Merge pull request #51 from seqeralabs/dev

Dev -> Master for v0.3.0 release
seqeralabs · Jul 1, 2024 · c9aec68 · c9aec68
2 parents 496dba5 + 9237376
commit c9aec68
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,22 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [[0.3.0](https://github.com/seqeralabs/nf-aggregate/releases/tag/0.3.0)] - 2024-07-01
+
+### Credits
+
+Special thanks to the following for their contributions to the release:
+
+- [Adam Talbot](https://github.com/adamrtalbot)
+- [Esha Joshi](https://github.com/ejseqera)
+- [Rob Syme](https://github.com/robsyme)
+
+Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
+
+### Enhancements & fixes
+
+[PR #49](https://github.com/seqeralabs/nf-aggregate/pull/49) - Add custom java truststore support and improved exception handling
+
 ## [[0.2.0](https://github.com/seqeralabs/nf-aggregate/releases/tag/0.2.0)] - 2024-05-29
 
 ### Credits

diff --git a/README.md b/README.md
@@ -54,6 +54,8 @@ nextflow run seqeralabs/nf-aggregate \
     -profile docker
 ```
 
+If you are using a Seqera Platform Enterprise instance that is secured with a private CA SSL certificate not recognized by default Java certificate authorities, you can specify a custom `cacerts` store path through the `--java_truststore_path` parameter and optionally, a password with the `--java_truststore_password`. This certificate will be used to achieve connectivity with your Seqera Platform instance through API and CLI.
+
 ## Output
 
 The results from the pipeline will be published in the path specified by the `--outdir` and will consist of the following contents:

diff --git a/main.nf b/main.nf
@@ -46,7 +46,9 @@ workflow {
         ch_multiqc_logo,
         params.seqera_api_endpoint,
         params.skip_run_gantt,
-        params.skip_multiqc
+        params.skip_multiqc,
+        params.java_truststore_path,
+        params.java_truststore_password
     )
 }
 

diff --git a/modules/local/plot_run_gantt/tests/main.nf.test b/modules/local/plot_run_gantt/tests/main.nf.test
@@ -17,6 +17,8 @@ nextflow_process {
                     """
                     input[0] = ['id': '4Bi5xBK6E2Nbhj', 'workspace': 'community/showcase']
                     input[1] = "https://api.tower.nf"
+                    input[2] = ""
+                    input[3] = ""
                     """
                 }
             }

diff --git a/modules/local/seqera_runs_dump/functions.nf b/modules/local/seqera_runs_dump/functions.nf
@@ -1,6 +1,14 @@
-
 @Grab('com.github.groovy-wslite:groovy-wslite:1.1.2;transitive=false')
 import wslite.rest.RESTClient
+import groovy.json.JsonSlurper
+
+// 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, client, authHeader) {
     def orgResponse = client.get(path: '/orgs', headers: authHeader)
@@ -14,15 +22,22 @@ Long getWorkspaceId(orgName, workspaceName, client, 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}"
         }
     }
     return null
 }
 
-Map getRunMetadata(meta, log, api_endpoint) {
+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}"]
@@ -39,11 +54,18 @@ Map getRunMetadata(meta, log, api_endpoint) {
                 return metaMap ?: [:]
             }
         }
-    } catch(Exception ex) {
+    } 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)
+            ↳ Status code ${ex.response?.statusCode} returned from request to ${ex.request?.url} (authentication headers excluded)
+        """.stripIndent()
+        log.error "Exception: ${ex.message}", ex
+    } catch (Exception ex) {
+        log.warn """
+        An error occurred while getting workflow details for workflow ${runId} in workspace ${meta.workspace}:
+            ↳ ${ex.message}
         """.stripIndent()
+        log.error "Exception: ${ex.message}", ex
     }
     return [:]
 }
diff --git a/modules/local/seqera_runs_dump/main.nf b/modules/local/seqera_runs_dump/main.nf
@@ -8,6 +8,8 @@ process SEQERA_RUNS_DUMP {
     input:
     val meta
     val api_endpoint
+    val java_truststore_path
+    val java_truststore_password
 
     output:
     tuple val(metaOut), path("${prefix}"), emit: run_dump
@@ -17,11 +19,15 @@ process SEQERA_RUNS_DUMP {
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
-    metaOut = meta + getRunMetadata(meta, log, api_endpoint)
+    metaOut = meta + getRunMetadata(meta, log, api_endpoint, java_truststore_path, java_truststore_password)
     fusion = metaOut.fusion ? '--add-fusion-logs' : ''
+    javaTrustStore = java_truststore_path ? "-Djavax.net.ssl.trustStore=${java_truststore_path}" : ''
+    javaTrustStorePassword = java_truststore_password ? "-Djavax.net.ssl.trustStorePassword=${java_truststore_password}" : ''
     """
     tw \\
         $args \\
+        $javaTrustStore \\
+        $javaTrustStorePassword \\
         --url=${api_endpoint} \\
         --access-token=$TOWER_ACCESS_TOKEN \\
         runs \\

diff --git a/modules/local/seqera_runs_dump/nextflow.config b/modules/local/seqera_runs_dump/nextflow.config
@@ -2,6 +2,7 @@ process {
     withName: 'SEQERA_RUNS_DUMP' {
         ext.args = { params.seqera_cli_extra_args ? params.seqera_cli_extra_args.split("\\s(?=--)") : '' }
         ext.args2 = { params.skip_run_gantt ? '' : '--add-task-logs' }
+        containerOptions = { params.java_truststore_path ? "--volume ${params.java_truststore_path}:${params.java_truststore_path}" : '' }
         publishDir = [
             path: { "${params.outdir}/${metaOut?.projectName?.replace("/", "_") ?: ""}/runs_dump" },
             mode: params.publish_dir_mode,

diff --git a/modules/local/seqera_runs_dump/tests/main.nf.test b/modules/local/seqera_runs_dump/tests/main.nf.test
@@ -15,6 +15,8 @@ nextflow_process {
                 """
                 input[0] = ['id': '4Bi5xBK6E2Nbhj', 'workspace': 'community/showcase']
                 input[1] = "https://api.tower.nf"
+                input[2] = ""
+                input[3] = ""
                 """
             }
         }

diff --git a/nextflow.config b/nextflow.config
@@ -18,6 +18,9 @@ params {
     // Seqera CLI options
     seqera_api_endpoint          = "https://api.cloud.seqera.io"
     seqera_cli_extra_args        = null
+    java_truststore_path         = null
+    java_truststore_password     = null
+
     // MultiQC options
     multiqc_config               = null
     multiqc_title                = null
@@ -219,6 +222,6 @@ manifest {
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.10.0'
     defaultBranch   = 'main'
-    version         = '0.2.0'
+    version         = '0.3.0'
     doi             = ''
 }
diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -48,6 +48,16 @@
                     "description": "Extra arguments to pass to the Seqera Platform CLI command in addition to defaults defined by the pipeline.",
                     "fa_icon": "fas fa-plus"
                 },
+                "java_truststore_path": {
+                    "type": "string",
+                    "description": "Path to custom cacerts Java truststore used by Seqera Platform.",
+                    "fa_icon": "fas fa-key"
+                },
+                "java_truststore_password": {
+                    "type": "string",
+                    "description": "Password for custom cacerts Java truststore used by Seqera Platform.",
+                    "fa_icon": "fas fa-key"
+                },
                 "skip_run_gantt": {
                     "type": "boolean",
                     "description": "Skip GANTT chart creation for each run.",

diff --git a/workflows/nf_aggregate/main.nf b/workflows/nf_aggregate/main.nf
@@ -13,13 +13,15 @@ include { paramsSummaryMap     } from 'plugin/nf-validation'
 workflow NF_AGGREGATE {
 
     take:
-    ids                   // channel: run ids read in from --input
-    multiqc_custom_config // channel: user specified custom config file used by MultiQC
-    multiqc_logo          // channel: logo rendered in MultiQC report
-    seqera_api_endpoint   //     val: Seqera Platform API endpoint URL
-    skip_run_gantt        //     val: Skip GANTT chart creation for each run
-    skip_multiqc          //     val: Skip MultiQC
-
+    ids                       // channel: run ids read in from --input
+    multiqc_custom_config     // channel: user specified custom config file used by MultiQC
+    multiqc_logo              // channel: logo rendered in MultiQC report
+    seqera_api_endpoint       //     val: Seqera Platform API endpoint URL
+    skip_run_gantt            //     val: Skip GANTT chart creation for each run
+    skip_multiqc              //     val: Skip MultiQC
+    java_truststore_path      //     val: Path to java truststore if using private certs
+    java_truststore_password  //     val: Password for java truststore if using private certs
+
     main:
 
     ch_versions = Channel.empty()
@@ -30,7 +32,9 @@ workflow NF_AGGREGATE {
     //
     SEQERA_RUNS_DUMP (
         ids,
-        seqera_api_endpoint
+        seqera_api_endpoint,
+        java_truststore_path ?: '',
+        java_truststore_password ?: ''
     )
     ch_versions = ch_versions.mix(SEQERA_RUNS_DUMP.out.versions.first())
 
@@ -40,9 +44,9 @@ workflow NF_AGGREGATE {
     SEQERA_RUNS_DUMP
         .out
         .run_dump
-        .filter { 
+        .filter {
             meta, run_dir ->
-                meta.fusion && !params.skip_run_gantt 
+                meta.fusion && !params.skip_run_gantt
         }
         .set { ch_runs_for_gantt }
 

diff --git a/workflows/nf_aggregate/tests/main.nf.test b/workflows/nf_aggregate/tests/main.nf.test
@@ -22,6 +22,8 @@ nextflow_workflow {
                 input[3] = 'https://api.tower.nf'
                 input[4] = false
                 input[5] = false
+                input[6] = ""
+                input[7] = ""
                 """
             }
         }