Change Log

v1.7.2 (2019-11-18)

Full Changelog

Fixed bugs:

File-Browser: Select All Bug #3467
Analysis import fails due to celery SoftTimeLimitExceeded #3435

Closed issues:

Bam File IGV Not Working #3465
Botocore incompatability with v1.12.98 #3388

Merged pull requests:

upgrade postgresql version #3489 (ilan-gold)
Adding some tests and better handling for non-ascii throughout #3488 (ilan-gold)
Fixing the Provenance Graph #3487 (ilan-gold)
Ilan gold/user registration bug #3486 (ilan-gold)
Fix Excessive File Downloading #3485 (ilan-gold)
Fix .bam file handling for visualizations #3484 (ilan-gold)
Set Up CloudWatch Alarms for CPU Utilization #3483 (ilan-gold)
Fix Dict/Unicode bug #3475 (ilan-gold)
Update AWS CLI to the latest version #3472 (hackdna)
Rename Files in Flight #3471 (ilan-gold)
Restructure Analysis Metadata Fetching for Celery #3461 (ilan-gold)

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:

Hide non-active members in groups. #3470 (jkmarx)
Disable search in library. #3469 (jkmarx)
Correct skipped variable when updated to new assay field. #3468 (jkmarx)
Python2 Package Updates/Changes #3464 (ilan-gold)
Jkmarx/fix file count #3462 (jkmarx)
Avoid refinery generated auxiliary_nodes in ds_file_count. #3458 (jkmarx)
Update Buggy Code in Advance of Python 3 Update #3457 (ilan-gold)
Update to instance name for user clarity #3454 (jkmarx)
Remove djangular dependency to support transition to python 3 #3453 (jkmarx)
Update version of cryptography to match install dependency version. #3450 (jkmarx)
Update version for security. #3449 (jkmarx)
Get Absolute URL Always Returns Absolute URL or Raises Error #3448 (ilan-gold)
Fix unit test to avoid order dependency in api response. #3447 (jkmarx)
Update release for security fix. #3445 (jkmarx)
Jkmarx/remove unused pyyaml #3443 (jkmarx)
Remove unused template dependency, Jinja2 #3442 (jkmarx)
Refactor Testing into Different Files #3441 (ilan-gold)
tool_manager Error Handling #3440 (ilan-gold)
Error Handling for the data_set_manager app #3439 (ilan-gold)
Jkmarx/update lodash dependency v2 #3438 (jkmarx)
Error Handling for core app #3437 (ilan-gold)
Update to latest version 9 for security upgrades. #3434 (jkmarx)
Jkmarx/fb select all feature #3433 (jkmarx)
Fix to available version. #3431 (jkmarx)
Hackdna/node fileuuid #3430 (hackdna)
Migrate UUIDField analysis_uuid in AnalysisResult #3427 (hackdna)
Jkmarx/move dependencies to npm #3426 (jkmarx)
Jkmarx/upgrade node js #3411 (jkmarx)

v1.7.0 (2019-07-19)

Full Changelog

Implemented enhancements:

New NavBar Configuration #3113
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
Fix padding #3425 (jkmarx)
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

Merged pull requests:

Migrate UUIDField uuid in Parameter model #3424 (hackdna)
Delete stale content types #3422 (hackdna)
Migrate UUIDField token_uuid in Invitation model #3421 (hackdna)
Fix UUIDField migrations in AnalysisStatus to allow upgrading django_extensions #3419 (hackdna)
Update UserProfile.uuid migrations to allow upgrading django_extensions #3418 (hackdna)
Migrate UUIDField uuid in Assay model #3416 (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)

v1.6.9.1 (2019-05-15)

Full Changelog

Implemented enhancements:

Replace requests library with urllib2 for data file import #3149
Update AWS deployment docs for v1.6.8 #3116
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
Provide a unique name to final RDS snapshot to avoid error #3090
Update FileStoreItem.get_file_size() to support S3 storage backend #3029
Update get_temp_dir() to support S3 storage backend #3028
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
Update AWS deployment docs for v1.6.7 #2923
Dashboard Performance Enhancement #2909
Allow for deletion of VisualizationTools from the UI #2897
New dashboard doesn't show Analysis information in DataSet Delete modal #2894
Hackdna/update upload box #3378 (hackdna)
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)
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)
Assign unique ID to final RDS snapshot #3091 (hackdna)
Migrate app server config from CloudFormation to Terraform #3089 (hackdna)
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)
Scottx611x/tool manager views cleanup #2991 (scottx611x)
Render vis-tool-user-not-allowed template with a 403 status #2990 (scottx611x)
Trim Tool's creation date in display\_name to the second #2985 (scottx611x)
Scottx611x/add test coverage for refinery import tasks #2984 (scottx611x)

Fixed bugs:

AWS Command Line Modal - missing bucket name #3374
AWS Command Line Modal Links should open new tab #3370
Newly Registered Users added to group cannot be demoted or deleted #3366
Collaboration - Unable to Promote User #3363
Unnecessary warning when importing data sets without data files #3360
Unable to upload RFC file #3359
Dashboard Collaboration - Invitation Request for Non-Managers Dashboard #3358
AWS Command Upload Modal #3357
Resizing description box covers up save button #3267
TypeError in data_sets API #3251
Landing Page - Attribute Label moves down when scrolling #3232
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
File Browser/Details unable to download zip #3212
User/files grid sort bug #3211
Failed to Load Resources - console error #3210
Landing Page - Embedded Videos not loading #3209
HTTP 500 in site_profiles API due to DoesNotExist in SiteProfileViewSet.get() #3200
HTTP 500 in analysis API due to AttributeError in get_object_list() #3199
Deleting a primary group bug #3189
Delete button appears active for visualizations owned by others #3186
User.DoesNotExist error in files API #3175
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
Prevent submitting data set until all data files have been uploaded #3114
Intermittent HTTP error when deploying puppetlabs-rabbitmq module #3098
test_user_registration_successful_recaptcha depends on environment #3083
Internal server error in get_owner_from_assay - MultipleObjectsReturned #3053
ReadTimeout in Tool.is_running() #3046
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
ConnectTimeout in django_docker_cleanup #2998
Internal Server Error in _check_max_running_containers #2988
FF only: Unable to add files during upload #2987
Dashboard text search doesn't interact with paging #2967
Error importing tabular metadata file - no samples displayed #2962
Firefox only: Click on left half of download button does nothing #2960
Filtering down to empty set causes facet sidebar to disappear #2958
DataSet api v2 improperly yields is\_owner: true #2957
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
Revise Metadata button in "Details" tab still clickable when disabled #2884
User/files multiple filtering bug #2879
History Card -> View Text Bugs #2878
Dashboard Filters -> Race conditions #2877
Primary Group Popover -> Missing Title #2876
Transfer Data Set Bug -> New Owner not updating UI Side #2875
File Browser UI-Bug Deactivate Drop Down #2874
Jkmarx/fix upload text for clarity #3377 (jkmarx)
Fix missing text on the s3 file upload page. #3376 (jkmarx)
Fix typo. #3375 (jkmarx)
Jkmarx/fix command line bugs #3371 (jkmarx)
Jkmarx/fix routing issue for demoting users #3369 (jkmarx)
Jkmarx/fix collaboration incorrect param #3364 (jkmarx)
Jkmarx/import hide confirm button #3362 (jkmarx)
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)
Add CORS config to S3 media bucket for igv.js #3227 (hackdna)
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)
Scottx611x/properly reflect admin dataset ownership #3074 (scottx611x)
Add error handling when saving files directly to S3 #3021 (hackdna)
Scottx611x/fix add users to public group timeout #2996 (scottx611x)
Scottx611x/fix refinery import pending state all local inputs #2976 (scottx611x)
Avoid adding UUIDs of FileStoreItems that have already been imported #2975 (scottx611x)

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 #3157
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
Generate SES user keys with aws_iam_access_key Terraform resource #3088
Upgrade Node Version to V8 #3064
Update EBS data volume configuration #3052
Implement backups for MEDIA_BUCKET #3042
Tighten S3 access policies #3020
Improve lifecycle management for data file storage bucket #3017
Remove unused Attribute Definition Model #3008
Meta-data update - modify existing node's content - UI #2982
Analyses Tab - Add owner sort #2973
ISA-Tab data set submission should end with blue 'Submit' button #2969
Missing comma in list (but maybe change it to <br>s?) #2961
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
FileBrowser add file functionality fails if DataSet's sources haven't been translated to their corresponding s3 upload buckets #2887
"Invite New Member" modal should have 2nd phase with only one button #2883

Merged pull requests:

Upgrade package to avoid travis error. #3373 (jkmarx)
Replace a custom noop with RunPython.noop in database migrations #3368 (hackdna)
Remove unused GroupManagement and UserAuthentication classes #3367 (hackdna)
Improve error handling during ISA-Tab parsing #3361 (hackdna)
Hackdna/update api urls #3348 (hackdna)
Add timezone helper in serializer. #3342 (jkmarx)
Hackdna/update urls #3341 (hackdna)
Update params per style guide. #3339 (jkmarx)
Jkmarx/update group view set params #3338 (jkmarx)
Update to match style guide for params for analysis view set #3337 (jkmarx)
Add unit tests. #3336 (jkmarx)
Jkmarx/refactor viewset names #3335 (jkmarx)
Update Django-related packages in preparation for v1.9 upgrade #3334 (hackdna)
Jkmarx/remove solr synonyms setting #3332 (jkmarx)
Remove amqplib and upgrade librabbitmq to version 2.0.0 #3331 (hackdna)
Jkmarx/remove neo4j #3330 (jkmarx)
Add comments to api for clarity. #3328 (jkmarx)
Hackdna/celery upgrade #3327 (hackdna)
Remove swagger. #3324 (jkmarx)
Upgrade Supervisor to version 4.0.0 #3322 (hackdna)
Remove tasty pie. #3318 (jkmarx)
Jkmarx/update client to invite api v2 #3317 (jkmarx)
Add get_group helper method. #3316 (jkmarx)
Jkmarx/create group invitations api #3314 (jkmarx)
Remove unused group api v1 resource. #3311 (jkmarx)
Update client to group memebers api v2. #3310 (jkmarx)
Jkmarx/add group member api #3309 (jkmarx)
Revert "Jkmarx/extend group api to delete" #3308 (jkmarx)
Jkmarx/extend group api to delete #3307 (jkmarx)
Hackdna/postgresql update #3304 (hackdna)
Jkmarx/update client with group api enhancements #3302 (jkmarx)
Jkmarx/extend group api to delete #3301 (jkmarx)
Jkmarx/extend group api return all user groups #3300 (jkmarx)
Extend api to create groups. #3299 (jkmarx)
Remove unused entries from .gitignore #3298 (hackdna)
Jkmarx/remove unused group management resource #3297 (jkmarx)
Hackdna/puppet modules #3296 (hackdna)
jkmarx/remove-unused-workflow-client-service #3295 (jkmarx)
Remove unused auth api resource. #3291 (jkmarx)
Remove unneccessary auth service. #3290 (jkmarx)
Remove unused shareable api resource and unused helpers. #3289 (jkmarx)
Remove dataSetResource #3288 (jkmarx)
Jkmarx/update client edit perms #3287 (jkmarx)
Refactor other view sets to use helper. #3286 (jkmarx)
Jkmarx/group patch perms #3285 (jkmarx)
Remove snapshot scheduler and its tags #3284 (hackdna)
Set refinery_s3_user_data to true on AWS by default #3281 (hackdna)
Change default EC2 instance type for app server to t2.medium #3278 (hackdna)
Hackdna/vagrantfile cleanup #3276 (hackdna)
Jkmarx/remove unused user apis #3275 (jkmarx)
Remove analysis resource api. #3274 (jkmarx)
Make EBS volume config more robust #3273 (hackdna)
Apache config update #3272 (hackdna)
Jkmarx/update client with analysis api v2 #3271 (jkmarx)
Hackdna/update file storage #3269 (hackdna)
Jkmarx/extend analysis api #3266 (jkmarx)
Jkmarx/groups api v2 #3265 (jkmarx)
Jkmarx/remove unused workflow views #3264 (jkmarx)
Jkmarx/remove workflow api v1 #3263 (jkmarx)
Jkmarx/angularize workflow page #3262 (jkmarx)
Jkmarx/remove attribute investigation publication resource #3260 (jkmarx)
Jkmarx/remove study and node resource #3259 (jkmarx)
Extend node v2 service. #3258 (jkmarx)
Jkmarx/switch study resource v2 #3257 (jkmarx)
Remove unused cypress test and fixtures. #3256 (jkmarx)
Remove unused template. #3255 (jkmarx)
Remove unused annotations. #3254 (jkmarx)
Remove protocol resource which is not used by client. #3253 (jkmarx)
Jkmarx/switch fb ds details to v2 #3252 (jkmarx)
Remove assays api. #3249 (jkmarx)
Jkmarx/remove explore satori #3246 (jkmarx)
Sort analyses by owner name. #3243 (jkmarx)
Hackdna/cmdline uploads #3242 (hackdna)
Delete README.md for Terraform #3237 (hackdna)
Revert "Jkmarx/fix position of text" #3235 (jkmarx)
Revert change to fix scrolling bug. #3234 (jkmarx)
Jkmarx/fix position of text #3233 (jkmarx)
After upload, check status for queuing. #3231 (jkmarx)
Fix submit button activating after canceling post successful uploads #3230 (jkmarx)
Jkmarx/fix metadata submit #3229 (jkmarx)
Integration tests for landing pages. #3228 (jkmarx)
Fix hiding text with adding absolute. #3226 (jkmarx)
Fix link to file browser. #3225 (jkmarx)
Jkmarx/fix wrong pointer navbar #3221 (jkmarx)
Hackdna/update deployment script #3220 (hackdna)
Update awscli and aws-shell to the latest versions #3218 (hackdna)
Jkmarx/show warning data import #3217 (jkmarx)
Load API options when event occurs. #3216 (jkmarx)
Turn off inifinite scrolling for short files lists. #3215 (jkmarx)
Fix main sort bug. #3214 (jkmarx)
Hackdna/puppet params #3208 (hackdna)
Fix case. #3207 (jkmarx)
Update AMI version of the web app instance #3205 (hackdna)
Jkmarx/avoid duplicate api calls #3204 (jkmarx)
Jkmarx/fix dashboard search bugs #3202 (jkmarx)
Hackdna/remove external auth #3201 (hackdna)
Fix deactivated button. #3198 (jkmarx)
Error handle for missing site profile. #3197 (jkmarx)
Remove duplicates. #3196 (jkmarx)
Updates pg list when deleting group. #3195 (jkmarx)
Show only non-manager groups on user page. #3194 (jkmarx)
Fix bug related to refreshing group list when sending invites. #3193 (jkmarx)
Fix alignment for pg dropdown. #3192 (jkmarx)
Fix padding issue. #3191 (jkmarx)
Jkmarx/fix pg delete bug #3190 (jkmarx)
Hide any column containing the name data file. #3188 (jkmarx)
Only return characteristics_attributes for user-files api. #3187 (jkmarx)
Fix firefox issue due to capturing events within button element. #3185 (jkmarx)
Jkmarx/update homepage services #3184 (jkmarx)
Scottx611x/django docker engine version bump #3183 (scottx611x)
Remove unused variables. #3182 (jkmarx)
Add site-profile api service. #3181 (jkmarx)
Consolidate Puppet config #3179 (hackdna)
Remove get_temp_dir() #3178 (hackdna)
Jkmarx/add config model #3177 (jkmarx)
Set a Workflow's description from the ToolDefinition that represents it #3174 (scottx611x)
Hackdna/remove mage2isa convert #3171 (hackdna)
Set wsgi_pass_authorization to 'On' #3170 (scottx611x)
Make git-info.sh more robust #3169 (hackdna)
Move banner to child templates. #3168 (jkmarx)
Jkmarx/minor ui changes #3165 (jkmarx)
Update states for new url. #3164 (jkmarx)
Remove unused variables. #3161 (jkmarx)
Disable submit button while uploading. #3160 (jkmarx)
Add workflow link to fb. #3159 (jkmarx)
Hide icons based on perms. #3158 (jkmarx)
Jkmarx/public view dashboard #3152 (jkmarx)
Update navbar in template. #3151 (jkmarx)
Update requests and certifi to latest versions #3148 (hackdna)
Jkmarx/landing page reorganize #3144 (jkmarx)
Resolve bug due to incorrect name reference. #3143 (jkmarx)
Update Vagrant box to v20181203.0.1 #3142 (hackdna)
Jkmarx/add video carousel #3140 (jkmarx)
Jkmarx/add twitter component #3138 (jkmarx)
Jkmarx/add twitter settings #3137 (jkmarx)
Add buttons. #3134 (jkmarx)
Jkmarx/pass refinery intro config #3132 (jkmarx)
Add buttons. #3128 (jkmarx)
Jkmarx/add analysis delete to fb #3127 (jkmarx)
Adjust styling and css for dashboard. #3123 (jkmarx)
Jkmarx/add tools list landing page #3122 (jkmarx)
Jkmarx/add chart component #3117 (jkmarx)
Scottx611x/file browser csv download #3106 (scottx611x)
Remove collaboration module. #3103 (jkmarx)
Migrate ELB config to Terraform #3101 (hackdna)
Remove the unused attributeDefinition model. #3093 (jkmarx)
Remove statistics. #3092 (jkmarx)
Add comments and delete unit test. #3081 (jkmarx)
Scottx611x/handle admin users specially when determining ownership #3080 (scottx611x)
Update button text for clarity. #3078 (jkmarx)
Wrap gets. #3077 (jkmarx)
Update color. #3076 (jkmarx)
Jkmarx/highlight related nodes #3075 (jkmarx)
Jkmarx/node api extend node paths #3073 (jkmarx)
Jkmarx/file browser add pop over #3072 (jkmarx)
Jkmarx/api prevent internal updates #3071 (jkmarx)
Jkmarx/file browser disable derived rows #3070 (jkmarx)
Update versions of installation prerequisites #3069 (hackdna)
Scottx611x/postgresql upgrade #3068 (scottx611x)
Jkmarx/file browser disguise tool columns #3067 (jkmarx)
Jkmarx/non edit background internal attributes #3065 (jkmarx)
Jkmarx/cell edit highlights #3063 (jkmarx)
Scottx611x/integrate trevors observable #3060 (scottx611x)
Jkmarx/file browser edit mode #3059 (jkmarx)
Jkmarx/file browser grey overlay #3058 (jkmarx)
Jkmarx/fix transfer ownership bug #3055 (jkmarx)
Add name variable to all Terraform modules #3054 (hackdna)
Refactor core test putting model tests in own file. #3051 (jkmarx)
Remove references to DJANGO_DOCKER_ENGINE_DATA_DIR #3047 (mccalluc)
Add expiration for partially and fully uploaded S3 objects #3043 (hackdna)
Update error handling for file operations #3041 (hackdna)
Jkmarx/update node api patch edit #3039 (jkmarx)
xvfb is no longer needed on travis (functionality provided by cypress) #3035 (mccalluc)
Mccalluc/lru tool management 0.1.2 #3034 (mccalluc)
Fix for tabular metadata file import to S3 failure #3022 (hackdna)
Add soft time limit for Celery tasks #3019 (hackdna)
Hackdna/data set manager tasks cleanup #3015 (hackdna)
Hackdna/core tasks cleanup #3014 (hackdna)
Data set manager utils cleanup #3009 (hackdna)
Hackdna/rewrite import file #3005 (hackdna)
Remove str cast. #3001 (jkmarx)
Jkmarx/cell edit #2997 (jkmarx)
Scottx611x/vis tool deletion #2992 (scottx611x)
Jkmarx/fix delete modal #2971 (jkmarx)
Jkmarx/fix data upload #2966 (jkmarx)
Jkmarx/darker text dashboard #2964 (jkmarx)
Fix sort bug due to syntax error. #2963 (jkmarx)
Jkmarx/fix perms api error #2959 (jkmarx)
Update indexing logic to handle for unknown file_import tasks #2956 (scottx611x)
Resolve bug and test due to solr format update. #2955 (jkmarx)
Add padding to hover for uniformity. #2954 (jkmarx)
Hover highlight for clarity. #2953 (jkmarx)
Resolves bug showing private facets. #2952 (jkmarx)
Missing quote mark in ERB template #2951 (mccalluc)
Jkmarx/solr user files bug #2950 (jkmarx)
Bump django-docker version #2947 (mccalluc)
Jkmarx/isa tab upload enhancement #2945 (jkmarx)
Jkmarx/limit events api response #2944 (jkmarx)
Scottx611x/remove selenium #2943 (scottx611x)
Disable buttons when user is not a member of a group. #2940 (jkmarx)
Default to primary group on loading. #2939 (jkmarx)
Jkmarx/data set v2 api filter enhancement #2938 (jkmarx)
Hide pagination for one page. #2937 (jkmarx)
Jkmarx/upgrade guardian #2936 (jkmarx)
Jkmarx/remove projects template #2932 (jkmarx)
Jkmarx/file browser default open description #2930 (jkmarx)
Fix bug related to missing params. #2929 (jkmarx)
Remove unused modules from requirements.txt #2928 (hackdna)
Fix bug, not checking every data set for validiness. #2926 (jkmarx)
Add group name to add modal. #2925 (jkmarx)
Fix import error. #2924 (jkmarx)
Jkmarx/client side pagination data set card #2921 (jkmarx)
Jkmarx/data set api pagination #2919 (jkmarx)
Jkmarx/refactor move to test vew redo #2916 (jkmarx)
Refactor unit tests. #2914 (jkmarx)
Jkmarx/node api v2 unit test #2913 (jkmarx)
Jkmarx/move node related to data set manager #2911 (jkmarx)
Jkmarx/unit test client #2910 (jkmarx)
Update styling to match other templates. #2908 (jkmarx)
Match template styling. #2907 (jkmarx)
Fix ui for adding group and member. #2905 (jkmarx)
Fix bug related to bootstrap popover font. #2904 (jkmarx)
Jkmarx/deselect tool #2903 (jkmarx)
Fix text for clarity. #2902 (jkmarx)
Update group list after deleting. #2901 (jkmarx)
Remove distracting tooltips #2900 (jkmarx)
Add limit to prevent truncating. #2899 (jkmarx)
Scottx611x/properly associate metadata file for tabular imports #2859 (scottx611x)

v1.6.5 (2018-07-20)

Full Changelog

Implemented enhancements:

Implement support for removing files from a data set #2817
Spam Registrations #2797
Perms Enhancement: Add Primary Group #2781
Perms Enhancements: change_data_set ownership #2780
Support for custom Tool launch names #2545
Why is analysis group centered in table? #2512
Higlass should be friendlier on launch #2357
Strip whitespace before indexing #2176
Getting more datasets when scrolling on the dashboard is slow #1550
DataSet2 - Optimize Column Width Algorithm #1048
Ui-scroll list is blocked during API calls #819
add "last accessed" table for base resources #600
DataSet API returns different types of objects #594
Fix styling for width and padding in analysis group. #2843 (jkmarx)
Hackdna/add files to dataset #2819 (hackdna)
Hackdna/import file s3 #2806 (hackdna)
Streamline private network adapter config #2793 (hackdna)
Make the EC2 Instant Type configurable #2788 (drj11)

Fixed bugs:

Revise Metadata button in "Details" tab still clickable when disabled #2884
History Card -> View Text Bugs #2878
Dashboard Filters -> Race conditions #2877
Primary Group Popover -> Missing Title #2876
Transfer Data Set Bug -> New Owner not updating UI Side #2875
File Browser UI-Bug Deactivate Drop Down #2874
Duplicate Events created for launched Analyses #2872
Remove User #2870
UnicodeEncodeError when updating test site's Solr index #2869
Import Data File -> Incorrect status during pending #2846
NodeSerializer cannot save valid Node instance serializations #2834
Unable to Delete Old Inactive User #2803
Admin Interface - Unable to access user profiles #2802
Inability to bring up clean vm with latest develop code #2795
Inability to Filter DataSets by Group in Firefox-Linux #2701
Check if .hitile is being ingested into HiGlass the right way #2361
Make sure list of file types supported by HiGlass is accurate #2358
Remove flakey Satori Cypress test #2348
Data set link from cross-dataset browser is missing ID, sometimes #2259
Scottx611x/fix add file source translation #2890 (scottx611x)
Properly create Attribute instances within factory boy utils #2871 (scottx611x)
Add permissions check to AddFilesToDataSetView #2821 (hackdna)
Make sure file system path matches data file name in file_store #2815 (hackdna)
Fix #2795 #2801 (hackdna)

Closed issues:

FileBrowser add file functionality fails if DataSet's sources haven't been translated to their corresponding s3 upload buckets #2887
Upgrade postgresql on all deployment platforms #2865
UI exposure for Docker logs #2847
Data Set Files Never Imported (ISA-Tab) #2840
Data file removal should only be allowed if a DataSet is "clean" #2829
DataSets should be able to report on their "Cleanliness" #2784
Perms Auditing: Events API #2779
Metadata/Data File Editing for Existing DataSets #2700
HiGlass should be initialized with all selected tracks as horizontals #2360
Meaningful test of update_annotated_nodes #2329
Test sorting of concatenated facet values #2167
"Public" filter count does not match count seen by the public #2144
Add data files to an existing data set #2037
UI Grid CSS Customizer #1867
Upgrade NPM to sporadic Travis errors #1768
404 not apparent to user if invalid genome selected #1524
Make dataset which incorporates all types supported by IGV #1453
More "@login_required" in view.py? #1346
Details always says "using 0 bytes" #1309

Merged pull requests:

Jkmarx/hot fix filtering race #2893 (jkmarx)
Fix checking ownership by user perms not group. #2886 (jkmarx)
Scottx611x/fix 2872 #2885 (scottx611x)
Deactive drop down when unclean and missing data file. #2882 (jkmarx)
Fix text on html. #2881 (jkmarx)
Correct uuid. #2873 (jkmarx)
Jkmarx/fix bug event refresh #2868 (jkmarx)
Jkmarx/add missing import #2867 (jkmarx)
Add node-uuid for importing added files. #2866 (jkmarx)
Update text for clarity. #2864 (jkmarx)
Avoid str cast causing ascii bug. #2863 (jkmarx)
Jkmarx/update clean status after launch #2862 (jkmarx)
Remove Satori test causing intermittent build failures #2861 (scottx611x)
Show PENDING state for datafiles added from the UI #2860 (scottx611x)
Jkmarx/remove public group anon user from api #2858 (jkmarx)
Jkmarx/add missing UUID #2857 (jkmarx)
Fix bug related to how modal closes. #2856 (jkmarx)
Jkamrx/fix node api remove datafile #2854 (jkmarx)
Jkmarx/fix add file bug ui #2853 (jkmarx)
Scottx611x/reintroduce pending import state #2852 (scottx611x)
Fix response object for unauthorized users. #2851 (jkmarx)
Jkmarx/update serializers fields syntax #2850 (jkmarx)
Jkmarx/fix meta data ui #2849 (jkmarx)
Jkmarx/update ui metadata #2848 (jkmarx)
Jkmarx/remove file ui #2845 (jkmarx)
Jkmarx/remove unused igv stuff #2844 (jkmarx)
Add Excel specific FileTypes and FileExtensions #2842 (scottx611x)
Jkmarx/update events ui #2841 (jkmarx)
Add unit tests for api. #2839 (jkmarx)
Jkmarx/connect add file service #2838 (jkmarx)
Hackdna/node api test update #2836 (hackdna)
Jkmarx data file modal unit tests #2835 (jkmarx)
Jkmarx/primary group ui unit tests #2833 (jkmarx)
Hyperlink DOIs against preferred resolver #2831 (katrinleinweber)
Scottx611x/add is clean to dataset api #2830 (scottx611x)
Jkmarx/primary group ui #2828 (jkmarx)
Remove unused code from core API module #2827 (hackdna)
Scottx611x/update dashboard to use events api #2824 (scottx611x)
Jkmarx/primary group api unit tests #2823 (jkmarx)
Core API cleanup #2822 (hackdna)
Jkmarx/add primary group api #2820 (jkmarx)
Jkmarx/data file replace modal #2818 (jkmarx)
Scottx611x/add access control to events api #2816 (scottx611x)
Jkmarx/replace data file ui #2814 (jkmarx)
Scottx611x/metadata revisions #2811 (scottx611x)
Mccalluc/more event logging #2809 (mccalluc)
Mccalluc/begin events api #2808 (mccalluc)
Jkmarx/update to registration form #2807 (jkmarx)
Update group api to return member_list which are only active. #2805 (jkmarx)
Jkmarx/ui tool launch input #2804 (jkmarx)
Jkmarx/data set owner transfer ui #2796 (jkmarx)
Jkmarx/data set owner transfer #2794 (jkmarx)
Update load_tools mgmt command to utilize nargs; #2790 (scottx611x)
Scottx611x/untouched dataset #2786 (scottx611x)
Jkmarx/extend data set V2 api #2785 (jkmarx)
Scottx611x/custom tool launch names api changes #2772 (scottx611x)
Scottx611x/datasets api performance gains #2757 (scottx611x)

v1.6.4 (2018-05-22)

Full Changelog

Implemented enhancements:

Scottx611x/serialize tool definitions #2747 (scottx611x)
Scottx611x/remove receiver subclasses decorator #2744 (scottx611x)
Update Solr queries to not limit # of docs returned #2711 (scottx611x)

Fixed bugs:

VisualizationTools can't be launched properly on DataSets with missing Data Files #2774
Inability to Import DataSets into "Own Space" #2773
Dashboard Results differ from Launch Pad #2759
VisualizationTool relaunches, but new tab is blank #2758
Data Set API Bug -> Group Filter #2742
Error accessing EBS data volume during WebInstance provisioning #2708
Index Files Not Being Generated for Newly Imported BAM Files #2705
Internal Server Error: /api/v1/viewconfs/ #2703
Internal Server Error: /assets/images/touchicon.png #2702
No DELETE request to Galaxy library API in successful analyses #2641
Avoid use of special characters in file names #2553
Creation Time for Visualization Tools in Visualizations Tab is in the Future #2527
IGV internal server error due to HTTP Error 404 #2450
Analysis Filters don't seem to work on some Analyses #2383
Provenance Graph loading error #2372
Treemap looses orange when mouse leaves data sets list #2132
Dashboard: Filter with Groups Bug #1724
Scottx611x/fix visualization launches #2775 (scottx611x)
Hot-fix: Fix relaunch bug. #2761 (jkmarx)
Scottx611x/fix process metadata table command #2740 (scottx611x)
Escape @ symbol to fix filter bug. #2733 (jkmarx)
Make data file names POSIX compliant #2732 (hackdna)
Jkmarx/fix vis ui #2730 (jkmarx)
File import bug fixes #2723 (hackdna)
Fix BAM index file generation #2712 (hackdna)

Closed issues:

Data Set Updates #2783
Superuser creation failure when stack doesn't reference backups #2738
Incorrect icon display after VisualizationTool selection #2720
Add Collection of Requested Metrics #2694
Dashboard Rev 1 #2679
Remove receiver_subclasses() decorator #2658
Remove NodeManager class #2649
Add file count to User Files browser #2620
Cloudman Upgrade #2468
Update Galaxy test workflows #2411
Remove file_server Django app #2393
Tool-Launched User Story #2245
Template 500 page not working / not sure it ever was #2077
When header wraps, top of body is obscured. #1876

Merged pull requests:

Fix Import into own space issue #2778 (scottx611x)
Jkmarx/fix icon #2777 (jkmarx)
Allow any permissible users to relaunch or view a tool. #2771 (jkmarx)
Order event and tools by creation_time. #2769 (jkmarx)
Jkmarx/dashboard search bug fix #2765 (jkmarx)
Jkmarx/tool launch add notice msg #2756 (jkmarx)
Jkmarx/refresh group list #2755 (jkmarx)
Jkmarx/min data set api #2754 (jkmarx)
Remove get_file_object() method and function #2753 (hackdna)
Jkmarx/fix group api bug #2752 (jkmarx)
Add data set totals to user files and file browser. #2749 (jkmarx)
Switch network adapter type to paravirtualized for increased performance #2748 (hackdna)
Adjust css errors. #2745 (jkmarx)
Add basic functionality for creating S3 user data object keys #2737 (hackdna)
Scottx611x/prettier tool auth page #2736 (scottx611x)
Remove isort. #2734 (jkmarx)
Remove rename() task and unnecessary code from rename_results() #2725 (hackdna)
Remove unused django-resumable Python module #2724 (hackdna)
Scottx611x/fix travis psycopg issue #2722 (scottx611x)
Jkmarx/dashboard #2721 (jkmarx)
Remove NodeManager class and related items #2715 (hackdna)
Remove the last remaining parts of the file_server Django app #2714 (hackdna)
Scottx611x/collect stats #2704 (scottx611x)
Scottx611x/provide vis tools with url to their input data #2677 (scottx611x)
Mccalluc/terraform ec2 for docker engine #2597 (mccalluc)

v1.6.3 (2018-03-29)

Full Changelog

Implemented enhancements:

Add VPC to Terraform infrastructure #2600
Global Analysis Popover - Add link for in-progress analyses #2516
Dataset is shared with me, but I can't actually edit metadata #2506
Refactor Analysis.attach\_outputs\_dataset #2415
VisualizationTool launches should have access to **all** of a Dataset's Node metadata information #2413
User/files Empty Columns #2350
"Data File Column" upload message uses internal absolute path #2323
Satori minor discrepancies between test doc and real world #2152
Satori: Jumpy context menu if column scroll, on FF #2136
First add-all-to-cart takes 4 seconds (with 119 data sets) #2129
Satori icon loading could be enhanced #1905
Postcss doesn't do anything #1778
When using ELB, log client IP #1389
RepoExplorer: show number of data sets related to hovered ontology term #975
RepoExplorer: double clicking on a node === rooting it #973
RepoExplorer: treemap should feature the same node context menu of the list graph #968
RepoExplorer: Add short explanation for precision and recall #966
RepoExplorer: Treemap: Add tooltip #963
Sample names from ISA-Tab are not being displayed #441
Hackdna/update apache config #2672 (hackdna)
Keep chunked uploads outside file_store dir and delete chunked upload… #2594 (hackdna)
Bring up the log level of httpstream and pysolr to INFO #2555 (hackdna)

Fixed bugs:

Missing Workflow tools for datasets with modify (non-owner) perms #2692
Unnecessary FileStoreItem instances created during analysis #2670
TemplateDoesNotExist errors in analysis_manager views #2668
Internal Server Error from /solr/core/select #2639
Remove related objects when deleting a data set #2632
Missing migration for chunked_upload app #2615
Potentially Flaky Unit Tests #2610
Workflow Visualization Bug #2609
Spurious slashes added to source name of data set files #2582
Edit Accession input box is not displayed correctly #2581
Non-idempotent test: core.tests.test\_get\_analysis\_list #2576
Visualization Tab - loading bug #2552
Testing suite fails to run #2537
"Import into own space" should not be available if I already own the dataset #2518
FileStoreItem.get_file_extension() returns None for certain FileTypes #2515
Satori treemap labels missing if URL has branchId=2 #2494
In "Two Bar" mode, recall and precision overlap after sort #2489
All Files Browser: Chrome is mis-encoding an API url #2425
Submit button on data set upload form is not changing its state on AWS #2412
User/Files Filtering Behavior #2352
Found set counts not (usually) preserved across Satori toggles #2339
search data sets + satori + title click = missized columns #2338
Tutorials don't work if the relevant component in Satori is minimized #2140
Satori: Context menu interferes with lock highlight propagation #2138
Satori: Nodes missing from node-link after sorting while zoomed #2135
Re-render truncated after zoom-out in Satori #2134
Satori menu toggle up missing icon on FF #2133
Adding search to satori query seems to produce result, but not rendered #1931
Satori tutorial: Data Set Summary link not working #1925
Satori tutorial can be instantiated on top of prior ones #1924
Limit to one dashboard filter menu at a time? #1923
Satori: Mis-sized if coming from preview with lock active #1921
Satori: Tree map loses lock state if window resize forces redraw #1920
Satori: lock state not mirrored between treemap and node list #1918
Satori treemap depth label mispositioned (FF only) #1916
Satori: Popover for current screen split mode remains even after mouse leaves #1915
Satori treemap info-"i" does nothing #1914
Satori: scroll node column down, change sort, and the column does not redraw #1913
Satori treemap depth controller: Click the up-arrow, but the down-arrow gets highlighted #1911
Satori treemap depth controller treats click as mousedown (FF only) #1910
Satori treemap depth controller requires mouse movement (Chrome only) #1909
Satori treemap labels not being cleaned up on redraw #1908
Inconsistent state if query cleared while data cart still open #1904
Typo, and bad style, on access-denied #1889
Analysis Filtering Discrepancy FF vs. Chrome #1728
DataSet deletion can break half-way #1580
Dashboard Preview - Min Window width Bug #1461
Delete related objects when analysis is deleted #1428
ontology info box mispositioned on FF only #1403
RepoExplorer: query-search search message hiccup #971
RepoExplorer: Some annotations are not highlighted #965
Fix perms to allow modify_perm users to view workflows. #2695 (jkmarx)
Hide button for owners. #2682 (jkmarx)
Update user/files to view datasets with read_all plus perms. #2659 (jkmarx)
Hackdna/delete files #2657 (hackdna)
Scottx611x/fix management commands #2606 (scottx611x)
Fix form alignment. #2601 (jkmarx)
Hackdna/fix isa tab parser bug #2556 (hackdna)

Closed issues:

Add content-disposition to cross-dataset file browser downloads. #2699
After completion of tutorial, checkbox does not appear until page is re-loaded #2696
Prettier please wait for visualizations #2621
FileRelationship: (fields.W340) null has no effect on ManyToManyField #2611
Remove workflow_manager Django app #2587
Data Set One - Solr Code #2567
Refactor FileStoreItem.get_datafile_url() #2563
Registration Redux Upgrade #2561
Odd (Spam) User accounts on the Beta Site #2543
Remove WorkflowDataInput, WorkflowDataInputMap, and WorkflowInputRelationships #2466
Remove DiskQuota #2465
Remove visualization_manager Django app #2464
Remove workflow_manager app #2463
Add "cell type" to cross dataset browser #2459
Add columns/facets to cross filebrowser to meet Shivdasani lab needs #2458
Update to Terraform v0.11 #2423
Extra closing quote in group help pop over #2362
File browser columns in config in reverse order #2208
Facet counts behave differently between cross-dataset and within-dataset #2178
Cross-dataset: Filename column should not be url encoded #2150
Missing tutorials? #2141
Data cart sizing inconsistent between FF/Chrome #2128
Satori never loads if data sets loads first? #2126
Satori "Zoom out" is really more of a zoom toggle? #1917
Tidy up enormous function in stack.py #1736
"Add all to data cart" does not do anything #1552
Replace REFINERY_URL_SCHEME with native Django options #1293
Remove bitstring package and related code #569
Upgrade to Django 1.8 #449

Merged pull requests:

Fix conditional and icon name. #2686 (jkmarx)
Jkmarx/import ui error msg #2685 (jkmarx)
Remove upload_bucket_name output from root and bucket_name_base outpu… #2683 (hackdna)
Remove unused analysis views #2676 (jkmarx)
Replace DownloadError with RuntimeError #2671 (hackdna)
Fix typo and reword text for clarifty> #2667 (jkmarx)
Jkmarx/remove file display #2666 (jkmarx)
Jkmarx/solr perms #2665 (jkmarx)
Hackdna/remove create task #2664 (hackdna)
Scottx611x/Add VPC to Terraform #2656 (scottx611x)
Scottx611x/delete related analysis objects #2655 (scottx611x)
Scottx611x/remove workflow models #2654 (scottx611x)
bump docker engine [skip ci] #2653 (mccalluc)
Jkmarx/remove dotted line #2652 (jkmarx)
Refactor file_store tests and models into separate files #2651 (hackdna)
Hackdna/update fabfile #2648 (hackdna)
Scottx611x/delete related Dataset & Analysis objects #2646 (scottx611x)
Scottx611x/persistent visualization urls #2638 (scottx611x)
Remove Python package bitstring #2635 (hackdna)
Hackdna/refactor file store #2634 (hackdna)
Scottx611x/remove workflow manager #2633 (scottx611x)
Jkmarx/fix facet query user files #2630 (jkmarx)
Jkmarx/remove migration warning redo #2629 (jkmarx)
Remove null_field which has no effect. #2625 (jkmarx)
Add chunked-upload migration. #2624 (jkmarx)
"Please wait" for vis tools #2622 (mccalluc)
Remove flaky tests. #2613 (jkmarx)
Jkmarx/dashboard file browser icon #2612 (jkmarx)
Jkmarx/visual no display #2608 (jkmarx)
Jkmarx/update management command argparse #2607 (jkmarx)
Jkmarx/hide user files column #2604 (jkmarx)
Remove DiskQuota model #2599 (hackdna)
Scottx611x/refactor attach outputs dataset #2591 (scottx611x)
Scottx611x/handle lack of galaxy input step inputs #2590 (scottx611x)
Jkmarx update deprecated 1 8 items #2588 (jkmarx)
Add --fake-initial to our migrate commands to provide the behavior … #2585 (scottx611x)
Jkmarx/outparse to argparse #2584 (jkmarx)
Jkmarx/remove unused m commands #2583 (jkmarx)
Clean up Puppet manifests #2579 (hackdna)
Ensure analysis api response order to make test more robust #2578 (scottx611x)
Update user/file facet/columns per user request. #2577 (jkmarx)
Remove post-css library, unused. #2574 (jkmarx)
Upgrade django storage. #2571 (jkmarx)
Remove solr_igv dependencies. #2570 (jkmarx)
Scottx611x/send over all dataset node info #2569 (scottx611x)
Centralize flake8 config for consistency and easy updates #2568 (hackdna)
Swap deprecated method out. #2566 (jkmarx)
Jkmarx/registration redux upgrade #2562 (jkmarx)
Upgrade django version to 1.8 #2560 (jkmarx)
Remove file server #2541 (hackdna)
Jkmarx/update httpresponse #2533 (jkmarx)

v1.6.2 (2018-01-26)

Full Changelog

Implemented enhancements:

load\_tools --visualizations Error message could be more helpful #2529
Lightning Bolt Icon is not a true representation of an Importing FilestoreItem's state #2382
Prettier tool names #2155
Data Set 2 - Update selection icon and select all icon #1833
Data-Set 2 Layout/CSS #1666
Move "URL shortcut" field from upload page to data set details in file browser #1629
provide list of download URLs for selection #326
Add a Django config for running tests #2536 (hackdna)
Provide additional information when logging a file import error from S3 #2444 (hackdna)

Fixed bugs:

Node indexing code needs to be updated to exclude Nodes associated with Output AnalysisNodeConnections w/ is_refinery_file == False #2522
If shortcut is reused, API fails, but UI does not update #2514
Table all blue when "uuid" is not exposed. #2511
Dataset Details tab: "Owner's information not available" #2505
Provvis stuck on "Loading graph": errors in console: provvis.js:5081 #2502
File Browser Input Group Popover Hover Bug #2495
ISA-Tab Error Bug - No exit or info #2493
Tutorial checkmarks not updated until page reload #2486
Revoked invitation: "View group information" link broken #2484
Incorrect REFINERY_DOWNLOAD_URL_s displayed for File Nodes without an associated file_import task #2481
Add read-meta perms to existing dataset objs w/ read perm #2455
EC2 data volume type is set to magnetic #2442
Download links not displayed in the data set view #2434
File Browser - Tooltips Linger #2431
Import Own Space Button - Fix color and padding #2401
Analysis results are not added to source data set #2294
Spurious Solr error 404 in Celery log #2290
Provenance Bug: URL fails to redirect #2285
Seeing unexpected values for "type" in file browser #2106
"study_uuid: AND assay_uuid:" solr syntax error #2063
provenance attributes menu not showing on FF #1466
Jkmarx/hot fix popover r1.6.2 #2509 (jkmarx)
Update ui tool_panel visibility based on perms. #2467 (jkmarx)
Jkmarx/fixes for vis tab #2449 (jkmarx)
Bug fix for checking the dataset object perms. #2445 (jkmarx)
Set EC2 instance root volume type to gp2 #2443 (hackdna)
Hide any users without profiles or a full_name. #2440 (jkmarx)
Jkmarx/popover fix #2439 (jkmarx)
Remove flaky tool tip. #2438 (jkmarx)

Closed issues:

Remove visualization_manager Django app #2540
Extra closing quote in help text #2482
Unable to create stack with currently pinned deployment/requirements.txt #2477
Remove old attribute order api #2476
Sharing/Permissions UI #2390
Details > History > "Import into own space" should get grey background #2356
file browser filters disappear as new facets applied #2091
With download url in solr, don't need the per-row api hits in file browser #2050
Refactor provvis global scope usage #1000

Merged pull requests:

bump django-docker-engine #2542 (mccalluc)
Scottx611x/better load tools error message #2530 (scottx611x)
Scottx611x/update node index preparation #2524 (scottx611x)
Jkmarx/hot fix isa tab r 1.6.2 #2523 (jkmarx)
Hide uuid attribute. #2521 (jkmarx)
Jkmarx/hot fix isa tab r 1.6.2 #2520 (jkmarx)
Jkmarx/hot fix owner name r 1.6.2 #2510 (jkmarx)
Scottx611x/fix 2481 #2490 (scottx611x)
Jkmarx/remove unused api #2479 (jkmarx)
Scottx611x/bump awscli version #2478 (scottx611x)
Remove slug ref from management command. #2475 (jkmarx)
Remove slug reference when importing meta data form. #2474 (jkmarx)
Remove slug edit from import form. #2473 (jkmarx)
Add default class and padding. #2472 (jkmarx)
Fix cog color. #2471 (jkmarx)
Scottx611x/create attribute orders for exsting datsets #2469 (scottx611x)
Jkmarx/download url index bug #2462 (jkmarx)
Bump django_docker_engine version #2460 (scottx611x)
scottx611x/update_existing_datasets_with_read_meta_perm #2457 (scottx611x)
Scottx611x/working heatmap scatterplot #2456 (scottx611x)
Bump codecov req #2453 (scottx611x)
Scottx611x/fix bugs from rushing yesterday #2452 (scottx611x)
Remove unused functions is_local, is_permanent, get_file_extension, g… #2448 (hackdna)
Scottx611x/expose extra directories #2447 (scottx611x)
Scottx611x/parameter updates #2446 (scottx611x)
Jkmarx/add visualization tab #2437 (jkmarx)
Scottx611x/expose vis tool status #2433 (scottx611x)
Jkmarx/share modal file browser #2421 (jkmarx)
Skip indexing for some files #2330 (mccalluc)
Jkmarx/refactor provvis code #2317 (jkmarx)

v1.6.1.1 (2017-12-13)

Full Changelog

Implemented enhancements:

ISA-Tab Upload: Wrong remove color button #1727
Allow deletion of the empty user data S3 buckets #2392 (hackdna)

Fixed bugs:

Results missing from some successful analyses #2426
Database migrations fail to apply automatically #2420
Assertion error in test_analysis_deletion #2408
KeyError when cancelling an Analysis before Galaxy Import stage #2397
Downloading more files from Galaxy than specified by workflow #2293
Assign unique name to each Celery worker #2404 (hackdna)
Remove data_set_manager test data zip files from .gitignore #2395 (hackdna)

Closed issues:

Collaboration Permissions - View Meta Data Level #2389
Remove the WorkflowFilesDL model #2173
Assay Files Refactor/Fix Unit Test #1621

Merged pull requests:

Fix duplicate migration error. #2430 (jkmarx)
Hotfix 1.6.1.1 #2428 (scottx611x)
Add UUIDField migrations for django-extensions update #2424 (hackdna)
Rename meta.module_name to model_name for Django 1.8 #2422 (hackdna)
Remove call to a deprecated method commit_unless_managed() #2418 (hackdna)
Restrict serializer to pickle and add expiration for django_docker_cl… #2417 (hackdna)
Scottx611x/only download exposed workflow outputs #2414 (scottx611x)
Specify base\_url in GalaxyInstance Factory #2410 (scottx611x)
Jkmarx/add dataset read meta #2409 (jkmarx)
Rename _meta.module_name to _meta.model_name for compatibility with D… #2406 (hackdna)
Rename get_query_set() to get_queryset() for compatibility with Djang… #2405 (hackdna)
Simplify Django logging config #2403 (hackdna)
Update django-extensions to the latest version that supports Django 1.7 #2402 (hackdna)
Remove unused custom template tag simple_name #2400 (hackdna)
Scottx611x/fix 2397 #2399 (scottx611x)
Remove unused package django-uuidfield #2396 (hackdna)
Scottx611x/remove workflow files dl model #2384 (scottx611x)
Add warning color to button. #2333 (jkmarx)

v1.6.1 (2017-11-27)

Full Changelog

Implemented enhancements:

Replace stack-s3.py with Terraform configuration #2307
File Browser sized just a little too large -> scroll bars on pane #2220
If a Tool launch fails, it fails silently #2211
WorkflowTools need to be mindful of Galaxy's RenameDatasetAction #2193
Django docker tmp needs separate EBS mount #2166
Meaningful error in UI when container count limit is hit #2113
Details tab, metadata edit: input boxes not pre-populated #2085
In Recent Analyses list, percentage complete should be top-aligned. #1895
Same page link on the Collaboration page #1884
Data Set 2 - Add modal notification when clearing launch config #1832
Separate requirements file for dev requirements #1387

Fixed bugs:

TypeError when adding a FileStoreItem using Django admin site #2380
Galaxy objs. persist when deleting/cancelling running Analyses #2375
"Select File Display Mode" popover can't be cleared #2354
Import ISATab not working #2345
"Import into Own Space" not working #2342
On Provenance, dynamically loaded JS 404s #2341
Data Set Table Configuration modal only triggers when clicking directly on wrench #2326
Potentially non-idempotent test? #2304
"./manage.py process_default_table" broken / never worked? #2296
Global Analysis Number doesn't update #2265
Attribute Filter Bug #2263
Config Button Color Mishap #2244
Internal server error in NodeSet API #2229
Provvis regression since 1.6.0 release #2221
If files have not completely downloaded, visualizations fail silently. #2204
Unable to cancel an Analysis #2171
Satori list graph tutorial 404 #2163
Analysis popover doesn't close on clicks between header and body #2122
Analysis filters do not work reliably in FB2 when url params already set #2081
Unit test errors and failures in data_set_manager #2067
Refinery freezes when trying to view Protocol Reference Parameters #2032
Analysis Filtering url is not picked up by File Browser 2 facet filtering #2027
filebrowser2: table rows disappear after adding filter #1926
Links in pop-overs are un-clickable #1886
Global analysis popover show/hide out of sync #1879
/user/files/ makes useless call to /api/v1/nodeset/ #1853
File Browser - Console Error #1478
ISATab DataSets seem to lack their symlinked isatab files on AWS instances brought up from snapshots #1455
Hackdna/filestoreitem fix #2386 (hackdna)
Jkmarx/release bug fix provvis #2347 (jkmarx)

Closed issues:

Separate file upload bucket from data storage bucket #2370
"Show Tool Panel" should be left aligned #2322
Try Karma reporter config instead of grepping on travis #2316
Remove COGNITO_DEVELOPER_PROVIDER_NAME from settings #2299
Google Analytics tracking code syntax error #2295
Tool launch error on 1.6.0 #2256
Handle ToolDefinition list visibility on a per-user per-Dataset basis #2253
test_csv() and test_user_files_csv() are brittle #2235
Remove splits in logic fromis\_tool\_based #2194
Add Node meta Info To VisualizationTool Launches #2189
attributes button on provvis not working #2185
Hovering over show/hide toggle in Analyses listing yields \_ character #2183
Satori list graph tutorial typos #2162
Cross-dataset is missing facet counts #2149
"This was a quick over" -> "overview" #2139
Remove download column from file browser #2094
"Following files ..." message should not be shown if everything is good #2048
bash hint for multi file download #2029
ISA-Tab parsing: report error messages #2026
Is data_sets_old/<uuid>/edit still needed? #2019
In FB2, Analyses should have name and not just UUID #1999
/user/files making unnecessary requests #1937
Add 'class="indicator"' to analysis status <li>s on dashboard? #1878
Find replacement for cfn-pyplates #1837
Restrict Tastypie serialization formats to JSON only #1836
ELB access logs should be enabled using CloudFormation #1809
Remove REFINERY_USER_AUTHENTICATED if unused #1765
List all files across Assays #1753
Remove INTERVAL_BETWEEN_CHECKS from settings #1209
Update Matrix View in New DataSet View #915
Assess Ansible, Puppet and Docker as possible provisioners for Vagrant #416

Merged pull requests:

Hackdna/remove sharename field #2388 (hackdna)
Hackdna/media files s3 prototype #2387 (hackdna)
Scottx611x/galaxy cleanup on delete or cancel #2385 (scottx611x)
Mccalluc/tools registry #2374 (mccalluc)
Update Google Analytics tracking code #2371 (hackdna)
Command-line multi-file download #2369 (mccalluc)
Mccalluc/dev docs #2368 (mccalluc)
Separate S3 upload bucket #2366 (hackdna)
Hackdna/cognito cleanup #2353 (hackdna)
Scottx611x/isa tab import fix #2346 (scottx611x)
Hackdna/terraform prototype #2337 (hackdna)
Update test to be more robust #2336 (scottx611x)
Scottx611x/galaxy connector pindown tests #2335 (scottx611x)
Scottx611x/less test output #2328 (scottx611x)
Mccalluc/file browser buttons #2327 (mccalluc)
Remove INTERVAL_BETWEEN_CHECKS. Fix #1209. #2325 (mccalluc)
Only show the body of the dialog if there actually are files to list. #2324 (mccalluc)
We do not need to see each successful GET under Cypress #2320 (mccalluc)
Try the "dots" reporter for karma... #2319 (mccalluc)
Increase size of root volume #2318 (mccalluc)
Scottx611x/ensure workflow outputs exist #2315 (scottx611x)
Add styling back to button. #2313 (jkmarx)
Jkmarx/remove unused spinner library #2312 (jkmarx)
Mccalluc/tasty pie no xml 2 #2311 (mccalluc)
Jkmarx/remove unused json2 #2310 (jkmarx)
Jkmarx/remove unused templates #2309 (jkmarx)
Jkmarx/remove static bootstrap #2308 (jkmarx)
Jkmarx/reorganize bootbox #2306 (jkmarx)
quieter grunt #2303 (mccalluc)
Mccalluc/misc travis log cleanup #2302 (mccalluc)
Mccalluc/exponential explosion #2300 (mccalluc)
Remove extra scrollbar cause by auto class on exterior panel. #2297 (jkmarx)
Jkmarx/provvis tab integration #2289 (jkmarx)
Remove unused JS global. Fix #1765. #2287 (mccalluc)
Remove unused JS global. Fix #1765. #2283 (mccalluc)
Mock USER_FILES_COLUMNS #2282 (mccalluc)
Scottx611x/set workflow tool analysis library_id #2280 (scottx611x)
Jkmarx/remove old node maps api #2279 (jkmarx)
Jkmarx/data set 1 cleanup #2278 (jkmarx)
Jkmarx/analysis tab url fix #2276 (jkmarx)
Scottx611x/tool manager test coverage #2271 (scottx611x)
Fix typo in generate\_tool\_definitions mgmt command #2270 (scottx611x)
Jkmarx/remove select workflows and igv module #2269 (jkmarx)
Jkmarx/decongest data set nav ui #2268 (jkmarx)
Jkmarx/global analysis count fix #2267 (jkmarx)
Fix field showing due to includes empty string returning true. #2266 (jkmarx)
Bump version #2264 (mccalluc)
Jkmarx/analysis filter bug #2262 (jkmarx)
Scottx611x/utilize parameters in vis tool launches #2258 (scottx611x)
Remove canEdit field and ng-if to show tools to all users. #2255 (jkmarx)
Scottx611x/show visualizations for all #2254 (scottx611x)
"Not" -> "Note", and linebreaks on <br> for readability in source. #2252 (mccalluc)
Remove node-mapping module and add third party dependency to refinery… #2250 (jkmarx)
Remove node-relationship module. #2249 (jkmarx)
Jkmarx/analysis launch ui removal #2248 (jkmarx)
Scottx611x/add force to generate tool definitions #2247 (scottx611x)
Fix button color. #2246 (jkmarx)
Scottx611x/fix node meta info query #2241 (scottx611x)
Jkmarx/fix analyses padding #2240 (jkmarx)
Mccalluc/cypress continued #2239 (mccalluc)
Remove underscroll from collapse icon. #2237 (jkmarx)
Jkmarx/metadata edit enhancement #2234 (jkmarx)
Fix spacing on status icon. #2233 (jkmarx)
Jkmarx/add modal tool launch error #2232 (jkmarx)
Fix visual bug with tool tip. #2231 (jkmarx)
Jkmarx/analysis global monitor update #2230 (jkmarx)
Scottx611x/galaxy rename dataset action #2228 (scottx611x)
Remove ProtocolReference and ProtocolReferenceParameter from admin ui #2226 (scottx611x)
Scottx611x/fix bower #2225 (scottx611x)
Mccalluc/provvis regression #2223 (mccalluc)
Scottx611x/is tool based cleanup #2222 (scottx611x)
Add missing library script. #2216 (jkmarx)
Mccalluc/fix provvis attributes menu on ff #2215 (mccalluc)
Update django-docker to 0.0.31 #2213 (mccalluc)
Update for boto3 version #2207 (drj11)
Mccalluc/sort filter facets on file browser #2115 (mccalluc)
Add error messages to isatab parser #2036 (scottx611x)

v1.6.0 (2017-10-02)

Full Changelog

Implemented enhancements:

Show zero-count facets in cross-dataset browser #2088
Sort "+" concatenated facet strings #2080
Allow associating uploaded data files with data sets imported from ISA archives #2053
user/files: update facet counts on each click #2005
user/files facet display should be the same as fb2 #2000
user/files: csv export does not include data urls #1968
Discrepancies between "Details" tab: file browser 1 vs. 2 #1890
Group creation modal text update #1883
Change annotation of workflows with single input. #268

Fixed bugs:

Launching Visualization tools fails #2184
Lack of cleanup for Docker temp files causes AWS root volume to reach capacity #2160
Visualization launch fails ~10% of the time? #2154
data set search: "fi" -> 5; "fib" -> 7 #2142
Show zero-count facets in file browser #2089
Details tab, metadata edit: updates not shown in dashboard #2087
cross-dataset browser: Download urls are sometimes still paths #2086
Details tab, metadata edit: save button doesn't seem to work #2084
Old file browser is broken #2083
Internal server error when accessing visualization URLs that do not exist #2079
HTTP 500 error when accessing data set API #2078
Cross-dataset: rows do not match facet counts #2069
all files download CSV fails on test if unfiltered (1000+ rows) #2064
data_sets (new) making unnecessary API calls #2043
user/files csv is broken: 500 #2004
Database connection error when launching AWS stack with custom RDS_SUPERUSER_PASSWORD #1990
/user/files: Why do zero-value facets even show up? #1973
File not found error for /static/images/icons.svg #1967
user/files filename sort doesn't work #1960
Check that user/files link to dataset works #1958
Publicly shared files are not visible when not logged in #1940
On production /user/files API has no results if not logged in #1912
filebrowser2: table rows disappear after scroll in short window #1900
Data set samples are not always displayed in file browser 2 #1882
Canceling analysis does not terminate file import tasks #1730
Provenance Graph Fails to Load #1654
Error importing expanded workflow into Galaxy for analysis #1454
RepoExplorer: initializing with custom root doesn't trigger a query #970
RepoExplorer: Two AND queries don't work as expected #962
RepoExplorer: List graph doesn't re-root on page load #961
Locking a node in the treemap doesn't highlight it in the list graph #954
analysis titles swapped when two analyses are launched simultaneously #631

Closed issues:

Just use pypi instead of git tags for django_docker_proxy versioning #2199
On chrome, provenance for some datasets never loads #2190
tool_manager/utils.py too fussy about types? #2108
Limit number of docker containers #2107
Move please-wait js to django_docker, and refinery only supplies text and style. #2105
Docker "please wait" page until visualization is available #2074
Only one file of two file upload shows up in data_sets at first, but reindex helps #2049
With the files facets collapsed by default, they should expand when there is a facet search #2023
Facet sorts done right #2008
Remove hide option from user/files columns #2003
Replace analysis urls with fb2 urls with appropriate facet #2002
simpler url: "user/files" should just be "files" #2001
/user/files: where is technology? #1972
Preserve facets when navigating from /user/files to filebrowser #1971
user/files: Update history as filters and sorts change #1959
user/files: updating filter or sort updates csv download #1957
user/files facets should be OR, not AND #1955
How to run esformatter? Does it have role in build? #1952
Update check data files functionality to support S3 #1874
Modify tabular metadata file upload form to use S3 #1711
Use django_docker_engine's purge_inactive() #1670
Turn on CORS on S3 #1669
Create documentation #1406
Create non-interactive, external tutorial #1405
RepoExplorer: treemap and list-graph should be collapsible #969
Merge Analysis().prepare_galaxy() into start_galaxy_analysis() #879
Provide status updates for each Galaxy file import #878
Remove unused templates? #783
Add support for Galaxy dataset collections #444

Merged pull requests:

Please-wait is now handled by django-docker #2209 (mccalluc)
Scottx611x/add detailed node info to container launches #2203 (scottx611x)
Update config.yaml.template #2200 (hackdna)
Mccalluc/api should return description 2087 #2197 (mccalluc)
Updating neo4j is slow and should only be done async #2196 (mccalluc)
Hackdna/static asset delivery fix #2195 (hackdna)
Mccalluc/remove old check from provvis 2190 #2191 (mccalluc)
Fix 2184 #2187 (scottx611x)
Introduce a new field with JSON in the API response #2186 (mccalluc)
Disable maximizing webdriver browser window in tests #2181 (hackdna)
With this, I can get to the old file browser #2179 (mccalluc)
Scottx611x/fix derived node attribute inheritance #2174 (scottx611x)
Use the latest django-docker #2172 (mccalluc)
Wait an hour before killing viz containers #2169 (mccalluc)
Hackdna/identity pool to s3 stack #2164 (hackdna)
Mccalluc/facet counts in cross data set browser #2161 (mccalluc)
window.open was causing us to hit pop-up blocker #2159 (mccalluc)
Better icon, as requested by Nils #2158 (mccalluc)
Enable detailed monitoring for EC2 instance #2146 (hackdna)
Reduce max memory for Solr on Vagrant #2131 (hackdna)
Increase wait to avoid Satori load race condition #2127 (mccalluc)
Hackna/neo4j deployment update #2123 (hackdna)
Mccalluc/irrelevent lines in node index tests #2120 (mccalluc)
Sort facet values #2119 (mccalluc)
Clean up display of FB buttons #2118 (mccalluc)
Replace bit.ly links with their targets #2117 (mccalluc)
Accept unicode, Remove explicit str #2114 (mccalluc)
Hit this limit in testing, just bumping max\_length value #2112 (scottx611x)
Make _mkdir() more robust #2111 (hackdna)
Mccalluc/limit docker instances #2110 (mccalluc)
Scottx611x/fix svg 404s #2109 (scottx611x)
Mccalluc/bring back get assays #2104 (mccalluc)
Purge docker containers after inactivity #2103 (mccalluc)
Hackdna/isa tab uploaded files #2102 (hackdna)
django docker please-wait page #2100 (mccalluc)
Scottx611x/fix same name analysis results #2099 (scottx611x)
Hackdna/file store settings update #2098 (hackdna)
Add two missing closing div tags and reformat code accordingly #2097 (hackdna)
Store full urls in solr index. Requires reindex. #2093 (mccalluc)
zero-valued facets #2092 (mccalluc)
Scottx611x/derived node attributes bugfix #2076 (scottx611x)
Mccalluc/merge facets #2073 (mccalluc)
download url in csv + map to ascii in csv #2072 (mccalluc)
fixes the facet updating #2071 (mccalluc)
Mccalluc/update url #2070 (mccalluc)
More robust test. Towards #2067 #2068 (mccalluc)
Scottx611x/analysis groups #2066 (scottx611x)
undo copy and paste #2062 (mccalluc)
Mccalluc/import into own space #2061 (mccalluc)
Mccalluc/details tab #2060 (mccalluc)
keep "import.html" this time; remove the others #2059 (mccalluc)
Remove unneeded js from cross-dataset file browser #2058 (mccalluc)
Jkmarx/data set clean up #2057 (jkmarx)
Prevent old_file_browser api calls and grid generation in current fil… #2056 (jkmarx)
Mccalluc/better fold on facet search #2055 (mccalluc)
Scottx611x/analysis names in fb2 workaround #2046 (scottx611x)
Mccalluc/update solr from celery #2044 (mccalluc)
Scottx611x/remove fastqc viz #2042 (scottx611x)
Mccalluc/user files csv filtering #2041 (mccalluc)
Keeping the same filters between the two pages just will not work. #2040 (mccalluc)
One last case I wanted to check #2038 (mccalluc)
Mccalluc/isatab test #2035 (mccalluc)
Scottx611x/Dataset Collection workflow output association #2024 (scottx611x)
No more column menus. Easy. #2022 (mccalluc)
Mccalluc/data sets to plain data sets #2021 (mccalluc)
Mccalluc/simplify facet css #2018 (mccalluc)
get_assays is buggy, and both are unused #2016 (mccalluc)
data_sets2 slugs #2011 (mccalluc)
Try to make this a little easier to read by replacing RE with constant #2010 (mccalluc)
Mccalluc/new style analyses urls #2009 (mccalluc)
user/files -> files; Not sure about csv #2007 (mccalluc)
Mccalluc/incremental fb rename #1998 (mccalluc)
Hackdna/s3 upload dataset integration #1997 (hackdna)
Fix for #1882 #1995 (scottx611x)
Allow for custom RDS\_SUPERUSER\_PASSWORDs to be set in config.yml #1991 (scottx611x)
Scottx611x/test galaxy cleanup #1989 (scottx611x)
Update phrasing to be more clear #1988 (scottx611x)
Remove unused templates #1987 (scottx611x)
Scottx611x/chucks recent prs #1986 (scottx611x)
More user friendly max-height #1985 (scottx611x)
I was sloppy earlier: We want to OR within, but AND across facets #1983 (mccalluc)
Mccalluc/preserve facets in fb2 #1981 (mccalluc)
Scottx611x/dataset collection updates #1980 (scottx611x)
Hide zero facets #1979 (mccalluc)
Title is unnecessary #1977 (mccalluc)
Mccalluc/search facet labels #1976 (mccalluc)
Mccalluc/max height #1975 (mccalluc)
Mccalluc/where is technology #1974 (mccalluc)
Mccalluc/make filename normal field #1969 (mccalluc)
Put the button back on the dashboard #1965 (mccalluc)
Mccalluc/user files sort by filename #1964 (mccalluc)
Fix #1955: AND -> OR #1963 (mccalluc)
Mccalluc/remove esformatter again #1962 (mccalluc)
Not using jshint since #942 #1953 (mccalluc)
More JS cleaning #1951 (mccalluc)
Mccalluc/user files sorting #1950 (mccalluc)
Scottx611x/workflow launching and monitoring #1949 (scottx611x)
Mccalluc/link user files to data sets #1944 (mccalluc)
Mccalluc/user files not logged in #1942 (mccalluc)
Mccalluc/public datasets regression #1941 (mccalluc)
Scottx611x/workflow launching #1939 (scottx611x)
Mccalluc/unnecessary evals #1935 (mccalluc)
"++" is not an operator in Python. #1934 (mccalluc)
Mccalluc/errors from landscape #1933 (mccalluc)
Mccalluc/no commit manually #1932 (mccalluc)
Mccalluc/upgrade travis #1930 (mccalluc)
isort everything #1927 (mccalluc)
I think we were only indexing the values we got the last time through #1875 (mccalluc)
Mccalluc/user files facets fixes #1869 (mccalluc)
Masking errors not helpful #1863 (mccalluc)
Mccalluc/cleanup data set manager models #1827 (mccalluc)
Terminate file_import tasks upon cancellation of an Analysis #1747 (scottx611x)

v1.5.8 (2017-07-17)

Full Changelog

Implemented enhancements:

Flekschas/satori v1.5 #1776 (flekschas)

Fixed bugs:

exploration views do not fully instantiate #1907
Search keywords are still highlighted after clearing the search #1583
Flekschas/satori v1.5 #1776 (flekschas)

Closed issues:

Upload Form: Sample Identifier Typo #1906
Number of References doesn't match expected? #1903
Add Satori to manual testing #1896

Merged pull requests:

Add svgxuse dependency to allow for external svgs to properly be loaded #1919 (scottx611x)

v1.5.7 (2017-07-11)

Full Changelog

Implemented enhancements:

IntroJs tutorials are not checked until user refreshes page #1774
Tool Panel Collapse #1645
Add description of backup and recovery on AWS to wiki #901
Flekschas/isa tab import no annotated node explosion #1763 (flekschas)

Fixed bugs:

Provisioning failure with NoMethodError in Puppet #1847
Handle Exceptions during rebuild\_index mgmt. command #1735
Handle AttributeError in DataSet REST API #1734
Flekschas/isa tab archive import bug fix #1762 (flekschas)

Closed issues:

finalize isort config #1830
UI: /user_files -> /user/files #1792
use isort to reorder imports, and add to flake8 #1770
avoid writing to config.yaml file #1751
Make sure EBS data volume is unmounted without errors on stack deletion #1722
Be able to Launch a ToolDefinition: Workflow with tools endpoint #1712
Import SCC public RNA-Seq & ChipSeq Datasets #1706
Data Set 2 - Launch Tool Validation UI #1701
UI - Grid Selection Display #1649
Node Groups Repurpose #1643
After migration of repo, reconnect travis #1493
On AWS the suggested EBS volume is too small #938

Merged pull requests:

Scottx611x/analysis custom name bugfix #1897 (scottx611x)
Annotated node explosion with tests #1887 (scottx611x)
Add refinery-base styling to buttons. #1870 (jkmarx)
Jkmarx/data set2 css update #1866 (jkmarx)
Data structure rather than string is more robust #1865 (mccalluc)
No more ajax error when not logged in (facets still empty, though) #1864 (mccalluc)
Jkmarx/add comments in tool launch #1862 (jkmarx)
ELB Logging in CloudFormation #1860 (drj11)
Fix concat bug when offset is 0. #1859 (jkmarx)
Jkmarx/add exit modal #1858 (jkmarx)
Mccalluc/make the facets do something #1857 (mccalluc)
Hackdna/s3 data upload #1856 (hackdna)
Mccalluc/connect user files facets api ui #1855 (mccalluc)
Scottx611x/run analysis refactoring #1854 (scottx611x)
Mccalluc/refactor search indexes #1850 (mccalluc)
Update text. #1849 (jkmarx)
Jkmarx/remove group bug #1846 (jkmarx)
Jkmarx/fix icon bug #1843 (jkmarx)
Jkmarx/remove group bug #1842 (jkmarx)
Scottx611x/workflow launching updates #1841 (scottx611x)
/api/v2/user/files/ now returns the facets I need #1840 (mccalluc)
Jkmarx/details owner name bug #1839 (jkmarx)
Mccalluc/user files facets #1838 (mccalluc)
Jkmarx/relocate config button #1835 (jkmarx)
Jkmarx/missing nav bar bug #1834 (jkmarx)
Sort django above other third party, and local above first part #1831 (mccalluc)
Fix color issue associate on deselecting a node. #1829 (jkmarx)
Jkmarx/reindex on remove #1828 (jkmarx)
Scottx611x/workflow launching #1825 (scottx611x)
Mccalluc/add fields to datasetmanager index #1824 (mccalluc)
Explain why we have a default haystack #1823 (mccalluc)
Jkmarx/add missing library #1821 (jkmarx)
Add depthNames data and replace types. #1820 (jkmarx)
Hackdna/s3 data upload backend #1819 (hackdna)
Scottx611x/analysis manager updates #1817 (scottx611x)
Jkmarx/row template updates #1816 (jkmarx)
Mccalluc/begin user files facets #1814 (mccalluc)
Mccalluc/better user files columns #1811 (mccalluc)
Jkmarx/parameter popover #1810 (jkmarx)
Jkmarx/panel view perms #1808 (jkmarx)
Add Contributing.md #1807 (scottx611x)
Fix launch button regardless of sizing. #1806 (jkmarx)
Scottx611x/tool manager updates #1805 (scottx611x)
Jkmarx/data set 2 fix button hide #1804 (jkmarx)
Fix bound bug by using the auto-resize ui-grid module. #1802 (jkmarx)
Fix parsing error. #1801 (jkmarx)
Refactor - simplify popover in input group. #1800 (jkmarx)
Scottx611x/tool manager updates #1799 (scottx611x)
Mccalluc/user file browser real data #1798 (mccalluc)
Jkmarx/data set 2 tools param #1797 (jkmarx)
Scottx611x/selenium bug fix #1795 (scottx611x)
Jkmarx/https fix #1793 (jkmarx)
Mccalluc/landscape smells #1791 (mccalluc)
Jkmarx/generalize attribute filter #1790 (jkmarx)
Update smaller services according to style guide. #1788 (jkmarx)
Jkmarx/file browser refactor services #1787 (jkmarx)
Update module and setting file to style guide. #1786 (jkmarx)
Jkmarx/file browser refactor ctrl #1785 (jkmarx)
Mccalluc/user files continued #1784 (mccalluc)
Refactor directives according to angular style guide. #1783 (jkmarx)
Jkmarx/data set 2 additional comments #1782 (jkmarx)
Jkmarx/persist workflow collapse #1781 (jkmarx)
Add scrolling to tool panel. #1780 (jkmarx)
Jkmarx/data set 2 input group column bug #1779 (jkmarx)
Move helper functions from main AWS stack into a separate utils file #1777 (hackdna)
Mccalluc/user files next steps #1772 (mccalluc)
isort prehook #1771 (mccalluc)
Scottx611x/cleanup tool containers #1766 (scottx611x)
Jkmarx/data set 2 remove bug #1761 (jkmarx)
Add popover in input group column. #1758 (jkmarx)
Jkmarx/data set 2 list display changes #1757 (jkmarx)
S3 bucket for config #1756 (drj11)
Jkmarx/display node data #1750 (jkmarx)
Mccalluc/all files empty ui start api #1749 (mccalluc)
Scottx611x/update index on post save #1748 (scottx611x)
Handle errors that have occured when rebuilding solr's index #1746 (scottx611x)
Jkmarx/add launch validation #1745 (jkmarx)
Jkmarx/remove node group #1744 (jkmarx)
Jkmarx/hide selection column #1743 (jkmarx)
Jkmarx/collapse tool panel #1742 (jkmarx)
Add event to close popover when clicking on select icon. #1741 (jkmarx)
Jkmarx/data set 2 input group display #1740 (jkmarx)
Scottx611x/dataset api error handling #1739 (scottx611x)
Jkmarx/data set 2 add selection nav #1737 (jkmarx)
Jkmarx/generate launch configs #1733 (jkmarx)

v1.5.6 (2017-05-15)

Full Changelog

Implemented enhancements:

Replace Makefile with AWS API calls using boto3. #1694
Tool Launch Configurations & ToolDefinition Updates #1672
Tabular Metadata Upload - Enhancements Cont. #1656
Input Tool: 'working panel/cart' #1604
Data Set 2 - Fix CSS on tabs #1451
add 'annotation' Solr query field to node set #385
keep a fixed URL (=UUID) for all versions of a data set #314
Address #1663 in README #1704 (ngehlenborg)
Jkmarx/tabular upload enhancements #1677 (jkmarx)

Fixed bugs:

Group Details: Empty Names #1726
Revise indexing of data sets in Refinery #1702
Help popover's partial not found #1673
Paired Input File Mapping - Safari Web Content Error #1663
PhantomJS causing OOM failures #1660
Data file upload failure when data set is submitted before files are uploaded #1659
Newly imported Datasets don't show up in the Exploration tool #1560
ProgrammingError during ELB health checks #1397
"core" and "data_set_manager" tests can't run separately #1353

Closed issues:

Changes to Upload page text #1729
Use stack name to generate RDS instance name #1718
Avoid explicitly setting Availability Zone. #1709
Collaboration/sharing updates #1707
Search discrepancy: cdx vs. cdx2 #1703
Can't cleanly delete CloudFormation stack due to circular dependency #1678
Data Set 2: File_Relationship Service #1662
on AWS, automatically rotate backups #1648
DataSet2 - Paired Input Analysis #1267
Download multiple files at once #1253
Enable tagging of CloudFormation stacks #1176
Configure serving UI assets (static files) from S3 #838

Merged pull requests:

Jkmarx/import text update #1732 (hackdna)
Jkmarx/import text update #1731 (jkmarx)
Scottx611x/migration bug fix #1723 (scottx611x)
Add REFINERY\_CUSTOM\_NAVBAR\_ITEM setting to display extra link #1721 (scottx611x)
Add reserved word list to data import upload page. #1720 (jkmarx)
Name RDS instance with the CloudFormation stack name #1719 (drj11)
Convert RDS backups to automatic snapshots #1717 (drj11)
Scottx611x/indexing updates #1716 (scottx611x)
Jkmarx/tools service #1715 (jkmarx)
Jkmarx/sharing text update #1714 (jkmarx)
Jkmarx/sharing bug #1713 (jkmarx)
Remove the explicit choice of AZ #1710 (drj11)
Sweep away the last remnants of the old Makefile #1708 (drj11)
Jkmarx/file relationship unit test #1700 (jkmarx)
Jkmarx/file browser factory refactor style #1698 (jkmarx)
Jkmarx/data set2 bug fixes #1697 (jkmarx)
Scottx611x/test folder cleanup #1696 (scottx611x)
Add script to create EBS Snapshot Scheduler stack. #1693 (drj11)
Scottx611x/tlc updates #1692 (scottx611x)
Add tags to the CloudFormation stack itself #1691 (drj11)
tag EC2 instances for backups #1690 (drj11)
Hackdna/storage stack #1689 (hackdna)
Jkmarx/data set2 indicator column #1688 (jkmarx)
Jkmarx/clean up ui grid defaults #1687 (jkmarx)
Jkmarx/remove unused data set2 visual mod #1686 (jkmarx)
Remove Makefile #1685 (drj11)
Add basic landscape.io config file #1684 (scottx611x)
Jkmarx/data set 2 form data validation #1683 (jkmarx)
Add help popover and adjust text. #1682 (jkmarx)
Jkmarx/data set 2 tool panel cont #1681 (jkmarx)
Require STACK_NAME in aws-config #1680 (drj11)
Hackdna/postgres conf update #1679 (hackdna)
Jkmarx/data set 2 grid selection #1676 (jkmarx)
Scottx611x/django docker engine integration #1674 (scottx611x)
Hackdna/ec2 ips django settings #1671 (hackdna)
Hackdna/s3 static files #1668 (hackdna)
Jkmarx/tool control panel #1667 (jkmarx)
Scottx611x/docker puppet install #1664 (scottx611x)
Fix typo in method call. #1657 (jkmarx)
Scottx611x/td api fixes #1653 (scottx611x)
Scottx611x/run selenium on travis only #1650 (scottx611x)

v1.5.5 (2017-04-03)

Full Changelog

Implemented enhancements:

Tool Data Cart : Ensure it works for any PAIR:LIST combos #1661
Tabular Metadata File Upload Enhancement Con't #1638
Meta Data Import - Fix "Optional Upload Data Files" Language #1637
"?" help icon should be consistent across pages #1633
create separate "Before You Get Started Section" #1632
Remove "Make Public" field from data set upload page #1628
remove base path field from file upload page #1627
add screenshot annotations to tutorial #1625
DataSet Enhancement - Add how-to intro #1616
load data from non-Galaxy directories #367
Jkmarx metadata upload enhancements #1639 (jkmarx)
Remove base path and make public. #1630 (jkmarx)
Jkmarx/data upload enhancements #1626 (jkmarx)

Fixed bugs:

spacing in About page layout is broken #1640
advanced section opens upon click anywhere on the row representing the collapsed section #1634
Analysis links in DataSet delete modals 404 #1589
Fix missing padding on about. #1641 (jkmarx)
Fix styling. #1636 (jkmarx)
Jkmarx/data set upload fixes #1635 (jkmarx)

Closed issues:

Attribute Filter UI Enhancement #1644
Tool Definitions API #1613
Display will change depending on tool selected #1605

Merged pull requests:

Scottx611x/fix analysis 404 #1658 (scottx611x)
Jkmarx/attribute filter updates #1647 (jkmarx)
Scottx611x/td api #1646 (scottx611x)
Jkmarx/tool launch module #1642 (jkmarx)
Scottx611x/acceptance test bugfix #1631 (scottx611x)
Add the ability to generate basic ToolDefinitons from properly annota… #1624 (scottx611x)
Scottx611x/td api url routing #1622 (scottx611x)
Scottx611x/td api #1620 (scottx611x)
Add security group #1606 (drj11)

v1.5.4 (2017-03-02)

Full Changelog

Implemented enhancements:

Data Upload Page Enhancement #1615
Update Collaboration Page Styling #1597
Data Set - Edit Capabilities #1591
Data Set / share API Adjustment #1191
Collapse advanced settings. #1617 (jkmarx)
Update years in license #1612 (ngehlenborg)
Modify /sharing to return only owner and share_list. #1611 (jkmarx)
Jkmarx/colloration styling update #1598 (jkmarx)
Jkmarx/edit data set #1595 (jkmarx)

Fixed bugs:

Url error #1608
Data set sharing list in File Browser 2 too comprehensive #1600
Empty last protocol step #1522
Upload Raw Data - Overall Progress Bar Issue #1300
Provenance graph breaks when analysis is lost #1098
Add conditional to remove unnamed protocols. #1609 (jkmarx)
Jkmarx/data set sharing api bug #1602 (jkmarx)

Closed issues:

Node Group API - is_current field use #1329
Unit Tests: Service to create uuids #1289
Cleanup Python module imports #890
provenance graph timeline can be shifted #816

Merged pull requests:

Utilize Transaction Management for case where Data already exists #1623 (scottx611x)
Jkmarx/data set edit adjustments #1610 (jkmarx)
Prevent console errors when in data set 2. #1607 (jkmarx)
Fix relative imports in management commands #1601 (hackdna)
Jkmarx/mock uuid service #1596 (jkmarx)

v1.5.3.1 (2017-01-23)

Full Changelog

v1.5.3 (2017-01-23)

Full Changelog

Implemented enhancements:

move repo into refinery-platform organization #1504
Tutorial Enhancement #1459
Refactor data-set-nav: don't use rootScope #943
Allow user to sort data set file browser based on node selection #892
deploy IGV WebStart directly from Refinery site #325
add compact mode to new workflow annotation #285
more detailed progress indicator (for power users?) #255
Workflow Page - Hide Edit Button Enhancement #1527
Navbar - Global Analysis Popover #1525
Collaboration UI - Membership Permissions #1474
Saved filter selector should be reset when "reset" is clicked #1314
Avoid duplicating fields if they are annotated as both a characteristic and a factor #446
Update data set total file size after data set changes #309
Jkmarx/colloration modal update #1565 (jkmarx)
Wrap delete model to check for user permissions. #1564 (jkmarx)
Edit new line in sample file for command line view. #1558 (jkmarx)
Add permissions conditional. #1555 (jkmarx)

Fixed bugs:

Data Set 2 Browser - Cont. Scroll Bug #1577
Error entering duplicate group name when creating a new group #1477
Analysis is reported as finished successfully while still running in Galaxy when AJAX call to analysis_status view results in a server error #451
Data Set 2 Browser - Fix URL for Duplicate Attribute Fields #1567
Data File Import: Uploading Bug #1542
Data Import Error Handling #1538
Data Set Preview - Missing Technology Field CSS #1526
Data Set 1 - Launch Web Based IGV #1520
Dashboard - Import into Own Space Bug #1519
Dashboard - Sharing Modal Bug #1518
API V1: Group Members can Delete Group #1426
DataSet2 Browser - Fastqc Viewer Bug #1409
DataSet2 - Attribute Filter Bug #1046
allow same name for characteristic and factor value fields in study/assay file #849
Jkmarx/data set2 cont scroll bug #1582 (jkmarx)
Jkmarx/group name duplicate error #1573 (jkmarx)
Jkmarx/data set 2 url bug #1568 (jkmarx)
Adjust html so analysis's column can't be hidden. #1566 (jkmarx)
Jkmarx/data set 2 attribute filter bugs #1562 (jkmarx)
Jkmarx/data set ui size update #1557 (jkmarx)
Add object to keep seperate preview items. #1556 (jkmarx)
Jkmarx/data set import file order bug #1545 (jkmarx)
Jkmarx/data set import delete files #1541 (jkmarx)
Jkmarx/data set preview hide empty technology #1535 (jkmarx)
Add pointer class to global analysis cog. #1533 (jkmarx)
Prevent limiting solr data returned. #1532 (jkmarx)
Jkmarx/sharing modal bug #1531 (jkmarx)

Closed issues:

"Add all to DataCart" star is broken #1579
Update Deprecated Grunt-AutoPrefixer to Grunt-PostCSS #1528
Find underlying issue behind needing to run specific app's migrations individually #1146
Load third-party UI dependencies in static via bower #1016
Importing ontologies and annotations from a pre imported Neo4J database should be automated #1401
Pin Javascript dependencies to exact versions #1288
Dashboard Preview- Console Error 401 for unowned data-set #1061
Update to AngularJS 1.5.x #986
Configure Apache using Puppet module #779
Upgrade to Django 1.7 #614

Merged pull requests:

Fix issue with Exploration tool #1588 (scottx611x)
Change default setting so modals can be esc. #1576 (jkmarx)
Update references to current repo for new refinery-platform organiz… #1574 (scottx611x)
Scottx611x/django 1.7 upgrade #1511 (scottx611x)
Flekschas/angular 1.5 #1559 (jkmarx)
Jkmarx/tech debt update does not exist #1553 (jkmarx)
Jkmarx/javascript dependency pin #1521 (jkmarx)

v1.5.2.1 (2016-12-19)

Full Changelog

Implemented enhancements:

Ontology hover style cause unnecessary redraws #1404

Fixed bugs:

Data set preview in repo mode doesn't work #1547
Repo mode #1546

Merged pull requests:

Scottx611x/django 1.7 upgrade apache settings fix #1544 (scottx611x)
Scottx611x/automate neo4 j installation #1536 (scottx611x)

v1.5.2 (2016-11-18)

Full Changelog

Implemented enhancements:

Collaboration Modals #1473
Data Set 2 - Deactivate Selected Filters #1508
IGV should always include gene annotation track #1494
Remove running Analysis cog animation from LaunchPad filter #1476
Data Set 2 - Persist UI-Grid Data #1446
Validation of saved sets #1342
Set selector should change on save #1341
Provide two button for quick asignment of files to paired input analyses #1019
Safari Only: IGV Download Opens Blank Tab #847
Scrollbar madness after isatab import #730
On Dashboard, Analysis list does not update status #693
Success message is shown each time a successful analysis is visited. #619
Deleting analyses within the django admin interface should not delete them permanently. #480
Update node set sizes after data set update #308
create "node detail" view with file download option in sample selection interface #243
Remove analysis monitor alerts in html, ctrl, service, etc #1517 (jkmarx)
Jkmarx/data set2 utility deactivate selected #1512 (jkmarx)
Jkmarx/node group refactor #1499 (jkmarx)
Jkmarx/data set2 persist ui grid data #1495 (jkmarx)
Jkmarx/data set2 analyses about refactor #1492 (jkmarx)
Remove unneccessary cog animation. #1488 (jkmarx)

Fixed bugs:

Problem loading remotely located bed file into web-based IGV #1487
Tabular files with a single row don't show up properly in data_sets 1 file browser #1463
Data Set 2 Utility/Refresh Bug #1506
Clicking IGV launch buttons is possible without selecting a species #1496
Index files are not created for BAM files generated by RNA-seq workflows #1491
Tabular Meta Data File - Cancelation #1475
Dashboard: Data Cart Selection Bug #1471
Dashboard Filter & Sorting Bug #1469
Dashboard Filter Bug #1468
tabular meta data file upload failing in Safari 10.0.0 #1465
Tabular Meta Data - Bug when upload fails #1458
Modification Date UI Bug - Test Site #1457
DataSet2 - Analyze Persist Node Group Selection #1325
Filter counts broken between digits #1310
Firefox: "Search" placeholder positioned too low #1306
Dashboard workflow loading animation seems to be linked to the data set loading. #934
Prov Vis: Button for change layering is not correct after Bootstrap 3 upgrade #806
Jkmarx/igv selection bug fix #1514 (jkmarx)
Jkmarx/data set2 utility persist bug #1507 (jkmarx)
Jkmarx/data set2 bug #1503 (jkmarx)
Jkmarx/data set1 attribute filter count bug #1501 (jkmarx)
Jkmarx/data import cancelation bug #1500 (jkmarx)
Jkmarx/prov vis bug #1498 (jkmarx)
Disable igv buttons until species selected. #1497 (jkmarx)
Jkamrx/dashboard filter bug #1490 (jkmarx)
Add helper method to exit error div.: #1486 (jkmarx)
Remove add data set method. #1485 (jkmarx)
Specifically set blob api for safari. #1482 (jkmarx)

Closed issues:

Remove all print statements from Python code #1195
Upgrade Puppet apt module to v2.3.0 #774
Update external Javascript packages to the latest stable versions #452

Merged pull requests:

Towards HiGlass UI #1509 (mccalluc)
Hackdna/neo4j repo key error #1505 (hackdna)

v1.5.1 (2016-10-20)

Full Changelog

Fixed bugs:

"datafile" field in FileStoreItem cannot be documented automatically #328

Closed issues:

Adding User to neo4J produces too much travis output #1376
Enable viewing BAM files in IGV #1264

v1.5.0 (2016-10-14)

Full Changelog

Implemented enhancements:

Ui-Grid Multi-sorting Feature Unneccessary #936
Data Set Import Update #1430
UI - Help Animation #1414
Make sure we have a desired reference genomes for IGV #1411
Shortcut not validated for being alphanumeric + "_" #1395
Waving help in banner is distracting after a while #1393
Handle multiple admins, rather than just taking the first email #1388
Data Set 2 Browser - Implement New Layout #1384
Separate selectors for UI state and actions could be confusing #1339
Redundant error messages when given email is invalid #1332
Data sets filter not available when not logged in #1316
Tabular Upload: Add a strip warning #1262
Data Set Preview -- Sharing Modal Needs more text #1246
Implement automatic backups on AWS #1053
Easy-to-usify collaboration #1017
Provide Deletion controls for DataSets and Analyses #866
Jkmarx/data import slug validation #1441 (jkmarx)
Jkmarx/collaboration add member enhancements #1440 (jkmarx)
Jkmarx/sharing modal enhancements #1436 (jkmarx)
Jkmarx/dataset2 igv #1433 (jkmarx)
Jkmarx/file upload text update #1432 (jkmarx)
Add warning of file strip. #1422 (jkmarx)

Fixed bugs:

Ontology Explorer doesn't work from dashboard when logged in? #1402
CSRF Error upon datafile upload (Only in Windows) #1370
Tutorial Bug, launching from about page #1472
different species applied to same url not respected #1464
UI - Failed Unit Test, Locally #1427
Analysis Redirect UI Bug #1415
DataSet2 - Persist Files URL when Filters Selected #1412
Strange completion percentage #1394
"Invite New Member" with bad email / hit return / no error #1333
Progress percentages for analyses need to be trimmed #1317
Firefox: Dataset "preview" URLs do not load preview #1312
"Permission Editor" "Save" does not close modal #1311
Users should not be able to remove themselves from "Public" group #1304
Affiliation not saved during account creation #1303
Workflow input names are not unique error during workflow import #1265
Inconsistent UI behavior and server error when canceling group creation #1248
Incorrect number of samples displayed in the sample browser during import #1241
handle node blacklist/whitelist in IGV launch #386
Jkmarx/data set web igv fix #1456 (jkmarx)
Jkmarx/data set 2 persist filter url #1450 (jkmarx)
Remove unused code, which may be causing login bug. #1449 (jkmarx)
Round percentages. #1442 (jkmarx)
Fix #1312 #1439 (flekschas)
Show filters only for logged in users. #1437 (jkmarx)
Enable share button only for data set owners. #1434 (jkmarx)
Jkmarx/account affiliation bug #1429 (jkmarx)
Jkmarx/public group bug fix #1424 (jkmarx)
Jkmarx/group create bug #1420 (jkmarx)
Update error message for missing emails. #1419 (jkmarx)

Closed issues:

Remove infrastructure and code for Sphinx docs #1240
Delete Sphinx docs directory #1431
"Group Editor" dialog is missing cancel button #1305
DataSet2: IGV #1271

Merged pull requests:

Hackdna/workflow import #1443 (hackdna)
Jkmarx/unify alert appearance #1448 (jkmarx)
AWS backups #1418 (drj11)
Jkmarx/dataset2 new layout #1413 (jkmarx)

v1.4.0 (2016-09-15)

Full Changelog

Implemented enhancements:

Data Set 2 Browser - Refactor Display Button #1373
Data Set 2 - New Run Analysis Launch #1372
Data Set 2 - Remove Orange Button Nav #1371
Upload Raw Data - UI Clarity #1299
Duplicate About in header and file browser tab #1245
Explore IGV.js and pileup.js integration options #1237
Tutorial overlays for end users #1226
Reword tabular file import instructions and add more help #1111
Two import buttons are confusing #797
Jkmarx/dataset2 launch analysis #1385 (jkmarx)
Jkmarx/dataset2 display refactor #1382 (jkmarx)
Jkmarx/dataset2 remove orange nav #1375 (jkmarx)

Fixed bugs:

Upload + Explore button should be in one row #1399
Data Import Bug in Safari #1361
System Administrator email missing #1340
UI suggests Data set files can be reordered, but they can't #1313
Metadata table preview does not persist #1291
DataSet2 - UI Grid Bug #1268
Jkmarx/data import safari fix #1383 (jkmarx)

Closed issues:

For the time being, support both old and new IGV #1356
Integrate ELB with the CloudFormation stack #1170

Merged pull requests:

Scottx611x/enable viewing bam in igv #1390 (scottx611x)
Change file browser link color when in preview mode. #1374 (jkmarx)

v1.3.0 (2016-08-26)

Full Changelog

Implemented enhancements:

Data Import Alert #1352
Data Import - Reorganize Tab and Content #1336
Data Import - Pre-select column selection #1323
Data Import Add Link to Metadata sample #1322
Data Import Update Text Order #1321
Upload Button Enhancement #1301
Add support for BCL files and .fq extension #1280
Data Set2 Browser: Prevent Empty Node Groups and Launch Analyses #1278
Data Set 2: Clear button should also reset attribute filters #1269
Update BackEnd to Strip WhiteSpaces in tab delimited metadata file generated as output from R #1260
Change layout of the metadata upload page #1255
Problem loading tab delimited metadata file generated as output from R #1252
Node Group API - Current Selection First #1244
NodeGroup API Update - Select All Nodes #1223
Integrate NodeGroup Api in Data Set 2 UI #1213
Create proof of concept for a tutorial/more verbose help for users throughout Refinery #1212
DataSet API - Add Fields #1190
Django Rest - Node Set API #1175
Dashboard - Data Set List Add Tooltip #1154
Analysis Cancel Permission UI #1151
DataSet2 - Add Fastqc Viewer #1047
DataSet View: Merge Sharing and Details Tab #907
Unknown or running analysis page doesn't contain any files #893
On AWS, choice of SSH keys is fixed #859
caching in file server backend #351
Bring unit tests for file store up to date #339
Recolor import button and file browser link. #1366 (jkmarx)
Update ISSUE_TEMPLATE.md #1359 (jkmarx)
Jkmarx/data import reorganize tabs #1345 (jkmarx)
Jkmarx/data import text update #1331 (jkmarx)
Jkmarx/node group api reformat #1263 (jkmarx)
Jkmarx/data set2 select all update #1234 (jkmarx)

Fixed bugs:

Error importing tabular metadata #1351
remote files get imported into file store despite 404 response #1318
Permission Editor not available for unshared data sets #1315
stalls if required fields on import not given #1308
Upload Raw Data #1298
Impossible to upload more than one data file #1292
Error during npm update #1283
Data file uploads failing #1282
DataSet2: Bug with Filters and Complement Nodes #1275
DataSet2 Analyze - Workflow Select Resets to Placeholder #1272
Update BackEnd to Strip WhiteSpaces in tab delimited metadata file generated as output from R #1260
Unhandled UnicodeEncodeError in visualization_manager #1254
Unable to launch IGV for RNA-seq's tophat_accepted_hits file (bam format) #1251
Data set name is not displayed correctly in the launch pad #1242
Make Django's ALLOWED_HOSTS work with AWS ELB Health Checks #1239
DataSet2 Infinite Scroll - Select All #1235
Can't import the massive dataset #1233
Incorrect message displayed when admin approves user account #1228
javascript spark-md5 error in firefox #1222
DataSet2 - Extra Input Box under UI-Select Drop-down #1217
Incorrect message displayed when deleting data sets #1216
Node Set Button - Reset Broken #1215
Workflow API V2 Exposes All Workflows #1207
Inactive workflows included in the total on Statistics page #1205
Error in browser console when viewing data set summary #1202
Admin user does not belong to the Public Group #1182
RabbitMQ GPG error during provisioning #1181
Undefined slug should be allowed #1166
Isa archives associated with a DataSet persist after DataSet deletion #1158
Start time is incorrect in analysis result emails #1155
Solr plugin for synonym resolution in wrong location #1153
account activation email needs to be more specific #1149
Solr error when importing ISA archives on AWS #1116
relaunching stack with RDS snapshot fails due to missing host and port in config.json #1099
Downloading input file after its been analyzed yields weird results. #1083
remote data automatically imported into Refinery even when not requested #1079
Add error handling to visualization_manager.views.get_file_name() #1058
DataSet 2 - Assay Attribute API -- Ranks Initially 0 #1035
Unable to using latest Debian #1024
figure out why Read the Docs can’t find the djcelery package #467
Fix conditional for updating current selection. #1285 (jkmarx)
Jkmarx/data set2 attribute filter fix #1279 (jkmarx)
Flekschas/satori fixes #1165 (flekschas)

Closed issues:

Analysis Node-Group Run - Update Exception Handling #1277
DataSet2 - Node Group Selection #1273
Remove share\_list field from API endpoints #1238
Django settings cannot be controlled from config.yaml on AWS #1232
This is just scott testing the slack integration #1230
Data Set 2 - Update Select-All Event #1224
AWS install breaks trying to install librarian-puppet #1220
Change Django settings to production configuration on AWS #1208
DataSet2 - FileStoreItem API Add Field #1199
DataSet2 - FileStoreAPI Display & Services #1198
FileStoreItem API #1192
Document process of installing Neo4J Ontologies/Annotations from Fritz's Database Backups #1159
Data Set Attribute Filter - CSS Spacing Issue #1152
DataSet2 - Implement Launch Analysis Single Input Workflows #1038
Attribute Order Model Update #891
Resource performance tests #365

Merged pull requests:

Jkmarx/dataset2 attribute fix #1363 (jkmarx)
Add support for .fq FileExtension and .BCL FileType/FileExtension #1327 (scottx611x)
On metadata file upload, remove leading/trailing white spaces on all … #1259 (jkmarx)
Add default to whitelist on reset. #1257 (jkmarx)
Add Private IP to ALLOWED_HOSTS #1249 (drj11)
Jkmarx/data set2 node group #1225 (jkmarx)
Fix location of solr plugin in AWS #1204 (drj11)
Jkmarx/file store api updates #1196 (jkmarx)
Scottx611x/auto import of data fix #1188 (scottx611x)

v1.2.0 (2016-05-23)

Full Changelog

Implemented enhancements:

show admin contact information on registration confirmation page #1148
Pair Analysis UI - Analysis Title shown instead of UUID #1134
Open sample files in a new browser window #1128
Data Set Browser - Filter Analysis Group Value -1 #1110
Clarify login interface #1109
analysis in initializing, failed, or unknown status should be linked to corresponding data set analysis tab #1100
Explain MD5 spinner and disable upload buttons properly #1081
Create tab test file for 13293 #1073
One can click on the global upload button multiple times #1071
Remove Analysis Email Capabilities #1069
Add visual indicator when custom files have been uploaded #1066
DataSet2 View, selected attributes filters should always be visible #1025
Data set summary panel should limit number of analysis shown #1014
Swap data set surrogate title and preview links #1012
Setup esformatter to autoformat JS #982
RepoExplorer: implement a way to clear the data cart #972
RepoExplorer: distinguish data cart from rest of the data set list more strongly #967
RepoExplorer: DataCart: Add distinct state when panel is opened #964
RepoExplorer: Visible depth is not stored in the URL #960
Protocol item's appearance should change #958
Implement UI-Grid Infinite Scroll #949
Refactor node-relationship.js #946
Refactor node-mapping #945
Replace jshint with eslint #942
Refactor and angularize full-height panels #935
Integrate Attributes Tab Capability into DataSet Files Table #906
Clean up UI JS root directory #904
Duplicated Angular API service #903
Recreate Data Set Table in Angular #897
Encode facet filters into URL query #896
Create Test Dataset with Multiple Studies and Assays #895
Consolidate AWS deployment configuration files #888
Assign a name to Refinery EC2 instance using CloudFormation #887
Assess whether git pre-hooks is good way to run stuff before committing. #885
Analysis Monitoring -- Add flag when backend pauses #876
Analysis Monitoring - Consolidate Progress Bars #869
Fix Current_Commit in production #857
Statistics Page Fix CSS Layout #850
Celery looses worker when the os runs low on memory #842
AWS deployment should use a separate EBS volume #837
AWS deployment should use RDS #835
Dataset Browser moved to the AngularJS #831
Prepare deployment scripts for use with EBS and RDS #805
Change start and end time format after some time. #687
Enable server side gzipping and caching in Apache #662
Group data set associated analyses by user #343
Add functionality to keep galaxy workflows, libraries, and histories #324
Create Sphinx documentation for database migration with South #319
*[8]* correct notifications about error states #298
Swap caret to table for data-set-explorer link. #1065 (jkmarx)
Jkmarx/add file download data set2 #1042 (jkmarx)
Flekschas/repo mode #1040 (flekschas)
Tag the root EBS #1037 (drj11)
Flekschas/rex paper #994 (flekschas)
Jkmarx/data set fix solr params #977 (jkmarx)
Jkmarx/data set encode facet filters #974 (jkmarx)
Flekschas/node mapping refactoring #947 (flekschas)
Flake8 #905 (flekschas)
Dashboard exploration neo4j outsourcing #882 (flekschas)

Fixed bugs:

DataSet Browser -- Column Config lacking css #1150
Remove all hardcoded references to 'vagrant' from all settings files #1147
REFINERY_DATA_IMPORT_DIR is not set correctly on AWS #1139
Move REFINERY_URL_SCHEME to config.json.erb #1136
Data sets are not displayed on the home page when served over HTTPS #1135
DataSet Browser, Analyze: Delete Modal Missing Template #1125
Analyze Ui Bug - Paired Workflow #1123
Data sample properties are not displayed during input mapping #1118
Sample drop area is not displayed when a new workflow input pair is created #1117
Registration: E-Mail is not required to be unique. #1113
Anaylsis Monitoring Api - rename cancel property #1108
Analysis monitor throws error when no object is returned by the API #1097
TypeError prevents analyses from completing successfully #1094
Fileupload broken when running in prod mode #1093
data set list on top of data set list filter when data set summary is open #1089
Failed custom upload interface broken #1082
Analysis Launch/Completion Emails Not Sent #1076
Check files dialog broken #1074
Dashboard - Owner Display #1064
Dashboard Preview: Abstract caret misdirection #1062
Unable to cancel Analyses #1057
IGV session file contains URLs without base URL for local files #1056
IGV launch file need to be created with session file instead of with sample meta data file #1055
Data Set - Pairs Analysis UI Missing #1052
Data Set Browser - Missing Table #1050
Console Error - Analyses Viewing Error in Data Set Explorer #1044
Console Error - Missing data-set-ui-node-mapping.html #1043
Dashboard Preview - Double Click Bug #1041
Workflow vis container grows when the window's width is changed #1030
Assay Attribute Api Does not return Exposed + Non-facet Fields #1028
Progress bar of custom file upload is broken #1022
Tabular file upload page broken #1021
Provvis shifted away when opening analyze #1020
IGV launcher has 2 empty entries #1018
The number of data files returned by the API is incorrect. #1013
The "forgot password" button is totally broken #1010
Can't login successfully on AWS instance #1008
Can't spin up Refinery instance on AWS #1003
Unable to upload large files into Galaxy #999
Invitation API is broken and UI doesn't reflect that error #998
Creating a new group dialog is closed on enter without any action #997
Extended group API errors trigger confusing error message #996
In vm, grunt test fails #989
grunt test --host fatel error #988
Impossible to delete node relationship #981
Solr index is not stored in EBS storage #980
Node mapping related issue #978
Data set page: columns appear twice #959
Make sure that all actions go through handler methods #957
Page freeze when deleting the number of the visible depth input #956
Sorted reverts after term querying #955
Attribute Filter Fields with ; break Solr Search #950
Supervisor is not starting automatically during AWS deployment #933
Attribute Filter Selection throws TypeError in Console #931
Apache is not configured to serve files from MEDIA_ROOT on AWS #928
URLs for downloading analysis results are incorrect on AWS #927
on AWS the supervisord.conf file is wrong. #923
Exploration tool throws an error when the returned number of nodes is zero #920
Analyses fail when more than one input or pair of inputs is used #911
Impossible to create input file mapping #910
Registration emails link to wrong URL (on AWS at least) #900
Analysis Monitor State Does Not Update after Galaxy Pauses #894
The AWS EC2 instance root volume (EBS) does not get tagged #875
Download link not displayed for MACS2 tabular output file #868
Internal server error on homepage #863
Dashboard: infinite scroll-list acts weirdly #852
Solr is generating lots of log files #841
Fix viewing property bug with correcting data scope. #1143 (jkmarx)
Add button styling which resolves issue #1123. #1126 (jkmarx)
Flekschas/rex paper #994 (flekschas)
Flekschas/node mapping refactoring #947 (flekschas)

Closed issues:

specific migrations #1145
Add variables to config.yaml.template #1138
Django AWS settings are hardcoded to inherit from dev settings #1137
AWS Installation notes do not feature an image #1106
Make all datetimes time zone aware #1090
allow taking ownership of public data sets via file re-import #1072
Filter data sets by group #1070
Analyses Disable Links for Failed/Unknown #1068
Rewrite analysis_manager.views.get_full_url() to make it reusable #1063
Update npm #1054
DataSet2 View: Update number of files selected #1039
Dataset2 View: Implement File Downloads #1026
ui-grid header sort hit/miss on touch device #1006
Combine CloudFormation stacks into a single template #1005
create repository mode #990
Update built-in accounts for AWS deployment #932
Configure availability zone at runtime #926
Add Custom Sorting Capabilities by Requesting from Attribute Files API #919
Integrate Ui-Scroll with Ui-Grid in New DataSet View #914
Having to create an IAM role for EC2 instance is confusing #912
/data directory on AWS is not mounted #883
Move UNTITLED_DATA_SET_TITLE from Django settings to DataSet model #864
Using git checksum breaks git checkout on AWS #861
The requirements of the AWS RDS are unclear #860
Integrate Analysis Tab with new Analysis Monitor Backend #856
Integrate Global Analysis with new Analysis Monitor Backend #855
Add Solr to TravisCI #851
Handle Analysis deletion properly #840
Enable tagging of all AWS resources during deployment #839
Launchpad search: add type ahead #768
Upgrade to Django 1.6 #612
Replace simplejson Python module #589
Read The Docs fails to build because of missing libraries #531
Eliminate Celery chords from analysis_manager #448
explore possibility of distributing Refinery (+ Galaxy) as an Amazon Machine Image #376

Merged pull requests:

Jkmarx/data set config button styling #1163 (jkmarx)
Add configurations for data volume #1144 (drj11)
Scottx611x/own public datasets #1124 (scottx611x)
Update analysis link on dashboard analysis list. #1091 (jkmarx)
Single CloudFormation stack #1080 (drj11)
Set analysis\_status properly to alleviate issue of overall state be… #1067 (scottx611x)
Jkmarx/data set attribute util #1032 (jkmarx)
Add a Name tag for EC2 Web UI #1029 (drj11)
Move solr data to persistent volume #1027 (drj11)
Flekschas/eslint #1023 (flekschas)
Return only the relative url, but still use the full url in vizualiza… #993 (scottx611x)
Jkmarx/data set infinite scroll #987 (jkmarx)
create the guest account as an inactive account #979 (drj11)
Configurable Site URL #976 (drj11)
Fix Apache's MEDIA_ROOT serving directory. #953 (drj11)
Create fresh role for EC2 instance #913 (drj11)
Pre commit hook #898 (flekschas)
Analysis monitor ui #889 (jkmarx)
Scottx611x/django 1.6 upgrade #886 (scottx611x)
Set the Availability Zone for the new EC2 instance #881 (drj11)
Fix postgresql for "vagrant provision" #865 (drj11)

v1.1.0 (2016-01-14)

Full Changelog

Implemented enhancements:

Notify #general Slack Channel of new migrations automatically #823
Include JS test coverage in codecov #821
Refinery / Bootstrap 3 buttons are hard to see #787
Move stylesheets (css+less) into the UI's source folder #781
Change Puppet manifest to deploy Neo4j as a system package #767
Fetching the owner uuid slows down the API #759
Fetching the sharing status slows down an API call dramatically #758
Remove "PROFILE VISIBILITY" and its usages #750
Header: tab order isn't consistent #725
Dataset page table controls unnecessary for prov vis and matrix view #723
Prov vis not space filling #722
Dataset page paired-input analysis cause extra scrollbar #717
Intermediate selection for select-all checkbox on the dataset page #716
Don't select all samples in data set view by default #709
Distinguish between my own and my collaborators analyses #675
Relocate canceling notification #653
include owner information in analysis API #646
Solr highlighter doesn't highlight cryptic words correctly in EdgeNGram field #547
initialize 'Current Selection' node set on creation and page load #387

Fixed bugs:

Admin interface doesn't support unicode characters #845
Sorting and filtering doesn't work. #813
Solr Sends back Facets with 0 Counts #811
Dataset sharing API is broken #809
Asset Loading Console Error: Select2.min #801
Tabular File Upload Table View: Column Misaligned #795
Galaxy analysis fails with AttributeError$"'tuple' object has no attribute 'lower'",$ in Celeryd #780
Vagrant provision fails in manage.py collectstatic and manage.py syncdb #776
get_file_size() for DataSets not working properly #773
NotUserNorGroup exception during workflow import #772
Migration fails #765
500 error while accessing /api/v1/analysis/ w/ AnonymousUser #764
Public Profiles not visible to other users #762
500 Error from Analysis API #761
Replace STATIC_URL with the static template tag in Django templates #746
Logo bug and scrollbar issues on the workflow page #744
Postgresql dies upon query for deletion of analysis with many inputs #742
Account activation being displayed twice #739
Cannot open the filter & sort dialog in Firefox #726
Node mapper throws error when something other than node is dragged onto it #720
Undefined nodeset query leads to 401 error #714
Internal Server Error: /solr/data_set_manager/select/ #705
Dataset page: table doesn't build properly on initial load #699
ISA archive is imported even if it has been imported previously #562
Duplicate base resource slugs are possible #4

Closed issues:

Replace ng-grid with ui-grid #754
Update to NodeJS 4.2.1 LTE #752
Create "Users" API #749
Test if prov vis works with current version of d3 and lodash #734
Text out of bounds when drop menus are clicked. #732
Uploading the test isatab archive leads to a Solr error #729
Share some Django settings with AngularJS #703
upgrade to Bootstrap 3.x.x #494
Clicking "View in IGV" multiple times in quick succession with lead to multiple sets of launch buttons in the dialog #7

Merged pull requests:

Document how to delete a stack #846 (drj11)

v1.0.0 (2015-09-17)

Full Changelog

Implemented enhancements:

On Dataset view, message if no attribute features are available #695
Remove downloads tabs from Dataset view #689
increase size of supervisord controlled log files to 5 MB #684
Dashboard hovering a previewed dataset search result leads to unexpected coloring. #681
Longterm running CSS3 animated spinners cause drop of framerate. #650
Dataset page shows content of all tabs for fragment of a second while loading. #640
Analyses tab uses space inefficient. #637
change URLs in analysis list in launch pad to point to analyses tab of data set #633
Preview is very slow for datasets with a high number of raw data files #629
Fetch permission data before enabling the permission modal #622
Limit the number of visible data sources #620
change button labels for panels to show/hide #604
enable data set sort by title/name #599
labels are trimmed in provenance graph #537
allow users to decide if they want to create a copy of analysis input files to store with analysis results #368
identify relevant references for similar systems #333

Fixed bugs:

Details Page - Edit Button Redirect #696
On Dataset Import the Content Flashes #692
Statistics counts datasets differently #691
Analyses icon has wrong title #688
Dataset Manager API does not have failsafe when solr is down #680
It's possible to create a group with no name #678
hide "do not show to user" facets from matrix browser #656
Unknown Analysis is Loading Details #655
Delay between when an analyses cancels and list updates #652
sample mapping summary is not displayed after samples are added to create an input pair #630
Delete the corresponding Solr doc when a data set is deleted #627
analysis progress on dataset page is delayed during download phase #598
global analysis progress percentage overlaps with icon/text #596
Analyses drop down flickers #590
Lots of ERROR logs from the status tool #518
no node sets are shown for publicly shared data sets #489
HTTP error 500 in ExternalToolStatus API #427
external tool status for celery unstable even though celery is running fine #377

Closed issues:

remove ExternalToolStatus code from back-end #669
analysis API is slow to return results #613
Add unit test task to grunt compile command #564
vagrant provision fails: Installing RDoc documentation #412
Create and publish a development Vagrant Box. #393
explore django-pipeline for JavaScript and CSS packaging #272

v0.0.4 (2015-08-11)

Full Changelog

Implemented enhancements:

Update Analysis Tab View Styling #585
show full user names on collaboration page #580
humanize dates on collaboration page #578
Admins should see all data sets on the dashboard #573
Command line ISATab import creates only soft link to the original file. #571
Separate code from configuration in Django settings #552
OwnableResource's get_owner() checks for add_ permission #540
Checking permissions for ownership makes API slow #539
Filtering on is_owner and is_public for data sets, projects etc. #529
Filters that do not change anything could be disabled. #514
Implement data file uploads using a web browser #508
indicate number of facet values in facet browser #506
Refine provenance change encoding #505
Make API for reading user information from group #500
update icons for cell label expand & collapse #499
change FASTQC workflow to produce ZIP archive output #471
Data uploads #466
Extract file name from file path for display in file selection browser #442
refine UI for sample selection page #335
*[8+]* stop requiring page reloads in workflow setup interface #300
implement "red button" script to set all jobs to error state in Galaxy #261

Fixed bugs:

permission editor shows manager groups #581
missing select2 dropdown list button arrow on hires displays #575
ISATAB parser fails to create a data set. #570
Home menu shows up on data-set views #548
$state is not defined in data set view #546
Impossible to import an ISA archive using web UI if it has been previously imported #545
404 error for map file for select2 #517
Missing refinerySharingController error on the landing page #488
Problem accessing public datasets as AnonymousUser #477
click + ctrl shortcuts in provenance visualization not working in Chrome on the Mac #460
Dialog box pops up saying canceling analysis failed when user cancels analysis #428
Launch analysis button is disabled with valid input selection #415
Crash when selecting an invalid mapping column for a new relationship. #288
Flipped assay and study UUID assignment in the UI #245

Closed issues:

admin user does not have data upload directory #535
deactivate sharing UI components until launch pad is Angularized #519
Superuser not recognized by admin login #475
Update Puppet modules to the latest versions #453
rewrite externalToolStatusService as a factory or as a proper service that does not return a value #375
Assignment of data files to workflow inputs in the data set view is not working correctly #6

v0.0.2 (2014-11-05)

Full Changelog

Implemented enhancements:

create transfer directory in VM to import data from host #438
Add UI app management infrastructure to Vagrant VM #389

Fixed bugs:

Fix RabbitMQ deployment error in the Puppet manifest #462
Incorrectly including CSS stylesheet with "link ref" instead of "link rel" #439

v0.0.1 (2014-05-07)

Full Changelog

Implemented enhancements:

Add zv9 (zebrafish) genome build for visualization in IGV #399
show correct input label if only one input has been dragged onto dropzone #381
*[3]* create workflow: SPP #291
Handle no connection to database server condition. #236
Handle error when RabbitMQ is down #234
Add API for stopping running analyses. #232
create "create_workflowengine" command #219
remove SUPPORTED_GENOMES in annotation_server and replace with list of default genomes from genome build table #217
Implement a view for canceling Galaxy jobs #213
*[1]* create documentation for Refinery workflow importing #203
*[1]* test if input relationships refer to existing workflow inputs #202
*[4]* test workflow tools annotations for correctness and completeness #201
*[2]* store workflow template dictionary in workflow model #200
*[4]* Send welcome email when user account is created using django-auth-ldap #197
update Park lab dev VM so it sends emails #195
Disable registration using REGISTRATION_OPEN setting from django-registration #191
*[6]* Implement functionality to add a custom message to every page #184
*[2]* Disable registration page on SCC VMs #182
*[4]* add (for now optional) "type" attribute to tool annotation in Galaxy workflow and apply it to workflow output files #181
make login button more visible #177
Add phantompeakqualtools as a workflow in Galaxy #175
redirect user to previous page after login if possible #172
show node set manager only when user is logged in #171
implement authentication using remote_user http header #167
link analysis results back to data model #163
Allow for tool output renaming based on tags for name and description #162
Make sure all new users are added to the Public group #147
determine length of row/column labels in matrix view and adjust matrix position #140
keep track of both data query and annotation query to avoid reset #139
Refactor sample selection #138
use NodeSet API to create NodeSet based on Solr query #134
Extend Galaxy API to provide functionality for downloading datasets. #131
Derived data files that contain a summary across samples are only being associated with a "single parent". (e.g. gene expression matrix or a phantompeakqualtools report). #129
Implement authentication against LDAP #127
Modify NodeSet model/API #126
Remove MEDIA_HOST variable #125
add help text to options for make_metadata_table #123
Move REFINERY_BASE_URL and REFINERY_INSTANCE_NAME from settings to a param for the init_refinery command. #122
implement support for markup in descriptions of core data structures (project, data set, workflow) #121
optparse support for import_metadata_table #120
Implement REST API for NodeSet model #119
Extend the galaxy instance model with a field that indicates whether http or local download should be used #117
add support for Array Data File and Derived Array Data File in ISA-Tab #114
sort sample table by first column #113
make a description field for DataSet and Workflow #112
add tgz as file type in FileStore #109
Create NodeSet model #106
create proper 404 and other error pages #103
handle blacklist/whitelist of file uuids when creating analysis and IGV session files #102
switch to using file server in sample selection view #101
block bulk download when viewing annotation tracks #100
allow user to choose how many table rows should be shown #99
replace icon checkboxes with real checkboxes #97
trim labels and add tool tips to matrix view #96
make ISArchive (and Pre-ISA) available for download #95
Make meta data table available as download #94
update facets using matrix selection and vice versa #93
implement bigBed file server item #92
add note on profile edit page after first log in that is optional #89
include species on genome build buttons in IGV modal #88
implement file server Python API for TDF files #87
keep track of individually (de)selected nodes in sample selection interface #86
expand genome_build_to_species_id in annotation_server #84
create "clear all" button for facet selection #83
(modal) warning on all pages if we detect IE #81
change edit buttons on profile page #79
tooltips for annotation/data buttons #78
add help buttons for "View in IGV" and "Download as Archive" #76
disable "Download as Archive" button when user is not logged in #75
optimize performance of TDF profile calculation #74
add tgz as file format #73
Remove "Solr Query" link from download page if running in non-debug mode. #71
in repository mode replace "Analysis" with "Downloads" wherever possible #70
limit number of files per zip download to 20 #69
remove checkboxes from sample selection page #68
make sequence length table (e.g. chromosome lengths) #67
in repository mode only show contents of catch-all project #66
clean up analysis results page for repository mode #65
make "genome build" model #63
Create django view for solr queries #62
send an email to admin when new user registers #61
find library to provide proper command line flags for custom commands #60
Bootbox js modals for opening up multiple igv instances #59
replace "Unnamed" in name of analysis with name of the workflow #58
add tag to galaxy workflows to mark them as templates for use with refinery #57
create "Forgot Password" link and reset password #56
use django-registration package and enforce unique email addresses for registration #55
add species information to nodes #54
Email notification when analysis has finished #53
parser should implicitly add missing empty fields at the end of non-header rows #52
make model for genes #51
serve genome sequence in given window #50
merge isa-tab importing backend code for view and command line input #49
create logging monitor for admin #48
put our Galaxy extensions into the main branch #47
fix new converter extra tab at end #46
ISA-Tab Logging #44
edit process_isatab command #43
Remove References to Refinery Repository from data_set_manager views #42
Correctly identify number of steps in workflow. Differs from number of steps defined in workflow file. #41
Remove references to Refinery Repository in Analysis Manager #40
Add ability to galaxy to download a collection of files, zip, and return a tar ball via the cluster #38
web UI for importing ISA-Tab files #37
accept ISArchives with and without subdirectories in the ISA-Tab parser #36
refactor file store to use symlinks #35
Finish galaxy analysis pipeline, download results to a stored directory #34
use galaxy workflow output flag to indicate what files are output #33
add support to file store to rename files #32
version data sets #31
add support for api keys #30
extend parser to work with ISA-Tab files that are a combination of multiple studies #28
implement basic file store API #27
implement JavaScript tdf parser #25
specify file store #24
progress updates for Galaxy workflows #22
get number of steps for a given Galaxy workflow #21
add support to retrieve galaxy file type from history #20
store analysis results in repository #19
Figure out Expansion Factor of SPP workflow #18
read through eXFrame's createISA.pl to get an idea of what they're doing #17
add execute flag to workflow engines #16
Create fixture for New ISA-Tab Model #15
Put link to E-R diagram in Wiki #14
store original isa-tab files and mage-tab files in file store #13

Fixed bugs:

Analyses with datasets in paused state are reported as running by Refinery. #407
deleting a workflow engine doesn't delete the corresponding external tool status #244
AttributeError is raised when accessing analysis status with an ID that doesn't exist. #231
"No such file or directory" error when installing Puppet firewall module while provisioning a new VM instance. #227
Fix RabbitMQ "node down error message during VM provisioning. #221
*[4]* fix duplicate import of ISArchive file in ISA-Tab importer #187
admin should be allowed to see all group pages #186
*[8]* FileStoreItem datafile sometimes is not created when file store contains broken symlinks. #180
workflow count shown on statistics page also includes inactive workflows #178
*[1]* pager shows extra page if number of items in data set == number of items per page #174
*[2]* selecting facet value should not close facet value list #173
change relationship between Investigation and DataSet from many-to-many to one-to-many #169
if there are only one or a few entries in the sample selection table the column selection menu gets cut off at the bottom #151
Assignment of data files to workflow inputs in the data set view is not working correctly #141
matrix does not maintain ordering after selection is made #136
labels on matrix are missing when switching back to matrix from table/list view #135
download of ISA-Tab/pre-ISA-Tab archive from data set detail page is broken #130
"Name" facet is not being split properly by the parser. Consider using just the filename when a full path is given. (Need to evaluate if this is generally applicable) #128
"Name" facet is parsing out each directory in absolute file paths #124
Fix names of imported files produced by tools installed from Galaxy toolshed. #116
unknown filetype produces error in file store #110
file store produces URLs with duplicate "file_store" component #107
data_set_manager documentation is throwing errors #104
No content in table until user changes filter in matrix #98
commit error on loading a bigbed file as an auxiliary file #91
Two Emails sent per user registration #90
FileServer add is creating BAM items instead of WIG items (calling create on wrong object) #82
fix naming of archive files downloaded from galaxy #80
fix problem with parentheses in filenames failing import into Galaxy #72
fix problem with analysis completion emails not being sent #64

Closed issues:

Handle analysis failure in Galaxy #394
Sample drag and drop does not work properly in Safari and Firefox. #380
Display analysis results in the data set view after workflow has finished running. #373
*[8]* Upload test workflows and dummy tools into the test toolshed #208
document LDAP settings #206
Troubleshoot IGV crash #190
update Galaxy on Refinery VMs #188
NodeSet permissions in REST API #156
Upgrade to Bootbox 3.0 #150
Upgrade to latest bootstrap #148
include license and author information at the top of each code file #143
deal with spam registrations #137
Host our own copy of externally loaded UI resources #133
check security of Solr setup #132
get a private github account #118
implement migration with South #115
add workflows to dev VM galaxy instance #111
set up development VM #108
document on wiki how to use Sphinx to generate documentation #105
UI Testing for Repository Mode Alpha Release #85
launch Refinery in debug mode #77
move logger settings into settings.py from local settings #45
add instructions on how to set up Sentry to wiki #39
find out best practices for Python/Django documentation #29
Update to Django 1.4 #26
write Refinery architecture overview #23
explore options for Django logging and monitoring #12
explain to richard, psalm and ilya how pivotal tracker works #11
Integration Refinery with Galaxy. Step 1: Creating a Galaxy Instance #10
Instructions for creating django super user didn't work #9
readme file has incorrect git clone url #8
Refinery doesn't work in Firefox (or Internet Explorer) #5

preview02 (2012-08-31)

Full Changelog

Closed issues:

Error starting a workflow #3
Test Issue 2 #2

preview01 (2012-05-02)

Closed issues:

Test Issue #1

* This Change Log was automatically generated by github_changelog_generator

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CHANGELOG.md

CHANGELOG.md

Change Log

v1.7.2 (2019-11-18)

v1.7.1 (2019-10-21)

v1.7.0 (2019-07-19)

v1.6.9.1 (2019-05-15)

v1.6.5 (2018-07-20)

v1.6.4 (2018-05-22)

v1.6.3 (2018-03-29)

v1.6.2 (2018-01-26)

v1.6.1.1 (2017-12-13)

v1.6.1 (2017-11-27)

v1.6.0 (2017-10-02)

v1.5.8 (2017-07-17)

v1.5.7 (2017-07-11)

v1.5.6 (2017-05-15)

v1.5.5 (2017-04-03)

v1.5.4 (2017-03-02)

v1.5.3.1 (2017-01-23)

v1.5.3 (2017-01-23)

v1.5.2.1 (2016-12-19)

v1.5.2 (2016-11-18)

v1.5.1 (2016-10-20)

v1.5.0 (2016-10-14)

v1.4.0 (2016-09-15)

v1.3.0 (2016-08-26)

v1.2.0 (2016-05-23)

v1.1.0 (2016-01-14)

v1.0.0 (2015-09-17)

v0.0.4 (2015-08-11)

v0.0.2 (2014-11-05)

v0.0.1 (2014-05-07)

preview02 (2012-08-31)

preview01 (2012-05-02)

Files

CHANGELOG.md

Latest commit

History

CHANGELOG.md

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Change Log

v1.7.2 (2019-11-18)

v1.7.1 (2019-10-21)

v1.7.0 (2019-07-19)

v1.6.9.1 (2019-05-15)

v1.6.5 (2018-07-20)

v1.6.4 (2018-05-22)

v1.6.3 (2018-03-29)

v1.6.2 (2018-01-26)

v1.6.1.1 (2017-12-13)

v1.6.1 (2017-11-27)

v1.6.0 (2017-10-02)

v1.5.8 (2017-07-17)

v1.5.7 (2017-07-11)

v1.5.6 (2017-05-15)

v1.5.5 (2017-04-03)

v1.5.4 (2017-03-02)

v1.5.3.1 (2017-01-23)

v1.5.3 (2017-01-23)

v1.5.2.1 (2016-12-19)

v1.5.2 (2016-11-18)

v1.5.1 (2016-10-20)

v1.5.0 (2016-10-14)

v1.4.0 (2016-09-15)

v1.3.0 (2016-08-26)

v1.2.0 (2016-05-23)

v1.1.0 (2016-01-14)

v1.0.0 (2015-09-17)

v0.0.4 (2015-08-11)

v0.0.2 (2014-11-05)

v0.0.1 (2014-05-07)

preview02 (2012-08-31)

preview01 (2012-05-02)