Merge pull request #31 in DAT/cbioportal_external from develop to master* commit '75f1942eda58f475d15946b665d6641e116d9585':
Linting
VDB-730: Update tests to use stable_id column name
VDB-730: Bump the patch number
VDB-730: Use PyMySQL as dependency
VDB-730: Update to use prompt password with set command
VDB-730: Update logging logic + use stable_id column name
VDB-730: Switch to using SQL Alchemy to connect to cbioportal database
Merge pull request #30 in DAT/cbioportal_external from bug/mysqlcursor_encode to develop* commit 'bde700dd4c9bdd1b86bb3e3ef68c37fcf76b862b':
Linting
VDB-730: Update tests to use stable_id column name
VDB-730: Bump the patch number
VDB-730: Use PyMySQL as dependency
VDB-730: Update to use prompt password with set command
VDB-730: Update logging logic + use stable_id column name
VDB-730: Switch to using SQL Alchemy to connect to cbioportal database
Merge pull request #29 in DAT/cbioportal_external from develop to master* commit 'f3f3916b54dfabbf93e303dfbe4e10f5425a3c4a':
Linting
SYS-56279: Update comment
SYS-56279: Update tests
SYS-56279: Bump the minor version number
SYS-56279: Delete unused parameter
SYS-56279: Add validate_input_file method from formatter module
SYS-56279: Use named arguments + add log argument
SYS-56279: Move validate_input_file method to upload module + delete default log...
Merge pull request #28 in DAT/cbioportal_external from bug/update_formatter_logging to develop* commit 'a0e6c6420056db773ac1d0b6f102602b04371a46':
Linting
SYS-56279: Update comment
SYS-56279: Update tests
SYS-56279: Bump the minor version number
SYS-56279: Delete unused parameter
SYS-56279: Add validate_input_file method from formatter module
SYS-56279: Use named arguments + add log argument
SYS-56279: Move validate_input_file method to upload module + delete default log...
Merge pull request #27 in DAT/cbioportal_external from develop to master* commit '5594abccc2f3a2cc471b1ed002b7a5eeee62df29':
VDB-723: Bump the minor version number
VDB-723: Add instructions for setting keyring passwords to access vardb and gsc_cbioportal databases
Merge pull request #26 in DAT/cbioportal_external from feature/improve_readme to develop* commit '4e18b0e756aa343b5404d5acac3198b2b909c401':
VDB-723: Bump the minor version number
VDB-723: Add instructions for setting keyring passwords to access vardb and gsc_cbioportal databases
Merge pull request #25 in DAT/cbioportal_external from develop to master* commit 'fbc65fff5e5f225352de5f731db25c23c25e8f20':
Bump the patch number
Add descriptions for the input parameters and reload_studies file
Use pog_comparator_sampling view
Filter normal libraries based on tc flag
Improve Readme
Merge pull request #24 in DAT/cbioportal_external from feature/improve_readme to develop* commit '23a8611ea7cb278a30cd4df480e1056b62a6e522':
Bump the patch number
Add descriptions for the input parameters and reload_studies file
Use pog_comparator_sampling view
Filter normal libraries based on tc flag
Improve Readme
Merge pull request #23 in DAT/cbioportal_external from develop to master* commit '26e5b3ceb82fa16f60f111e8b92ca2433d711a63': (64 commits)
VDB-714: Update test to add log parameter
VDB-714: Add logging from the beginning to log database activities and errors
VDB-704: Add log directory as input argument to store the formatter logs + update tests
VDB-704: Add log directory as input argument to store the formatter logs + update tests
VDB-704: Place mariadb re...
Merge pull request #22 in DAT/cbioportal_external from feature/improve_import_process to develop* commit 'ea482dbe10825379134a663fea3666ff01a7804d': (64 commits)
VDB-714: Update test to add log parameter
VDB-714: Add logging from the beginning to log database activities and errors
VDB-704: Add log directory as input argument to store the formatter logs + update tests
VDB-704: Add log directory as input argument to store the formatter logs + update tests
VDB-704: Place mariadb re...
