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[WIP] test script and venv requirements #55

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[WIP] test script and venv requirements #55

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2524563
test script and venv requirements
cat-bro Oct 21, 2020
a9b4ba0
remove parsec init, venv creation and sourcing of variables
cat-bro Oct 21, 2020
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2 changes: 2 additions & 0 deletions requirements.txt
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Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
planemo==0.72.0
galaxy-parsec==1.13.0
3 changes: 2 additions & 1 deletion run_galaxy_workflow_tests.sh
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Expand Up @@ -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
Expand All @@ -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
26 changes: 26 additions & 0 deletions test_workflows.sh
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@@ -0,0 +1,26 @@
#!/bin/bash

workflow_list=workflows_to_test.txt
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Suggested change
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
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I've never seen this construction before, cool! 👍

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 {} +
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planemo test_reports test_output/merged_test_output.json --test_output merged_test_output.html
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Merged test reports will be SO much nicer!!