databiosphere/data-explorer-indexers issues and pull requests

#163 - Update apiVersion for PodDisruptionBudget

Pull Request - State: closed - Opened by wnojopra over 1 year ago

#162 - Bump certifi from 2020.4.5.2 to 2022.12.7 in /bigquery

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#161 - Bump protobuf from 3.12.2 to 3.18.3 in /bigquery

Pull Request - State: open - Opened by dependabot[bot] almost 3 years ago
Labels: dependencies

#160 - Bump urllib3 from 1.25.9 to 1.26.5 in /bigquery

Pull Request - State: open - Opened by dependabot[bot] almost 3 years ago
Labels: dependencies

#159 - Bump urllib3 from 1.24.2 to 1.26.5 in /indexer_util

Pull Request - State: open - Opened by dependabot[bot] about 4 years ago
Labels: dependencies

#158 - PR to move our ECK changes to main-dev branch

Pull Request - State: open - Opened by wnojopra about 5 years ago

#157 - Run yapf with indent 2 on elasticsearch directory.

Pull Request - State: closed - Opened by mbookman about 5 years ago

#156 - Initial checkin of "es-config.py status" command.

Pull Request - State: closed - Opened by mbookman about 5 years ago

#155 - Enable private cluster with master authorized network by default.

Pull Request - State: closed - Opened by wnojopra about 5 years ago - 3 comments

#154 - Initial checkin of new elasticsearch deployment tools.

Pull Request - State: closed - Opened by mbookman about 5 years ago

#153 - Support 'columns_to_ignore', an optional list of BigQuery column name…

Pull Request - State: closed - Opened by wnojopra about 5 years ago

#152 - Update data explorer indexer to run on Python 3

Pull Request - State: closed - Opened by wnojopra almost 6 years ago - 2 comments

#151 - Update data explorer indexer to run on Python 3

Pull Request - State: closed - Opened by wnojopra almost 6 years ago - 1 comment

#150 - Bump urllib3 from 1.24.1 to 1.24.2 in /indexer_util

Pull Request - State: closed - Opened by dependabot[bot] almost 6 years ago
Labels: dependencies

#149 - Undo some of the changes for Baseline

Pull Request - State: closed - Opened by melissachang almost 6 years ago

#148 - Changed unknown to Unknown

Pull Request - State: closed - Opened by lgolowich almost 6 years ago

#147 - Expand README discussion of samples and time series

Pull Request - State: closed - Opened by melissachang almost 6 years ago

#146 - Changes needed for reindexing Baseline internal

Pull Request - State: closed - Opened by melissachang almost 6 years ago - 2 comments

#145 - Increase put_mapping timeout

Pull Request - State: closed - Opened by melissachang almost 6 years ago

#144 - Added support for unknown times.

Pull Request - State: closed - Opened by lgolowich almost 6 years ago

#143 - Removed participant and sample id columns from fields index

Pull Request - State: closed - Opened by lgolowich about 6 years ago

#142 - Added floating point support, updated configuration

Pull Request - State: closed - Opened by lgolowich about 6 years ago

#141 - Have setup-gcloud.sh work with JSON files with comments

Pull Request - State: closed - Opened by melissachang about 6 years ago

#140 - Added time series support

Pull Request - State: closed - Opened by lgolowich about 6 years ago

#139 - Document how to change user for local indexing

Pull Request - State: closed - Opened by melissachang about 6 years ago - 1 comment

#138 - Script for deleting oldest cluster

Pull Request - State: closed - Opened by wnojopra over 6 years ago

#137 - Create standalone script setup-gcloud.sh

Pull Request - State: closed - Opened by melissachang over 6 years ago

#136 - Minor script fixes - set project before listing clusters

Pull Request - State: closed - Opened by wnojopra over 6 years ago

#135 - Use simple analyzer on indexes.

Pull Request - State: closed - Opened by wnojopra over 6 years ago - 3 comments

#134 - Update scripts to reindex with no downtime

Pull Request - State: closed - Opened by wnojopra over 6 years ago - 1 comment

#133 - participant_id column should be case insensitive

Issue - State: closed - Opened by wnojopra over 6 years ago - 3 comments

#132 - Turn on autoupgrade for GKE cluster

Pull Request - State: closed - Opened by melissachang over 6 years ago

#131 - Use sample_id_column name from config instead of hard coded 'sample_id'

Pull Request - State: closed - Opened by wnojopra over 6 years ago

#130 - Willyn/bulk at end

Pull Request - State: closed - Opened by wnojopra over 6 years ago - 4 comments

#129 - Bold some lines in deployment scripts

Pull Request - State: closed - Opened by melissachang over 6 years ago

#128 - In README, change indexer role from BigQuery Job User to BigQuery Admin

Pull Request - State: closed - Opened by melissachang over 6 years ago

#127 - Performance improvement: Construct documents in memory before indexing

Issue - State: open - Opened by melissachang over 6 years ago - 5 comments

#126 - Add timestamp formatting strings for datetime fields

Pull Request - State: closed - Opened by wnojopra over 6 years ago

#125 - Move local-ui-index-gke instructions to deploy README

Pull Request - State: closed - Opened by melissachang over 6 years ago

#124 - Use PodDisruptionBudgets to prevent ES breaking after nodes are auto-upgraded

Pull Request - State: closed - Opened by melissachang over 6 years ago

#123 - Fix default number of master and data replicas

Pull Request - State: closed - Opened by melissachang over 6 years ago

#122 - Indexing fails on Baseline data due to Timestamp field

Issue - State: closed - Opened by wnojopra over 6 years ago

#121 - Reindex with zero downtime

Issue - State: closed - Opened by melissachang over 6 years ago - 6 comments

#120 - Allow customizing disk space for GKE deployment

Issue - State: closed - Opened by melissachang over 6 years ago - 2 comments

#119 - Minor changes to ES-from-GKE instructions

Pull Request - State: closed - Opened by melissachang over 6 years ago

#118 - Add instructions for having local UI read from ES on GKE

Pull Request - State: closed - Opened by melissachang over 6 years ago

#117 - Upgrade requests lib

Pull Request - State: closed - Opened by wnojopra over 6 years ago - 1 comment

#116 - Set ttl on table-export bucket

Issue - State: open - Opened by melissachang over 6 years ago

#115 - Index view

Pull Request - State: closed - Opened by wnojopra over 6 years ago

#114 - Kubernetes Deployment Optimization and Improvements

Pull Request - State: closed - Opened by bfcrampton over 6 years ago

#113 - Fix instructions for indexing large tables locally

Pull Request - State: closed - Opened by melissachang over 6 years ago

#112 - Add note about Compute SA to deploy readme

Pull Request - State: closed - Opened by melissachang over 6 years ago

#111 - Ignore .yaml-e files (mac)

Pull Request - State: closed - Opened by bfcrampton over 6 years ago

#110 - Add 'Set zone' step to Elasticsearch deployment

Pull Request - State: closed - Opened by melissachang over 6 years ago

#109 - Update to kubernetes API v1

Pull Request - State: closed - Opened by bfcrampton over 6 years ago - 1 comment

#108 - Add more documentation on fields index

Pull Request - State: closed - Opened by melissachang over 6 years ago

#107 - README tips for indexing large tables

Pull Request - State: closed - Opened by melissachang over 6 years ago

#106 - Minor README changes after deploying UKBB indexer

Pull Request - State: closed - Opened by melissachang over 6 years ago

#105 - Increase request timeout to 300s

Pull Request - State: closed - Opened by melissachang over 6 years ago

#104 - Fail script if command fails

Pull Request - State: closed - Opened by melissachang over 6 years ago

#103 - indexing doesn't work with repeated records

Issue - State: open - Opened by melissachang over 6 years ago

#102 - multi_match slow on GKE compared to local

Issue - State: closed - Opened by melissachang over 6 years ago - 1 comment

#101 - Add env for customizing ES heap size

Pull Request - State: closed - Opened by bfcrampton over 6 years ago

#100 - Fix creation of nested samples mappings

Pull Request - State: closed - Opened by bfcrampton over 6 years ago - 2 comments

#99 - Views no longer supported by the BigQuery indexer

Issue - State: closed - Opened by mbookman over 6 years ago - 6 comments

#98 - Update kubernetes configs to support indexing large datasets

Pull Request - State: closed - Opened by bfcrampton over 6 years ago

#97 - Use localhost over EXTERNAL_IP

Pull Request - State: closed - Opened by bfcrampton over 6 years ago

#96 - Update deployment docs after having deployed

Pull Request - State: closed - Opened by melissachang over 6 years ago

#95 - Only create samples export file if there are samples in dataset

Pull Request - State: closed - Opened by bfcrampton over 6 years ago - 2 comments

#94 - Support indexing very large BigQuery tables

Pull Request - State: closed - Opened by bfcrampton over 6 years ago

#93 - Use static mapping creation

Pull Request - State: closed - Opened by bfcrampton over 6 years ago - 1 comment

#92 - Preview: Indexer groupby

Pull Request - State: open - Opened by RoriCremer almost 7 years ago - 2 comments

#91 - Saturn -> Terra

Pull Request - State: closed - Opened by melissachang almost 7 years ago

#90 - Indexer performance for very large tables (> 2Gb)

Issue - State: closed - Opened by bfcrampton almost 7 years ago - 3 comments

#89 - Remove BILLING_PROJECT_ID flag

Pull Request - State: closed - Opened by melissachang almost 7 years ago - 1 comment

#88 - Add deploy.json to circle ci config

Pull Request - State: closed - Opened by malathi13 almost 7 years ago

#87 - Include the index name and the service account name as part of bucket

Pull Request - State: closed - Opened by malathi13 almost 7 years ago

#86 - Fix the bug in indexing views

Pull Request - State: closed - Opened by malathi13 almost 7 years ago

#85 - Elaborate on why we use scripts for samples tables

Pull Request - State: closed - Opened by melissachang almost 7 years ago

#84 - Wait before creating samples JSON export file

Pull Request - State: closed - Opened by bfcrampton almost 7 years ago

#83 - Add nested fields to the fields index

Pull Request - State: closed - Opened by malathi13 almost 7 years ago

#82 - Create nested mappings for sub nested schema

Pull Request - State: closed - Opened by malathi13 almost 7 years ago

#81 - Write samples JSON file to GCS on indexing

Pull Request - State: closed - Opened by bfcrampton almost 7 years ago

#80 - Migrate 1000 genomes table name

Pull Request - State: closed - Opened by bfcrampton almost 7 years ago

#79 - Clarify documentation about ID columns in BQ indexer.

Pull Request - State: closed - Opened by danxmoran almost 7 years ago

#78 - BQ indexer times out in requests to ES on dataset with many samples per participant

Issue - State: open - Opened by danxmoran almost 7 years ago - 20 comments

#77 - Start migration 1000 genomes dataset

Pull Request - State: closed - Opened by bfcrampton almost 7 years ago

#76 - Support . and : in project id

Pull Request - State: closed - Opened by melissachang almost 7 years ago

#75 - Add integration test golden files for fields and mappings

Pull Request - State: closed - Opened by bfcrampton almost 7 years ago

#74 - Add fastq to sample_file_columns

Pull Request - State: closed - Opened by melissachang almost 7 years ago

#73 - BQ indexer fails when "participant_id_column" points to a repeated field

Issue - State: closed - Opened by danxmoran almost 7 years ago - 8 comments

#72 - Trim 1000 genomes sample file columns

Pull Request - State: closed - Opened by bfcrampton almost 7 years ago

#71 - Update 1000 genomes dataset config

Pull Request - State: closed - Opened by bfcrampton almost 7 years ago - 2 comments

#70 - Document fields index in READMEs

Pull Request - State: closed - Opened by melissachang almost 7 years ago

#69 - Delete index at beginning of integration test instead of end

Pull Request - State: closed - Opened by melissachang almost 7 years ago

#68 - Add a prefix to sample facet fields

Pull Request - State: closed - Opened by malathi13 almost 7 years ago

#67 - Rename cols -> columns

Pull Request - State: closed - Opened by bfcrampton almost 7 years ago

#66 - Minor changes to BigQuery deploy README

Pull Request - State: closed - Opened by melissachang almost 7 years ago - 2 comments

#65 - Added a _fields index with a document per field.

Pull Request - State: closed - Opened by malathi13 almost 7 years ago

#64 - Add integration test for sample indexing

Pull Request - State: closed - Opened by bfcrampton almost 7 years ago - 1 comment

GitHub / databiosphere/data-explorer-indexers issues and pull requests