After upgrading Guava to the latest version, 31.1-jre, and eliminating outdated imports from the pom.xml file, the ProtAnnot feature is now visible in the master IGB. However, Dr. Freese suggests that including the entire Guava library in Protannot might be excessive, as Protannot only requires a few specific components from Guava. I have uploaded the modified code to the repository for future reference: https://bitbucket.org/kaushik-gopu/kgopu_proant/branch/IGBF-3349

A quick note:

If ProtAnnot is going to rely on the platform (IGB) to provide the necessary package, we need to specify which version of IGB is needed, since the currently released version of IGB does not have this. This is difficult.

In light of this difficulty, it might be good for ProtAnnot to package its required library along with the App and not use the library provided by the framework. If we do this, then ProtAnnot developers would not have to keep track of all the myriad 3rd-party libraries that are getting packaged with IGB as part of the platform.

Instead of mentioning specific versions, we can use version="0" in the plugins so that they can dynamically pick the version being used by IGB at runtime. This approach will save us from hardcoding specific version numbers. However, it's important to note that modifying the dependency versions to align with IGB's version might be time-consuming. This is because every time we upgrade a dependency in IGB, we would need to review all the plugins and adjust their respective versions accordingly.

To sum up, even though every plugin has its own pom.xml to manage dependencies, they are only valid for compile time. They look over IGB for dependencies and import the necessary ones, which we basically mention in <Import-Package> </Import-Package>, and use them during runtime. either we can make plugins version independent or change the versions whenever there is an dependency upgrade happens in IGB.

Reference: https://stackoverflow.com/questions/36188935/how-to-exclude-version-numbers-from-import-package-with-maven-bundle-plugin

Summary of discussion:

• Try this: set the "import-packages" bundle plugin configuration to * and then report back as to what the bundle plugin inserted into the corresponding section of the MANIFEST
• We think that probably the best solution that properly balances flexibility and safety is to specify version 16 as the acceptable guava package version. We think that this will ensure that the ProtAnnot app will be able to properly function in currently released and future versions IGB.
• We note that ProtAnnot is indeed explicitly importing the above package in its java code.
• We note also that at some point in the past, someone edited the import-packages directive to maven bundle plugin, making it specify which packages to import into the bundle and which versions. See: this commit.
• We recalled that App Store somehow or other needs to be able to figure out which versions of IGB a given App version can be installed into. [~aloraine] remembers (but could be wrong) that App Store code parses the bundled MANIFEST to determine IGB compatibility. This means that an App developer, one way or another, has to somehow insert some kind of text into the MANIFEST's OSGI-specific import packages statement that indicate IGB version.
• [~aloraine] requests Kaushik Gopu and/or Nowlan Freese write about / document this issue and these concerns in a way that will help future developers of Apps to understand the platform and its use.

                        <Import-Package>
                            com.apple.eawt,
                            org.lorainelab.igb.*;version=9.1.0,
                            *
                        </Import-Package>

leads to:

Import-Package: org.lorainelab.igb.genoviz.extensions;version="9.1.0",or
 g.lorainelab.igb.genoviz.extensions.glyph;version="9.1.0",org.lorainela
 b.igb.image.exporter.service;version="9.1.0",org.lorainelab.igb.javafx;
 version="9.1.0",org.lorainelab.igb.menu.api;version="9.1.0",org.loraine
 lab.igb.menu.api.model;version="9.1.0",org.lorainelab.igb.services;vers
 ion="9.1.0",com.affymetrix.common;version="[9.1,10)",com.affymetrix.gen
 ometry;version="[9.1,10)",com.affymetrix.genometry.comparator;version="
 [9.1,10)",com.affymetrix.genometry.event;version="[9.1,10)",com.affymet
 rix.genometry.span;version="[9.1,10)",com.affymetrix.genometry.symmetry
 ;version="[9.1,10)",com.affymetrix.genometry.symmetry.impl;version="[9.
 1,10)",com.affymetrix.genometry.thread;version="[9.1,10)",com.affymetri
 x.genometry.util;version="[9.1,10)",com.affymetrix.genoviz.awt;version=
 "[1.1,2)",com.affymetrix.genoviz.bioviews;version="[1.1,2)",com.affymet
 rix.genoviz.event;version="[1.1,2)",com.affymetrix.genoviz.glyph;versio
 n="[1.1,2)",com.affymetrix.genoviz.swing;version="[1.1,2)",com.affymetr
 ix.genoviz.util;version="[1.1,2)",com.affymetrix.genoviz.widget;version
 ="[1.1,2)",com.affymetrix.genoviz.widget.tieredmap;version="[1.1,2)",co
 m.affymetrix.igb.shared;version="[9.1,10)",com.affymetrix.igb.swing;ver
 sion="[9.1,10)",com.affymetrix.igb.swing.jide;version="[9.1,10)",com.go
 ogle.common.base;version="[16.0,17)",com.google.common.collect;version=
 "[16.0,17)",com.google.common.eventbus;version="[16.0,17)",javax.swing,
 javax.swing.border,javax.swing.table,javax.xml.bind,javax.xml.bind.anno
 tation,javax.xml.namespace,javax.xml.parsers,javax.xml.xpath,net.miginf
 ocom.layout,net.miginfocom.swing,org.apache.commons.io;version="[1.4,2)
 ",org.apache.commons.lang3.text;version="[3.4,4)",org.osgi.service.comp
 onent;version="[1.2,2)",org.slf4j;version="[1.7,2)",org.w3c.dom,org.xml
 .sax,com.apple.eawt

Note that the google version is still being set to between 16 and 17, unsure of why. This version of protannot does appear to work correctly in IGB 9.1.10 (IGB with version 16 of google).

Documentation on maven-bundle-plugin Import-Package: https://felix.apache.org/documentation/subprojects/apache-felix-maven-bundle-plugin-bnd.html

<Import-Package>
The <Import-Package> instruction is a list of packages that are required by the bundle’s contained packages. The default for this header is "", resulting in importing all referred packages. This header rarely has to be explicitly specified. However, in certain cases when there is an unwanted import, such an import can be removed by using a negation package pattern. The package patterns work in the same way as for <Export-Package>, which means they are ordered. For example, if you wanted to import all packages except org.foo.impl you would specify "!org.foo.impl,"

<Import-Package> is assumed to be "*", which imports everything referred to by the bundle content, but not contained in the bundle. Any exported packages are also imported by default, to ensure a consistent class space.

Testing Protannot on my system, completely omitting the Import-Package results in the manifest containing the same/similar Import-Package section as if I had included *. This version of ProtAnnot works in IGB 9.1.10 using google version 16.

works in 9.1.12

com.google.common.base;version=32.1.1,
com.google.common.collect;version=32.1.1,
com.google.common.eventbus;version=32.1.1,

works in 9.1.12 and 9.1.10

com.google.common.base;version=16.0,
com.google.common.collect;version=16.0,
com.google.common.eventbus;version=16.0,

works in 9.1.12 and 9.1.10

com.google.common.base;version="\"[16.0,33)\"",
com.google.common.collect;version="\"[16.0,33)\"",
com.google.common.eventbus;version="\"[16.0,33)\"",

One other interesting comment on Stackoverflow: https://stackoverflow.com/questions/36187308/how-to-configure-maven-bundle-plugin

Add an empty <Export-Package/> tag : by default, this plugin export all packages but .internal. .impl.. If your package doesn't use this convention, you risk to export internal classes of your bundle.

As Nowlan Freese suggested, I would also like to go with the same approach(exclusion of upper bound version) because, it is compatible with any newer version and most importantly we don't need to make any version changes in future whenever we upgrade some dependency in IGB. assigning base version to package means it is compatible with any version >= base version.
Below are the details about changes that were commited to repo.
*commit
*branch
Moving to first level review.

For some reason when I'm connected to the UNCC VPN I get "bad gateway" errors from bitbucket. Moving back to "Needs first level review" since I can't actually test this now while I'm using the VPN.

Request for Kaushik Gopu:

Please build new xml and jar files for the new branch and deploy to the Downloads section of the fork so that I can test it.

Tested Kaushik's protannot branch locally on Mac following the testing guidelines outlined in IGBF-3381.

IGB release-9.1.10
Installed version 9.1.3 of ProtAnnot through the App Manager. After adding Kaushik's protannot as a new repository the app manager showed that I could update protannot from 9.1.3 to 9.1.4. ProtAnnot worked correctly.

IGB main-JDK8
With the default app manager repositories ProtAnnot is not available. After adding Kaushik's protannot as a new repository the app manager showed that I could install protannot version 9.1.4. ProtAnnot worked correctly.

Looking at the commit, I don't think we should make changes to the version logic for non Google/Guava dependencies. Please limit the changes to just Google/Guava. We may need to make additional changes to versions in IGBF-3393 or when we are able to get the R6 declarative services annotations working in IGB.

*Reverted non guava version changes. here is the commit.
*pipeline build was successful.
*moving to first level review.

Retested following testing outlined in previous commit, everything is working.

Please squash commits then submit pull request.

Regarding running out of build minutes, I contacted Bitbucket and this was the response:

John commented:

Hi Nowlan,

Thank you for reaching out to Atlassian. My name is John and I'm from the Billing and Licensing team. I'll be happy to look into your request.

Unfortunately, we can't increase build minutes for Bitbucket standard Free plans (max 5 users). However, upon taking a look into your account, you may be eligible to receive a free academic Bitbucket Cloud subscription that is intended for members (students, professors, and so forth) of colleges and universities (criteria listed below). This may be a good direction for increasing build minutes.

Special pricing is available for qualified Academic institutions. The following organizations are eligible for an Atlassian Academic License:

Collegiate-level or higher educational institutions: vocational schools, junior colleges, colleges, universities, or scientific or technical schools that are accredited by a national accrediting agency.
Administrative offices & boards of education: Provincial, district, regional, national and state administrative offices and authorities of the Educational Institutions defined above.
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Public libraries
Collegiate-level or higher home-school programs
Research institutes that are affiliated with an accredited university.
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Training and teaching organizations that are accredited by a statutory government qualifications body.
You can apply and provide details of your academic institution by requesting a Bitbucket academic subscription. Our team will then review the application and get back to you. We can further proceed, once approved.

I hope the above information helps.

I have used the link to submit my information for an academic subscription.

UPDATE: I am now on a University license.

commits squashed
Pull request submitted

Tested on IGB 9.1.10 and main-JDK8. Everything is working correctly. On 9.1.10 with ProtAnnot 9.1.3 installed, I could see the update button in the App Manager to update to 9.1.4.

Closing ticket.