Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f52028f40093af71632e530c79a83bd7148944ed https://github.com/galaxyproject/galaxy/commit/f52028f40093af71632e530c79a83... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/1.fastqsanger.bz2 A lib/galaxy/datatypes/test/1.fastqsanger.gz M test/unit/datatypes/test_datatypes_registry.py Log Message: ----------- Fixes at least 4 more bugs related to sniffing of compressed datatypes. - Incorrect parsing of default auto sniff flag value. - Not respecting flag value when adding to dict of compressed sniffers. - Not checking the right value when checking for compressed datatype instances to add to sniff order. - Not filtering out the sniffers from being automatically added during the default stage of sniffer handling where all types with sniff are added at the end. This last point is the most complicated. I added a hack with #6091 so that the compressed sniffers would only return True if in validation mode or explicitly enabled. I'm not convinced that approached worked and I'm definitely convinced it was a bad approach. The better, cleaner approach is to just always let the sniffer return its truth regardless of validation mode or not and instead only add it to the list of sniffers if it should be enabled. This is what I was assuming would happen but I found this method append_to_sniff_order that was adding sniffers back in that I didn't want added. Commit: 8a58711e391de36b62fc20dc4db5f8ccd55f786d https://github.com/galaxyproject/galaxy/commit/8a58711e391de36b62fc20dc4db5f... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/datatypes/data.py M tools/data_source/upload.py Log Message: ----------- Remove validate_mode prop for sniffing, no longer needed with previous fixes. This does undo an attempt that Nate made to auto sniff fastq.gz files when they can't be converted anyway, but that was kind of broken in its own way.

From Gitter:

jmchilton: natefoo "# Link mode can't decompress anyway, so enable sniffing for keep-compressed datatypes even when auto_decompress is enabled" Did you test this hack? I get the thought process but it seems like it results in uploaded fastq.gz files defaulting to fastqcssanger.gz? Maybe it didn't at some point though? Nate Coraor: ummmmmmmmmmmm maybe probably not John Chilton: I have four fixes for compressed datatypes that all fall apart because of this hack... can I just use the configured sniff order or do you want me to try to preserve this and write a test case Nate Coraor: nah go ahead and de-hack John Chilton: There is a good argument to be made for making the behavior more consistent anyway right? Cool thanks Commit: 2d103a09bce34ac64a5decdff316a92f9223c54c https://github.com/galaxyproject/galaxy/commit/2d103a09bce34ac64a5decdff316a... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Fix sniff_compressed_dynamic_datatypes_default config option not propagating to upload tool. Resolving the default when unspecified in the XML before writing out datatype confs fixes this. This makes this option always explicit in the datatypes conf that is shared with the upload tool. Commit: 67257da24b484f093c6cdba68d4e0d0c358ac571 https://github.com/galaxyproject/galaxy/commit/67257da24b484f093c6cdba68d4e0... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Fixes for compressed datatype fixes thanks to @nsoranzo. Commit: 7b4b2a0f77f35cefc691782b51a9a12dec0da5be https://github.com/galaxyproject/galaxy/commit/7b4b2a0f77f35cefc691782b51a9a... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Fix for lack of feedback on rule builder job failures. Present users with the job standard error and also check for binary sniffing problems and report them with a pretty message suggesting specifying a file type. Commit: f06adba766a987aa8ac59ed99d537008e76a4913 https://github.com/galaxyproject/galaxy/commit/f06adba766a987aa8ac59ed99d537... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/1.fastqsanger.bz2 A lib/galaxy/datatypes/test/1.fastqsanger.gz M test/unit/datatypes/test_datatypes_registry.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #6115 from jmchilton/dynamic_compressed_types_fix_5 [18.05] More compressed datatype sniffing fixes. Commit: a4f99c8cc9514765a68e2c9296c813e7b9f23674 https://github.com/galaxyproject/galaxy/commit/a4f99c8cc9514765a68e2c9296c81... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Merge pull request #6121 from jmchilton/rule_builder_error_better [18.05] Fix for lack of feedback on rule builder job failures. Commit: 4c92aca576c24b96fa0adeb7903283ed44b4012a https://github.com/galaxyproject/galaxy/commit/4c92aca576c24b96fa0adeb790328... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- Fix GIE volume usage Commit: c76e21c030958d7bafd95cc6d13257350bc9acf6 https://github.com/galaxyproject/galaxy/commit/c76e21c030958d7bafd95cc6d1325... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- Consistency in container_path : host_path Commit: e2d516be2a0580277f5e8aeaa8d55558640abb92 https://github.com/galaxyproject/galaxy/commit/e2d516be2a0580277f5e8aeaa8d55... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- Merge pull request #6128 from dannon/fix_cli_gies [18.05] Fix GIE volume wrangling Commit: 9dd6773ced15df7b22d2d23ee0466701c92cfbf3 https://github.com/galaxyproject/galaxy/commit/9dd6773ced15df7b22d2d23ee0466... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/1.fastqsanger.bz2 A lib/galaxy/datatypes/test/1.fastqsanger.gz M lib/galaxy/visualization/plugins/interactive_environments.py M test/unit/datatypes/test_datatypes_registry.py M tools/data_source/upload.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/c9c7455c6688...9dd6773ced15 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.