messages, error handling, WDL ingest #117
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- pytest markers - reduced calls to galaxy load_xmltool() - added all test data locally (no more downloading using toolshed api)
- moved all wrappers to tests/data/galaxy/wrappers - avoids making any galaxy toolshed API requests during tests - added tests which do use galaxy toolshed API requests to check this functionality still works. locally: - base suite = 58 sec - release suite = 215 sec
- broken - updating calls to parse_expression()
TODO - messages: print to top of file - fix wdl translate
TODO: - WDL ingest messages - Galaxy ingest messages
still TODO: - GXY ingest messages - WDL address runtime inputs - adapt other translate units for WDL shell and native parsers
STILL TODO - WDL -> NXF handle runtime exprs - WDL -> NXF unwrapping of shell script sometimes has unnecessary nested brackets - WDL -> CWL unwrapping can be cleaner than stringformatter - WDL -> CWL unwrapping can needs proper indenting - WDL implement scatter on multiple inputs using zip()
STILL TODO - WDL -> NXF handle runtime exprs - WDL -> NXF unwrapping of shell script sometimes has unnecessary nested brackets - WDL -> CWL unwrapping can be cleaner than stringformatter - WDL -> CWL unwrapping can needs proper indenting - WDL implement scatter on multiple inputs using zip()
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