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Releases: refinery-platform/refinery-platform

Version 1.6.5

20 Jul 20:27
@scottx611x scottx611x
v1.6.5
30567f8
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Version 1.6.5
  • Add support for revising a DataSet's metadata while preserving data files that have been uploaded prior
  • Add support for uploading/removing data files directly from the FileBrowser
  • Add "Primary Group" functionality to be able to filter DataSets on one's main Group of interest
  • Add recording of more Events in Dashboard history panel
  • Add support for custom Tool Launch naming
  • Address /api/v1/data_sets performance issues
  • Various other bug fixes/enhancements

NOTE:

Will need to run the following to update the Solr index and add a new version of the heatmap-scatterplot visualization tool, respectively:

  • ./manage.py update_index
  • ./manage.py load_tools --visualizations heatmap-scatterplot --force

Implemented enhancements:

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

Fixed bugs:

  • Import Data File -> Incorrect status during pending #2846
  • NodeSerializer cannot save valid Node instance serializations #2834
  • Unable to Delete Old Inactive User #2803
  • Admin Interface - Unable to access user profiles #2802
  • Inability to bring up clean vm with latest develop code #2795
  • Inactive User Accounts Displayed in Public Group Members List #2792
  • Remove flakey Satori Cypress test #2348
  • Data set link from cross-dataset browser is missing ID, sometimes #2259
  • Add permissions check to AddFilesToDataSetView #2821 (hackdna)
  • Make sure file system path matches data file name in file_store #2815 (hackdna)
  • Fix #2795 #2801 (hackdna)

Closed issues:

  • Upgrade postgresql on all deployment platforms #2865
  • Data Set Files Never Imported (ISA-Tab) #2840
  • Data file removal should only be allowed if a DataSet is "clean" #2829
  • DataSets should be able to report on their "Cleanliness" #2784
  • Perms Auditing: Events API #2779
  • Metadata/Data File Editing for Existing DataSets #2700
  • Add data files to an existing data set #2037
  • 404 not apparent to user if invalid genome selected #1524
  • Make dataset which incorporates all types supported by IGV #1453
  • Details always says "using 0 bytes" #1309

Merged pull requests:

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Version 1.6.4

22 May 15:43
@scottx611x scottx611x
v1.6.4
f36dfda
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Version 1.6.4
  • Implementation of alpha version of new dashboard ui code & design
  • Code to periodically collect site statistics
  • Development/deployment of a new vis tool wrapping Taggle
  • Various other bug fixes/enchancements

NOTE:

  • Will need to run the following to update new/existing VisualizationTools:
    • ./manage.py load_tools --visualizations multiqc
    • ./manage.py load_tools --visualizations heatmap-scatterplot
    • ./manage.py load_tools --visualizations caleydo-taggle
    • ./manage.py load_tools --visualizations higlass --force
    • ./manage.py load_tools --visualizations igv --force

Fixed bugs:

  • Data Set API Bug -> Group Filter #2742
  • Error accessing EBS data volume during WebInstance provisioning #2708
  • Index Files Not Being Generated for Newly Imported BAM Files #2705
  • Internal Server Error: /api/v1/viewconfs/ #2703
  • Internal Server Error: /assets/images/touchicon.png #2702
  • No DELETE request to Galaxy library API in successful analyses #2641
  • Avoid use of special characters in file names #2553
  • Creation Time for Visualization Tools in Visualizations Tab is in the Future #2527
  • IGV internal server error due to HTTP Error 404 #2450
  • Analysis Filters don't seem to work on some Analyses #2383
  • Treemap looses orange when mouse leaves data sets list #2132
  • Dashboard: Filter with Groups Bug #1724
  • Dataset Import Body does not clear Navbar #793
  • Escape @ symbol to fix filter bug. #2733 (jkmarx)
  • Make data file names POSIX compliant #2732 (hackdna)
  • Jkmarx/fix vis ui #2730 (jkmarx)
  • File import bug fixes #2723 (hackdna)
  • Fix BAM index file generation #2712 (hackdna)

Closed issues:

  • Superuser creation failure when stack doesn't reference backups #2738
  • Incorrect icon display after VisualizationTool selection #2720
  • Add Collection of Requested Metrics #2694
  • Dashboard Rev 1 #2679
  • Remove receiver_subclasses() decorator #2658
  • Remove NodeManager class #2649
  • Add file count to User Files browser #2620
  • Cloudman Upgrade #2468
  • Update Galaxy test workflows #2411
  • Remove file_server Django app #2393
  • Tool-Launched User Story #2245

Merged pull requests:

Assets 2

Version 1.6.3

29 Mar 20:52
@scottx611x scottx611x
v1.6.3
8f071da
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Version 1.6.3

Technical Debt Focused Release:

NOTE:

  • Will need to "reset" migrations for the file_server app after deployment with ./manage.py migrate --fake file_server zero to prepare for file_server migrations removal in the next release (#2393)
    • When prompted that: The following content types are stale and need to be deleted type yes (#2599)
  • Will need to run ./manage.py update_index due to changes from: #2630
  • Will need to run ./manage.py load_tools --visualizations igv --force due to changes from here
  • We now utilize a VPC as part of our cloud deployment infrastructure. The Terraform portion of our stack deployment has been updated to reflect this change and can be found here

Implemented enhancements:

  • Add VPC to Terraform infrastructure #2600
  • Global Analysis Popover - Add link for in-progress analyses #2516
  • Dataset is shared with me, but I can't actually edit metadata #2506
  • Refactor Analysis.attach\_outputs\_dataset #2415
  • VisualizationTool launches should have access to **all** of a Dataset's Node metadata information #2413
  • User/files Empty Columns #2350
  • "Data File Column" upload message uses internal absolute path #2323
  • Satori minor discrepancies between test doc and real world #2152
  • Satori: Jumpy context menu if column scroll, on FF #2136
  • First add-all-to-cart takes 4 seconds (with 119 data sets) #2129
  • Satori icon loading could be enhanced #1905
  • Postcss doesn't do anything #1778
  • When using ELB, log client IP #1389
  • RepoExplorer: show number of data sets related to hovered ontology term #975
  • RepoExplorer: double clicking on a node === rooting it #973
  • RepoExplorer: treemap should feature the same node context menu of the list graph #968
  • RepoExplorer: Add short explanation for precision and recall #966
  • RepoExplorer: Treemap: Add tooltip #963
  • Analyses tab view is slow to load when there are many sets #610
  • add support for Per tile sequence quality view in FASTQC report #605
  • Sample names from ISA-Tab are not being displayed #441
  • implement periodically running test workflow to monitor system performance and readiness #347
  • Hackdna/update apache config #2672 (hackdna)
  • Keep chunked uploads outside file_store dir and delete chunked upload… #2594 (hackdna)
  • Bring up the log level of httpstream and pysolr to INFO #2555 (hackdna)

Fixed bugs:

  • Unnecessary FileStoreItem instances created during analysis #2670
  • TemplateDoesNotExist errors in analysis_manager views #2668
  • Internal Server Error from /solr/core/select #2639
  • Remove related objects when deleting a data set #2632
  • Missing migration for chunked_upload app #2615
  • Potentially Flaky Unit Tests #2610
  • Workflow Visualization Bug #2609
  • Spurious slashes added to source name of data set files #2582
  • Edit Accession input box is not displayed correctly #2581
  • Non-idempotent test: core.tests.test\_get\_analysis\_list #2576
  • Visualization Tab - loading bug #2552
  • Testing suite fails to run #2537
  • "Import into own space" should only be available for ISAtabs #2519
  • "Import into own space" should not be available if I already own the dataset #2518
  • FileStoreItem.get_file_extension() returns None for certain FileTypes #2515
  • Satori treemap labels missing if URL has branchId=2 #2494
  • In "Two Bar" mode, recall and precision overlap after sort #2489
  • All Files Browser: Chrome is mis-encoding an API url #2425
  • User/Files Filtering Behavior #2352
  • Found set counts not (usually) preserved across Satori toggles #2339
  • search data sets + satori + title click = missized columns #2338
  • Tutorials don't work if the relevant component in Satori is minimized #2140
  • Satori: Context menu interferes with lock highlight propagation #2138
  • Satori: Nodes missing from node-link after sorting while zoomed #2135
  • Re-render truncated after zoom-out in Satori #2134
  • Satori menu toggle up missing icon on FF #2133
  • Adding search to satori query seems to produce result, but not rendered #1931
  • Satori tutorial: Data Set Summary link not working #1925
  • Satori tutorial can be instantiated on top of prior ones #1924
  • Limit to one dashboard filter menu at a time? #1923
  • Satori: Mis-sized if coming from preview with lock active #1921
  • Satori: Tree map loses lock state if window resize forces redraw #1920
  • Satori: lock state not mirrored between treemap and node list #1918
  • Satori treemap depth label mispositioned (FF only) #1916
  • Satori: Popover for current screen split mode remains even after mouse leaves #1915
  • Satori treemap info-"i" does nothing #1914
  • Satori: scroll node column down, change sort, and the column does not redraw #1913
  • Satori treemap depth controller: Click the up-arrow, but the down-arrow gets highlighted #1911
  • Satori treemap depth controller treats click as mousedown (FF only) #1910
  • Satori treemap depth controller requires mouse movement (Chrome only) #1909
  • Satori treemap labels not being cleaned up on redraw [#1908](https://github.com/refinery-platform/refinery-platform/issu...
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Version 1.6.2

24 Jan 16:44
@scottx611x scottx611x
v1.6.2
91a0067
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Version 1.6.2

NOTE: When updating to use this release the following haystack management command will have to be run to rebuild the Solr index: ./manage.py rebuild_index

Implemented enhancements:

  • Lightning Bolt Icon is not a true representation of an Importing FilestoreItem's state #2382
  • Prettier tool names #2155
  • Data Set 2 - Update selection icon and select all icon #1833
  • Data-Set 2 Layout/CSS #1666
  • Move "URL shortcut" field from upload page to data set details in file browser #1629
  • provide list of download URLs for selection #326
  • Provide additional information when logging a file import error from S3 #2444 (hackdna)
  • ISA-Tab Upload: Wrong remove color button #1727
  • Allow deletion of the empty user data S3 buckets #2392 (hackdna)

Fixed bugs:

  • Add read-meta perms to existing dataset objs w/ read perm #2455
  • EC2 data volume type is set to magnetic #2442
  • Download links not displayed in the data set view #2434
  • File Browser - Tooltips Linger #2431
  • Import Own Space Button - Fix color and padding #2401
  • Spurious Solr error 404 in Celery log #2290
  • Provenance Bug: URL fails to redirect #2285
  • Seeing unexpected values for "type" in file browser #2106
  • "study_uuid: AND assay_uuid:" solr syntax error #2063
  • provenance attributes menu not showing on FF #1466
  • Update ui tool_panel visibility based on perms. #2467 (jkmarx)
  • Jkmarx/fixes for vis tab #2449 (jkmarx)
  • Bug fix for checking the dataset object perms. #2445 (jkmarx)
  • Set EC2 instance root volume type to gp2 #2443 (hackdna)
  • Hide any users without profiles or a full_name. #2440 (jkmarx)
  • Jkmarx/popover fix #2439 (jkmarx)
  • Remove flaky tool tip. #2438 (jkmarx)
  • Results missing from some successful analyses #2426
  • Database migrations fail to apply automatically #2420
  • Assertion error in test_analysis_deletion #2408
  • KeyError when cancelling an Analysis before Galaxy Import stage #2397
  • Downloading more files from Galaxy than specified by workflow #2293
  • Assign unique name to each Celery worker #2404 (hackdna)
  • Remove data_set_manager test data zip files from .gitignore #2395 (hackdna)

Closed issues:

  • Sharing/Permissions UI #2390
  • Details > History > "Import into own space" should get grey background #2356
  • file browser filters disappear as new facets applied #2091
  • With download url in solr, don't need the per-row api hits in file browser #2050
  • Refactor provvis global scope usage #1000
  • Decouple access control for data set metadata from access control for data samples #486
  • Collaboration Permissions - View Meta Data Level #2389
  • Remove the WorkflowFilesDL model #2173
  • Assay Files Refactor/Fix Unit Test #1621

Merged pull requests:

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Hotfix v1.6.1.1

13 Dec 21:40
@scottx611x scottx611x
v1.6.1.1
8a4fc91
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Hotfix v1.6.1.1

Hotfix release to allow for some ISATab datasets that exhibited the error from here to upload properly.

Assets 2

Version 1.6.1

27 Nov 22:17
@hackdna hackdna
v1.6.1
d29c885
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Version 1.6.1

Miscellaneous UI and back-end enhancements, bug fixes and automated testing improvements.

Note: ./manage.py migrate will have to be run manually to remove stale contenttypes for: NodeSet, NodeRelationship, and NodePair
Note: you should delete and re-create the storage stack because it now contains Cognito resources.

Assets 2

Version 1.6.0

02 Oct 17:23
@scottx611x scottx611x
v1.6.0
b301acb
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Version 1.6.0

Implemented enhancements:

  • Show zero-count facets in cross-dataset browser #2088
  • 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:

  • Show zero-count facets in file browser #2089
  • cross-dataset browser: Download urls are sometimes still paths #2086
  • 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
  • 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:

  • Limit number of docker containers #2107
  • 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
  • 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:

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Version 1.5.8

17 Jul 12:57
@scottx611x scottx611x
v1.5.8
8d80f47
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Version 1.5.8

Implemented enhancements:

Fixed bugs:

  • Search keywords are still highlighted after clearing the search #1583
  • Flekschas/satori v1.5 #1776 (flekschas)
Assets 2

Version 1.5.7

11 Jul 19:41
@scottx611x scottx611x
v1.5.7
6b115d1
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Version 1.5.7

Note: ./manage.py migrate will have to be run manually to remove stale contenttypes for: NodeGroup

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

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
Assets 2

Version 1.5.6

15 May 16:21
@hackdna hackdna
v1.5.6
7367df5
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Version 1.5.6

Enhancements and improvements:

  • AWS deployment and stack management
  • Data set import and file upload
  • Data set browser 2
  • Collaboration functionality
  • Other miscellaneous bug fixes and enhancements
Assets 2