From 8cac61c5184c265e2f00f3c128f3f324d565b7f6 Mon Sep 17 00:00:00 2001
From: Victor Lin <13424970+victorlin@users.noreply.github.com>
Date: Mon, 23 Sep 2024 14:51:58 -0700
Subject: [PATCH] Set pipefail in setup scripts

This was added in places where it's been necessary. Setting it in shared
setup scripts simplifies tests and allows future tests to use pipes
without the need to set pipefail explicitly.

A couple calls with non-zero exit codes have been exposed. These still
fall under expected behavior.
---
 tests/functional/_setup.sh                                       | 1 +
 tests/functional/ancestral/cram/_setup.sh                        | 1 +
 tests/functional/curate/cram/_setup.sh                           | 1 +
 tests/functional/curate/cram/validate-records.t                  | 1 -
 tests/functional/export_v2/cram/_setup.sh                        | 1 +
 tests/functional/filter/cram/_setup.sh                           | 1 +
 tests/functional/filter/cram/filter-mismatched-sequences-error.t | 1 +
 tests/functional/frequencies/cram/_setup.sh                      | 1 +
 tests/functional/merge/cram/_setup.sh                            | 1 +
 tests/functional/merge/cram/merge.t                              | 1 -
 tests/functional/parse.t                                         | 1 +
 tests/functional/refine/cram/_setup.sh                           | 1 +
 tests/functional/titers/cram/_setup.sh                           | 1 +
 tests/functional/translate/cram/_setup.sh                        | 1 +
 tests/functional/tree/cram/_setup.sh                             | 1 +
 15 files changed, 13 insertions(+), 2 deletions(-)

diff --git a/tests/functional/_setup.sh b/tests/functional/_setup.sh
index 65f24344d..f755d7e72 100644
--- a/tests/functional/_setup.sh
+++ b/tests/functional/_setup.sh
@@ -1 +1,2 @@
 export AUGUR="${AUGUR:-$TESTDIR/../../bin/augur}"
+set -o pipefail
diff --git a/tests/functional/ancestral/cram/_setup.sh b/tests/functional/ancestral/cram/_setup.sh
index 032447690..9c29b1c17 100644
--- a/tests/functional/ancestral/cram/_setup.sh
+++ b/tests/functional/ancestral/cram/_setup.sh
@@ -1 +1,2 @@
 export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
+set -o pipefail
diff --git a/tests/functional/curate/cram/_setup.sh b/tests/functional/curate/cram/_setup.sh
index 032447690..9c29b1c17 100644
--- a/tests/functional/curate/cram/_setup.sh
+++ b/tests/functional/curate/cram/_setup.sh
@@ -1 +1,2 @@
 export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
+set -o pipefail
diff --git a/tests/functional/curate/cram/validate-records.t b/tests/functional/curate/cram/validate-records.t
index f5b9bdaa2..7d00a38d7 100644
--- a/tests/functional/curate/cram/validate-records.t
+++ b/tests/functional/curate/cram/validate-records.t
@@ -25,7 +25,6 @@ error when it encounters the record with mismatched fields.
 Passing the records through multiple augur curate commands should raise the
 same error when it encounters the record with mismatched fields.
 
-  $ set -o pipefail
   $ cat records.ndjson \
   >   | ${AUGUR} curate passthru \
   >   | ${AUGUR} curate passthru \
diff --git a/tests/functional/export_v2/cram/_setup.sh b/tests/functional/export_v2/cram/_setup.sh
index 032447690..9c29b1c17 100644
--- a/tests/functional/export_v2/cram/_setup.sh
+++ b/tests/functional/export_v2/cram/_setup.sh
@@ -1 +1,2 @@
 export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
+set -o pipefail
diff --git a/tests/functional/filter/cram/_setup.sh b/tests/functional/filter/cram/_setup.sh
index 032447690..9c29b1c17 100644
--- a/tests/functional/filter/cram/_setup.sh
+++ b/tests/functional/filter/cram/_setup.sh
@@ -1 +1,2 @@
 export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
+set -o pipefail
diff --git a/tests/functional/filter/cram/filter-mismatched-sequences-error.t b/tests/functional/filter/cram/filter-mismatched-sequences-error.t
index 5930234fa..38ad9a95b 100644
--- a/tests/functional/filter/cram/filter-mismatched-sequences-error.t
+++ b/tests/functional/filter/cram/filter-mismatched-sequences-error.t
@@ -39,6 +39,7 @@ Repeat with sequence and strain outputs. We should get the same results.
   \s*0 .* (re)
   $ grep "^>" filtered.fasta | wc -l
   \s*0 (re)
+  [1]
 
 Repeat without any sequence-based filters.
 Since we expect metadata to be filtered by presence of strains in input sequences, this should produce no results because the intersection of metadata and sequences is empty.
diff --git a/tests/functional/frequencies/cram/_setup.sh b/tests/functional/frequencies/cram/_setup.sh
index 032447690..9c29b1c17 100644
--- a/tests/functional/frequencies/cram/_setup.sh
+++ b/tests/functional/frequencies/cram/_setup.sh
@@ -1 +1,2 @@
 export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
+set -o pipefail
diff --git a/tests/functional/merge/cram/_setup.sh b/tests/functional/merge/cram/_setup.sh
index 032447690..9c29b1c17 100644
--- a/tests/functional/merge/cram/_setup.sh
+++ b/tests/functional/merge/cram/_setup.sh
@@ -1 +1,2 @@
 export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
+set -o pipefail
diff --git a/tests/functional/merge/cram/merge.t b/tests/functional/merge/cram/merge.t
index d40f50e6e..87b29ad79 100644
--- a/tests/functional/merge/cram/merge.t
+++ b/tests/functional/merge/cram/merge.t
@@ -1,7 +1,6 @@
 SETUP
 
   $ source "$TESTDIR"/_setup.sh
-  $ set -o pipefail
 
 
 BASIC USAGE
diff --git a/tests/functional/parse.t b/tests/functional/parse.t
index 7e055b382..d73007507 100644
--- a/tests/functional/parse.t
+++ b/tests/functional/parse.t
@@ -107,6 +107,7 @@ This should use the first field as the id field and the metadata should not have
   - strain\tvirus\taccession\tdate\tregion\tcountry\tdivision\tcity\tdb\tsegment\tauthors\turl\ttitle\tjournal\tpaper_url (esc)
   ---
   + col1\tvirus\tcol3\tdate\tregion\tcountry\tdivision\tcity\tdb\tsegment\tauthors\turl\ttitle\tjournal\tpaper_url (esc)
+  [1]
   $ rm -f "$TMP/sequences.fasta" "$TMP/metadata.tsv"
 
 Parse compressed Zika sequences into sequences and metadata.
diff --git a/tests/functional/refine/cram/_setup.sh b/tests/functional/refine/cram/_setup.sh
index 032447690..9c29b1c17 100644
--- a/tests/functional/refine/cram/_setup.sh
+++ b/tests/functional/refine/cram/_setup.sh
@@ -1 +1,2 @@
 export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
+set -o pipefail
diff --git a/tests/functional/titers/cram/_setup.sh b/tests/functional/titers/cram/_setup.sh
index 95f4b5dda..a19898b77 100644
--- a/tests/functional/titers/cram/_setup.sh
+++ b/tests/functional/titers/cram/_setup.sh
@@ -1,2 +1,3 @@
 pushd "$TESTDIR" > /dev/null
 export AUGUR="${AUGUR:-../../../../bin/augur}"
+set -o pipefail
diff --git a/tests/functional/translate/cram/_setup.sh b/tests/functional/translate/cram/_setup.sh
index d04045ec2..e53284585 100644
--- a/tests/functional/translate/cram/_setup.sh
+++ b/tests/functional/translate/cram/_setup.sh
@@ -1,2 +1,3 @@
 export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
 export SCRIPTS="$TESTDIR/../../../../scripts"
+set -o pipefail
diff --git a/tests/functional/tree/cram/_setup.sh b/tests/functional/tree/cram/_setup.sh
index 032447690..9c29b1c17 100644
--- a/tests/functional/tree/cram/_setup.sh
+++ b/tests/functional/tree/cram/_setup.sh
@@ -1 +1,2 @@
 export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
+set -o pipefail