empty list
• parse_node_data_and_metadata needs to internally look for the div property on the tree instance instead of an external JSON or metadata file

[jameshadfield]

Ran into this today so adding a message here as a reminder. John's summation ☝️ is still accurate I believe, although --metadata is optional!

[jameshadfield]

Six monthly update 😂

PR #727 added some functional test coverage of augur export v2 including a minimal example.

• Currently a coloring must be provided (via node-data or metadata file) as the schema requires at least 1. Note that technically the dataset file is produced, and auspice can display it, but the command exits with code 2. The schema should be relaxed here.

[huddlej]

This issue came up at office hours today (and last week) where someone wanted to make a Nextclade dataset and needed to create an Auspice JSON version of their Newick tree for their custom dataset. This user did not have any node data JSON files and did not need any, but they were forced to mockup a nearly-empty JSON file to get augur export to work the way they wanted.

[huddlej]

This issue came up again at office hour from a different person. Even just allowing --node-data to be optional would be a huge win for people.