SciCrunch / sparc-curation / 629

Builds Branch Commit Type Ran Committer Via Coverage
629 master update to use new openpyxl conventions get_active_sheet() method -> active property template schema version can legitimately be None if a NoDataError occurs, in which case we just have to proceed, there may be some other consequences of that dow... push tgbugs travis-ci pending completion   set done
628 master better handling of error cases for malformed headers in manifests self.norm_to_orig_header is not present in all failure modes push tgbugs travis-ci pending completion   set done
627 master simple core pipeline, structure validation, norm Pios to int ids structure validation on way to being able to list folders associated with specimens push tgbugs travis-ci pending completion   set done
626 master datasets MetadataFile can't error on match yet metadata_element is shared between headers right now, will have to get that sorted out, and the error will show up later with how!? if it happens again push tgbugs travis-ci pending completion   set done
624 master dev guide new section on clarity for the better future workflow retrieve extract transform validate etv can be rearranged, interwoven etc. the critical part is that retrieve happens only once per phase based on new information that has come to l... push tgbugs travis-ci pending completion   set done
623 master sparcur.simple.retrieve first pass of retrieve for single datasets the implementation is a bit verbose and repetitive, but it seems like it more or less is working as expected, we clone only that single dataset into the full hierarchy and stick i... push tgbugs travis-ci pending completion   set done
622 master paths upstream.mkdir can fail, pull no joblib if n_jobs <= 1 push tgbugs travis-ci pending completion   set done
620 master finish impl of exclude uploaded, remove title trailing whitespace the trailing whitespace in dataset names (which occures in more than one dataset!!!) breaks the code for accessing alternate data streams on windows NTFS files system, which breaks... push tgbugs travis-ci pending completion   set done
619 master add sparcur_internal folder and github interation push tgbugs travis-ci pending completion   set done
618 master setup.org add section for enabling long paths on windows transiently documenting my broken fix and solution and related bugs for the long paths issue on windows using the //?/ prefix and added ability to retrieve files from blackfynn whose state... push tgbugs travis-ci pending completion   set done
617 master dev guide updated, fetch_files to use a filter function general improvements to the organization and clarity of the extract portion of the pipeline, moved a few things to utils to reduce noise push tgbugs travis-ci pending completion   set done
616 master dev guide python ir example, validate extract step also supporting changes needed for the extract step change bids_root to dataset_root, with a note that we can probably do away with this check now since dataset_description should always be at t... push tgbugs travis-ci pending completion   set done
615 master reports for hubmap, path_ir, fix tab tables also switch to preview ttl for reports the path_ir implementation required the creation of register_all_types which will need to be kept in sync with any additional type conversions that are added in t... push tgbugs travis-ci pending completion   set done
614 master queries.org add dataset sample source push tgbugs travis-ci pending completion   set done
612 master add docs/queries.org push tgbugs travis-ci pending completion   set done