> ## Documentation Index
> Fetch the complete documentation index at: https://docs.open-metadata.org/llms.txt
> Use this file to discover all available pages before exploring further.

# Run the Epic FHIR Connector Externally

> Configure Epic FHIR ingestion using YAML to automate FHIR resource metadata collection.

export const CodePanel = ({children, fileName = 'config.yaml', showLineNumbers = false}) => {
  const codePanelRef = useRef(null);
  const codeContentRef = useRef(null);
  const isProgrammaticScroll = useRef(false);
  const hoverTimeout = useRef(null);
  useEffect(() => {
    let tries = 0;
    const wrapLines = () => {
      const root = codeContentRef.current;
      if (!root) return;
      const pres = Array.from(root.querySelectorAll('pre'));
      if (!pres.length) {
        if (tries++ < 20) requestAnimationFrame(wrapLines);
        return;
      }
      let globalLine = 1;
      pres.forEach(pre => {
        const code = pre.querySelector('code') || pre;
        if (!code || code.dataset.wrapped === 'true') return;
        const raw = code.textContent || '';
        let lines = raw.split('\n');
        while (lines[0] === '') lines.shift();
        while (lines[lines.length - 1] === '') lines.pop();
        code.innerHTML = lines.map(line => {
          const ln = globalLine++;
          const num = showLineNumbers ? `<span class="line-number">${ln}</span>` : '';
          const safe = line.replace(/</g, '&lt;').replace(/>/g, '&gt;') || ' ';
          return `<span class="code-line" data-line="${ln}">${num}${safe}</span>`;
        }).join('');
        code.dataset.wrapped = 'true';
      });
    };
    wrapLines();
  }, [children, showLineNumbers]);
  useEffect(() => {
    const panel = codePanelRef.current;
    const content = codeContentRef.current;
    if (!panel || !content) return;
    const waitForLines = () => {
      const codeLines = content.querySelectorAll('.code-line');
      if (!codeLines.length) {
        requestAnimationFrame(waitForLines);
        return;
      }
      setupHighlighting(codeLines);
    };
    const setupHighlighting = codeLines => {
      const layout = panel.closest('.split-layout');
      const sections = layout.querySelectorAll('.content-section');
      const parseLines = str => {
        if (!str) return [];
        const out = [];
        str.split(',').forEach(p => {
          if (p.includes('-')) {
            const [s, e] = p.split('-').map(Number);
            for (let i = s; i <= e; i++) out.push(i);
          } else {
            const n = Number(p);
            if (!isNaN(n)) out.push(n);
          }
        });
        return out;
      };
      const clearHighlight = () => {
        codeLines.forEach(l => l.classList.remove('highlighted'));
      };
      const highlight = lines => {
        clearHighlight();
        lines.forEach(n => {
          const el = content.querySelector(`.code-line[data-line="${n}"]`);
          if (el) el.classList.add('highlighted');
        });
      };
      const scrollToLines = lines => {
        if (!lines.length) return;
        const first = lines[0];
        const targetLine = lines.length > 1 ? first : lines[0];
        const el = content.querySelector(`.code-line[data-line="${targetLine}"]`);
        if (!el) return;
        isProgrammaticScroll.current = true;
        const containerRect = content.getBoundingClientRect();
        const elRect = el.getBoundingClientRect();
        const offset = elRect.top - containerRect.top + content.scrollTop;
        const TOP_PADDING = 16;
        content.scrollTo({
          top: Math.max(offset - TOP_PADDING, 0),
          behavior: 'smooth'
        });
        setTimeout(() => {
          isProgrammaticScroll.current = false;
        }, 200);
      };
      const activate = (section, scroll) => {
        if (section.classList.contains('active')) return;
        sections.forEach(s => s.classList.remove('active'));
        section.classList.add('active');
        const lines = parseLines(section.dataset.lines);
        highlight(lines);
        if (scroll) scrollToLines(lines);
      };
      const observer = new IntersectionObserver(entries => {
        if (isProgrammaticScroll.current) return;
        entries.forEach(e => {
          if (e.isIntersecting) activate(e.target, false);
        });
      }, {
        threshold: 0.3,
        rootMargin: '-80px 0px -40% 0px'
      });
      sections.forEach(section => {
        observer.observe(section);
        section.addEventListener('click', () => activate(section, true));
        section.addEventListener('mouseenter', () => {
          clearTimeout(hoverTimeout.current);
          hoverTimeout.current = setTimeout(() => activate(section, true), 80);
        });
      });
      if (sections[0]) activate(sections[0], false);
    };
    waitForLines();
  }, []);
  const handleCopy = e => {
    const btn = e.currentTarget;
    const codeLines = codeContentRef.current?.querySelectorAll('.code-line');
    if (!codeLines || codeLines.length === 0) return;
    const text = Array.from(codeLines).map(line => {
      const clone = line.cloneNode(true);
      const lineNumber = clone.querySelector('.line-number');
      if (lineNumber) lineNumber.remove();
      return clone.textContent;
    }).join('\n');
    if (!text) return;
    navigator.clipboard.writeText(text).then(() => {
      btn.dataset.copied = 'true';
      setTimeout(() => btn.dataset.copied = 'false', 1500);
    });
  };
  return <div className="code-panel" ref={codePanelRef}>
      <div className="code-header">
        {fileName}
        <button className="copy-btn" aria-label="Copy full code" data-copied="false" onClick={handleCopy}>
          <svg className="icon-copy" viewBox="0 0 15 16" fill="currentColor">
            <path d="M10.113 3.124H2.205C1.463 3.124.86 3.655.86 4.31v10.005c0 .654.603 1.186 1.345 1.186h7.908c.742 0 1.345-.532 1.345-1.186V4.31c0-.655-.606-1.186-1.345-1.186Z" />
            <path d="M13.138.5H5.229c-.742 0-1.344.531-1.344 1.186 0 .23.209.414.47.414s.47-.184.47-.414c0-.197.182-.357.404-.357h7.909c.223 0 .404.16.404.357V11.69c0 .196-.181.356-.404.356-.262 0-.47.184-.47.415 0 .23.208.415.47.415.742 0 1.344-.532 1.344-1.186V1.686C14.482 1.03 13.88.5 13.138.5Z" />
          </svg>

          <svg className="icon-check" viewBox="0 0 20 20" fill="currentColor">
            <path fillRule="evenodd" d="M16.707 5.293a1 1 0 010 1.414l-7.25 7.25a1 1 0 01-1.414 0l-3.25-3.25a1 1 0 011.414-1.414l2.543 2.543 6.543-6.543a1 1 0 011.414 0z" clipRule="evenodd" />
          </svg>
        </button>
      </div>

      <div className="code-content" ref={codeContentRef}>
        {children}
      </div>
    </div>;
};

export const ContentSection = ({id, title, lines, children}) => <div className="content-section" data-content-id={id} data-lines={lines}>
    {title && <h4>{title}</h4>}
    {children}
  </div>;

export const ContentPanel = ({children}) => <div className="content-panel">{children}</div>;

export const CodePreview = ({children}) => {
  const [instanceId] = useState(() => `preview-${Math.random().toString(36).slice(2)}`);
  useEffect(() => {
    const nav = document.querySelector('nav') || document.querySelector('header') || document.querySelector('[class*="nav"]');
    if (nav) {
      document.documentElement.style.setProperty('--navbar-height', `${nav.offsetHeight}px`);
    }
  }, []);
  return <div className="split-layout" data-preview-id={instanceId}>
      {children}
    </div>;
};

export const ConnectorDetailsHeader = ({name, icon, stage, availableFeatures, unavailableFeatures = [], availableFeaturesCollate = []}) => {
  const showSubHeading = availableFeatures?.length > 0 || unavailableFeatures?.length > 0 || availableFeaturesCollate?.length > 0;
  const totalAvailableFeatures = [...availableFeatures || [], ...availableFeaturesCollate || []];
  return <div className="container">
      <div className="Heading">
        <div className="flex items-center gap-3">
          {icon && <div className="IconContainer">
              <img src={icon} alt={name} noZoom className="ConnectorIcon" />
            </div>}
          <h1 className="ConnectorName">{name}</h1>
          <span className={`StageBadge ${stage === 'PROD' ? 'prod' : 'beta'}`}>
            {stage}
          </span>
        </div>
      </div>
      {showSubHeading && <div className="SubHeading">
          <div className="FeaturesHeading">Feature List</div>
          <div className="FeaturesList">
            {totalAvailableFeatures.map(feature => <div className="FeatureTag AvailableFeature" key={feature}>
                ✓ {feature}
              </div>)}
            {unavailableFeatures.map(feature => <div className="FeatureTag UnavailableFeature" key={feature}>
                ✕ {feature}
              </div>)}
          </div>
        </div>}
    </div>;
};

<ConnectorDetailsHeader icon="/public/images/connectors/epic.png" name="Epic" stage="BETA" availableFeatures={["Metadata"]} unavailableFeatures={["Data Profiler", "Data Quality", "dbt", "Lineage", "Column-level Lineage", "Query Usage", "Owners", "Tags", "Sample Data", "Reverse Metadata (Collate Only)", "Auto-Classification", "Stored Procedures"]} />

In this section, we provide guides and references to use the Epic FHIR connector.
Configure and schedule Epic metadata workflows from the Collate UI:

* [Requirements](#requirements)
* [Metadata Ingestion](#metadata-ingestion)

<ExternalIngestionDeployment />

## Requirements

To run the Epic ingestion, install the Python package:

```bash theme={null}
pip3 install "openmetadata-ingestion[epic]"
```

## Metadata Ingestion

All connectors are defined as JSON Schemas.
[Here](https://github.com/open-metadata/OpenMetadata/blob/main/openmetadata-spec/src/main/resources/json/schema/entity/services/connections/database/epicConnection.json) you can find the structure to create a connection to Epic.
The ingestion workflow itself follows the general [workflow schema](https://github.com/open-metadata/OpenMetadata/blob/main/openmetadata-spec/src/main/resources/json/schema/metadataIngestion/workflow.json).

### 1. Define the YAML Config

<CodePreview>
  <ContentPanel>
    <ContentSection id={1} title="Source Configuration" lines="1-3">
      Configure the source type and service name for your Epic FHIR connector.
    </ContentSection>

    <ContentSection id={2} title="FHIR Server URL" lines="7">
      **fhirServerUrl**: Base URL of the Epic FHIR server.
    </ContentSection>

    <ContentSection id={3} title="FHIR Version" lines="8">
      **fhirVersion**: FHIR specification version supported (`R4`, `STU3`, or `DSTU2`).
    </ContentSection>

    <ContentSection id={4} title="Database Name" lines="10">
      **databaseName**: Optional name for the database in OpenMetadata. Defaults to `epic`.
    </ContentSection>

    <ContentSection id={5} title="Filter Patterns" lines="34-54">
      **schemaFilterPattern / tableFilterPattern**: Regex filters to limit which FHIR resource categories (schemas) or resource types (tables) are ingested.
    </ContentSection>

    <ContentSection id={6} title="Source Config" lines="11-54">
      #### Source Configuration - Source Config

      The `sourceConfig` is defined [here](https://github.com/open-metadata/OpenMetadata/blob/main/openmetadata-spec/src/main/resources/json/schema/metadataIngestion/databaseServiceMetadataPipeline.json):

      <div>
        **markDeletedTables**: To flag tables as soft-deleted if they are not present anymore in the source system.
      </div>

      <div>
        **markDeletedStoredProcedures**: Optional configuration to soft delete stored procedures in OpenMetadata if the source stored procedures are deleted. Also, if the stored procedures is deleted, all the associated entities like lineage, etc., with that stored procedures will be deleted.

        **markDeletedSchemas**: Optional configuration to soft delete schemas stored in OpenMetadata if the source schema is deleted. Setting this flag to true will only keep filtered schema and delete any other schemas that do not match schemaFilterPattern or do not exist at source.

        **markDeletedDatabases**: Additional optional configuration for soft deletion, providing granular option to select which particular entities should be deleted.

        **includeTables**: true or false, to ingest table data. Default is true.
      </div>

      <div>
        **includeViews**: true or false, to ingest views definitions.
      </div>

      <div>
        **includeTags**: Optional configuration to toggle the tags ingestion.
      </div>

      <div>
        **includeOwners**: Set the 'Include Owners' toggle to control whether to include owners to the ingested entity if the owner email matches with a user stored in the OM server as part of metadata ingestion. If the ingested entity already exists and has an owner, the owner will not be overwritten.
      </div>

      <div>
        **includeStoredProcedures**: Optional configuration to toggle the Stored Procedures ingestion.
      </div>

      <div>
        **includeDDL**: Optional configuration to toggle the DDL Statements ingestion.
      </div>

      <div>
        **overrideMetadata** *(boolean)*: Set the 'Override Metadata' toggle to control whether to override the existing metadata in the OpenMetadata server with the metadata fetched from the source. If the toggle is set to true, the metadata fetched from the source will override the existing metadata in the OpenMetadata server. If the toggle is set to false, the metadata fetched from the source will not override the existing metadata in the OpenMetadata server. This is applicable for fields like description, tags, owner and displayName.
      </div>

      <div>
        **queryLogDuration**: Configuration to tune how far we want to look back in query logs to process Stored Procedures results.
      </div>

      <div>
        **queryParsingTimeoutLimit**: Configuration to set the timeout for parsing the query in seconds.
      </div>

      <div>
        **useFqnForFiltering**: Regex will be applied on fully qualified name (e.g service\_name.db\_name.schema\_name.table\_name) instead of raw name (e.g. table\_name).
      </div>

      <div>
        **databaseFilterPattern**, **schemaFilterPattern**: Note that the filter supports regex as include or exclude. You can find examples [here](/connectors/ingestion/workflows/metadata/filter-patterns/database)
      </div>

      <div>
        **tableFilterPattern**: Note that the filter supports regex as include or exclude. You can find examples [here](/connectors/ingestion/workflows/metadata/filter-patterns/table)
      </div>

      <div>
        **threads (beta)**: The number of threads to use when extracting the metadata using multithreading.
      </div>

      <div>
        **databaseMetadataConfigType** *(string)*: Database Source Config Metadata Pipeline type.
      </div>

      <div>
        **incremental (beta)**: Incremental Extraction configuration. Currently implemented for:

        * [BigQuery](/connectors/ingestion/workflows/metadata/incremental-extraction/bigquery)
        * [Redshift](/connectors/ingestion/workflows/metadata/incremental-extraction/redshift)
        * [Snowflake](/connectors/ingestion/workflows/metadata/incremental-extraction/snowflake)
      </div>
    </ContentSection>

    <ContentSection id={7} title="Sink Configuration" lines="55-57">
      To send the metadata to OpenMetadata, it needs to be specified as `type: metadata-rest`.
    </ContentSection>

    <ContentSection id={8} title="Workflow Configuration" lines="58-74">
      <div>
        The main property here is the `openMetadataServerConfig`, where you can define the host and security provider of your OpenMetadata installation.
      </div>

      <div>
        **Logger Level**

        You can specify the `loggerLevel` depending on your needs. If you are trying to troubleshoot an ingestion, running with `DEBUG` will give you far more traces for identifying issues.
      </div>

      <div>
        **JWT Token**

        JWT tokens will allow your clients to authenticate against the OpenMetadata server. To enable JWT Tokens, you will get more details [here](/deployment/security/enable-jwt-tokens).

        You can refer to the JWT Troubleshooting section [link](/deployment/security/jwt-troubleshooting) for any issues in your JWT configuration.
      </div>

      <div>
        **Store Service Connection**

        If set to `true` (default), we will store the sensitive information either encrypted via the Fernet Key in the database or externally, if you have configured any [Secrets Manager](/deployment/secrets-manager).

        If set to `false`, the service will be created, but the service connection information will only be used by the Ingestion Framework at runtime, and won't be sent to the OpenMetadata server.
      </div>

      <div>
        **SSL Configuration**

        If you have added SSL to the [OpenMetadata server](/deployment/security/enable-ssl), then you will need to handle the certificates when running the ingestion too. You can either set `verifySSL` to `ignore`, or have it as `validate`, which will require you to set the `sslConfig.caCertificate` with a local path where your ingestion runs that points to the server certificate file.

        Find more information on how to troubleshoot SSL issues [here](/deployment/security/enable-ssl/ssl-troubleshooting).
      </div>

      <div>
        **ingestionPipelineFQN**

        Fully qualified name of ingestion pipeline, used to identify the current ingestion pipeline.
      </div>
    </ContentSection>
  </ContentPanel>

  <CodePanel fileName="epic_config.yaml">
    ```yaml theme={null}
    source:
      type: epic
      serviceName: epic_fhir
      serviceConnection:
        config:
          type: Epic
          fhirServerUrl: https://fhir.epic.com/interconnect-fhir-oauth/api/FHIR/R4  # REQUIRED
          fhirVersion: R4  # REQUIRED
          # Optional:
          # databaseName: epic
    ```

    ```yaml theme={null}
      sourceConfig:
        config:
          type: DatabaseMetadata
          markDeletedTables: true
          markDeletedStoredProcedures: true
          markDeletedSchemas: true
          markDeletedDatabases: true
          includeTables: true
          includeViews: true
          # includeTags: true
          # includeOwners: false
          # includeStoredProcedures: true
          # includeDDL: true
          # overrideMetadata: false
          # queryLogDuration: 1
          # queryParsingTimeoutLimit: 300
          # useFqnForFiltering: false
          # threads: 1
          # databaseMetadataConfigType: ()
          # incremental:
          #   enabled: true
          #   lookbackDays: 7
          #   safetyMarginDays: 1
          # databaseFilterPattern:
          #   includes:
          #     - database1
          #     - database2
          #   excludes:
          #     - database3
          #     - database4
          # schemaFilterPattern:
          #   includes:
          #     - schema1
          #     - schema2
          #   excludes:
          #     - schema3
          #     - schema4
          # tableFilterPattern:
          #   includes:
          #     - users
          #     - type_test
          #   excludes:
          #     - table3
          #     - table4
    ```

    ```yaml theme={null}
    sink:
      type: metadata-rest
      config: {}
    ```

    ```yaml theme={null}
    workflowConfig:
      loggerLevel: INFO  # DEBUG, INFO, WARNING or ERROR
      openMetadataServerConfig:
        hostPort: "http://localhost:8585/api"
        authProvider: openmetadata
        securityConfig:
          jwtToken: "{bot_jwt_token}"
        ## Store the service Connection information
        storeServiceConnection: true  # false
        ## Secrets Manager Configuration
        # secretsManagerProvider: aws, azure or noop
        # secretsManagerLoader: airflow or env
        ## If SSL, fill the following
        # verifySSL: validate  # or ignore
        # sslConfig:
        #   caCertificate: /local/path/to/certificate
    # ingestionPipelineFQN: <service name>.<ingestion name> ## e.g., "my_redshift.metadata"
    ```
  </CodePanel>
</CodePreview>