[IGBF-3379] Edit SCR annotations to use R6 instead of R5 syntax and observe the effects - JIRA UNCC

Details

Type: Task
Status: Closed (View Workflow)
Priority: Major
Resolution: Done
Affects Version/s: None
Fix Version/s: 10.0.0 Major Release
Labels:
None

Story Points:
4
Epic Link:
Implement r6 Annotations in IGB
Sprint:
Summer 4 2023 June 26, Summer 5 2023 July 10, Summer 6 2023 July 24, Summer 7 2023 Aug 7, Summer 8 2023 Aug 21

Description

In previous work, we observed that updating SCR syntax to match the OSGI SCR R6 coincided with inability to run IGB using JDK 11.

We do not know why this occurred.

To get a better understanding of how SCR annotations are used in IGB, update the annotations to use R6 instead of R5 syntax, using the master branch of the team repository, version 9.1.12.

Hopefully, we will see how the changes affect IGB and in what way. For example, if we observe wiring errors, we would like to know why these wiring errors would occur if there is only a change in the Component syntax.

This task emerged from work on a different ticket. See this comment from that ticket.

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IGBF-3379_coreIGB-bundle.txt
40 kB
25/Jul/23 3:57 PM
main-JDK8_coreIGB-bundle.txt
30 kB
25/Jul/23 3:57 PM

Issue Links

blocks

IGBF-3417 Investigate: Update mi-Bundle to work with main-JDK8-r6

Closed

relates to

IGBF-3422 Investigate Test Failure that is occurring in QuickloadUtilsTest class.

Closed

IGBF-3425 Investigate FileNotFoundException when loading data from BioViz Connect

Closed

IGBF-3427 Investigate script handler GUI locking IGB

Closed

IGBF-3371 Identify OSGI and declarative services versions in IGB-JDK11, IGB-JDK8, osgi-book-inventory

Closed

IGBF-3393 Investigate updating ProtAnnot to R6 annotations

Closed

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Karthik Raveendran added a comment - 10/Jul/23 9:53 AM - edited

Migration of aQute annotations to OSGI Release 6 annotations have been pushed: https://bitbucket.org/KarthikRavee91/karthikfork-igb/commits/538f8efed53dedd96bdf232234153b398844c1e7

The changes are mostly in library imports and attributes of the annotations:

@Component
- provide :: service
@Reference
- 'multiple = true, optional = true' :: cardinality = ReferenceCardinality.MULTIPLE
  'multiple = true, optional = false' :: cardinality = ReferenceCardinality.AT_LEAST_ONE
  'multiple=false & optional = true' :: cardinality = ReferenceCardinality.OPTIONAL
  'multiple = true' :: cardinality = ReferenceCardinality.AT_LEAST_ONE
  'optional=false' :: cardinality = ReferenceCardinality.MANDATORY
  'dynamic = true' :: policy = ReferencePolicy.DYNAMIC

Changes in pom.xml is also included:

<plugin>
                    <groupId>org.apache.felix</groupId>
                    <artifactId>maven-bundle-plugin</artifactId>
                    <version>4.2.1</version>
</plugin>

<dependency>
                <groupId>org.osgi</groupId>
                <artifactId>org.osgi.service.component.annotations</artifactId>
                <version>1.5.1</version>
            </dependency>

            <dependency>
                <groupId>org.osgi</groupId>
                <artifactId>org.osgi.annotation</artifactId>
                <version>6.0.0</version>
            </dependency>

            <dependency>
                <groupId>org.osgi</groupId>
                <artifactId>org.osgi.service.metatype.annotations</artifactId>
                <version>1.4.1</version>
            </dependency>

            <dependency>
                <groupId>org.osgi</groupId>
                <artifactId>osgi.cmpn</artifactId>
                <version>6.0.0</version>
                <scope>provided</scope>
            </dependency>

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Karthik Raveendran added a comment - 10/Jul/23 9:53 AM - edited Migration of aQute annotations to OSGI Release 6 annotations have been pushed: https://bitbucket.org/KarthikRavee91/karthikfork-igb/commits/538f8efed53dedd96bdf232234153b398844c1e7 The changes are mostly in library imports and attributes of the annotations: @Component provide :: service @Reference 'multiple = true, optional = true' :: cardinality = ReferenceCardinality.MULTIPLE 'multiple = true, optional = false' :: cardinality = ReferenceCardinality.AT_LEAST_ONE 'multiple=false & optional = true' :: cardinality = ReferenceCardinality.OPTIONAL 'multiple = true' :: cardinality = ReferenceCardinality.AT_LEAST_ONE 'optional=false' :: cardinality = ReferenceCardinality.MANDATORY 'dynamic = true' :: policy = ReferencePolicy.DYNAMIC Changes in pom.xml is also included: <plugin> <groupId>org.apache.felix</groupId> <artifactId>maven-bundle-plugin</artifactId> <version>4.2.1</version> </plugin> <dependency> <groupId>org.osgi</groupId> <artifactId>org.osgi.service.component.annotations</artifactId> <version>1.5.1</version> </dependency> <dependency> <groupId>org.osgi</groupId> <artifactId>org.osgi.annotation</artifactId> <version>6.0.0</version> </dependency> <dependency> <groupId>org.osgi</groupId> <artifactId>org.osgi.service.metatype.annotations</artifactId> <version>1.4.1</version> </dependency> <dependency> <groupId>org.osgi</groupId> <artifactId>osgi.cmpn</artifactId> <version>6.0.0</version> <scope>provided</scope> </dependency>

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Kaushik Gopu added a comment - 22/Aug/23 12:38 PM - edited

after installing mi-bundle and recreating the issue in various IGB releases, observed the following results:

I can see the see the same exception in the release 9.1.10 and 9.1.12.
However, when I was trying to install mi-bundle in earlier versions, before 9.1.10, the installation is not happening. In other words, when I hit the install button, nothing is getting triggered and there were no errors in the logs as well. its not only with mi- bundle, but also with rest of the plugins. A lot of things has changed since 9.1.10 release, and that could be one of the reason.
created a separate ticket and will be posting further updates about this issue on that ticket.

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Kaushik Gopu added a comment - 22/Aug/23 12:38 PM - edited after installing mi-bundle and recreating the issue in various IGB releases, observed the following results: I can see the see the same exception in the release 9.1.10 and 9.1.12. However, when I was trying to install mi-bundle in earlier versions, before 9.1.10, the installation is not happening. In other words, when I hit the install button, nothing is getting triggered and there were no errors in the logs as well. its not only with mi- bundle, but also with rest of the plugins. A lot of things has changed since 9.1.10 release, and that could be one of the reason. created a separate ticket and will be posting further updates about this issue on that ticket.

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Karthik Raveendran added a comment - 25/Aug/23 9:56 AM

Windows Testing is complete. See above comment

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Karthik Raveendran added a comment - 25/Aug/23 9:56 AM Windows Testing is complete. See above comment

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Molly Davis added a comment - 29/Aug/23 3:49 PM - edited

Mac Testing is complete.

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Molly Davis added a comment - 29/Aug/23 3:49 PM - edited Mac Testing is complete.

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Nowlan Freese added a comment - 30/Aug/23 2:20 PM - edited

Testing on Mac macOS 13.5.1

BioViz Connect - I am able to load data, however I am seeing an error for java.io.FileNotFoundException cache/data.dat. However, this issue is present in IGB 9.1.10 and 9.1.8 so it is unrelated to R6 annotations. New ticket - ~~IGBF-3425~~
Data Provider - The secure quickload link does not appear to be responding. This issue is present in IGB 9.1.10 so it is unrelated to R6. New ticket - IGBF-3426
Script Handler - There is an issue where an IGB script loaded through the menu causes IGB to freeze (tested on 9.1.10, 9.1.8, 9.1.6 with the same effect). If the script file is dragged and dropped into IGB it works fine, it is only when the user attempts to load the script through the menu interface that it causes IGB to freeze. The issue is unrelated to R6 annotations. New ticket - ~~IGBF-3427~~
File Handler - Genotyping Results - I am unsure how the syms are supposed to appear when loading data, but they seem to be invisible (tested on 9.1.10). The issue is unrelated to R6 annotations.

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Nowlan Freese added a comment - 30/Aug/23 2:20 PM - edited Testing on Mac macOS 13.5.1 BioViz Connect - I am able to load data, however I am seeing an error for java.io.FileNotFoundException cache/data.dat. However, this issue is present in IGB 9.1.10 and 9.1.8 so it is unrelated to R6 annotations. New ticket - IGBF-3425 Data Provider - The secure quickload link does not appear to be responding. This issue is present in IGB 9.1.10 so it is unrelated to R6. New ticket - IGBF-3426 Script Handler - There is an issue where an IGB script loaded through the menu causes IGB to freeze (tested on 9.1.10, 9.1.8, 9.1.6 with the same effect). If the script file is dragged and dropped into IGB it works fine, it is only when the user attempts to load the script through the menu interface that it causes IGB to freeze. The issue is unrelated to R6 annotations. New ticket - IGBF-3427 File Handler - Genotyping Results - I am unsure how the syms are supposed to appear when loading data, but they seem to be invisible (tested on 9.1.10). The issue is unrelated to R6 annotations.

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Nowlan Freese added a comment - 30/Aug/23 3:30 PM

Tests are complete. Issues unrelated to R6 have new tickets.

Closing ticket.

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Nowlan Freese added a comment - 30/Aug/23 3:30 PM Tests are complete. Issues unrelated to R6 have new tickets. Closing ticket.

Edit SCR annotations to use R6 instead of R5 syntax and observe the effects

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