usegalaxy-eu · cat-bro · Oct 21, 2020 · Oct 21, 2020 · hexylena · Oct 21, 2020
diff --git a/.gitignore b/.gitignore
@@ -1,2 +1,3 @@
 .venv/
 tool_test_output.*
+.secret.env
diff --git a/requirements.txt b/requirements.txt
@@ -0,0 +1,2 @@
+planemo==0.72.0
+galaxy-parsec==1.13.0
diff --git a/run_galaxy_workflow_tests.sh b/run_galaxy_workflow_tests.sh
@@ -14,6 +14,7 @@ planemo $PLANEMO_OPTIONS test \
 	--galaxy_user_key "$GALAXY_USER_KEY" \
 	--no_shed_install \
 	--engine external_galaxy \
+	--test_output_json test_output.json \
 	"$1";
 planemo_exit_code=$?
 set -e
@@ -26,6 +27,6 @@ else
 	# Otherwise immediately delete
 	history_id=$(parsec histories get_histories --name "$history_name" | jq -r .[0].id)
 	parsec histories delete_history --purge $history_id
-	echo "<html><head></head><body>Test was completely successful</body></html>"> history.html
+	echo "<html><head></head><body>Test was completely successful</body></html>" > history.html
 fi
 exit $planemo_exit_code
diff --git a/test_workflows.sh b/test_workflows.sh
@@ -0,0 +1,37 @@
+#!/bin/bash
+
+# if GALAXY_URL and GALAXY_USER_KEY are not set, try to set them from local untracked file
+[ ! $GALAXY_URL ] || [ ! $GALAXY_USER_KEY ] && source .secret.env
+export GALAXY_URL GALAXY_USER_KEY
+
+virtualenv -p python3 .venv; . .venv/bin/activate
+pip install -r requirements.txt
+
+# initalise parsec with url and api key.  Remove any existing parsec configuration stored in the home directory
+rm -f ~/.parsec.yml ||:
+parsec init --url $GALAXY_URL --api_key $GALAXY_USER_KEY # caution: if ~/.parsec.yml already exists at this point it will not be updated
+
+workflow_list=workflows_to_test.txt
-workflow_list=workflows_to_test.txt
+workflow_list=$(mktemp)
-workflow_list=workflows_to_test.txt
+workflow_list=$(mktemp)
+# # get list of local workflows with tests (ignoring training folder)
+find . \( -name '*-test.yml' ! -path './training*' \) | sed 's/^\.\///g' | sed 's/-test.yml/.ga/g' > $workflow_list
+
+# # clone training-material repo
+git clone --depth 1 https://github.com/galaxyproject/training-material.git
+
+# # get list of training-material workflows with tests
+find 'training-material' -path '*-test.yml' | sed 's/-test.yml/.ga/g' >> $workflow_list
+
+[ -d test_output ] && rm -rf test_output
+mkdir test_output
+
+# run test for each workflow and store json report
+cat $workflow_list | while read line || [[ -n $line ]]; do
+   ./run_galaxy_workflow_tests.sh $line
+   mv test_output.json test_output/$(sed 's/\//__/g' <<< $line).test_output.json
+   mv history.html test_output/$(sed 's/\//__/g' <<< $line).history.html
+done
+
+# merge json reports and create html report from merged report
+find 'test_output' -name '*test_output.json' -exec sh -c 'planemo merge_test_reports "$@" test_output/merged_test_output.json' sh {} +
+planemo test_reports test_output/merged_test_output.json  --test_output merged_test_output.html
+