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| 1 | +#!/usr/bin/env cram |
| 2 | + |
| 3 | +Setup. |
| 4 | + |
| 5 | + $ [[ -n "$AWS_ACCESS_KEY_ID" && -n "$AWS_SECRET_ACCESS_KEY" ]] || exit 80 |
| 6 | + |
| 7 | + $ : "${IMAGE:=localhost:5000/nextstrain/base:latest}" |
| 8 | + $ (docker image inspect "$IMAGE" || docker image pull "$IMAGE") &>/dev/null |
| 9 | + |
| 10 | + $ export NEXTSTRAIN_AWS_BATCH_VERBOSE=0 |
| 11 | + |
| 12 | +Workdir ZIP archive is downloaded and extracted. |
| 13 | + |
| 14 | + $ export NEXTSTRAIN_AWS_BATCH_WORKDIR_URL="s3://nextstrain-tmp/$(python3 -c 'import uuid; print(uuid.uuid4())').zip" |
| 15 | + |
| 16 | + $ aws s3 cp --quiet "$TESTDIR/data/workdir-without-overlays.zip" "$NEXTSTRAIN_AWS_BATCH_WORKDIR_URL" |
| 17 | + |
| 18 | + $ docker run --rm --env=NEXTSTRAIN_AWS_BATCH_{WORKDIR_URL,VERBOSE} --env=AWS_{ACCESS_KEY_ID,SECRET_ACCESS_KEY,SESSION_TOKEN} "$IMAGE" \ |
| 19 | + > /sbin/entrypoint-aws-batch bash -euo pipefail -c 'ls -l' |
| 20 | + download: s3://nextstrain-tmp/*.zip to ../build.zip (glob) |
| 21 | + Archive: /nextstrain/build.zip |
| 22 | + extracting: reticulating |
| 23 | + extracting: splines |
| 24 | + total 0 |
| 25 | + -rw-rw-r-- 1 nextstrain nextstrain 0 Mar 10 21:46 reticulating |
| 26 | + -rw-rw-r-- 1 nextstrain nextstrain 0 Mar 10 21:46 splines |
| 27 | + upload: ../build.zip to s3://nextstrain-tmp/*.zip (glob) |
| 28 | + |
| 29 | +Overlays are handled. |
| 30 | + |
| 31 | + $ export NEXTSTRAIN_AWS_BATCH_WORKDIR_URL="s3://nextstrain-tmp/$(python3 -c 'import uuid; print(uuid.uuid4())').zip" |
| 32 | + |
| 33 | + $ aws s3 cp --quiet "$TESTDIR/data/workdir-with-augur-auspice-overlays.zip" "$NEXTSTRAIN_AWS_BATCH_WORKDIR_URL" |
| 34 | + |
| 35 | + $ docker run --rm --env=NEXTSTRAIN_AWS_BATCH_{WORKDIR_URL,VERBOSE} --env=AWS_{ACCESS_KEY_ID,SECRET_ACCESS_KEY,SESSION_TOKEN} "$IMAGE" \ |
| 36 | + > /sbin/entrypoint-aws-batch bash -euo pipefail -c 'ls -lR . ../augur ../auspice' |
| 37 | + download: s3://nextstrain-tmp/*.zip to ../build.zip (glob) |
| 38 | + removing ../augur/ for overlay |
| 39 | + removing ../auspice/ for overlay |
| 40 | + Archive: /nextstrain/build.zip |
| 41 | + extracting: reticulating |
| 42 | + extracting: splines |
| 43 | + creating: ../augur/ |
| 44 | + creating: ../augur/a/ |
| 45 | + creating: ../augur/a/b/ |
| 46 | + creating: ../augur/a/b/c/ |
| 47 | + extracting: ../augur/a/b/c/world.txt |
| 48 | + extracting: ../augur/a/b/c/hello.txt |
| 49 | + creating: ../augur/augur/ |
| 50 | + extracting: ../augur/augur/__init__.py |
| 51 | + extracting: ../augur/README.md |
| 52 | + creating: ../auspice/ |
| 53 | + .: |
| 54 | + total 0 |
| 55 | + -rw-rw-r-- 1 nextstrain nextstrain 0 Mar 10 21:46 reticulating |
| 56 | + -rw-rw-r-- 1 nextstrain nextstrain 0 Mar 10 21:46 splines |
| 57 | + |
| 58 | + ../augur: |
| 59 | + total 12 |
| 60 | + -rw-rw-r-- 1 nextstrain nextstrain 22 Mar 10 21:45 README.md |
| 61 | + drwxrwxr-x 3 nextstrain nextstrain 4096 Mar 10 21:32 a |
| 62 | + drwxrwxr-x 2 nextstrain nextstrain 4096 Mar 10 21:46 augur |
| 63 | + |
| 64 | + ../augur/a: |
| 65 | + total 4 |
| 66 | + drwxrwxr-x 3 nextstrain nextstrain 4096 Mar 10 21:32 b |
| 67 | + |
| 68 | + ../augur/a/b: |
| 69 | + total 4 |
| 70 | + drwxrwxr-x 2 nextstrain nextstrain 4096 Mar 10 21:33 c |
| 71 | + |
| 72 | + ../augur/a/b/c: |
| 73 | + total 8 |
| 74 | + -rw-rw-r-- 1 nextstrain nextstrain 6 Mar 10 21:32 hello.txt |
| 75 | + -rw-rw-r-- 1 nextstrain nextstrain 6 Mar 10 21:32 world.txt |
| 76 | + |
| 77 | + ../augur/augur: |
| 78 | + total 4 |
| 79 | + -rw-rw-r-- 1 nextstrain nextstrain 34 Mar 10 21:46 __init__.py |
| 80 | + |
| 81 | + ../auspice: |
| 82 | + total 0 |
| 83 | + upload: ../build.zip to s3://nextstrain-tmp/*.zip (glob) |
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