Releases: Sage-Bionetworks/agora-data-tools
Releases · Sage-Bionetworks/agora-data-tools
0.5.1
0.5.0
What's Changed
- [IBCDPE-766] Adds
distribution_data
GX suite by @BWMac in #140 - [IBCDPE-789] Adds
network
GX Suite by @BWMac in #141 - [IBCDPE-765] Adds
biodomain_info
GX Suite by @BWMac in #142 - [IBCDPE-795] Adds
rna_distribution_data
GX Suite by @BWMac in #144 - [IBCDPE-1066] Updates
gx_enabled
logic by @BWMac in #147 - Added transform to proteomics data sets to remove CON__ entries by @jaclynbeck-sage in #146
- [IBCDPE-794] Adds
proteomics
GX Suite by @BWMac in #143 - [IBCDPE-954] Adds
proteomics_srm
GX Suite by @BWMac in #145 - Biomarkers transform for ModelAD by @beatrizsaldana in #148
- MG45 - ADT: Pathology data ETL by @beatrizsaldana in #149
New Contributors
- @beatrizsaldana made their first contribution in #148
Full Changelog: 0.4.2...0.5.0
0.4.2
0.4.1
0.4.0
0.3.0
What's Changed
- Added transform for biodomain_info by @jaclynbeck-sage in #79
- AG-1143/transform distribution data testing by @jaclynbeck-sage in #82
- AG-1147/AG-1148/AG-1098: Add tests for rna seq data and rna distribution data by @jaclynbeck-sage in #80
- jbeck/AG-1145/transform overall scores testing by @jaclynbeck-sage in #81
- AG-1146/transform proteomics distribution testing by @jaclynbeck-sage in #83
- AG-841: Add ingest/merge of tep_adi_info into gene_info transform by @jaclynbeck-sage in #84
- AG-1196: Sort gene_info.biodomains to generate consistent ordering by @JessterB in #86
- AG-1191: Consume updated tep_adi source file by @JessterB in #87
- AG-1161 Updated gene_info transform with renamed columns by @jaclynbeck-sage in #88
- AG-1150: Update source file and provenance versions to pick up IU nom… by @JessterB in #89
- AG-1239: Bump team_info source version to pick up corrected data by @JessterB in #91
- [IBCDPE-386] Adds CI step to publish GHCR container by @BWMac in #92
- [IBCDPE-386] Update README.md by @BWMac in #93
- [IBCDPE-683] Updates Python Versions by @BWMac in #94
- Ag-866/Ag-1227 Process SRM DE data by @jaclynbeck-sage in #90
- AG-1117: Add new ensembl info fields to gene_info transform by @jaclynbeck-sage in #95
- [IBCDPE-527] Makes
syn
always required by @BWMac in #97 - [IBCDPE-688] Great Expectations Implementation for Metabolomics Data by @BWMac in #96
- [IBCDPE-430] Support shared source file definitions in config by @BWMac in #99
- [IBCDPE-430] Remove the top level array in the configuration files by @BWMac in #98
- Updated GWAS pre-processing step to remove HASGs from BioMart by @jaclynbeck-sage in #100
- [IBCDPE-421] Deprecates
agoradatatools/etl/test.py
by @BWMac in #101 - [IBCDPE-734] Updates
pyarrow
Version by @BWMac in #102 - [IBCDPE-712] Implement Great Expectations for the
genes_biodomains
Datset by @BWMac in #103 - AG-1305: Validate '23 new nominations and related data updates by @JessterB in #104
- AG-1305: Bump source file versions to pick up misc data fixes by @JessterB in #105
- AG-1305: Bump harmonized_targets source version to pick up 2 late nominations by @JessterB in #106
- AG-1305: Bump exp_val provenance version to align with source version by @JessterB in #107
- AG-1305: Bump source file versions in config.yaml for prod processing by @JessterB in #108
- AG-1305: Pick up final source file adjustments for 23 nominations by @JessterB in #109
- AG-1305: Bump targets source version to collapse metabolom(e)(ics) GCT filters by @JessterB in #110
- [IBCDPE-419] Initial Setup of
pre-commit
for ADT by @BWMac in #112 - [AG-1314] JSON Schema Validation GX Prototyping by @BWMac in #111
- Updated nest_fields util function by @jaclynbeck-sage in #114
- [IBCDPE-791] Implement Great Expectations for the
overall_scores
Dataset by @BWMac in #115 - SRM remove multiple ENSGs per peptide by @jaclynbeck-sage in #113
- [IBCDPE-790] Implement Great Expectations for the
neuropath_corr
Dataset by @BWMac in #116 - [IBCDPE-792] Implement Great Expectations for the
proteomics_distribution_data
Dataset by @BWMac in #118 - [IBCDPE-793] Implement Great Expectations for the
proteomics_tmt
Dataset by @BWMac in #119 - [IBCDPE-800] Bumps pandas and synapseclient versions by @BWMac in #122
- [IBCDPE-798] Implements GX Expectation Suite for
team_info
Dataset by @BWMac in #123 - Updated biodomains file to v5 by @jaclynbeck-sage in #125
- Jbeck/ag 1144/transform gene info testing by @jaclynbeck-sage in #121
- Fix genes_biodomains transform to drop duplicate rows by @jaclynbeck-sage in #127
- Bumped version of target_exp_validation_harmonized by @jaclynbeck-sage in #128
- [AG-1386] Implement Error Catching for GX Data Validation by @BWMac in #129
- [IBCDPE-797] Adds
target_exp_validation_harmonized
Expectation Suite by @BWMac in #126 - [IBCDPE-835] Revamps GX Report Uploads by @BWMac in #130
- [AG-1385] Fixes JSON Schema expectation passing when it should fail by @BWMac in #131
- Update gene metadata file to remove biomart-only genes by @jaclynbeck-sage in #132
- [IBCDPE-946] Adds Optional Uploading by @BWMac in #133
- Updates CI Workflow by @BWMac in #134
Full Changelog: 0.2.0...0.3.0
0.2.0
What's Changed
- AG-1001: Align config.yaml with test_config.yaml by @JessterB in #73
- [AG-1105] Data-Driven Test for
transform_genes_biodomains
by @BWMac in #74 - [Mg-8] Create mouse gene metadata file by @jaclynbeck-sage in #75
- Added tests and test input/output for the team_info transform by @jaclynbeck-sage in #77
- AG-1154: Added biodomains column to gene_info transform by @jaclynbeck-sage in #78
- [IBCDPE-572] Add in contribution guide by @thomasyu888 in #72
Full Changelog: 0.1.0...0.2.0
0.1.0
What's Changed
- Ag 896 add ensembl version by @jaclynbeck-sage in #68
- Update python installation instructions by @thomasyu888 in #69
- Fixed pandas SettingWithCopy warning by @jaclynbeck-sage in #67
- [AG-1041] Adds timestamp logging for processing runs by @BWMac in #71
- [AG-838] Support independent transforms by @BWMac in #70
Full Changelog: 0.0.2...0.1.0
0.0.2
What's Changed
- AG-992: Update dataset & filename: biodomains -> genes_biodomains by @JessterB in #53
- Ag-935 rna distribution updates by @jaclynbeck-sage in #54
- Fixed logic for determining if rna or protein was changed in AD by @jaclynbeck-sage in #55
- [IBCDPE-394] NumpyEncoder Tests by @BWMac in #57
- Created eQTL preprocessing script to update eQTL data with Solly's data by @jaclynbeck-sage in #58
- Added n_terms and enrichment_pct calculations to biodomains output by @jaclynbeck-sage in #56
- [AG-1017] test data workflow name change by @BWMac in #59
- [AG-809] Synapse Upload Versions by @BWMac in #60
- [AG-1016] CI pipeline should indicate failure when file upload fails by @BWMac in #62
- AG-995: Update wiki IDs to new versions for scores update by @JessterB in #64
- [IBCDPE-409] Implement
agora-data-tools
CLI by @BWMac in #66
Full Changelog: 0.0.1...0.0.2
0.0.1
What's Changed
- Refactoring of the gene_info dataset by @mfazza in #1
- Data Release 2.5.0 by @mfazza in #2
- Adding dynamic login by @mfazza in #3
- adding testing file by @mfazza in #4
- AG-500: adding documentation by @mfazza in #5
- AG-621 by @mfazza in #6
- AG-500 by @mfazza in #7
- 2.6.5 by @mfazza in #8
- AG-500: found a problem with overall scores by @mfazza in #9
- Ag 557 by @mfazza in #10
- AG-605 by @mfazza in #11
- AG-560 and AG-557: TMT distribution data and renaming of cor_p_val by @thomasyu888 in #13
- [AG-698] Updates to develop branch by @thomasyu888 in #14
- Adjust pipelines to be executed via gh-actions by @thomasyu888 in #15
- Update documentation by @thomasyu888 in #16
- Add dockerfile by @thomasyu888 in #18
- Dev to main by @thomasyu888 in #17
- AG-780 Update configs & README by @JessterB in #19
- Merge main to dev to sync branches by @JessterB in #20
- AG-701 - disable TREAT-AD score processing by @JessterB in #21
- AG-701: Disable TREAT-AD scores in test_config.yaml by @JessterB in #22
- Temporarily reenable TREAT-AD score processing in test-config only by @JessterB in #24
- Disable TREAT-AD score processing by @JessterB in #25
- AG-826: Update & reenable overall_scores processing by @JessterB in #26
- AG-827: Update and reenable distribution_data processing by @JessterB in #27
- AG-825 ADT: Reconfigure TMT proteomics to use new source files by @j-hendrickson-sage in #28
- AG-825 by @JessterB in #29
- Add in public dockerhub and fix some markdown issues by @thomasyu888 in #32
- Update Dockerfile by @BWMac in #33
- AG-915: pin source file versions for nextflowtower validation by @JessterB in #34
- AG-915: Pin iGAP source file version for nft validation by @JessterB in #35
- [IBCDPE-411]/test extract by @BWMac in #36
- [IBCDPE-395]/adds ci pytest by @BWMac in #38
- Ag 469 update ensembl ID list by @jaclynbeck-sage in #30
- Notebook to update GWAS list by @jaclynbeck-sage in #31
- AG-888: Pin source file versions and clean up configs by @JessterB in #39
- AG-826: Revert neuropath handling changes until we are ready for it by @JessterB in #41
- AG-492: Update config.yaml to process new source file versions by @JessterB in #42
- Removed unnecessary results.json creation and upload to synapse by @jaclynbeck-sage in #43
- AG-889: Process new version of scores source data by @JessterB in #44
- Modified nest_fields to allow dropping columns from the nested dictionary by @jaclynbeck-sage in #45
- Update load functions by @jaclynbeck-sage in #46
- [IBCDPE-414] - test process tests by @BWMac in #48
- AG-932/AG-958: Add biodomains dataset by @JessterB in #47
- [IBCDPE-416] - Fixes/Re-Writes Tests for
utils.py
by @BWMac in #50 - Deprecate processing with github actions by @thomasyu888 in #49
- [IBCDPE-413]/test load.py by @BWMac in #51
- [IBCDPE-415] transform tests by @BWMac in #52
New Contributors
- @mfazza made their first contribution in #1
- @thomasyu888 made their first contribution in #13
- @j-hendrickson-sage made their first contribution in #28
- @BWMac made their first contribution in #33
- @jaclynbeck-sage made their first contribution in #30
Full Changelog: https://github.com/Sage-Bionetworks/agora-data-tools/commits/0.0.1