Releases: d3b-center/d3b-cds-manifest-prep
Releases · d3b-center/d3b-cds-manifest-prep
🏷 Release 1.0.1
Release 1.0.1
Fixes for sequenicng_file columns
fixes some of the columns in sequencing file
Summary
- Emojis: 🐛 x1
- Categories: Fixes x1
New features and changes
- #150 - 🐛 Fix sequencing file mappings - 2e81148f by chris-s-friedman
🏷 Release 1.0.0
Release 1.0.0
CDS Release 2 first draft
This is the first draft of the full release for cds v2. This takes the ideas
behind the first cds release and changes some configuration based upon the
spec provided by CDS - Specifically that all of the documents are in one large
excel file.
Summary
- Emojis: 🍱 x1, 🐛 x4, ? x3, ♻️ x1, ✨ x2, 🎨 x1, 🌱 x1
- Categories: Additions x4, Fixes x4, Ops x1, Other Changes x4
New features and changes
- #146 - 🍱 add updated sequencing file and excel output - f91cefab by chris-s-friedman
- #145 - 🐛 don't save index to excel files - df23893d by chris-s-friedman
- #144 - 🐛 get file gatherer working - afddb9f7 by chris-s-friedman
- #143 - Sequencing file cache location - 15894491 by chris-s-friedman
- #142 - 🐛 get study_tables to have appropriate column values - b4584307 by chris-s-friedman
- #141 - add sequencing_file and updates to study and study_admin, start work on excel_writer - 41fadbd0 by chris-s-friedman
- #140 - ♻️ move cli options into a common function - 2971b5b2 by chris-s-friedman
- #139 - Sequencing file update - 6df1b620 by chris-s-friedman
- #138 - ✨ M1TEAM-64 V1.x prep - f154c2c3 by chris-s-friedman
- #137 - 🎨 remove breakpoint when building jhu manifest - b0dd7ea1 by chris-s-friedman
- #136 - 🐛 load the jhu sample manifest when creating the file-sample-participant map - b65c934e by chris-s-friedman
- #135 - ✨ M1TEAM-74 remove jhu samples from the x01 fsp - 7aeb8f3c by chris-s-friedman
- #133 - 🌱 Add file-sample-participant mapping for the CBTN X01 - d13c2105 by chris-s-friedman
🏷 Release 0.14.1
Release 0.14.1
This is the final manifest sent to CDS for release 1
updated sample information from redcap
One sample was updated in redcap and another sample had some database updates.
This release has those sample updates.
Summary
- Emojis: 🍱 x1, 🔥 x1
- Categories: Additions x1, Removals x1
New features and changes
- #128 - 🍱 updated sample manifest after redcap updates - 31e48521 by chris-s-friedman
- #127 - 🔥 Remove unused data files - 71426ec3 by chris-s-friedman
🏷 Release 0.14.0
Release 0.14.0
Updates to diagnoses
This release includes a few updates to diagnoses:
- remove diagnoses from the histologies file that were manually assigned, that are attached to normal samples.
- Only include normal samples in the diagnosis-sample mapping table.
- test that only and all tumor samples are in the diagnosis-sample mapping table.
- if a participant's only samples in CDS are normal, and all of those samples only come from events that have only normal samples, extract the diagnoses from other events for the participant. Set the diagnosis ID to be based of the C-ID instead of the 7316 ID.
Summary
- Emojis: 🐛 x2, ✅ x1
- Categories: Additions x1, Fixes x2
New features and changes
- #124 - 🐛 Fix histologies file - 01269fdf by chris-s-friedman
- #123 - ✅ add test for diagnosis_sample map file - 38d8ddaa by chris-s-friedman
- #122 - 🐛 missing diagnoses and remove normal samples from bs_dx - ce3e2a9d by chris-s-friedman
🏷 Release 0.13.0
Release 0.13.0
Set diagnosis as an attribute of event, not aliquot
Set diagnosis as an attribute of event, not aliquot. Set diagnosis IDs as the 7316 (event) ID.
Summary
- Emojis: ✨ x2, ♻️ x1
- Categories: Additions x3
New features and changes
- #118 - ✨ New diagnosis ids - 9a5216fd by chris-s-friedman
- #117 - ✨ add qc of diagnoses - 0392c252 by chris-s-friedman
- #116 - ♻️ move qc functions to submodules of qc - 8dd03057 by chris-s-friedman
🏷 Release 0.12.0
Release 0.12.0
Use updated base and read counts
Some values were mungled by excel. this unmungles those values.
Summary
- Emojis: 🍱 x2
- Categories: Additions x2
New features and changes
- #113 - 🍱 updated genomic_info table with correct bases and read counts - fe87d481 by chris-s-friedman
- #112 - 🍱 updated nci submit from bix - a3a05dbc by chris-s-friedman
🏷 Release 0.11.1
Release 0.11.1
Remove last not reported diagnoses
Updates the diagnosis table with the last diagnosis that were not reported.
Summary
- Emojis: 🍱 x2, 🚑️ x1
- Categories: Additions x2, Other Changes x1
New features and changes
- #110 - 🍱 remove not reported diagnoses from diagnosis manifest - c9d85ba8 by chris-s-friedman
- #109 - 🚑️ remove duplicated entries from histologies - 951ae3cb by chris-s-friedman
- #108 - 🍱 update histologies file with manual diagnoses - 7ab9493c by chris-s-friedman
🏷 Release 0.11.0
Release 0.11.0
Use updated histologies file
updates the histologies file used for the diagnosis manifest. This is related to #100. This isn't a complete fix,but fixes all the oligo samples.
Summary
- Emojis: 🍱 x1, ✨ x2, 🔥 x1
- Categories: Additions x3, Removals x1
New features and changes
- #106 - 🍱 updated histologies data - 15f41c79 by chris-s-friedman
- #105 - ✨ Generate histologies file - e8b59bfa by chris-s-friedman
- #104 - 🔥 remove unused module for utils - 6fd29a6d by chris-s-friedman
- #103 - ✨ sort values of all the output manifests - a49e7140 by chris-s-friedman
🏷 Release 0.10.1
Release 0.10.1
Add build_manifest docstrings and return manifests
- add docstrings for 🧑💻
- return output manifests in build_manifest functions. this is so that outputs can be handled in the future. Note that diagnosis output is different from other manifest outputs because it's a tuple of both the diagnosis_table and diagnosis_sample_mapping.
Summary
- Emojis: 📝 x1, ✨ x1
- Categories: Additions x1, Documentation x1
New features and changes
- #101 - 📝 add docstrings for build_manifest functions - 6b8bb461 by chris-s-friedman
- #99 - ✨ return output tables in build functions - 4962ea90 by chris-s-friedman
🏷 Release 0.10.0
Release 0.10.0
qc sample diagnosis and fix diagnoses
- qc the sample-diagnosis mapping file
- As discovered in #92, some samples have multiple diagnoses. after investigating this, some diagnoses were found to be mapped to incorrect participants. this fixes that.
Summary
- Emojis: 🐛 x1, ✨ x1
- Categories: Additions x1, Fixes x1
New features and changes
- #93 - 🐛 reset indices of diagnosis table before splitting and joining - 2100a145 by chris-s-friedman
- #91 - ✨ add testing for samples in sample diagnoses manifest - ab70ba0e by chris-s-friedman