Releases: d3b-center/d3b-cds-manifest-prep
Releases · d3b-center/d3b-cds-manifest-prep
🏷 Release 0.9.0
Release 0.9.0
Force column Order and fix diagnosis IDs
- Column order is now enforced. In previous releases, column order was unstable and could change. Now column order is enforced directly before saving tables to file.
- Per #84, diagnosis IDs were not unique. diagnosis IDs are now made unique.
Summary
- Emojis: 🐛 x2, ✨ x1
- Categories: Additions x1, Fixes x2
New features and changes
- #89 - 🐛 file id comes before sample in genomic_info - 79f5627e by chris-s-friedman
- #88 - 🐛 fix issue where diagnosis ids weren't unique - bd17f4b8 by chris-s-friedman
- #83 - ✨ order columns in output manifests - 3be104af by chris-s-friedman
🏷 Release 0.8.1
Release 0.8.1
Summary
- Emojis: 🐛 x1
- Categories: Fixes x1
New features and changes
- #80 - 🐛 add sample missing from bix manifest - 2986844d by chris-s-friedman
🏷 Release 0.8.0
Release 0.8.0
Use the new bix mapping to generate genomic_info table
The seed for generating the genomic_info table is now changed to the new mapping manifest.
Summary
- Emojis: 🍱 x3
- Categories: Other Changes x3
New features and changes
- #77 - 🍱 Use the new mapping table for more accurate genomic info - 6b0e20bf by chris-s-friedman
- #76 - 🍱 use csv instead of xlsx for bix manifest - 4d6453c9 by chris-s-friedman
- #74 - 🍱 add new bix manifest to seed genomic_info table - 410d266a by chris-s-friedman
🏷 Release 0.7.1
Release 0.7.1
Pull file endpoint updates
The file endpoint was updated to fix issues related to #31 as well as issues with file format. some bam.bai files had the file_format of bam, when they should have had the format bai. After consulting with @zhangb1, also found that file_format values for .n2.results, .BEST.results, and some .theta2.total.cns needed to be updated.
After all of these updates were made in the dataservice, the cds submission packet was regenerated for this release.
Summary
- Emojis: 🍱 x1
- Categories: Other Changes x1
New features and changes
- #72 - 🍱 re-generated manifest to get file updates from ds - d728e87d by chris-s-friedman
Contributors
zhangb1
Assets 3
🏷 Release 0.7.0
Release 0.7.0
Updated seed mapping file
Removed 33 files from the file sample participant mapping.
Summary
- Emojis: 🍱 x1
- Categories: Other Changes x1
New features and changes
- #70 - 🍱 remove 33 dgd files from mapping and regenerate - be6747f0 by chris-s-friedman
🏷 Release 0.6.0
Release 0.6.0
Updated Diagnoses
Updated logic for picking diagnosis from pathology_diagnosis, broad_histology, and pathology_free_text_diagnosis
Summary
- Emojis: ✨ x1, 🚨 x1, 🍱 x3, 🐛 x1, ♻️ x2, 📝 x2, 🔥 x1
- Categories: Additions x1, Documentation x2, Removals x1, Fixes x2, Other Changes x5
New features and changes
- #67 - ✨ use pathology_free_text for participants missing dx - d0893aa5 by chris-s-friedman
- #66 - 🚨 fix markdownlint warnings - b4654405 by chris-s-friedman
- #64 - 🍱 add updated outputs in diagnosis table - 610e161f by chris-s-friedman
- #63 - 🐛 diagnosis_id did not work unless finding_missing_dx - db34f40b by chris-s-friedman
- #62 - ♻️ make searching for missing dx in the ds optional - b63d29a3 by chris-s-friedman
- #61 - 📝 add documentation for diagnosis table - 2bfc6bef by chris-s-friedman
- #60 - 🔥 remove a breakpoint in diagnosis generator - 01741bba by chris-s-friedman
- #59 - ♻️ extract diagnosis from histology in its own func - 983092cb by chris-s-friedman
- #58 - 📝 add readme for package data - e952d805 by chris-s-friedman
- #57 - 🍱 use openpedcan histologies table - ce3d9432 by chris-s-friedman
- #56 - 🍱 use openpedcan histology file - 5f272039 by chris-s-friedman
🏷 Release 0.5.3
Release 0.5.3
Two big changes here:
- automatically updating the file-sample-participant map in the output directory
- handle the issue #32
Summary
- Emojis: 🐛 x2, ✨ x1
- Categories: Additions x1, Fixes x2
New features and changes
- #54 - 🐛 handle participants that are missing diagnoses - af74b616 by chris-s-friedman
- #53 - 🐛 save the fsp map - bbc8b048 by chris-s-friedman
- #52 - ✨ save the seed mapping file to the output directory - 2054dd96 by chris-s-friedman
🏷 Release 0.5.2
Release 0.5.2
Summary
- Emojis: 🐛 x1, 🔧 x1, ✨ x1
- Categories: Additions x1, Fixes x1, Other Changes x1
New features and changes
- #50 - 🐛 didn't uncomment the important parts - 0da3fa18 by chris-s-friedman
- #47 - 🔧 add prerelease to config - ebcbe783 by chris-s-friedman
- #46 - ✨ setup pre-release script to update readme and submission bug_report - 1cf9c881 by chris-s-friedman
🏷 Release 0.5.1
Release 0.5.1
Setup issue and PR templates
Summary
- Emojis: 🐛 x6, 🔧 x1, 🚸 x1
- Categories: Fixes x7, Other Changes x1
New features and changes
- #44 - 🐛 set correct submission issue bug frontmatter - a6c75c1f by chris-s-friedman
- #43 - 🐛 set submission_issue opts to labels for checkbox - ee9311a2 by chris-s-friedman
- #42 - 🐛 options for effected files must be hashable - 1da54eb6 by chris-s-friedman
- #41 - 🐛 submission issue template wants strings - b66fdc04 by chris-s-friedman
- #40 - 🐛 fix_submission_package_bug_report - bae5acaf by chris-s-friedman
- #39 - 🐛 submission_bug_report is yml - 5a946a22 by chris-s-friedman
- #38 - 🔧 add issue templates - 437ab049 by chris-s-friedman
- #37 - 🚸 output zip directory has version number in top level inside zip - 2ddff1d6 by chris-s-friedman
🏷 Release 0.5.0
Release 0.5.0
Summary
- Emojis: 🍱 x1, 🚑️ x3, 🚸 x2, 🚚 x1
- Categories: Fixes x2, Other Changes x5
New features and changes
- #29 - 🍱 updated submission_packet after changes from 0.2.0 - 166d7760 by chris-s-friedman
- #28 - 🚑️ Fix imports - 254053a1 by chris-s-friedman
- #27 - 🚑️ specify package_name for version - 29ab5eac by chris-s-friedman
- #26 - 🚸 add --version option - 14140b24 by chris-s-friedman
- #25 - 🚑️ reuirements needs click - 9577eaa4 by chris-s-friedman
- #24 - 🚸 bundle file-sample-participant map with package - 9108322a by chris-s-friedman
- #23 - 🚚 move old zip package to zip directory - d95315f7 by chris-s-friedman