[curate rename] Add tests

Tests describe desired output, not current output

tests/functional/curate/cram/rename/drop-columns.t

@@ -0,0 +1,29 @@
+
+Setup
+
+  $ export AUGUR="${AUGUR:-$TESTDIR/../../../../../bin/augur}"
+
+  $ cat >records.ndjson <<~~
+  > {"strain": "s_1", "country": "c_1", "accession": "a_1"}
+  > {"strain": "s_2", "country": "c_2", "accession": "a_2"}
+  > {"strain": "s_3", "country": "c_3", "accession": "a_3"}
+  > ~~
+
+Rename the strain column to accession -- we don't move the strain column to where accession was,
+We simply rename it and drop the (old) accession column. The alternate (which I don't like) produces:
+{"country": "c_1", "accession": "s_1"}
+{"country": "c_2", "accession": "s_2"}
+{"country": "c_3", "accession": "s_3"}
+
+  $ $AUGUR curate rename --field-map "strain=accession" --force < <(cat records.ndjson)
+  {"accession": "s_1", "country": "c_1"}
+  {"accession": "s_2", "country": "c_2"}
+  {"accession": "s_3", "country": "c_3"}
+
+Similarly, renaming accession to strain re-names the column "in-place" and drops the (old) strain column
+
+  $ $AUGUR curate rename --field-map "accession=strain" --force < <(cat records.ndjson)
+  {"country": "c_1", "strain": "a_1"}
+  {"country": "c_2", "strain": "a_2"}
+  {"country": "c_3", "strain": "a_3"}
+

tests/functional/curate/cram/rename/force-behaviour.t

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+Setup
+
+  $ export AUGUR="${AUGUR:-$TESTDIR/../../../../../bin/augur}"
+
+
+  $ cat >records.ndjson <<~~
+  > {"accession": "record_1", "country": ""}
+  > {"accession": "record_2", "country": "country_2"}
+  > ~~
+
+Test that --force is required if a key exists, irregardless of its associated value
+(This was not the behaviour in the precursor command `transform-field-names`)
+
+  $ $AUGUR curate rename --field-map "accession=country" < <(cat records.ndjson) 1> out1.ndjson
+  WARNING: skipping rename of accession because record already has a field named country.
+
+  $ diff records.ndjson out1.ndjson
+

tests/functional/curate/cram/rename/general.t

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+Setup
+
+  $ export AUGUR="${AUGUR:-$TESTDIR/../../../../../bin/augur}"
+
+The tests here use NDJSON I/O and don't explicitly test TSV I/O as we rely
+on the general curate infrastructure to enforce that each row has the same
+fields. See <https://github.com/nextstrain/augur/issues/1510> for more
+
+  $ cat >records.ndjson <<~~
+  > {"accession": "record_1", "country": "country_1"}
+  > {"accession": "record_2", "country": "country_2"}
+  > ~~
+
+The --field-map argument is requried (error text not checked as it includes the entire argparse usage text)
+
+  $ $AUGUR curate rename < <(cat records.ndjson) 2>/dev/null
+  [2]
+
+Rename "accession" to "strain" -- the order should be preserved (i.e. strain is first column)
+
+  $ $AUGUR curate rename --field-map "accession=strain" < <(cat records.ndjson)
+  {"strain": "record_1", "country": "country_1"}
+  {"strain": "record_2", "country": "country_2"}
+
+
+Rename "accession" to "country" - single error message is reported as we won't overwrite without --force
+and we don't change the data
+
+  $ $AUGUR curate rename --field-map "accession=country" < <(cat records.ndjson) > out2.ndjson
+  WARNING: skipping rename of accession because record already has a field named country.
+
+  $ diff records.ndjson out2.ndjson
+
+Rename "accession" to "country" using --force
+
+  $ $AUGUR curate rename --field-map "accession=country" --force < <(cat records.ndjson)
+  {"country": "record_1"}
+  {"country": "record_2"}
+
+Asking to rename multiple columns to the same new name is an error!
+
+  $ $AUGUR curate rename --field-map "accession=foo" "country=foo" < <(cat records.ndjson)
+  ERROR: Asked to rename multiple fields to 'foo'.
+  [2]
+
+Asking to rename a non-existant column raises a warning. Using a warning not an error allows the command
+to be idempotent.
+
+  $ $AUGUR curate rename --field-map "strain=foo" < <(cat records.ndjson) 1> out3.ndjson
+  WARNING: Asked to rename field 'strain' (to 'foo') but it doesn't exist in the input data.
+
+  $ diff records.ndjson out3.ndjson
+
+
+Rename will re-order fields to match the first observed record (with any necessary changes applied)
+This produces NDJSON output which more closely matches TSV output.
+
+  $ cat >records.unordered.ndjson <<~~
+  > {"accession": "record_1", "country": "country_1"}
+  > {"country": "country_2", "accession": "record_2"}
+  > ~~
+
+  $ $AUGUR curate rename --field-map "accession=id" --force < <(cat records.unordered.ndjson)
+  {"id": "record_1", "country": "country_1"}
+  {"id": "record_2", "country": "country_2"}
+
+
+Using --field-map without a single '=' char is an error
+  $ $AUGUR curate rename --field-map "accession" < <(cat records.ndjson)
+  ERROR: The field-map 'accession' must contain a single '=' character.
+  [2]
+
+Using --field-map with more than a single '=' char is an error
+  $ $AUGUR curate rename --field-map "accession=id=strain" < <(cat records.ndjson)
+  ERROR: The field-map 'accession=id=strain' must contain a single '=' character.
+  [2]
+
+Using --field-map with spaces surrounding field names is OK (as long as you quote the arg appropriately)
+  $ $AUGUR curate rename --field-map " accession = strain " < <(cat records.ndjson)
+  {"strain": "record_1", "country": "country_1"}
+  {"strain": "record_2", "country": "country_2"}
+
+Using --field-map with an empty "old field" doesn't make sense
+  $ $AUGUR curate rename --field-map "=accession" < <(cat records.ndjson)
+  ERROR: The field-map '=accession' doesn't specify a name for the existing field.
+  [2]
+
+Using --field-map with an empty "new field" doesn't (yet) make sense
+  $ $AUGUR curate rename --field-map "accession=" < <(cat records.ndjson)
+  ERROR: The field-map 'accession=' doesn't specify a name for the new field.
+  [2]