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Merge ShedToolLineage and StockLineage to ToolLineage #4119
This means we don't rely on the Tool Shed metadata anymore and instead
3 times, most recently
May 29, 2017
I couldn't love the ambition of this pull request more - this is fantastic. We should probably stipulate that there potentially degenerate cases where this provides a different lineage than what the tool shed would have provided before - which only effectively matters if a different tool really appears at the top of the lineage. I don't know if any actual repository exhibits such a lineage - but the fix in that case is pretty easy I think - just push out a new version of that tool with a new corrected absolute greater version and upgrade to that.
We can potentially delete even more client code that sets up those lineages and reads them from the server now right? That doesn't have to be done as part of this PR - but we should create an issue stipulate that we can do that I think.
Right, that could potentially happen. We could include this, and the solution to that problem in the release notes, right? And/Or we could go through the toolshed and see if that would happen -- I think the API exposes everything we need to do this remotely.
A corner-case may be versions like 1.0beta-1 appearing after 1.0 in the lineage, but we could solve this by switching to a version parser that implements pep440, like https://packaging.pypa.io/en/latest/version/#packaging.version.parse instead of LooseVersion.
We can definitely remove the lineage mako in the admin settings and remove the ToolVersionManager on the galaxy side. For now I think we may need to keep the ToolVersion and ToolVersionAssociation on the Tool Shed side for older Galaxy versions.
Jul 5, 2017
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I like this PR a lot but I noticed an issue when loading a previously imported workflow and I think it might be related.
I can debug this more and provide additional information if needed.
but that is not a new error ...