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fix(tests): Fix false negative cram tests #1666

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fix(tests): Fix false negative cram tests #1666

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8aa5ead
Warn against some misuse of regex paths
corneliusroemer Nov 9, 2024
e596b50
fix type error
corneliusroemer Nov 9, 2024
21d2227
Add `root['meta']['updated']` to default exclude paths to simplify di…
corneliusroemer Nov 9, 2024
7c99d29
Use exclude-paths over exclude-regex-paths when possible
corneliusroemer Nov 9, 2024
75c7976
Fix #1665
corneliusroemer Nov 9, 2024
9327a7d
Fix small error when refactoring
corneliusroemer Nov 9, 2024
11587e5
Actual output changed but this was hidden by tests being broken, @jam…
corneliusroemer Nov 9, 2024
bd8d892
Save some lines in test files by excluding all generated_by by default
corneliusroemer Nov 9, 2024
ba3c43f
Another test failure that was masked, should be double checked but se…
corneliusroemer Nov 9, 2024
6b55555
Add changelog entry
corneliusroemer Nov 9, 2024
3dacd2d
Add warning to dev docs
corneliusroemer Nov 9, 2024
27d18b4
Update scripts/diff_jsons.py
corneliusroemer Nov 12, 2024
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3 changes: 3 additions & 0 deletions CHANGES.md
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Expand Up @@ -11,10 +11,13 @@

* index: Previously specifying a directory that does not exist in the path to `--output` would result in an incorrect error stating that the input file does not exist. It now shows the correct path responsible for the error. [#1644][] (@victorlin)
* curate format-dates: Update help docs and improve failure messages to show use of `--expected-date-formats`. [#1653][] (@joverlee521)
* tests: Fix false negative tests due to incorrect use of DeepDiff's `--exclude-regex-path` option. [#1665][] [#1666][] (@corneliusroemer)

[#1644]: https://github.com/nextstrain/augur/issues/1644
[#1653]: https://github.com/nextstrain/augur/pull/1653
[#1656]: https://github.com/nextstrain/augur/pull/1656
[#1665]: https://github.com/nextstrain/augur/issues/1665
[#1666]: https://github.com/nextstrain/augur/pull/1666

## 26.0.0 (17 September 2024)

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2 changes: 2 additions & 0 deletions docs/contribute/DEV_DOCS.md
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Expand Up @@ -89,6 +89,8 @@ To compare JSON outputs with stochastic numerical values, use `scripts/diff_json

Both tree and JSON comparison scripts rely on [deepdiff](https://deepdiff.readthedocs.io/en/latest/) for underlying comparisons.

When using `diff_jsons.py`'s `--exclude-regex-paths` argument, make sure to escape any special regex characters, in particular square brackets: do this `\['seqid'\]`, not this `['seqid']`. See [#1655](https://github.com/nextstrain/augur/issues/1665) for what happens if you don't.

#### When to use which type of test

1. Unit tests should be used for the [public API](https://docs.nextstrain.org/projects/augur/en/stable/api/public/index.html).
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13 changes: 12 additions & 1 deletion scripts/diff_jsons.py
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Expand Up @@ -3,6 +3,7 @@
import argparse
import deepdiff
import json
import re

from augur.argparse_ import ExtendOverwriteDefault

Expand All @@ -15,12 +16,22 @@
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']", "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)")

args = parser.parse_args()

# Test for most fatal errors in regex path usage
# Exclude regexes should never match `'`, otherwise the diff is always going to pass
Comment on lines +25 to +26
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Should this include " as well? I'm assuming root['generated_by'] and root["generated_by"] are both valid.

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I think that the path that deep diff uses to match against uses a single quote not double quote. Hence excluding only single quote. Does that make sense?

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I just tested with both ['seqid'] and ["seqid"]:

   $ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" "$TESTDIR/../data/clades.json" clades_no-labels.json --exclude-regex-paths "['seqid']"
-  {'dictionary_item_removed': [root['branches']]}
+  Traceback (most recent call last):
+    File "/Users/vlin/Dropbox/repos/nextstrain/augur/tests/functional/clades/cram/../../../../scripts/diff_jsons.py", line 30, in <module>
+      raise Exception(
+  Exception: Exclude regex ['seqid'] matches `'` which means this diff will always pass which is probably not what you want.
+  You probably forgot to escape something in your regex. See for example: https://stackoverflow.com/a/79173188/7483211
+  [1]
   $ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" "$TESTDIR/../data/clades.json" clades_no-labels.json --exclude-regex-paths '["seqid"]'
-  {'dictionary_item_removed': [root['branches']]}
+  {}

It looks like " should get the same treatment.

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Ah yeah, there's a bunch more things that should not not be allowed to be matched, things like [ and ] and any single letter. But in a way it's not super clearcut as someone might want to exclude everything but a single path (they should use an include path instead then) - so I don't know how far we want to go here. Including " sounds good though, no harm I can see.

for regex in args.exclude_regex_paths or []:
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nit

Adding or [] (e596b50) doesn't seem useful:

  • We don't run mypy/pyright on this file
  • A better solution would be to set default=[] on add_argument()

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@corneliusroemer corneliusroemer Nov 12, 2024 •
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Just because we don't run mypy doesn't mean that we shouldn't prevent type errors from happening? The error actually happens irrespective of running mypy. It's not mypy erroring it's a real runtime error.

Why is changing the defaults better?

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Why is changing the defaults better?

Setting the default up top allows for a valid assumption that args.exclude_regex_paths is always iterable. Otherwise we would have to do another args.exclude_regex_paths or [] if using it as an iterable somewhere else in the code for whatever reason.

result = re.compile(regex).search("'")
if result is not None:
print(
f"Exclude regex {regex} matches `'` which means this diff will always pass which is probably not what you want.\n"
"You probably forgot to escape something in your regex. See for example: https://stackoverflow.com/a/79173188/7483211"
)
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with open(args.first_json, "r") as fh:
first_json = json.load(fh)

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2 changes: 1 addition & 1 deletion tests/functional/ancestral/cram/ambiguous-positions.t
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Expand Up @@ -36,7 +36,7 @@ Setup

$ python3 "$SCRIPTS/diff_jsons.py" \
> expected.json "nt_muts.json" \
> --exclude-regex-paths "root\['annotations'\]" "root\['generated_by'\]" "root\['reference'\]"
> --exclude-paths "annotations" "generated_by" "reference"
{}

$ python3 "$SCRIPTS/compare-json-vcf.py" \
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6 changes: 2 additions & 4 deletions tests/functional/ancestral/cram/case-sensitive.t
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Expand Up @@ -15,8 +15,7 @@ Change the _reference_ to lowercase

$ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" \
> "$TESTDIR/../data/simple-genome/nt_muts.ref-seq.json" \
> "nt_muts.ref-seq.json" \
> --exclude-paths "root['generated_by']"
> "nt_muts.ref-seq.json"
{}


Expand All @@ -37,6 +36,5 @@ be lowecase which will be compared against the uppercase reference

$ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" \
> "$TESTDIR/../data/simple-genome/nt_muts.ref-seq.json" \
> "nt_muts.ref-seq.json" \
> --exclude-paths "root['generated_by']"
> "nt_muts.ref-seq.json"
{}
6 changes: 2 additions & 4 deletions tests/functional/ancestral/cram/general.t
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Expand Up @@ -19,8 +19,7 @@ node-data JSON we diff against.

$ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" \
> "$TESTDIR/../data/simple-genome/nt_muts.ref-seq.json" \
> "nt_muts.ref-seq.json" \
> --exclude-paths "root['generated_by']"
> "nt_muts.ref-seq.json"
{}

Same as above but without providing a `--root-sequence`. The effect of this on behaviour is:
Expand All @@ -39,6 +38,5 @@ mutations (as there's nothing to compare the root node to)

$ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" \
> "$TESTDIR/../data/simple-genome/nt_muts.no-ref-seq.json" \
> "nt_muts.no-ref-seq.json" \
> --exclude-paths "root['generated_by']"
> "nt_muts.no-ref-seq.json"
{}
2 changes: 1 addition & 1 deletion tests/functional/ancestral/cram/infer-amino-acid-sequences-with-root-sequence.t
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Expand Up @@ -20,7 +20,7 @@ ancestor).
Check that the reference length was correctly exported as the nuc annotation

$ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" \
> --exclude-regex-paths "['seqid']" -- \
> --exclude-regex-paths "\['seqid'\]" -- \
> "$TESTDIR/../data/ancestral_mutations_with_root_sequence.json" \
> "$CRAMTMP/$TESTFILE/ancestral_mutations.json"
{}
2 changes: 1 addition & 1 deletion tests/functional/ancestral/cram/vcf-multi-allele.t
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion tests/functional/ancestral/cram/vcf.t
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Expand Up @@ -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,
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8 changes: 6 additions & 2 deletions tests/functional/ancestral/data/ancestral_mutations_with_root_sequence.json
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Large diffs are not rendered by default.

3 changes: 1 addition & 2 deletions tests/functional/clades/cram/membership-and-label.t
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Expand Up @@ -13,6 +13,5 @@ Test custom membership key + label key. The only change should be the key names

$ 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']"
$ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" "$TESTDIR/../data/clades.json" clades_sed.json
{}
3 changes: 1 addition & 2 deletions tests/functional/clades/cram/no-label.t
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Expand Up @@ -11,6 +11,5 @@ Test the ability to _not_ export a branch label (same logic as not exporting the
> --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']"
$ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" "$TESTDIR/../data/clades.json" clades_no-labels.json
{'dictionary_item_removed': [root['branches']]}
9 changes: 3 additions & 6 deletions tests/functional/clades/cram/root-clade-identification.t
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Expand Up @@ -12,8 +12,7 @@ This is an oversight and ideally would be fixed
> --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']"
$ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" "$TESTDIR/../data/toy_clades_1.json" toy_clades_1.json
{}

A clade which exists at the root is identified (and correctly propogated) if the root sequence
Expand All @@ -25,8 +24,7 @@ is explicitly set.
> --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']"
$ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" "$TESTDIR/../data/toy_clades_2.json" toy_clades_2a.json
{}

A clade which exists at the root is identified (and correctly propogated) without a root sequence
Expand All @@ -38,6 +36,5 @@ if the (branch leading to the) root has the clade-defining mutation.
> --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']"
$ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" "$TESTDIR/../data/toy_clades_2.json" toy_clades_2b.json
{}
2 changes: 1 addition & 1 deletion tests/functional/refine/cram/not-timetree-mutations-per-site.t
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Expand Up @@ -28,5 +28,5 @@ Confirm that trees match expected topology and branch lengths, given that the ou
> "$TESTDIR/../data/mutations_per_site_branch_lengths.json" \
> branch_lengths.json \
> --significant-digits 0 \
> --exclude-paths "root['generated_by']['version']" "root['input_tree']"
> --exclude-paths "generated_by" "input_tree"
{}
2 changes: 1 addition & 1 deletion tests/functional/refine/cram/not-timetree-mutations.t
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Expand Up @@ -29,5 +29,5 @@ Confirm that trees match expected topology and branch lengths, given that the ou
> "$TESTDIR/../data/integer_branch_lengths.json" \
> branch_lengths.json \
> --significant-digits 0 \
> --exclude-paths "root['generated_by']['version']" "root['input_tree']" "root['alignment']"
> --exclude-paths "generated_by" "input_tree" "alignment"
{}
4 changes: 2 additions & 2 deletions tests/functional/translate/cram/general.t
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Expand Up @@ -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,
Expand All @@ -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\['annotations'\]\['.+'\]\['(seqid|type)'\]"
{}
11 changes: 5 additions & 6 deletions tests/functional/translate/cram/genes.t
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Expand Up @@ -21,9 +21,9 @@ as a feature ('nuc' in this case)
amino acid mutations written to .+ (re)

$ python3 "$SCRIPTS/diff_jsons.py" \
> "$DATA/aa_muts.json" \
> "aa_muts.genes-args.json" \
> --exclude-regex-paths "seqid" "gene1" "root['meta']['updated']"
> "$DATA/aa_muts.json" \
> "aa_muts.genes-args.json" \
> --exclude-regex-paths "seqid" "gene1"
{}
Using a text file rather than command line arguments

Expand All @@ -43,7 +43,6 @@ Using a text file rather than command line arguments
amino acid mutations written to .+ (re)

$ python3 "$SCRIPTS/diff_jsons.py" \
> "aa_muts.genes-args.json" \
> "aa_muts.genes-txt.json" \
> --exclude-paths "root['meta']['updated']"
> "aa_muts.genes-args.json" \
> "aa_muts.genes-txt.json"
{}
2 changes: 1 addition & 1 deletion tests/functional/translate/cram/gff.t
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion tests/functional/translate/cram/root-mutations.t
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Expand Up @@ -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'}}
2 changes: 1 addition & 1 deletion tests/functional/translate/cram/translate-with-genbank.t
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Expand Up @@ -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\['annotations'\]\['.+'\]\['seqid'\]"
{}
2 changes: 1 addition & 1 deletion tests/functional/translate/cram/translate-with-gff-and-gene-name.t
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Expand Up @@ -26,7 +26,7 @@ Other than the sequence ids which will include a temporary path, the JSONs
should be identical.

$ python3 "${SCRIPTS}/diff_jsons.py" \
> --exclude-regex-paths "['seqid']" -- \
> --exclude-regex-paths "\['seqid'\]" -- \
> "${DATA}/zika/aa_muts_gff.json" \
> aa_muts.json
{}
2 changes: 1 addition & 1 deletion tests/functional/translate/cram/translate-with-gff-and-gene.t
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Expand Up @@ -23,7 +23,7 @@ Translate amino acids for genes using a GFF3 file where the gene names are store
amino acid mutations written to .* (re)

$ python3 "${SCRIPTS}/diff_jsons.py" \
> --exclude-regex-paths "['seqid']" -- \
> --exclude-regex-paths "\['seqid'\]" -- \
> "${DATA}/zika/aa_muts_gff.json" \
> aa_muts.json
{}
2 changes: 1 addition & 1 deletion tests/functional/translate/cram/translate-with-gff-and-locus-tag.t
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Expand Up @@ -23,7 +23,7 @@ This is an identical test setup as `translate-with-gff-and-gene.t` but using loc
amino acid mutations written to .* (re)

$ python3 "${SCRIPTS}/diff_jsons.py" \
> --exclude-regex-paths "['seqid']" -- \
> --exclude-regex-paths "\['seqid'\]" -- \
> "${DATA}/zika/aa_muts_gff.json" \
> aa_muts.json
{}
2 changes: 1 addition & 1 deletion tests/functional/translate/cram/vcf-with-root-mutation.t
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Expand Up @@ -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\['annotations'\]\['.+'\]\['seqid'\]"
{}
2 changes: 1 addition & 1 deletion tests/functional/translate/cram/vcf.t
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Expand Up @@ -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 ----------------------------------
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14 changes: 12 additions & 2 deletions tests/functional/translate/data/zika/aa_muts_gff.json
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Original file line number Diff line number Diff line change
Expand Up @@ -13,11 +13,18 @@
"start": 457,
"strand": "+",
"type": "gene"
},
"nuc": {
"end": 10769,
"seqid": "genemap.gff",
"start": 1,
"strand": "+",
"type": "##sequence-region pragma"
}
},
"generated_by": {
"program": "augur",
"version": "16.0.3"
"version": "26.0.0"
},
"nodes": {
"BRA/2016/FC_6706": {
Expand Down Expand Up @@ -91,7 +98,10 @@
}
},
"NODE_0000006": {
"aa_muts": {},
"aa_muts": {
"CA": [],
"PRO": []
},
"aa_sequences": {
"CA": "MKNPKKKSGGFRIVNMLKRGVARVSPFGGLKRLPAGLLLGHGPIRMVLAILAFLRFTAIKPSLGLINRWGSVGKKEAMEIIKKFKKDLAAMLRIINARKEKKRRGADTSVGIVGLLLTTAMA",
"PRO": "AEVTRRGSAYYMYLDRNDAGEAISFPTTLGMNKCYIQIMDLGHMCDATMSYECPMLDEGVEPDDVDCWCNTTSTWVVYGTCHHKKGEARRSRR"
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