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Atlassian to eClinicalWorks integration — real-time, two-way sync

Keep Atlassian and eClinicalWorks in sync without custom scripts. Cut weeks of integration work, eliminate silent data drift, and give your team a single, reliable source of truth.

  • SOC 2 and 6 other compliance frameworks
  • POC with real engineers in minutes

Adopted by fast-scaling companies moving mission-critical data in real time

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Why teams connect Atlassian and eClinicalWorks

Stop re-entering the same information in Atlassian and eClinicalWorks: Stacksync keeps the records they share consistent in real time, in both directions.

Two tools in the daily stack often hold overlapping information: the same people, the same companies, or the same pieces of work, described twice. The tools do different jobs, so consolidating is not the answer; the overlap just needs to stop drifting.

Stacksync syncs Confluence Pages, Confluence Spaces, Jira Issues, Jira Projects in Atlassian with Practitioners, Observations, Medications, Allergies in eClinicalWorks in real time. You choose which records overlap, map the fields that should match, and pick a direction or let changes flow both ways. From then on, an update made in either tool is reflected in the other within seconds, without exports or copy-paste.

Because the sync is field-level, each tool keeps its own extras; only the shared data is held in agreement.

Common use cases

  • Keep Jira and a second tracker (for example a customer's Jira instance) aligned during co-delivery projects.
  • Sync Confluence page metadata into a knowledge index so other tools can link to current documentation.
  • Feed appointment events to reminder and messaging platforms to reduce no-shows.
  • Keep provider directories consistent between eClinicalWorks and scheduling or marketing systems.

Where eClinicalWorks is where the team documents or plans: keep its data fed

Information that originates in Atlassian stays current in eClinicalWorks instead of going stale after a one-time paste.

Handoffs between teams

When work started in one tool continues in the other, the shared fields travel with it automatically.

Where both tools track people or companies: one consistent record

Contact and company details corrected in either tool update the other, so nobody works from the old version.

What you can sync between Atlassian and eClinicalWorks

Representative objects on each side — any object or custom field can map to any target. Schemas are auto-detected; types are converted between the two systems.

Atlassian objects eClinicalWorks objects
Issue Comments Threaded discussion synced into linked tickets in external systems. Appointments Scheduling records available via FHIR and HL7 SIU messages, synced for reminders and outreach.
Attachments Files on issues mirrored to paired records where needed. Encounters Visit records tying diagnoses, providers, and billing context together.
Custom Fields Instance-specific fields (customfield IDs) that carry most business-specific data in syncs. Practitioners Provider records used to keep directories and scheduling systems consistent.
Workflows and Statuses Status transitions mapped to stages in the paired system. Observations Labs and vitals, delivered via FHIR resources or HL7 ORU result messages.
Users and Groups Assignees and reporters matched to identities in other tools. Medications Prescription and medication-list data within the patient record.
Confluence Pages Documentation content readable and writable through the Confluence REST API. Allergies Allergy and intolerance entries in the clinical record.
What ships with Atlassian ⇄ eClinicalWorks

Connect Atlassian and eClinicalWorks for flexible, real-time data sync.

Real-time sync, workflow automation, event queues, EDI, and monitoring, for every Atlassian–eClinicalWorks connection.

Real-time

Two-way sync

Changes in Atlassian or eClinicalWorks instantly reflect in both systems. No stale data, no manual imports.

No-code + pro-code

Workflow automation

Trigger automated workflows whenever Atlassian or eClinicalWorks data changes, update records, fire webhooks, or kick off sequences without brittle API scripts.

At scale

Event queues

Handle millions of events per minute without losing a single Atlassian or eClinicalWorks record.

Observability

Monitoring

Track your Atlassian ⇄ eClinicalWorks sync health, view errors, and replay failed events in one click.

Trading partners

EDI

Transform legacy EDI complexity into simple database interactions between Atlassian and eClinicalWorks.

How the Atlassian and eClinicalWorks connectors work

Atlassian

Integration surface
REST APIs per product (Jira Cloud and Confluence Cloud)
Authentication
OAuth 2.0 (3LO) for apps or API tokens with basic auth for scripts
Change detection
Webhooks on issue and page events, plus JQL polling on the updated timestamp for backfill
Capabilities
read · write · webhooks

eClinicalWorks

Integration surface
FHIR R4 REST API plus HL7 v2 interfaces (ADT, SIU, ORU) through an interface engine
Authentication
OAuth 2.0 / SMART on FHIR for the FHIR API; site-configured credentials for HL7 interface connections
Change detection
HL7 interface feeds push event messages as they occur; the FHIR API is polled
Capabilities
read · write
Rate limits
Subject to the platform's API rate limits and interface throughput agreements
How it works

How to connect Atlassian to eClinicalWorks — three steps, no code

Configure and sync within minutes, no code. Whether you sync 50k or 100M+ records, Stacksync handles the queues, infra, and plumbing. Integrations are non-invasive and need zero setup on your systems.

  1. 01

    Connect your apps

    Authenticate Atlassian and eClinicalWorks with each platform's native method — OAuth, API keys, or service accounts — plus secure options like SSH tunneling, IP whitelisting, and VPC peering.

    • OAuth 2.0
    • SSH tunnel
    • VPC peering
    Atlassian connected
    eClinicalWorks connected
    OAuth 2.0
    SSH tunnel
    SSL certificate
    VPC peering
  2. 02

    Choose tables

    Pick the Atlassian and eClinicalWorks objects to sync — Stacksync auto-detects both schemas, including custom fields where the platform exposes them. Sync to existing tables, or let Stacksync create new ones with ideal data types.

    • Standard objects
    • Custom objects
    • Auto-schema
    objects · Atlassian ⇄ eClinicalWorks
    Customers 12,480
    Sales Orders 8,213
    Invoices 5,902
    Items 1,344
  3. 03

    Map fields

    Fields map automatically even when names and types differ. Stacksync handles transformation and type casting for you, zero configuration required.

    • Auto-map
    • Type casting
    • Transforms
    Atlassian eClinicalWorks
    Company company_name text
    Email email text
    Amount amount numeric
    Created created_at timestamp
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FAQ

Atlassian and eClinicalWorks integration FAQ

SECURITY

Security teams love Stacksync

As a data company, we understand the importance of keeping your data secure. Stacksync is built with security best practices to keep your data safe at every layer, and is DPF-certified for US, EU, UK and CH data transfers.

Learn more about security
SOC 2 type II
ISO 27001
HIPAA BAA
GDPR
CCPA
CSA STAR
DPF US-EU-UK-CH
→ SECURITY WITH BENEFITS

SSO & SCIM

Let your users access Stacksync from your centralized user management systems. Works with Okta, Azure, Google SSO and more.

Alerts

Immediately get alerted about record syncing issues over email, Slack, PagerDuty and WhatsApp. Resolve issues from a centralized dashboard with retry and revert options.

Secure connection options

Securely connects to your systems with:

OAuth 2 SSH Tunnelling SSL certificates IP Whitelisting VPN gateway VPC peering and more

Related integrations

Every pair below is a real-time, two-way sync. Search all 386 integrations available for Atlassian and eClinicalWorks.

Popular · 8 of 386
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