Skip to content

Releases: refinery-platform/refinery-platform

Version 1.7.2

19 Nov 16:49
@ilan-gold ilan-gold
v1.7.2
dd4287c
Compare
Choose a tag to compare
Version 1.7.2 Latest
Latest
  • Resolve Analysis import fail due to celery SoftTimeLimitExceeded
  • Fix auxiliary file generation allowing correct importing as well as exporting for viz
  • Fix several Provenance visualization graph bugs
  • Begin refactor of tasks

Command to be run on deployment:
./manage.py load_tools --visualizations igv --force

Assets 2

Version 1.7.1

21 Oct 20:23
@ilan-gold ilan-gold
v1.7.1
5a4630b
Compare
Choose a tag to compare
Version 1.7.1

Summary of changes:

  • Compliance with WCAG 2.1 Level AA
  • A select-all feature for the file browser
  • Dependency upgrades
  • Beginning the transition to Python3 by updating bad Python2 code/packages

v1.7.1 (2019-10-21)

Full Changelog

Implemented enhancements:

  • Enable compliance with WCAG 2.1 Level AA #3429
  • FIle Browser - Fix Padding Input Group List #3423
  • No easy way to add lots of files to a visualisation tool #3268
  • Import - Check Data File Enhancement #3236
  • Site_profiles API returns HTTP 404 #3203
  • Update Site Profiles API #3446 (ilan-gold)
  • Fail fast on Travis when running Django tests #3428 (hackdna)

Fixed bugs:

  • 500 Error UserDoesNotExist #3463

Closed issues:

  • Pass in Context for ToolSerializer #3455
  • Remove djangular #3452
  • data_set_manager has test with non-determinstic behavior #3444
  • Update jquery-fileupload library #3420
  • User/files Enhance Filter #3119
  • Update Tutorial (intro.js) #3109

Merged pull requests:

Assets 2

Version 1.7.0

19 Jul 18:25
@jkmarx jkmarx
v1.7.0
3abb3aa
Compare
Choose a tag to compare
Version 1.7.0

1.7.0 (2019-07-15)

Full Changelog

Implemented enhancements:

  • New NavBar Configuration #3113
  • Update Icons #2726
  • Re-index only data sets that are not yet public in make_data_sets_public command #621
  • Add extra details on dashboard. #3399 (jkmarx)

Fixed bugs:

  • Fix Cancel button functionality on FB Details tab #3415
  • Applying site updates using Fabric is broken #3403
  • Solr service fails to start in Vagrant during second boot #3400
  • UnicodeEncodeError in events API #3386
  • Analyses Show Different Names Depending on Location #3379
  • ImproperlyConfigured error in workflows API #3352
  • Unwanted Download Facet (File Browser) #3277
  • Collaboration - Send Invite Bug #1655
  • Suggested edits for currently implemented tutorials #1417
  • Fix data set edit bug. #3417 (jkmarx)
  • Display the tools display name for analysis model. #3401 (jkmarx)
  • Limit workflow api urls. #3398 (jkmarx)
  • Hide attributes related to downloading files. #3382 (jkmarx)

Closed issues:

  • CryptographyDeprecationWarning when running Fabric #3404
  • Missing Dependency - linux-image-extra-3.13.0-170-generic #3387
  • Fix names of REST API view classes #3345
  • Fixture default-pages.json is unused #3333
  • Upgrade to Ubuntu 16.04 LTS #3118
  • Upgrade Puppet to version 4.10 or greater #3096
  • Make it less likely that users invite people to the wrong group #2906
  • Spurious log message when using manage.py #2810
  • Replace puppetlabs-docker_platform with puppetlabs-docker #2727
  • Remove copy_dataset() task #2662
  • Confusing error page if invitation token reused #1898
  • Replace puppetlabs-rabbitmq module with puppet-rabbitmq #1185
  • introduce requireJS to handle JS libraries and scripts #342

Merged pull requests:

  • Fix UUIDField migrations in AnalysisStatus to allow upgrading django_extensions #3419 (hackdna)
  • Update UserProfile.uuid migrations to allow upgrading django_extensions #3418 (hackdna)
  • Downgrade django-storages #3414 (hackdna)
  • Upgrade bower for critical update. #3410 (jkmarx)
  • Update ec2 configs. #3409 (jkmarx)
  • Hackdna/deployment code cleanup #3408 (hackdna)
  • Upgrade PostgreSQL to version 10.9 #3407 (hackdna)
  • Upgrade paramiko to v2.5.0 #3405 (hackdna)
  • Remove old and unused fixture. #3402 (jkmarx)
  • Jkmarx/upgrade puppet version #3397 (jkmarx)
  • Update storage setting per docs. #3395 (jkmarx)
  • Migrate UUIDField galaxy_workflow_task_group_id in AnalysisStatus model #3394 (hackdna)
  • Migrate UUIDField galaxy_export_task_group_id in AnalysisStatus model #3393 (hackdna)
  • Migrate UUIDField galaxy_import_task_group_id in AnalysisStatus model #3392 (hackdna)
  • Jkmarx/upgrade to ubuntu 16 #3391 (jkmarx)
  • Fix Cypress error on Travis CI #3390 (hackdna)
  • Migrate UUIDField refinery_import_task_id in AnalysisStatus model #3389 (hackdna)
  • Raise faker module log level to INFO to avoid spurious messages #3385 (hackdna)
  • Update UUIDField in UserProfile model #3384 (hackdna)
  • Jkmarx/finish api view names update #3381 (jkmarx)
  • Jkmarx/correct core api view names #3380 (jkmarx)
Assets 2

Version 1.6.9.1

15 May 19:14
@hackdna hackdna
v1.6.9.1
4c0b2fb
Compare
Choose a tag to compare
Version 1.6.9.1

Hotfix release to update PostgreSQL package to v10.8

Assets 2

Version 1.6.9

13 May 14:30
@jkmarx jkmarx
v1.6.9
93e7262
Compare
Choose a tag to compare
Version 1.6.9

1.6.9 (2019-04-29)

Full Changelog

Implemented enhancements:

  • Update AWS deployment docs for v1.6.8 #3116
  • New dashboard doesn't show Analysis information in DataSet Delete modal #2894
  • Statistics Page - Slow Loading #2488
  • Sorting data sets on launch pad is hard without more feed back #2143
  • Intro JS for the launchpad broken in repo mode #1773
  • Workflow Detail Page: Toggle Bug #1725
  • DataSet Explorer: the preview link's tooltip can stay permanently #1540
  • Sorting Datasets by name is case-dependent #1530
  • Data set summary panel should contain a list of all direct ontology annotations #1015
  • Study API takes long time when the dataset has many files associated to it #738
  • Enhance Data Set Description #643
  • Handle stale session condition. #323
  • Add components to launch download script modal. #3294 (jkmarx)
  • Add command line admin tools to AWS instance and Vagrant VM #3293 (hackdna)
  • Put Solr data dirs outside the source tree on both AWS and Vagrant #3283 (hackdna)
  • Set number of CPU cores in Vagrant to two to match t2.medium on AWS #3282 (hackdna)
  • Update RDS backup window #3280 (hackdna)

Fixed bugs:

  • Resizing description box covers up save button #3267
  • TypeError in data_sets API #3251
  • Explore Page -> View in File Browser button broken #3224
  • Landing Page - Text hides behind dropdown when activated #3222
  • IGV unable to access input files #3219
  • File Browser - Grid Disappears #3213
  • Failed to Load Resources - console error #3210
  • Landing Page - Embedded Videos not loading #3209
  • HTTP 500 in analysis API due to AttributeError in get_object_list() #3199
  • User.DoesNotExist error in files API #3175
  • Prevent submitting data set until all data files have been uploaded #3114
  • Error importing tabular metadata file - no samples displayed #2962
  • Error in browser console on GET requests #2832
  • High response times and system load after adding data sets #2789
  • Neo4j is accessible without authentication on AWS #2549
  • Wrong highlighting, old popover stuck, first page of tutorial #2485
  • HTTP 500 error in DataSet API #2451
  • JS error in workflow visualization #2379
  • Spurious error message in SharableResourceAPIInterface #2378
  • Data sets text search hides sort options #2363
  • Spurious slashes added to source name of data set files #2340
  • FF Depth bug even worse when rooted on particular nodes #2137
  • Data Set summary is exposed on private sets even with no login #1888
  • Intro JS for the launchpad broken in repo mode #1773
  • Dataset sharing/unsharing with Public Group leaves UI artifacts #1618
  • Reference loading indictator should timeout #1587
  • Ontology term box tabs are mis-positioned on FF #1551
  • Jumpy dataset list on the data explorer #1549
  • DataSet Explorer: the preview link's tooltip can stay permanently #1540
  • Django-Rest Swagger Broken on Test Site #1470
  • Dataset API always returns is_owner=true #826
  • settings.CONVERSION_DIR is used but not set in Django settings #588
  • Fix incorrect field reference. #3356 (jkmarx)
  • Fix bug due to incorrect reference. #3355 (jkmarx)
  • Add missing context. #3354 (jkmarx)
  • Fix close button position. #3353 (jkmarx)
  • Add missing serializer fields. #3350 (jkmarx)
  • Fix text which shouldn't be shown. #3349 (jkmarx)
  • Fix missing cancel button. #3347 (jkmarx)
  • Fix bug due to missing lookup field. #3346 (jkmarx)
  • Resolve loading error. #3344 (jkmarx)
  • Fix missing delete analysis button. #3343 (jkmarx)
  • Fix hiding of buttons on resize. #3340 (jkmarx)
  • Add missing serializer field to resolve ui bug. #3325 (jkmarx)
  • Fix bug with incorrect logic. #3323 (jkmarx)
  • Add label stying to prevent label hiding. #3321 (jkmarx)
  • Raise error when user object is not found. #3312 (jkmarx)
  • Avoid unneccessary api call. #3303 (jkmarx)
  • Jkmarx/fix analysis auto call bug #3292 (jkmarx)

Closed issues:

  • Address all current Celery configuration deprecations #3326
  • Upgrade Supervisor to v3.2.0 or higher #3320
  • Command line user data uploads for new data sets #3240
  • Upgrade PostgreSQL to v10.6 #3180
  • Launch Pad/Explore Remove #3162
  • Change default app server instance type to t2 ...
Read more
Assets 2

Version 1.6.8

27 Feb 13:33
@jkmarx jkmarx
v1.6.8
c0b2669
Compare
Choose a tag to compare
Version 1.6.8

Commands to run:
./manage.py ebs_to_s3
./manage.py update_index
./manage.py load_tools --workflows --force

Implemented enhancements:

  • Replace requests library with urllib2 for data file import #3149
  • New Layout of User Dashboard #3112
  • Public view of Dashboard #3111
  • Implement EBS to S3 data migration tool #3107
  • Enable S3 server access logging on media bucket #3105
  • Update get_temp_dir() to support S3 storage backend #3028
  • Update AWS deployment docs for v1.6.7 #2923
  • Merge tags.yaml into config.yaml #2640
  • Add name length constraints to stack.py script #2286
  • Reorder dashboard buttons to suggest "Explore" is a fold out? #2125
  • *[8]* create video to explain Refinery #284
  • Hackdna/docker instance count #3167 (hackdna)
  • Add app server instance count to Terraform config #3166 (hackdna)
  • Simplify and make file extension handling more robust #3155 (hackdna)
  • Hackdna/ftp import #3153 (hackdna)
  • Hackdna/EBS to S3 migration tool #3136 (hackdna)
  • Restrict allowed origins in CORS rules for static and media S3 buckets #3130 (hackdna)
  • Enable S3 server access logging for media bucket #3129 (hackdna)
  • Hackna/s3 backup #3125 (hackdna)
  • Simplify quickstart deployment on AWS #3115 (hackdna)

Fixed bugs:

  • HTTP 500 in site_profiles API due to DoesNotExist in SiteProfileViewSet.get() #3200
  • Deleting a primary group bug #3189
  • Delete button appears active for visualizations owned by others #3186
  • Adding files to existing data sets does not work in Firefox #3173
  • Launch Pad State Update #3150
  • Terraform parsing error in vars.tf #3135
  • Don't require page refresh to see newly invited user #3124
  • test_user_registration_successful_recaptcha depends on environment #3083
  • ReadTimeout in Tool.is_running() #3046
  • FF only: Unable to add files during upload #2987
  • Dashboard text search doesn't interact with paging #2967
  • Firefox only: Click on left half of download button does nothing #2960
  • svgxuse.min.js in error log #2145
  • Why is user/files slow? #2006
  • Delete related objects when workflow is deleted #1425
  • Dataset Import Body does not clear Navbar #793
  • Handle botocore.exceptions.ClientError #3176 (hackdna)
  • Set MEDIA_URL correctly when using S3 backend for user data #3145 (hackdna)
  • Fix defaults in config.json template #3131 (hackdna)

Closed issues:

  • Vis Tab Bug #3133
  • Relocate current launchpad to /explore #3110
  • Update Tutorial.md #3108
  • Streamline HTTPS configuration #3100
  • ISATab Metadata Import "Submit" button should be disabled after initial click #3097
  • Upgrade Node Version to V8 #3064
  • Implement backups for MEDIA_BUCKET #3042
  • Tighten S3 access policies #3020
  • Improve lifecycle management for data file storage bucket #3017
  • Home Page Rev 1 #2680
  • How should we handle Python coding style for open/close tokens spanning multiple lines? #2675
  • user/files ignore duplicate fieldnames #2603
  • Migrate stack.py to Terraform #2602
  • Consistency in UI for launch pad filtering / sorting #2147
  • CSS cleanup: priority-button style repeated on import-button #2065
  • Metadata field naming conflicts #1699
  • Avoid having separate tags file. #1386
  • Created manager group names are cryptic #1307

Merged pull requests:

Read more
Assets 2

Version 1.6.7

13 Nov 15:44
@scottx611x scottx611x
v1.6.7
1a93a1b
Compare
Choose a tag to compare
Version 1.6.7

Note: This release upgraded the version of PostgreSQL being used from 9.3.x to 10.x. The steps required to deploy a production instance with these changes can be found here

Implemented enhancements:

  • Update FileStoreItem.get_file_size() to support S3 storage backend #3029
  • Update FileStoreItem.rename_datafile() to support S3 storage backend #3027
  • Update FileStoreItem.is_local() to support S3 storage backend #3026
  • Update FileStoreItem.get_absolute_path() to support S3 storage backend #3025
  • Update FileStoreItem.get_datafile_url() to support S3 storage backend #3024
  • Specify a timeout for the file import task #3018
  • Force deletion of S3 buckets when destroying Terraform stack #3010
  • Meta-data update - modify existing node's content (back-end) #2977
  • Allow for deletion of VisualizationTools from the UI #2897
  • Inspect Solr query builder, some queries generate lots of Boolean expressions #952
  • Add django-pgcli #848
  • Admin owns everything? #825
  • Disable selection of 0 count facets. #3079 (jkmarx)
  • Migrate WebInstanceProfile to Terraform #3066 (hackdna)
  • Migrate SES user config to Terraform #3062 (hackdna)
  • Migrate database config for RDS to Puppet #3061 (hackdna)
  • Migrate RDS instance to Terraform #3056 (hackdna)
  • Migrate ELB and app server security groups to Terraform #3050 (hackdna)
  • Migrate S3 log bucket code to Terraform #3049 (hackdna)
  • Enable tagging of all resources managed by Terraform #3048 (hackdna)
  • Update rename_datafile() #3040 (hackdna)
  • Remove get_absolute_path() #3038 (hackdna)
  • Remove is_local() #3036 (hackdna)
  • Update get_datafile_url() #3033 (hackdna)
  • Update get_file_size() to support S3 storage backend #3030 (hackdna)
  • Delete static and upload file buckets even if not empty #3013 (hackdna)
  • Scottx611x/add recaptcha to registration form #3006 (scottx611x)

Fixed bugs:

  • Internal server error in get_owner_from_assay - MultipleObjectsReturned #3053
  • Transfer Data Set Bug #3045
  • Tabular metadata file is imported incorrectly to S3 #3023
  • Can't change permissions on dataset #3016
  • Internal Server Error: /api/v2/events/ #2999
  • Filtering down to empty set causes facet sidebar to disappear #2958
  • User/files multiple filtering bug #2879
  • "Hamburger" flicker on expand / collapse #2764
  • Default not to list static assets s3 bucket contents? #2762
  • Recent Analyses Popover spacing #2351
  • FileBrowser2: Change columns and the grid disappears #1902
  • Scottx611x/properly reflect admin dataset ownership #3074 (scottx611x)
  • Add error handling when saving files directly to S3 #3021 (hackdna)

Closed issues:

  • Meta-data update - modify existing node's content - UI #2982
  • ISA-Tab data set submission should end with blue 'Submit' button #2969
  • Upgrade PostgreSQL to version 10 #2707
  • Rewrite import_file task #2359
  • Get NodeIndexTests to use create_dataset_with_necessary_models #1948
  • Why does Node have FK to Study? #1929
  • Account activation welcome email is incorrect #1578
  • Implement data life cycle policies for UPLOAD_BUCKET #421

Merged pull requests:

Read more
Assets 2

Version 1.6.6.2

17 Sep 17:10
@jkmarx jkmarx
v1.6.6.2
04b3c79
This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
GPG key ID: 4AEE18F83AFDEB23
Expired
Learn about vigilant mode.
Compare
Choose a tag to compare
Version 1.6.6.2

This hotfix release resolves a bug in the events api caused by a str casting.

Assets 2

Version 1.6.6.1

17 Sep 13:14
@scottx611x scottx611x
v1.6.6.1
26cd009
Compare
Choose a tag to compare
Version 1.6.6.1

This is a hotfix release solely to get a larger EC2 instance type for our docker host running our VisualizationTools

Assets 2

Version 1.6.6

30 Aug 22:12
@scottx611x scottx611x
v1.6.6
2a63aec
Compare
Choose a tag to compare
Version 1.6.6

NOTE:

Will need to run the following to update the Solr index and add theintervene visualization tool, respectively:

  • ./manage.py update_index
  • ./manage.py load_tools --visualizations intervene

Implemented enhancements:

  • Dashboard Performance Enhancement #2909
  • Add Tools #2782
  • Dashboard Alpha: History panel dates out of order #2768
  • Provenance help wording #2767
  • Tool panel notifications can push launcher down off the screen #2766
  • Better Organization for ToolPanel selection/ tool_definitions api response #2544
  • update style of group join confirmation page #2436
  • File Browser UI - deselect / reset tool #2391
  • Retrieve Cognito identity pool ID directly from AWS API #2205
  • DataSet Upload Intro JS logs comments to the console #1775
  • UI - Uniform Modals #1489
  • File Broswer/ Visualiztion should utilize auxiliary\_file\_generation\_task\_state #1484
  • Data Set 2 - Save position on dynamic scroll #1452
  • create workflow: FASTQ replicate merging #293
  • create workflow: BAM replicate merging #292

Fixed bugs:

  • Handle ValueError in generate_solr_params #2931
  • Internal Server Error when Fetching Studies for a DataSet #2922
  • CSV download and script to get all files are truncated #2892
  • Handle ValueError in insert_facet_field_filter #2729
  • User-files filter bug #2710
  • Text in third tutorial is centered #2697
  • Data Set Import -> Associated data files waiting to be uploaded bug #2691
  • User/Files Attributes Fields #2678
  • FileStoreItem pointing to tabular metadata file has incorrect source #2669
  • RuntimeError in files API #2623
  • UnicodeEncodeError in UserProfile #2557
  • Public files momentarily not viewable (when not logged in) #2554
  • WebDriverException in test_HiGlass #2538
  • Various Django admin pages yield 500 errors on AWS-deployed Refinery Instances #2165
  • Intermittent Travis CI build failure in test_visualization_container_launch_IGV #1996
  • Second search for "ce" seems to bring up a number of title-less datasets #1922
  • Synonym search sometimes causes weird results #1011
  • Galaxy workflow import fails when Galaxy returns HTTP 500 error. #280

Closed issues:

  • Upgrade Guardian 1.4.9 #2935
  • Download links don't show after closing the Tool Panel #2895
  • UI does not update after group delete #2889
  • Distracting "Register" and "Login" tool tips #2888
  • "Invite New Member" modal should have 2nd phase with only one button #2883
  • Node functionality is split between core and data_set_manager #2837
  • Upgrade PostgreSQL version to 9.3.20 #2548
  • Tool Launch: Input files ? popover shows ui artifact on hover #2526
  • File browser sidebar rendering in short windows #2364
  • Remove igv & higlass Selenium tests in favor of a lightweight example #2238
  • Cross-dataset browser: genotype facets max out at 100? #2148
  • groups: Blank lines / random order (but do we even need it?) #2121
  • Remove unused templates #1993
  • user/files infinite scroll #1956
  • Understand solr errors in logs for /user/files #1938
  • filebrowser2: "File Display" selector positioning #1901
  • Password reset page missing box / button #1877
  • Data Set 2 - Correct font in node selection popover #1871
  • Implement data set preview panel for data sets with multiple studies #1001

Merged pull requests:

Read more
Assets 2