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Change Log

v1.6.1.1 (2017-12-13)

Full Changelog

Merged pull requests:

v1.6.1 (2017-11-07)

Full Changelog

Implemented enhancements:

  • 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
  • show all results of FASTQC analysis in FASTQC viewer and allow user to scroll through #659
  • allow lexicographical or alphanumeric sorting of facet attribute values #337
  • allow searching in facet values #336
  • *[8]* select assay (via study) to view in sample selection interface #299
  • add cartesian distortion to matrix view #260

Fixed bugs:

  • Data Set Table Configuration modal only triggers when clicking directly on wrench #2326
  • "./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

Closed issues:

  • "Show Tool Panel" should be left aligned #2322
  • Try Karma reporter config instead of grepping on travis #2316
  • 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
  • "Following files ..." message should not be shown if everything is good #2048
  • 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
  • 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
  • Migrate Travis CI config to Trusty build environment #800

Merged pull requests:

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 workflow ID changes in Galaxy #778
  • Add support for Galaxy dataset collections #444

Merged pull requests:

v1.5.8 (2017-07-17)

Full Changelog

Implemented enhancements:

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
  • modify workflow definitions to include file type in input names #266

Merged pull requests:

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
  • check workflow annotation for undeclared fields #286
  • import galaxy workflows through admin interface #276
  • 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:

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
  • 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
  • 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:

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
  • 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
  • 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
  • Set up search query logger #509
  • Rename add_nodeset permission to something like own_nodeset #312

Merged pull requests:

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
  • create workflow groups #470
  • queue analyses in Refinery to allow launch while Galaxy is unavailable #406
  • add support for timeout test for updates from galaxy during analysis #353
  • start discussion about "stop/pause" job API extension with Galaxy team #330
  • deploy IGV WebStart directly from Refinery site #325
  • prevent IGV from receiving non-genome-browser data #302
  • add compact mode to new workflow annotation #285
  • update TDF generation in SPP workflow #264
  • more detailed progress indicator (for power users?) #255
  • Edit data sets #253
  • 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
  • *[4+]* not all workflow outputs downloaded if output file is fed into multiple downstream tools #254
  • 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
  • Fix bug due to dependency order typo. #1585 (jkmarx)
  • 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
  • yvanlebras: new volunteer via Mozilla Science Lab Collaborate #666
  • create optimized packages for jquery UI #334
  • 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:

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
  • Analysis randomly failing because of authorization error #431
  • Fix data set preview + permanent expanded window in repo mode #1548 (flekschas)

Merged pull requests:

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 the latest version #774
  • Update external Javascript packages to the latest stable versions #452

Merged pull requests:

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

Merged pull requests:

  • Remove all occurrences of print currently within our codebase #1483 (scottx611x)
  • Fix caching bug where # of Analyses run on a DataSet wasn't updated #1481 (scottx611x)
  • Fix search text placement to work in Firefox as well #1480 (scottx611x)

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

Merged pull requests:

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)
  • Jkmarx/dataset2 analysis bug #1368 (jkmarx)

Closed issues:

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

Merged pull requests:

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
  • Preselect "current selection" for running analyses #690
  • provide option to keep Galaxy history if workflow fails #357
  • caching in file server backend #351
  • Bring unit tests for file store up to date #339
  • Create development documentation using Sphinx. #304
  • 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 sample file #1335 (jkmarx)
  • Jkmarx/data import default selection #1334 (jkmarx)
  • Jkmarx/data import text update #1331 (jkmarx)
  • Jkmarx/node group ui update #1286 (jkmarx)
  • Jkmarx/node group api reformat #1263 (jkmarx)
  • Jkmarx/metadata upload stripped file #1261 (jkmarx)
  • Jkmarx/data set2 select all update #1234 (jkmarx)
  • Jkmarx/node group api update #1227 (jkmarx)
  • Jkmarx/node group api v2 #1214 (jkmarx)
  • Jkmarx/data set2 sharing details merge #1193 (jkmarx)
  • Jkmarx/data set2 fastqc viewer #1180 (jkmarx)
  • Jkmarx/analysis cancel owner check #1177 (jkmarx)
  • Jkmarx/add tooltip data set preview #1174 (jkmarx)
  • Flekschas/angularize import #1167 (flekschas)

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
  • Jkmarx/data import md5 fix #1358 (jkmarx)
  • Jkmarx/data import form valid #1355 (jkmarx)
  • Jkmarx/data set import remove overall bar #1354 (jkmarx)
  • Jkmarx/data set2 workflow fix #1320 (jkmarx)
  • Jkmarx/display view fix #1297 (jkmarx)
  • Jkmarx/data upload multiple file error #1296 (jkmarx)
  • Fix conditional for updating current selection. #1285 (jkmarx)
  • Jkmarx/data set2 attribute filter fix #1279 (jkmarx)
  • Jkmarx/data set2 select all fix #1243 (jkmarx)
  • Fix error in service import. #1203 (jkmarx)
  • Add no wrap class to attribute filter count. #1178 (jkmarx)
  • Jkmarx/analysis timezone bug #1173 (jkmarx)
  • Jkmarx/data set2 attribute rank bug #1169 (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:

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
  • Django REST Api btwn Dataset Browser UI & Solr #830
  • Add Tooltip for Filedown Icon and Lightening Bolt #817
  • Update Core CSS to the USPTO Style Guide #808
  • Uniform Views Across Browsers #807
  • Prepare deployment scripts for use with EBS and RDS #805
  • Add latest commit hash to site #741
  • Change start and end time format after some time. #687
  • Empty selection selectable #671
  • 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
  • Find a way to "freeze" node sets #307
  • Implement delete functionality for Analysis REST API #306
  • *[4]* stop requiring page reloads in sample selection interface #301
  • *[8]* correct notifications about error states #298
  • allow user to view only those table rows selected with node selection #259
  • Jkmarx/paired analysis enhance properties #1162 (jkmarx)
  • Download files in new tab. #1131 (jkmarx)
  • Flekschas/satori fixes #1120 (flekschas)
  • Flekschas/email login #1115 (flekschas)
  • Flekschas/upload fixes #1088 (flekschas)
  • Webworkerify MD5 calculation to keep the UI usable when a large file is checked. #1087 (flekschas)
  • Swap caret to table for data-set-explorer link. #1065 (jkmarx)
  • Jkmarx/add file download tool tip #1045 (jkmarx)
  • Jkmarx/add file download data set2 #1042 (jkmarx)
  • Flekschas/repo mode #1040 (flekschas)
  • Tag the root EBS #1037 (drj11)
  • Flekschas/dashboard preview tweaks #1033 (flekschas)
  • Flekschas/rex paper #994 (flekschas)
  • Jkmarx/data set fix solr params #977 (jkmarx)
  • Jkmarx/data set encode facet filters #974 (jkmarx)
  • Flekschas/node relationship refactoring #948 (flekschas)
  • Flekschas/node mapping refactoring #947 (flekschas)
  • Flekschas/ontology unit annotation fix #940 (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
  • No AnonymousUser #1103
  • 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
  • Remove related objects when deleting a workflow #711
  • Remove related objects when deleting a data set #710
  • Started analyses never stop (visually) running when Galaxy is down #641
  • Results from Galaxy test tool workflows are not displayed correctly by Refinery #476
  • Analyses successfully completed in Galaxy are stuck at 100% in the execution stage. #408
  • Analysis monitoring checks analysis status before a history is created in Galaxy. #282
  • files with file extensions not registered in Refinery will not be assigned to new derived data file nodes #250
  • Fix viewing property bug with correcting data scope. #1143 (jkmarx)
  • Jkmarx/analyze pair mapping bug #1129 (jkmarx)
  • Jkmarx/analyze modal delete template #1127 (jkmarx)
  • Add button styling which resolves issue #1123. #1126 (jkmarx)
  • Flekschas/satori fixes #1120 (flekschas)
  • Jkmarx/analysis monitor bug2 #1119 (jkmarx)
  • Jkmarx/dashboard analysis link #1105 (jkmarx)
  • Flekschas/upload prod fix #1096 (flekschas)
  • Jkmarx/analysis disable emails #1084 (jkmarx)
  • Jkmarx/analysis cancel bug #1060 (jkmarx)
  • Jkmarx/fix igv bug #1059 (jkmarx)
  • Correct missing partial address. #1051 (jkmarx)
  • Jkmarx/analyses timeview bug #1049 (jkmarx)
  • Jkmarx/attribute api bug fix #1034 (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
  • Add Simple Email Service to AWS stack #836
  • Remove views analysis_run() and repository_run() from analysis_manager #827
  • Launchpad search: add type ahead #768
  • Update ui-select2 to ui-select as ui-select2 is deprecated #719
  • Upgrade to Django 1.6 #612
  • Replace simplejson Python module #589
  • Analysis Monitoring Backend Issues #554
  • 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
  • explore advantages (and disadvantages) of using a model to manage file types #305
  • Update to Celery 3.x #248

Merged pull requests:

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
  • Enable incremental search on substring of data set accession number #745
  • Lauch Pair Analysis -- Rename/Delete Should Have Pointer #728
  • 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
  • Accession number is not stored when importing new isatabs #715
  • Don't select all samples in data set view by default #709
  • Collaboration View: New Group should have cancel #700
  • Remove filter option ("own" and "public") for public users #685
  • Add Model fields to Django Admin using list_display #677
  • Distinguish between my own and my collaborators analyses #675
  • do not show paginator if there is only one page #658
  • Relocate canceling notification #653
  • redirect user to analysis tab after analysis has launched #648
  • show analysis owner name and link to owner profile in analysis list in analyses tab of a data set #647
  • include owner information in analysis API #646
  • show owner name and link to owner profile in data set preview #645
  • include owner information in data set API #644
  • Solr highlighter doesn't highlight cryptic words correctly in EdgeNGram field #547
  • initialize 'Current Selection' node set on creation and page load #387
  • Process ArrayExpress #340
  • Create deployment documentation using Sphinx #303
  • move Galaxy file store directory into Vagrant VM #279
  • Celery task cleanup #265

Fixed bugs:

  • Admin interface doesn't support unicode characters #845
  • Custom sharing icons broken. #824
  • Statistics API is broken #820
  • analysis monitoring states not displayed correctly #815
  • Sorting and filtering doesn't work. #813
  • Even dataset table rows are transparent #812
  • Solr Sends back Facets with 0 Counts #811
  • Missing Facet Field for Solr Request #810
  • Dataset sharing API is broken #809
  • Refactor global CSS #803
  • Sync Postgres Updates with Solr #802
  • Asset Loading Console Error: Select2.min #801
  • Dataset View: Missing NodeSelect Dropdown #799
  • Upload Metadata: Tabular File Errors #796
  • Tabular File Upload Table View: Column Misaligned #795
  • Fix Neo4j errors in unit tests #794
  • Dataset Import Body does not clear Navbar #793
  • Launching analysis is impossible #792
  • Dataset filters not displaying nicely #791
  • Tabular metadata file upload form is not displayed correctly #790
  • Unable to save Datasets (and anything else that extends BaseResource) with empty slugs in Django Admin #789
  • Failing analyses #788
  • 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
  • bower prune fails while vagrant provision #775
  • get_file_size() for DataSets not working properly #773
  • NotUserNorGroup exception during workflow import #772
  • Error occuring using core management commands #771
  • Supervisord fails to start Solr after Vagrant VM is provisioned #766
  • 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
  • Django complains about duplicate key being loaded from fixture #760
  • migrations of data set table are failing #757
  • The prov vis is half cut on initial load #755
  • Dataset View Pagination Issue #753
  • Universal Analytics not working #747
  • 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
  • DataSet View, pagination does not show on initial load #737
  • <label> tags have a pointer on hover #736
  • Global Running Analysis Does Not Update Until Popover Activated #735
  • Pair Analysis - Cannot delete node pair #733
  • Pair Analysis 501 Error #731
  • Cannot Upload New Dataset #727
  • Cannot open the filter & sort dialog in Firefox #726
  • Admin can't share datasets #724
  • Layout breaks for paired input analyses #721
  • Node mapper throws error when something other than node is dragged onto it #720
  • 400 error when mapping files for analysis #718
  • Undefined nodeset query leads to 401 error #714
  • User registration activation shows meaningless error #712
  • Dataset page shows model for 500 error multiple times. #706
  • Internal Server Error: /solr/data_set_manager/select/ #705
  • Dataset page: table doesn't build properly on initial load #699
  • Provenance View: Loading Icon Placement #698
  • Provenance View: Sometimes Loading icon does not stop spinning #697
  • Table header partially overlaps with the first row #686
  • Empty dataset page for "15826: ChipSeq of MLL1 in mouse leukemic blast cells" at refinery-dev #670
  • Galaxy Database File Cleanup, Post Analysis #567
  • ISA archive is imported even if it has been imported previously #562
  • show error message when launching of IGV session fails #371
  • Duplicate base resource slugs are possible #4

Closed issues:

  • ISA-tab upload fails in branch bootstrap3_upgrade #784
  • Dashboard: Bootstrap3_upgrade #782
  • Provenance View: Bootstrap3 Upgrade #777
  • Batch Uploading of isatabs #770
  • Replace ng-grid with ui-grid #754
  • Update to NodeJS 4.2.1 LTE #752
  • Create "Users" API #749
  • Set up tracking of Angular pages using Google Analytics #748
  • Test jsdoc compiler #743
  • 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
  • Test backup strategy #704
  • Share some Django settings with AngularJS #703
  • Update Javascript Filenames and Directory to meet Code Style Guide #583
  • upgrade to Bootstrap 3.x.x #494
  • upgrade to FontAwesome 4.x.x #493
  • Evaluate Django REST Framework as a replacement for Tastypie #491
  • Replace urllib2 with requests library #465
  • Upgrade Solr from version 4.4.0 to 5.x #457
  • Change update_refinery() in Fabric script to make it work with the vagrant VM #432
  • explore integration of BioJS #429
  • Evaluate use of Amazon RDS vs a locally hosted Postgresql instance #422
  • Prototype of automatic deployment to AWS #420
  • create rst file for every Refinery app #329
  • find a way to document javascript #327
  • Upload data analysis workflows to the Galaxy toolshed. #290
  • Clicking "View in IGV" multiple times in quick succession with lead to multiple sets of launch buttons in the dialog #7

Merged pull requests:

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
  • remove old data set index #660
  • Longterm running CSS3 animated spinners cause drop of framerate. #650
  • data set description content is showing up in launch pad #642
  • Dataset page shows content of all tabs for fragment of a second while loading. #640
  • Analyses tab uses space inefficient. #637
  • Global analyses icon shows text cursor when hovering with the mouse. #636
  • 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
  • recent analysis tooltip/list should show on cogwheel icon and analysis count #625
  • Fetch permission data before enabling the permission modal #622
  • Limit the number of visible data sources #620
  • use default analysis icon colors in data set preview #618
  • Filter icon displayed twice for a short time #609
  • change button labels for panels to show/hide #604
  • add tooltips for sharing/ownership icon to data set list in launchpad #602
  • add support for sorting and filtering for analyses/projects and workflows #601
  • enable data set sort by title/name #599
  • Bootstrap's tooltip doesn't show an arrow when positioning it top or right. #592
  • labels are trimmed in provenance graph #537
  • Projects is a dead end #513
  • Provviz info bar: DOI wording is confusing #511
  • terminate with error message if workflow fails in galaxy #370
  • 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
  • allow matrix to be transposed (dimensions are swapped) #332
  • implement general handling of ajax queries in Refinery #263
  • minify all CSS and JavaScript #262
  • Implement deployment to OS X, CentOS and Debian using Fabric. #247

Fixed bugs:

  • Details Page - Edit Button Redirect #696
  • analysis progress indicator row does not fully collapse #694
  • On Dataset Import the Content Flashes #692
  • Statistics counts datasets differently #691
  • Analyses icon has wrong title #688
  • Add proper error handling for the dashboard when Solr is down #682
  • Dataset Manager API does not have failsafe when solr is down #680
  • It's possible to create a group with no name #678
  • Default analysis name shown for (running) analyses #676
  • "vagrant up" fails in gem install librarian-puppet -v 2.1.0 step #665
  • Console Error Thrown When Canceling Analysis #664
  • https://refinery-dev.stemcellcommons.org/data\_set\_manager/ leads to 500 error #661
  • height of panels does not always get updated upon window resize #657
  • hide "do not show to user" facets from matrix browser #656
  • Unknown Analysis is Loading Details #655
  • Running Analyses Collapse/Expand Arrow Not Responsive #654
  • Delay between when an analyses cancels and list updates #652
  • Global analyses popover flashes "No Analyses" while loading #651
  • Scrollbar madness on the dataset page #649
  • analysis and visualization controls not showing in production mode #638
  • Dataset page routing seems to be broken #634
  • sample mapping summary is not displayed after samples are added to create an input pair #630
  • jshint is failing when Grunt is executed by Puppet during Vagrant VM provisioning #628
  • Delete the corresponding Solr doc when a data set is deleted #627
  • download and preview indicator not showing in data set file browser in Safari #626
  • analysis elapsed time not showing on analysis tab #624
  • page numbers for analysis list on analysis tab are 0-based #623
  • resizing of browser window duplicates entries in data set list in the launchpad #617
  • fix line breaks in "recent analyses" view #615
  • Permission Popup doesn't take user permission into account #611
  • Double click on radio filtering only works when the filtering leads to zero results. #608
  • remove commas shown in FastQC viewer #606
  • correct location of arrow for global analysis progress list #603
  • analysis progress on dataset page is delayed during download phase #598
  • global analysis progress percentage overlaps with icon/text #596
  • humanized time stamps don't work in Safari #595
  • Table view header issue #593
  • analysis on shared data sets not visible #591
  • Analyses drop down flickers #590
  • Routing for dataview tabs do not route properly #584
  • Uploading files through the data file uploader causes high CPU usage #549
  • Lots of ERROR logs from the status tool #518
  • no node sets are shown for publicly shared data sets #489
  • Spurious check_tool_status errors #447
  • HTTP error 500 in ExternalToolStatus API #427
  • Unable to configure IGV for the selected file set. #396
  • external tool status for celery unstable even though celery is running fine #377
  • bulk download or viewing of annotation tracks should not include the full set of data tracks #239

Closed issues:

  • Alert User Somehow when Solr is down #683
  • Items longer than selected option within a Data Set's Display dropdown are cut off. #674
  • remove ExternalToolStatus code from back-end #669
  • remove ExternalToolStatus code from front-end #668
  • Allow assignment of states to multiple locations #635
  • analysis API is slow to return results #613
  • rename user-facing instances of "subanalysis" into "analysis group" #607
  • dataset "BCL11A cistrome in mouse erythroleukemia (MEL) cells" exists twice in SCC #597
  • Add unit test task to grunt compile command #564
  • Update Angular to 1.4 #496
  • Shirish Goyal: new volunteer via Mozilla Science Lab Collaborate #454
  • vagrant provision fails: Installing RDoc documentation #412
  • Create and publish a development Vagrant Box. #393
  • Add attribution section to license #320
  • explore django-pipeline for JavaScript and CSS packaging #272
  • remove old styles in static/core & static/galaxy-connector #271

Merged pull requests:

  • Only issue warning when provisioning. #667 (drj11)

v0.0.4 (2015-08-11)

Full Changelog

Implemented enhancements:

  • Update Analysis Tab View Styling #585
  • Analysis drop down shown even though there are no analysis #582
  • 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
  • Analysis Monitoring Front End Issues #553
  • Separate code from configuration in Django settings #552
  • allow naming of analyses before launch #541
  • OwnableResource's get_owner() checks for add_ permission #540
  • Checking permissions for ownership makes API slow #539
  • Update lodash to v3 #530
  • Filtering on is_owner and is_public for data sets, projects etc. #529
  • Add fields to indicate is_public, is_owner, etc in the Sharable Resource API #524
  • Filters that do not change anything could be disabled. #514
  • When creating a project "slug" changes to "shortcut name" #512
  • While browsing a data set: tabs that have no content could be deactivated #510
  • Implement data file uploads using a web browser #508
  • only show facets with more than 1 facet value #507
  • indicate number of facet values in facet browser #506
  • Refine provenance change encoding #505
  • Make API for updating members #501
  • Make API for reading user information from group #500
  • update icons for cell label expand & collapse #499
  • improve how text is trimmed in dataset file table #497
  • extend external tool status indicator #495
  • Prevent the Analyze tab from being displayed to unauthenticated users #479
  • change FASTQC workflow to produce ZIP archive output #471
  • Freeze Header Row in List View #468
  • Data uploads #466
  • Improve analysis progress monitoring UI #450
  • Extract file name from file path for display in file selection browser #442
  • support metadata table upload through the browser UI #436
  • add support for timeout test for connecting to galaxy #354
  • refine UI for sample selection page #335
  • create theme for modencode site #321
  • *[8+]* stop requiring page reloads in workflow setup interface #300
  • cancel analysis if error state returned by Galaxy (based on overall history state) #297
  • *[20]* improve progress indicators #296
  • support canceling of analyses #295
  • Automate Django superuser creation. #275
  • implement "red button" script to set all jobs to error state in Galaxy #261
  • *[4]* change how analysis status is displayed in launch pad #242
  • make favicon.ico for Refinery #240

Fixed bugs:

  • Unknown provider: analysesOffsetFilterProvider <- analysesOffsetFilter #587
  • permission editor shows manager groups #581
  • TypeError: Cannot read property 'indexOf' of undefined when searching for data sets #576
  • missing select2 dropdown list button arrow on hires displays #575
  • dataset keyword search broken #572
  • ISATAB parser fails to create a data set. #570
  • ISATAB file import fails due to UnicodeDecodeError #563
  • Search results get duplicated sometimes #561
  • launchpad display issue in Safari #556
  • retrieval of publication information in launchpad preview fails when accessing Refinery via https #555
  • link to analysis results broken in dashboard #550
  • 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
  • Default state is not set when opening a dataset #544
  • ISA-Tab parser fails on data set from Scientific Data website #536
  • Uncaught ReferenceError: analysisView is not defined #533
  • Admin interface not displaying CSS #528
  • Can't register new user. #527
  • Isatab isa_16182_919177.zip fails #526
  • changes to parse_isatab return type are breaking downstream code #523
  • newly created node sets are not shown in analyze tab on data set page #522
  • ExternalToolStatus: TypeError: Cannot set property '...' of undefined #521
  • $log undefined in externalToolStatusFactory #520
  • 404 error for map file for select2 #517
  • Horizontal width of dataset table view adds unnecessary scrollbar #504
  • Execution of workflows on multiple input files produces 200MB+ files in media directory #503
  • High CPU utilization by Javascript UI during analysis monitoring #498
  • file download links are not shown in publicly shared data sets #490
  • Missing refinerySharingController error on the landing page #488
  • TypeError on landing page in sharing.js #487
  • Display dropdown does not switch to corresponding Provenance or Matrix tab #485
  • Launching analysis not always possible using current selection #483
  • Missing project_user variable when using Fabric #481
  • Samples in public datasets are not displayed for unauthenticated users #478
  • Problem accessing public datasets as AnonymousUser #477
  • ISA-Tab upload URL field should perform 'trim' before upload #474
  • Selecting all samples doesn't work properly in the data set view #473
  • ViewDoesNotExist exception on GET request to / #464
  • click + ctrl shortcuts in provenance visualization not working in Chrome on the Mac #460
  • Provenance graph not displayed for newly imported datasets #458
  • public data sets don't display for users who are not logged in #443
  • Dialog box pops up saying canceling analysis failed when user cancels analysis #428
  • Launch analysis button is disabled with valid input selection #415
  • Catch-All Projects are created without an owner #402
  • Analysis status view briefly shows "Analysis execution is pending" after analysis results have been downloaded. #397
  • Crash when selecting an invalid mapping column for a new relationship. #288
  • Unable to hide columns in sample table #283
  • Analysis status on the home page keeps making GET requests for corresponding Galaxy histories even when Analysis status is set to SUCCESS. #273
  • External tool error messages are not styled #269
  • Flipped assay and study UUID assignment in the UI #245

Closed issues:

  • grunt watch is failing when run outside VM #579
  • add angularjs-humanize library #577
  • link collaboration page from base template #574
  • abstract in launchpad data set preview is broken #560
  • Eliminate verbs from REST API URLs. #559
  • video at vimeo is private #558
  • download links in node info panel are incorrect #557
  • import all SCC data set into FAS dev instance #551
  • names should be shown for all nodes in provenance graph #538
  • admin user does not have data upload directory #535
  • rename user-facing/UI instances of "metadata table" into "Tabular File" #534
  • TypeError: Cannot set property 'GALAXY' of undefined #525
  • deactivate sharing UI components until launch pad is Angularized #519
  • add accession number field to data set model #516
  • Rewrite calculate_checksum() to accept a file object instead of file path #515
  • Login Tooltip flickering #492
  • guardian.shortcuts assign method unable to make change permission false #484
  • Superuser not recognized by admin login #475
  • Switching to develop #472
  • Devasena Inupakutika (di1c13): new volunteer via Mozilla Science Lab Collaborate #455
  • Update Puppet modules to the latest versions #453
  • Modify analysis progress reporting to use total number of datasets in history from run_workflow() #426
  • Show the name(s) of currently running tool(s) when displaying analysis progress #425
  • Update deployment process to use Ubuntu 14.04 LTS Vagrant box #417
  • Use $watch to get externalToolStatus service updates instead of polling with $timeout. #395
  • Uncaught TypeError: Cannot call method 'getDocumentList' of null #392
  • 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
  • create simplified tab-delimited file import command #437
  • set maximum size for provenance graph elements #434
  • capture referral URL when users are redirected to ISA-Tab upload page #413
  • Add UI app management infrastructure to Vagrant VM #389
  • Update galaxy on VM (dev) to be run using apache/nginx #338

Fixed bugs:

  • Fix RabbitMQ deployment error in the Puppet manifest #462
  • Download of files from SRA is failing #445
  • sharing data set with public group causes error when viewing data set #440
  • Incorrectly including CSS stylesheet with "link ref" instead of "link rel" #439
  • download of ISA-Tab archives is failing #433
  • Internal server error when a workflow that doesn't exist is accessed #430
  • output of IGV tile or count not imported correctly into Refinery #405

Closed issues:

  • make text scaling independent of graph scaling #456
  • investigate if MM/DD/YYYY is a valid date format for ISA-Tab #410
  • change supervisord config to store logs in a separate "log" folder #384
  • explore using BioBlend as an abstraction layer for the Galaxy API #313

v0.0.1 (2014-05-07)

Full Changelog

Implemented enhancements:

  • remove horizontal scroll bars in data set UI where not needed #404
  • Add zv9 (zebrafish) genome build for visualization in IGV #399
  • Add an option to use Apache and mod_wsgi on the Vagrant VM #388
  • replace analysis uuid in file browser table with analysis name #383
  • show correct input label if only one input has been dragged onto dropzone #381
  • enforce usernames to be lowercase only #345
  • *[3]* create workflow: SPP #291
  • *[?]* cancel running analyses #257
  • Updating creating node relationships #241
  • Handle no connection to database server condition. #236
  • Handle error when RabbitMQ is down #234
  • Do not send analysis failure email if analysis was cancelled by user. #233
  • Add API for stopping running analyses. #232
  • Create a custom version of SPP tool based on the Modencode version and upload it to the test tool shed. #230
  • serve workflow graph through Workflow API #229
  • add support for sending emails from Vagrant VM #226
  • Revise directory structure to better separate deployment configuration from the rest of the code. #225
  • Add support for Galaxy to the Vagrant VM. #224
  • test if celery is running before trying to import isa-tab through custom command #223
  • switch email backend from console to file #222
  • create "create_workflowengine" command #219
  • check if Solr is running #218
  • remove SUPPORTED_GENOMES in annotation_server and replace with list of default genomes from genome build table #217
  • Report analysis failure if one of the input files cannot be downloaded or read from disk #216
  • Create a simplified installation procedure using Vagrant and Puppet. #215
  • Implement a view for canceling Galaxy jobs #213
  • *[16]* catch exceptions from all critical calls to Galaxy in the AnalysisManager #212
  • Implement processing of special characters when importing tab-delimited metadata files. #211
  • Remove reset and change password links from views when LDAP auth is enabled. #210
  • *[4]* filter samples/files by "analysis"/"workflow"/"workflow step" #209
  • *[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
  • *[12]* handle packaged downloads separately from analyses #199
  • password reminder email sent notice should be on login page #198
  • *[4]* Send welcome email when user account is created using django-auth-ldap #197
  • update Park lab dev VM so it sends emails #195
  • Variable input workflows with additional steps beyond "Archiving" #193
  • *[4]* Customize login page with info necessary to obtain FAS RC account. #192
  • Disable registration using REGISTRATION_OPEN setting from django-registration #191
  • do not delete workflows by default, instead archive them #189
  • *[4]* access forbidden page should distinguish between anonymous and logged in users #185
  • *[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
  • *[8]* Analysis REST API #179
  • make login button more visible #177
  • *[4]* implement mapping from URLs to file system paths when importing files into refinery #176
  • 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
  • NodeSets need to be owned by users #170
  • implement setting remote_user http request header #168
  • implement authentication using remote_user http header #167
  • *[2]* set workflow as inactive and do not delete when new workflows are being imported #166
  • link analysis results back to data model #163
  • Allow for tool output renaming based on tags for name and description #162
  • add GTF as a file type #159
  • Add all the currently used config variables with sensible default values and comments to settings.py. #157
  • Update view "IGV" when looking at analysis results #155
  • show project owner on project detail page #154
  • distinguish public and private resources on landing page #153
  • Make sure all new users are added to the Public group #147
  • Add default NodeRelationshipType for single input workflows #146
  • remove ISA_TAB_TEMP_DIR references and replace with mkdtmp (?) #145
  • let users chose how many entries they want to see per list page #142
  • 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
  • Crash when trying to access a data set shared by a user that was subsequently deleted. #401
  • Clicking on the "Public" link under Groups on the Profile page results in an error #400
  • all analyses are showing up for all users with login credentials #398
  • successfully finished analyses showing up as running with 0% on launch pad #390
  • analysis facet selector on data set page not loading in most cases #382
  • Page not found (404) is produced when trying to access an analysis result file of 0 bytes in size. #289
  • Analysis results are not downloaded after successful workflow run. #274
  • Server error: GenomeBuild matching query does not exist. #246
  • deleting a workflow engine doesn't delete the corresponding external tool status #244
  • Celery down error message appears at random. #238
  • Celery/Galaxy/Solr down error message appears intermittently #237
  • admin interface not accessible when Galaxy instance is down #235
  • AttributeError is raised when accessing analysis status with an ID that doesn't exist. #231
  • workflow page can't be viewed when Galaxy instance is down #228
  • "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
  • Creating workflow engines via the admin UI does not allow workflow import. #220
  • problem with LDAP settings after login #207
  • *[1]* allow workflow without defined input relationship #204
  • *[2]* User sometimes is redirected to registration page after logging in. #196
  • *[4]* fix duplicate import of ISArchive file in ISA-Tab importer #187
  • admin should be allowed to see all group pages #186
  • *[4]* only first 20 nodes from node set are passed to analysis #183
  • *[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
  • analyses are accessible with direct link without requirement to login #165
  • description field in Galaxy Instance model should not be required #164
  • "invert selection" button sometimes doesn't switch blacklist state #160
  • clicking checkbox in Solr Document table field selection dropdown doesn't work (clicking on the name does) #158
  • FIREFOX: selection state of attributes on "attribute" tab is not saved #152
  • 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
  • analysis email notifications incorrect in default mode #144
  • 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
  • Problem adding and navigating input node pairs. #391
  • Sample drag and drop does not work properly in Safari and Firefox. #380
  • scroll only table but not dropzones #379
  • node relationship drop zones sometimes do not work #378
  • Display analysis results in the data set view after workflow has finished running. #373
  • Disallow launching of analyses when Galaxy is down. #372
  • remove images/scc_logo.png if not needed any longer #270
  • document ArrayExpress, taxonomy and UCSC settings #214
  • *[8]* Upload test workflows and dummy tools into the test toolshed #208
  • document LDAP settings #206
  • Create a Github repository for Galaxy tools and workflows used by Refinery #205
  • Update help/documentation for the process_metadata_table command. #194
  • Troubleshoot IGV crash #190
  • update Galaxy on Refinery VMs #188
  • upgrade D3 to version 3.0 #161
  • NodeSet permissions in REST API #156
  • Upgrade to Bootbox 3.0 #150
  • upgrade to FontAwesome 3.0 #149
  • 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