0.5.1

What's Changed

• [AG-1557] Fixes ModelAD File size must be at least one byte Error by @BWMac in #150

Full Changelog: 0.5.0...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

What's Changed

• MG-88: Create harmonized biomarkers source file by @JessterB in #137
• MG-40: Create harmonized pathology source file by @JessterB in #138
• [IBCDPE-769] Adds gene_info Expectation Suite by @BWMac in #139

Full Changelog: 0.4.1...0.4.2

0.4.1

What's Changed

• [IBCDPE-796] Adds rnaseq_differential_expression expectation suite by @BWMac in #136

Full Changelog: 0.4.0...0.4.1

0.4.0

What's Changed

• [IBCDPE-947] GX Validation Record Keeping by @BWMac in #135

Full Changelog: 0.3.0...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