Add the openfn package to platform. Also fixed CU-86bzwyh69 #322
Conversation
WalkthroughThe Changes
Sequence Diagram(s)sequenceDiagram
participant User
participant System
participant Config
participant DockerCompose
User->>System: Request to update configuration
System->>Config: Add openfn package
Config-->>System: Package added confirmation
System->>DockerCompose: Configure openfn and worker services
DockerCompose-->>System: Services configured
System-->>User: Configuration updated successfully
Possibly related PRs
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Actionable comments posted: 7
Outside diff range, codebase verification and nitpick comments (7)
openfn/importer/workflows/docker-compose.config.yml (1)
19-22: Consider a more robust restart policy for production.The current restart policy (
condition: none) is suitable for development but consider using a more robust policy likeon-failureoralwaysfor production environments to ensure service reliability.- condition: none + condition: on-failureopenfn/importer/postgres/docker-compose.config.yml (1)
23-26: Consider a more robust restart policy for production.The current restart policy (
condition: none) is suitable for development but consider using a more robust policy likeon-failureoralwaysfor production environments to ensure service reliability.- condition: none + condition: on-failuredocumentation/packages/openfn/README.md (1)
5-11: Specify language for code block in usage section.To improve readability and follow best practices, specify the language for the code block in the usage section.
-`instant package init -n openfn --dev` +```bash +instant package init -n openfn --dev +```openfn/swarm.sh (3)
66-68: Consider logging the stack destruction.In the
destroy_packagefunction, consider adding a log statement before destroying the stack to provide more context in the logs.log info "Destroying stack $STACK"
70-89: Enhance error messaging inmain.The
mainfunction logs an error if an invalid action is provided. Consider providing more detailed guidance on valid options.log error "Invalid action: $ACTION. Valid options are: init, up, down, or destroy."
1-1: Add Executable Permissions toswarm.sh.The file
openfn/swarm.shcurrently lacks executable permissions. To execute this script directly, set the executable bit usingchmod +x openfn/swarm.sh.
- Current permissions:
-rw-r--r--- Required action:
chmod +x openfn/swarm.shAnalysis chain
Ensure executable permissions.
Since this is a shell script, ensure that it has executable permissions set in the repository.
Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify that the swarm.sh script has executable permissions. # Test: Check file permissions. Expect: Executable bit set. ls -l openfn/swarm.shLength of output: 88
openfn/package-metadata.json (1)
4-4: Remove HTML entities in the description.The description contains HTML entities (
') which should be replaced with the appropriate character (')."description": "Lightning ⚡ (OpenFn v2) is a workflow automation platform that's used to automate critical business processes and integrate information systems.",
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Files ignored due to path filters (1)
openfn/importer/postgres/package-lock.jsonis excluded by!**/package-lock.json
Files selected for processing (12)
- config.yaml (1 hunks)
- documentation/packages/openfn/README.md (1 hunks)
- documentation/packages/openfn/environment-variables.md (1 hunks)
- kafka-mapper-consumer/docker-compose.config.yml (1 hunks)
- openfn/docker-compose.dev.yml (1 hunks)
- openfn/docker-compose.yml (1 hunks)
- openfn/importer/postgres/create-db.js (1 hunks)
- openfn/importer/postgres/docker-compose.config.yml (1 hunks)
- openfn/importer/postgres/package.json (1 hunks)
- openfn/importer/workflows/docker-compose.config.yml (1 hunks)
- openfn/package-metadata.json (1 hunks)
- openfn/swarm.sh (1 hunks)
Files skipped from review due to trivial changes (3)
- config.yaml
- openfn/docker-compose.dev.yml
- openfn/importer/postgres/package.json
Additional context used
Markdownlint
documentation/packages/openfn/README.md
24-24: null
Fenced code blocks should have a language specified(MD040, fenced-code-language)
Gitleaks
openfn/package-metadata.json
31-31: Uncovered a JSON Web Token, which may lead to unauthorized access to web applications and sensitive user data.
(jwt)
Additional comments not posted (14)
openfn/importer/workflows/docker-compose.config.yml (4)
1-6: Use specific Node.js version and global npm package installation.Using a specific Node.js version (
node:18-alpine3.20) ensures consistency across environments. Installing npm packages globally (npm install -g @openfn/cli) is suitable for CLI tools but be mindful of potential version conflicts.
14-18: Good use of environment variables and external network.Using environment variables for sensitive information like API keys and URLs is a best practice. The external network
postgres_publicensures connectivity with the database.
24-44: Dynamic config names and external network definition are well-implemented.Using dynamic names for configuration files based on digests ensures uniqueness and traceability. The external network
postgres_publicis correctly defined.
7-13: Verify configuration files availability and correctness.Ensure that the configuration files (
cdr-ndr.yaml,config.json,project.yaml) are present in the specified paths and contain the correct configurations for your deployment.openfn/importer/postgres/docker-compose.config.yml (4)
1-6: Use specific Node.js version and npm package installation.Using a specific Node.js version (
node:erbium-alpine) ensures consistency across environments. Installing npm packages (npm i) is necessary for running thecreate-db.jsscript.
12-22: Good use of environment variables and external network.Using environment variables for sensitive information like database credentials is a best practice. The external network
postgres_publicensures connectivity with the database.
28-43: Dynamic config names and external network definition are well-implemented.Using dynamic names for configuration files based on digests ensures uniqueness and traceability. The external network
postgres_publicis correctly defined.
7-11: Verify configuration files availability and correctness.Ensure that the configuration files (
package.json,create-db.js) are present in the specified paths and contain the correct configurations for your deployment.documentation/packages/openfn/README.md (2)
29-31: Documentation section is well-structured.The link to the official documentation is appropriate and provides additional resources for users.
15-27: Exercise caution with sensitive information in documentation.Providing demo credentials in documentation can be risky. Ensure these credentials are intended for public use and consider alternative methods for sharing sensitive information.
Tools
Markdownlint
24-24: null
Fenced code blocks should have a language specified(MD040, fenced-code-language)
openfn/docker-compose.yml (1)
1-40: Configuration looks good!The Docker Compose file is well-structured and uses environment variables effectively for configuration. Ensure that all environment variables used are defined in the environment where this Docker Compose file will be deployed.
kafka-mapper-consumer/docker-compose.config.yml (1)
30-30: Change approved!The update to the digest variable name aligns with the service's context, which should improve clarity in the configuration.
Verification successful
Verification complete: No issues found with the updated digest variable usage.
The variable
kafka_mapper_consumer_openhimConfig_js_DIGESTis used only in the specified line within thedocker-compose.config.ymlfile, indicating consistent usage within this context. No further occurrences were found in thekafka-mapper-consumerdirectory.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the impact of the updated digest variable. # Test: Search for the updated digest variable usage. # Expect: The new variable should be used consistently across the codebase. rg --type yaml 'kafka_mapper_consumer_openhimConfig_js_DIGEST' kafka-mapper-consumer/Length of output: 236
openfn/importer/postgres/create-db.js (1)
60-72: Overall logic is sound.The script correctly handles database and user creation, checking for existence before attempting to create them. Ensure that error handling covers all potential failure points.
openfn/swarm.sh (1)
28-32: Verify the existence of utility scripts.The
import_sourcesfunction assumes that the utility scripts exist at the specified paths. Ensure these files are present and accessible.
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brett-onions
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
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Actionable comments posted: 1
Outside diff range, codebase verification and nitpick comments (1)
openfn/importer/postgres/create-db.js (1)
67-67: Improve error logging for better debugging.Consider logging the full error object instead of just the message to get more context about the error.
- console.error("Error in db operations:", error.message); + console.error("Error in db operations:", error);
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Files selected for processing (1)
- openfn/importer/postgres/create-db.js (1 hunks)
Additional context used
Biome
openfn/importer/postgres/create-db.js
[error] 52-52: expected
,but instead foundawaitRemove await
(parse)
[error] 54-54: expected
,but instead found;Remove ;
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Additional comments not posted (3)
openfn/importer/postgres/create-db.js (3)
3-10: Securely handle sensitive data.Avoid using hardcoded fallback values for sensitive information like passwords. Use environment variables or secret management tools to manage these values securely.
35-35: Use parameterized queries to prevent SQL injection.The current use of string interpolation for creating the database is vulnerable to SQL injection. Use parameterized queries instead.
51-51: Fix syntax error and use parameterized queries.There is a syntax error due to a missing closing parenthesis. Additionally, use parameterized queries to prevent SQL injection.
- await client.query( - 'CREATE USER $1 WITH ENCRYPTED PASSWORD $2;', [newUser, newUserPassword] + await client.query( + 'CREATE USER $1 WITH ENCRYPTED PASSWORD $2;', [newUser, newUserPassword] + );Likely invalid or redundant comment.
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Actionable comments posted: 1
Outside diff range, codebase verification and nitpick comments (4)
openfn/importer/workflows/example/cdr-ndr.yaml (2)
16-20: Remove trailing spaces.Trailing spaces are present in multiple lines, which can lead to formatting inconsistencies. Consider removing them for cleaner code.
- const parsedData = JSON.parse(state.data.body); - console.log(parsedData); - state.resource = parsedData.entry[0].resource; - console.log('show only the resource:: ', state.resource); - return state; + const parsedData = JSON.parse(state.data.body); + console.log(parsedData); + state.resource = parsedData.entry[0].resource; + console.log('show only the resource:: ', state.resource); + return state;Also applies to: 34-35, 37-37, 84-84, 86-87, 92-93, 115-116, 118-123
Tools
yamllint
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29-29: Typographical Error: Correct comment spelling.The comment contains a typographical error: "Removig" should be "Removing."
- //Removig PII here before sending it to NDR + //Removing PII here before sending it to NDRopenfn/importer/workflows/example/project.yaml (2)
16-20: Remove trailing spaces.Trailing spaces are present in multiple lines, which can lead to formatting inconsistencies. Consider removing them for cleaner code.
- const parsedData = JSON.parse(state.data.body); - console.log(parsedData); - state.resource = parsedData.entry[0].resource; - console.log('show only the resource:: ', state.resource); - return state; + const parsedData = JSON.parse(state.data.body); + console.log(parsedData); + state.resource = parsedData.entry[0].resource; + console.log('show only the resource:: ', state.resource); + return state;Also applies to: 34-35, 37-37, 84-84, 86-87, 92-93, 115-116, 118-123
Tools
yamllint
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29-29: Typographical Error: Correct comment spelling.The comment contains a typographical error: "Removig" should be "Removing."
- //Removig PII here before sending it to NDR + //Removing PII here before sending it to NDR
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Files selected for processing (3)
- openfn/importer/workflows/example/cdr-ndr.yaml (1 hunks)
- openfn/importer/workflows/example/config.json (1 hunks)
- openfn/importer/workflows/example/project.yaml (1 hunks)
Additional context used
Gitleaks
openfn/importer/workflows/example/config.json
4-4: Uncovered a JSON Web Token, which may lead to unauthorized access to web applications and sensitive user data.
(jwt)
yamllint
openfn/importer/workflows/example/cdr-ndr.yaml
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openfn/importer/workflows/example/project.yaml
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Actionable comments posted: 0
Outside diff range, codebase verification and nitpick comments (3)
openfn/docker-compose.yml (3)
6-6: Consider simplifying the command for readability.The command for the
openfnservice is complex and could be broken down into a script or multiple lines for better readability and maintainability.command: > sh -c ' /app/bin/lightning eval "Lightning.Release.migrate()" && /app/bin/lightning eval "Lightning.Demo.reset_demo()" && /app/bin/lightning start '
34-44: Environment Variables Not Set forworkerServiceThe following environment variables required for the
workerservice are not set, which may lead to issues in its operation:
OpenFn_WORKER_IMAGEWORKER_LIGHTNING_PUBLIC_KEYWORKER_SECRETNODE_ENVEnsure these variables are properly defined in your environment or in a
.envfile used by Docker Compose. This is crucial for the correct functioning of theworkerservice.Analysis chain
workerservice configuration looks good. Verify environment variables.The configuration for the
workerservice is clear and concise. Ensure that all environment variables are correctly set.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify that all environment variables for the worker service are set correctly. # Test: List all environment variables used and check if they are set. env_vars=( "OpenFn_WORKER_IMAGE" "WORKER_LIGHTNING_PUBLIC_KEY" "WORKER_SECRET" "NODE_ENV" ) for var in "${env_vars[@]}"; do if [ -z "${!var}" ]; then echo "Warning: $var is not set." fi doneLength of output: 621
12-22: Environment Variables Not SetThe following environment variables are not set in the current environment, which might lead to issues if they are required for the application to function properly:
DATABASE_URLDISABLE_DB_SSLIS_RESETTABLE_DEMOLISTEN_ADDRESSLOG_LEVELORIGINSPRIMARY_ENCRYPTION_KEYSECRET_KEY_BASEWORKER_RUNS_PRIVATE_KEYWORKER_SECRETKAFKA_TRIGGERS_ENABLED(note: this variable is not listed in thedocker-compose.ymlsnippet provided)Please ensure these variables are correctly set in the environment where the Docker Compose file will be used.
Analysis chain
Verify environment variables for correctness.
Ensure that all environment variables are correctly set in the environment where this Docker Compose file will be used. This includes checking for any missing or incorrectly named variables.
Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify that all environment variables are set correctly. # Test: List all environment variables used and check if they are set. env_vars=( "DATABASE_URL" "DISABLE_DB_SSL" "IS_RESETTABLE_DEMO" "LISTEN_ADDRESS" "LOG_LEVEL" "ORIGINS" "PRIMARY_ENCRYPTION_KEY" "SECRET_KEY_BASE" "WORKER_RUNS_PRIVATE_KEY" "WORKER_SECRET" "KAFKA_TRIGGERS_ENABLED" ) for var in "${env_vars[@]}"; do if [ -z "${!var}" ]; then echo "Warning: $var is not set." fi doneLength of output: 1641
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Files selected for processing (3)
- openfn/docker-compose.dev.yml (1 hunks)
- openfn/docker-compose.yml (1 hunks)
- openfn/importer/postgres/create-db.js (1 hunks)
Files skipped from review as they are similar to previous changes (2)
- openfn/docker-compose.dev.yml
- openfn/importer/postgres/create-db.js
Additional comments not posted (2)
openfn/docker-compose.yml (2)
1-1: Version declaration is correct.The version '3.9' is a valid and recent Docker Compose version.
49-55: Network settings are appropriate. Verify network existence.The use of external networks
kafka_publicandpostgresis appropriate. Ensure these networks exist and are correctly configured in the Docker environment.
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Files ignored due to path filters (1)
test/cucumber/package-lock.jsonis excluded by!**/package-lock.json
Files selected for processing (4)
- config.yaml (2 hunks)
- test/cucumber/features/single-mode/openfn.feature (1 hunks)
- test/cucumber/features/single-mode/recipe.feature (1 hunks)
- test/cucumber/package.json (1 hunks)
Files skipped from review as they are similar to previous changes (1)
- config.yaml
Additional comments not posted (3)
test/cucumber/features/single-mode/openfn.feature (2)
4-13: ScenarioInit OpenFnis well-defined.The scenario comprehensively tests the initialization of the OpenFn package, including service startups and network connections.
14-24: ScenarioDestroy OpenFnis well-defined.The scenario thoroughly tests the destruction of the OpenFn package, ensuring all services, volumes, configs, and networks are removed.
test/cucumber/package.json (1)
34-34: New test commandtest:single:openfnis correctly added.The command for testing the OpenFn feature is well-integrated and follows the existing pattern.
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Actionable comments posted: 6
🧹 Outside diff range and nitpick comments (8)
openfn/package-metadata.json (2)
1-7: LGTM! Consider version number strategy.The basic metadata looks good. However, given that this seems to be a configuration for a production-ready platform (OpenFn v2), you might want to reconsider the version number "0.0.1".
Consider adopting a more meaningful versioning strategy that aligns with your release cycle and the maturity of the platform.
28-29: Specify a version for the worker image.Good job on using a specific version for the OpenFn image. This practice ensures consistency across different environments.
However, for the worker image, consider specifying a version instead of using the 'latest' tag. Using 'latest' can lead to inconsistencies and unexpected behavior in production environments.
Example:
"OpenFn_WORKER_IMAGE": "openfn/ws-worker:v1.2.3"Replace "v1.2.3" with the appropriate version number. This ensures that you have control over which version of the worker is being used in your environment.
openfn/importer/workflows/example/project.yaml (6)
8-40: LGTM: parse-bundle job is well-structured.The job effectively parses and sorts incoming data bundles. The logging of resource type counts is a helpful feature for monitoring and debugging.
Consider adding more detailed error logging for the JSON parsing step. For example:
if (typeof data === "string") { try { data = JSON.parse(data); } catch (error) { console.error(`Error parsing JSON: ${error.message}`); // Handle the error appropriately } }This will provide more context if there are issues with malformed JSON input.
41-111: LGTM with suggestions: Register-Organization job is functional but could be improved.The job successfully creates and registers an organization based on the first patient's managing organization. However, there are a few areas for potential improvement:
Using the first patient's managing organization might not be suitable for all scenarios. Consider adding a comment explaining this choice or implementing a more robust selection method.
Error handling for the HTTP request is missing.
Consider adding error handling for the HTTP request:
put(`/fhir/Organization/${$.orgId}`, { body: $.mappedOrganization, headers: { 'content-type': 'application/json' }, }).then((response) => { console.log('Organization registered successfully!'); return response; }).catch((error) => { console.error('Error registering organization:', error); // Handle the error appropriately });This will provide better visibility into any issues that occur during the organization registration process.
113-1129: LGTM with suggestions: Comprehensive mapping jobs with room for improvement.The map-encounters, map-patients, and map-medications jobs provide thorough mapping of resources to FHIR format. The use of utility functions and constants for mapping is commendable. However, there are areas for potential improvement:
Some parts of the code, especially in the map-medications job, are quite complex. Consider breaking down large functions into smaller, more manageable pieces.
Additional inline comments would be helpful for understanding the more complex mapping logic.
There's some code duplication in error handling and logging that could be refactored into utility functions.
Consider creating utility functions for common operations. For example:
const logWarning = (message, context) => { console.log(`WARNING: ${message}`, context); }; const findResourceById = (resources, id, type) => { const resource = resources.find(e => e.resource.id === id)?.resource; if (!resource) { logWarning(`COULD NOT FIND MATCHING ${type} FOR ${id}`); } return resource; };These functions could be used throughout the code to reduce duplication and improve readability.
🧰 Tools
yamllint
[error] 158-158: trailing spaces
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[error] 401-401: trailing spaces
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1131-1164: LGTM with a minor suggestion: send-to-NDR job is well-implemented.The job successfully sends the final bundle to the NDR and includes error handling. This is crucial for ensuring data integrity and tracking issues.
Consider enhancing the error logging to provide more context:
.catch(async (response, state) => { const err = JSON.parse(response.body) console.error('Error from NDR FHIR:', { status: response.status, statusText: response.statusText, error: err }); state.issue = err.issue; return state })This will provide more detailed information about the HTTP response in case of an error, which can be helpful for debugging.
1165-1189: LGTM with suggestions: send-errors-to-kafka-topic job is a good error handling mechanism.The job effectively sends error messages and failed bundles to separate Kafka topics, which is excellent for error tracking and potential retry mechanisms.
Consider adding error handling for the Kafka POST requests:
post('/openfn/fhir-errors', { body: JSON.stringify($.issue), headers: { 'content-type': 'application/json' }, }).then(() => { console.log('Successfully sent error to Kafka topic fhir-errors'); }).catch((error) => { console.error('Failed to send error to Kafka topic fhir-errors:', error); }); post('/openfn/dead-queue', { body: $.bundle, headers: { 'content-type': 'application/json' }, }).then(() => { console.log('Successfully sent failed bundle to Kafka topic dead-queue'); }).catch((error) => { console.error('Failed to send bundle to Kafka topic dead-queue:', error); });This will provide visibility into any issues that occur when sending data to Kafka topics.
158-158: Minor: Remove trailing spaces.The static analysis tool yamllint reported trailing spaces on lines 158 and 401. While these don't affect functionality, it's good practice to remove them for code cleanliness.
Please remove the trailing spaces from lines 158 and 401.
Also applies to: 401-401
🧰 Tools
yamllint
[error] 158-158: trailing spaces
(trailing-spaces)
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📒 Files selected for processing (4)
- openfn/importer/workflows/docker-compose.config.yml (1 hunks)
- openfn/importer/workflows/example/config.json (1 hunks)
- openfn/importer/workflows/example/project.yaml (1 hunks)
- openfn/package-metadata.json (1 hunks)
🧰 Additional context used
Gitleaks
openfn/importer/workflows/example/config.json
4-4: Uncovered a JSON Web Token, which may lead to unauthorized access to web applications and sensitive user data.
(jwt)
openfn/package-metadata.json
31-31: Uncovered a JSON Web Token, which may lead to unauthorized access to web applications and sensitive user data.
(jwt)
yamllint
openfn/importer/workflows/example/project.yaml
[error] 158-158: trailing spaces
(trailing-spaces)
[error] 401-401: trailing spaces
(trailing-spaces)
🔇 Additional comments not posted (5)
openfn/importer/workflows/docker-compose.config.yml (3)
17-20: Review deployment configuration for production readinessThe current deployment configuration might not be suitable for a production environment.
- The single replica without a restart policy could lead to downtime if the container fails.
- For a configuration service, you might want to consider using a
deploymode that ensures the task runs once and then stops.Consider the following adjustments:
If this is intended for production use, add a restart policy:
restart_policy: condition: on-failure max_attempts: 3If this is a one-time setup task, consider using a separate Docker Compose file for initialization tasks, or use a
deploymode that runs once:deploy: mode: global placement: constraints: - node.role == managerPlease clarify the intended use of this service (one-time setup vs. long-running service) to determine the most appropriate configuration.
27-37:⚠️ Potential issueReview config file paths and consider environment-specific configurations
The current configuration uses files from an
./exampledirectory, which may not be suitable for production use.Consider the following improvements:
Use environment-specific paths instead of
./example:configs: config.json: file: ${CONFIG_PATH:-./config/production}/config.json project.yaml: file: ${PROJECT_PATH:-./config/production}/project.yamlImplement a strategy for managing different configurations across environments (development, staging, production).
Ensure that sensitive information in these config files is properly secured, possibly by using Docker secrets for sensitive data instead of config files.
To ensure the correct files are being used, you can add a step in your deployment process to verify the content of the configs:
#!/bin/bash # Verify config files echo "Content of config.json:" cat ${CONFIG_PATH:-./config/production}/config.json echo "Content of project.yaml:" cat ${PROJECT_PATH:-./config/production}/project.yamlReview the output to confirm that the correct configuration files are being used for your target environment.
22-25: Verify the security of thepostgres_publicnetworkThe use of an external network named
postgres_publicraises potential security concerns.Please confirm that:
- This network is not actually exposed to the public internet.
- Appropriate security measures (like firewalls, VPNs, or other network isolation techniques) are in place to protect this network.
Consider renaming the network to something less ambiguous, like
postgres_internal, if it's not meant to be public.Review the output to ensure the network configuration aligns with your security requirements.
openfn/importer/workflows/example/project.yaml (2)
1-7: LGTM: Initial configuration looks good.The workflow name and description are clear and concise. The credential setup appears to be correct for the intended purpose.
1190-1231: LGTM: Workflow configuration is well-structured.The workflow configuration is logically organized with a clear sequence of job executions. The use of a conditional edge for error handling (send-to-NDR -> send-errors-to-kafka-topic) is a good practice that ensures errors are properly captured and processed.
The webhook trigger and job sequence align well with the overall purpose of the workflow. The configuration provides a robust pipeline for processing and validating healthcare data.
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Actionable comments posted: 8
🧹 Outside diff range and nitpick comments (6)
openfn/importer/workflows/example/state.json (5)
1-17: Consider enhancing project metadata and reviewing retention policy.While the project configuration is well-structured, consider the following improvements:
- The project name "jembi-cdc-ahie" could be more descriptive to better reflect its purpose.
- The description "POC test project for ART patient use case" is brief. Consider expanding it to provide more context about the project's goals and scope.
- The retention policy is set to "retain_all". Review if this is appropriate for long-term data management, as it may lead to unnecessary data storage.
18-151: Enhance workflow naming and documentation.The workflow configuration is comprehensive, but consider the following improvements:
- The workflow name "1-process-cdr-bundle" uses a numeric prefix. Consider adopting a more descriptive naming convention that doesn't rely on ordering, e.g., "process-cdr-bundle".
- Some edges could benefit from more descriptive condition labels. For example, the edge "send-to-NDR->send-errors-to-kafka-topic" has a condition label "import errors", which could be more specific.
- The kafka trigger is enabled, but there's no description of its purpose or expected payload. Consider adding documentation about the trigger's role in the workflow.
86-92: Enhance "parse-bundle" job documentation and error handling.The "parse-bundle" job could benefit from the following improvements:
- Add comments explaining the purpose and expected input/output of the job.
- Implement error handling for the JSON parsing operation.
- Consider moving the complex logic into a separate, testable function.
128-134: Improve error handling in "send-errors-to-kafka-topic" job.The error handling job could be enhanced:
- Add more detailed logging of the error information.
- Implement retries for the Kafka topic posts.
- Consider adding alerting or monitoring for critical errors.
1-155: Overall, the workflow configuration is comprehensive but has room for improvement.The
state.jsonfile provides a detailed configuration for the CDR bundle processing workflow. While it's functional, consider the following overall improvements:
- Adopt more consistent and descriptive naming conventions across the project, workflow, and jobs.
- Enhance documentation throughout, especially for complex job logic and trigger configurations.
- Refactor inline JavaScript code in job bodies into separate, testable functions.
- Implement more robust error handling and logging across all jobs.
- Review and standardize the use of project credentials across jobs.
- Consider breaking down larger jobs into smaller, more focused tasks for better maintainability.
These enhancements will improve the overall quality, maintainability, and reliability of the workflow.
openfn/importer/workflows/example/project.yaml (1)
1209-1310: LGTM: Bundle building and workflow configuration look good.The "build-bundle" job effectively constructs the final FHIR bundle, and the workflow configuration properly defines the job sequence and execution conditions.
Consider adding more detailed logging in the "build-bundle" job to facilitate debugging and monitoring. For example:
console.log(`Bundle construction started. Total resources: ${Object.values(state).flat().length}`); // ... existing bundle building logic ... console.log(`Bundle construction completed. Final bundle size: ${JSON.stringify(bundle).length} bytes`);This additional logging would provide more insights into the bundle building process, which could be helpful for performance monitoring and troubleshooting.
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- openfn/docker-compose.yml (1 hunks)
- openfn/importer/workflows/docker-compose.config.yml (1 hunks)
- openfn/importer/workflows/example/config.json (1 hunks)
- openfn/importer/workflows/example/project.yaml (1 hunks)
- openfn/importer/workflows/example/state.json (1 hunks)
- openfn/package-metadata.json (1 hunks)
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- openfn/importer/workflows/docker-compose.config.yml
- openfn/importer/workflows/example/config.json
- openfn/package-metadata.json
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openfn/docker-compose.yml (5)
1-3: LGTM: Docker Compose version and services structure.The Docker Compose file version 3.9 is appropriate for modern features, and the services structure is well-defined.
14-23: Caution: Potential exposure of sensitive information.Some environment variables (e.g.,
SECRET_KEY_BASE,PRIMARY_ENCRYPTION_KEY,WORKER_SECRET) likely contain sensitive information. Ensure these are not logged or exposed in any way.Consider using Docker secrets for sensitive information. Here's a script to check if any of these variables are currently set in the environment:
#!/bin/bash # Check for sensitive environment variables sensitive_vars=("SECRET_KEY_BASE" "PRIMARY_ENCRYPTION_KEY" "WORKER_SECRET" "WORKER_RUNS_PRIVATE_KEY") for var in "${sensitive_vars[@]}"; do if env | grep -q "^$var="; then echo "Warning: $var is set in the environment" fi done
34-48: Verify the WebSocket connection to the OpenFn service.The worker service connects to the OpenFn service using a WebSocket. Ensure that the URL and port are correctly configured and that the OpenFn service is set up to accept this connection.
#!/bin/bash # Check if the OpenFn service is exposing the expected port grep -q "LISTEN_ADDRESS=.*:4000" openfn/docker-compose.yml && echo "OpenFn service is configured to listen on port 4000" || echo "Warning: OpenFn service may not be configured to listen on port 4000" # Verify that the worker's command uses the correct WebSocket URL grep -q "ws://openfn:\${URL_PORT-4000}/worker" openfn/docker-compose.yml && echo "Worker is configured to connect to OpenFn service" || echo "Warning: Worker may not be configured to connect to OpenFn service correctly"
50-56: LGTM: Network configuration. Verify external networks.The use of external networks for Kafka and PostgreSQL is a good practice for modularity. However, ensure that these networks are properly set up in your environment.
Run the following script to verify the existence of the external networks:
#!/bin/bash # Check for the existence of the required external networks networks=("kafka_public" "postgres_public") for network in "${networks[@]}"; do if docker network ls | grep -q "$network"; then echo "Network $network exists" else echo "Warning: Network $network does not exist" fi done
25-30: Verify the health check test command.The health check test uses an environment variable
${DOCKER_WEB_HEALTHCHECK_TEST}with a fallback. Ensure this variable is properly set in your environment or consider using a fixed value for consistency.✅ Verification successful
Health check test command is correctly using the fallback value when the environment variable is not set.
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#!/bin/bash # Verify if DOCKER_WEB_HEALTHCHECK_TEST is set in the environment if env | grep -q DOCKER_WEB_HEALTHCHECK_TEST; then echo "DOCKER_WEB_HEALTHCHECK_TEST is set" else echo "DOCKER_WEB_HEALTHCHECK_TEST is not set, using default value" fiLength of output: 843
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#!/bin/bash # Directly check if DOCKER_WEB_HEALTHCHECK_TEST is set if [ -z "${DOCKER_WEB_HEALTHCHECK_TEST}" ]; then echo "DOCKER_WEB_HEALTHCHECK_TEST is not set" else echo "DOCKER_WEB_HEALTHCHECK_TEST is set to: ${DOCKER_WEB_HEALTHCHECK_TEST}" fiLength of output: 102
openfn/importer/workflows/example/project.yaml (2)
1-7: LGTM: Initial configuration looks good.The workflow name and description are clear, and the credential for "openhim ndr" is properly defined.
1-1310: Overall, the workflow is well-structured with room for some improvements.This YAML file defines a comprehensive workflow for processing and submitting healthcare data, particularly for ART patients. The workflow effectively handles data parsing, mapping, and submission to the NDR.
Key strengths:
- Detailed mapping of various healthcare resources to FHIR format.
- Error handling and reporting to Kafka topics.
- Well-defined job sequence and execution conditions.
Suggested improvements:
- Enhance error handling in data parsing and organization registration.
- Refactor complex mapping jobs for better readability and maintainability.
- Implement a retry mechanism for NDR submissions.
- Optimize Kafka error reporting by combining messages.
- Add more detailed logging throughout the workflow.
Implementing these suggestions would further improve the robustness, maintainability, and reliability of the workflow.
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This project's new adaptor has a new release and is under a different adaptor name ("fhir-ndr-et")
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Actionable comments posted: 9
🧹 Outside diff range and nitpick comments (7)
documentation/packages/openfn/README.md (4)
7-11: Consider expanding the Usage sectionWhile the provided command is clear, consider adding more context to enhance user understanding:
- Briefly explain what the
instantCLI tool is and how to install it if not already available.- Clarify what the
--devflag does in this context.- Provide a brief explanation of what happens after running this command.
These additions would help users, especially those new to the package or the
instanttool, to get started more easily.
29-36: Enhance Kafka trigger configuration instructionsThe Kafka trigger configuration instructions are helpful, but they could be improved for clarity and completeness.
Consider the following enhancements:
- Use a numbered list for the configuration steps to make them easier to follow.
- Provide more context for the configuration details (e.g., explain what CDR and NDR stand for).
- Consider using a table or bullet points for the configuration parameters (topic, hosts, etc.) to improve readability.
- Expand on the warning about disabling the trigger, explaining the potential consequences of not doing so.
38-40: Enhance the Documentation sectionWhile the link to the official documentation is helpful, this section could be expanded to provide more value to users.
Consider the following additions:
- Briefly list some of the key topics covered in the official documentation to give users an idea of what they can expect to find.
- If applicable, mention any other resources available (e.g., API reference, tutorials, community forums).
- Encourage users to contribute to the documentation if it's open-source.
24-27: Specify language for fenced code blockTo improve the formatting and potential syntax highlighting of the README, specify a language for the fenced code block containing the demo credentials.
Update the fenced code block as follows:
-``` +```plaintext username: [email protected] password: instant101<details> <summary>🧰 Tools</summary> <details> <summary>🪛 Markdownlint</summary><blockquote> 24-24: null Fenced code blocks should have a language specified (MD040, fenced-code-language) </blockquote></details> </details> </blockquote></details> <details> <summary>openfn/importer/workflows/example/state.json (3)</summary><blockquote> `15-17`: **Consider reviewing the data retention policy.** The current retention policy is set to "retain_all". While this ensures no data loss, it may have implications for storage costs and data privacy compliance (e.g., GDPR). Consider implementing a more granular retention policy based on data criticality and regulatory requirements. --- `58-66`: **Document the error handling condition.** The error handling edge uses a JavaScript expression condition (`state.issue`). While this is likely checking for the presence of an error, it would be beneficial to add a comment explaining the specific conditions under which errors are sent to the Kafka topic. This will improve maintainability and make it easier for other developers to understand the error handling logic. --- `154-155`: **Consider enabling Multi-Factor Authentication (MFA).** Given the sensitive nature of healthcare data being processed in this workflow, it's recommended to enable MFA for additional security. This can help prevent unauthorized access and comply with healthcare data protection regulations. </blockquote></details> </blockquote></details> <details> <summary>📜 Review details</summary> **Configuration used: CodeRabbit UI** **Review profile: CHILL** <details> <summary>📥 Commits</summary> Files that changed from the base of the PR and between 97daf986687866c791fbcde9e4c291c95f12eed3 and 2490ccd4eb42f7d0b22810811d05799bb04b588c. </details> <details> <summary>📒 Files selected for processing (5)</summary> * documentation/packages/openfn/README.md (1 hunks) * openfn/docker-compose.yml (1 hunks) * openfn/importer/workflows/example/project.yaml (1 hunks) * openfn/importer/workflows/example/state.json (1 hunks) * openfn/package-metadata.json (1 hunks) </details> <details> <summary>🚧 Files skipped from review as they are similar to previous changes (2)</summary> * openfn/docker-compose.yml * openfn/package-metadata.json </details> <details> <summary>🧰 Additional context used</summary> <details> <summary>🪛 Markdownlint</summary><blockquote> <details> <summary>documentation/packages/openfn/README.md</summary><blockquote> 24-24: null Fenced code blocks should have a language specified (MD040, fenced-code-language) </blockquote></details> </blockquote></details> <details> <summary>🪛 yamllint</summary><blockquote> <details> <summary>openfn/importer/workflows/example/project.yaml</summary><blockquote> [error] 1205-1205: trailing spaces (trailing-spaces) </blockquote></details> </blockquote></details> </details> <details> <summary>🔇 Additional comments (5)</summary><blockquote> <details> <summary>documentation/packages/openfn/README.md (1)</summary><blockquote> `1-5`: **LGTM: Clear and concise introduction** The introduction effectively communicates the purpose of the `openfn` package and its target audience. It provides a good overview for users new to the package. </blockquote></details> <details> <summary>openfn/importer/workflows/example/project.yaml (4)</summary><blockquote> `1-11`: **LGTM: Well-structured workflow configuration.** The initial configuration for the "jembi-cdc-ahie" workflow is well-organized and clearly defined. It includes appropriate credential setup and a logical job structure for processing ART patient data. --- `1209-1262`: **LGTM: Well-implemented bundle building process.** The "build-bundle" job effectively constructs the final FHIR bundle from the processed resources. It includes proper handling of resource creation vs. update, and the logging of bundle statistics is helpful for monitoring. The implementation is clean and efficient. --- `1264-1267`: **LGTM: Appropriate trigger configuration.** The Kafka webhook trigger is properly defined and enabled, providing a suitable entry point for the workflow. --- `1268-1310`: **LGTM: Well-defined workflow sequence.** The edges section effectively defines the workflow sequence with appropriate conditions for job execution. The use of a custom JS expression for error handling adds flexibility to the workflow, allowing for proper routing of errors to the Kafka topic. </blockquote></details> </blockquote></details> </details> <!-- This is an auto-generated comment by CodeRabbit for review status -->
upgrade adaptor version project.yaml
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Actionable comments posted: 11
🧹 Outside diff range and nitpick comments (1)
openfn/importer/workflows/example/project.yaml (1)
1-1310: Summary of review for openfn/importer/workflows/example/project.yamlThis workflow for processing ART patient data is comprehensive and well-structured. However, there are several areas where improvements can be made:
Code Organization: Many jobs, particularly "map-patients" and "map-medications", are overly complex and could benefit from being broken down into smaller, more manageable functions or separate jobs.
Error Handling: While some error handling is present, it could be more robust and consistent across all jobs. Implementing a global error handling strategy would improve the workflow's resilience.
Logging: More detailed and structured logging throughout the workflow would enhance observability and make debugging easier.
Performance: Some jobs, like "build-bundle", could benefit from performance optimizations.
Configurability: Consider making the workflow more configurable by moving hardcoded values to configuration files where appropriate.
Testing: While not directly addressed in the review, implementing unit tests for individual mapping functions and integration tests for the workflow would greatly improve reliability.
Addressing these points will result in a more maintainable, robust, and efficient workflow. Despite these areas for improvement, the overall structure and approach of the workflow are sound and provide a good foundation for processing ART patient data.
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openfn/importer/workflows/example/project.yaml (1)
1-11: Workflow setup looks good!The initial configuration for the "jembi-cdc-ahie" workflow is well-structured. It clearly defines the purpose (ART patient use case), includes necessary credentials, and sets up the first job "parse-bundle".
Co-authored-by: Kelvin Murumba <[email protected]>
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🧹 Outside diff range and nitpick comments (4)
openfn/docker-compose.yml (4)
5-5: Standardize environment variable naming convention.The environment variable
OpenFn_IMAGEuses inconsistent casing. Consider using uppercase with underscores for all environment variables (e.g.,OPENFN_IMAGE) to maintain consistency with other variables in the file.
33-38: Consider enhancing the health check.While the basic health check is good, consider adding validation of critical dependencies (database, Kafka) in your health check endpoint.
53-53: Improve WebSocket URL configuration.The WebSocket URL construction could be more robust. Consider:
- Using a dedicated environment variable for the full WebSocket URL
- Adding URL validation
- command: [ 'pnpm', 'start:prod', '-l', 'ws://openfn:${URL_PORT-4000}/worker' ] + command: [ 'pnpm', 'start:prod', '-l', '${OPENFN_WORKER_WS_URL:-ws://openfn:4000/worker}' ]
58-64: Standardize network naming convention.The network naming is inconsistent:
kafka_publicvspostgres_public- Network name doesn't match the external name for postgres
postgres: - name: postgres_public + name: postgres_public external: true
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openfn/docker-compose.yml (2)
21-32: Standardize environment variable naming with OPENFN prefix.
For better organization and clarity, consider prefixing OpenFn-specific environment variables with OPENFN_.
environment:
- - DATABASE_URL=${DATABASE_URL}
+ - DATABASE_URL=${OPENFN_DATABASE_URL}
- - DISABLE_DB_SSL=${DISABLE_DB_SSL}
+ - DISABLE_DB_SSL=${OPENFN_DISABLE_DB_SSL}
# ... apply similar changes to other variables14-15: 🛠️ Refactor suggestion
Improve maintainability by separating setup steps.
The current command combines multiple operations into a single line, making it difficult to maintain and debug. Consider creating separate initialization scripts.
Create separate scripts and modify the command:
+ # Add these files to the Docker image
+ # /app/scripts/migrate.sh
+ #!/bin/sh
+ /app/bin/lightning eval 'Lightning.Release.migrate()'
+
+ # /app/scripts/setup_user.sh
+ #!/bin/sh
+ /app/bin/lightning eval 'Lightning.Setup.setup_user(...)'
+
command: >
- sh -c "/app/bin/lightning eval 'Lightning.Release.migrate()' && /app/bin/lightning eval 'Lightning.Setup.setup_user(%{first_name: \"Test\",...' && /app/bin/lightning start"
+ sh -c "/app/scripts/migrate.sh && /app/scripts/setup_user.sh && /app/bin/lightning start"
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🧹 Outside diff range and nitpick comments (3)
openfn/importer/postgres/docker-compose.config.yml (1)
23-26: Review restart policy configurationThe current
restart_policywithcondition: nonemeans the container won't restart even if the database initialization fails. Consider usingon-failureto handle temporary database connectivity issues.deploy: replicas: 1 restart_policy: - condition: none + condition: on-failure + max_attempts: 3openfn/docker-compose.yml (1)
33-38: Improve health check configurationThe health check configuration has potential issues:
- The test command uses an environment variable without a default value
- The interval might be too frequent for a production environment
healthcheck: - test: '${ DOCKER_WEB_HEALTHCHECK_TEST:-curl localhost:4000/health_check}' + test: ['CMD-SHELL', 'curl -f http://localhost:4000/health_check || exit 1'] - interval: '10s' + interval: '30s' timeout: '3s' - start_period: '5s' + start_period: '30s' retries: 3openfn/package-metadata.json (1)
1-7: Consider using plain text for the description.The description contains an HTML entity (
') for an apostrophe. Consider using a plain apostrophe instead for better readability in JSON.- "description": "Lightning ⚡ (OpenFn v2) is a workflow automation platform that's used to automate critical business processes and integrate information systems.", + "description": "Lightning ⚡ (OpenFn v2) is a workflow automation platform that's used to automate critical business processes and integrate information systems.",
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🔇 Additional comments (7)
openfn/docker-compose.yml (3)
14-15:
Critical: Remove hardcoded credentials from command
The command contains hardcoded sensitive information (email: "[email protected]", password: "instant101") which is a security risk.
19-20:
Set reasonable default resource limits
Setting resource limits to 0 (unlimited) could lead to resource exhaustion.
Also applies to: 47-48
53-53: Verify WebSocket connection URL configuration
The worker service connects to the OpenFn service using WebSocket. Ensure the URL and port are correctly configured and the connection is secure.
✅ Verification successful
Based on the search results, I can verify that:
- The OpenFn service has a
LISTEN_ADDRESSenvironment variable configured in bothpackage-metadata.jsonanddocker-compose.yml. - The default port 4000 is used in the WebSocket URL (
${URL_PORT-4000}), which matches theOPENFN_ORIGINSconfiguration that includeshttp://localhost:4000. - The worker service is configured to connect to the OpenFn service using the internal Docker network hostname
openfn.
Let me verify the network configuration to ensure the services can communicate:
WebSocket configuration is correctly set up
The WebSocket connection is properly configured:
- The worker service connects to the OpenFn service using the internal Docker network hostname
- The default port 4000 aligns with the
OPENFN_ORIGINSconfiguration - Both services are on the same Docker networks (
kafka_publicandpostgres), ensuring network connectivity - The WebSocket URL uses the format
ws://openfn:4000/worker, which follows standard WebSocket protocol conventions
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test/cucumber/features/single-mode/recipe.feature (1)
34-34: Verify service dependencies for OpenFn
The OpenFn service depends on both Kafka and Postgres networks. Ensure it starts after these dependencies are ready.
✅ Verification successful
Based on the docker-compose files analysis, I can see that the OpenFn service is properly configured with network dependencies. The service is connected to both kafka_public and postgres networks, and these networks are defined as external networks in the configuration. Additionally, the service has a healthcheck configured that ensures it's running properly.
Service dependencies are correctly configured
- OpenFn service is connected to required networks (kafka_public and postgres)
- Service has proper healthcheck configuration
- Networks are properly defined as external networks
- Service startup order is managed through Docker Compose dependency resolution
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openfn/package-metadata.json (3)
9-10:
Enable SSL for database connections in production.
Disabling SSL (OPENFN_DISABLE_DB_SSL: "true") for database connections poses a security risk, especially in production environments. This could expose sensitive data during transmission.
Consider enabling SSL by default and only disabling it explicitly in development environments:
- "OPENFN_DISABLE_DB_SSL": "true",
+ "OPENFN_DISABLE_DB_SSL": "${OPENFN_DISABLE_DB_SSL:-false}",17-17:
Critical: Remove exposed private key.
The private key is exposed in plain text within the configuration file. This is a severe security risk as private keys should never be stored in version control.
Store the private key securely using environment variables or a secure key management system:
- "OPENFN_WORKER_RUNS_PRIVATE_KEY": "LS0tLS1CRUdJTiBQUklWQVRFIEtFWS0tLS0t...",
+ "OPENFN_WORKER_RUNS_PRIVATE_KEY": "${OPENFN_WORKER_RUNS_PRIVATE_KEY}",37-39:
Secure FHIR server communications.
Two security concerns in the FHIR server configuration:
- Using HTTP instead of HTTPS for healthcare data transmission
- Hardcoded credentials in the configuration file
Consider these improvements:
- "FHIR_SERVER_BASE_URL": "http://openhim-core:5001",
- "FHIR_SERVER_USERNAME": "openfn_client",
- "FHIR_SERVER_PASSWORD": "openfn_client_password"
+ "FHIR_SERVER_BASE_URL": "${FHIR_SERVER_BASE_URL}",
+ "FHIR_SERVER_USERNAME": "${FHIR_SERVER_USERNAME}",
+ "FHIR_SERVER_PASSWORD": "${FHIR_SERVER_PASSWORD}"Also, ensure that HTTPS is used in production environments for secure transmission of healthcare data.
Likely invalid or redundant comment.
Summary by CodeRabbit
New Features
openfnpackage to enhance functionality and integration capabilities.openfnandworkerservices in the Docker configuration for improved application deployment.openfn_db_configadded for managing the OpenFn PostgreSQL database.Documentation
openfnpackage outlining its purpose and usage.package-metadata.jsonfor essential configuration and deployment metadata.Chores
openfnservice.