From 7883082fdc38313d61a1b4e6940bace3bdcf158c Mon Sep 17 00:00:00 2001
From: jmoore <josh@glencoesoftware.com>
Date: Tue, 27 Apr 2021 21:30:36 +0200
Subject: [PATCH] Fix retcode and properly test shape

---
 environment.yml                                    |  3 +--
 generate_data/jzarr/generate_data.sh               | 14 +++++++++++---
 .../main/java/zarr_implementations/jzarr/App.java  |  6 +++---
 3 files changed, 15 insertions(+), 8 deletions(-)

diff --git a/environment.yml b/environment.yml
index 117263cb..87f38352 100644
--- a/environment.yml
+++ b/environment.yml
@@ -11,7 +11,7 @@ dependencies:
   - zlib
   - blosc
   - nodejs
-  - z5py >= 2.0.10
+  - z5py
   - python == 3.7.9
   - scikit-image
   - pytest
@@ -20,5 +20,4 @@ dependencies:
   - pandas
   - tabulate
   - pip:
-      - pyn5
       - git+https://github.com/grlee77/zarrita.git@codec_update
diff --git a/generate_data/jzarr/generate_data.sh b/generate_data/jzarr/generate_data.sh
index 2bbcd7f5..c6aa8268 100755
--- a/generate_data/jzarr/generate_data.sh
+++ b/generate_data/jzarr/generate_data.sh
@@ -2,8 +2,16 @@
 # https://stackoverflow.com/a/6393573/2700168
 cd "${0%/*}"
 
+set -e
+set -u
+set -x
+
 mvn clean package
-java -cp target/jzarr-1.0.0.jar zarr_implementations.jzarr.App "$@"
+java -cp target/jzarr-1.0.0.jar zarr_implementations.jzarr.App "$@" && {
+    # Workaround for: https://github.com/bcdev/jzarr/issues/25
+    find ../../data/jzarr* -name .zarray -exec sed -ibak 's/>u1/|u1/' {} \;
+} || {
+    echo jzarr failed
+    exit 2
+}
 
-# Workaround for: https://github.com/bcdev/jzarr/issues/25
-find ../../data/jzarr* -name .zarray -exec sed -ibak 's/>u1/|u1/' {} \;
diff --git a/generate_data/jzarr/src/main/java/zarr_implementations/jzarr/App.java b/generate_data/jzarr/src/main/java/zarr_implementations/jzarr/App.java
index 1b65b6e7..61bc2503 100644
--- a/generate_data/jzarr/src/main/java/zarr_implementations/jzarr/App.java
+++ b/generate_data/jzarr/src/main/java/zarr_implementations/jzarr/App.java
@@ -78,10 +78,10 @@ public static void main(String args[]) throws Exception {
             String dsname = args[2];
             ZarrArray verification = ZarrGroup.open(fpath).openArray(dsname);
             int[] shape = verification.getShape();
-            if (!Arrays.equals(new int[]{}, shape)) {
+            if (!Arrays.equals(SHAPE, shape)) {
                 throw new RuntimeException(String.format(
-                            "shape-mismatch expected:{} found:{}",
-                            SHAPE, shape
+                            "shape-mismatch expected:%s found:%s",
+                            Arrays.toString(SHAPE), Arrays.toString(shape)
                 ));
             }
             return;  // EARLY EXIT