Bug fixed: when uploading a gzipped FASTQ file through upload1 tool on a
machine with SQLite 3.3.6, it was detected as 'sqlite' datatype and not
decompressed.
In fact, the sqlite3 command 'pragma schema_version' on any file returns
without error on this SQLite version.
Tools will pair off (or triplize, quadraplate, quintukify, etc...) based only on the index of the elements in the collection (so any N element list can be used in the same tool execution as any other N element list). Originally, I had decided to require the element identifiers to be the same in both collections (allows mixing a matching fewer collections in tools - but probably less likely to mismatch in a way the user did not intend). At any rate - I changed that decision and updated tool execution appropriately but not every aspect workflow collection 'pairing' - this fixes that and closes out this card https://trello.com/c/m5PiF1lR.
In very partical terms tools would ideally be consuming collection pairs - but for those that are still consuming two separate files (i.e. all of them) one can use two lists of datasets with pairs at matching indices and feed them into these tools - for workflows this doesn't work without this patch unless the identifiers and the indices match on these collections.
Thanks for Michael Crusoe and takadonet for the bug reports.
See full conversation on https://bitbucket.org/galaxy/galaxy-central/commits/07508592cb65845474b9f3e0f781260c.
Would like to better and allow slugs of deleted items to be reused - they cannot be for workflows for instance. Because the slugs are not really handled uniformly though - pages do not have this problem and deleted pages can have their slugs reused because this is included in a check in the web controller which directly assigns valid slugs at that point. Slugs for deleted histories cannot be re-used - but they couldn't be prior to this commit - so this isn't making things worse in that respect.
[STABLE] For _ensure_valid_session with use_remote_user set, when galaxy_session.user.email != remote_user_email invalidate the session UNLESS allowing user impersonation and the remote user is an admin.
For instance 10.6084/m9.figshare.979190 reported by Michael Crusoe. JavaScript parser didn't like @data entries produced by figshare and when requesting the entry dx.doi.org returns a 403 response for type accept type text/bibliography, also allowing application/x-bibtex fixes this. Interestingly dx.doi.org throws 500 exceptions if application/x-bibtex is the only acceptable type or appears first for some other DOIs.
Was displaying warning message about history citations being potentially incomplete for tools - which if they have annotated citations we should assume they are complete.
... so internals of tool XML description are only utilized in the galaxy.tools module (and submodules). Add some unit tests for this new method for finding externally referenced files.
Previous commit ensured that topsort is stable - but keys are reshuffled by position prior to being sent to topsort - in case their are "ties" when sorting by position ensure that import order is preserved before sorting on position.
This is all very dry and seemingly persnickety - but at any rate - after this commit I am fairly confident that Galaxy will import newly saved workflows that have been exported in the same order they were exported in. This means that 64a25838085978c250a0486b516bb2c8e7c3b850 is more correct.
Dannon Baker