refinery-platform/refinery-platform issues and pull requests

#3536 - Bump debug, grunt-contrib-watch and phantomjs-prebuilt in /refinery/ui

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

#3535 - Bump qs, grunt-contrib-watch, body-parser and phantomjs-prebuilt in /refinery/ui

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

#3534 - Bump certifi from 2018.11.29 to 2022.12.7

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

#3533 - Bump flower from 0.9.1 to 1.2.0

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

#3532 - Bump angular from 1.5.9 to 1.8.3 in /refinery/ui

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

#3531 - Bump codecov from 2.0.11 to 2.0.16

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

#3530 - Bump grunt from 1.0.1 to 1.5.3 in /refinery/ui

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

#3529 - Bump grunt from 1.0.1 to 1.5.2 in /refinery/ui

Pull Request - State: closed - Opened by dependabot[bot] almost 3 years ago - 1 comment
Labels: dependencies, javascript

#3528 - Bump paramiko from 2.5.0 to 2.10.1 in /deployment

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

#3527 - Bump karma from 4.3.0 to 6.3.16 in /refinery/ui

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

#3526 - Bump follow-redirects from 1.9.0 to 1.14.8 in /refinery/ui

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

#3525 - Bump karma from 4.3.0 to 6.3.14 in /refinery/ui

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago - 1 comment
Labels: dependencies, javascript

#3524 - Bump follow-redirects from 1.9.0 to 1.14.7 in /refinery/ui

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago - 1 comment
Labels: dependencies, javascript

#3523 - Bump celery from 3.1.26.post2 to 5.2.2

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

#3522 - Bump aws-sdk from 2.49.0 to 2.814.0 in /refinery/ui

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

#3521 - Bump django from 1.8.18 to 2.2.24

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

#3520 - Bump glob-parent from 5.1.0 to 5.1.2 in /refinery/ui

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

#3519 - Bump chart.js from 2.8.0 to 2.9.4 in /refinery/ui

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

#3518 - Bump hosted-git-info from 2.1.5 to 2.8.9 in /refinery/ui

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

#3517 - Bump lodash from 4.17.15 to 4.17.21 in /refinery/ui

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

#3516 - Bump grunt from 1.0.1 to 1.3.0 in /refinery/ui

Pull Request - State: closed - Opened by dependabot[bot] almost 4 years ago - 1 comment
Labels: dependencies, javascript

#3515 - Bump django-debug-toolbar from 1.9.1 to 1.11.1

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

#3514 - Bump pygments from 1.6rc1 to 2.7.4

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

#3513 - Bump djangorestframework from 3.3.3 to 3.11.2

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

#3512 - Bump ini from 1.3.4 to 1.3.8 in /refinery/ui

Pull Request - State: open - Opened by dependabot[bot] about 4 years ago - 1 comment
Labels: dependencies, javascript

#3511 - Bump cryptography from 2.5 to 3.2

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

#3510 - Bump http-proxy from 1.18.0 to 1.18.1 in /refinery/ui

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

#3509 - Bump lodash from 4.17.15 to 4.17.19 in /refinery/ui

Pull Request - State: closed - Opened by dependabot[bot] over 4 years ago - 1 comment
Labels: dependencies, javascript

#3508 - Bump angular from 1.5.9 to 1.8.0 in /refinery/ui

Pull Request - State: closed - Opened by dependabot[bot] over 4 years ago - 1 comment
Labels: dependencies, javascript

#3507 - Bump websocket-extensions from 0.1.1 to 0.1.4 in /refinery/ui

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

#3506 - Bump django from 1.8.18 to 1.11.29

Pull Request - State: closed - Opened by dependabot[bot] over 4 years ago - 1 comment
Labels: dependencies, python

#3505 - Bump jquery from 2.1.1 to 3.5.0 in /refinery/ui

Pull Request - State: open - Opened by dependabot[bot] almost 5 years ago
Labels: dependencies, javascript

#3504 - Bump django from 1.8.18 to 1.11.28

Pull Request - State: closed - Opened by dependabot[bot] about 5 years ago - 1 comment
Labels: dependencies, python

#3503 - Control NAT gateway deployment

Pull Request - State: open - Opened by hackdna about 5 years ago - 1 comment
Labels: deployment, feature, aws, fix-2x-small

#3502 - Hackdna/python3

Pull Request - State: closed - Opened by hackdna about 5 years ago - 1 comment
Labels: deployment, technical debt, server, fix-4x-medium

#3501 - Bump sshpk from 1.9.2 to 1.16.1 in /refinery/ui

Pull Request - State: open - Opened by dependabot[bot] about 5 years ago - 1 comment
Labels: dependencies, javascript

#3500 - Bump eslint from 2.4.0 to 4.18.2 in /refinery/ui

Pull Request - State: open - Opened by dependabot[bot] about 5 years ago - 1 comment
Labels: dependencies, javascript

#3499 - Bump is-my-json-valid from 2.13.1 to 2.20.0 in /refinery/ui

Pull Request - State: open - Opened by dependabot[bot] about 5 years ago
Labels: dependencies, javascript

#3498 - Bump stringstream from 0.0.5 to 0.0.6 in /refinery/ui

Pull Request - State: open - Opened by dependabot[bot] about 5 years ago - 1 comment
Labels: dependencies, javascript

#3497 - Refactor Celery

Pull Request - State: open - Opened by ilan-gold about 5 years ago - 1 comment

#3496 - Bump angular from 1.5.9 to 1.7.9 in /refinery/ui

Pull Request - State: closed - Opened by dependabot[bot] about 5 years ago - 1 comment
Labels: dependencies, javascript

#3495 - Add NPM package-lock.json to version control

Pull Request - State: closed - Opened by hackdna about 5 years ago - 1 comment
Labels: enhancement, ui, deployment, client, fix-1x-quick

#3494 - Ilan gold/igv bug fix

Pull Request - State: closed - Opened by ilan-gold over 5 years ago - 1 comment

#3493 - remove usage of chain and do FileImportTask as post-process step

Pull Request - State: closed - Opened by ilan-gold over 5 years ago - 11 comments

#3492 - remove usage of chain and do FileImportTask as post-process step

Pull Request - State: closed - Opened by ilan-gold over 5 years ago - 1 comment

#3491 - IGV Bug Fix

Pull Request - State: closed - Opened by ilan-gold over 5 years ago - 2 comments

#3490 - Celery Chain Does Not Fail

Issue - State: closed - Opened by ilan-gold over 5 years ago - 2 comments

#3489 - upgrade postgresql version

Pull Request - State: closed - Opened by ilan-gold over 5 years ago - 1 comment

#3488 - Adding some tests and better handling for non-ascii throughout

Pull Request - State: closed - Opened by ilan-gold over 5 years ago - 1 comment

#3487 - Fixing the Provenance Graph

Pull Request - State: closed - Opened by ilan-gold over 5 years ago - 1 comment

#3486 - Ilan gold/user registration bug

Pull Request - State: closed - Opened by ilan-gold over 5 years ago - 2 comments

#3485 - Fix Excessive File Downloading

Pull Request - State: closed - Opened by ilan-gold over 5 years ago - 1 comment

#3484 - Fix .bam file handling for visualizations

Pull Request - State: closed - Opened by ilan-gold over 5 years ago - 2 comments

#3483 - Set Up CloudWatch Alarms for CPU Utilization

Pull Request - State: closed - Opened by ilan-gold over 5 years ago - 2 comments

#3482 - Bump jquery from 2.1.1 to 3.4.1 in /refinery/ui

Pull Request - State: closed - Opened by dependabot[bot] over 5 years ago - 2 comments
Labels: dependencies, javascript

#3481 - Bump angular from 1.5.9 to 1.7.8 in /refinery/ui

Pull Request - State: closed - Opened by dependabot[bot] over 5 years ago - 2 comments
Labels: dependencies, javascript

#3480 - Bump flower from 0.9.1 to 0.9.2

Pull Request - State: closed - Opened by dependabot[bot] over 5 years ago - 2 comments
Labels: dependencies, python

#3479 - Bump ecdsa from 0.11 to 0.13.3 in /deployment

Pull Request - State: open - Opened by dependabot[bot] over 5 years ago - 1 comment
Labels: dependencies, python

#3478 - Bump django from 1.8.18 to 1.11.23

Pull Request - State: closed - Opened by dependabot[bot] over 5 years ago - 1 comment
Labels: dependencies, python

#3477 - Bump djangorestframework from 3.3.3 to 3.9.1

Pull Request - State: closed - Opened by dependabot[bot] over 5 years ago - 1 comment
Labels: dependencies, python

#3476 - Upgrade to Python 3.6+

Issue - State: open - Opened by hackdna over 5 years ago
Labels: deployment, security, technical debt, server

#3475 - Fix Dict/Unicode bug

Pull Request - State: closed - Opened by ilan-gold over 5 years ago - 2 comments

#3474 - Update to Python3.5

Pull Request - State: closed - Opened by ilan-gold over 5 years ago - 1 comment

#3473 - Refactor Celery and Analysis Handling

Issue - State: open - Opened by ilan-gold over 5 years ago
Labels: celery, technical debt

#3472 - Update AWS CLI to the latest version

Pull Request - State: closed - Opened by hackdna over 5 years ago - 1 comment
Labels: deployment, technical debt, fix-1x-quick, aws

#3471 - Rename Files in Flight

Pull Request - State: closed - Opened by ilan-gold over 5 years ago - 1 comment

#3470 - Hide non-active members in groups.

Pull Request - State: closed - Opened by jkmarx over 5 years ago - 1 comment

#3467 - File-Browser: Select All Bug

Issue - State: closed - Opened by jkmarx over 5 years ago
Labels: bug, ui, dataset, important

#3465 - Bam File IGV Not Working

Issue - State: closed - Opened by ilan-gold over 5 years ago - 3 comments
Labels: celery, server

#3464 - Python2 Package Updates/Changes

Pull Request - State: closed - Opened by ilan-gold over 5 years ago - 1 comment

#3461 - Restructure Analysis Metadata Fetching for Celery

Pull Request - State: closed - Opened by ilan-gold over 5 years ago - 1 comment

#3451 - Update mockcache

Issue - State: open - Opened by ilan-gold over 5 years ago - 4 comments
Labels: deployment, technical debt, server

#3436 - Readme update

Pull Request - State: open - Opened by ilan-gold over 5 years ago

#3435 - Analysis import fails due to celery SoftTimeLimitExceeded

Issue - State: closed - Opened by gmnelson over 5 years ago - 6 comments
Labels: galaxy, bug, celery

#3388 - Botocore incompatability with v1.12.98

Issue - State: closed - Opened by jkmarx over 5 years ago
Labels: deployment, technical debt, aws

#3319 - Switch to the new Celery API

Issue - State: open - Opened by hackdna almost 6 years ago
Labels: celery, technical debt, server

#3305 - Upgrade to Celery 4 or higher

Issue - State: open - Opened by hackdna almost 6 years ago - 1 comment
Labels: celery, technical debt, server

#3104 - Clock skew on EC2 instance

Issue - State: closed - Opened by hackdna over 6 years ago - 2 comments
Labels: bug, deployment, server, aws

#2995 - Update AngularJS to v1.7.x

Issue - State: open - Opened by hackdna over 6 years ago - 1 comment
Labels: ui, deployment, security, technical debt, client

#2989 - ProtocolError in _proxy_view

Issue - State: open - Opened by hackdna over 6 years ago - 1 comment
Labels: bug, visualization, server, tools, docker

#2965 - CPU utilization continuously high

Issue - State: closed - Opened by hackdna over 6 years ago - 7 comments
Labels: bug, important, server, performance, aws

#2917 - Certain user accounts fail to activate

Issue - State: closed - Opened by hackdna over 6 years ago - 2 comments
Labels: accounts, core, bug, important, server, HSCI requested

#2718 - Rewrite generate_bam_index()

Issue - State: closed - Opened by hackdna almost 7 years ago
Labels: bug, files, technical debt, important, server, cloud

#2713 - Avoid generating BAM index file under FILE_STORE_BASE_DIR tree

Issue - State: closed - Opened by hackdna almost 7 years ago - 2 comments
Labels: bug, files, important, server, cloud, HSCI requested

#2642 - Repeated identical requests to Galaxy API

Issue - State: closed - Opened by hackdna almost 7 years ago - 7 comments
Labels: analysis, galaxy, bug, server, performance

#2619 - Upgrade to Python 3.x

Issue - State: closed - Opened by hackdna almost 7 years ago - 3 comments
Labels: deployment, technical debt, server

#2616 - Upgrade to Ubuntu 18.04 LTS

Issue - State: open - Opened by hackdna almost 7 years ago - 2 comments
Labels: deployment, security, technical debt, server, cloud, travis-ci, fix-8x-large

#2572 - Django Upgrade to 1.11

Issue - State: open - Opened by jkmarx about 7 years ago
Labels: deployment, security, technical debt, important, server

#2519 - "Import into own space" should only be available for ISAtabs

Issue - State: open - Opened by mccalluc about 7 years ago - 4 comments
Labels: bug, ui, files

#2501 - Provenance Graph fails to load on some DataSets

Issue - State: closed - Opened by mccalluc about 7 years ago - 12 comments
Labels: bug, ui, provenance

#2498 - Commandline download-all doesn't actually download everything

Issue - State: open - Opened by mccalluc about 7 years ago - 1 comment
Labels: bug, feature

#2416 - Celery RuntimeWarning E_WOULDBLOCK

Issue - State: open - Opened by hackdna about 7 years ago
Labels: analysis, bug, celery, important, server

#2277 - "Exponential explosion" when trying to upload 2 line CSV

Issue - State: open - Opened by mccalluc over 7 years ago - 1 comment
Labels: bug, dataset, metadata, important, import

#2013 - /files_download -> /files?download=csv

Issue - State: open - Opened by mccalluc over 7 years ago
Labels: feature

#1966 - user/files: links to data_sets should highlight the file we came from

Issue - State: open - Opened by mccalluc over 7 years ago - 1 comment
Labels: feature

#1848 - Data-Set 2 Node Selection Popover

Issue - State: open - Opened by jkmarx over 7 years ago - 9 comments
Labels: enhancement, workflow, ui, dataset, files

#1755 - EBS snapshots are not tagged

Issue - State: closed - Opened by drj11 over 7 years ago - 1 comment
Labels: cloud

#1377 - Be able to save the state of a visualization tool?

Issue - State: open - Opened by scottx611x over 8 years ago - 7 comments
Labels: visualization, question

#1348 - Define a model to capture genome information

Issue - State: open - Opened by ngehlenborg over 8 years ago - 2 comments
Labels: database, visualization, api, feature, server

#1157 - Correct support for Django ADMINS setting

Issue - State: open - Opened by scottx611x over 8 years ago - 3 comments
Labels: bug, deployment, technical debt

GitHub / refinery-platform/refinery-platform issues and pull requests