export v2: "accession" missing from node attributes when used as the metadata ID column

[victorlin]

Originally noticed in nextstrain/rsv#29 (comment).

Current Behavior

In augur export v2, the accession node attribute gets exported as long as it's an available node attribute. The problem comes when "accession" is used as the metadata ID column - it is no longer available in the current implementation.

I think this is an oversight of 3be4d18.

augur/tests/functional/export_v2/cram/metadata-with-accession.t

Lines 19 to 33 in bb4c4ca

	Run export with metadata that contains "accession", and use "accession" as the ID column.
	Currently, this results in losing the accession from the node attributes.
	$ ${AUGUR} export v2 \
	> --tree "$TESTDIR/../data/tree.nwk" \
	> --metadata "$TESTDIR/../data/dataset1_metadata_with_strain_and_accession.tsv" \
	> --metadata-id-columns accession \
	> --node-data "$TESTDIR/../data/div_node-data.json" "$TESTDIR/../data/location_node-data.json" \
	> --auspice-config "$TESTDIR/../data/auspice_config1.json" \
	> --maintainers "Nextstrain Team" \
	> --output dataset.json > /dev/null
	$ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" "$TESTDIR/../data/dataset_with_accession.json" dataset.json \
	> --exclude-paths "root['meta']['updated']" "root['meta']['maintainers']"
	{'dictionary_item_removed': [root['tree']['children'][0]['node_attrs']['accession'], root['tree']['children'][1]['children'][0]['node_attrs']['accession'], root['tree']['children'][1]['children'][1]['node_attrs']['accession'], root['tree']['children'][2]['children'][0]['node_attrs']['accession'], root['tree']['children'][2]['children'][1]['node_attrs']['accession'], root['tree']['children'][2]['children'][2]['node_attrs']['accession']]}

Expected behavior

The "accession" column can both (1) be used as the metadata ID column and (2) exported as a node attribute.

augur/tests/functional/export_v2/cram/metadata-with-accession.t

Lines 30 to 32 in 72f645c

	$ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" "$TESTDIR/../data/dataset_with_accession.json" dataset.json \
	> --exclude-paths "root['meta']['updated']" "root['meta']['maintainers']"
	{}

Possible solution

0ec4cc6