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Merge pull request #62 from seqeralabs/dev
Dev -> Master for 0.5.0 release
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@@ -11,61 +11,21 @@ on: | |
| types: [published] | ||
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| jobs: | ||
| EditorConfig: | ||
| pre-commit: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | ||
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| - uses: actions/setup-node@v3 | ||
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| - name: Install editorconfig-checker | ||
| run: npm install -g editorconfig-checker | ||
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| - name: Run ECLint check | ||
| run: editorconfig-checker -exclude README.md $(find .* -type f | grep -v '.git\|.py\|.md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile') | ||
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| Prettier: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
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| - uses: actions/setup-node@v3 | ||
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| - name: Install Prettier | ||
| run: npm install -g prettier | ||
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| - name: Run Prettier --check | ||
| run: prettier --check ${GITHUB_WORKSPACE} | ||
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| PythonBlack: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
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| - name: Check code lints with Black | ||
| uses: psf/black@stable | ||
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| # If the above check failed, post a comment on the PR explaining the failure | ||
| - name: Post PR comment | ||
| if: failure() | ||
| uses: mshick/add-pr-comment@v1 | ||
| - name: Set up Python 3.12 | ||
| uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 | ||
| with: | ||
| message: | | ||
| ## Python linting (`black`) is failing | ||
| To keep the code consistent with lots of contributors, we run automated code consistency checks. | ||
| To fix this CI test, please run: | ||
| * Install [`black`](https://black.readthedocs.io/en/stable/): `pip install black` | ||
| * Fix formatting errors in your pipeline: `black .` | ||
| Once you push these changes the test should pass, and you can hide this comment :+1: | ||
| python-version: "3.12" | ||
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| We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help! | ||
| - name: Install pre-commit | ||
| run: pip install pre-commit | ||
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| Thanks again for your contribution! | ||
| repo-token: ${{ secrets.GITHUB_TOKEN }} | ||
| allow-repeats: false | ||
| - name: Run pre-commit | ||
| run: pre-commit run --all-files | ||
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| nf-core: | ||
| runs-on: ubuntu-latest | ||
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@@ -84,7 +44,7 @@ jobs: | |
| - name: Install dependencies | ||
| run: | | ||
| python -m pip install --upgrade pip | ||
| pip install nf-core | ||
| pip install git+https://github.com/nf-core/[email protected] | ||
| - name: Run nf-core lint | ||
| env: | ||
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@@ -6,4 +6,4 @@ process { | |
| saveAs: { filename -> filename.equals('versions.yml') ? null : filename } | ||
| ] | ||
| } | ||
| } | ||
| } | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,78 +1,65 @@ | ||
| @Grab('com.github.groovy-wslite:groovy-wslite:1.1.2;transitive=false') | ||
| import wslite.rest.RESTClient | ||
| import groovy.json.JsonSlurper | ||
| import nextflow.exception.ProcessException | ||
| import groovy.json.JsonBuilder | ||
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| // Set system properties for custom Java trustStore | ||
| def setTrustStore(trustStorePath, trustStorePassword) { | ||
| System.setProperty("javax.net.ssl.trustStore", trustStorePath) | ||
| if (trustStorePassword) { | ||
| System.setProperty("javax.net.ssl.trustStorePassword", trustStorePassword) | ||
| Long getWorkspaceId(orgName, workspaceName, api_endpoint, authHeader) { | ||
| Map response | ||
| try { | ||
| def responseString = new URL("${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 ${workspaceName}", e) | ||
| } | ||
| } | ||
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| Long getWorkspaceId(orgName, workspaceName, client, authHeader) { | ||
| def orgResponse = client.get(path: '/orgs', headers: authHeader) | ||
| if (orgResponse.statusCode == 200) { | ||
| def orgMap = orgResponse.json?.organizations.collectEntries { org -> [org.name, org.orgId] } | ||
| def orgId = orgMap.get(orgName) | ||
| if(!orgId) log.warn "Could not find organization '${orgName}'" | ||
| def orgId = response | ||
| ?.organizations | ||
| ?.collectEntries { org -> [org.name, org.orgId] } | ||
| ?.get(orgName) | ||
| if(!orgId) log.warn "Could not find organization '${orgName}'" | ||
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| // GET the workspaces in this org | ||
| def workspaceReponse = client.get(path: "/orgs/${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 | ||
| } | ||
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| Map getRunMetadata(meta, log, api_endpoint, trustStorePath, trustStorePassword) { | ||
| def runId = meta.id | ||
| def (orgName, workspaceName) = meta.workspace.tokenize("/") | ||
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| if (trustStorePath) { | ||
| log.info "Setting custom truststore: ${trustStorePath}" | ||
| setTrustStore(trustStorePath, trustStorePassword) | ||
| } | ||
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| 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 [:] | ||
| } | ||
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| 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() | ||
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| 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} | ||
| """.stripIndent() | ||
| log.error "Exception: ${ex.message}", ex | ||
| throw new ProcessException("Failed to get workflow details for workflow ${runId} in workspace ${meta.workspace}", ex) | ||
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| throw new nextflow.exception.ProcessException("Failed to get workflow details for workflow ${runId} in workspace ${meta.workspace}", ex) | ||
| } | ||
| return [:] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,3 +1,3 @@ | ||
| includeConfig '../../modules/local/seqera_runs_dump/nextflow.config' | ||
| includeConfig '../../modules/local/plot_run_gantt/nextflow.config' | ||
| includeConfig '../../modules/nf-core/multiqc/nextflow.config' | ||
| includeConfig '../../modules/nf-core/multiqc/nextflow.config' |