diff --git a/.github/workflows/cloud_tests_full.yml b/.github/workflows/cloud_tests_full.yml new file mode 100644 index 0000000..46fa6ce --- /dev/null +++ b/.github/workflows/cloud_tests_full.yml @@ -0,0 +1,95 @@ +name: full-sized tests on cloud providers +run-name: Submitting workflow to all cloud providers using full sized data +on: + release: + types: [published] + inputs: + platform: + description: "Platform to run test" + default: "all" + workflow_dispatch: + inputs: + platform: + description: "Platform to run test" + required: true + default: "all" + type: choice + options: + - all + - aws + - azure + - gcp +jobs: + run-full-tests-on-aws: + if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'aws' }} + runs-on: ubuntu-latest + strategy: + matrix: + aligner: ["star_salmon", "star_rsem"] + steps: + - uses: seqeralabs/action-tower-launch@v1 + with: + workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} + access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} + compute_env: ${{ secrets.TOWER_CE_AWS_CPU }} + workdir: "${{ secrets.TOWER_BUCKET_AWS }}/work/testpipeline/work-${{ github.sha }}" + run_name: "aws_testpipeline_${{ matrix.aligner }}" + profiles: test + parameters: | + { + "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}", + "outdir": "${{ secrets.TOWER_BUCKET_AWS }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}" + } + - uses: actions/upload-artifact@v3 + with: + name: Tower debug log file + path: tower_action_*.log + run-full-tests-on-gcp: + if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'gcp' }} + runs-on: ubuntu-latest + strategy: + matrix: + aligner: ["star_salmon", "star_rsem"] + steps: + - uses: seqeralabs/action-tower-launch@v1 + with: + workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} + access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} + compute_env: ${{ secrets.TOWER_CE_GCP_CPU }} + workdir: "${{ secrets.TOWER_BUCKET_GCP }}/work/testpipeline/work-${{ github.sha }}" + run_name: "gcp_testpipeline_${{ matrix.aligner }}" + profiles: test + parameters: | + { + "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}", + "outdir": "${{ secrets.TOWER_BUCKET_GCP }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}" + } + - uses: actions/upload-artifact@v3 + with: + name: Tower debug log file + path: tower_action_*.log + run-full-tests-on-azure: + if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'azure' }} + runs-on: ubuntu-latest + strategy: + matrix: + aligner: ["star_salmon", "star_rsem"] + steps: + - uses: seqeralabs/action-tower-launch@v1 + with: + workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} + access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} + compute_env: ${{ secrets.TOWER_CE_AZURE_CPU }} + workdir: "${{ secrets.TOWER_BUCKET_AZURE }}/work/testpipeline/work-${{ github.sha }}" + run_name: "azure_testpipeline_${{ matrix.aligner }}" + profiles: test + parameters: | + { + "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}", + "outdir": "${{ secrets.TOWER_BUCKET_AZURE }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}", + "igenomes_base": "${{ secrets.TOWER_IGENOMES_BASE_AZURE }}" + } + - uses: actions/upload-artifact@v3 + with: + name: Tower debug log file + path: tower_action_*.log diff --git a/assets/slackreport.json b/assets/slackreport.json new file mode 100644 index 0000000..043d02f --- /dev/null +++ b/assets/slackreport.json @@ -0,0 +1,34 @@ +{ + "attachments": [ + { + "fallback": "Plain-text summary of the attachment.", + "color": "<% if (success) { %>good<% } else { %>danger<%} %>", + "author_name": "sanger-tol/readmapping v${version} - ${runName}", + "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico", + "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>", + "fields": [ + { + "title": "Command used to launch the workflow", + "value": "```${commandLine}```", + "short": false + } + <% + if (!success) { %> + , + { + "title": "Full error message", + "value": "```${errorReport}```", + "short": false + }, + { + "title": "Pipeline configuration", + "value": "<% out << summary.collect{ k,v -> k == "hook_url" ? "_${k}_: (_hidden_)" : ( ( v.class.toString().contains('Path') || ( v.class.toString().contains('String') && v.contains('/') ) ) ? "_${k}_: `${v}`" : (v.class.toString().contains('DateTime') ? ("_${k}_: " + v.format(java.time.format.DateTimeFormatter.ofLocalizedDateTime(java.time.format.FormatStyle.MEDIUM))) : "_${k}_: ${v}") ) }.join(",\n") %>", + "short": false + } + <% } + %> + ], + "footer": "Completed at <% out << dateComplete.format(java.time.format.DateTimeFormatter.ofLocalizedDateTime(java.time.format.FormatStyle.MEDIUM)) %> (duration: ${duration})" + } + ] +} diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy index 2fc0a9b..25a0a74 100755 --- a/lib/NfcoreTemplate.groovy +++ b/lib/NfcoreTemplate.groovy @@ -32,6 +32,25 @@ class NfcoreTemplate { } } + // + // Generate version string + // + public static String version(workflow) { + String version_string = "" + + if (workflow.manifest.version) { + def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' + version_string += "${prefix_v}${workflow.manifest.version}" + } + + if (workflow.commitId) { + def git_shortsha = workflow.commitId.substring(0, 7) + version_string += "-g${git_shortsha}" + } + + return version_string + } + // // Construct and send completion email // @@ -61,7 +80,7 @@ class NfcoreTemplate { misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp def email_fields = [:] - email_fields['version'] = workflow.manifest.version + email_fields['version'] = NfcoreTemplate.version(workflow) email_fields['runName'] = workflow.runName email_fields['success'] = workflow.success email_fields['dateComplete'] = workflow.complete @@ -145,6 +164,64 @@ class NfcoreTemplate { output_tf.withWriter { w -> w << email_txt } } + // + // Construct and send a notification to a web server as JSON + // e.g. Microsoft Teams and Slack + // + public static void IM_notification(workflow, params, summary_params, projectDir, log) { + def hook_url = params.hook_url + + def summary = [:] + for (group in summary_params.keySet()) { + summary << summary_params[group] + } + + def misc_fields = [:] + misc_fields['start'] = workflow.start + misc_fields['complete'] = workflow.complete + misc_fields['scriptfile'] = workflow.scriptFile + misc_fields['scriptid'] = workflow.scriptId + if (workflow.repository) misc_fields['repository'] = workflow.repository + if (workflow.commitId) misc_fields['commitid'] = workflow.commitId + if (workflow.revision) misc_fields['revision'] = workflow.revision + misc_fields['nxf_version'] = workflow.nextflow.version + misc_fields['nxf_build'] = workflow.nextflow.build + misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp + + def msg_fields = [:] + msg_fields['version'] = NfcoreTemplate.version(workflow) + msg_fields['runName'] = workflow.runName + msg_fields['success'] = workflow.success + msg_fields['dateComplete'] = workflow.complete + msg_fields['duration'] = workflow.duration + msg_fields['exitStatus'] = workflow.exitStatus + msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None') + msg_fields['errorReport'] = (workflow.errorReport ?: 'None') + msg_fields['commandLine'] = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "") + msg_fields['projectDir'] = workflow.projectDir + msg_fields['summary'] = summary << misc_fields + + // Render the JSON template + def engine = new groovy.text.GStringTemplateEngine() + // Different JSON depending on the service provider + // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format + def json_path = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json" + def hf = new File("$projectDir/assets/${json_path}") + def json_template = engine.createTemplate(hf).make(msg_fields) + def json_message = json_template.toString() + + // POST + def post = new URL(hook_url).openConnection(); + post.setRequestMethod("POST") + post.setDoOutput(true) + post.setRequestProperty("Content-Type", "application/json") + post.getOutputStream().write(json_message.getBytes("UTF-8")); + def postRC = post.getResponseCode(); + if (! postRC.equals(200)) { + log.warn(post.getErrorStream().getText()); + } + } + // // Print pipeline summary on completion // @@ -154,7 +231,7 @@ class NfcoreTemplate { if (workflow.stats.ignoredCount == 0) { log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-" } else { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed successfully, but with errored process(es) ${colors.reset}-" + log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-" } } else { log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-" @@ -242,6 +319,7 @@ class NfcoreTemplate { // public static String logo(workflow, monochrome_logs) { Map colors = logColours(monochrome_logs) + String workflow_version = NfcoreTemplate.version(workflow) String.format( """\n ${dashedLine(monochrome_logs)} @@ -250,7 +328,7 @@ class NfcoreTemplate { ${colors.blue} |\\ | |__ __ / ` / \\ |__) |__ ${colors.yellow}} {${colors.reset} ${colors.blue} | \\| | \\__, \\__/ | \\ |___ ${colors.green}\\`-._,-`-,${colors.reset} ${colors.green}`._,._,\'${colors.reset} - ${colors.purple} ${workflow.manifest.name} v${workflow.manifest.version}${colors.reset} + ${colors.purple} ${workflow.manifest.name} ${workflow_version}${colors.reset} ${dashedLine(monochrome_logs)} """.stripIndent() ) diff --git a/nextflow.config b/nextflow.config index 0d1e9e9..c3d4b2a 100644 --- a/nextflow.config +++ b/nextflow.config @@ -31,6 +31,7 @@ params { email_on_fail = null plaintext_email = false monochrome_logs = false + hook_url = null help = false validate_params = true show_hidden_params = false diff --git a/nextflow_schema.json b/nextflow_schema.json index 5c6266a..58682c4 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -213,6 +213,13 @@ "fa_icon": "fas fa-palette", "hidden": true }, + "hook_url": { + "type": "string", + "description": "Incoming hook URL for messaging service", + "fa_icon": "fas fa-people-group", + "help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.", + "hidden": true + }, "multiqc_config": { "type": "string", "description": "Custom config file to supply to MultiQC.", diff --git a/workflows/testpipeline.nf b/workflows/testpipeline.nf index 8b1f8de..6bf61b6 100644 --- a/workflows/testpipeline.nf +++ b/workflows/testpipeline.nf @@ -114,6 +114,9 @@ workflow.onComplete { NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report) } NfcoreTemplate.summary(workflow, params, log) + if (params.hook_url) { + NfcoreTemplate.IM_notification(workflow, params, summary_params, projectDir, log) + } } /*