Merge pull request #1658: clades: Update Cram tests

tests/functional/clades/cram/_setup.sh

@@ -0,0 +1,2 @@
+export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
+set -o pipefail

tests/functional/clades/cram/membership-and-label.t

@@ -0,0 +1,18 @@
+Integration tests for augur clades.
+
+  $ source "$TESTDIR"/_setup.sh
+
+Test custom membership key + label key. The only change should be the key names
+
+  $ ${AUGUR} clades \
+  >   --tree "$TESTDIR/../data/tree.nwk" \
+  >   --mutations "$TESTDIR/../data/aa_muts.json" "$TESTDIR/../data/nt_muts_small.json" \
+  >   --clades "$TESTDIR/../data/clades.tsv" \
+  >   --membership-name lineage --label-name origin \
+  >   --output-node-data clades_custom.json &>/dev/null
+
+  $ cat clades_custom.json | sed "s/lineage/clade_membership/" | sed "s/origin/clade/" > clades_sed.json
+
+  $ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" "$TESTDIR/../data/clades.json" clades_sed.json \
+  >   --exclude-paths "root['generated_by']"
+  {}

tests/functional/clades/cram/multiple-mutations-error.t

@@ -0,0 +1,12 @@
+Integration tests for augur clades.
+
+  $ source "$TESTDIR"/_setup.sh
+
+Multiple mutations at the same position on a single branch are a fatal error
+
+  $ ${AUGUR} clades \
+  >   --tree "$TESTDIR/../data/toy_tree.nwk" \
+  >   --mutations "$TESTDIR/../data/toy_muts_multiple.json" \
+  >   --clades "$TESTDIR/../data/toy_clades_nuc.tsv"
+  ERROR: Multiple mutations at the same position on a single branch were found: Node A (nuc), Node AB (geneName)
+  [2]

tests/functional/clades/cram/no-label.t

@@ -0,0 +1,16 @@
+Integration tests for augur clades.
+
+  $ source "$TESTDIR"/_setup.sh
+
+Test the ability to _not_ export a branch label (same logic as not exporting the membership)
+
+  $ ${AUGUR} clades \
+  >   --tree "$TESTDIR/../data/tree.nwk" \
+  >   --mutations "$TESTDIR/../data/aa_muts.json" "$TESTDIR/../data/nt_muts_small.json" \
+  >   --clades "$TESTDIR/../data/clades.tsv" \
+  >   --label-name none \
+  >   --output-node-data clades_no-labels.json &>/dev/null
+
+  $ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" "$TESTDIR/../data/clades.json" clades_no-labels.json \
+  >   --exclude-paths "root['generated_by']"
+  {'dictionary_item_removed': [root['branches']]}

tests/functional/clades/cram/root-clade-identification.t

@@ -0,0 +1,43 @@
+Integration tests for augur clades.
+
+  $ source "$TESTDIR"/_setup.sh
+
+A clade which exists at the root is not identified by inferring the root state
+(i.e. we don't infer the root state to be A if we observe a subsequent A10T mutation)
+This is an oversight and ideally would be fixed
+
+  $ ${AUGUR} clades \
+  >   --tree "$TESTDIR/../data/toy_tree.nwk" \
+  >   --mutations "$TESTDIR/../data/toy_muts_no_ref.json" \
+  >   --clades "$TESTDIR/../data/toy_clades_nuc.tsv" \
+  >   --output-node-data toy_clades_1.json &>/dev/null
+
+  $ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" "$TESTDIR/../data/toy_clades_1.json" toy_clades_1.json \
+  >   --exclude-paths "root['generated_by']"
+  {}
+
+A clade which exists at the root is identified (and correctly propogated) if the root sequence
+is explicitly set.
+
+  $ ${AUGUR} clades \
+  >   --tree "$TESTDIR/../data/toy_tree.nwk" \
+  >   --mutations "$TESTDIR/../data/toy_muts_ref.json" \
+  >   --clades "$TESTDIR/../data/toy_clades_nuc.tsv" \
+  >   --output-node-data toy_clades_2a.json &>/dev/null
+
+  $ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" "$TESTDIR/../data/toy_clades_2.json" toy_clades_2a.json \
+  >   --exclude-paths "root['generated_by']"
+  {}
+
+A clade which exists at the root is identified (and correctly propogated) without a root sequence
+if the (branch leading to the) root has the clade-defining mutation.
+
+  $ ${AUGUR} clades \
+  >   --tree "$TESTDIR/../data/toy_tree.nwk" \
+  >   --mutations "$TESTDIR/../data/toy_muts_explicit_root_mutation.json" \
+  >   --clades "$TESTDIR/../data/toy_clades_nuc.tsv" \
+  >   --output-node-data toy_clades_2b.json &>/dev/null
+
+  $ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" "$TESTDIR/../data/toy_clades_2.json" toy_clades_2b.json \
+  >   --exclude-paths "root['generated_by']"
+  {}

tests/functional/clades/cram/simple.t

@@ -0,0 +1,15 @@
+Integration tests for augur clades.
+
+  $ source "$TESTDIR"/_setup.sh
+
+Test augur clades with simple Zika input files and hierarchical clades.
+
+  $ ${AUGUR} clades \
+  >   --tree "$TESTDIR/../data/tree.nwk" \
+  >   --mutations "$TESTDIR/../data/aa_muts.json" "$TESTDIR/../data/nt_muts_small.json" \
+  >   --clades "$TESTDIR/../data/clades.tsv" \
+  >   --output-node-data clades.json &>/dev/null
+
+  $ python3 "$TESTDIR/../../../../scripts/diff_jsons.py"  "$TESTDIR/../data/clades.json" clades.json \
+  >   --exclude-paths "root['generated_by']"
+  {}