the update to Agile 6.4.3 appears to have taken care of the problem; however, I did run into an issue right after the upgrade which required the integrity check to fix. Afterwards my imports are back to running as expected... the longest I've had to wait on the reindex is 14 minutes for a large project.
I'm on version 6.1.3 and standalone. I'm testing project imports bringing 50 projects into our Enterprise Jira and the re-index portion of import is extremely slow. example.. 400 issues taking 43 minutes. the one i am working on now is at 3 hrs 26 minutes and is 85% complete. I was looking at the logs and I'm getting the "Could not retrieve LexoRank value for issue[id=34208]. Indexing max LexoRank value instead." message which I believe is a bug in Agile. I'm researchign that now, but it appears it should have been corrected in Agile 188.8.131.52 and I am at 6.4.2. I will say, I have run previously all imports with no issue, but was prior to my last upgrade of Agile. Sorry don't remember what it was prior.
I've searched around and I've found a registered issue on Atlassian JIRA that says that there are some issues with this plugin and it should be fixed in the newest version of the plugin. Here it is: https://jira.atlassian.com/browse/GHS-10872
There are other one who has a workaround for a similiar problem.
Please let us know if you find any answer to this.
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