fix: check if fusion is enabled via the Platform API #57
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| @@ -49,8 +50,10 @@ Map getRunMetadata(meta, log, api_endpoint, trustStorePath, trustStorePassword) | |||
| def workflowResponse = client.get(path: "/workflow/${runId}", query: ["workspaceId":workspaceId], headers: authHeader) | |||
| if (workflowResponse.statusCode == 200) { | |||
| def metaMap = workflowResponse?.json?.workflow?.subMap("runName", "workDir", "projectName") | |||
| def config = new ConfigSlurper().parse( workflowResponse?.json?.workflow?.configText ) | |||
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This line fails to load in the config just for viralrecon but works for other pipelines.
A quick way to reproduce would be to download the raw functions.nf and append the lines below at the end of the file. This would assume you have access to the workspaces below via exporting TOWER_ACCESS_TOKEN for Seqera Cloud.
def meta = [id:'LanYfJk1vaHuD', workspace:'scidev/azure'] // WORKS: no fusion / nf-core/rnaseq
// def meta = [id:'3Z627eCb3HqUy3', workspace:'seqeralabs/showcase'] // WORKS: with fusion / nf-core/rnaseq
// def meta = [id:'13gHs3OF4AYPI5', workspace:'scidev/azure'] // FAILS: no fusion / nf-core/viralrecon
def api_endpoint = 'https://api.cloud.seqera.io/'
def java_truststore_path = ''
def java_truststore_password = ''
metaOut = getRunMetadata(meta, log, api_endpoint, java_truststore_path, java_truststore_password)
println(metaOut)
You can then run the file directly as a Nextflow script to test:
nextflow run functions.nf
The fix in this PR is much more fragile because we are unable to load the config into a map and then checking whether Fusion is enabled. Instead, we are using a regex to check whether fusion is enabled via a pattern match in the config string.
This isn't a great solution but we can't think of anything more robust right now and can make improvements in the future.
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Will merge this in for now to get a release out. We can patch with a better solution later as mentioned in #55 |
Alternative implementation to #56