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Releases: ENCODE-DCC/encoded

patch release for v93

25 Nov 04:24
@hitz hitz
v93.1
1ec8b73
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patch release for v93 
v93.1

ENCD-4978 update bcrypt and pip3 (#3051)
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v93.0 (snovault 1.0.38)

23 Nov 01:18
@hitz hitz
v93.0
18521a0
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v93.0 (snovault 1.0.38) 
1.	ENCD-4970 Make reference-epignome cells render on IE11 (#3041)
2.	ENCD-4973-raw-schema (#3042)
3.	ENCD-4968-update-snovault-1.0.38 (#3040)
4.	ENCD-4930-flag-read1-without-read2 (#3036)
5.	ENCD-4687-add-adapter-files-to-library (#3033)
6.	ENCD-4949-Fix-IE11 (#3039)
7.	ENCD-4908-turn-on-swap-in-deployment (#3037)
8.	ENCD-2304 Reference epigenome matrix (#3032)
9.	ENCD-4912-update-matching-md5-audit (#3005)
10.	ENCD-4896-Add-mirna-annotations-to-file-and-analysis-step (#3030)
11.	ENCD-4898-add-pipeline-assay-audit (#3021)
12.	ENCD-4851 remove duplicated dataset (#3035)
13.	ENCD-2529-fix-default-required-properties-in-json-schema (#3015)
14.	ENCD-4822-update-hgnc-file-to-fix-missing-suggest-genes (#2934)
15.	ENCD-2401 fix IHEC trackhub JSON (#3028)
16.	ENCD-4926-add-michael-schatz-to-aliases (#3011)
17.	ENCD-4848-display-juicebox-name-for-hic (#3038)
18.	ENCD-4934-add-perturbed-property-to-biosample (#3026)
19.	ENCD-4939-change-memlimit-kill-to-terminate
20.	ENCD-4938-add-forensic-logging-to-deployment
21.	ENCD-4937-add-single-node-name-arg
22.	ENCD-4911-increase-upload-limit-to-5gb
23.	ENCD-4947-Fix-deploy-tag-bug-that-pulls-origin-dev
24.	ENCD-4025-update-schema-md (#2985)
25.	ENCD-4842-new-gm-property-introduced-elements (#3031)
26.	ENCD-4929 add control type to FCC experiments (#3018)
27.	ENCD-4933-remove-library-treatment-facet (#3016)
28.	ENCD-4932 Fix links and formatting in Experiment Series audit (#3017)
29.	ENCD-4946-add-new-annotation-type (#3020)
30.	ENCD-4921-add-pacbio-sequel-to-file (#3004)
31.	ENCD-4944 remove oneOf from target schema (#3027)
32.	ENCD-4906-add-treatment-info-metadata (#2995)
33.	SNO-125-switch-batch-download-to-query-string (#2998)
34.	ENCD-4905-add-search-view-tests (#2974)
35.	ENCD-4950-update-deploy-defaults-for-pg11 (#3029)
36.	ENCD-4873-update-audit-search-label (#3019)
37.	SNO-118-simple-query-string (#3013)
38.	SNO-123-limit-es-scan (#3024)
39.	ENCD-4935-reduce-compute-circle-ci-tests (#3003)
40.	ENCD-4914-fix-test-timeout (#3012)
41.	ENCD-4904-add-ingrid-as-user
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v92.0

15 Nov 01:08
@caseylitton caseylitton
v92.0
d1a1685
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v92.0 
	1.	ENCD-4924 fix bugs in moving controls (#3001)
	2.	ENCD-4928-run-npm-once (#3002)
	3.	ENCD-4925-increase-circle-es-heap (#2999)
	4.	ENCD-4895-adjust-long-read-RNA-audit (#2982)
	5.	ENCD-4920-update-snovault-1.0.37 (#2997)
	6.	ENCD-3336-Upgrade-postgres-11 (#2976)
	7.	ENCD-4892 region search refresh (#2978)
	8.	ENCD-4861 add enum to user groups(#2964)
	9.	ENCD-4849-fix-description-misalignment-in-docs (#2958)
	10.	ENCD-4840-Add-Donor-accession-boost-value (#2975)
	11.	ENCD-4674 move Control from Target to Experiment (#2866)
	12.	ENCD-4894 Exclude long read RNA-seq from RNA fragment size audit and add tests for missing read_length (#2969)
	13.	ENCD-4900 Add status check for matching md5 sum audit (#2972)
	14.	ENCD-4903-image-update (#2983)
	15.	[HOTFIX] SNO-120-stream-large-json (#2980)
	16.	ENCD-4885 add entry for functional characterization assays (#2981)
	17.	ENCD-4916-fix-circleci (#2986)
	18.	ENCD-4816 Summary release date source change (#2961)
	19.	ENCD-4722 install Valis as component (#2937)
	20.	ENCD-4855 Extra-wide search facets (#2948)
	21.	ENCD-4876-add-assembly-annotations (#2956)
	22.	ENCD-4865 remove fcc assay term names from experiements (#2952)
	23.	SNO-115-delete-old-search-code (#2966)
	24.	ENCD-4731 Add audits for experiment series (#2960)
	25.	ENCD-4890-library-target-size-range (#2970)
	26.	ENCD-4901-redirect-file-downloads (#2968)
	27.	ENCD-4902-fix-graph-x-tick (#2971)
	28.	ENCD-4887-fix-audit-detail-bugs (#2957)
	29.	ENCD-4862-fix-audit-script error (#2962)
	30.	ENCD-4836-bring-back-alt-color-report-view-table (#2963)
	31.	ENCD-4854 Change severity of missing controlled by audit (#2953)
	32.	ENCD-4858-table-border (#2949)
	33.	ENCD-4863-audit-paths (#2940)
	34.	ENCD-4866 fix sorttable comment (#2947)
	35.	ENCD-4868-update-organ-slims (#2954)
	36.	ENCD-4888-add-admin-access-key-to-insert (#2946)
	37.	ENCD-4079-fix-npm-audit-errors (#2913)
	38.	ENCD-4816 Summary release date source change (#2961)
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EncodeD release v91.0

09 Oct 23:25
@hitz hitz
v91.0
3339ecb
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EncodeD release v91.0 
1. ENCD-4891-region-search-crash-with-position (#2955)
2. ENCD-4878-update-robots-txt (#2939)
3. ENCD-4884-allow-apache-conf-variables-on-deploy
4. ENCD-4718-Refactor-deployment-based-on-build-type
5. ENCD-4881-fix-NTR-audit-detail (#2943)
6. ENCD-4879-workaround-for-improper-date (#2942)
7. ENCD-4880-restore-disabled-buttons (#2941)
8. ENCD-4875-update-snovault-1.0.36 (#2936)
9. ENCD-4803-new-search-views (#2928)
10. ENCD-4871-summary-dates (#2935)
11. ENCD-4398-allow-unprivileged-login-for-cart(#2869)
12. ENCD-4753-fix-audit-details-and-cleanup (#2927)
13. ENCD-4838 Remove Experiment Classification from Experiment Schema (#2929)
14. ENCD-4856 break up test suite for circle-ci (#2932)
15. ENCD-4826 updated chip-seq qc (#2930)
16. ENCD-4846 Fix microRNA raw data table headers (#2933)
17. ENCD-4820-update-ontology (#2917)
18. ENCD-4690-remove-cln-msg-in-file-assoc-graph (#2903)
19. ENCD-4050-replace-momentjs (#2914)
20. ENCD-4832 remove border on empty results (#2926)
21. ENCD-4844-Add-Jessica-to-users
22. ENCD-4837 assay title facet for experimental series (#2921)
23. ENCD-4213-replace-cookie-monster (#2906)
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EncodeD release v90

01 Oct 00:00
@hitz hitz
v90.0
140a88a
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EncodeD release v90 
v90.0 (released) snovault 1.0.34

---------------------------------------
1. ENCD-4828 Remove extra div and style .box.facets (#2919)
2. ENCD-4827 Restore old link underlines (#2918)
3. ENCD-4824 Make Safari search box styling the same as others (#2915)
4. ENCD-4825 Return button style and clean up CSS (#2916)
5. ENCD-4817 Fix default value (#2902)
6. ENCD-4538 Fixed minor typos and formatting inconsistencies (#2895)
7. ENCD-4376 new ATAC-seq QC (#2907)
8. ENCD-4819 Use not-allowed cursor on disabled inputs, buttons (#2909)
9. ENCD-4818 downgrade ChIP-seq QM schema versions (#2908)
10. ENCD-4788-add-mg-kg-treat (#2900)
11. ENCD-4714-move-pg-deploy-echos-to-file (#2905)
12. ENCD-4794 update bulk RNA QC (#2901)
13. ENCD-4680 Remove and replace Bootstrap styling (#2894)
14. ENCD-4783-set-iam-role-on-deploy (#2904)
15. ENCD-4797 Add new file FCC output_type elements reference (#2899)
16. ENCD-4789 Add wranglers' uuids to antibody_characterization.json (#2898)
17. ENCD-4776 Add Bonita's info to user.json (#2897)
18. ENCD-4800 Fix Chrome slow scrolling with scrollable facets (#2892)
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v89-hotfix-1

18 Sep 20:31
@caseylitton caseylitton
v89-hotfix-1
c7e4f98
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v89-hotfix-1 
v89-hotfix1-ENCD-4817-fix-default-value
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Release v89.0

20 Aug 23:03
@hitz hitz
v89.0
a03b242
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Release v89.0

v89.0 (released) snovault 1.0.34

  1. ENCD-4811 Change breadcrumb pluralization (#2893)
  2. ENCD-4801 fix bugs related to award embedding in AntibodyLot (#2890)
  3. ENCD-4539-pipelines-missing-alt-accession (#2879)
  4. ENCD-4802 update ChIP-seq QMs (#2891)
  5. ENCD-4641 new ChIP-seq quality metrics (#2789)
  6. ENCD-4779 fix default tracks (#2884)
  7. ENCD-4664 FCC experiment modeling (#2882)
  8. ENCD-4768 Add matching md5sum property (#2870)
  9. ENCD-4769 Add dataset properties on ExperimentPage (#2888)
  10. ENCD-4711-update-sn-atac-name (#2889)
  11. ENCD-4785 correcting md5 uniqueness behavior (#2881)
  12. ENCD-4778 Add link for Mouse Dev Series collection to drop down menu (#2874)
  13. ENCD-4775 default to mm10 over mm9 (#2883)
  14. ENCD-4773 fix browser styles on IE 11 (#2872)
  15. ENCD-4750 rename duplicated health status column (#2876)
  16. ENCD-4791 remove Quick View (#2886)
  17. ENCD-4745 biosample characterization audit update (#2880)
  18. ENCD-4730-change-menu-item-names-for-matrices (#2877)
  19. ENCD-4740-fix-broken-report-link (#2862)
  20. ENCD-4729-fix-add-minus-btn-on-graph (#2885)
  21. ENCD-4228-genetic-mod-missing-alter-acc (#2878)
  22. ENCD-4752 read_structure for fastq files (#2868)
  23. ENCD-4646-add-search-btn-top-nav (#2871)
  24. ENCD-4608 ENCODE4 antibody review (#2849)
  25. ENCD-4744 Added erez-aiden to aliases list (#2873)
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v88.0 (released) snovault 1.0.34

30 Jul 16:27
@jenjou jenjou
v88.0
804f95d
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v88.0 (released) snovault 1.0.34 
---------------------------------------
1. ENCD-4761 Fix table display for non-anno and exp pages (#2861)
2. ENCD-4762 make-search-fields-consistent (#2860)
3. ENCD-3904 remove-quotation-marks (#2850)
4. ENCD-4715 Integrate Valis browser (#2809)
5. ENCD-4760 Update to snovault 1.0.34 (#2858)
6. SNO-108 improve-search-new (#2856)
7. ENCD-4724 md5 uniqueness adjustment (#2855)
8. ENCD-4720 change-es-deploy-arg-to-bool (#2853)
9. ENCD-4692 Add mechanism for audit details to include links (#2854)
10. SNO-106 fix-spec-char-500-error (#2851)
11. ENCD-4685 matrix-vertical-scroll (#2836)
12. ENCD-4717 adding output types (#2839)
13. ENCD-4682 Award title required (#2831)
14. ENCD-4677 Update biosample characterization audit (#2847)
15. ENCD-3567 Upgrade React JS 15.6.0 (#2841)
16. ENCD-4697 add biosample summary to experiment series (#2842)
17. ENCD-4701 Update STAR quality metric for chimeric reads (#2843)
18. ENCD-4706 store-circleci-results (#2848)
19. ENCD-4702 remove-dup-gm-column-in-biosample (#2846)
20. ENCD-4684 remove-facet-duplication (#2844)
21. ENCD-4511 make-pool-table (#2820)
22. ENCD-4699 Fix Javascript crash display series file tables (#2829)
23. ENCD-4063 ambulance-icon-for-only-logged-in-users (#2819)
24. SNO-105 fix-batchupgrade-tests-sno103 (#211)
25. ENCD-4772 Fix context usage with GM object pages (#2865)
26. ENCD-4771 gene locations for mouse incorrectly padded (#2864)
27. ENCD-4770 Only filter revoked files when needed (#2863)
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v87.0 (released) snovault 1.0.32/1.0.33

26 Jul 21:35
@caseylitton caseylitton
v87.0
7bab075
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v87.0 (released) snovault 1.0.32/1.0.33 
---------------------------------------
1. ENCD-4723 update-snovault-1.0.33 (#2840)
2. ENCD-4716 Update cloud init deployment (#2830)
3. ENCD-4713 manually-install-oracle-java-11 (#2830)
4. ENCD-4719 Use 16 processes demo batchupgrade (#2830)
5. ENCD-4665 organize-cluster-cloud-yamls (#2830)
6. ENCD-4688 remove-unused-code-from-deploy (#2830)
7. ENCD-4704 Fix frozen column for Safari (#2825)
8. ENCD-4708 Fix the target column on experiment series page (#2828)
9. SNO-102 use-openjdk-java-for-circleci (#2832)
10. ENCD-4703 test-submitter-user-circleci-fix (#2824)
11. ENCD-4654 change ChIP-seq to TF ChIP-seq (#2806)
12. ENCD-4698 update-snovault-1.0.32 (#2822)
13. ENCD-4662 Experiment series (#2812)
14. ENCD-4659 batch-download-unit-test (#2815)
15. ENCD-4514 add MouseDevSeries internal tag (#2821)
16. ENCD-4106 Remove kyoto from aliases and dbxrefs (#2803)
17. ENCD-4672 Remove news page and instead link to generic search (#2811)
18. ENCD-4653 add AWS link (#2798)
19. ENCD-4415 Add GM perturbation property (#2816)
20. ENCD-4694 restrict use of FCC in experiments (#2817)
21. ENCD-4471 add-prod-id-source-treatment (#2808)
22. ENCD-4671 port tests circleci (#2810)
23. ENCD-4062 Fix read name details dependency (#2797)
24. ENCD-4613 Changed cRE to cCRE with batch upgrades and tests (#2763)
25. ENCD-4656 Fix BDD Travis CI test failures (#2793)
26. ENCD-4651 add new analysis step type (#2785)
27. ENCD-4586 Freeze left column of matrix (#2799)
28. SNO-100 Parallelize batchupgrade script
29. SNO-92 fix-batch-upgrade-logging
30. SNO-101 Refactor batchupgrade
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v86.0 (released) snovault 1.0.31

07 Jun 18:37
@caseylitton caseylitton
v86.0
1b587f4
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v86.0 (released) snovault 1.0.31 
--------------------------------
1. ENCD-4676 add-nagios-role-deployment (#2796)
2. ENCD-4666 update-snovault-1.0.31 (#2790)
3. ENCD-4657 add-s3-uri-to-metadata (#2786)
4. ENCD-4639 Organize demo cloud yaml (#2773)
5. ENCD-4634 Add database to file_format (#2770)
6. ENCD-4541 Add multiple facets to cart view pages (#2780)
7. ENCD-4633 Update saucelabs connect version 4.5.3 (#2788)
8. ENCD-4609 Exclude fccs institutional certification (#2764)
9. ENCD-4631 add new qc object for gencode categories (#2787)
10. ENCD-4492 audit-to-chk-fq-non-fq-pair (#2776)
11. ENCD-4084 date selector facet (#2759)
12. ENCD-4600 Add MIME type for ab1 attachment (#2774)
13. SNO-93 user-count-does-not-match (#2758)
14. ENCD-4647 Display QC metric properties with multitype (#2783)
15. SNO-90 added-advanced-search (#2729)
16. ENCD-4648 always-show-cloud-metadata (#2777)
17. ENCD-4642 Stop home banner truncation (#2781)
18. ENCD-4599 fix audit detail typo (#2765)
19. ENCD-4400 added-creative-commons-logo (#2750)
20. ENCD-4611 update 2 polyA assay_titles (#2761)
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