Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fce2dd3ae801cd13a542388746b84f9cca2a4c48 https://github.com/galaxyproject/galaxy/commit/fce2dd3ae801cd13a542388746b84... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/config.py R lib/galaxy/datatypes/converters/fastagz_to_fasta.xml R lib/galaxy/datatypes/converters/fastqbz2_to_fastq.xml R lib/galaxy/datatypes/converters/fastqcssangerbz2_to_fastqcssanger.xml R lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml R lib/galaxy/datatypes/converters/fastqgz_to_fastq.xml R lib/galaxy/datatypes/converters/fastqilluminabz2_to_fastqillumina.xml R lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml R lib/galaxy/datatypes/converters/fastqsangerbz2_to_fastqsanger.xml R lib/galaxy/datatypes/converters/fastqsangergz_to_fastqsanger.xml R lib/galaxy/datatypes/converters/fastqsolexabz2_to_fastqsolexa.xml R lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml R lib/galaxy/datatypes/converters/genbankgz_to_genbank.xml A lib/galaxy/datatypes/converters/gz_to_uncompressed.xml M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/webapps/galaxy/api/datatypes.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Eliminate compressed datatype boiler plate. Just annotate auto_compressed_types="gz|bz2|gz,bz2" in datatypes_conf.xml and get for free: - The compressed datatype with correct extension, no need to have a class definition. - Converters from the compressed datatype to the uncompressed datatype. - A sniffer in the correct order. Additionally, the hacky way we were controlling whether types would be sniffed or not has been improved. This can now be set in the datatypes_conf.xml file or read from a global Galaxy configuration option for options that haven't been explicitly set on a per-datatype basis in the configuration (sniff_compressed_dynamic_datatypes_default). This should simplify all future datatypes moving in this direction and introduces the possibility of also just loading them in dynamically as needed based on what the tools in the tool panel annotate for inputs and outputs. See a tool with an input of type "genbank.gz" should be enough to trigger this someday I hope. Commit: 379714e5beace2ca7b31eab064f22862902b1831 https://github.com/galaxyproject/galaxy/commit/379714e5beace2ca7b31eab064f22... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- remove sniffers that no longer exist from sample config Commit: b9fe69fb8b46ffc2c9842d672c547413439f12d8 https://github.com/galaxyproject/galaxy/commit/b9fe69fb8b46ffc2c9842d672c547... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/config.py R lib/galaxy/datatypes/converters/fastagz_to_fasta.xml R lib/galaxy/datatypes/converters/fastqbz2_to_fastq.xml R lib/galaxy/datatypes/converters/fastqcssangerbz2_to_fastqcssanger.xml R lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml R lib/galaxy/datatypes/converters/fastqgz_to_fastq.xml R lib/galaxy/datatypes/converters/fastqilluminabz2_to_fastqillumina.xml R lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml R lib/galaxy/datatypes/converters/fastqsangerbz2_to_fastqsanger.xml R lib/galaxy/datatypes/converters/fastqsangergz_to_fastqsanger.xml R lib/galaxy/datatypes/converters/fastqsolexabz2_to_fastqsolexa.xml R lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml R lib/galaxy/datatypes/converters/genbankgz_to_genbank.xml A lib/galaxy/datatypes/converters/gz_to_uncompressed.xml M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/webapps/galaxy/api/datatypes.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge pull request #5794 from jmchilton/dynamic_compressed_types Infrastructure for dynamic compressed datatypes Compare: https://github.com/galaxyproject/galaxy/compare/21c10e960b21...b9fe69fb8b46