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Bugfix/submission alias clash #77

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Bugfix/submission alias clash #77

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20 changes: 18 additions & 2 deletions modules/local/registerstudy/tests/main.nf.test
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Original file line number Diff line number Diff line change
@@ -1,3 +1,17 @@
def writeStudyMetadataJson = { String alias ->
def metadata = new File(System.getProperty("user.dir"), "modules/local/registerstudy/tests/study_metadata_${alias}.json")

@mberacochea mberacochea Jun 26, 2026

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I would use a tmp file instead

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"
Expand All @@ -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
Expand Down Expand Up @@ -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
Expand Down
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