moved get and clean to scripts

Author: bendhouseart

.gitmodules

@@ -2,12 +2,12 @@
 	path = bids-specification
 	url = https://github.com/bids-standard/bids-specification
 	branch = master
-[submodule "test/test_data/petdicoms"]
-	path = test/test_data/petdicoms
-	url = https://github.com/openneuropet/petdicoms.git
 [submodule "test/test_data/dcm_qa_nih"]
 	path = test/test_data/dcm_qa_nih
 	url = https://github.com/neurolabusc/dcm_qa_nih.git
 [submodule "test/test_data/dcm_qa_uih"]
 	path = test/test_data/dcm_qa_uih
 	url = https://github.com/neurolabusc/dcm_qa_uih.git
+[submodule "test/test_data/petdicoms"]
+	path = test/test_data/petdicoms
+	url = https://github.com/openneuropet/petdicoms.git

Makefile

@@ -6,32 +6,8 @@ test/test_data:
 
 # Initialize and update submodules for test data
 gettestdata: test/test_data
-	@if [ ! -d "test/test_data/dcm_qa_nih" ]; then \
-		git submodule add --force https://github.com/neurolabusc/dcm_qa_nih.git test/test_data/dcm_qa_nih; \
-	fi
-	@if [ ! -d "test/test_data/dcm_qa_uih" ]; then \
-		git submodule add --force https://github.com/neurolabusc/dcm_qa_uih.git test/test_data/dcm_qa_uih; \
-	fi
-	@if [ ! -d "test/test_data/petdicoms" ]; then \
-		git submodule add --force https://github.com/openneuropet/petdicoms.git test/test_data/petdicoms; \
-	fi
-	git submodule update --init test/test_data/dcm_qa_nih
-	git submodule update --init test/test_data/dcm_qa_uih
-	git submodule update --init test/test_data/petdicoms
-	# Prevent accidental commits to submodules
-	git config submodule.test/test_data/dcm_qa_nih.ignore dirty
-	git config submodule.test/test_data/dcm_qa_uih.ignore dirty
-	git config submodule.test/test_data/petdicoms.ignore dirty
+	test/gettestdata
 
 # Clean test data (remove submodules and their directories)
 clean-testdata:
-	git submodule deinit -f test/test_data/dcm_qa_nih
-	git submodule deinit -f test/test_data/dcm_qa_uih
-	git submodule deinit -f test/test_data/petdicoms
-	git rm -f test/test_data/dcm_qa_nih
-	git rm -f test/test_data/dcm_qa_uih
-	git rm -f test/test_data/petdicoms
-	rm -rf .git/modules/test/test_data/dcm_qa_uih
-	rm -rf .git/modules/test/test_data/dcm_qa_nih
-	rm -rf .git/modules/test/test_data/petdicoms
-	rm -rf test/test_data 
+	test/cleantestdata

test/cleantestdata

@@ -0,0 +1,13 @@
+#! /usr/bin/env bash
+# cleans up the testdata we have in this folder
+
+git submodule deinit -f test/test_data/dcm_qa_nih
+git submodule deinit -f test/test_data/dcm_qa_uih
+git submodule deinit -f test/test_data/petdicoms
+git rm -f test/test_data/dcm_qa_nih
+git rm -f test/test_data/dcm_qa_uih
+git rm -f test/test_data/petdicoms
+rm -rf .git/modules/test/test_data/dcm_qa_uih
+rm -rf .git/modules/test/test_data/dcm_qa_nih
+rm -rf .git/modules/test/test_data/petdicoms
+rm -rf test/test_data

test/gettestdata

@@ -0,0 +1,27 @@
+#! /usr/bin/env bash
+
+if [ ! -d "test/test_data/dcm_qa_nih" ]; then
+	git submodule add --force https://github.com/neurolabusc/dcm_qa_nih.git test/test_data/dcm_qa_nih
+fi
+if [ ! -d "test/test_data/dcm_qa_uih" ]; then
+	git submodule add --force https://github.com/neurolabusc/dcm_qa_uih.git test/test_data/dcm_qa_uih
+fi
+if [ ! -d "test/test_data/petdicoms" ]; then
+	git submodule add --force https://github.com/openneuropet/petdicoms.git test/test_data/petdicoms
+fi
+git submodule update --init test/test_data/dcm_qa_nih
+git submodule update --init test/test_data/dcm_qa_uih
+git submodule update --init test/test_data/petdicoms
+# Prevent accidental commits to submodules
+git config submodule.test/test_data/dcm_qa_nih.ignore dirty
+git config submodule.test/test_data/dcm_qa_uih.ignore dirty
+git config submodule.test/test_data/petdicoms.ignore dirty
+# Unzip petdicoms data
+echo "Unzipping petdicoms data..."
+cd test/test_data/petdicoms/sourcedata || exit 1
+for zip in *.zip; do
+	if [ -f "$zip" ]; then
+		echo "Unzipping $zip..."
+		unzip -q -o "$zip" -d "${zip%.zip}"
+	fi
+done