diff --git a/modules/local/registerstudy/tests/main.nf.test b/modules/local/registerstudy/tests/main.nf.test index 7da4837..b3da1cc 100644 --- a/modules/local/registerstudy/tests/main.nf.test +++ b/modules/local/registerstudy/tests/main.nf.test @@ -1,3 +1,17 @@ +def writeStudyMetadataJson = { String alias -> + def metadata = new File(System.getProperty("user.dir"), "modules/local/registerstudy/tests/study_metadata_${alias}.json") + metadata.text = """\ +{ + "alias": "${alias}", + "study_title": "Example metagenome study", + "study_abstract": "Description of the study aims and methods.", + "existing_study_type": "Metagenomics" +} +""" + metadata.deleteOnExit() + return metadata.absolutePath +} + nextflow_process { name "Test Process REGISTERSTUDY" script "../main.nf" @@ -8,13 +22,14 @@ nextflow_process { tag "registerstudy" test("registerstudy - submission to ENA test server (JSON metadata)") { + def studyMetadata = writeStudyMetadataJson("study-example-json-registerstudy") when { process { """ input[0] = [ [ id:'example_study' ], - file(params.pipelines_testdata_base_path + 'test_data/study_metadata/study_metadata.json', checkIfExists: true) + file("${studyMetadata}", checkIfExists: true) ] input[1] = true input[2] = false @@ -59,13 +74,14 @@ nextflow_process { test("registerstudy - stub") { options "-stub" + def studyMetadata = writeStudyMetadataJson("study-example-json-registerstudy-stub") when { process { """ input[0] = [ [ id:'example_study' ], - file(params.pipelines_testdata_base_path + 'test_data/study_metadata/study_metadata.json', checkIfExists: true) + file("${studyMetadata}", checkIfExists: true) ] input[1] = true input[2] = false