Data-sharing Applications Team
  1. Data-sharing Applications Team

vardb_etl_anonymize

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  1. Data-sharing Applications Team
  2. vardb_etl_anonymize

Commits

AuthorCommitMessageCommit dateIssues
Caralyn ReisleCaralyn Reisle
9c0a1f5ac2cMMerge pull request #7 in DAT/vardb_etl_anonymize from feature/VDB-727-transfer-crons to master* commit '0325960a8ef750cdbe620b082cb2a05e52ba4b79': Add version to keyring install Update readme instructionsVDB-727
Caralyn ReisleCaralyn Reisle
0325960a8efAdd version to keyring install
Caralyn ReisleCaralyn Reisle
0b42e628133Update readme instructions
Darryl D'SouzaDarryl D'Souza
a8a1c311800MMerge pull request #6 in DAT/vardb_etl_anonymize from develop to master* commit 'b9f3a42d408eb58cd70e6f224885b6f0a67b7bb7': (37 commits) Linting Add setup.cfg to repo for ignoring some of the flake8 erros VDB-520: Add flake8 and black to list of dependencies + linting Update .gitignore VDB-520: Preserve module related arguments within it VDB-520: Replace vdb with dat VDB-520: Replace vdb with dat VDB-520: Update comment to add gcc path VDB-520: ...VDB-520
Darryl D'SouzaDarryl D'Souza
b9f3a42d408MMerge pull request #5 in DAT/vardb_etl_anonymize from feature/tumour_char_bam_cron to develop* commit 'd5eac90ef7a48fdb576eb7df337cd91c05e88f79': (37 commits) Linting Add setup.cfg to repo for ignoring some of the flake8 erros VDB-520: Add flake8 and black to list of dependencies + linting Update .gitignore VDB-520: Preserve module related arguments within it VDB-520: Replace vdb with dat VDB-520: Replace vdb with dat VDB-520: Update comment to add gcc path VDB-520: ...VDB-520
Darryl D'SouzaDarryl D'Souza
d5eac90ef7aLinting
Darryl D'SouzaDarryl D'Souza
dedd97cebcfAdd setup.cfg to repo for ignoring some of the flake8 erros
Darryl D'SouzaDarryl D'Souza
be504f39d6dVDB-520: Add flake8 and black to list of dependencies + lintingVDB-520
Darryl D'SouzaDarryl D'Souza
395b31629f4Update .gitignore
Darryl D'SouzaDarryl D'Souza
7d7587f38a7VDB-520: Preserve module related arguments within itVDB-520
Darryl D'SouzaDarryl D'Souza
85a66540857VDB-520: Replace vdb with datVDB-520
Darryl D'SouzaDarryl D'Souza
9ace03e247bVDB-520: Replace vdb with datVDB-520
Darryl D'SouzaDarryl D'Souza
cc3c71bb888VDB-520: Update comment to add gcc pathVDB-520
Darryl D'SouzaDarryl D'Souza
0581659488bVDB-520: Delete redundant comments matching variable namesVDB-520
Darryl D'SouzaDarryl D'Souza
68e2527353eVDB-520: Use the arguments module to access the argumentsVDB-520
Darryl D'SouzaDarryl D'Souza
84ccc38edc9VDB-520: Add module to store the argumentsVDB-520
Darryl D'SouzaDarryl D'Souza
35648eae64aVDB-520: Add instructions to ssh to the hadoop server + adding the gcc path to the environment PATH variableVDB-520
Darryl D'SouzaDarryl D'Souza
dac436c32cfVDB-520: Use relative importsVDB-520
Darryl D'SouzaDarryl D'Souza
b95a7987fe5VDB-520: Use global variables for wolverine_vardb parameters and update the testsVDB-520
Darryl D'SouzaDarryl D'Souza
8537380552cVDB-520: Call the methods to initialize bioapps and vardb respectivelyVDB-520
Darryl D'SouzaDarryl D'Souza
b85ba8acccaVDB-520: Call the methods to initialize and connect to vardbVDB-520
Darryl D'SouzaDarryl D'Souza
c35b62057c4VDB-520: Club the separate classes for BioApps and vardb into a single class.Initalize and connect the database object using two separate functionsVDB-520
Darryl D'SouzaDarryl D'Souza
b22d616f441VDB-520: Group the common hadoop and vardb arguments into functionsVDB-520
Darryl D'SouzaDarryl D'Souza
1c026ecd7bcVDB-520: Use a single try-finally clause with appropriate checksVDB-520
Darryl D'SouzaDarryl D'Souza
f7d92a22e78VDB-520: Use single letter switches and expand a few long names in argumentsVDB-520
Darryl D'SouzaDarryl D'Souza
8b8d0bade30VDB-520: Add buildout endpoint for tumour_char_bamsVDB-520
Darryl D'SouzaDarryl D'Souza
20fa9f762eaVDB-520: Add example to update tumour_char_bams table in vardbVDB-520
Darryl D'SouzaDarryl D'Souza
f9aba33c253VDB-520: Update argument parser switches to use single letters.Use variant database name in long arguments.VDB-520
Darryl D'SouzaDarryl D'Souza
d9f1803e2d5VDB-520: Rename solexa to bioappsVDB-520
Darryl D'SouzaDarryl D'Souza
c98e8427979VDB-520: Add version numbers to dependenciesVDB-520
Darryl D'SouzaDarryl D'Souza
ea613448608VDB-520: Update instruction to set password for access to wolverine_vardb databaseVDB-520
Darryl D'SouzaDarryl D'Souza
63b06940138VDB-520: Add instructions to set password for access to vardb and solexa databasesVDB-520
Darryl D'SouzaDarryl D'Souza
eb70671b12fVDB-520: Update commentVDB-520
Darryl D'SouzaDarryl D'Souza
748d927c96eVDB-520: Add password requirement to connect to solexa databaseVDB-520
Darryl D'SouzaDarryl D'Souza
f5f13332675VDB-520: Delete sqlalchemy as a requirement.Bump the minor version number.VDB-520
Darryl D'SouzaDarryl D'Souza
008fe4ce0afVDB-520: Update calls to database module classes and methodsVDB-520
Darryl D'SouzaDarryl D'Souza
36dbaa2bbebVDB-520: Validation for updating tumour_char_bams tableVDB-520
Darryl D'SouzaDarryl D'Souza
cfdb686e8b4VDB-520: Sample input test data file for validating tumour_char_bams table updateVDB-520
Darryl D'SouzaDarryl D'Souza
1fddaa59554VDB-520: Add module to update tumour_char_bams table in vardbVDB-520
Darryl D'SouzaDarryl D'Souza
6ee0f8cd9b7VDB-520: Update the calls to the database module classes and methodsVDB-520
Darryl D'SouzaDarryl D'Souza
fb284eb8dbdVDB-520: Add queries for tumour_char_bamsVDB-520
Darryl D'SouzaDarryl D'Souza
b7afffdcb90VDB-520: Refactor the module to use psycopg2 instead of sql alchemyVDB-520
Darryl D'SouzaDarryl D'Souza
8966f619e81MMerge pull request #4 in VDB/vardb_etl_anonymize from develop to master* commit '6c3ed4ef4729e65080aa933c48af0175449649b3': VDB-547: Bump the patch number VDB-547: Do not catch the exception and let the stack trace be printed out VDB-547: Print out a success message on completion VDB-547: Query to truncate the existing anonymize_patient_id table and reload the new dataVDB-547
Darryl D'SouzaDarryl D'Souza
6c3ed4ef472VDB-547: Bump the patch numberVDB-547
Darryl D'SouzaDarryl D'Souza
91e2d0c0452MMerge pull request #3 in VDB/vardb_etl_anonymize from feature/truncate_query to develop* commit '9b11dcf3703e77bc15a93c2fb41fa3a1af454110': VDB-547: Do not catch the exception and let the stack trace be printed out VDB-547: Print out a success message on completion VDB-547: Query to truncate the existing anonymize_patient_id table and reload the new dataVDB-547
Darryl D'SouzaDarryl D'Souza
9b11dcf3703VDB-547: Do not catch the exception and let the stack trace be printed outVDB-547
Darryl D'SouzaDarryl D'Souza
cd3abb6e53eVDB-547: Print out a success message on completionVDB-547
Darryl D'SouzaDarryl D'Souza
0a13ecf157cVDB-547: Query to truncate the existing anonymize_patient_id table and reload the new dataVDB-547
Darryl D'SouzaDarryl D'Souza
3e2f502b35eMMerge pull request #2 in VDB/vardb_etl_anonymize from develop to master* commit '57722e67e462a9827a84d6a5f8107becac5a0a47': (28 commits) VDB-519: Update the Major version number VDB-519: Add quotes around username VDB-519: Update instructions to add keyring password VDB-519: Add instructions to add password to keyring for db access VDB-519: Add instructions to add db access password to keyring VDB-519: Delete the instruction to install the test package...VDB-519
Darryl D'SouzaDarryl D'Souza
57722e67e46VDB-519: Update the Major version numberVDB-519