Add root['meta']['updated'] to default exclude paths to simplify di…

…ff_jsons.py invocations

scripts/diff_jsons.py

@@ -16,7 +16,7 @@
     parser.add_argument("first_json", help="first JSON to compare")
     parser.add_argument("second_json", help="second JSON to compare")
     parser.add_argument("--significant-digits", type=int, default=5, help="number of significant digits to use when comparing numeric values")
-    parser.add_argument("--exclude-paths", nargs="+", action=ExtendOverwriteDefault, help="list of paths to exclude from consideration when performing a diff", default=["root['generated_by']['version']"])
+    parser.add_argument("--exclude-paths", nargs="+", action=ExtendOverwriteDefault, help="list of paths to exclude from consideration when performing a diff", default=["root['generated_by']['version']", "root['meta']['updated']"])
     parser.add_argument("--exclude-regex-paths", nargs="+", action="extend", help="list of path regular expressions to exclude from consideration when performing a diff")
     parser.add_argument("--ignore-numeric-type-changes", action="store_true", help="ignore numeric type changes in the diff (e.g., int of 1 to float of 1.0)")
 

tests/functional/ancestral/cram/vcf-multi-allele.t

@@ -24,7 +24,7 @@ See <https://github.com/nextstrain/augur/issues/1380> for the bug this is testin
   $ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" \
   >   "$DATA/nt_muts.ref-seq.json" \
   >   nt_muts.json \
-  >   --exclude-regex-paths "root\['nodes'\]\['.+'\]\['sequence'\]" "root\['generated_by'\]"
+  >   --exclude-regex-paths "root\['nodes'\]\['.+'\]\['sequence'\]"
   {'iterable_item_added': {"root['nodes']['sample_B']['muts'][0]": 'A30G'}}
 
   $ cat > expected.vcf <<EOF

tests/functional/ancestral/cram/vcf.t

@@ -21,7 +21,7 @@ but it will have the reference sequence attached.
   $ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" \
   >   "$DATA/nt_muts.ref-seq.json" \
   >   "nt_muts.vcf-input.ref-seq.json" \
-  >   --exclude-regex-paths "root\['nodes'\]\['.+'\]\['sequence'\]" "root\['generated_by'\]"
+  >   --exclude-regex-paths "root\['nodes'\]\['.+'\]\['sequence'\]"
   {}
 
 Here's the same mutations as in $DATA/nt_muts.ref-seq.json,

tests/functional/translate/cram/general.t

@@ -18,7 +18,7 @@ which validate the output will fail as it's missing a 'nuc' annotation.
   $ python3 "$SCRIPTS/diff_jsons.py" \
   >   "$DATA/aa_muts.json" \
   >   "aa_muts.json" \
-  >   --exclude-regex-paths "root\['annotations'\]\['.+'\]\['seqid'\]" "root['meta']['updated']" 
+  >   --exclude-regex-paths "root\['annotations'\]\['.+'\]\['seqid'\]"
   {}
 
 Same as above but using a GenBank file. This changes the 'type' of the annotations,
@@ -33,5 +33,5 @@ but this is irrelevant for Auspice's use and simply reflects the reference sourc
   $ python3 "$SCRIPTS/diff_jsons.py" \
   >   "$DATA/aa_muts.json" \
   >   "aa_muts.genbank.json" \
-  >   --exclude-regex-paths "root\['annotations'\]\['.+'\]\['seqid'\]" "root\['annotations'\]\['.+'\]\['type'\]" "root['meta']['updated']" 
+  >   --exclude-regex-paths "root\['annotations'\]\['.+'\]\['(seqid|type)'\]"
   {}

tests/functional/translate/cram/genes.t

@@ -23,7 +23,7 @@ as a feature ('nuc' in this case)
   $ python3 "$SCRIPTS/diff_jsons.py" \
   >   "$DATA/aa_muts.json" \
   >   "aa_muts.genes-args.json" \
-  >   --exclude-regex-paths "seqid" "gene1" "root['meta']['updated']"
+  >   --exclude-regex-paths "seqid" "gene1"
   {}
 Using a text file rather than command line arguments
 
@@ -45,5 +45,4 @@ Using a text file rather than command line arguments
   $ python3 "$SCRIPTS/diff_jsons.py" \
   >   "aa_muts.genes-args.json" \
   >   "aa_muts.genes-txt.json" \
-  > --exclude-paths "root['meta']['updated']"
   {}

tests/functional/translate/cram/gff.t

@@ -77,7 +77,7 @@ GFF file with 'region' removed, so the only genome information is the ##sequence
   $ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" \
   >   "$DATA/aa_muts.json" \
   >   "aa_muts.pragma-only.json" \
-  >   --exclude-regex-paths "root\['annotations'\]\['.+'\]\['seqid'\]" "root['meta']['updated']"
+  >   --exclude-regex-paths "root\['annotations'\]\['.+'\]\['seqid'\]"
   {}
 
 GFF file with no genome coordinate information

tests/functional/translate/cram/root-mutations.t

@@ -27,5 +27,5 @@ is unchanged (MPCG*). There is also a mutation E4G at the root node to compensat
   $ python3 "$SCRIPTS/diff_jsons.py" \
   >   "$DATA/aa_muts.json" \
   >   "aa_muts.json" \
-  >   --exclude-regex-paths "root\['annotations'\]\['.+'\]\['seqid'\]" "root['meta']['updated']"
+  >   --exclude-regex-paths "root\['annotations'\]\['.+'\]\['seqid'\]"
   {'values_changed': {"root['reference']['gene1']": {'new_value': 'MPCE*', 'old_value': 'MPCG*'}}, 'iterable_item_added': {"root['nodes']['node_root']['aa_muts']['gene1'][0]": 'E4G'}}

tests/functional/translate/cram/translate-with-genbank.t

@@ -18,5 +18,5 @@ Translate amino acids for genes using a GenBank file.
   amino acid mutations written to .* (re)
 
   $ python3 "$SCRIPTS/diff_jsons.py" $DATA/zika/aa_muts_genbank.json aa_muts.json \
-  >  --exclude-regex-paths "root\['annotations'\]\['.+'\]\['seqid'\]" "root['meta']['updated']"
+  >  --exclude-regex-paths "root\['annotations'\]\['.+'\]\['seqid'\]"
   {}

tests/functional/translate/cram/vcf-with-root-mutation.t

@@ -43,5 +43,5 @@ node is E (and so are all the other nodes))
   $ python3 "$SCRIPTS/diff_jsons.py" \
   >   aa_muts.truth.json \
   >   aa_muts.json \
-  >   --exclude-regex-paths "root\['annotations'\]\['.+'\]\['seqid'\]" "root['meta']['updated']"
+  >   --exclude-regex-paths "root\['annotations'\]\['.+'\]\['seqid'\]"
   {}

tests/functional/translate/cram/vcf.t

@@ -26,7 +26,7 @@ Setup
   $ python3 "$SCRIPTS/diff_jsons.py" \
   >   "$DATA/aa_muts.json" \
   >   aa_muts.json \
-  >   --exclude-regex-paths "root\['annotations'\]\['.+'\]\['seqid'\]" "root['meta']['updated']"
+  >   --exclude-regex-paths "root\['annotations'\]\['.+'\]\['seqid'\]"
   {}
 
 ------------------------------   MISSING TEST   ----------------------------------