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Notes on how to update an existing Tripal site to Tripal4 using the move chado approach. #82
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In regards to step 3, if you encounter this error:
You can fix it by running this command before loading:
No actual harm is done if the extension already exists:
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I have a few existing entities that are linked to by external sources. I will probably want to keep the block of existing entity_id values unused so that later a reference can be made and it is not used by something else. So to alter the first available entity_id, I am testing this
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@pdtouch, this is the issue I was referring to. You can use the same approach to move your chado instance from Tripal 2 to Tripal 4 as what is described here. Just make sure your chado is version 1.3 It can have extra tables and columns but those tables/columns that are in chado 1.3 must match the chado spec exactly. |
After running the trp-check-terms drush command and fixing the various issues that it suggested (either automatically through its functionality or manually), tried the prepare step and got the following errors (sequentially):
This error repeated itself every time I tried the prepare step. Each time, I'd manually go in and set the offending row to is_obsolete=1 and try again. After a few times I noticed it only happened with the synonym_type and tripal_contact CVs I don't know if this is a case that should be caught by the trp-check-terms command or if the Chado prepare step needs to be modified so it skips existing entries. |
Pull Request #88
Currently the way I am working to upgrade KnowPulse to Tripal 4 involves
tempchado
orteacup
drush trp-check-terms --chado_schema=chado
command that's currently in PR Drush command to update chado instance to match Tripal Term expectations tripal#1895.The plan is to add a command in the future that help pull over url alias' from your Drupal 7 site for existing pages.
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