[ALS-5422] Add persistence.xml to visualization resource #161
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The visualization resource is failing to start due to an error injecting persistence unit into CDI managed bean. It is unable to find a persistence unit named ''.
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* [ALS-5422] Add persistence.xml to visualization resource (#161) The visualization resource is failing to start due to an error injecting persistence unit into CDI managed bean. It is unable to find a persistence unit named ''. * [ALS-0000] Fix aggregate resource - Very confused as to how this was working before * [ALS-5422] Add persistence.xml to visualization resource (#161) (#162) (#163) The visualization resource is failing to start due to an error injecting persistence unit into CDI managed bean. It is unable to find a persistence unit named ''. --------- Co-authored-by: Luke Sikina <[email protected]>
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* [ALS-5422] Add persistence.xml to visualization resource (#161) (#162) The visualization resource is failing to start due to an error injecting persistence unit into CDI managed bean. It is unable to find a persistence unit named ''. * Sync new Release/0008 with Master (#168) * [ALS-5422] Add persistence.xml to visualization resource (#161) The visualization resource is failing to start due to an error injecting persistence unit into CDI managed bean. It is unable to find a persistence unit named ''. * [ALS-0000] Fix aggregate resource - Very confused as to how this was working before * [ALS-5422] Add persistence.xml to visualization resource (#161) (#162) (#163) The visualization resource is failing to start due to an error injecting persistence unit into CDI managed bean. It is unable to find a persistence unit named ''. --------- Co-authored-by: Luke Sikina <[email protected]> * [ALS-5061] Remove HSAPIResource (#166) [ALS-5061] Remove HSAPIResource (#166) * [ALS-3978] Update version handling in multiple pom.xml files (#167) * [ALS-3978] Update version handling in multiple pom.xml files This commit removes hardcoded versions of dependencies from individual pom.xml files and introduces them into the root pom.xml's properties section. This centralizes the control of dependency versions to prevent inconsistencies and makes future updates more straightforward. This change covers several libraries including Guava, JUnit Jupiter, Mockito, and others. * Update library versions and clean up pom.xml Upgraded dependencies including Jackson, Guava, JUnit, Hibernate, HttpClient, and Commons-IO. Also, improved the management of versions via property variables and cleaned up inconsistent formatting. Removed an unnecessary comment related to Mockito version compatibility. * Remove specific version references in pom.xml files The changes encompass the removal of explicit version references in the project's pom.xml files. By relying on property variables, this maintenance update enhances dependency management flexibility. Specific version comments also have been removed to eliminate clutter and improve overall file readability. * Update pom.xml to use property variables for versions The changes primarily involve updating the pom.xml file to use property variables instead of hardcoding the version numbers. This is a better approach as it improves the flexibility in managing dependencies. This change also results in cleaner and more readable code by removing unnecessary explicit version references. * Downgrade Spring version in pom.xml The Spring version has been downgraded in the pom.xml file from 6.1.1 to 5.3.31. This is due to java version requirement of 17+ for 6.x --------- Co-authored-by: Luke Sikina <[email protected]>
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* [ALS-5422] Add persistence.xml to visualization resource (#161) (#162) The visualization resource is failing to start due to an error injecting persistence unit into CDI managed bean. It is unable to find a persistence unit named ''. * ALS-5387: Remove stack from resources table * ALS-5387: More robust implementation of feature --------- Co-authored-by: Gcolon021 <[email protected]> Co-authored-by: GeorgeC <[email protected]>
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Mar 26, 2024
* [ALS-5827] Enable search by CA id - If a uuid does not match a query, instead search for common area UUID - If we have a collision, I'm buying a lottery ticket * [ALS-5787] Open Access StatViz is not showing "Other" (#180) * Update key length handling in limitKeySize The limitKeySize method in the VisualizationUtil class has been updated to ensure key uniqueness when keys exceed a certain length. A more robust method of shortening the keys has been implemented: if the key is longer than 45 characters, it is cut off and replaced with "..." and additional characters are appended to ensure uniqueness if needed. This helps limit key size while preserving uniqueness. * Add VisualizationUtilTests and refine key shortening logic Added a new test class, VisualizationUtilTests to validate the functionality of the VisualizationUtil class. Adjusted the 'limitKeySize' method to ensure key uniqueness when keys are shortened to a maximum length of 45 characters. If shortened keys are not unique, additional trailing characters are included until uniqueness is achieved. * Add check on length before substring * Update pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/VisualizationUtil.java * Update pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/VisualizationUtil.java * Update pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/VisualizationUtil.java * Update pic-sure-resources/pic-sure-visualization-resource/src/test/java/edu/harvard/hms/dbmi/avillach/resource/visualization/service/VisualizationUtilTests.java Co-authored-by: Luke Sikina <[email protected]> * Fix import for modified unit test * Refactor and add test cases for key size limiting function Refactors existing code by simplifying key size limiting logic in VisualizationUtil and added several new unit tests to ensure its correct behavior with different input scenarios including long keys, empty maps, null maps, and uniqueness near middle. * Update null handling in VisualizationUtil's limitKeySize Changed the handling of null input in VisualizationUtil's limitKeySize from returning a new HashMap to throwing an IllegalArgumentException. Also, updated the corresponding test to check for this exception instead of comparing with an empty map. --------- Co-authored-by: Luke Sikina <[email protected]> * Refine the condition for empty return in DataProcessingService (#184) Adjusted the condition under which an empty HashMap is returned in the DataProcessingService. Now, an empty HashMap will only be returned when both the maximum and minimum values in the data are 0, and the number of bins is also 0. This change takes into account situations where the data contains values but the min and max are both 0. * ALS-5387: Remove stack from resources table (#186) * [ALS-5422] Add persistence.xml to visualization resource (#161) (#162) The visualization resource is failing to start due to an error injecting persistence unit into CDI managed bean. It is unable to find a persistence unit named ''. * ALS-5387: Remove stack from resources table * ALS-5387: More robust implementation of feature --------- Co-authored-by: Gcolon021 <[email protected]> Co-authored-by: GeorgeC <[email protected]> --------- Co-authored-by: Luke Sikina <[email protected]> Co-authored-by: Luke Sikina <[email protected]> Co-authored-by: ramari16 <[email protected]>
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Apr 2, 2024
* [ALS-5827] Enable search by CA id - If a uuid does not match a query, instead search for common area UUID - If we have a collision, I'm buying a lottery ticket * [ALS-5787] Open Access StatViz is not showing "Other" (#180) * Update key length handling in limitKeySize The limitKeySize method in the VisualizationUtil class has been updated to ensure key uniqueness when keys exceed a certain length. A more robust method of shortening the keys has been implemented: if the key is longer than 45 characters, it is cut off and replaced with "..." and additional characters are appended to ensure uniqueness if needed. This helps limit key size while preserving uniqueness. * Add VisualizationUtilTests and refine key shortening logic Added a new test class, VisualizationUtilTests to validate the functionality of the VisualizationUtil class. Adjusted the 'limitKeySize' method to ensure key uniqueness when keys are shortened to a maximum length of 45 characters. If shortened keys are not unique, additional trailing characters are included until uniqueness is achieved. * Add check on length before substring * Update pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/VisualizationUtil.java * Update pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/VisualizationUtil.java * Update pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/VisualizationUtil.java * Update pic-sure-resources/pic-sure-visualization-resource/src/test/java/edu/harvard/hms/dbmi/avillach/resource/visualization/service/VisualizationUtilTests.java Co-authored-by: Luke Sikina <[email protected]> * Fix import for modified unit test * Refactor and add test cases for key size limiting function Refactors existing code by simplifying key size limiting logic in VisualizationUtil and added several new unit tests to ensure its correct behavior with different input scenarios including long keys, empty maps, null maps, and uniqueness near middle. * Update null handling in VisualizationUtil's limitKeySize Changed the handling of null input in VisualizationUtil's limitKeySize from returning a new HashMap to throwing an IllegalArgumentException. Also, updated the corresponding test to check for this exception instead of comparing with an empty map. --------- Co-authored-by: Luke Sikina <[email protected]> * Refine the condition for empty return in DataProcessingService (#184) Adjusted the condition under which an empty HashMap is returned in the DataProcessingService. Now, an empty HashMap will only be returned when both the maximum and minimum values in the data are 0, and the number of bins is also 0. This change takes into account situations where the data contains values but the min and max are both 0. * ALS-5387: Remove stack from resources table (#186) * [ALS-5422] Add persistence.xml to visualization resource (#161) (#162) The visualization resource is failing to start due to an error injecting persistence unit into CDI managed bean. It is unable to find a persistence unit named ''. * ALS-5387: Remove stack from resources table * ALS-5387: More robust implementation of feature --------- Co-authored-by: Gcolon021 <[email protected]> Co-authored-by: GeorgeC <[email protected]> * [ALS-6222] Status endpoints now filters resources (#189) The database contains both open and auth hpds even if it wasn't deployed. This means we attempt to check for a resource that doesn't exist. This results in our service always showing degraded. --------- Co-authored-by: Luke Sikina <[email protected]> Co-authored-by: Luke Sikina <[email protected]> Co-authored-by: ramari16 <[email protected]>
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Apr 10, 2024
* [ALS-5827] Enable search by CA id - If a uuid does not match a query, instead search for common area UUID - If we have a collision, I'm buying a lottery ticket * [ALS-5787] Open Access StatViz is not showing "Other" (#180) * Update key length handling in limitKeySize The limitKeySize method in the VisualizationUtil class has been updated to ensure key uniqueness when keys exceed a certain length. A more robust method of shortening the keys has been implemented: if the key is longer than 45 characters, it is cut off and replaced with "..." and additional characters are appended to ensure uniqueness if needed. This helps limit key size while preserving uniqueness. * Add VisualizationUtilTests and refine key shortening logic Added a new test class, VisualizationUtilTests to validate the functionality of the VisualizationUtil class. Adjusted the 'limitKeySize' method to ensure key uniqueness when keys are shortened to a maximum length of 45 characters. If shortened keys are not unique, additional trailing characters are included until uniqueness is achieved. * Add check on length before substring * Update pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/VisualizationUtil.java * Update pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/VisualizationUtil.java * Update pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/VisualizationUtil.java * Update pic-sure-resources/pic-sure-visualization-resource/src/test/java/edu/harvard/hms/dbmi/avillach/resource/visualization/service/VisualizationUtilTests.java Co-authored-by: Luke Sikina <[email protected]> * Fix import for modified unit test * Refactor and add test cases for key size limiting function Refactors existing code by simplifying key size limiting logic in VisualizationUtil and added several new unit tests to ensure its correct behavior with different input scenarios including long keys, empty maps, null maps, and uniqueness near middle. * Update null handling in VisualizationUtil's limitKeySize Changed the handling of null input in VisualizationUtil's limitKeySize from returning a new HashMap to throwing an IllegalArgumentException. Also, updated the corresponding test to check for this exception instead of comparing with an empty map. --------- Co-authored-by: Luke Sikina <[email protected]> * Refine the condition for empty return in DataProcessingService (#184) Adjusted the condition under which an empty HashMap is returned in the DataProcessingService. Now, an empty HashMap will only be returned when both the maximum and minimum values in the data are 0, and the number of bins is also 0. This change takes into account situations where the data contains values but the min and max are both 0. * ALS-5387: Remove stack from resources table (#186) * [ALS-5422] Add persistence.xml to visualization resource (#161) (#162) The visualization resource is failing to start due to an error injecting persistence unit into CDI managed bean. It is unable to find a persistence unit named ''. * ALS-5387: Remove stack from resources table * ALS-5387: More robust implementation of feature --------- Co-authored-by: Gcolon021 <[email protected]> Co-authored-by: GeorgeC <[email protected]> * [ALS-6222] Status endpoints now filters resources (#189) The database contains both open and auth hpds even if it wasn't deployed. This means we attempt to check for a resource that doesn't exist. This results in our service always showing degraded. --------- Co-authored-by: Luke Sikina <[email protected]> Co-authored-by: Gcolon021 <[email protected]> Co-authored-by: Luke Sikina <[email protected]> Co-authored-by: ramari16 <[email protected]> Co-authored-by: GeorgeC <[email protected]>
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May 6, 2024
* 2024-04-11-Release (#192) * [ALS-5827] Enable search by CA id - If a uuid does not match a query, instead search for common area UUID - If we have a collision, I'm buying a lottery ticket * [ALS-5787] Open Access StatViz is not showing "Other" (#180) * Update key length handling in limitKeySize The limitKeySize method in the VisualizationUtil class has been updated to ensure key uniqueness when keys exceed a certain length. A more robust method of shortening the keys has been implemented: if the key is longer than 45 characters, it is cut off and replaced with "..." and additional characters are appended to ensure uniqueness if needed. This helps limit key size while preserving uniqueness. * Add VisualizationUtilTests and refine key shortening logic Added a new test class, VisualizationUtilTests to validate the functionality of the VisualizationUtil class. Adjusted the 'limitKeySize' method to ensure key uniqueness when keys are shortened to a maximum length of 45 characters. If shortened keys are not unique, additional trailing characters are included until uniqueness is achieved. * Add check on length before substring * Update pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/VisualizationUtil.java * Update pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/VisualizationUtil.java * Update pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/VisualizationUtil.java * Update pic-sure-resources/pic-sure-visualization-resource/src/test/java/edu/harvard/hms/dbmi/avillach/resource/visualization/service/VisualizationUtilTests.java Co-authored-by: Luke Sikina <[email protected]> * Fix import for modified unit test * Refactor and add test cases for key size limiting function Refactors existing code by simplifying key size limiting logic in VisualizationUtil and added several new unit tests to ensure its correct behavior with different input scenarios including long keys, empty maps, null maps, and uniqueness near middle. * Update null handling in VisualizationUtil's limitKeySize Changed the handling of null input in VisualizationUtil's limitKeySize from returning a new HashMap to throwing an IllegalArgumentException. Also, updated the corresponding test to check for this exception instead of comparing with an empty map. --------- Co-authored-by: Luke Sikina <[email protected]> * Refine the condition for empty return in DataProcessingService (#184) Adjusted the condition under which an empty HashMap is returned in the DataProcessingService. Now, an empty HashMap will only be returned when both the maximum and minimum values in the data are 0, and the number of bins is also 0. This change takes into account situations where the data contains values but the min and max are both 0. * ALS-5387: Remove stack from resources table (#186) * [ALS-5422] Add persistence.xml to visualization resource (#161) (#162) The visualization resource is failing to start due to an error injecting persistence unit into CDI managed bean. It is unable to find a persistence unit named ''. * ALS-5387: Remove stack from resources table * ALS-5387: More robust implementation of feature --------- Co-authored-by: Gcolon021 <[email protected]> Co-authored-by: GeorgeC <[email protected]> * [ALS-6222] Status endpoints now filters resources (#189) The database contains both open and auth hpds even if it wasn't deployed. This means we attempt to check for a resource that doesn't exist. This results in our service always showing degraded. --------- Co-authored-by: Luke Sikina <[email protected]> Co-authored-by: Gcolon021 <[email protected]> Co-authored-by: Luke Sikina <[email protected]> Co-authored-by: ramari16 <[email protected]> Co-authored-by: GeorgeC <[email protected]> * ALS-6375: Suppress showing user 0 results in open-pic-sure (#193) --------- Co-authored-by: Luke Sikina <[email protected]> Co-authored-by: Gcolon021 <[email protected]> Co-authored-by: Luke Sikina <[email protected]> Co-authored-by: ramari16 <[email protected]> Co-authored-by: GeorgeC <[email protected]>
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May 9, 2024
* [ALS-5827] Enable search by CA id - If a uuid does not match a query, instead search for common area UUID - If we have a collision, I'm buying a lottery ticket * [ALS-5787] Open Access StatViz is not showing "Other" (#180) * Update key length handling in limitKeySize The limitKeySize method in the VisualizationUtil class has been updated to ensure key uniqueness when keys exceed a certain length. A more robust method of shortening the keys has been implemented: if the key is longer than 45 characters, it is cut off and replaced with "..." and additional characters are appended to ensure uniqueness if needed. This helps limit key size while preserving uniqueness. * Add VisualizationUtilTests and refine key shortening logic Added a new test class, VisualizationUtilTests to validate the functionality of the VisualizationUtil class. Adjusted the 'limitKeySize' method to ensure key uniqueness when keys are shortened to a maximum length of 45 characters. If shortened keys are not unique, additional trailing characters are included until uniqueness is achieved. * Add check on length before substring * Update pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/VisualizationUtil.java * Update pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/VisualizationUtil.java * Update pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/VisualizationUtil.java * Update pic-sure-resources/pic-sure-visualization-resource/src/test/java/edu/harvard/hms/dbmi/avillach/resource/visualization/service/VisualizationUtilTests.java Co-authored-by: Luke Sikina <[email protected]> * Fix import for modified unit test * Refactor and add test cases for key size limiting function Refactors existing code by simplifying key size limiting logic in VisualizationUtil and added several new unit tests to ensure its correct behavior with different input scenarios including long keys, empty maps, null maps, and uniqueness near middle. * Update null handling in VisualizationUtil's limitKeySize Changed the handling of null input in VisualizationUtil's limitKeySize from returning a new HashMap to throwing an IllegalArgumentException. Also, updated the corresponding test to check for this exception instead of comparing with an empty map. --------- Co-authored-by: Luke Sikina <[email protected]> * Refine the condition for empty return in DataProcessingService (#184) Adjusted the condition under which an empty HashMap is returned in the DataProcessingService. Now, an empty HashMap will only be returned when both the maximum and minimum values in the data are 0, and the number of bins is also 0. This change takes into account situations where the data contains values but the min and max are both 0. * ALS-5387: Remove stack from resources table (#186) * [ALS-5422] Add persistence.xml to visualization resource (#161) (#162) The visualization resource is failing to start due to an error injecting persistence unit into CDI managed bean. It is unable to find a persistence unit named ''. * ALS-5387: Remove stack from resources table * ALS-5387: More robust implementation of feature --------- Co-authored-by: Gcolon021 <[email protected]> Co-authored-by: GeorgeC <[email protected]> * [ALS-6222] Status endpoints now filters resources (#189) The database contains both open and auth hpds even if it wasn't deployed. This means we attempt to check for a resource that doesn't exist. This results in our service always showing degraded. * Sync changes between master and release branch (#194) * 2024-04-11-Release (#192) * [ALS-5827] Enable search by CA id - If a uuid does not match a query, instead search for common area UUID - If we have a collision, I'm buying a lottery ticket * [ALS-5787] Open Access StatViz is not showing "Other" (#180) * Update key length handling in limitKeySize The limitKeySize method in the VisualizationUtil class has been updated to ensure key uniqueness when keys exceed a certain length. A more robust method of shortening the keys has been implemented: if the key is longer than 45 characters, it is cut off and replaced with "..." and additional characters are appended to ensure uniqueness if needed. This helps limit key size while preserving uniqueness. * Add VisualizationUtilTests and refine key shortening logic Added a new test class, VisualizationUtilTests to validate the functionality of the VisualizationUtil class. Adjusted the 'limitKeySize' method to ensure key uniqueness when keys are shortened to a maximum length of 45 characters. If shortened keys are not unique, additional trailing characters are included until uniqueness is achieved. * Add check on length before substring * Update pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/VisualizationUtil.java * Update pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/VisualizationUtil.java * Update pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/VisualizationUtil.java * Update pic-sure-resources/pic-sure-visualization-resource/src/test/java/edu/harvard/hms/dbmi/avillach/resource/visualization/service/VisualizationUtilTests.java Co-authored-by: Luke Sikina <[email protected]> * Fix import for modified unit test * Refactor and add test cases for key size limiting function Refactors existing code by simplifying key size limiting logic in VisualizationUtil and added several new unit tests to ensure its correct behavior with different input scenarios including long keys, empty maps, null maps, and uniqueness near middle. * Update null handling in VisualizationUtil's limitKeySize Changed the handling of null input in VisualizationUtil's limitKeySize from returning a new HashMap to throwing an IllegalArgumentException. Also, updated the corresponding test to check for this exception instead of comparing with an empty map. --------- Co-authored-by: Luke Sikina <[email protected]> * Refine the condition for empty return in DataProcessingService (#184) Adjusted the condition under which an empty HashMap is returned in the DataProcessingService. Now, an empty HashMap will only be returned when both the maximum and minimum values in the data are 0, and the number of bins is also 0. This change takes into account situations where the data contains values but the min and max are both 0. * ALS-5387: Remove stack from resources table (#186) * [ALS-5422] Add persistence.xml to visualization resource (#161) (#162) The visualization resource is failing to start due to an error injecting persistence unit into CDI managed bean. It is unable to find a persistence unit named ''. * ALS-5387: Remove stack from resources table * ALS-5387: More robust implementation of feature --------- Co-authored-by: Gcolon021 <[email protected]> Co-authored-by: GeorgeC <[email protected]> * [ALS-6222] Status endpoints now filters resources (#189) The database contains both open and auth hpds even if it wasn't deployed. This means we attempt to check for a resource that doesn't exist. This results in our service always showing degraded. --------- Co-authored-by: Luke Sikina <[email protected]> Co-authored-by: Gcolon021 <[email protected]> Co-authored-by: Luke Sikina <[email protected]> Co-authored-by: ramari16 <[email protected]> Co-authored-by: GeorgeC <[email protected]> * ALS-6375: Suppress showing user 0 results in open-pic-sure (#193) --------- Co-authored-by: Luke Sikina <[email protected]> Co-authored-by: Gcolon021 <[email protected]> Co-authored-by: Luke Sikina <[email protected]> Co-authored-by: ramari16 <[email protected]> Co-authored-by: GeorgeC <[email protected]> --------- Co-authored-by: Luke Sikina <[email protected]> Co-authored-by: Gcolon021 <[email protected]> Co-authored-by: Luke Sikina <[email protected]> Co-authored-by: ramari16 <[email protected]> Co-authored-by: GeorgeC <[email protected]>
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The visualization resource is failing to start due to an error injecting persistence unit into CDI managed bean. It is unable to find a persistence unit named ''.