The method `write_from()` of `SingleFileSource` and `BaseFilesSource` reads a local file from `native_path` and saves it to `target_path` on a file source.
This commit allows the service backing the file source to choose which will be the path of the saved file, meaning that `target_path` and the actual path where the file can be recovered later do not have to match. The latter is the return value of `write_from()`.
Therefore, all usages of `write_from()` have also been refactored to consider the paths chosen by the file source's backing service. In addition, when exporting a history, the URI that the service backing the file source assigns to it will be saved to the history export result metadata object.
- Downstream I want a way to load plugins from outside the ConfiguredFileSources class.
- Adds some more typing as I went in there and refactored things.
When enabling the `warn_unused_ignores = True` option of mypy, this
was making the `test_galaxy_packages` tests fail with:
```
mypy .
Traceback (most recent call last):
File "/tmp/gxpkgtestenvu3fgDr/bin/mypy", line 8, in <module>
sys.exit(console_entry())
File "/tmp/gxpkgtestenvu3fgDr/lib/python3.10/site-packages/mypy/__main__.py", line 15, in console_entry
main()
File "mypy/main.py", line 100, in main
File "mypy/main.py", line 182, in run_build
File "mypy/build.py", line 192, in build
File "mypy/build.py", line 266, in _build
File "mypy/build.py", line 2942, in dispatch
File "mypy/build.py", line 3333, in process_graph
File "mypy/build.py", line 3414, in process_fresh_modules
File "mypy/build.py", line 2110, in fix_cross_refs
File "mypy/fixup.py", line 52, in fixup_module
File "mypy/fixup.py", line 127, in visit_symbol_table
File "mypy/lookup.py", line 49, in lookup_fully_qualified
AssertionError: Cannot find component 'util' for 'galaxy.util'
make: *** [Makefile:96: mypy] Error 1
```
Moreover, installing packages in editable mode was hiding some issues
with how files from other packages were accessed.
davelopez