0.0.1

What's Changed

• Add monitor cron by @thomasyu888 in #2
• Add new users to be notified by @xindiguo in #3
• Add stats team to the list by @xindiguo in #4
• Add code to create BPC mappings by @thomasyu888 in #5
• Update clinical supp survival file by @thomasyu888 in #6
• Create separate survival treatment file by @thomasyu888 in #8
• Add other SP code by @thomasyu888 in #7
• Use unified mapping by @thomasyu888 in #10
• Make sure to exclude regimen drugs that contain the str investigational drug by @thomasyu888 in #11
• Add support for priority column for clinical files by @thomasyu888 in #12
• Add in retraction policy by @thomasyu888 in #13
• Update version of table to use by @thomasyu888 in #15
• Allow for this respository to be installed by @thomasyu888 in #17
• Update mapping version by @thomasyu888 in #16
• hardcode mapping for laterality by @thomasyu888 in #19
• regimen abbreviation formed from all words of a drug by @hhunterzinck in #22
• drug regimen abbreviations with ncit codes by @hhunterzinck in #24
• Support PANC cohort by @thomasyu888 in #21
• dockerize geniesp by @hhunterzinck in #25
• Back compatibility by @hhunterzinck in #26
• Run black ./geniesp to lint code by @thomasyu888 in #36
• Add in new package setup by @thomasyu888 in #35
• Add contribution guide by @thomasyu888 in #34
• Edit setup by @thomasyu888 in #39
• add bladder class by @hhunterzinck in #40
• validation script for bpc to cbio mapping file by @hhunterzinck in #33
• adapt new variable names and cohorts by @hhunterzinck in #43
• add functionality and checks to mapping file validation by @hhunterzinck in #46
• Remove null start dates by @thomasyu888 in #47
• fix panc files by @hhunterzinck in #50
• Add code of conduct by @thomasyu888 in #57
• Remove low-memory pandas warning by @thomasyu888 in #54
• Use pd.concat instead of dataframe.append by @thomasyu888 in #55
• update genomic data release file by @hhunterzinck in #58
• account for missing AGENT by @hhunterzinck in #60
• fix hack by @hhunterzinck in #62
• update mapping table by @hhunterzinck in #64
• Create metadata files by @thomasyu888 in #38
• Don't create folder if staging by @thomasyu888 in #56
• additional validation checks for bpc to cbio portal mapping file by @hhunterzinck in #66
• add troubleshooting guide first draft by @hhunterzinck in #68
• update derived variable name and other misc fixes by @hhunterzinck in #69
• update nsclc 2.0-public column header by @hhunterzinck in #71
• cohort generic doc links for meta study file and minor fixes by @hhunterzinck in #74
• fix inconsistencies between cBioPortal and clinical files by @hhunterzinck in #76
• update meta study desc by @hhunterzinck in #81
• remove data catalog dependency by @hhunterzinck in #82
• update cbio panc column name by @hhunterzinck in #91
• modify timeline dx generation by @hhunterzinck in #93
• sor col name reference by @hhunterzinck in #97
• rad therapy dataset name and mapping table updates by @hhunterzinck in #99
• remove gh-action by @thomasyu888 in #100
• [IBCDPE-261] Make sure blank values are filled with NA by @thomasyu888 in #102
• Update main genie release used to 12.0-public by @thomasyu888 in #103
• Change AGE_AT_SEQUENCING to integer by @thomasyu888 in #104
• [GEN-90] Add nextflow wf by @thomasyu888 in #105
• [GEN-261] retract samples from clinical survival treatment file by @thomasyu888 in #106
• [GEN-264] Rename the seg file to be more in line with other cbioportal files by @thomasyu888 in #107
• [GEN-286] Make sure meta seg file is named correctly by @thomasyu888 in #108
• [GEN-94] Add initial commit to get start date by @thomasyu888 in #109
• [GEN-335] sequence file drop duplicates by @thomasyu888 in #110
• [GEN-384] Include data sv in bpc releases by @thomasyu888 in #111
• function per file by @hhunterzinck in #95
• [GEN-507] Add in performance status variable by @thomasyu888 in #112
• [GEN-460] Staging runs should upload to a different Synapse folder by @thomasyu888 in #113
• [GEN-628] Update PFS status variables by @thomasyu888 in #114
• [GEN-746] timeline performance status RESULT column must be integers by @thomasyu888 in #115
• [GEN-778] Add timeline treatment to NSCLC by @thomasyu888 in #117
• [GEN-766, GEN-870] Retract using release files and use consortium release by @thomasyu888 in #116
• Update README.md by @Chelsea-Na in #120
• [GEN-889] Updating validate_map.py by @Chelsea-Na in #122
• [GEN-848, GEN-860] Add in ECOG values by @thomasyu888 in #119
• [GEN-950] Support NA values in AGE_AT_SEQUENCING by @thomasyu888 in #123
• [GEN-949] Add in retraction table synids by @thomasyu888 in #124
• [GEN-954] Remove GRS by @thomasyu888 in #125
• [GEN-1004] Update bpc_redcap_export_mapping.py by @Chelsea-Na in #127
• [GEN-1083] use 15.4-release by @thomasyu888 in #129
• [GEN-1062] Use GRS instead of data dictionary for drug mapping by @thomasyu888 in #128
• Subset genomic regions file and upload to synapse by @thomasyu888 in #130
• Remove hard coded in CRC for treatment Rad by @thomasyu888 in #131
• [GEN-1200] Use "cohort_internal" by @thomasyu888 in #132
• [GEN-1202] Update bpc_config.py by @Chelsea-Na in #133
• Update bpc_redcap_export_mapping.py by @Chelsea-Na in #135
• [GEN-1222] Fix retraction and add RT back into the mix for NSCLC by @thomasyu888 in #136
• GEN-1220 mapping file validation error by @xindiguo in #139
• [GEN-1273, GEN-1275] Update PFS to different value by @thomasyu888 in #140
• [GEN-1174] Don't use temporary retraction table by @thomasyu888 in #137

New Contributors

• @thomasyu888 made their first contribution in #2
• @xindiguo made their first contribution in #3
• @hhunterzinck made their first contribution in #22
• @Chelsea-Na made their first contribution in #120

Full Changelog: https://github.com/Sage-Bionetworks/GENIE-Sponsored-Projects/commits/0.0.1