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Remove dependency on external library/grape
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,78 +1,65 @@ | ||
| @Grab('com.github.groovy-wslite:groovy-wslite:1.1.2;transitive=false') | ||
| import wslite.rest.RESTClient | ||
| import groovy.json.JsonSlurper | ||
| import nextflow.exception.ProcessException | ||
| import groovy.json.JsonBuilder | ||
|
|
||
| // Set system properties for custom Java trustStore | ||
| def setTrustStore(trustStorePath, trustStorePassword) { | ||
| System.setProperty("javax.net.ssl.trustStore", trustStorePath) | ||
| if (trustStorePassword) { | ||
| System.setProperty("javax.net.ssl.trustStorePassword", trustStorePassword) | ||
| Long getWorkspaceId(orgName, workspaceName, api_endpoint, authHeader) { | ||
| Map response | ||
| try { | ||
| def responseString = new URL("${api_endpoint}/orgs").getText(requestProperties: authHeader) | ||
| response = new groovy.json.JsonSlurper().parseText(responseString) | ||
| } catch (Exception e) { | ||
| log.warn "Could not fetch organization ${orgName} from API endpoint ${api_endpoint}" | ||
| throw new nextflow.exception.ProcessException("Failed to get organization details for ${orgName} in workspace ${workspaceName}", e) | ||
| } | ||
| } | ||
|
|
||
| Long getWorkspaceId(orgName, workspaceName, client, authHeader) { | ||
| def orgResponse = client.get(path: '/orgs', headers: authHeader) | ||
| if (orgResponse.statusCode == 200) { | ||
| def orgMap = orgResponse.json?.organizations.collectEntries { org -> [org.name, org.orgId] } | ||
| def orgId = orgMap.get(orgName) | ||
| if(!orgId) log.warn "Could not find organization '${orgName}'" | ||
| def orgId = response | ||
| ?.organizations | ||
| ?.collectEntries { org -> [org.name, org.orgId] } | ||
| ?.get(orgName) | ||
| if(!orgId) log.warn "Could not find organization '${orgName}'" | ||
|
|
||
| // GET the workspaces in this org | ||
| def workspaceReponse = client.get(path: "/orgs/${orgId}/workspaces", headers: authHeader) | ||
| if (workspaceReponse.statusCode == 200) { | ||
| def workspaceMap = workspaceReponse.json?.workspaces.collectEntries { ws -> [ws.name, ws.id]} | ||
| return workspaceMap?.get(workspaceName) | ||
| } else { | ||
| log.error "Failed to fetch workspaces for orgId: ${orgId}, statusCode: ${workspaceResponse.statusCode}" | ||
| } | ||
| try { | ||
| def workspaceReponse = new URL("${api_endpoint}/orgs/${orgId}/workspaces").getText(requestProperties: authHeader) | ||
| def workspaceMap = new groovy.json.JsonSlurper() | ||
| .parseText(workspaceReponse) | ||
| ?.workspaces | ||
| ?.collectEntries { ws -> [ws.name, ws.id]} | ||
| return workspaceMap?.get(workspaceName) | ||
| } catch (Exception e) { | ||
| log.error "Failed to fetch workspaces for orgId: ${orgId}" | ||
| return null | ||
| } | ||
| return null | ||
| } | ||
|
|
||
| Map getRunMetadata(meta, log, api_endpoint, trustStorePath, trustStorePassword) { | ||
| def runId = meta.id | ||
| def (orgName, workspaceName) = meta.workspace.tokenize("/") | ||
|
|
||
| if (trustStorePath) { | ||
| log.info "Setting custom truststore: ${trustStorePath}" | ||
| setTrustStore(trustStorePath, trustStorePassword) | ||
| } | ||
|
|
||
| def client = new RESTClient(api_endpoint) | ||
| def token = System.getenv("TOWER_ACCESS_TOKEN") | ||
| def authHeader = ["Authorization": "Bearer ${token}"] | ||
| def workspaceId = getWorkspaceId(orgName, workspaceName, api_endpoint, authHeader) | ||
| def endpointUrl = "${api_endpoint}/workflow/${runId}?workspaceId=${workspaceId}" | ||
| if(!workspaceId) { | ||
| log.error "Failed to get workspaceId for ${orgName}/${workspaceName}" | ||
| return [:] | ||
| } | ||
|
|
||
| try { | ||
| 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 configText = new JsonBuilder(workflowResponse?.json?.workflow?.configText) | ||
| def pattern = /fusion\s*\{\\n\s*enabled\s*=\s*true/ | ||
| def matcher = configText.toPrettyString() =~ pattern | ||
| metaMap.fusion = matcher.find() | ||
| def workflowResponseString = new URL(endpointUrl).getText(requestProperties: authHeader) | ||
| def workflowResponse = new groovy.json.JsonSlurper().parseText(workflowResponseString) | ||
| def metaMap = workflowResponse | ||
| ?.workflow | ||
| ?.subMap("runName", "workDir", "projectName") | ||
| def configText = new groovy.json.JsonBuilder(workflowResponse?.workflow?.configText) | ||
| def pattern = /fusion\s*\{\\n\s*enabled\s*=\s*true/ | ||
| def matcher = configText.toPrettyString() =~ pattern | ||
| metaMap.fusion = matcher.find() | ||
|
|
||
| return metaMap ?: [:] | ||
| } | ||
| } | ||
| } catch (wslite.rest.RESTClientException ex) { | ||
| log.warn """ | ||
| Could not get workflow details for workflow ${runId} in workspace ${meta.workspace}: | ||
| ↳ Status code ${ex.response?.statusCode} returned from request to ${ex.request?.url} (authentication headers excluded) | ||
| """.stripIndent() | ||
| log.error "Exception: ${ex.message}", ex | ||
| throw new ProcessException("Failed to get workflow details for workflow ${runId} in workspace ${meta.workspace}", ex) | ||
| return metaMap ?: [:] | ||
| } catch (Exception ex) { | ||
| log.warn """ | ||
| An error occurred while getting workflow details for workflow ${runId} in workspace ${meta.workspace}: | ||
| ↳ ${ex.message} | ||
| Could not get workflow details for workflow ${runId} in workspace ${meta.workspace}: | ||
| ↳ From request to ${endpointUrl} (authentication headers excluded) | ||
| """.stripIndent() | ||
| log.error "Exception: ${ex.message}", ex | ||
| throw new ProcessException("Failed to get workflow details for workflow ${runId} in workspace ${meta.workspace}", ex) | ||
|
|
||
| throw new nextflow.exception.ProcessException("Failed to get workflow details for workflow ${runId} in workspace ${meta.workspace}", ex) | ||
| } | ||
| return [:] | ||
| } |