Dev #322
Dev #322
Conversation
…ge-github-actions update on release and merge config
…mbi/JeMPI into CU-86bz306ft_Benchmark-Linker-and-API
…r-guide-for-UI Cu 86c060qh5 documentation add user guide for UI
…lation-Scripts CU-86c029q15 - Update Windows Installation Scripts
…n-Java-Prerequisites
…on-loading-without-data Cu 86c04wpae dashboard oops error on loading without data
…n-Java-Prerequisites
…Installation-Java-Prerequisites updated java installation prerequisite
WalkthroughThe pull request encompasses various changes across multiple files, primarily focusing on configuration adjustments, Dockerfile updates, and formatting improvements. Key modifications include the addition of specific Java version settings in Dockerfiles, enhancements to timeout and connection parameters in Akka HTTP server configurations, and updates to the Changes
Possibly related PRs
Poem
Recent review detailsConfiguration used: CodeRabbit UI Files selected for processing (2)
Files skipped from review due to trivial changes (1)
Additional comments not posted (1)
Thank you for using CodeRabbit. We offer it for free to the OSS community and would appreciate your support in helping us grow. If you find it useful, would you consider giving us a shout-out on your favorite social media? TipsChatThere are 3 ways to chat with CodeRabbit:
Note: Be mindful of the bot's finite context window. It's strongly recommended to break down tasks such as reading entire modules into smaller chunks. For a focused discussion, use review comments to chat about specific files and their changes, instead of using the PR comments. CodeRabbit Commands (Invoked using PR comments)
Other keywords and placeholders
CodeRabbit Configuration File (
|
![coderabbitai[bot]](https://avatars.githubusercontent.com/in/347564?s=60&v=4){kind=small}
There was a problem hiding this comment.
Actionable comments posted: 27
Outside diff range and nitpick comments (29)
JeMPI_Apps/JeMPI_ETL/src/main/resources/application.conf (1)
4-4: Monitor the request processing times and implement rate limiting.Increasing the
request-timeoutto 60 seconds can help accommodate longer-running requests. However, setting it too high can make the server vulnerable to Denial-of-Service (DoS) attacks. Please monitor the request processing times and adjust the value if needed. Also, consider implementing rate limiting to protect against DoS attacks.JeMPI_Apps/JeMPI_AsyncReceiver/src/main/resources/application.conf (1)
3-5: Consider a more moderate timeout value to balance performance and resource usage.Increasing the
idle-timeout,request-timeout, andlinger-timeoutto 60 seconds can help accommodate longer-running requests and idle connections, potentially improving user experience. However, setting the timeouts to a relatively high value might lead to resource exhaustion if there are many slow or idle connections, as the server will keep these connections open for a longer duration.It's important to strike a balance between accommodating slower connections and preventing resource exhaustion. Consider monitoring the server performance with these new timeout values and adjust them if needed. A more moderate timeout value, such as 30 seconds, might be a good middle ground to start with.
documentation/road-map.md (2)
1-6: Provide more details on the planned enhancements.The "Next Release" section provides a good overview of the key focus areas. Consider adding more details on the specific UI/UX enhancements and role-based access control features planned to give readers a better understanding of what to expect in the next release.
7-12: Provide more specificity on the performance and UX goals.The "Future Goals" section outlines some ambitious and exciting goals. To make it even more informative, consider providing more specificity on:
- The new technology options being explored to increase performance by an order of magnitude.
- The specific aspects of the UX that will be focused on to make JeMPI the easiest MPI to install, use, and maintain.
This will give readers a clearer picture of the direction and scope of the planned improvements.
JeMPI_Apps/build-app-image.sh (1)
13-13: Consider the impact on build time and the necessity of rebuilding all layers.The
--no-cacheoption ensures that the latest dependencies and configurations are always used, potentially leading to more consistent and up-to-date application images. This change is suitable for local development or testing environments.However, please note that rebuilding all layers from scratch can significantly increase the build time, especially for large applications with many dependencies. Consider the necessity of rebuilding all layers and the impact on build time.
For CI/CD pipelines, it's generally recommended to use cached layers to optimize the build process, as the dependencies and configurations are typically managed through version control and are less likely to change frequently.
devops/benchmarking/README.md (1)
3-8: Consider pinning the extension versions.The Docker command for building the xk6 binary looks good. However, consider pinning the versions of the xk6-kafka and xk6-exec extensions to avoid potential issues if there are breaking changes in the future.
For example, you can update the command to:
docker run --rm -it -u "$(id -u):$(id -g)" -v "${PWD}:/xk6" grafana/xk6 build v0.43.1 \ - --with github.com/mostafa/xk6-kafka@latest \ + --with github.com/mostafa/xk6-kafka@v0.1.0 \ - --with github.com/grafana/xk6-exec@latest + --with github.com/grafana/xk6-exec@v0.1.0JeMPI_Apps/JeMPI_UI/src/components/dashboard/widgets/BetaFscoreWidget.tsx (1)
5-17: Great work on improving type safety and centralizing the formatting logic!The introduction of the
DataPropsandBetaFscoreWidgetPropsinterfaces enhances the clarity and maintainability of the component by explicitly defining the structure of the expected props. This change improves type safety and makes the code more self-documenting.The
formatValuefunction is a nice addition that centralizes the formatting logic for numerical values. It handles non-finite values gracefully and replaces the direct calls totoFixed(5), reducing code duplication and improving readability.One minor suggestion for the
formatValuefunction:-const formatValue = (value: number | undefined): number => - Number.isFinite(value) ? Number(value?.toFixed(5)) : 0; +const formatValue = (value: number | undefined): number => + value === undefined ? 0 : Number.isFinite(value) ? Number(value.toFixed(5)) : 0;This change explicitly handles
undefinedvalues by returning zero, making the function's behavior clearer and avoiding the use of the optional chaining operator (?.) when it's not needed.devops/benchmarking/api-read.js (1)
27-57: Consider removing the console log statement.The function is correctly defined and implements the load test scenario. The function uses the
requestsPerUserSecondconstant to maintain the desired load.However, the function logs the response body, which may not be necessary for a load test and can add overhead to the test.
Consider removing the console log statement:
- // Log the request body - console.log(res.body);documentation/backup-and-restore.md (2)
30-40: Helpful addition of Python installation instructions!The instructions for Python installation and using
python-dotenvto manage environment variables are helpful for users setting up the backup and restore process.Use a heading instead of emphasis for "Python Installation".
To improve the document structure and readability, consider using a heading (e.g.,
###) instead of emphasis (**) for the "Python Installation" text.Apply this change:
-**Python Installation** +### Python InstallationTools
Markdownlint
30-30: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
64-70: Helpful addition of the manual backup process instructions!The instructions for performing a manual backup using
pg_dumpand verifying the success of the backup process are helpful for users.Use headings instead of emphasis for "Manual Backup Process" and "Verify if process was successful".
To improve the document structure and readability, consider using headings (e.g.,
###) instead of emphasis (**) for the "Manual Backup Process" and "Verify if process was successful" texts.Apply these changes:
-**Manual Backup Process** +### Manual Backup Process -**Verify if process was successful** +### Verify if process was successfulTools
Markdownlint
64-64: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
68-68: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
devops/windows/base-docker-wsl/conf/env/create-env-linux-low-1.sh (3)
50-59: Sensitive information in development setup is acceptable.Gitleaks flagged the Keycloak client secret and session secret as potentially exposing sensitive information. While this is true, having these values in a development environment setup script is acceptable.
For production environments, consider using a secrets management solution to securely store and access sensitive information.
Tools
Gitleaks
53-53: Detected a Generic API Key, potentially exposing access to various services and sensitive operations.
(generic-api-key)
55-55: Detected a Generic API Key, potentially exposing access to various services and sensitive operations.
(generic-api-key)
106-106: Clarify the purpose of echoing dots.Echoing a string of dots at line 106 seems to serve no functional purpose. If it is used as a visual separator or progress indicator, consider adding a comment to explain the intent.
If it serves no specific purpose, consider removing it to improve code clarity.
Line range hint
1-106: Comprehensive development environment setup.The script provides a comprehensive setup for a development environment by exporting various environment variables. It includes configurations for project paths, databases, services, Keycloak, memory limits, and UI settings, promoting configurability and customization.
The use of relative paths and variables for constructing absolute paths enhances the portability of the script.
As a suggestion for further improvement, consider using a dotenv file (e.g.,
.env) to manage the environment variables in a more organized manner. This can make it easier to maintain and modify the configurations.Tools
Shellcheck
[warning] 96-96: Declare and assign separately to avoid masking return values.
(SC2155)
Gitleaks
53-53: Detected a Generic API Key, potentially exposing access to various services and sensitive operations.
(generic-api-key)
55-55: Detected a Generic API Key, potentially exposing access to various services and sensitive operations.
(generic-api-key)
JeMPI_Apps/JeMPI_LibShared/src/main/java/org/jembi/jempi/shared/kafka/MyKafkaConsumerByTopic.java (1)
42-54: LGTM! Consider adding a TODO comment for the empty method.The changes introduce a
ConsumerRebalanceListenerto handle partition revocation and assignment. Committing offsets before a rebalance in theonPartitionsRevokedmethod is a good practice to ensure that the consumer's state is preserved and no messages are lost during the transition. This improves the reliability of message processing.The empty
onPartitionsAssignedmethod indicates a placeholder for potential future handling of partition assignments. Consider adding a TODO comment to make it explicit.@Override public void onPartitionsAssigned(final Collection<TopicPartition> partitions) { + // TODO: Handle partition assignment if needed - // Handle partition assignment if needed }JeMPI_Apps/JeMPI_LibMPI/src/main/java/org/jembi/jempi/libmpi/dgraph/DgraphClient.java (1)
89-106: Great work on implementing the retry mechanism!The
runWithRetriesmethod encapsulates the retry logic nicely, making the code more readable and maintainable. The error handling and logging are also implemented correctly.Consider adding a brief JavaDoc comment to explain the purpose and behavior of the
runWithRetriesmethod, as it is a crucial part of the retry mechanism.devops/JeMPI_TestData/Reference/DataGenerator.py (1)
Line range hint
24-189: Excellent improvements to thegenerate_datasetfunction!The modifications to the function signature and the usage of the
argsparameter greatly enhance the configurability of the dataset generation process. The simplification of the record number generation logic and the return of the generated file path are also valuable changes that improve readability and usability.Just one minor suggestion:
Remove the unused import of
src.helperas indicated by the static analysis hint:-from src import helper, basefunctions +from src import basefunctionsdocumentation/installation/standalone-installation.md (3)
41-45: Use a heading for the note and specify the language for the code block.The added note provides important configuration information for non-root user installations. The command to source the Java path is helpful for users.
However, please consider the following suggestions to improve the documentation:
- Use a heading (e.g.,
###) instead of emphasis for the note to make it more prominent.- Specify the language (e.g.,
bash) for the fenced code block to enable syntax highlighting.Apply this diff to address the suggestions:
-**Note: when installing with a non-root user set java directory** +### Note: Set Java directory when installing with a non-root user -``` +```bash source "/home/${USER}/.sdkman/candidates/java/current"<details> <summary>Tools</summary> <details> <summary>Markdownlint</summary><blockquote> 41-41: null Emphasis used instead of a heading (MD036, no-emphasis-as-heading) --- 42-42: null Fenced code blocks should have a language specified (MD040, fenced-code-language) </blockquote></details> </details> --- `178-181`: **Use a heading for the note.** The added note provides important instructions for server installations. The example command for setting the `SERVER_IP` variable is helpful for users. However, please consider using a heading (e.g., `###`) instead of emphasis for the note to make it more prominent. Apply this diff to address the suggestion: ```diff -**Note: for server installations, manually set SERVER_IP for environment variable before executing the script** +### Note: Set SERVER_IP environment variable for server installationsTools
Markdownlint
178-178: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
182-182: Remove the empty line.The empty line at the end of the code block is unnecessary and can be removed for better readability.
Apply this diff to remove the empty line:
-devops/benchmarking/linker-test.js (6)
5-13: Improve configuration object for better clarity.Consider making the following improvements to the configuration object:
- Add a more detailed comment for the
corruptionsetting, explaining its purpose and valid range.- Express the
logsTimeoutvalue in seconds or minutes for better readability.
23-28: Improve housekeeping logic for better maintainability and safety.Consider making the following improvements to the housekeeping logic:
- Define the file paths as constants or configuration variables for better maintainability.
- Use
rm -rfinstead ofrm -fto recursively remove directories and their contents safely.
30-42: Improve test data generation logic for better reliability and efficiency.Consider making the following improvements to the test data generation logic:
- Make the path to the
DataGenerator.pyscript configurable or use an absolute path to ensure reliability.- Consider having the Python script output the number of records directly, instead of using
wc -lto count the lines.
55-86: Improve file copy logic for better code organization and logging.Consider making the following improvements to the file copy logic:
- Extract the retry logic into a separate function for better code organization and reusability.
- Make the debugging logs more concise and informative, focusing on the essential information.
88-195: Improve linker monitoring logic for better code organization and user experience.Consider making the following improvements to the linker monitoring logic:
- Refactor the code to extract the log parsing logic into separate functions for better code organization and readability.
- Define the magic strings used for log matching (e.g., "TEA TIME", "Stream closed") as constants for better maintainability.
- Enhance the progress display to provide more visually appealing output, such as using progress bars or colored text.
197-229: Improve log saving and duration calculation logic for better organization and simplicity.Consider making the following improvements to the log saving and duration calculation logic:
- Enhance the log file naming convention to include additional information, such as the test run timestamp or iteration number.
- Extract the duration calculation logic into a separate function for better code organization and reusability.
- Simplify the duration display logic by using a library like
moment.jsfor formatting.JeMPI_Apps/JeMPI_Linker/src/main/java/org/jembi/jempi/linker/backend/BackEnd.java (1)
202-229: Approve the refactoring changes to enhance error handling and streamline the control flow.The refactoring improves readability and maintainability by reducing the complexity of nested conditions and ensuring that all error handling is centralized. The changes align with the AI-generated summary.
Consider extracting the logic for handling the case where
contentTypeis notBATCH_INTERACTIONinto a separate method to further reduce the complexity of theasyncLinkInteractionHandlermethod.For example:
private Behavior<Request> handleNonBatchInteraction(AsyncLinkInteractionRequest req) { return Behaviors.withTimers(timers -> { timers.startSingleTimer(SINGLE_TIMER_TIMEOUT_KEY, TeaTimeRequest.INSTANCE, Duration.ofSeconds(GlobalConstants.TIMEOUT_TEA_TIME_SECS)); req.replyTo.tell(new AsyncLinkInteractionResponse(null)); return Behaviors.same(); }); } private Behavior<Request> asyncLinkInteractionHandler(final AsyncLinkInteractionRequest req) { try { if (req.batchInteraction.contentType() != InteractionEnvelop.ContentType.BATCH_INTERACTION) { return handleNonBatchInteraction(req); } // Rest of the method logic... } catch (Exception e) { // Exception handling... } // Timer logic... }documentation/user-interface-guide.md (3)
47-47: Add the missing period after "e.g.".The abbreviation "e.g." should have a period at the end.
-e.g Find all males in village x +e.g. Find all males in village xTools
LanguageTool
[uncategorized] ~47-~47: The abbreviation “e.g.” (= for example) requires two periods.
Context: ...perform filtering instead of blocking. (e.g Find all males in village x) **Similar...(E_G)
217-217: Consider rephrasing to be more concise.The phrasing "In order to view the details of a patient, select the relevant row." is a bit wordy.
Consider a more concise rephrasing, such as:
To view a patient's details, select the relevant row.Tools
LanguageTool
[style] ~217-~217: Consider a shorter alternative to avoid wordiness.
Context: ... of a patient, select the relevant row. In order to view the details of a patient, select t...(IN_ORDER_TO_PREMIUM)
519-519: Add the missing period after "etc".The abbreviation "etc" should have a period at the end.
-Select comparator function from a dropdown field eg "Exact", "Low Fuzziness" etc +Select comparator function from a dropdown field eg "Exact", "Low Fuzziness" etc.Tools
LanguageTool
[uncategorized] ~519-~519: The noun “dropdown” is spelled as one word.
Context: ...eld - Select comparator function from a drop down field eg “Exact”, “Low Fuzziness” etc -...(LOCKDOWN)
[style] ~519-~519: In American English, abbreviations like “etc.” require a period.
Context: ... down field eg “Exact”, “Low Fuzziness” etc - Add a second row of input fields by s...(ETC_PERIOD)
Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Files ignored due to path filters (1)
JeMPI_Apps/JeMPI_UI/yarn.lockis excluded by!**/yarn.lock,!**/*.lock
Files selected for processing (73)
- .github/workflows/entry-on-merge.yml (1 hunks)
- .gitignore (1 hunks)
- JeMPI_Apps/JeMPI_API/docker/Dockerfile (1 hunks)
- JeMPI_Apps/JeMPI_API/src/main/resources/application.conf (2 hunks)
- JeMPI_Apps/JeMPI_API_KC/docker/Dockerfile (1 hunks)
- JeMPI_Apps/JeMPI_API_KC/src/main/resources/application.conf (2 hunks)
- JeMPI_Apps/JeMPI_AsyncReceiver/docker/Dockerfile (1 hunks)
- JeMPI_Apps/JeMPI_AsyncReceiver/src/main/java/org/jembi/jempi/async_receiver/Main.java (1 hunks)
- JeMPI_Apps/JeMPI_AsyncReceiver/src/main/resources/application.conf (1 hunks)
- JeMPI_Apps/JeMPI_BackupRestoreAPI/docker/Dockerfile (1 hunks)
- JeMPI_Apps/JeMPI_BackupRestoreAPI/src/main/resources/application.conf (1 hunks)
- JeMPI_Apps/JeMPI_Bootstrapper/docker/Dockerfile (1 hunks)
- JeMPI_Apps/JeMPI_Controller/docker/Dockerfile (1 hunks)
- JeMPI_Apps/JeMPI_Controller/src/main/resources/application.conf (1 hunks)
- JeMPI_Apps/JeMPI_EM_Scala/docker/Dockerfile (1 hunks)
- JeMPI_Apps/JeMPI_ETL/docker/Dockerfile (1 hunks)
- JeMPI_Apps/JeMPI_ETL/src/main/resources/application.conf (1 hunks)
- JeMPI_Apps/JeMPI_LibAPI/src/main/java/org/jembi/jempi/libapi/BackEnd.java (2 hunks)
- JeMPI_Apps/JeMPI_LibAPI/src/main/java/org/jembi/jempi/libapi/ProxyRoutes.java (1 hunks)
- JeMPI_Apps/JeMPI_LibMPI/src/main/java/org/jembi/jempi/libmpi/dgraph/DgraphClient.java (3 hunks)
- JeMPI_Apps/JeMPI_LibShared/src/main/java/org/jembi/jempi/shared/config/Config.java (2 hunks)
- JeMPI_Apps/JeMPI_LibShared/src/main/java/org/jembi/jempi/shared/kafka/MyKafkaConsumerByTopic.java (2 hunks)
- JeMPI_Apps/JeMPI_LibShared/src/main/java/org/jembi/jempi/shared/models/GlobalConstants.java (1 hunks)
- JeMPI_Apps/JeMPI_Linker/docker/Dockerfile (1 hunks)
- JeMPI_Apps/JeMPI_Linker/src/main/java/org/jembi/jempi/linker/Ask.java (1 hunks)
- JeMPI_Apps/JeMPI_Linker/src/main/java/org/jembi/jempi/linker/Main.java (2 hunks)
- JeMPI_Apps/JeMPI_Linker/src/main/java/org/jembi/jempi/linker/SPInteractions.java (3 hunks)
- JeMPI_Apps/JeMPI_Linker/src/main/java/org/jembi/jempi/linker/SPMU.java (1 hunks)
- JeMPI_Apps/JeMPI_Linker/src/main/java/org/jembi/jempi/linker/backend/BackEnd.java (1 hunks)
- JeMPI_Apps/JeMPI_Linker/src/main/resources/application.conf (2 hunks)
- JeMPI_Apps/JeMPI_UI/Dockerfile (2 hunks)
- JeMPI_Apps/JeMPI_UI/src/components/browseRecords/BrowseRecords.tsx (3 hunks)
- JeMPI_Apps/JeMPI_UI/src/components/dashboard/Dashboard.tsx (4 hunks)
- JeMPI_Apps/JeMPI_UI/src/components/dashboard/widgets/BetaFscoreWidget.tsx (1 hunks)
- JeMPI_Apps/JeMPI_UI/src/components/notificationWorklist/NotificationWorklist.tsx (3 hunks)
- JeMPI_Apps/JeMPI_UI/src/pages/settings/Settings.tsx (0 hunks)
- JeMPI_Apps/JeMPI_UI/src/pages/settings/probabilistic/Probabilistic.tsx (5 hunks)
- JeMPI_Apps/JeMPI_UI/src/pages/settings/probabilistic/ProbabilisticConstants.tsx (1 hunks)
- JeMPI_Apps/build-app-image.sh (1 hunks)
- devops/JeMPI_TestData/Reference/DataGenerator.py (4 hunks)
- devops/benchmarking/README.md (1 hunks)
- devops/benchmarking/api-read.js (1 hunks)
- devops/benchmarking/api-write.js (1 hunks)
- devops/benchmarking/kafka-monitor.js (1 hunks)
- devops/benchmarking/linker-test.js (1 hunks)
- devops/linux/docker/conf/env/create-env-linux-low-1.sh (1 hunks)
- devops/linux/docker/conf/keycloak/import-jempi-dev-realm.json (1 hunks)
- devops/linux/docker/d-stack-1-build-___-reboot.sh (1 hunks)
- devops/linux/docker/data-config/config.json (1 hunks)
- devops/linux/docker/deployment/deploy-local.sh (2 hunks)
- devops/linux/docker/deployment/scripts/d-stack-up-app-containers.sh (1 hunks)
- devops/windows/base-docker-linux/conf/env/conf-env-high-1-pc.template (7 hunks)
- devops/windows/base-docker-linux/conf/env/conf-env-low-1-pc.template (1 hunks)
- devops/windows/base-docker-linux/conf/env/create-env-linux-high-1.sh (1 hunks)
- devops/windows/base-docker-linux/conf/env/create-env-linux-low-1.sh (3 hunks)
- devops/windows/base-docker-linux/helper/scripts/d-stack-01-create-dirs.sh (1 hunks)
- devops/windows/base-docker-wsl/conf/env/conf-env-high-1-pc.template (4 hunks)
- devops/windows/base-docker-wsl/conf/env/conf-env-low-1-pc.template (1 hunks)
- devops/windows/base-docker-wsl/conf/env/create-env-linux-high-1.sh (1 hunks)
- devops/windows/base-docker-wsl/conf/env/create-env-linux-low-1.sh (3 hunks)
- devops/windows/base-docker-wsl/helper/scripts/d-stack-01-create-dirs.sh (1 hunks)
- devops/windows/deployment/deploy-local-windows.ps1 (3 hunks)
- devops/windows/run--base-docker-linux/start.ps1 (3 hunks)
- devops/windows/run--base-docker-wsl/start-with-bootstraper.ps1 (4 hunks)
- devops/windows/run--base-docker-wsl/start.ps1 (4 hunks)
- documentation/SUMMARY.md (1 hunks)
- documentation/backup-and-restore.md (3 hunks)
- documentation/configuration-user-guide.md (2 hunks)
- documentation/installation/standalone-installation.md (3 hunks)
- documentation/keycloak/README.md (1 hunks)
- documentation/road-map.md (1 hunks)
- documentation/sso.md (1 hunks)
- documentation/user-interface-guide.md (1 hunks)
Files not reviewed due to no reviewable changes (1)
- JeMPI_Apps/JeMPI_UI/src/pages/settings/Settings.tsx
Files skipped from review due to trivial changes (13)
- .github/workflows/entry-on-merge.yml
- JeMPI_Apps/JeMPI_API_KC/docker/Dockerfile
- JeMPI_Apps/JeMPI_AsyncReceiver/docker/Dockerfile
- JeMPI_Apps/JeMPI_AsyncReceiver/src/main/java/org/jembi/jempi/async_receiver/Main.java
- JeMPI_Apps/JeMPI_BackupRestoreAPI/docker/Dockerfile
- JeMPI_Apps/JeMPI_Bootstrapper/docker/Dockerfile
- JeMPI_Apps/JeMPI_Controller/docker/Dockerfile
- JeMPI_Apps/JeMPI_ETL/docker/Dockerfile
- JeMPI_Apps/JeMPI_Linker/docker/Dockerfile
- JeMPI_Apps/JeMPI_UI/Dockerfile
- devops/linux/docker/data-config/config.json
- documentation/SUMMARY.md
- documentation/keycloak/README.md
Additional context used
Markdownlint
documentation/sso.md
48-48: null
Bare URL used(MD034, no-bare-urls)
documentation/backup-and-restore.md
30-30: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
64-64: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
68-68: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
documentation/installation/standalone-installation.md
41-41: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
42-42: null
Fenced code blocks should have a language specified(MD040, fenced-code-language)
178-178: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
documentation/user-interface-guide.md
121-121: Expected: 0; Actual: 1
Inconsistent indentation for list items at the same level(MD005, list-indent)
569-569: Expected: 0; Actual: 1
Inconsistent indentation for list items at the same level(MD005, list-indent)
570-570: Expected: 0; Actual: 1
Inconsistent indentation for list items at the same level(MD005, list-indent)
571-571: Expected: 0; Actual: 1
Inconsistent indentation for list items at the same level(MD005, list-indent)
121-121: Expected: 0; Actual: 1
Unordered list indentation(MD007, ul-indent)
414-414: Expected: 0; Actual: 1
Unordered list indentation(MD007, ul-indent)
415-415: Expected: 0; Actual: 1
Unordered list indentation(MD007, ul-indent)
569-569: Expected: 0; Actual: 1
Unordered list indentation(MD007, ul-indent)
570-570: Expected: 0; Actual: 1
Unordered list indentation(MD007, ul-indent)
571-571: Expected: 0; Actual: 1
Unordered list indentation(MD007, ul-indent)
578-578: Expected: 0; Actual: 3
Unordered list indentation(MD007, ul-indent)
579-579: Expected: 0; Actual: 3
Unordered list indentation(MD007, ul-indent)
2-2: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
4-4: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
22-22: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
63-63: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
76-76: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
88-88: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
103-103: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
114-114: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
118-118: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
125-125: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
132-132: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
145-145: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
153-153: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
167-167: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
173-173: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
175-175: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
190-190: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
194-194: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
212-212: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
220-220: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
239-239: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
247-247: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
272-272: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
278-278: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
291-291: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
311-311: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
329-329: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
331-331: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
357-357: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
361-361: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
381-381: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
383-383: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
390-390: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
405-405: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
419-419: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
428-428: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
434-434: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
448-448: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
470-470: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
474-474: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
480-480: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
498-498: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
514-514: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
540-540: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
12-12: null
Images should have alternate text (alt text)(MD045, no-alt-text)
16-16: null
Images should have alternate text (alt text)(MD045, no-alt-text)
20-20: null
Images should have alternate text (alt text)(MD045, no-alt-text)
139-139: null
Images should have alternate text (alt text)(MD045, no-alt-text)
363-363: null
Images should have alternate text (alt text)(MD045, no-alt-text)
388-388: null
Images should have alternate text (alt text)(MD045, no-alt-text)
417-417: null
Images should have alternate text (alt text)(MD045, no-alt-text)
472-472: null
Images should have alternate text (alt text)(MD045, no-alt-text)
Shellcheck
devops/linux/docker/d-stack-1-build-___-reboot.sh
[warning] 24-24: Declare and assign separately to avoid masking return values.
(SC2155)
[warning] 25-25: Declare and assign separately to avoid masking return values.
(SC2155)
[warning] 34-34: Declare and assign separately to avoid masking return values.
(SC2155)
[error] 81-81: Arrays implicitly concatenate in [[ ]]. Use a loop (or explicit * instead of @).
(SC2199)
[warning] 81-81: Remove quotes from right-hand side of =~ to match as a regex rather than literally.
(SC2076)
[warning] 84-84: Quote to prevent word splitting/globbing, or split robustly with mapfile or read -a.
(SC2206)
[error] 92-92: Argument mixes string and array. Use * or separate argument.
(SC2145)
devops/windows/base-docker-linux/conf/env/create-env-linux-low-1.sh
[warning] 4-4: Declare and assign separately to avoid masking return values.
(SC2155)
[warning] 4-4: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
[warning] 6-6: Declare and assign separately to avoid masking return values.
(SC2155)
[warning] 6-6: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
[warning] 10-10: Declare and assign separately to avoid masking return values.
(SC2155)
[warning] 10-10: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
devops/windows/base-docker-wsl/conf/env/create-env-linux-low-1.sh
[warning] 4-4: Declare and assign separately to avoid masking return values.
(SC2155)
[warning] 4-4: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
[warning] 6-6: Declare and assign separately to avoid masking return values.
(SC2155)
[warning] 6-6: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
[warning] 96-96: Declare and assign separately to avoid masking return values.
(SC2155)
devops/windows/base-docker-linux/conf/env/create-env-linux-high-1.sh
[warning] 4-4: Declare and assign separately to avoid masking return values.
(SC2155)
[warning] 4-4: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
[warning] 6-6: Declare and assign separately to avoid masking return values.
(SC2155)
[warning] 6-6: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
[warning] 17-17: Declare and assign separately to avoid masking return values.
(SC2155)
[warning] 19-19: Declare and assign separately to avoid masking return values.
(SC2155)
devops/windows/base-docker-wsl/conf/env/create-env-linux-high-1.sh
[warning] 4-4: Declare and assign separately to avoid masking return values.
(SC2155)
[warning] 4-4: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
[warning] 6-6: Declare and assign separately to avoid masking return values.
(SC2155)
[warning] 6-6: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
[warning] 17-17: Declare and assign separately to avoid masking return values.
(SC2155)
[warning] 19-19: Declare and assign separately to avoid masking return values.
(SC2155)
Gitleaks
devops/windows/base-docker-linux/conf/env/create-env-linux-low-1.sh
53-53: Detected a Generic API Key, potentially exposing access to various services and sensitive operations.
(generic-api-key)
55-55: Detected a Generic API Key, potentially exposing access to various services and sensitive operations.
(generic-api-key)
devops/windows/base-docker-wsl/conf/env/create-env-linux-low-1.sh
53-53: Detected a Generic API Key, potentially exposing access to various services and sensitive operations.
(generic-api-key)
55-55: Detected a Generic API Key, potentially exposing access to various services and sensitive operations.
(generic-api-key)
devops/windows/base-docker-linux/conf/env/create-env-linux-high-1.sh
66-66: Detected a Generic API Key, potentially exposing access to various services and sensitive operations.
(generic-api-key)
68-68: Detected a Generic API Key, potentially exposing access to various services and sensitive operations.
(generic-api-key)
devops/windows/base-docker-wsl/conf/env/create-env-linux-high-1.sh
66-66: Detected a Generic API Key, potentially exposing access to various services and sensitive operations.
(generic-api-key)
68-68: Detected a Generic API Key, potentially exposing access to various services and sensitive operations.
(generic-api-key)
LanguageTool
documentation/configuration-user-guide.md
[uncategorized] ~74-~74: Possible missing comma found.
Context: ...Probabilistic** In the Probabilistic tab the user can define the linking thresh...(AI_HYDRA_LEO_MISSING_COMMA)
documentation/user-interface-guide.md
[uncategorized] ~47-~47: The abbreviation “e.g.” (= for example) requires two periods.
Context: ...perform filtering instead of blocking. (e.g Find all males in village x) **Similar...(E_G)
[grammar] ~209-~209: A word may be missing after ‘a’.
Context: ...FILTER button to view the results a. If no results are found, the system dis...(THE_SENT_END)
[style] ~217-~217: Consider a shorter alternative to avoid wordiness.
Context: ... of a patient, select the relevant row. In order to view the details of a patient, select t...(IN_ORDER_TO_PREMIUM)
[uncategorized] ~517-~517: The noun “dropdown” is spelled as one word.
Context: ...g : - Select the operator values from a drop down field eg “And” and “Or” - Select common...(LOCKDOWN)
[uncategorized] ~518-~518: The noun “dropdown” is spelled as one word.
Context: ...Or” - Select common field values from a drop down field - Select comparator function from...(LOCKDOWN)
[uncategorized] ~519-~519: The noun “dropdown” is spelled as one word.
Context: ...eld - Select comparator function from a drop down field eg “Exact”, “Low Fuzziness” etc -...(LOCKDOWN)
[style] ~519-~519: In American English, abbreviations like “etc.” require a period.
Context: ... down field eg “Exact”, “Low Fuzziness” etc - Add a second row of input fields by s...(ETC_PERIOD)
[duplication] ~520-~520: Possible typo: you repeated a word
Context: ...nd row of input fields by selecting the add add icon button - Save rule by selecting th...(ENGLISH_WORD_REPEAT_RULE)
Ruff
devops/JeMPI_TestData/Reference/DataGenerator.py
8-8:
src.helperimported but unusedRemove unused import:
src.helper(F401)
Additional comments not posted (212)
.gitignore (1)
15-18: LGTM!The changes to the
.gitignorefile are appropriate and help maintain a cleaner repository by excluding unnecessary files from version control. The additions include:
.metalsdirectory, which is commonly used for Scala development.devops/benchmarking/k6path, which likely contains configuration files or output data from load testing using the k6 tool.devops/windows/base-docker-wsl/configanddevops/windows/base-docker-wsl/csvpaths, which likely contain configuration files and data related to a Windows Docker setup using WSL.These files and directories can be safely ignored by Git.
JeMPI_Apps/JeMPI_API/docker/Dockerfile (1)
1-1: Verify application compatibility with the specified Java version.Setting a default Java version ensures consistency and reproducibility of the Docker image builds. However, please ensure that the application is compatible with the specified Java version
21.0.1-tem.If the specified Java version is a custom or non-standard version, consider using a standard LTS (Long-Term Support) version of Java for better stability and long-term support, unless there are specific requirements for using the custom version.
JeMPI_Apps/JeMPI_ETL/src/main/resources/application.conf (2)
3-3: Monitor the impact of the increasedidle-timeout.Increasing the
idle-timeoutto 60 seconds can help accommodate longer idle connections without prematurely closing them. However, setting it too high can lead to resource exhaustion if there are many idle connections. Please monitor the server resources and adjust the value if needed.
5-5: LGTM!Increasing the
linger-timeoutto 60 seconds can help accommodate longer network delays. The change looks good to me.JeMPI_Apps/JeMPI_Controller/src/main/resources/application.conf (3)
3-3: Monitor server performance with the increased idle timeout.The change to increase the
idle-timeoutfrom 10 seconds to 60 seconds may improve the server's handling of scenarios where connections remain idle for extended periods. However, this also means that the server will hold onto resources for a longer duration for each idle connection.Please monitor the server's resource utilization and connection handling capacity under load to ensure that the increased timeout does not adversely impact the server's performance. If you observe any resource constraints or degraded performance, consider tuning the timeout value based on the observed usage patterns and server capacity.
4-4: Review request processing logic and consider granular timeout configuration.The change to increase the
request-timeoutfrom 5 seconds to 60 seconds may improve the server's handling of longer-running requests. However, this also means that the server will hold onto resources for a longer duration for each request, potentially impacting the server's resource utilization and responsiveness.Please review the request processing logic and any external dependencies to ensure that the increased timeout is appropriate and does not mask any underlying issues. If a request is taking an exceptionally long time, it may indicate an issue that needs to be addressed.
Additionally, consider implementing a more granular timeout configuration based on the nature and expected duration of different request types, if applicable. This can help optimize the server's resource utilization and responsiveness for different scenarios.
5-5: Assess client requirements and monitor resource utilization.The change to increase the
linger-timeoutfrom 5 seconds to 60 seconds may be beneficial if clients are expected to send additional data after receiving a response. This allows the connection to remain open for a longer duration to handle such cases.However, please assess whether the increased linger timeout aligns with the expected behavior and requirements of the clients interacting with the server. If clients are not expected to send additional data after receiving a response, the increased timeout may unnecessarily hold onto resources.
Additionally, monitor the server's resource utilization with the increased linger timeout and consider adjusting the value based on the observed client behavior and server capacity to optimize resource usage.
JeMPI_Apps/JeMPI_EM_Scala/docker/Dockerfile (1)
1-1: LGTM!Setting a default value for the
JAVA_VERSIONargument is a good practice as it ensures that the Docker image will use a specific Java version if no version is provided during the build process. This change enhances build consistency and reduces potential errors related to version specification.devops/benchmarking/README.md (3)
10-10: LGTM!The command for benchmarking the Linker looks good.
12-14: LGTM!The commands for benchmarking the API look good.
16-16: Clarify the status of the Kafka monitoring implementation.The command for monitoring Kafka looks good. However, the section is marked as "WIP, for future reference". Can you please clarify the current status of the Kafka monitoring implementation? Is it ready to be used or still a work in progress?
JeMPI_Apps/JeMPI_Linker/src/main/resources/application.conf (4)
12-15: Monitor the impact of the increased timeout values on server resources and application performance.Increasing the
idle-timeout,request-timeout, andlinger-timeoutvalues to 400s allows longer processing times for requests, which can be beneficial for scenarios with high latency or resource-intensive operations.However, please keep an eye on the server resources and application performance after deploying these changes. Long timeouts might tie up server resources if not used judiciously.
You can use monitoring tools like Prometheus or Grafana to track metrics such as CPU usage, memory usage, request latency, and error rates. If you notice any performance degradation or resource exhaustion, consider fine-tuning these timeout values based on your application's specific requirements.
20-21: LGTM!Increasing the
parallelism-minandparallelism-maxvalues to 8 and 64, respectively, can improve the throughput of actor processing by allowing more threads to be utilized concurrently. The chosen values seem reasonable for a production environment.
35-35: Monitor the memory usage and garbage collection after deploying the changes.Increasing the
fixed-pool-sizeof themy-blocking-dispatcherto 1024 can enhance the performance of blocking tasks by providing more threads. This can help reduce wait times and improve overall application responsiveness.However, please monitor the memory usage and garbage collection after deploying these changes. Ensure that the system has enough memory to accommodate the increased number of threads without causing excessive garbage collection or out-of-memory errors.
You can use tools like JConsole or VisualVM to monitor the JVM memory usage and garbage collection behavior. If you observe any memory-related issues, consider adjusting the
fixed-pool-sizevalue or tuning the JVM memory settings (e.g., increasing the heap size) accordingly.
7-10: Verify if the system has enough resources to handle the specified number of connections and open requests.The changes to introduce the
host-connection-poolsection withmax-connectionsandmax-open-requestsset to 1024 are aimed at scaling the connection handling capabilities of the server, which is a good improvement.However, please ensure that the system has enough resources (CPU, memory, etc.) to handle this many connections and open requests effectively. You can run load tests or performance tests to verify this.
To assist with the verification, you can use the following script to check the system resources:
If the system resources are not sufficient, consider adjusting the
max-connectionsandmax-open-requestsvalues accordingly.devops/linux/docker/deployment/scripts/d-stack-up-app-containers.sh (1)
29-33: LGTM!The code segment is correctly implemented and follows the bash syntax. The purpose of the code segment is to conditionally start a Keycloak test server for Single Sign-On (SSO) support, which is a good addition to the script. The code segment is well-integrated into the existing script and does not disrupt the overall flow. The code segment uses the
pushdandpopdcommands to navigate to thehelper/keycloakdirectory and back, which is a good practice to ensure that the script's working directory is not changed. The code segment uses thesourcecommand to execute thestart-keycloak-test-server.shscript, which is a common practice in bash scripts to execute a script in the current shell environment. The code segment uses theifstatement to check the value of theREACT_APP_ENABLE_SSOenvironment variable, which is a common practice in bash scripts to conditionally execute code based on the value of an environment variable.JeMPI_Apps/JeMPI_UI/src/components/dashboard/widgets/BetaFscoreWidget.tsx (1)
26-26: Proper usage of theformatValuefunction.The
formatValuefunction is correctly used to format thevalueprop of theCountWidgetcomponents. This ensures consistent formatting of the precision, recall_precision, and recall values throughout the component.Also applies to: 32-32, 38-38
devops/windows/base-docker-wsl/helper/scripts/d-stack-01-create-dirs.sh (1)
33-37: LGTM!The added lines for creating new directories look good to me:
- Using
mkdir -pis the correct way to create directories.- Reading the directory paths from environment variables is a good practice for configuration management.
- Creating dedicated directories for backups, configs and CSV files helps in organizing the file system.
devops/windows/base-docker-linux/helper/scripts/d-stack-01-create-dirs.sh (4)
36-38: LGTM!Creating a dedicated directory for PostgreSQL database storage and setting its ownership to the PostgreSQL user and group is a good practice for better organization, isolation, and security.
40-40: LGTM!Creating a dedicated directory for system configuration files is a good practice for better organization and separation of concerns.
41-41: LGTM!Creating a dedicated directory for CSV files is a good practice for better organization and separation of data files from other files and directories.
43-43: Verify backup process and schedule.Creating a dedicated directory for PostgreSQL backups is a good practice for better organization and management of backup files. However, I couldn't find any commands in this script to perform the actual backups.
Please verify if there are any scripts or commands to perform the PostgreSQL backups and if they are scheduled to run regularly. Regular backups are essential for data protection and disaster recovery.
You can run the following script to search for any PostgreSQL backup related scripts or configurations in the repository:
JeMPI_Apps/JeMPI_LibShared/src/main/java/org/jembi/jempi/shared/config/Config.java (1)
20-30: LGTM!The code changes introduce a more flexible approach to determine the configuration file path based on the operating system. It first checks for the existence of a configuration file at a specific path tailored for Ubuntu systems. If this path does not exist, it falls back to an alternative path defined by the
SYSTEM_CONFIG_DIRSenvironment variable, which is more suitable for Windows systems.The changes enhance the application's ability to adapt to different environments by dynamically selecting the appropriate configuration file path based on the operating system and the presence of the file, thereby improving its robustness and usability.
The implementation follows the intended logic as described in the AI-generated summary and is implemented correctly.
[consistent_summary]
devops/benchmarking/api-read.js (4)
1-3: LGTM!The imports are correct and necessary for the script.
5-7: LGTM!The constant is correctly defined and can be used to control the load on the API.
9-25: LGTM!The custom metrics and options are correctly defined. The thresholds for errors and request duration are reasonable.
41-42: Verify the expected API request method and payload.There is an inconsistency between the commented out POST request and the active GET request:
- The commented out POST request sends a payload to the API endpoint.
- The active GET request does not send a payload.
It's unclear if the API endpoint expects a POST request with a payload or a GET request without a payload.
Please verify the expected API request method and payload, and update the script accordingly.
JeMPI_Apps/JeMPI_UI/src/pages/settings/probabilistic/ProbabilisticConstants.tsx (4)
53-53: LGTM!The code segment correctly assigns the value of
rule.reviewThresholdRange?.lowtominReviewThresholdif it exists, otherwise it falls back todefaultValues.minReviewThreshold. The change to remove the.toString()method call is appropriate to preserve the original type of the value.
54-54: LGTM!The code segment correctly assigns the value of
rule.linkThresholdtolinkThresholdif it exists, otherwise it falls back todefaultValues.linkThreshold. The change to directly assign the value without converting it to a string is appropriate.
56-56: LGTM!The code segment correctly assigns the value of
rule.reviewThresholdRange?.hightomaxReviewThresholdif it exists, otherwise it falls back todefaultValues.maxReviewThreshold. The change to remove the.toString()method call is appropriate to preserve the original type of the value.
57-57: LGTM!The code segment correctly assigns the value of
rule.marginWindowSizetomarginWindowSizeif it exists, otherwise it falls back todefaultValues.marginWindowSize. The change to directly assign the value without converting it to a string is appropriate.documentation/sso.md (2)
45-45: LGTM!The updated image path improves the clarity and accessibility of the image reference by removing the parent directory reference
../.
50-50: LGTM!The updated image paths improve the clarity and accessibility of the image references by removing the parent directory reference
../.Also applies to: 54-54
devops/benchmarking/kafka-monitor.js (5)
1-7: LGTM!The comment block provides a clear and concise description of the file's purpose.
8-34: LGTM!The code segment correctly imports the required modules, defines the necessary constants and instances, and creates the topic only once using the current virtual user check.
36-42: LGTM!The threshold ensures that the test fails if there are any errors while reading messages from Kafka.
43-75: LGTM!The code segment correctly reads 10 messages from Kafka and performs the necessary checks on the messages. It uses the schemaRegistry.deserialize method to deserialize the key and value of the message and the String.fromCharCode method to convert the header value from a byte array to a string.
77-84: LGTM!The code segment correctly deletes the topic only once using the current virtual user check and closes the reader and connection.
devops/windows/base-docker-wsl/conf/env/conf-env-low-1-pc.template (1)
21-25: LGTM!The code segment is correctly exporting the new environment variables related to system and API configurations. The variable names are descriptive, follow a consistent naming convention, and their values are being set from other environment variables, which is a good practice. There are no security concerns with exporting these variables as they don't seem to contain sensitive information.
These variables are likely being used in other parts of the system for configuration purposes, so it's important to ensure that they are being used correctly and consistently throughout the codebase.
JeMPI_Apps/JeMPI_BackupRestoreAPI/src/main/resources/application.conf (3)
6-6: Ensure the idle timeout is optimal for your use case.Increasing the
idle-timeoutto 60 seconds allows connections to remain idle for a longer duration before being closed by the server. This change may be beneficial if your clients have long periods of inactivity between requests.However, please monitor your server resources and adjust this timeout if you notice any resource constraints due to a large number of idle connections.
8-8: Ensure the linger timeout is optimal for your use case.Increasing the
linger-timeoutto 60 seconds allows connections to linger for a longer duration after a request has been completed. This change may be beneficial if your clients send multiple requests over the same connection.However, please monitor your server resources and adjust this timeout if you notice any resource constraints due to a large number of lingering connections.
7-7: Verify if the increased request timeout is necessary.Increasing the
request-timeoutto 60 seconds allows more time for a request to be completed before it times out. This change may be necessary if your server handles long-running requests that take more than 5 seconds to complete.However, if you notice that certain requests are consistently taking close to 60 seconds or timing out, it may indicate a performance issue. In such cases, please investigate and optimize those requests to improve the response times.
Run the following script to verify the request durations:
devops/linux/docker/d-stack-1-build-___-reboot.sh (5)
21-72: LGTM!The
process_appfunction follows a clear sequence of steps to scale down, build, push, and scale up an app. The logic is correct and easy to understand.Tools
Shellcheck
[warning] 24-24: Declare and assign separately to avoid masking return values.
(SC2155)
[warning] 25-25: Declare and assign separately to avoid masking return values.
(SC2155)
[warning] 34-34: Declare and assign separately to avoid masking return values.
(SC2155)
80-86: LGTM!The code segment correctly processes valid apps using the
process_appfunction and keeps track of invalid apps. The logic is sound and easy to follow.Tools
Shellcheck
[error] 81-81: Arrays implicitly concatenate in [[ ]]. Use a loop (or explicit * instead of @).
(SC2199)
[warning] 81-81: Remove quotes from right-hand side of =~ to match as a regex rather than literally.
(SC2076)
[warning] 84-84: Quote to prevent word splitting/globbing, or split robustly with mapfile or read -a.
(SC2206)
91-93: LGTM!The code segment correctly notifies the user of any invalid apps that were ignored. The logic is clear and concise.
Tools
Shellcheck
[error] 92-92: Argument mixes string and array. Use * or separate argument.
(SC2145)
1-9: LGTM!The script's header and documentation are well-written and informative. The shebang line and shell options are correctly set, and the purpose, usage, and current status of the script are clearly documented.
10-19: LGTM!The configuration and input validation setup is well-organized and follows good practices. Loading environment variables from configuration files separates configuration from code, and defining valid apps in an array allows for easy validation of input arguments. Initializing an empty array for invalid apps is a good way to keep track of invalid input.
devops/linux/docker/conf/env/create-env-linux-low-1.sh (1)
68-69: LGTM!Commenting out the previous values for
REACT_APP_JEMPI_BASE_API_PORTandREACT_APP_ENABLE_SSOis a good practice to keep the history of the changes.JeMPI_Apps/JeMPI_Linker/src/main/java/org/jembi/jempi/linker/Main.java (3)
34-39: Excellent addition of the supervision strategy!Introducing a supervision strategy for the
BackEndactor is a great way to handle failures gracefully. Resuming the actor on failure ensures that it continues to operate even if it encounters an exception, improving the overall resilience of the system. Enabling logging for the supervision strategy provides better visibility into the failures and restarts of the actor, which is crucial for monitoring and debugging purposes.
45-45: Good addition of the logging statement.The logging statement provides useful information about the state of the system, indicating that the SPMU is opened. This helps in understanding the sequence of events during the startup of the application.
49-63: Great improvements to the actor behavior!The changes to the actor behavior enhance the observability and resilience of the actor system:
Handling the
Terminatedsignal and logging the termination reason improves the observability of the actor lifecycle events. This helps in understanding why an actor was terminated and aids in debugging.Logging a message when the actor is restarted provides insight into the actor's state transitions. This is useful for monitoring the health of the actor system.
Wrapping the behavior in a supervision strategy ensures that failures are managed effectively. Resuming the actor on failure with logging enabled ensures that the actor continues to operate and that failures are logged for further analysis.
Overall, these changes make the actor system more robust and maintainable.
JeMPI_Apps/JeMPI_API/src/main/resources/application.conf (5)
7-8: LGTM!The changes to increase the
max-connectionsandmax-open-requestssettings to 1024 are reasonable for enhancing the server's capacity to handle concurrent connections and requests in a production environment.
11-13: LGTM!Increasing the
idle-timeout,request-timeout, andlinger-timeoutsettings to 60 seconds is a good change to allow for longer wait times before closing idle connections. This could potentially improve user experience during high-latency scenarios.
15-16: LGTM!Setting the
max-to-strict-bytesto 128 MB and allowing for dynamic adjustment via the${?JEMPI_FILE_IMPORT_MAX_SIZE_BYTE}environment variable is a good change. It provides a reasonable default limit while also allowing for flexibility based on deployment needs.
23-24: LGTM!Increasing the
parallelism-minto 64 and setting theparallelism-maxto 64 are good changes to enhance the ability to handle concurrent tasks in a production environment.
88-88: LGTM!Increasing the
fixed-pool-sizeto 1024 for themy-blocking-dispatcheris a good change to improve throughput and responsiveness under load by increasing the number of threads available for blocking operations.documentation/backup-and-restore.md (3)
25-29: Great addition of the prerequisites section!Specifying the PostgreSQL version requirement ensures users have the necessary setup for backup and restore operations. This improves the clarity and completeness of the documentation.
62-63: Corrected image reference for the backup process.Fixing the image reference ensures proper linking and improves the clarity of the documentation.
89-89: Corrected image reference for the restore process.Fixing the image reference ensures proper linking and improves the clarity of the documentation.
devops/windows/base-docker-linux/conf/env/create-env-linux-low-1.sh (8)
5-5: LGTM!The code segment is correctly setting the
PROJECT_PATH_UIenvironment variable using the value ofPROJECT_PATH_APPS_ROOT.
8-8: LGTM!The code segment is correctly setting the
PROJECT_DATA_APPS_DIRenvironment variable using the value ofPROJECT_DIR.
11-15: LGTM!The code segment is correctly setting the environment variables related to configuration files and directories.
32-36: LGTM!The code segment is correctly setting the environment variables related to PostgreSQL databases.
42-49: LGTM!The code segment is correctly setting the environment variables related to ports for various services.
56-56: LGTM!The code segment is correctly setting the
JEMPI_FILE_IMPORT_MAX_SIZE_BYTEenvironment variable to a human-readable value of128m.
60-65: LGTM!The code segment is correctly setting the environment variables related to the React application.
78-78: LGTM!The code segment is correctly setting the
EM_SCALA_RAM_LIMITenvironment variable to a value of16G.devops/windows/base-docker-wsl/conf/env/create-env-linux-low-1.sh (7)
5-5: LGTM!The code segment looks good. It correctly uses the previously defined
PROJECT_PATH_APPS_ROOTvariable to construct thePROJECT_PATH_UIpath.
8-8: LGTM!The code segment looks good. It correctly uses the previously defined
PROJECT_DIRvariable to construct thePROJECT_DATA_APPS_DIRpath.
11-15: LGTM!The code segment looks good. It correctly uses the previously defined
PROJECT_DIRvariable to construct paths for various configuration files and directories.
32-36: LGTM!The code segment looks good. It exports environment variables for various PostgreSQL database names.
82-89: LGTM!The RAM limits for various services look reasonable for a development environment. The higher RAM limit for the EM Scala service (
EM_SCALA_RAM_LIMIT) seems justified given its memory requirements.
91-96: LGTM!The UI configuration settings look appropriate for a development environment. Setting
NODE_ENVto "development",REACT_APP_MOCK_BACKENDto "false", andREACT_APP_ENABLE_SSOto "false" aligns with the development setup.The calculation and export of
REACT_APP_MAX_UPLOAD_CSV_SIZE_IN_BYTESis also correct.Tools
Shellcheck
[warning] 96-96: Declare and assign separately to avoid masking return values.
(SC2155)
Line range hint
1-106: Code changes align with the AI-generated summary.The code changes in the script align with the AI-generated summary. The summary accurately captures the addition of various environment variables for project directories, database configurations, API settings, HTTP ports, Keycloak configurations, memory limits, and UI configurations.
No inconsistencies found between the code and the summary.
Tools
Shellcheck
[warning] 96-96: Declare and assign separately to avoid masking return values.
(SC2155)
Gitleaks
53-53: Detected a Generic API Key, potentially exposing access to various services and sensitive operations.
(generic-api-key)
55-55: Detected a Generic API Key, potentially exposing access to various services and sensitive operations.
(generic-api-key)
devops/windows/base-docker-linux/conf/env/create-env-linux-high-1.sh (9)
4-5: LGTM!The code segment is setting the
PROJECT_PATH_APPS_ROOTandPROJECT_PATH_UIenvironment variables usingbuiltin cdand command substitution, which is a common and acceptable pattern in bash scripts.Tools
Shellcheck
[warning] 4-4: Declare and assign separately to avoid masking return values.
(SC2155)
[warning] 4-4: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
8-8: LGTM!The code segment is correctly setting the
PROJECT_DATA_APPS_DIRenvironment variable.
11-15: LGTM!The code segment is correctly setting various environment variables related to system configuration and API configuration.
17-27: LGTM!The code segment is correctly setting various environment variables related to node placement and IP addresses.
Tools
Shellcheck
[warning] 17-17: Declare and assign separately to avoid masking return values.
(SC2155)
[warning] 19-19: Declare and assign separately to avoid masking return values.
(SC2155)
34-35: LGTM!The code segment is correctly setting the
SCALE_ZERO_02andSCALE_ZERO_03environment variables to 0.
41-41: LGTM!The code segment is correctly setting the
SCALE_LINKERenvironment variable to 3.
45-49: LGTM!The code segment is correctly setting various environment variables related to PostgreSQL databases.
55-62: LGTM!The code segment is correctly setting various environment variables related to API ports.
69-93: LGTM!The code segment is correctly setting various environment variables related to file import size limit, UI configuration, and RAM limits for various services.
devops/windows/base-docker-wsl/conf/env/create-env-linux-high-1.sh (9)
8-8: LGTM for adding application data path variable.The addition of the
PROJECT_DATA_APPS_DIRenvironment variable is a good practice for maintaining a structured development environment.
11-15: LGTM for adding system configuration variables.The addition of environment variables for system configuration directory and configuration file names is a good practice for maintaining a structured development environment.
34-35: LGTM for adding scaling parameters.The addition of the
SCALE_ZERO_02andSCALE_ZERO_03environment variables with values set to 0 suggests a shift in resource allocation, which is essential for managing the services in the development environment.
41-41: LGTM for updating linker scaling parameter.Increasing the
SCALE_LINKERvalue from 1 to 3 indicates a potential need for more resources for the linker service, which is essential for managing the service in the development environment.
45-49: LGTM for adding PostgreSQL database variables.The addition of environment variables for multiple PostgreSQL databases, such as
users_db,notifications_db,audit_db, andkc_test_db, indicates a more complex data management strategy, which is essential for maintaining a structured development environment.
56-61: LGTM for adding HTTP port variables.The addition of environment variables for HTTP ports of various services, all set to 50000, centralizes the API access point, which is essential for maintaining a consistent development environment.
76-81: LGTM for adding UI environment variables.The addition of environment variables for the UI, such as
NODE_ENV,REACT_APP_JEMPI_BASE_API_HOST,REACT_APP_JEMPI_BASE_API_PORT,REACT_APP_MOCK_BACKEND, andREACT_APP_ENABLE_SSO, helps maintain a consistent development environment for the UI.
87-87: LGTM for updating HAProxy RAM limit.Reducing the
HAPROXY_RAM_LIMITvalue from 32G to 8G indicates a potential optimization of resource usage, which is essential for managing the service in the development environment.
90-100: LGTM for adding service RAM limits and UI settings.The addition of environment variables for RAM limits of various services, such as async receiver, ETL, controller, EM Scala, linker, API, and UI, helps optimize resource usage for the services in the development environment.
The UI settings, such as the base URL, mock backend, and SSO enablement, are also defined to maintain a consistent development environment for the UI.
documentation/configuration-user-guide.md (4)
38-40: LGTM!The changes to the list of actions that the user can perform in the design view of the deterministic tab are accurate and improve the clarity of the documentation.
44-44: LGTM!The grammatical correction to the action that the user can perform in the design view of the deterministic tab is accurate and improves the clarity of the documentation.
49-49: LGTM!The grammatical correction to the description of the sub tabs of the blocking tab is accurate and improves the clarity of the documentation.
63-71: LGTM!The changes to the list of actions that the user can perform in the design view of the blocking tab are accurate and improve the clarity of the documentation.
JeMPI_Apps/JeMPI_Linker/src/main/java/org/jembi/jempi/linker/SPMU.java (1)
58-58: LGTM!Replacing the hardcoded timeout value with a reference to a constant from
GlobalConstantsis a good refactoring that improves maintainability. The change is straightforward and does not introduce any issues.devops/windows/base-docker-linux/conf/env/conf-env-low-1-pc.template (1)
21-25: LGTM!The introduction of new environment variables for system and API configurations aligns well with the PR objective of enhancing configuration management. Setting the values from other environment variables allows for flexibility in managing the configurations. The code segment has no syntax or logical issues.
JeMPI_Apps/JeMPI_API_KC/src/main/resources/application.conf (5)
7-8: Verify the impact of increasing the host connection pool settings.The changes to increase the
max-connectionsandmax-open-requestsparameters to 1024 can improve the server's capacity to handle concurrent connections and requests. However, it's important to verify the impact of these changes on the server's performance and resource utilization under the expected load.Consider running load tests and monitoring the server's resource utilization (CPU, memory, network) to ensure that the new settings are appropriate for the production environment.
11-13: Monitor the impact of increasing the server timeout settings.The changes to increase the
idle-timeout,request-timeout, andlinger-timeoutparameters to 60 seconds can allow for longer wait times before connections are closed, potentially improving user experience during high-load scenarios. However, it's important to monitor the impact of these changes on the server's performance and user experience.Consider monitoring the following metrics:
- Number of open connections
- Connection duration
- Request latency
- Server resource utilization (CPU, memory, network)
If the server is unable to handle the load and the connections are being closed prematurely, you may need to adjust the timeout values or optimize the server's performance.
15-16: LGTM!Linking the
max-to-strict-bytesparameter to an environment variableJEMPI_FILE_IMPORT_MAX_SIZE_BYTEis a good practice for allowing dynamic configuration based on external settings. This can be useful for adjusting the maximum request size limit without modifying the code.
23-24: Verify the impact of increasing the default dispatcher parallelism settings.The changes to increase the
parallelism-minandparallelism-maxparameters to 8 and 64, respectively, can allow for greater concurrency in task execution. However, it's important to verify the impact of these changes on the server's performance and resource utilization under the expected load.Consider running load tests and monitoring the server's resource utilization (CPU, memory) to ensure that the new settings are appropriate for the production environment.
115-115: Consider adjusting the fixed-pool-size value based on resource utilization.The change to increase the
fixed-pool-sizeparameter to 1024 for the blocking dispatcher can improve the server's capacity to handle blocking operations. However, setting the value too high may lead to resource exhaustion if not properly tuned.Consider monitoring the server's resource utilization (CPU, memory) under the expected load and adjusting the
fixed-pool-sizevalue based on the observed utilization. You may need to lower the value if the server is experiencing high CPU or memory usage.JeMPI_Apps/JeMPI_LibShared/src/main/java/org/jembi/jempi/shared/kafka/MyKafkaConsumerByTopic.java (1)
5-5: LGTM!The imports are necessary for the introduced
ConsumerRebalanceListenerand there are no issues.Also applies to: 9-9, 14-14
devops/benchmarking/api-write.js (6)
1-7: LGTM!The imports are correct and necessary for the script.
8-14: LGTM!The configuration object is well-structured and contains relevant test parameters.
16-41: LGTM!The k6 options object is correctly configured with reasonable thresholds and metrics.
43-73: LGTM!The setup function is well-structured and performs the necessary setup steps correctly.
75-81: LGTM!The SharedArray usage and counter initialization are correct.
82-139: LGTM!The main test function is well-structured and performs the necessary test steps correctly. The error handling and logging are sufficient.
JeMPI_Apps/JeMPI_LibShared/src/main/java/org/jembi/jempi/shared/models/GlobalConstants.java (4)
67-67: LGTM!The reduction in the number of Dgraph reconnect retries from 20 to 5 aligns with the objective of quicker failure responses in Dgraph reconnections.
69-69: LGTM!Setting a fixed query timeout of 60 seconds decouples it from the retry mechanism and seems like a reasonable value.
70-70: LGTM!The introduction of a separate timeout for Akka operations is a good practice. The calculation of the timeout value based on the retry count, sleep duration, and query duration is correct.
72-72: Verify the impact of the change and add a comment to explain the reason.The significant increase in the tea time timeout from 5 to 30 seconds could potentially impact the overall performance of the system. Please verify that this change does not introduce any performance issues.
Also, consider adding a comment to explain the reason for the significant increase in the timeout value. This will help in understanding the rationale behind the change in the future.
JeMPI_Apps/JeMPI_LibMPI/src/main/java/org/jembi/jempi/libmpi/dgraph/DgraphClient.java (3)
5-5: LGTM!The removal of the
TxnConflictExceptionimport statement aligns with the changes made to the transaction conflict handling mechanism.
16-16: LGTM!The addition of the
java.util.function.Supplierimport statement is necessary for the implementation of the new retry mechanism in therunWithRetriesmethod.
111-124: Excellent refactoring of the transaction methods!The use of the
runWithRetriesmethod in theexecuteReadOnlyTransactionanddoMutateTransactionmethods greatly improves the code readability and maintainability by removing the repetitive retry logic. The error handling and logging are also preserved, which is crucial for debugging purposes.Also applies to: 128-145
devops/windows/deployment/deploy-local-windows.ps1 (4)
13-13: LGTM!Updating to the latest stable version of Java is a good practice. The URL update looks correct.
38-45: LGTM!The improved logic for starting WSL looks good. It prevents unnecessary attempts to start WSL if it is already running, optimizing the script's execution flow.
91-94: LGTM!The updated logic in the "Build and Reboot" choice of the switch statement looks good. It suggests a more streamlined approach to managing the application lifecycle by focusing on stopping and starting the application.
91-94: Skipping duplicate review.This code segment was already reviewed in the previous comment.
JeMPI_Apps/JeMPI_Linker/src/main/java/org/jembi/jempi/linker/SPInteractions.java (5)
51-53: LGTM!The code change correctly creates a
completableFutureto handle the asynchronous operation of linking the patient interaction.
59-73: Robust error handling and logging!The code change enhances the error handling and logging of the asynchronous operation. Setting the interrupt status when an
InterruptedExceptionoccurs is a good practice. Logging the failed interaction helps in identifying and debugging issues.I noticed that
this.closeInteractionStream()is commented out. Can you provide more context on the updated stream closing logic and if the commented out code can be removed?
75-76: LGTM!The code change correctly handles the exceptions that can occur when getting the result of the
completableFuture. Logging an error message when the backend actor is not available helps in identifying the issue.
107-110: What is the updated stream closing logic?I noticed that the
closeInteractionStream()method is commented out. Can you provide more context on why it's commented out and what the updated stream closing logic is? If the method is no longer needed, consider removing the commented out code to keep the codebase clean.
15-15: LGTM!The import statement for
GlobalConstantsis correctly added.devops/windows/base-docker-linux/conf/env/conf-env-high-1-pc.template (18)
13-15: LGTM!The new environment variable exports for the API service are correctly implemented and follow the existing pattern in the file.
16-18: LGTM!The new environment variable exports for the backup restore API service are correctly implemented and follow the existing pattern in the file.
19-21: LGTM!The new environment variable exports for the API KC service are correctly implemented and follow the existing pattern in the file.
22-24: LGTM!The new environment variable exports for the linker service are correctly implemented and follow the existing pattern in the file.
25-27: LGTM!The new environment variable exports for the controller service are correctly implemented and follow the existing pattern in the file.
28-30: LGTM!The new environment variable exports for the ETL service are correctly implemented and follow the existing pattern in the file.
37-42: LGTM!The new environment variable exports for system configuration and CSV directories are correctly implemented and follow the existing pattern in the file.
54-55: LGTM!The new environment variable exports for Dgraph zero-02 and zero-03 directories are correctly implemented and follow the existing pattern in the file.
60-63: LGTM!The new environment variable exports for PostgreSQL database, PostgreSQL backup, and Dgraph backup directories are correctly implemented and follow the existing pattern in the file.
69-69: LGTM!The renaming of the environment variable for the EM service directory from
DATA_DIR_EMtoDATA_DIR_EM_SCALAis correctly implemented and follows the existing pattern in the file.
80-81: LGTM!The new environment variable exports for Dgraph zero-02 and zero-03 scale configurations are correctly implemented and follow the existing pattern in the file.
93-93: LGTM!The renaming of the environment variable for the EM service placement from
PLACEMENT_EMtoPLACEMENT_EM_SCALAis correctly implemented and follows the existing pattern in the file.
102-103: LGTM!The new environment variable exports for Kafka-02 and Kafka-03 placement configurations are correctly implemented and follow the existing pattern in the file.
105-110: LGTM!The new environment variable exports for Dgraph zero-02, zero-03, alpha-02, and alpha-03 placement configurations are correctly implemented and follow the existing pattern in the file.
113-117: LGTM!The new environment variable exports for Keycloak test server placement and placement configurations for nodes 1, 2, and 3 are correctly implemented and follow the existing pattern in the file.
122-125: LGTM!The new environment variable exports for PostgreSQL users, notifications, audit, and Keycloak test databases are correctly implemented and follow the existing pattern in the file.
140-140: LGTM!The renaming of the environment variable for the EM service RAM limit from
EM_RAM_LIMITtoEM_SCALA_RAM_LIMITis correctly implemented and follows the existing pattern in the file.
Line range hint
147-175: LGTM!The new environment variable exports for API and UI configurations are correctly implemented and follow the existing pattern in the file.
devops/windows/base-docker-wsl/conf/env/conf-env-high-1-pc.template (13)
13-14: LGTM!The new environment variables for the API service configuration look good. Using parameterized values is a good practice.
16-17: LGTM!The new environment variables for the backup and restore API service configuration look good. Using parameterized values is a good practice.
19-20: LGTM!The new environment variables for the API service integrated with Keycloak (KC) look good. Using parameterized values is a good practice.
22-23: LGTM!The new environment variables for the linker service configuration look good. Using parameterized values is a good practice.
28-29: LGTM!The new environment variables for the ETL service configuration look good. Using parameterized values is a good practice.
37-41: LGTM!The new environment variables for system directories and API configuration files look good. Using parameterized values is a good practice.
54-55: LGTM!The new environment variables for Dgraph zero instance data directories look good. Using parameterized values is a good practice.
64-71: LGTM!The new environment variables for data directories of various services look good. Using parameterized values is a good practice.
79-80: LGTM!The new environment variables for scaling Dgraph zero instances look good. Using parameterized values is a good practice.
88-97: LGTM!The new environment variables for placement of various services on
NODE1look good. Using parameterized values is a good practice.
101-102: LGTM!The updated environment variables for placement of Kafka, Dgraph zero, Dgraph alpha, and Keycloak test server instances across multiple nodes look good. Using parameterized values is a good practice.
Also applies to: 104-105, 107-108, 112-113
114-116: LGTM!The new environment variables for placement of services across multiple nodes look good. Using parameterized values is a good practice.
121-124: LGTM, but verify the usage of the commented-out code.The new environment variables related to PostgreSQL databases, resource limits for various services, API configuration, and UI configuration look good. Using parameterized values is a good practice.
However, the commented-out code at line range 160-164 seems to be conditionally setting the
REACT_APP_JEMPI_BASE_API_PORTbased on the value ofREACT_APP_ENABLE_SSO.Please verify if this code is still needed. If not, consider removing it to keep the configuration clean and maintainable.
Run the following script to verify the usage of the commented-out code:
Also applies to: 135-143, 145-157, 160-164, 166-174
Verification successful
Commented-out code for
REACT_APP_JEMPI_BASE_API_PORTis redundant.The
REACT_APP_JEMPI_BASE_API_PORTvariable is actively used and set with a default value in multiple scripts across different environments. The commented-out code appears to be unnecessary unless it serves a specific conditional purpose. Consider removing it to maintain a clean and maintainable configuration.
JeMPI_Apps/JeMPI_UI/docker-entrypoint.shdevops/windows/base-docker-linux/conf/env/create-env-linux-low-1.shdevops/windows/base-docker-linux/conf/env/create-env-linux-high-1.shdevops/windows/base-docker-wsl/conf/env/create-env-linux-high-1.shdevops/windows/base-docker-wsl/conf/env/create-env-linux-low-1.shdevops/linux/docker/conf/env/create-env-linux-high-1.shdevops/linux/docker/conf/env/create-env-linux-low-1.shdevops/linux/docker/conf/env/create-env-wsl-low-1.shScripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the usage of the commented-out code that conditionally sets `REACT_APP_JEMPI_BASE_API_PORT`. # Test: Search for the usage of `REACT_APP_JEMPI_BASE_API_PORT`. Expect: No usage outside the commented-out code. rg --type-not markdown --type-not make --type shell -C 5 $'REACT_APP_JEMPI_BASE_API_PORT'Length of output: 118
Script:
#!/bin/bash # Description: Verify the usage of the commented-out code that conditionally sets `REACT_APP_JEMPI_BASE_API_PORT`. # Test: Search for the usage of `REACT_APP_JEMPI_BASE_API_PORT`. Expect: No usage outside the commented-out code. rg --type-not markdown --type-not make --type sh -C 5 $'REACT_APP_JEMPI_BASE_API_PORT'Length of output: 8823
JeMPI_Apps/JeMPI_UI/src/components/notificationWorklist/NotificationWorklist.tsx (5)
70-71: LGTM!Setting
keepPreviousDatatotrueis a good practice to improve the user experience by showing stale data while new data is being fetched.
71-79: LGTM!The
onSuccesscallback is a nice addition to automatically adjust the date filter when no records are found for the current day. This enhances the component's responsiveness to user input.
109-116: LGTM!The reformatting of the
DateTimePickercomponent for the start date filter improves code readability without altering functionality.
119-125: LGTM!The reformatting of the
DateTimePickercomponent for the end date filter improves code readability without altering functionality.
225-236: LGTM!The reformatting of the export statement for the
NotificationWorklistcomponent and theCustomTextFieldcomponent improves code consistency without altering functionality.devops/linux/docker/deployment/deploy-local.sh (1)
58-59: LGTM!The changes enhance the functionality of the script:
- Installing
unzipandzippackages ensures the necessary utilities for handling zip files are available during the SDKMAN installation process.- Sourcing the SDKMAN initialization script after installing SBT is crucial for making SDKMAN commands available in the current shell session.
Good job on improving the script!
Also applies to: 77-77
JeMPI_Apps/JeMPI_Linker/src/main/java/org/jembi/jempi/linker/Ask.java (1)
167-167: Verify the appropriateness of the new timeout value.The timeout duration for the
AskPattern.askcall in thelinkInteractionmethod has been changed fromGlobalConstants.TIMEOUT_DGRAPH_QUERY_SECStoGlobalConstants.TIMEOUT_DGRAPH_AKKA_SECS. This change suggests that the expected response time for asynchronous interactions with the backend is different when using Akka compared to Dgraph queries.Please ensure that the new timeout value is appropriate for the specific use case and doesn't introduce any unintended consequences or performance issues. Consider adding a comment to explain the reason for the change and provide additional context for future maintainers.
JeMPI_Apps/JeMPI_UI/src/components/dashboard/Dashboard.tsx (3)
5-5: LGTM!The import statement for
IconButtonis correct and necessary for the changes made later in the file.
25-25: LGTM!The import statement for
useNavigateis correct and necessary for the changes made later in the file to enable programmatic navigation.
Line range hint
58-165: LGTM!The changes look good and enhance the user experience:
- The
useNavigatehook is correctly used to enable programmatic navigation to the/notificationsroute when theIconButtonis clicked.- The
IconButtonis correctly configured with theNotificationAddicon and appropriate styling for normal and hover states.- Users can now access notifications directly from the dashboard, improving the interactivity and user experience.
devops/JeMPI_TestData/Reference/DataGenerator.py (1)
16-22: LGTM!The
parse_argumentsfunction is well-implemented and follows best practices for parsing command-line arguments using theargparsemodule. The argument names, default values, and help messages are clear and informative.documentation/installation/standalone-installation.md (1)
38-38: LGTM!The Java installation command has been updated to use the recommended version 21.0.3-tem. This aligns with the changes mentioned in the summary.
devops/benchmarking/linker-test.js (1)
16-19: LGTM!The k6 options object is correctly defined, setting the test duration to 48 hours and the number of iterations to 10.
JeMPI_Apps/JeMPI_UI/src/pages/settings/probabilistic/Probabilistic.tsx (4)
143-173: LGTM!The
Slidercomponent is well-structured and the functionality is clear. TheonChangehandler correctly updates the form values based on the slider changes, and the color-coding of the thumbs enhances the user experience by visually distinguishing the different thresholds.
187-187: LGTM!Adding the
type="number"attribute to theTextFieldcomponent for thelinkThresholdfield is a good practice to enforce numeric input and enhance the user experience. This change aligns with the alteration list and does not introduce any issues.
217-217: LGTM!Adding the
type="number"attribute to theTextFieldcomponent for theminReviewThresholdfield is a good practice to enforce numeric input and enhance the user experience. This change aligns with the alteration list and does not introduce any issues.
260-260: LGTM!Adding the
type="number"attribute to theTextFieldcomponents for themaxReviewThresholdandmarginWindowSizefields is a good practice to enforce numeric input and enhance the user experience. These changes align with the alteration list and do not introduce any issues.Also applies to: 304-304
JeMPI_Apps/JeMPI_UI/src/components/browseRecords/BrowseRecords.tsx (3)
76-77: LGTM!The change is standardizing the string used for comparison, which is a good practice for consistency.
Line range hint
120-140: LGTM!The changes introduce a new control flow that dynamically adjusts the date filter based on the query results, improving the user experience by ensuring relevant data is displayed. The logic is sound and the implementation is accurate.
131-132: LGTM!Setting
keepPreviousDatatotrueis a good practice for improving the user experience by showing the previous data while the new data is being fetched.devops/windows/run--base-docker-linux/start.ps1 (5)
7-8: LGTM!The code changes are consistent with the AI-generated summary. Copying the same configuration file for both applications seems intentional.
10-11: LGTM!The code changes are consistent with the AI-generated summary. The script introduces new copy operations for the configuration files.
81-84: LGTM!The code changes are consistent with the AI-generated summary. The script establishes a new variable
$config_dirthat captures the current working directory, which is used to set several new system configuration parameters in the subsequent code segments.
86-89: LGTM!The code changes are consistent with the AI-generated summary. The script utilizes the
$config_dirvariable to set several new system configuration parameters, which are used to configure the API application.
279-282: LGTM!The code changes are consistent with the AI-generated summary. The script passes the new system configuration parameters as arguments to the API application.
devops/windows/run--base-docker-wsl/start.ps1 (10)
10-11: LGTM!The code segment correctly copies the required configuration files to the appropriate directory.
83-86: LGTM!The code segment correctly uses
Push-LocationandPop-Locationcommands to temporarily change the current directory and sets the$config_dirvariable to the path of the config directory, which can be used later in the script. This is a good practice.
88-91: LGTM!The code segment correctly sets several variables related to configuration file names and paths using the
$config_dirvariable set in the previous code segment. The variable names are descriptive and follow a consistent naming convention, which makes the code more readable.
112-114: LGTM!The code segment correctly copies the required configuration file to the resources directory of the JeMPI_API application before building the applications.
288-288: LGTM!The code segment correctly passes the system configuration directory path (
$def_system_config_dir) to the API application, which was set in a previous code segment.
289-289: LGTM!The code segment correctly passes the API configuration reference filename (
$API_CONFIG_REFERENCE_FILENAME) to the API application, which was set in a previous code segment.
290-290: LGTM!The code segment correctly passes the API configuration master filename (
$API_CONFIG_MASTER_FILENAME) to the API application, which was set in a previous code segment.
291-291: LGTM!The code segment correctly passes the API fields configuration filename (
$API_FIELDS_CONFIG_FILENAME) to the API application, which was set in a previous code segment.
7-8: Verify the configuration requirements and consider using variables for file paths.Please confirm if both
JeMPI_APIandJeMPI_API_KCapplications require the sameconfig-reference-link-dp-api.jsonconfiguration file. If they have different configuration requirements, copying the same file to both applications could lead to inconsistencies.Also, consider using variables for the file paths to make the script more maintainable. Hardcoded paths can make the script brittle if the directory structure changes.
93-94: Consider using a variable for the system configuration directory path and provide more information about the environment variable.The
SYSTEM_CONFIG_DIRSvariable is being set to a hardcoded path, which could make the script brittle if the directory structure changes. Consider using a variable for the path to make the script more maintainable.Also, please provide more information about the purpose and usage of the
MY_VARIABLEenvironment variable. Setting it at the machine level could affect other processes or scripts, so it's important to understand its intended use.devops/windows/run--base-docker-wsl/start-with-bootstraper.ps1 (11)
7-8: LGTM!The changes are consistent with the AI-generated summary. Copying the same configuration file to both
JeMPI_APIandJeMPI_API_KCprojects suggests that they share the same API configuration.
10-11: LGTM!The changes are consistent with the AI-generated summary. Copying the reference configuration files to the
base-docker-wsl/configdirectory suggests a restructuring of how configurations are managed for the JeMPI applications.
83-86: LGTM!The changes introduce a new variable
$config_dirto store the path of thebase-docker-wsl/configdirectory. This variable is likely used in subsequent parts of the script to reference the configuration directory path.
88-91: LGTM!The changes introduce new variables to store configuration-related values. These variables are likely used in subsequent parts of the script to reference the configuration files and directories.
114-116: LGTM!The changes are consistent with the AI-generated summary. Copying the
config-api.jsonfile to the resources of theJeMPI_APIproject ensures that the necessary configuration is available for this component during the build process.
117-119: LGTM!The changes are consistent with the AI-generated summary. Copying the
config-api.jsonfile to the resources of theJeMPI_Bootstrapperproject ensures that the necessary configuration is available for this component during the build process.
301-301: LGTM!The changes pass the value of
$def_system_config_diras an argument to the API process. This is likely used by the API process to locate the system configuration directory.
302-302: LGTM!The changes pass the value of
$API_CONFIG_REFERENCE_FILENAMEas an argument to the API process. This is likely used by the API process to locate the reference configuration file.
303-303: LGTM!The changes pass the value of
$API_CONFIG_MASTER_FILENAMEas an argument to the API process. This is likely used by the API process to locate the master configuration file.
304-304: LGTM!The changes pass the value of
$API_FIELDS_CONFIG_FILENAMEas an argument to the API process. This is likely used by the API process to locate the API fields configuration file.
93-94: Verify the purpose and usage of the new variables.The changes introduce new environment variable settings, which is consistent with the AI-generated summary. Setting
SYSTEM_CONFIG_DIRSsuggests an enhancement in the configuration management aspect of the script, and setting a machine-level environment variableMY_VARIABLEindicates a need for this variable to be accessible system-wide.To verify the purpose and usage of the new variables, run the following script:
JeMPI_Apps/JeMPI_LibAPI/src/main/java/org/jembi/jempi/libapi/ProxyRoutes.java (1)
535-535: LGTM!Replacing the hardcoded timeout value with a constant reference is a good practice. It improves maintainability and allows for easier configuration of the timeout duration across the codebase.
documentation/user-interface-guide.md (6)
2-75: The "Getting Started" section looks good!It provides a clear overview of the top navigation bar and important terms and definitions related to the JeMPI system.
Tools
LanguageTool
[uncategorized] ~47-~47: The abbreviation “e.g.” (= for example) requires two periods.
Context: ...perform filtering instead of blocking. (e.g Find all males in village x) **Similar...(E_G)
Markdownlint
2-2: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
4-4: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
22-22: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
63-63: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
12-12: null
Images should have alternate text (alt text)(MD045, no-alt-text)
16-16: null
Images should have alternate text (alt text)(MD045, no-alt-text)
20-20: null
Images should have alternate text (alt text)(MD045, no-alt-text)
76-172: The "Dashboard" section provides great details!The content thoroughly explains the 3 dashboard tabs with the help of informative screenshots. Nicely done!
Tools
Markdownlint
121-121: Expected: 0; Actual: 1
Inconsistent indentation for list items at the same level(MD005, list-indent)
121-121: Expected: 0; Actual: 1
Unordered list indentation(MD007, ul-indent)
76-76: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
88-88: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
103-103: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
114-114: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
118-118: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
125-125: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
132-132: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
145-145: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
153-153: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
167-167: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
139-139: null
Images should have alternate text (alt text)(MD045, no-alt-text)
173-328: The "Browse" section is exceptionally detailed and well-instructed!The step-by-step instructions, combined with the illustrative screenshots, provide an excellent walkthrough of the Browse Patients functionality. The details for filtering patients, viewing patient details, editing golden records, and relinking are thoroughly covered, making it easy for users to understand and follow. Great work!
Tools
LanguageTool
[grammar] ~209-~209: A word may be missing after ‘a’.
Context: ...FILTER button to view the results a. If no results are found, the system dis...(THE_SENT_END)
[style] ~217-~217: Consider a shorter alternative to avoid wordiness.
Context: ... of a patient, select the relevant row. In order to view the details of a patient, select t...(IN_ORDER_TO_PREMIUM)
Markdownlint
173-173: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
175-175: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
190-190: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
194-194: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
212-212: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
220-220: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
239-239: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
247-247: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
272-272: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
278-278: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
291-291: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
311-311: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
329-418: The "Notifications" section is thoroughly detailed and clearly instructed!The content comprehensively covers the Notifications Worklist functionality, providing step-by-step instructions for handling notifications, refining searches, relinking patient records, and creating new golden records. The included screenshots effectively illustrate the steps. The level of detail and clarity is excellent!
Tools
Markdownlint
414-414: Expected: 0; Actual: 1
Unordered list indentation(MD007, ul-indent)
415-415: Expected: 0; Actual: 1
Unordered list indentation(MD007, ul-indent)
329-329: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
331-331: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
357-357: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
361-361: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
381-381: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
383-383: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
390-390: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
405-405: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
363-363: null
Images should have alternate text (alt text)(MD045, no-alt-text)
388-388: null
Images should have alternate text (alt text)(MD045, no-alt-text)
417-417: null
Images should have alternate text (alt text)(MD045, no-alt-text)
419-473: The "Import" section provides good coverage of the functionality!The content adequately details the Import data and metadata screen, providing instructions for configuring machine learning, setting threshold values, and generating reports. The included screenshots helpfully illustrate the interface. The section provides a solid overview of the Import functionality.
Tools
Markdownlint
419-419: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
428-428: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
434-434: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
448-448: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
470-470: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
472-472: null
Images should have alternate text (alt text)(MD045, no-alt-text)
474-579: The "Configuration Settings" section provides comprehensive coverage with clear instructions!The content thoroughly details the Configuration Settings screen and its various tabs, providing clear instructions for editing common properties, deterministic rules, blocking rules, probabilistic thresholds, and node properties. The included screenshots effectively illustrate the interface elements being described. The section offers a comprehensive and well-instructed overview of the Configuration Settings functionality. Excellent work!
Tools
LanguageTool
[uncategorized] ~517-~517: The noun “dropdown” is spelled as one word.
Context: ...g : - Select the operator values from a drop down field eg “And” and “Or” - Select common...(LOCKDOWN)
[uncategorized] ~518-~518: The noun “dropdown” is spelled as one word.
Context: ...Or” - Select common field values from a drop down field - Select comparator function from...(LOCKDOWN)
[uncategorized] ~519-~519: The noun “dropdown” is spelled as one word.
Context: ...eld - Select comparator function from a drop down field eg “Exact”, “Low Fuzziness” etc -...(LOCKDOWN)
[style] ~519-~519: In American English, abbreviations like “etc.” require a period.
Context: ... down field eg “Exact”, “Low Fuzziness” etc - Add a second row of input fields by s...(ETC_PERIOD)
[duplication] ~520-~520: Possible typo: you repeated a word
Context: ...nd row of input fields by selecting the add add icon button - Save rule by selecting th...(ENGLISH_WORD_REPEAT_RULE)
Markdownlint
569-569: Expected: 0; Actual: 1
Inconsistent indentation for list items at the same level(MD005, list-indent)
570-570: Expected: 0; Actual: 1
Inconsistent indentation for list items at the same level(MD005, list-indent)
571-571: Expected: 0; Actual: 1
Inconsistent indentation for list items at the same level(MD005, list-indent)
569-569: Expected: 0; Actual: 1
Unordered list indentation(MD007, ul-indent)
570-570: Expected: 0; Actual: 1
Unordered list indentation(MD007, ul-indent)
571-571: Expected: 0; Actual: 1
Unordered list indentation(MD007, ul-indent)
578-578: Expected: 0; Actual: 3
Unordered list indentation(MD007, ul-indent)
579-579: Expected: 0; Actual: 3
Unordered list indentation(MD007, ul-indent)
474-474: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
480-480: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
498-498: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
514-514: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
540-540: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
JeMPI_Apps/JeMPI_LibAPI/src/main/java/org/jembi/jempi/libapi/BackEnd.java (2)
471-478: LGTM!The code segment enhances the robustness of file handling by providing a fallback mechanism for file storage. It allows the application to adapt to different deployment environments by using an environment variable to specify an alternative file storage location. The usage of the
Filesclass for checking directory existence and moving files is a good practice.
519-529: LGTM!The code segment allows for greater flexibility in locating configuration files, accommodating different deployment environments. It uses the
Paths.getmethod to construct file paths, which is a good practice for cross-platform compatibility. The code handles the case when the specific configuration file does not exist by falling back to a default location specified by an environment variable.
| local name=$(docker ps -f name=$service --format "{{.Names}}") | ||
| local scale=$(docker service inspect --format='{{.Spec.Mode.Replicated.Replicas}}' $service || echo 1) |
There was a problem hiding this comment.
Declare and assign variables separately.
To avoid masking return values, declare and assign variables separately as suggested by the static analysis hints.
Apply this diff to fix the issues:
- local name=$(docker ps -f name=$service --format "{{.Names}}")
+ local name
+ name=$(docker ps -f name=$service --format "{{.Names}}")
- local scale=$(docker service inspect --format='{{.Spec.Mode.Replicated.Replicas}}' $service || echo 1)
+ local scale
+ scale=$(docker service inspect --format='{{.Spec.Mode.Replicated.Replicas}}' $service || echo 1)
- local app_dir=$(find ../../../JeMPI_Apps/ -maxdepth 1 -type d -iname "jempi_$app" | head -n 1)
+ local app_dir
+ app_dir=$(find ../../../JeMPI_Apps/ -maxdepth 1 -type d -iname "jempi_$app" | head -n 1)Also applies to: 34-34
Tools
Shellcheck
[warning] 24-24: Declare and assign separately to avoid masking return values.
(SC2155)
[warning] 25-25: Declare and assign separately to avoid masking return values.
(SC2155)
| sleep 1 | ||
|
|
||
| for app in "$@"; do | ||
| if [[ " ${valid_apps[@]} " =~ " ${app} " ]]; then |
There was a problem hiding this comment.
Use a loop and quote the regex.
To avoid potential issues and improve code quality, address the following static analysis hints:
- Use a loop instead of implicit array concatenation in
[[ ]]. - Quote the right-hand side of
=~to match as a regex rather than literally. - Use
mapfileorread -ato split the array robustly.
Apply this diff to fix the issues:
- if [[ " ${valid_apps[@]} " =~ " ${app} " ]]; then
+ for valid_app in "${valid_apps[@]}"; do
+ if [[ "$valid_app" =~ "$app" ]]; then
process_app $app
+ break
+ fi
+ done
- invalid_apps+=($app)
+ mapfile -t invalid_apps < <(printf '%s\n' "$app")Also applies to: 84-84
Tools
Shellcheck
[error] 81-81: Arrays implicitly concatenate in [[ ]]. Use a loop (or explicit * instead of @).
(SC2199)
[warning] 81-81: Remove quotes from right-hand side of =~ to match as a regex rather than literally.
(SC2076)
|
|
||
| # Notify user of invalid apps | ||
| if [ ${#invalid_apps[@]} -ne 0 ]; then | ||
| echo "The following apps are not valid and were ignored: ${invalid_apps[@]}" |
There was a problem hiding this comment.
Use * to expand the array.
To avoid mixing string and array, use * to expand the array as suggested by the static analysis hint.
Apply this diff to fix the issue:
- echo "The following apps are not valid and were ignored: ${invalid_apps[@]}"
+ echo "The following apps are not valid and were ignored: ${invalid_apps[*]}"Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| echo "The following apps are not valid and were ignored: ${invalid_apps[@]}" | |
| echo "The following apps are not valid and were ignored: ${invalid_apps[*]}" |
Tools
Shellcheck
[error] 92-92: Argument mixes string and array. Use * or separate argument.
(SC2145)
| export REACT_APP_JEMPI_BASE_API_PORT=50001 | ||
| export REACT_APP_ENABLE_SSO="true" |
There was a problem hiding this comment.
Tip
Codebase Verification
Issues with API Port Configuration and UI Default Port Setting
The API port is still configured to use 50000 in multiple places, and the UI's default port setting is also 50000. Please ensure the following updates are made:
-
Update all instances of
API_HTTP_PORTto50001where necessary to reflect the new configuration. -
Change the default value of
REACT_APP_JEMPI_BASE_API_PORTinJeMPI_Apps/JeMPI_UI/docker-entrypoint.shto50001. -
devops/linux/docker/conf/stack/docker-stack-low-1.yml -
devops/linux/docker/conf/stack/docker-stack-high-1.yml -
JeMPI_Apps/JeMPI_UI/docker-entrypoint.sh
Analysis chain
Verify the API port and UI configuration.
The changes to enable SSO using Keycloak look good. However, please ensure the following:
- The API is running on the new port
50001. - The UI is configured to communicate with the API on the new port
50001.
Run the following script to verify the API port and UI configuration:
Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify the API port and UI configuration.
# Test 1: Search for the API port configuration. Expect: Port 50001.
rg --type-add 'config:*.{ts,js,json,yaml,yml}' -g '!node_modules' -g '!dist' -g '!build' -i 'API_HTTP_PORT'
# Test 2: Search for the UI configuration. Expect: API port 50001.
rg --type-add 'config:*.{ts,js,json,yaml,yml}' -g '!node_modules' -g '!dist' -g '!build' -i 'REACT_APP_JEMPI_BASE_API_PORT'
Length of output: 11913
| export KC_REALM_NAME="jempi-dev" | ||
| export KC_API_URL="http://keycloak-test-server:8080" | ||
| export KC_JEMPI_CLIENT_ID="jempi-oauth" | ||
| export KC_JEMPI_CLIENT_SECRET="Tbe3llP5OJIlqUjz7K1wPp8YDAdCOEMn" | ||
| export KC_JEMPI_CLIENT_SECRET="Nsuhj2lQiCgSE7eVPLBgnLEEeaijufeh" |
There was a problem hiding this comment.
Don't hardcode secret values in the script.
Hardcoding secret values in the script is not a good practice as it can lead to security vulnerabilities if the script is committed to version control.
Consider storing the secret value in a separate file or using a secrets management system.
Do you want me to suggest a secrets management system or open a GitHub issue to track this task?
Tools
Gitleaks
53-53: Detected a Generic API Key, potentially exposing access to various services and sensitive operations.
(generic-api-key)
| - saves and updates the link score to 3.0. | ||
| - notification state is updated from New/Open to Closed. |
There was a problem hiding this comment.
Fix the list indentation.
The list items "- saves and updates the link score to 3.0." and "- notification state is updated from New/Open to Closed." are incorrectly indented. They should be indented one level more to match their parent list item.
Apply this diff to fix it:
-The system:
- - saves and updates the link score to 3.0.
- - notification state is updated from New/Open to Closed.
+The system:
+ - saves and updates the link score to 3.0.
+ - notification state is updated from New/Open to Closed.Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| - saves and updates the link score to 3.0. | |
| - notification state is updated from New/Open to Closed. | |
| The system: | |
| - saves and updates the link score to 3.0. | |
| - notification state is updated from New/Open to Closed. |
Tools
Markdownlint
414-414: Expected: 0; Actual: 1
Unordered list indentation(MD007, ul-indent)
415-415: Expected: 0; Actual: 1
Unordered list indentation(MD007, ul-indent)
| - Select the operator values from a drop down field eg “And” and “Or” | ||
| - Select common field values from a drop down field | ||
| - Select comparator function from a drop down field eg “Exact”, “Low Fuzziness” etc | ||
| - Add a second row of input fields by selecting the add add icon button |
There was a problem hiding this comment.
Remove the duplicated word "add".
The word "add" is duplicated in the phrase "add add icon button".
-Add a second row of input fields by selecting the add add icon button
+Add a second row of input fields by selecting the add icon buttonCommittable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| - Add a second row of input fields by selecting the add add icon button | |
| - Add a second row of input fields by selecting the add icon button |
Tools
LanguageTool
[duplication] ~520-~520: Possible typo: you repeated a word
Context: ...nd row of input fields by selecting the add add icon button - Save rule by selecting th...(ENGLISH_WORD_REPEAT_RULE)
| **Open Notifications** | ||
| - No. of New & Open notifications | ||
| Closed notifications | ||
| - No. of Closed notifications |
There was a problem hiding this comment.
Fix the list indentation inconsistency.
The list item "Closed notifications" is indented incorrectly. It should be at the same level as "Open Notifications".
Apply this diff to fix it:
-Closed notifications
- - No. of Closed notifications
+- Closed notifications
+ - No. of Closed notificationsCommittable suggestion was skipped due to low confidence.
Tools
Markdownlint
121-121: Expected: 0; Actual: 1
Inconsistent indentation for list items at the same level(MD005, list-indent)
121-121: Expected: 0; Actual: 1
Unordered list indentation(MD007, ul-indent)
| **Blocking**: Reducing the search space by grouping records by similar attributes into blocks. | ||
|
|
||
| **Candidate records**: A short list of Golden Records generated as a result of blocking. The records on this short list are referred to as candidate (golden) records, as they are potential candidates for linking. | ||
|
|
||
| **Patient Interaction record**: Stores demographic information of the patient e.g. name, surname, DOB, gender, address, etc. This information together with the unique source system ID is used to uniquely identify patients. | ||
|
|
||
| **Patient ID**: Unique identifier of the patient record assigned by the JeMPI upon entry. | ||
|
|
||
| **Golden record (GR)**: A golden record is created for a patient if this is the first and/or only patient record to be stored in the database. This is the same as a master record. The golden record links records based on a match score, i.e., determines that 2 or more patient records belong to the same person. | ||
|
|
||
| Always has the most up-to-date information for a patient by consensus among the golden record's interactions. | ||
|
|
||
| **Golden ID**: Unique identifier of the Golden record. | ||
|
|
||
| **Link Threshold (LTH)**: Predetermined values that allocate the match status of two records based on the probabilistic score generated by the comparison algorithm. | ||
| **M & U values**: The matching (M) and unmatching (U) values derived for each record field. | ||
| - The m values can be expressed as data quality and calculated as the ratio of matching attributes given that they belong to the same record. | ||
| - The u values can be expressed as data uniqueness and calculated as the ratio of matching values given that they do not belong to the same record. | ||
| -Because the status of matching records is unknown, m and u values are calculated using the Expectation | ||
| Maximization algorithm. |
There was a problem hiding this comment.
Fix the list formatting inconsistency.
There is an inconsistent indentation for the list items "The m values..." and "The u values..." at lines 40-41. They should be indented to match the indentation of their parent list item.
Apply this diff to fix it:
-The m values can be expressed as data quality and calculated as the ratio of matching attributes given that they belong to the same record.
-The u values can be expressed as data uniqueness and calculated as the ratio of matching values given that they do not belong to the same record.
+- The m values can be expressed as data quality and calculated as the ratio of matching attributes given that they belong to the same record.
+- The u values can be expressed as data uniqueness and calculated as the ratio of matching values given that they do not belong to the same record.Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| **Blocking**: Reducing the search space by grouping records by similar attributes into blocks. | |
| **Candidate records**: A short list of Golden Records generated as a result of blocking. The records on this short list are referred to as candidate (golden) records, as they are potential candidates for linking. | |
| **Patient Interaction record**: Stores demographic information of the patient e.g. name, surname, DOB, gender, address, etc. This information together with the unique source system ID is used to uniquely identify patients. | |
| **Patient ID**: Unique identifier of the patient record assigned by the JeMPI upon entry. | |
| **Golden record (GR)**: A golden record is created for a patient if this is the first and/or only patient record to be stored in the database. This is the same as a master record. The golden record links records based on a match score, i.e., determines that 2 or more patient records belong to the same person. | |
| Always has the most up-to-date information for a patient by consensus among the golden record's interactions. | |
| **Golden ID**: Unique identifier of the Golden record. | |
| **Link Threshold (LTH)**: Predetermined values that allocate the match status of two records based on the probabilistic score generated by the comparison algorithm. | |
| **M & U values**: The matching (M) and unmatching (U) values derived for each record field. | |
| - The m values can be expressed as data quality and calculated as the ratio of matching attributes given that they belong to the same record. | |
| - The u values can be expressed as data uniqueness and calculated as the ratio of matching values given that they do not belong to the same record. | |
| -Because the status of matching records is unknown, m and u values are calculated using the Expectation | |
| Maximization algorithm. | |
| **Blocking**: Reducing the search space by grouping records by similar attributes into blocks. | |
| **Candidate records**: A short list of Golden Records generated as a result of blocking. The records on this short list are referred to as candidate (golden) records, as they are potential candidates for linking. | |
| **Patient Interaction record**: Stores demographic information of the patient e.g. name, surname, DOB, gender, address, etc. This information together with the unique source system ID is used to uniquely identify patients. | |
| **Patient ID**: Unique identifier of the patient record assigned by the JeMPI upon entry. | |
| **Golden record (GR)**: A golden record is created for a patient if this is the first and/or only patient record to be stored in the database. This is the same as a master record. The golden record links records based on a match score, i.e., determines that 2 or more patient records belong to the same person. | |
| Always has the most up-to-date information for a patient by consensus among the golden record's interactions. | |
| **Golden ID**: Unique identifier of the Golden record. | |
| **Link Threshold (LTH)**: Predetermined values that allocate the match status of two records based on the probabilistic score generated by the comparison algorithm. | |
| **M & U values**: The matching (M) and unmatching (U) values derived for each record field. | |
| - The m values can be expressed as data quality and calculated as the ratio of matching attributes given that they belong to the same record. | |
| - The u values can be expressed as data uniqueness and calculated as the ratio of matching values given that they do not belong to the same record. | |
| -Because the status of matching records is unknown, m and u values are calculated using the Expectation | |
| Maximization algorithm. |
| "temporary": false, | ||
| "userLabel" : "My password", | ||
| "createdDate" : 1685983298938, | ||
| "secretData" : "{\"value\":\"avydCqOak8Hkxbaat5k1SchwuF0e+nMJC7sEmTM1oAg=\",\"salt\":\"OeiBGFRcnjFaguM2myRzJA==\",\"additionalParameters\":{}}", | ||
| "credentialData" : "{\"hashIterations\":27500,\"algorithm\":\"pbkdf2-sha256\",\"additionalParameters\":{}}" | ||
| "value": "dev_password_only" |
There was a problem hiding this comment.
Critical Security Vulnerability: Plain Text Password Storage
Storing passwords in plain text is a severe security vulnerability that exposes users to significant risks. If the database is compromised, attackers would have direct access to user passwords, enabling account takeover and unauthorized access.
Industry standards and security best practices strongly recommend storing user passwords using secure hashing algorithms like bcrypt, PBKDF2, or scrypt. These algorithms incorporate salting and multiple iterations to make password cracking attempts computationally infeasible.
It is crucial to adhere to best practices and comply with regulations such as GDPR, HIPAA, and PCI-DSS, which often mandate the use of strong password hashing to protect sensitive user data.
To mitigate this vulnerability, I strongly recommend reverting to the previous hashed password structure or implementing a secure password hashing mechanism immediately. Failure to do so may result in severe consequences, including data breaches, reputational damage, legal liabilities, and financial penalties.
There was a problem hiding this comment.
@MatthewErispe Been through the lot and tested locally, all seems good.
There was a problem hiding this comment.
Actionable comments posted: 1
Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Files selected for processing (1)
- devops/linux/docker/conf/keycloak/import-jempi-dev-realm.json (1 hunks)
Additional comments not posted (2)
devops/linux/docker/conf/keycloak/import-jempi-dev-realm.json (2)
395-395: LGTM!Adding the
"temporary": falsefield to indicate that the password is not temporary is acceptable.
Line range hint
1-426: Review the entire Keycloak configuration for security best practices.While reviewing the specific code changes, it is crucial to take a step back and assess the entire Keycloak configuration for adherence to security best practices. The modifications made to user details and the introduction of plain text password storage could have implications beyond just the specific user object.
Please review the complete Keycloak realm configuration to ensure that:
- Secure password hashing algorithms are consistently used throughout the configuration.
- User details are managed in a secure and maintainable manner.
- Authentication and authorization settings align with the desired security posture.
- Any other security-related configurations, such as session management, token settings, and client policies, follow industry best practices.
Conducting a thorough review of the entire configuration will help identify and address any potential security vulnerabilities or misconfigurations.
…s-Undefined Cu 86c0af52c keycloak user shows as undefined
Summary by CodeRabbit
Release Notes
New Features
max-connectionsandmax-open-requeststo 1024.Improvements
idle-timeout,request-timeout, andlinger-timeout, improving handling of long-running requests.21.0.1-temin Dockerfiles for consistent build environments.Bug Fixes
Chores
.gitignoreto exclude unnecessary files and directories, maintaining a cleaner repository.