From 14ff471f06dfa7ac3fbde09f7642010129c89754 Mon Sep 17 00:00:00 2001
From: jmoore <josh@glencoesoftware.com>
Date: Fri, 17 Sep 2021 09:31:47 +0200
Subject: [PATCH 1/3] Enable ZarrReader tests

This script downloads the latest bftools.zip script,
checks out the latest ZarrReader code, builds it,
and launches the two together against each of the
sources defined.
---
 scripts/zarr_reader_open | 15 +++++++++++++++
 suites.yml               |  3 +++
 2 files changed, 18 insertions(+)
 create mode 100755 scripts/zarr_reader_open

diff --git a/scripts/zarr_reader_open b/scripts/zarr_reader_open
new file mode 100755
index 0000000..1fde92f
--- /dev/null
+++ b/scripts/zarr_reader_open
@@ -0,0 +1,15 @@
+#!/usr/bin/env bash
+set -e
+set -u
+
+
+test -e bftools || {
+    test -e bftools.zip || wget https://downloads.openmicroscopy.org/bio-formats/latest/artifacts/bftools.zip
+    unzip bftools
+}
+
+test -e ZarrReader  || git clone git://github.com/ome/ZarrReader 1>&2
+cd ZarrReader
+mvn package -DskipTests # 1>&2
+cd ..
+env BF_CP=ZarrReader/target/*.jar bftools/showinf -nopix "$@"
diff --git a/suites.yml b/suites.yml
index 1079cdc..666e18d 100644
--- a/suites.yml
+++ b/suites.yml
@@ -7,3 +7,6 @@
 
 - name: checksum
   script: zarr_checksum
+
+- name: reader
+  script: zarr_reader_open

From 2d4d55e5d1150ddee2a5c479d4bf204c71bb711d Mon Sep 17 00:00:00 2001
From: jmoore <josh@glencoesoftware.com>
Date: Sun, 19 Sep 2021 17:19:26 +0200
Subject: [PATCH 2/3] Passing zarr_reader_open

 * append `.zattrs` to all .zarr arguments
 * define INVOCATION_DIR to speed up tests
---
 scripts/zarr_reader_open | 27 +++++++++++++++++++++------
 test_suite.py            |  4 +++-
 2 files changed, 24 insertions(+), 7 deletions(-)

diff --git a/scripts/zarr_reader_open b/scripts/zarr_reader_open
index 1fde92f..4f8190b 100755
--- a/scripts/zarr_reader_open
+++ b/scripts/zarr_reader_open
@@ -1,15 +1,30 @@
 #!/usr/bin/env bash
+
 set -e
 set -u
+set -x
+
 
+echo =======================
+echo Current Directory: $PWD
+echo Invocation Directory: ${INVOCATION_DIR}
+echo =======================
 
-test -e bftools || {
+# Install bftools if missing
+test -e ${INVOCATION_DIR}/bftools || {
+    pushd ${INVOCATION_DIR}
     test -e bftools.zip || wget https://downloads.openmicroscopy.org/bio-formats/latest/artifacts/bftools.zip
     unzip bftools
+    popd
+}
+
+# Build ZarrReader if not built
+test -e ${INVOCATION_DIR}/ZarrReader  || {
+    git clone git://github.com/ome/ZarrReader ${INVOCATION_DIR}/ZarrReader
+    pushd ${INVOCATION_DIR}ZarrReader
+    mvn package -DskipTests # 1>&2
+    popd
 }
 
-test -e ZarrReader  || git clone git://github.com/ome/ZarrReader 1>&2
-cd ZarrReader
-mvn package -DskipTests # 1>&2
-cd ..
-env BF_CP=ZarrReader/target/*.jar bftools/showinf -nopix "$@"
+export BF_CP=${INVOCATION_DIR}/ZarrReader/target/\*
+${INVOCATION_DIR}/bftools/showinf -nopix "$@"/.zattrs
diff --git a/test_suite.py b/test_suite.py
index b5ebb8f..9d3fcbf 100644
--- a/test_suite.py
+++ b/test_suite.py
@@ -180,7 +180,9 @@ def source(request: SubRequest, tmpdir: py.path.local) -> typing.Iterator[Source
 def suite(request: SubRequest, tmpdir: os.PathLike) -> typing.Iterator[Suite]:
     doc = request.param
     script = doc["script"]
-    script = f"{request.config.invocation_dir}/scripts/{script}"
+    idir = f"{request.config.invocation_dir}"
+    os.environ["INVOCATION_DIR"] = idir
+    script = f"{idir}/scripts/{script}"
     yield Suite(script)
 
 

From 7ed18c764d9cc86dc42030783bedbf9ff06845a5 Mon Sep 17 00:00:00 2001
From: jmoore <josh@glencoesoftware.com>
Date: Sun, 19 Sep 2021 18:13:09 +0200
Subject: [PATCH 3/3] Set format to prevent long searches over HTTP

---
 scripts/zarr_reader_open | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/scripts/zarr_reader_open b/scripts/zarr_reader_open
index 4f8190b..0072d7f 100755
--- a/scripts/zarr_reader_open
+++ b/scripts/zarr_reader_open
@@ -4,6 +4,7 @@ set -e
 set -u
 set -x
 
+export INVOCATION_DIR=${INVOCATION_DIR:-$PWD}
 
 echo =======================
 echo Current Directory: $PWD
@@ -27,4 +28,4 @@ test -e ${INVOCATION_DIR}/ZarrReader  || {
 }
 
 export BF_CP=${INVOCATION_DIR}/ZarrReader/target/\*
-${INVOCATION_DIR}/bftools/showinf -nopix "$@"/.zattrs
+${INVOCATION_DIR}/bftools/showinf -format Zarr -nopix "$@"/.zattrs