Upgrade syntax using `pyupgrade --py36-plus` .
Manually drop several `six` imports.
Also:
- Remove broken pr_cache in scripts/bootstrap_history.py
- Fix broken prefix removal in lib/galaxy/tool_util/deps/mulled/mulled_build.py
Also, when sniffing binary files, sniff images together with the other
formats and respect sniff order.
Also remove `is_multi_byte` from:
- `stream_to_open_named_file()`
- `stream_to_file()`
Remove the now unused `get_image_ext()` and `Binary.is_sniffable_binary()`
and all the calls to `Binary.register_sniffable_binary_format()`.
Also, merge its 3 parameters `gzip_only`, `bz2_only`, `zip_only` into
`compressed_formats` (a list of allowed formats).
As a consequence of the changes in `get_fileobj()`, update:
- `files_diff()`
- `get_file_peek()`, which now determines that a file is binary when a
`UnicodeDecodeError` exception is raised and doesn't need
`is_multi_byte` any more
- `iter_headers()` and `get_headers()`, which now return Unicode and don't
need `is_multi_byte` parameter any more
As a consequence of the changes in `get_file_peek()`, update:
- `set_peek()`, which now doesn't need `is_multi_byte` any more
As a consequence of the changes in `get_headers()`, update:
- `guess_ext` and `is_column_based()`, which now determine that a file is
binary when a `UnicodeDecodeError` exception is raised and don't need
`is_multi_byte` any more
As a consequence of the changes to `guess_ext`, update:
- `handle_uploaded_dataset_file() doesn't need `is_multi_byte` any more
Also, remove duplicated calls to `get_file_peek()` in
lib/galaxy/datatypes/molecules.py and lib/galaxy/datatypes/msa.py
The `is_multi_byte` was not removed from the signature of `get_file_peek()`
and `set_peek()` in order to preserve compatibility for ToolShed datatypes,
thanks @jmchilton for the review.
Add support for a single "import_module" to be passed to the new load_datatypes() method in the datatypes registry. This provides the ability to load a single class module from an installed tool shed repository along with a datatypes_conf.xml file included in the installed repository and pass them to the new load_datatypes() method. In the future, multiple imported modules may be allowed. The datatypes_conf.xml file included in the repository must conform to a slightly different definition than the same named file that comes with the distribution. This new definition will be documented in the Galaxy tool shed wiki.
We now have the ability to load new data types into the Galaxy server from an installed tool shed repository without restarting the Galaxy server.
greater than config.output_size_limit, no data will be retrieved and an error message will be provided to the user.
Tools using this script have been updated to provide the max file size on the command line.
Resolves ticket #93.
These are now used to store the list of chromosomes for species as well as the index for MAF files.
MAF tools have been enhanced to make use of index files when available.
TODO: When datasets are purged from disk, these files should also be purged.
Dannon Baker