From 8ef82e738d79e472a4060b3ee13fab4cf56521cf Mon Sep 17 00:00:00 2001 From: chris-s-friedman Date: Tue, 17 Jan 2023 15:41:04 -0500 Subject: [PATCH] :label: Release 0.14.0 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit ## Release 0.14.0 ### Updates to diagnoses This release includes a few updates to diagnoses: 1. remove diagnoses from the histologies file that were manually assigned, that are attached to normal samples. 2. Only include normal samples in the diagnosis-sample mapping table. 3. test that only and all tumor samples are in the diagnosis-sample mapping table. 4. 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](https://github.com/d3b-center/d3b-cds-manifest-prep/pull/124) - 🐛 Fix histologies file - [01269fdf](https://github.com/d3b-center/d3b-cds-manifest-prep/commit/01269fdffb570810e6df5c310713a70b7e6e01b9) by [chris-s-friedman](https://github.com/chris-s-friedman) - [#123](https://github.com/d3b-center/d3b-cds-manifest-prep/pull/123) - ✅ add test for diagnosis_sample map file - [38d8ddaa](https://github.com/d3b-center/d3b-cds-manifest-prep/commit/38d8ddaa1584c951f314e78d34fe4c2dbf46e409) by [chris-s-friedman](https://github.com/chris-s-friedman) - [#122](https://github.com/d3b-center/d3b-cds-manifest-prep/pull/122) - 🐛 missing diagnoses and remove normal samples from bs_dx - [ce3e2a9d](https://github.com/d3b-center/d3b-cds-manifest-prep/commit/ce3e2a9deb6d8a517be556a0ea252ecf7d58f002) by [chris-s-friedman](https://github.com/chris-s-friedman) --- .../submission_pkg_bug_report.yml | 1 + CHANGELOG.md | 25 ++++++++++++++++++- README.md | 1 + 3 files changed, 26 insertions(+), 1 deletion(-) diff --git a/.github/ISSUE_TEMPLATE/submission_pkg_bug_report.yml b/.github/ISSUE_TEMPLATE/submission_pkg_bug_report.yml index 5193b58..d746147 100644 --- a/.github/ISSUE_TEMPLATE/submission_pkg_bug_report.yml +++ b/.github/ISSUE_TEMPLATE/submission_pkg_bug_report.yml @@ -24,6 +24,7 @@ body: label: Version ID description: Select the version number relating to this bug options: # new_versions_here + - "0.14.0" - "0.13.0" - "0.12.0" - "0.11.1" diff --git a/CHANGELOG.md b/CHANGELOG.md index e630ed2..df84fe6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,28 @@ # D3B CDS Manifest Prep Change History +## Release 0.14.0 + +### Updates to diagnoses + +This release includes a few updates to diagnoses: + +1. remove diagnoses from the histologies file that were manually assigned, that are attached to normal samples. +2. Only include normal samples in the diagnosis-sample mapping table. +3. test that only and all tumor samples are in the diagnosis-sample mapping table. +4. 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](https://github.com/d3b-center/d3b-cds-manifest-prep/pull/124) - 🐛 Fix histologies file - [01269fdf](https://github.com/d3b-center/d3b-cds-manifest-prep/commit/01269fdffb570810e6df5c310713a70b7e6e01b9) by [chris-s-friedman](https://github.com/chris-s-friedman) +- [#123](https://github.com/d3b-center/d3b-cds-manifest-prep/pull/123) - ✅ add test for diagnosis_sample map file - [38d8ddaa](https://github.com/d3b-center/d3b-cds-manifest-prep/commit/38d8ddaa1584c951f314e78d34fe4c2dbf46e409) by [chris-s-friedman](https://github.com/chris-s-friedman) +- [#122](https://github.com/d3b-center/d3b-cds-manifest-prep/pull/122) - 🐛 missing diagnoses and remove normal samples from bs_dx - [ce3e2a9d](https://github.com/d3b-center/d3b-cds-manifest-prep/commit/ce3e2a9deb6d8a517be556a0ea252ecf7d58f002) by [chris-s-friedman](https://github.com/chris-s-friedman) + + ## Release 0.13.0 ### Set diagnosis as an attribute of event, not aliquot @@ -353,4 +376,4 @@ Updated logic for picking diagnosis from pathology_diagnosis, broad_histology, a - [#4](https://github.com/d3b-center/d3b-cds-manifest-prep/pull/4) - ✨ Add tools to generate manifests - [82049711](https://github.com/d3b-center/d3b-cds-manifest-prep/commit/820497117ae34a6b01e69d93b44814508a99d371) by [chris-s-friedman](https://github.com/chris-s-friedman) - [#3](https://github.com/d3b-center/d3b-cds-manifest-prep/pull/3) - ✨ Begin working on single entrypoint script - [ad18a5f0](https://github.com/d3b-center/d3b-cds-manifest-prep/commit/ad18a5f0459886ad9b21f2dd858c7b189f6b2a69) by [chris-s-friedman](https://github.com/chris-s-friedman) - [#2](https://github.com/d3b-center/d3b-cds-manifest-prep/pull/2) - move qc script into its own step in pipeline - [c952f080](https://github.com/d3b-center/d3b-cds-manifest-prep/commit/c952f08037f59f15c1178d46179638995bf842d9) by [chris-s-friedman](https://github.com/chris-s-friedman) -- [#1](https://github.com/d3b-center/d3b-cds-manifest-prep/pull/1) - 🚧 move files from kf_support and add extra cleanup - [de9dc1c6](https://github.com/d3b-center/d3b-cds-manifest-prep/commit/de9dc1c63cdef88ef973fef42e3553bcd6eb1ec8) by [chris-s-friedman](https://github.com/chris-s-friedman) +- [#1](https://github.com/d3b-center/d3b-cds-manifest-prep/pull/1) - 🚧 move files from kf_support and add extra cleanup - [de9dc1c6](https://github.com/d3b-center/d3b-cds-manifest-prep/commit/de9dc1c63cdef88ef973fef42e3553bcd6eb1ec8) by [chris-s-friedman](https://github.com/chris-s-friedman) \ No newline at end of file diff --git a/README.md b/README.md index 6ab55c7..578c28b 100644 --- a/README.md +++ b/README.md @@ -17,6 +17,7 @@ pip install git+https://github.com/d3b-center/d3b-cds-manifest-prep.git ## Data +The most recently generated manifest can be found [here](https://github.com/d3b-center/d3b-cds-manifest-prep/releases/tag/0.14.0). The most recently generated manifest can be found [here](https://github.com/d3b-center/d3b-cds-manifest-prep/releases/tag/0.13.0). The most recently generated manifest can be found [here](https://github.com/d3b-center/d3b-cds-manifest-prep/releases/tag/0.12.0). The most recently generated manifest can be found [here](https://github.com/d3b-center/d3b-cds-manifest-prep/releases/tag/0.11.1).