entrypoint-aws-batch: Remove existing /nextstrain/{augur,auspice,fauna}/ for overlays

Makes these overlays work the same on AWS Batch as they do in local
containers (Docker or Singularity): the overlays fully replace the
image's copy.  This addresses a caveat noted the Nextstrain CLI commit
adding AWS Batch overlay support¹ that was further discussed in review.²

ZIP archive directory members always end in "/", so we test only for the
presence of ../{augur,auspice,fauna}/ in the archive.  This works
consistently for workdir archives with overlays produced by Nextstrain
CLI, but it isn't foolproof for archives produced other ways.  For
example, it is possible for a ../augur/x/y/z path to be present in the
archive without ../augur/ also being present.  In that case, nothing
will be deleted.  This could be seen as a bug or a feature.

¹ <nextstrain/cli@99168ac>
² <nextstrain/cli#419 (comment)>

Author: tsibley

entrypoint-aws-batch

@@ -10,6 +10,10 @@ fi
 case "$NEXTSTRAIN_AWS_BATCH_WORKDIR_URL" in
     s3://*.zip)
         aws s3 cp --no-progress "$NEXTSTRAIN_AWS_BATCH_WORKDIR_URL" "$PWD.zip"
+        (zipinfo -1 "$PWD.zip" ../{augur,auspice,fauna}/ 2>/dev/null || true) | while read -r dir; do
+            echo "removing $dir for overlay"
+            rm -rf "$dir"
+        done
         unzip -: -o "$PWD.zip"
         ;;
     s3://*)

tests/aws-batch-workdir-url.t

@@ -0,0 +1,83 @@
+#!/usr/bin/env cram
+
+Setup.
+
+  $ [[ -n "$AWS_ACCESS_KEY_ID" && -n "$AWS_SECRET_ACCESS_KEY" ]] || exit 80
+
+  $ : "${IMAGE:=localhost:5000/nextstrain/base:latest}"
+  $ (docker image inspect "$IMAGE" || docker image pull "$IMAGE") &>/dev/null
+
+  $ export NEXTSTRAIN_AWS_BATCH_VERBOSE=0
+
+Workdir ZIP archive is downloaded and extracted.
+
+  $ export NEXTSTRAIN_AWS_BATCH_WORKDIR_URL="s3://nextstrain-tmp/$(python3 -c 'import uuid; print(uuid.uuid4())').zip"
+
+  $ aws s3 cp --quiet "$TESTDIR/data/workdir-without-overlays.zip" "$NEXTSTRAIN_AWS_BATCH_WORKDIR_URL"
+
+  $ docker run --rm --env=NEXTSTRAIN_AWS_BATCH_{WORKDIR_URL,VERBOSE} --env=AWS_{ACCESS_KEY_ID,SECRET_ACCESS_KEY,SESSION_TOKEN} "$IMAGE" \
+  >   /sbin/entrypoint-aws-batch bash -euo pipefail -c 'ls -l'
+  download: s3://nextstrain-tmp/*.zip to ../build.zip (glob)
+  Archive:  /nextstrain/build.zip
+   extracting: reticulating            
+   extracting: splines                 
+  total 0
+  -rw-rw-r-- 1 nextstrain nextstrain 0 Mar 10 21:46 reticulating
+  -rw-rw-r-- 1 nextstrain nextstrain 0 Mar 10 21:46 splines
+  upload: ../build.zip to s3://nextstrain-tmp/*.zip (glob)
+
+Overlays are handled.
+
+  $ export NEXTSTRAIN_AWS_BATCH_WORKDIR_URL="s3://nextstrain-tmp/$(python3 -c 'import uuid; print(uuid.uuid4())').zip"
+
+  $ aws s3 cp --quiet "$TESTDIR/data/workdir-with-augur-auspice-overlays.zip" "$NEXTSTRAIN_AWS_BATCH_WORKDIR_URL"
+
+  $ docker run --rm --env=NEXTSTRAIN_AWS_BATCH_{WORKDIR_URL,VERBOSE} --env=AWS_{ACCESS_KEY_ID,SECRET_ACCESS_KEY,SESSION_TOKEN} "$IMAGE" \
+  >   /sbin/entrypoint-aws-batch bash -euo pipefail -c 'ls -lR . ../augur ../auspice'
+  download: s3://nextstrain-tmp/*.zip to ../build.zip (glob)
+  removing ../augur/ for overlay
+  removing ../auspice/ for overlay
+  Archive:  /nextstrain/build.zip
+   extracting: reticulating            
+   extracting: splines                 
+     creating: ../augur/
+     creating: ../augur/a/
+     creating: ../augur/a/b/
+     creating: ../augur/a/b/c/
+   extracting: ../augur/a/b/c/world.txt  
+   extracting: ../augur/a/b/c/hello.txt  
+     creating: ../augur/augur/
+   extracting: ../augur/augur/__init__.py  
+   extracting: ../augur/README.md      
+     creating: ../auspice/
+  .:
+  total 0
+  -rw-rw-r-- 1 nextstrain nextstrain 0 Mar 10 21:46 reticulating
+  -rw-rw-r-- 1 nextstrain nextstrain 0 Mar 10 21:46 splines
+  
+  ../augur:
+  total 12
+  -rw-rw-r-- 1 nextstrain nextstrain   22 Mar 10 21:45 README.md
+  drwxrwxr-x 3 nextstrain nextstrain 4096 Mar 10 21:32 a
+  drwxrwxr-x 2 nextstrain nextstrain 4096 Mar 10 21:46 augur
+  
+  ../augur/a:
+  total 4
+  drwxrwxr-x 3 nextstrain nextstrain 4096 Mar 10 21:32 b
+  
+  ../augur/a/b:
+  total 4
+  drwxrwxr-x 2 nextstrain nextstrain 4096 Mar 10 21:33 c
+  
+  ../augur/a/b/c:
+  total 8
+  -rw-rw-r-- 1 nextstrain nextstrain 6 Mar 10 21:32 hello.txt
+  -rw-rw-r-- 1 nextstrain nextstrain 6 Mar 10 21:32 world.txt
+  
+  ../augur/augur:
+  total 4
+  -rw-rw-r-- 1 nextstrain nextstrain 34 Mar 10 21:46 __init__.py
+  
+  ../auspice:
+  total 0
+  upload: ../build.zip to s3://nextstrain-tmp/*.zip (glob)