Version 1.5.5

Full Changelog

Implemented enhancements:

• 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
• change Galaxy settings to stop copying files into the system #366
• 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
• 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
• Display will change depending on tool selected #1605

Merged pull requests:

• Jkmarx/attribute filter updates #1647 (jkmarx)
• 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)

Version 1.5.4

Full Changelog

Implemented enhancements:

• Update Collaboration Page Styling #1597
• Data Set - Edit Capabilities #1591
• Data Set / share API Adjustment #1191
• Fix Layout for Minimize Window #818
• Dataset page wastes space on small screens #786
• Test core.NodeSetListResourceTest.test\_get\_nodeset\_list fails. #586
• implement user authentication via API keys or tokens #359
• Bring unit tests for file server up to date #322
• Start using Modernizr #267
• 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
• Set up search query logger #509
• Rename add_nodeset permission to something like own_nodeset #312

Merged pull requests:

• 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)
• Improve AWS resource tags handling #1592 (hackdna)
• Jkmarx/import module refactor #1590 (jkmarx)
• Jkmarx/jshint rule change #1584 (jkmarx)

Version 1.5.3.1

Update intro.js and Python modules related to urllib3 to the latest versions

Version 1.5.3

• Update to Django 1.7
• Optimize large file uploads
• Configure Apache using Puppet module
• Re-enable default Apache vhost to use for ELB health checks
• Move repo into refinery-platform organization
• UI bug fixes

Version 1.5.2.1

• Update PostgreSQL engine version to 9.3.14
• Prevent automatic engine upgrades
• Update factory_boy module

Version 1.5.2

Implemented enhancements:

• Data Set 2 - Deactivate Selected Filters #1508
• IGV should always include gene annotation track #1494
• Collaboration Modals #1473
• 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
• 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
• 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)

Fixed bugs:

• 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
• Problem loading remotely located bed file into web-based IGV #1487
• Tabular Meta Data File - Cancelation #1475
• Dashboard Filter & Sorting Bug #1469
• Dashboard Filter Bug #1468
• Tabular files with a single row don't show up properly in data_sets 1 file browser #1463
• DataSet2 - Analyze Persist Node Group Selection #1325
• Filter counts broken between digits #1310
• 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)

Closed issues:

• Upgrade Puppet apt module to the latest version #774
• Update external Javascript packages to the latest stable versions #452

Merged pull requests:

• Add gene annotation track to IGV. Fix #1494. #1516 (mccalluc)
• Scottx611x/resolve manual fake issue #1515 (scottx611x)
• This helper script has been moved to its own repo #1513 (mccalluc)
• Jkmarx/higlass ui #1510 (jkmarx)
• Towards HiGlass UI #1509 (mccalluc)
• Hackdna/neo4j repo key error #1505 (hackdna)
• Fix for tabular metadata uploads that only contain one row #1479 (scottx611x)

Version 1.5.1

Hotfixes:

• Specifically set blob api for safari. #1482
• Fix search text placement to work in Firefox as well #1480
• Fix caching bug where # of Analyses run on a DataSet wasn't updated after an Analysis deletion #1481
• Remove add data set method. #1485
• Remove unneccessary cog animation. #1488
• Hotfix for issue #1491

Version 1.5.0

Implemented enhancements:

• 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
• 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
• Ui-Grid Multi-sorting Feature Unneccessary #936
• 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:

• UI - Failed Unit Test, Locally #1427
• Analysis Redirect UI Bug #1415
• DataSet2 - Persist Files URL when Filters Selected #1412
• Ontology Explorer doesn't work from dashboard when logged in? #1402
• Strange completion percentage #1394
• CSRF Error upon datafile upload (Only in Windows) #1370
• "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
• Reset password form should check if the email exists in the system #1250
• 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:

• Delete Sphinx docs directory #1431
• "Group Editor" dialog is missing cancel button #1305
• DataSet2: IGV #1271
• Remove infrastructure and code for Sphinx docs #1240
• The dataset nav feature needs refactoring #639
• Convert documentation from reStructuredText to Markdown #482

Merged pull requests:

• Jkmarx/unify alert appearance #1448 (jkmarx)
• Remove wobbly Help animation upon User's first login #1447 (scottx611x)
• Scottx611x/deletion from ui #1445 (scottx611x)
• Hackdna/workflow import #1443 (hackdna)
• Mccalluc/remove sphinx #1438 (mccalluc)
• Mccalluc/travis fast fail #1423 (mccalluc)
• AWS backups #1418 (drj11)
• Jkmarx/dataset2 new layout #1413 (jkmarx)

Version 1.4.0

v1.4.0

Release version 1.4.0

Version 1.3.0

v1.3.0

Release version 1.3.0