Sage-Bionetworks/Genie

Issues

• Abstract clinical validation functions

  #305 opened 4 years ago
  1

• Support pre-redacted values in YEAR columns

  #304 opened 5 years ago
  0

• Remove test parameter from database_to_staging and consortium_to_public

  #302 opened 2 years ago
  0

• maf files with too many column headers don't fail when read in

  #298 opened 5 years ago
  0

• Remap capitalized MAF headers into standard MAF headers

  #296 opened 5 years ago
  1

• Document if test is an integration test

  #295 opened 2 years ago
  0

• PHI cutoff should be greater or equal to 90 years in days

  #283 opened 5 years ago
  1

• R sweave requires texlive

  #280 opened 5 years ago
  0

• Processing error due to empty clinical file list

  #278 opened 5 years ago
  0

• Put write_invalid_reasons into main

  #277 opened 4 years ago
  0

• Check for empty rows in MAF file....

  #276 opened 5 years ago
  0

• Fix createmafdb

  #274 opened 5 years ago
  0

• Allow for `format_registry` to be passed in as an argument.

  #271 opened 4 years ago
  0

• Pass in list of interval columns to redact values

  #268 opened 5 years ago
  0

• Pass in database mapping synid for dashboardTemplate.Rmd

  #267 opened 4 years ago
  0

• Add in SEQ_PIPELINE

  #262 opened 5 years ago
  1

• Don't use argparse for R scripts, as that uses python

  #261 opened 5 years ago
  1

• Fix dashboard_markdown_template

  #258 opened 5 years ago
  1

• Pass in entity to processing

  #245 opened 4 years ago
  1

• --filetype flag isn't working

  #241 opened 5 years ago
  0

• tests shouldn't use specific genie classes

  #225 opened 4 years ago
  1

• pandas >= 0.23.0 required

  #215 opened 5 years ago
  1

• processing kwargs need to be linted

  #205 opened 4 years ago
  1

• Make __main__ consist of all the command line functions

  #204 opened 4 years ago
  1

• Use synapse to download exon / gene gtf

  #201 opened 3 years ago
  1

• store file type in validation status table

  #197 opened 5 years ago
  1

• use file type, not file name extension, if filtering of files is needed

  #196 opened 5 years ago
  1

• Test AWS infrastructure with develop

  #190 opened 5 years ago
  1

• Add tests to refactored database to staging

  #189 opened 4 years ago
  0

• example_file_format.validateFilename should be something like example_file_format.validate_file_type

  #185 opened 4 years ago
  1

• cna does syn.store, blocking removal of newPath

  #179 opened 4 years ago
  4

• Should processing in each file format include uploading to synapse?

  #152 opened 4 years ago
  0

• Tests are not all unit tests

  #148 opened 5 years ago
  1

• Move away from dict registry of classes

  #140 opened 5 years ago
  1

• get all entity information in rename_file

  #135 opened 5 years ago
  3

• Explore python data.tables

  #134 opened 5 years ago
  0

• Use pandas.dataframe.query feature

  #132 opened 5 years ago
  1

• raw_input not part of python 3

  #125 opened 6 years ago
  0

• define structure for 'fileinfo' rows

  #124 opened 5 years ago
  1

• update docstring for input_to_database._check_valid

  #123 opened 6 years ago
  1

• use same order to return (message, valid) from validate in other functions

  #122 opened 6 years ago
  1

• Split create_new_maf_db function into smaller functions

  #121 opened 4 years ago
  1

• Use thread argparse in input_to_database

  #119 opened 3 years ago
  1

• PROCESS_FILES said to be in a place where it isn't

  #117 opened 6 years ago
  1

• Turn camel case -> underscores

  #115 opened 5 years ago
  0

• test aws infrastructure with test_input_to_db branch

  #114 opened 5 years ago
  0

• Use separate loggers for different modules

  #109 opened 5 years ago
  0

• do not suggest saving username and password to bashrc

  #108 opened 6 years ago
  0

• Use different sentinel than 'None' to do something different with oncotree

  #107 opened 2 years ago
  0

• Instantiate classes

  #106 opened 5 years ago
  2