That should make the test less flakey. While in theory we should be able
to replace scheduled workflow jobs with cached jobs, this is not what
we're testing here, and I assume it doesn't work for now.
Turns out integers are used as is in `random.seed()`, but strings are
hashed (in the version 1 protocol), and the hashing isn't stable. So
instead we hack around this by using `ord()` on each character and
concatenating the digits. Yucky, but probably better than using numpy
and putting this tool on the list of tools that inherit galaxy's
environment (or adding a requirement tag and resolving with conda ...).
- Switch select_tag to group_tag as a parameter name - since it is restricted to group_tags and we don't call data parameters select_data.
- Add minimal XSD documentation for this new parameter type.
- Add example tools - for single and multiple tags.
- Add API tests for these tools and the tag handling.
Unlike upload 1.0, use different 'src' types to distinguish between URLs and pasted content - in the abstract this is better because it is more structured and practically this allows 'pasting' spreadsheets that start with URLs for instance (that is sometimes useful).
This doesn't quite work because of the dynamic output collection,
which fails with:
```
galaxy.tools.parameters.output_collect DEBUG 2018-06-06 18:40:38,784 (3) Add dynamic collection datasets to history for output [reverse] (171.970 ms)
galaxy.tools.parameters.output_collect ERROR 2018-06-06 18:40:38,839 Problem gathering output collection.
Traceback (most recent call last):
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/parameters/output_collect.py", line 340, in collect_dynamic_outputs
collection_builder.populate()
File "/Users/mvandenb/src/galaxy/lib/galaxy/dataset_collections/builder.py", line 88, in populate
elements = self.build_elements()
File "/Users/mvandenb/src/galaxy/lib/galaxy/dataset_collections/builder.py", line 59, in build_elements
new_elements[identifier] = element.build()
AttributeError: 'HistoryDatasetAssociation' object has no attribute 'build'
```
This seems to happen because the inner collection is wrongly detected as
nested. In general I doubt that mapping over colleciton output works
with dynamically discovered output collections.
It is jarring to users that works for collection inputs but not multiple data inputs, especially because the IUC discourages collection inputs when multiple data inputs would work.
This doesn't quite work because of the dynamic output collection,
which fails with:
```
galaxy.tools.parameters.output_collect DEBUG 2018-06-06 18:40:38,784 (3) Add dynamic collection datasets to history for output [reverse] (171.970 ms)
galaxy.tools.parameters.output_collect ERROR 2018-06-06 18:40:38,839 Problem gathering output collection.
Traceback (most recent call last):
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/parameters/output_collect.py", line 340, in collect_dynamic_outputs
collection_builder.populate()
File "/Users/mvandenb/src/galaxy/lib/galaxy/dataset_collections/builder.py", line 88, in populate
elements = self.build_elements()
File "/Users/mvandenb/src/galaxy/lib/galaxy/dataset_collections/builder.py", line 59, in build_elements
new_elements[identifier] = element.build()
AttributeError: 'HistoryDatasetAssociation' object has no attribute 'build'
```
This seems to happen because the inner collection is wrongly detected as
nested. In general I doubt that mapping over colleciton output works
with dynamically discovered output collections.
It is jarring to users that works for collection inputs but not multiple data inputs, especially because the IUC discourages collection inputs when multiple data inputs would work.
Nicola Soranzo