🤩 Added Treatment Data to `pbta_all`

What's Changed

• 🔨 Update PBTA 20240322 by @migbro in #60
• 🔧 Fix Missing Field by @migbro in #61
• ✨ Add Treatment Views to pbta_all by @migbro in #62

Full Changelog: v1.2.0...v1.3.0

🚀 OpenPedCan v15 and tll_sd_aq9kvn5p_2019 (Teachey) Added

• OpenPedCan v15 Added, with several bug fixes and adjustments to evolving realities of the project
• Added new KF study and refactored another in terms of config file

What's Changed

• 🛠️ refactor/rename Lupo study to new ID by @migbro in #56
• 🚀 Add OpenPedCan v15 by @migbro in #57
• ✏️ add teachey by @migbro in #59
• ✏️ update openpedcan desc by @migbro in #58

Full Changelog: v1.1.0...v1.2.0

✨ Clinical Data Diff Tool

Added a tool to identify and summarize changes slated to be made to an existing study on the portal based on the cBio formatted data_clinical files. It does the following for each of sample and patient views:

• Create a list, one per line, per ID, per attribute, of what would change if the data were loaded
• Output list of IDs that would be removed from the portal, if any
• Output list of IDs that would be added if any
• Create summary of the number of changes of each attribute type printed to STDOUT
  Also contains study updates

What's Changed

• 🚀 Add dbgap chdm, Update Mioncoseq by @migbro in #54
• ✨ add server scraper by @migbro in #55

Full Changelog: v1.0.1...v1.1.0

🔧 Fix Pandas, Numpy Calls

A recent upgrade in software versions used for pandas and numpy has caused some functions being used to be deprecated. This PR fixes that, and will be followed with an accompanying docker image and software list.

What's Changed

• 🔧 Fixes for numpy pandas compatibility by @migbro in #53

Full Changelog: v1.0.0...v1.0.1

🧹Cleanup Legacy

• Minor change to PBTA config to accommodate new file_type entries in manifests
• Removed many legacy files to cleanup repo
• Will make this now public as most changes are related to config file updates, less so software

What's Changed

• 🔨 Added new file type by @migbro in #52

Full Changelog: v0.9.1...v1.0.0

📝 Config updates

Several studies have had their configs updated to pull from the most recent sources

What's Changed

• 🚀 Update configs by @migbro in #51

Full Changelog: v0.9.0...v0.9.1

🛠️ Refactor Data Clinical Header

Biggest change is ditching using dbt to get headers for data_clinical_* files and using a flat file. The complexity of a 5 header line requirement makes using a db table too cumbersome to update and maintain. Also updated database pulls

What's Changed

• Feature/switch gatk cnv to cbio in wide format by @sakshamphul in #46
• 🛠️ clin data refactor by @migbro in #50

Full Changelog: 0.8.1...v0.9.0

🔧 Bug fix and new studies

• 🐛 ensure that sample IDs are imported as str, no matter how inty they look
• added new study configs

What's Changed

• 🛠️ New configs, bug fixes, improvements by @migbro in #47

Full Changelog: v0.8.0...0.8.1

🚀OpenPedCan v12 Release

Mostly updates to accommodate OpenPedcan v12, and some minor bug fixes

What's Changed

• 🚀 OpenPedcan v12 Release by @migbro in #41

Full Changelog: v0.7.1...v0.8.0

v0.7.1

What's Changed

• 🔨 Study Config Updates and bug fixes by @migbro in #34

Full Changelog: v0.7.0...v0.7.1