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Remove fusion retrieval to circumvent failures with nested config imports #56

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Remove fusion retrieval to circumvent failures with nested config imports #56

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06af994
this works, but is brittle and ugly
FriederikeHanssen Jul 25, 2024
93d83b3
remove fusion retrieval
FriederikeHanssen Jul 26, 2024
9727960
Merge remote-tracking branch 'origin/dev' into configs
FriederikeHanssen Jul 26, 2024
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7 changes: 2 additions & 5 deletions modules/local/seqera_runs_dump/functions.nf
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Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@
@Grab('com.github.groovy-wslite:groovy-wslite:1.1.2;transitive=false')
import wslite.rest.RESTClient
import groovy.json.JsonSlurper
import nextflow.exception.ProcessException

// Set system properties for custom Java trustStore
Expand Down Expand Up @@ -31,6 +30,7 @@ Long getWorkspaceId(orgName, workspaceName, client, authHeader) {
}

Map getRunMetadata(meta, log, api_endpoint, trustStorePath, trustStorePassword) {

def runId = meta.id
def (orgName, workspaceName) = meta.workspace.tokenize("/")

Expand All @@ -47,11 +47,9 @@ Map getRunMetadata(meta, log, api_endpoint, trustStorePath, trustStorePassword)
def workspaceId = getWorkspaceId(orgName, workspaceName, client, authHeader)
if (workspaceId) {
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 )
metaMap.fusion = config.fusion.enabled

return metaMap ?: [:]
}
}
Expand All @@ -69,7 +67,6 @@ Map getRunMetadata(meta, log, api_endpoint, trustStorePath, trustStorePassword)
""".stripIndent()
log.error "Exception: ${ex.message}", ex
throw new ProcessException("Failed to get workflow details for workflow ${runId} in workspace ${meta.workspace}", ex)

}
return [:]
}
3 changes: 2 additions & 1 deletion modules/local/seqera_runs_dump/main.nf
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Expand Up @@ -20,9 +20,10 @@ process SEQERA_RUNS_DUMP {
def args2 = task.ext.args2 ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
metaOut = meta + getRunMetadata(meta, log, api_endpoint, java_truststore_path, java_truststore_password)
fusion = metaOut.fusion ? '--add-fusion-logs' : ''
fusion = '' //metaOut.fusion ? '--add-fusion-logs' : '' see issue: https://github.com/seqeralabs/nf-aggregate/issues/55
javaTrustStore = java_truststore_path ? "-Djavax.net.ssl.trustStore=${java_truststore_path}" : ''
javaTrustStorePassword = java_truststore_password ? "-Djavax.net.ssl.trustStorePassword=${java_truststore_password}" : ''

"""
tw \\
$args \\
Expand Down
10 changes: 6 additions & 4 deletions workflows/nf_aggregate/main.nf
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Expand Up @@ -45,10 +45,12 @@ workflow NF_AGGREGATE {
SEQERA_RUNS_DUMP
.out
.run_dump
.filter {
meta, run_dir ->
meta.fusion && !params.skip_run_gantt
}
// This field is currently not set, see issue: https://github.com/seqeralabs/nf-aggregate/issues/55
// .filter {
// meta, run_dir ->

// meta.fusion && !params.skip_run_gantt
// }
.set { ch_runs_for_gantt }

PLOT_RUN_GANTT (
Expand Down
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