- Better error handling (check for bad characters when creating collections).
- Implement a strict mode parameter to do even more validation.
- Rework tabular vs txt mode to be explicit user choice.
- Mirror fix in release_17.01 for datasets not having a history,
I think it needs to be touched up but the basic operation seems to work so far. I think what remains to be done is:
- Validate uniqueness of identifiers and provide nice messages if they are not unique.
- Validate that at least the required number of lines are present in the file and provide a nice message if not.
- Add strict mode to ensure exactly the correct number of lines is added.
- Find where validation of identifiers happens in the API and apply same validation here - try not to let unsafe identifiers be created.
- Consider more advanced modes - selecting a column, apply a regex replace, pick two columns for nested lists, etc.... None of this may need to be needed in the first iteration.
- Consider another mode where a collection is labelled against an existing collection - should that be a separate tool of the same tool.
Having a BaseFastq class allows Fastq and FastqGz classes to inherit from
BaseFastq. FastqGz is therfor not a Fastq datatype and goes through the
converter.
Also add 2 tools to demonstrate that compressed fastq will be converted to
uncompressed fastq if the tool specifies `format="fastq"`, while
`format="fastq.gz"` leaves files compressed.
The tool test can be run with:
```
planemo test --galaxy_root . test/functional/tools/compressed_fastq_no_conversion.xml
planemo test --galaxy_root . test/functional/tools/compressed_fastq_conversion.xml
```
Note that fastq conversion appears to required a galaxy user session, and
planemo testing fails. Interactive testing with `planemo serve` is not affected
and works fine.
- Rename expected output Log from input Log. This relieves a concern I had that the tests were just working because the inputs and outputs match.
- Add another "unregistered" output file to the output directory and add a test for it. This verifies that such files are infact tested.
- Add a nested "unregistered" output file to the output directory and add a test for it. This verifies that nested files are tested.
These files are being moved to https://github.com/galaxyproject/galaxy-test-data.
Files used by framework functional tests remain. This drops the size of the test-data directory from 73M down to less than 1.3M.
Tool test is mildly useful to verify this works for single execution - but more useful as basis for future changesets testing mixed collection and subcollection mapping tool executions.
-framework will still cause just a small set of non-default, non-user facing tools to be tested and exerise various aspects of the tool and test frameworks, but now an argument can be passed in -with_framework_test_tools to allow these tools to be used as part of the normal test framework (i.e. when not using -framework). This serves two purposes - to ensure the feature coverage of existing tests remains high as the tests are migrated out of the distribution and to allow a set of tests to be available for functional (e.g. API tests) that users don't need to see.
Dannon Baker