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Slack api integration

Skill HolobiomicsLab/asb-skill-collections/collections/metabolomics/v2/skills/slack-api-integration

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npx -y skills add HolobiomicsLab/asb-skill-collections --skill slack-api-integration

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Use when rapid QC-MS detects a QC failure (e.g., internal standard retention time drift, m/z deviation, or intensity anomaly) during an active LC-MS instrument run and users have configured Slack as a notification target.

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SKILL.md

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Slack API Integration for Realtime QC-Fail Notifications

Summary

Dispatch realtime alerts to Slack channels when LC-MS quality control checks fail during instrument runs. This skill connects QC failure detection to user notification channels, enabling rapid response to data quality issues without manual monitoring.

When to use

Apply this skill when Rapid QC-MS detects a QC failure (e.g., internal standard retention time drift, m/z deviation, or intensity anomaly) during an active LC-MS instrument run and users have configured Slack as a notification target. Use when human intervention or awareness is time-critical and asynchronous notification (rather than polling) is preferred.

When NOT to use

  • Slack is not configured as a notification target in the system; fall back to email or other channels.
  • Users have disabled realtime notifications and prefer batch or manual log review.
  • Slack API credentials are invalid, revoked, or the workspace/channel no longer exists; graceful fallback and logging are required.

Inputs

  • QC check result with fail status (timestamp, check type, severity)
  • System configuration containing Slack channel ID and API credentials
  • Alert metadata (internal standard m/z, retention time, intensity thresholds)

Outputs

  • Slack message posted to configured channel
  • Dispatch log entry (timestamp, status: success/failure, message ID)
  • Delivery confirmation or error traceback

How to apply

Monitor QC check results for fail status during data acquisition. When a fail is detected, extract alert metadata (timestamp, check type, severity level) from the QC event. Retrieve the configured Slack channel ID and webhook endpoint from system configuration. Construct a notification payload with the alert details and dispatch it via the Slack API to the target channel. Log the dispatch status and confirm message delivery. Rationale: realtime push notification ensures users are informed immediately rather than discovering failures after instrument completion, enabling prompt troubleshooting of instrument or sample preparation issues.

Related tools

  • Slack API (Sends notification payloads to Slack channels and manages message delivery confirmation)
  • Email service (Alternative notification channel when Slack is unavailable or not configured)

Evaluation signals

  • Slack message appears in the configured channel within seconds of QC fail detection.
  • Message payload contains correct metadata: timestamp of QC check, check type (e.g., 'internal standard intensity'), severity level, and sample/run identifier.
  • Dispatch log records successful delivery with Slack message ID; failed dispatches log error reason (network, invalid credentials, channel not found).
  • Alert is not duplicated; only one message per unique QC failure event.
  • Message formatting is human-readable and includes actionable information (e.g., which sample, which check, remediation hint).

Limitations

  • Requires valid Slack workspace, channel, and API credentials; expired or revoked tokens will silently fail unless error handling is comprehensive.
  • Network latency or Slack API rate limits may delay notification delivery by seconds to minutes.
  • Slack API changes or deprecation may require code updates; this skill is tightly coupled to Slack's webhook and message API.
  • Only tested and deployed in Rapid QC-MS context; generalization to other QC or monitoring systems may require adaptation.
  • Alert fatigue: if QC thresholds are too permissive, users may receive excessive Slack notifications, reducing signal-to-noise ratio.

Evidence

  • [intro] Realtime updates on QC fails in the form of Slack or email notifications: "Realtime updates on QC fails in the form of Slack or email notifications"
  • [other] Parse QC-fail event and extract alert metadata (timestamp, check type, severity); Retrieve configured notification targets (Slack channel ID or email address); Dispatch notification payload via Slack API: "Parse QC-fail event and extract alert metadata (timestamp, check type, severity). 3. Retrieve configured notification targets (Slack channel ID or email address) from system configuration. 4."
  • [readme] Rapid QC-MS provides Automated and user-defined quality control checks during instrument runs: "Automated and user-defined quality control checks during instrument runs"

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