Revision b8b30009cf8f95e00d9487dd73d264c8837c23fb authored by Casey Litton on 28 February 2020, 01:27:31 UTC, committed by GitHub on 28 February 2020, 01:27:31 UTC
ENCD-5132-update-deployment-amis (#3174)
CHANGES.rst
Changes
=======
v97rc1 (unreleased) snovault 1.0.41 - pre v96.1 ubuntu18/py376 merge
--------------------------------------------------------------------
1. ENCD-5071-audit-script-error-when-control-is-series (#3164)
2. ENCD-4626-fix-test-save-change-antibody (#3145)
3. ENCD-4365-roadmap-collection-view (#3142)
4. ENCD-5121-doc-section-publication-data (#3162)
5. ENCD-5073-multiple-targets-FCC (#3154)
6. ENCD-5097-add-Ingrid-to-AntibodyCharacterization-reviewed-by (#3148)
7. ENCD-5033-index-user-made-accounts (#3158)
8. ENCD-4953-calculated-tags-property-experiment (#3155)
9. ENCD-5072 Library construction platform display (#3168)
10. ENCD-5106-add-control-link-FCE (#3151)
11. ENCD-5101-add-target-to-annotation-summary-page (#3165)
12. ENCD-5124-fix-vis-indexing-failure-on-RNA-seq-annotation (#3161)
13. ENCD-5074-exclude-single-cell-from-read-count-audit (#3153)
14. ENCD-5083-restrict-IHEC-dbxref-to-RefEpi-and-Annotation (#3147)
15. ENCD-5034-encyclopedia-v6-addition (#3152)
16. ENCD-4917-new-target-matrix (#3071)
17. ENCD-5075 Adding the change for depmap (#3141)
18. ENCD-5081 add-pooled-clone-sequencing-types (#3144)
19. ENCD-5084-draft-1 (#3149)
20. ENCD-5096-draft-1 (#3150)
21. ENCD-5091 Rebuilt package-lock.json (#3140)
22. ENCD-5077 Remove unnecessary prints (#3146)
v96.1 (unreleased) snovault 1.0.41
----------------------------------
1. SNO-142 Minor fixes for ubutnu 18 on v96x1rc1 (#3167)
2. SNO-141-update-osx-catalina-readme (#3167)
3. ENCD-5120-1st-post-master-merge-fix-u18-py369 (#3160)
4. ENCD-5112 Update deploy ami map for all builds (#3109)
5. SNO-140 Allow shorting uuids with flag (#3109)
6. SNO-139 Log detailed initial indexing times (#3109)
7. ENCD-3983-update-to-ubuntu-18 (#3109)
8. ENCD-4961-make-base-amis-encd-deployment (#3109)
9. ENCD-4960-add-aws-pems-for-deployment (#3109)
10. SNO-132 Update to py37 lrowe pr with fixes (#3109)
11. ENCD-5061-echo-filenames-in-deploy-scirpt (#3109)
12. ENCD-5060-add-py-requirements-file (#3109)
13. ENCD-5059-fix-pylint-in-deploy-script (#3109)
v96.0 (released) snovault 1.0.40
--------------------------------
1. ENCD-5089-add-back-account-creation-msg (#3139)
2. ENCD-5088-graphlib-crash (#3137)
3. ENCD-5086-remove-chip-seq-matrix-from-menu (#3136)
4. ENCD-5047-no-dependencies-output-types (#3135)
5. ENCD-4943-fix-bad-ancient-URL-forwards (#3129)
6. ENCD-5049 add MINT mixture to library object (#3132)
7. ENCD-5056-computation-model-object (#3128)
8. ENCD-5037-valis-library-update (#3119)
9. ENCD-5026 toolbar updates (#3133)
10. ENCD-5057-add-experiment-audit-for-no-processed-data (#3126)
11. ENCD-5078-fcc-insert (#3134)
12. ENCD-5068-update-regex-pattern-for-IHEC-dbxref (#3123)
13. ENCD-4172 improved PublicationData embedding (#3130)
14. ENCD-4975-three-library-properties-restricted-to-enum (#3108)
15. ENCD-5054-revise-biosample-search-result-link-age-display (#3118)
16. ENCD-5065-account-creation-error-msg (#3110)
17. ENCD-5050-nanopore-file-dependency (#3121)
18. ENCD-5032 add reset to genome browser (#3106)
19. ENCD-5020-create-account-on-any-page (#3112)
20. ENCD-5022-ENTEx-updates (#3122)
21. ENCD-5053-Display target_expression_percentile (#3127)
22. ENCD-4948 Facet registry (#3120)
23. ENCD-4936-add-location-to-gene (#3083)
24. ENCD-5043-add-icLASER-assay (#3115)
25. ENCD-5055-update-audit-detail-insufficient-read-length-rna (#3116)
26. ENCD-5025-create-account-created-messagebox (#3107)
27. ENCD-5048 annotation schema change for FCC controls (#3114)
28. ENCD-5066-calculate-s3-uri-for-all-files (#3117)
v95.0 (released) snovault 1.0.40
---------------------------------------
1. ENCD-5064 update the detail message in "inconsistent genetic modification tags" audit (#3113)
2. ENCD-5058 fix pip version (#3111)
3. ENCD-4899 additions to robots.txt (#3055)
4. ENCD-5008 Analyses property (#3100)
5. ENCD-5015 functional characterization series (#3099)
6. ENCD-4999 Add PRO-cap assay term (#3101)
7. SNO-129-add-fielded-generator-response (#3077)
8. ENCD-5005 replace GO properties with GO links (#3098)
9. ENCD-5044-update-to-snovault-1-40 (#3104)
10. ENCD-4995 adding read index_of (#3095)
11. ENCD-4987 Add audits for eclip queried_RNP_size_range (#3090)
12. ENCD-3086-add-dataset-to-file (#2977)
13. ENCD-4655 remove recombinant protein category of target (#3070)
14. ENCD-4986-fix-summary-page-filter-miscount (#3081)
15. ENCD-4997-adjust-GM-schema-for-FCC-expts (#3096)
16. ENCD-5004-update-assay-titles-ontology (#3093)
17. ENCD-4956-add-content-to-schema (#3089)
18. ENCD-5014-new-FCE-property-target-expression-percentile (#3097)
19. ENCD-5013 Allow elements_reference to link to Annotations (#3086)
20. ENCD-5010-Reduce-min-read-length-miRNA (#3092)
21. ENCD-5027-fix-refseq-dbxref-link (#3087)
22. ENCD-4998 Revise time units pluralization (#3082)
23. ENCD-4951-add-4dn-expt-dbxref (#3084)
24. ENCD-5036 freeze setuptools for wale at v43 (#3091)
25. ENCD-4790 replicates in Valis (#3068)
26. ENCD-5023 fix advanced query search BDD test (#3088)
27. ENCD-5007-home-svg-chrome-bug (#3080)
v94.0 (released) snovault 1.0.39
---------------------------------------
1. ENCD-5002 Removed month_released from facet list for scRNA series (#3074)
2. ENCD-5001-SCREEN-link-updates (#3076)
3. ENCD-4994-fix-broken-img-tag-appearance-ie11 (#3073)
4. ENCD-4996-fix-IE-shading (#3075)
5. ENCD-4993-update-snovault-1.0.39
6. ENCD-4222 Implement ENTEx matrix (#3067)
7. ENCD-4882 Removed month_released property from Dataset and Page (#3049)
8. ENCD-4965-quality-metrics-now-required-property (#3064)
9. ENCD-4983-new-file-output_type-personalized-genome-assembly (#3065)
10. ENCD-4810 md5 self audit (#3063)
11. ENCD-4967-broken-E11-fixes (#3043)
12. ENCD-4812-award-link-embedded (#3069)
13. ENCD-4971-add-TagRFP-enum-GM (#3062)
14. ENCD-4972-calculate-FCC-control-assay-titles (#3061)
15. ENCD-4969 Update missing raw data in replicate audit (#3046)
16. ENCD-4922 single cell RNA series (#3066)
17. ENCD-4859-clarify-undetermined-replication-type-audit (#3059)
18. ENCD-4488-tighten-annotation-schema (#3045)
19. ENCD-4984-add-ENCODE3-to-scRNA-without-controls (#3057)
20. ENCD-4942 remove control category of target (#3058)
21. ENCD-4872 open ENCODE4 antibody standards to ENCODE3 antibodies (#3022)
22. ENCD-4979-fix-reference-to-HTTPFound (#3060)
23. ENCD-4976 Remove scRNA-seq from RIN audit (#3056)
24. ENCD-4557-limit-reviewers-cannot-edit-characterization (#3054)
25. ENCD-4974-cricket-typo-fixes (#3048)
26. ENCD-4966-remove-default-replicate (#3047)
27. ENCD-4980-upgrade-pip-circleci (#3053)
v93.1 (released) snovault 1.0.38
---------------------------------------
1. ENCD-4978 update bcrypt and pip3 (#3051)
v93.0 (released) 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
v92.0 (released) snovault 1.0.37
---------------------------------------
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)
v91.0 (released) snovault 1.0.36
---------------------------------------
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)
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)
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)
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)
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
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)
v85.2 (unreleased) snovault 1.0.30
--------------------------------
1. ENCD-4650 update-snovault-1.0.30 (#2778)
2. ENCD-4620 indexing-failures (#2775)
v85.1 (released)
--------------------------------
1. ENCD-4628 Add a mechanism for a home page banner (#2768)
v85.0 (released) snovault 1.0.29
--------------------------------
1. ENCD-4625 Fix target upgrade for chromatin remodeler (#2755)
2. ENCD-4624 update-snovault-1.0.29 (#2754)
3. ENCD-4392 update-to-java-11 (#2726)
4. SNO-91 update-java-ref (#2753)
5. SNO-87 fix-profile-trailing-slash (#2710)
6. ENCD-4619 Add experiment classification to data insert (#2752)
7. ENCD-4361 validate-schema-set-status (#2748)
8. ENCD-4558 add 2 new FCC assays
9. ENCD-4563 shorten 3 assay titles
10. ENCD-4579 update to EFO3 and update ontology.json and docs
11. ENCD-4536 long read RNA audit (#2735)
12. ENCD-4535 long rna qc (#2673)
13. SNO-86 escape-search-text (#2709)
14. ENCD-3642 fix-file-format-download (#2746)
15. ENCD-4602 Update link on home page button (#2744)
16. ENCD-4606 Add error correction step type (#2747)
17. ENCD-4493 Limit RIN audit to certain assays (#2743)
18. ENCD-4593 add histone and control chip-seq titles (#2741)
19. ENCD-4504 miRNA audits (#2736)
20. ENCD-4503 micro RNA qc (#2679)
21. ENCD-4570 Add M21 V29 V30 genome annotations (#2745)
22. ENCD-4544 deleted the file atacseq qm json file (#2738)
23. ENCD-3108 Add new target categories (#2742)
24. SNO-88 fix-user-search-count (#2722)
25. ENCD-4589 Add an experimental audit for biosample characterization. (#2739)
26. ENCD-4316 Make generic matrix-rendering component. (#2728)
27. ENCD-4575 software-column-used-by (#2737)
28. ENCD-4545 Update visualization browser list (#2730)
29. ENCD-4597 show-all-datasets (#2733)
84.0 (released) snovault 1.0.28
-------------------------------
1. ENCD-4591 add-title-column-back (#2723)
2. ENCD-4590 fix-facet-num-line (#2725)
3. ENCD-4592 Update to Java 9 in travis (#2724)
4. ENCD-4585 Update to snovault 1.0.28 (#2721)
5. SNO-89 Fix backoff error key in indexer (#2720)
6. ENCD-4559 x-limit-zero-results (#2711)
7. ENCD-4349 restrict gm reagents (#2672)
8. ENCD-4578 Fix s3 to s3 allow flag in deployment (#2708)
9. ENCD-4243 Make dataset biosample boost values consistent (#2712)
10. ENCD-4527 walkme-production-snippet (#2690)
11. ENCD-4581 Temp install java 8 through aws (#2718)
12. ENCD-4577 Add documents on characterization page (#2716)
13. ENCD-4565 remove back slashes from search terms (#2714)
14. ENCD-4576 Change header links and add FAQ script (#2715)
15. ENCD-4556 Remove lane reqs for massspec characs (#2700)
16. ENCD-4311 href-column-is-blank (#2713)
17. SNO-85 facet-reappearing (#2676)
18. ENCD-4506 make fragmentation method a list (#2683)
19. ENCD-4542 Display biosample table on GM pages (#2699)
20. ENCD-4407 update the columns and facet titles
21. ENCD-4548 fix fallback images on collection pages (#2703)
22. ENCD-4560 update typeaheads after selections (#2702)
23. ENCD-4497 get rid of duplicate columns using titles
24. ENCD-4564 add target typeahead to AntibodyLot pages (#2707)
25. ENCD-4412 Add Clear Cart item to cart menu (#2695)
26. ENCD-4554 fix-annotation-url (#2697)
83.0 (released) / snovault 1.0.27
-----------------
1. ENCD-4569 Update snovault to 1.0.27 (#2704)
2. ENCD-4562 Setup s3tos3 copy on test (#2698)
3. ENCD-4555 Fix key errors in vis indexing (#2696)
4. ENCD-4543 fix-status-hierarchy (#2677)
5. ENCD-4550 Fix deploy console output (#2691)
6. ENCD-4170 exclude-restricted-files (#2670)
7. ENCD-4510 Fix human donor children calc prop (#2684)
8. ENCD-4513 add collections links to menu (#2681)
9. ENCD-3919 index-vis-blobs-on-deploy (#2685)
10. ENCD-4517 Add new property introduced_elements to user interface (#2671)
11. SNO-83 rotate jpg and tiff attachment based on EXIF (#2667)
12. ENCD-3952 add new assay category, mpra, update ontology.json
13. ENCD-4347 add efo derives from capability, remove unnecessary slimming
14. ENCD-4384 Update assay name ISO-seq to long read RNA-seq
15. ENCD-4489 add imputation annotation_type (#2654)
16. ENCD-4414 Allow users to add exp to carts from series (#2665)
17. ENCD-4507 Handle long cart operations (#2661)
18. ENCD-4494 remove-duplicate-embedding (#2659)
19. ENCD-4521 add-insert-user-meenakshi (#2653)
20. ENCD-4469 Add stimulation to treatment type (#2646)
21. ENCD-3422 datasets-table-publication (#2660)
22. ENCD-4524 update audit matrix (#2662)
23. ENCD-4526 Change date format for Pages (#2663)
24. ENCD-4477 added-changelogs (#2668)
25. ENCD-4530 Fix duplicate alternate accessions (#2669)
26. ENCD-4464 add GM category enums (#2634)
27. ENCD-4523 Fix ENSEMBL visualization (#2645)
82.0 (released) / snovault 1.0.26
-----------------
1. ENCD-4509 Add test back (#2640)
2. ENCD-4518 Fix javascript error for sorting dates (#2642)
3. ENCD-4481 Update to snovault 1.0.26 (#2639)
4. ENCD-4500 remove-uploading-private-status-list (#2636)
5. ENCD-3901 Support multiple carts per user (#2614)
6. ENCD-4487 reset-upload-bucket (#2635)
7. ENCD-4505 fix-file-bucket-audit (#2638)
8. ENCD-4482 adding lane to characterizations review (#2624)
9. ENCD-4483 Cleanup deploy output and short aws name(#2626)
10. ENCD-4353 Refactor-out-matrix-and-result (#2539)
11. SNO-80 Typeahead for facets (#2632)
12. ENCD-3877 annotation-download-btn
13. ENCD-4474 model restriction map (#2617)
14. ENCD-4473 add-MPRA-assay (#2623)
15. ENCD-4418 Add ontology dbxrefs to biosample page (#2637)
16. ENCD-4305 Turn Superseded by into links on exp file pages (#2633)
17. ENCD-4457 organoid age (#2631)
18. ENCD-4485 bug report camel case (#2629)
19. ENCD-4467 Numerical facets sorted by value not frequency (#2628)
20. ENCD-3877 annotation-download-btn
21. ENCD-4449 use top level class files property for Annotation
22. ENCD-4401 remove-approvalrequired (#2616)
23. ENCD-4217 Rendering error series objects (#2627)
24. ENCD-4484 Allow deployment set ssh id file (#2625)
25. ENCD-4348 Restrict ontologies for in vitro diff cells (#2620)
26. ENCD-4476 add-spaces-schema (#2615)
27. SNO-73 Add uuid queue module
28. ENCD-4456 Override update objs in vis reg indexers
29. ENCD-4450 add two sources to alias namespace (#2618)
30. ENCD-4475 Fix pub priv bucket variables (#2613)
81.0 (released) / snovault 1.0.25
-----------------
1. ENCD-4462 fixing the AB characterization view bug (#2606)
2. ENCD-4463 embed BiosampleType in antibody characterization (#2603)
3. ENCD-4460 Update AnalysisStep changelog (#2605)
4. ENCD-4461 Revert libraries for exp type matrix (#2602)
5. ENCD-4429 Lower audit severity for missing reagents in GM (#2601)
6. ENCD-4458 Update snovault 1.0.25 (#2600)
7. ENCD-4240 Allow review characterizations (#2591)
8. ENCD-4425 Update audits exp and genetic mod targets (#2598)
9. ENCD-4445 Handle login for related files in file tables. (#2597)
10. ENCD-4455 Notify indexer for file update bucket (#2599)
11. ENCD-4453 Add idx file format (#2594)
12. ENCD-4427 file-bucket-audit (#2580)
13. ENCD-4298 Ontology update colon and PLAC-seq (#2590)
14. ENCD-4251 Combine reorganize technical replicates (#2567)
15. ENCD-4431 Change report file download name (#2571)
16. ENCD-4444 Highlight selected facet terms numbers (#2587)
17. ENCD-4408 mobile menu readability (#2593)
18. ENCD-4420 Remove biosample type name id props (#2585)
19. ENCD-4014 library restriction enzyme audit (#2537)
20. ENCD-4419 use biosample ontology for audit (#2589)
21. ENCD-4435 Add ENCv5 ccre internal_tags to datasets (#2588)
22. ENCD-4406 exclude fly RNAi from reagents audit (#2570)
23. ENCD-4227 add-PLAC-seq-to-assays (#2584)
24. ENCD-4405 Add enrichment to analysis step types enum (#2582)
25. ENCD-4416 Revise audit_inherit list of AntibodyLots (#2583)
26. ENCD-4402 Add Jennifer Z to submitters (#2572)
27. ENCD-4397 introducing GM in metadata tsv (#2557)
28. ENCD-4439 add PLAC-seq in generate-ontology (also #2590)
80.0 (released) / snovault 1.0.24
-----------------
1. ENCD-4423 Update dalliance to version 1.0 (#2566)
2. ENCD-4417 Update to snovault 1.0.24 (#2563)
3. ENCD-3971 Update node npm to version 10 (#2553)
4. ENCD-4359 Fix recursive is_part_of audit function (#2552)
5. ENCD-4325 Juicebox browser (#2554)
6. ENCD-4360 connect biosample type (#2560)
7. ENCD-4396 Citation note (#2555)
8. ENCD-4388 excluding not relevant experiments form RE audits (#2551)
9. ENCD-4355 add introduced gene link (#2559)
10. ENCD-4375 Restore SRA dbxrefs linkouts (#2558)
11. ENCD-4393 add-gene-alignments (#2556)
12. ENCD-4369 Install redis server (#2543)
13. ENCD-4377 Add Ubiquitination to target mod enum (#2550)
14. ENCD-4399 fix-linux-travis-option (#2547)
79.0 (released) / snovault 1.0.22-23
-----------------
1. ENCD-4340 get-or-create-carts-with-types (#2541)
2. ENCD-4372 Update to snovault 1.0.23 (#2546)
3. ENCD-4367 Update simple for queue module (#2542)
4. ENCD-4371 Update to snovault 1.0.22 (#2544)
5. ENCD-4335 Remove npm shrinkwrap again (#2540)
6. ENCD-4312 genetic modification audit (#2528)
7. ENCD-3665 add file format dependency (#2523)
8. ENCD-4333 Add release candidate options to deploy (#2503)
9. ENCD-4323 Promote released objects (#2535)
10. ENCD-4346 Added new output type for HiC files (#2531)
11. ENCD-4334 Added status facet to Matrix view on y axis (#2520)
12. ENCD-4299 Fix anti body lot target_organisms (#2529)
13. ENCD-4358 add cell-free sample BiosampleType (#2536)
14. ENCD-4306 remove-improper-styling (#2524)
15. ENCD-4338 Allow repo to be specified on deploy (#2509)
16. ENCD-4327 changed audit level for missing step run (#2513)
17. ENCD-4201 Add Jen to test data insert (#2518)
18. ENCD-4328 disable-btn-unavail-files (#2521)
19. ENCD-4218 fix biodalliance visualize multiple datasets (#2522)
20. ENCD-4315 cleanup-mutated-gene (#2526)
21. ENCD-4273 Inconsistent antibody handling (#2530)
22. ENCD-4319 improve BiosampleType (#2516)
23. ENCD-4308 fix-audit-clear-filter (#2499)
24. ENCD-4324 Added-min-width-to-y-axis-label (#2506)
25. ENCD-4265 matrix-audit-text-update (#2507)
26. ENCD-4250 Make target synthetic organism as tag (#2510)
27. ENCD-4272 no-add-treatments (#2514)
28. ENCD-4326 Fix HTML entities for quotes (#2511)
29. ENCD-4297 Fix back button behavior and page jumping (#2515)
30. ENCD-3855 Filter ReEpig by assay facet by title (#2517)
78.0 (released) / snovault 1.0.21
-----------------
1. ENCD-4332 Update to snovault 1.0.21 (#2502)
2. ENCD-4301 Refactor index UUID server (#2485)
3. ENCD-4263 Only show released quality metrics (#2450)
4. ENCD-4195 Update ontology with mintchip slims (#2500)
5. ENCD-4321 Fix import of ExperimentTable (#2498)
6. ENCD-4317 Update snovault to 1.0.20 (#2494)
7. ENCD-4205 biosample type (#2442)
8. ENCD-4245 skip-restricted-acl (#2490)
9. ENCD-4279 Biosample preservation (#2493)
10. ENCD-4033 Search page type-specific header (Req SNO-66) (#2492)
11. ENCD-4281 fix-audit-text-message (#2465)
12. ENCD-4223 Make internal_tags badges clickable to search pages (#2467)
13. ENCD-4289 Update genetic modification tags metadata (#2491)
14. ENCD-4244 audit-error-page (#2461)
15. ENCD-4271 fix-treatment-tem-id-regex (#2475)
16. ENCD-4231 matched set controls (#2474)
17. ENCD-4295 fix target title in JSON (#2486)
18. ENCD-4291 changed modification_type to category in gm schema (#2478)
19. ENCD-4252 disable-download-restricted-files-admin (#2481)
20. ENCD-4300 Remove checkfiles folder (#2484)
21. ENCD-4288 Update requests to 2.20.0 (#2483)
22. ENCD-4195 ontology update sept18 (#2489)
23. ENCD-4267 Remove redirect from apache config (#2459)
24. ENCD-4142 Update calc prop assembly on dataset (#2437)
25. ENCD-4255 fix-biosample-audit-bug (#2470)
26. ENCD-4282 Add PGP internal_tags badge (#2468)
27. ENCD-4256 Fix region search back button functionality (#2463)
28. ENCD-4280 Remove table margin (#2462)
29. ENCD-4239 Add biosample to query string on matrix (#2460)
30. ENCD-4199 Ignore npm shrinkwrap (#2477)
77.1 (released) / 3998 Bug Fix
-----------------
1. ENCD-3998 Target upgrade to return gene uuid (#2466)
77.0 (released) / snovault 1.0.19
-----------------
1. ENCD-4237 bdd-test-for-search (#2435)
2. ENCD-4274 Update to snovault 1.0.19 (#2446)
3. ENCD-3159 Initial shopping cart (#2430)
4. ENCD-4209 Add index flags to indexers and fix logs (#2402)
5. ENCD-4000 represent histone modification in Target (#2416)
6. ENCD-3998 Link target to gene and link gene from targets. (#2416)
7. ENCD-4229 Fix no story news news crash (#2445)
8. ENCD-3701 Update events from search page text box (#2428)
9. ENCD-4185 s3-public-url (#2425)
10. ENCD-4257 Revert copy to deepcopy for matrix factory(#2439)
11. ENCD-4220 Remove references to release ready status (#2436)
12. ENCD-4176 fix BDSC links (#2434)
13. ENCD-4254 Raise file validation error audit level in exp (#2433)
76.0 (released) / snovault 1.0.18
-----------------
1. ENCD-3926 Refactor search related views (#2422) (#2424)
2. ENCD-4202 fixing missing control audit (#2398)
3. ENCD-4197 Red audit for missing step_run (#2397)
4. ENCD-4221 Fix button styles (#2414)
5. ENCD-4207 Added emma to user file (#2403)
6. ENCD-4177 Adding btn to convert page to JSON (#2411)
7. ENCD-3830 Make text area fields in forms (#2405)
8. ENCD-4206 calc prop rebased (#2418)
9. ENCD-4190 no-hypen-on-experiment-values (#2399)
10. ENCD-4200 show-facebook-share-btn (#2401)
11. ENCD-4196 Reduce cloud init size (#2392)
12. ENCD-4208 Add png addition to qc mime types (#2400)
13. ENCD-4216 Add RefSeq to dbxrefs in gene schema (#2410)
14. ENCD-4173 Add Paul to test user inserts (#2404)
15. ENCD-4171 Reset default audit inherit (#2393)
75.1 (released)
-----------------
1. ENCD-4214 Update to snovault 1.0.17 (#2406)
75.0 (released)
-----------------
1. ENCD-4204 Update to snovault 1.0.16 (#2394)
2. ENCD-4193 block-on-orange-audit (#2390)
3. ENCD-4153 alter-select-distinct-values (#2389)
4. ENCD-4135 integrity-num (#2375)
5. ENCD-4188 add khine to testdata (#2391)
6. ENCD-4187 fix ENSEMBL links for mouse. (#2380)
7. ENCD-4160 Added Casey, Jason, and Zack to users (#2371)
8. ENCD-4159 adjusting GM characterization audit (#2366)
9. ENCD-4038 Adding matrix bdd tests (#2335)
10. ENCD-4182 Patch dbxref pattern in Gene. (#23
11. ENCD-4166 RIN internal action audit (#2365)
74.0 (released)
-----------------
1. ENCD-4169 Update to snovault 1.0.15
2. ENCD-4131 set-status-endpoint (#2363)
3. ENCD-4168 add-embed-cache-to-ini (#2367)
4. ENCD-4167 Explicitly set availability zone in deploy script (#2361)
5. ENCD-4163 Update to snovault 1.0.14 (#2360)
6. ENCD-3997 Create Gene object (#2307)
7. ENCD-4083 Allow aws s3 to s3 file transfer (#2358)
8. ENCD-4162 update snovault 1.0.13 (#2359)
9. ENCD-4136 Add dry run arg for deployment (#2357)
10. ENCD-4123 audit chip (#2343)
11. ENCD-4154 Remove unused search type arg (#2355)
12. ENCD-4141 Add alias namespaces (#2344)
13. ENCD-4152 Make organism scientific_name required (#2354)
14. ENCD-4107 Added experiment_class to experiment schema (#2330)
15. ENCD-4134 add RIN number property to Library (#2348)
16. ENCD-3732 replicate-sorting (#2329)
17. ENCD-4146 Restore FileDownloadButton constructor (#2352)
18. ENCD-4149 Allow bin test log arg for workbook loading (#2351)
19. ENCD-4144 Fix failing impersonation test button size (#2350)
20. ENCD-4118 set minimum value to 0 for ch coordinates in GM (#2347)
21. ENCD-4143 Add asserts to status trigger tests
73.0 (released)
-----------------
1. ENCD-4129 update-to-snovault-1.0.12 (#2336)
2. ENCD-4064 release-endpoint (#2281)
3. ENCD-4017 Fulfill ECP requests for home page additions. (#2326)
4. ENCD-4105 Add DGGR dbxref processing (#2325)
5. ENCD-4108 audit matched (#2324)
6. ENCD-4089 Deactivated-rep-num-in-annot-table (#2315)
7. ENCD-4074 toolip-overlay (#2313)
8. ENCD-4102 changed audit from WARNING to ERROR (#2327)
9. ENCD-3903 add documentation for schema page (#2332)
10. ENCD-3563 updated sc replication audit (#2322)
11. ENCD-4087 fixed-flybase-search (#2312)
12. ENCD-4051 Change schemas to set minimum int values (#2309)
72.0 (released)
-----------------
1. ENCD-4103 Fix tests broken by SNO-41 (#2317)
2. ENCD-4098 Update to snovault 1.0.11 (#2314)
3. ENCD-4072 Remove es master from deployment (#2302)
4. ENCD-4086 Analysis-Step schema (#2305)
5. ENCD-4048 rep-num-in-pub-n-exp (#2311)
6. ENCD-4093 Fix initial region indexing failure (#2308)
7. ENCD-3728 Fix build error (#2306)
8. ENCD-4020 Allowing specification of Sets as controls (#2296)
9. ENCD-4055 removed-some-styling-on-raw-data (#2277)
10. ENCD-4057 properly-format-data-on-biosample-page (#2276)
11. ENCD-4088 Remove extra code added in ENCD-3306 (#2310)
12. ENCD-4040 vis index replicate conditional (#2294)
13. ENCD-3718 return-404-when-file-not-found (#2278)
14. ENCD-4073 Revert accidental blocked dataset status expansion (#2291)
15. ENCD-4077 Fix deploy volume size type (#2304)
16. ENCD-3776 move-to-standard-status (#2295)
17. ENCD-4078 Remove unused statuses (#2293)
18. ENCD-4058 expanding-matrix-creates-unaligned-header (#2280)
19. ENCD-4085 Add weiwei as a submitter (#2298)
20. ENCD-4081 Add Yunhai as a submitter in local test. (#2288)
71.0 (released)
-----------------
01. ENCD-4046 update to snovault 1.0.10, add CHANGES (#2275)
02. ENCD-3306-fix-line-in-table (#2271)
03. ENCD-4045 gdpr auth0 (#2274)
04. ENCD-3695-upgrade-to-boto3 (#2272)
05. ENCD-3883-add-pmi-data (#2263)
06. ENCD-3727 added hypen for long words (#2270)
07. Add zoldello (Phil) as an authorized submitter for the test environments. ENCD-4049
08. ENCD-4019 adding readname_details field to the file.json (#2260)
09. ENCD-4042 Update genetic mods for functional characterization experiments (#2262)
10. ENCD-3629 Refactor and redesign status displays. (#2246)
11. ENCD-4034 SVG tooltip and minor JS clean up (#2255)
12. ENCD-3911 Added a break above document box (#2256)
13. ENCD-3364 fixed text and link button misalignment (#2257)
70.0 (released)
-----------------
01. ENCD-4037 Update snovault 1.0.9 (#2258)
02. ENCD-4029 Update to snovault 1.0.8 (#2254)
03. ENCD-3889 supersedes refepi (#2247)
04. ENCD-3871-target-standard-status (#2252)
05. ENCD-4011 Fix wrong vars in buildout candidate config file (#2241)
06. ENCD-3867 Display proper replicate_type string (#2249)
07. ENCD-4015 adding an audit for read_count and test for it (#2242)
08. ENCD-4010 fixing a typo in the samtools flagstat quality metric (#2238)
09. ENCD-3995 Update file output_type (#2239)
10. ENCD-4016 adding community to users (#2243)
11. ENCD-3957 Add biosample accession to report columns (#2250)
12. ENCD-3970 Add encore badge (#2251)
13. ENCD-4008-fix-source-title (#2253)
14. ENCD-4007-nginx-proxy-header (#2244)
15. ENCD-3981 remove histone modification (#2240)
16. ENCD-3963 Remove antibody accession column (#2233)
17. ENCD-3974 Update biosample organoid (#2234)
18. ENCD-3641 fix navigate to file download URI (#2237)
69.0 (released)
-----------------
01. REG-9 Fix vis button for region search (#2210)
02. ENCD-3986 Update to snovault 1.0.7 (#2229)
03. ENCD-3950 Require date_submitted in submitted experiments (#2224)
04. ENCD-3923 Allow es to deploy separately from encoded
05. ENCD-3620 Update deploy options for region search
06. ENCD-3621 Refactor deploy script
07. ENCD-3980 Organize ini files and vars
08. ENCD-3216 Hide antibody characterizations via user access level (#2225)
09. ENCD-3726 adding platform to library (#2223)
10. ENCD-3959 Add int and bool to displayed QC types (#2212)
11. ENCD-3973 Redo how GM characterization documents get displayed (#2219)
12. ENCD-3979 Fix zc buildout for pypi update (#2221)
13. ENCD-3961 eslint AirBnB npm package updates (#2214)
68.0 (released)
-----------------
01. ENCD-3965 Update to snovault 1.0.6 (#2209)
02. ENCD-3934 fix plate location in library (#2208)
03. ENCD-3944 Add organ slim shims & update ontology.json (#2201)
04. ENCD-3934 Update to original 3934 commit (#2207)
05. ENCD-3739 rewriting chip control read depth audit (#2188)
06. ENCD-3775-started-to-in-progress (#2202)
07. ENCD-3451 Summary page (#2200)
08. ENCD-2992 Remove unused status (#2206)
09. ENCD-3960 Fix batch download lookup column test (#2205)
10. ENCD-3935 adding new biosample type "single cell" (#2193)
11. ENCD-3898 adding an audit flagging "tagging" GM without characterization (#2187)
12. ENCD-3886 Update deploy machine instance types (#2181)
13. ENCD-3863 Eliminate repeated values in report TSV (#2136)
14. ENCD-3938 Adding new Series type "AggregateSeries" (#2190)
15. ENCD-3934 adding "barcode_details" to library schema (#2197)
16. ENCD-3189 Traverse root using external_accession key from files (#2178)
17. ENCD-3645 & ENCD-3716 Strip white spaces from values (#2194)
18. ENCD-3716 Strip white spaces from values (#2194)
19. ENCD-3773-pipeline-status (#2189)
20. ENCD-3870-publication-status-mixin (#2191)
21. ENCD-3780-remove-ready-for-review (#2192)
22. ENCD-3772-remove-virtual (#2195)
23. ENCD-1 Add treatments amount, duration to metadata.tsv
24. ENCD-2845 Quick fix for biosamples with both the sexes
25. ENCD-3868 - Adding unit tests for batch_download helpers
26. ENCD-3823 & ENCD-3864 - Filter out restricted files and refactor batch_download
27. ENCD-3864 - Filter out restricted files and refactor batch_download
67.1 (released)
---------------
1. ENCD-3916 Fix for broken metadata queries (#2179)
67.0 (released)
-----------------
01. ENCD-3915 Remove chromedriver lock from Travis (#2174)
02. ENCD-3892 Update to snovault 1.0.5 (#2173)
03. ENCD-3809 Add run_types for pacbio and oxford nanopore (#2172)
04. ENCD-3839 Remove schemas for the deleted objects (#2167)
05. ENCD-3891 Fix file test for duplicates in derived_from (#2162)
06. ENCD-3908 Update indexer doc for march 2018 update
07. ENCD-3913 Update regionsearch MAX_CLAUSES request_timeout
08. ENCD-3900 Increase demo volume size
09. ENCD-3756 Remove scorefilter in dnase visuals
10. ENCD-3907 Adopting UCSC bigNarrowPeak type
11. ENCD-3260 Refactor visualization
12. ENCD-3602 Migrate indexers to region and secondary
13. ENCD-3894 Move NIH cert audit to experiment (#2166)
14. ENCD-3840 Add link to linkFrom linkTo schema properties (#2168)
15. ENCD-3899 Fix exp audit trigger on non-encode pipelines (#2170)
16. ENCD-3604 Update boost to include GM accessions (#2171)
17. ENCD-3848 Remove immortalize from cell line (#2164)
18. ENCD-3854 Fix report description column sort error (#2150)
19. ENCD-3893 Add NIH cert to biosample facets (#2165)
20. ENCD-3828 Update redacted alignments (#2163)
21. ENCD-3841 Add collapsing sections on schema pages (#2154)
22. ENCD-3880 Add Alembic documentation (#2152)
23. ENCD-3821 Show biosample characterization doc links (#2145)
24. ENCD-3882 Update DOI preferred resolver url (#2135)
25. ENCD-3879 Pin Alembic version (#2151)
66.0 (released)
---------------
01. ENCD-3878 Update to snovault version 1.0.4 (#2148)
02. ENCD-3834 Add Alembic framework for Postgres migrations (#2142)
03. ENCD-3869 Downgrade chromedriver version 2.33 (#2143)
04. ENCD-3827 Fix ES5 version in README (#2141)
05. ENCD-3698 Add Institutional certifications to biosample (#2140)
06. ENCD-1934 Format schema displays (#2115)
07. ENCD-3865 Update to snovault version 1.0.3 (#2139)
08. ENCD-3836 Small heap single machine (#2137)
09. ENCD-3819 Add biosample preservation method (#2122)
10. ENCD-3835 Fix inconsistent platforms audit HiSeq2K 2.5K (#2133)
11. ENCD-3341 Add new output_types to file json (#2132)
12. ENCD-3853 Remove UCSC logos (#2134)
13. ENCD-3757 Adjust histone broad peak read depth audit (#2125)
14. ENCD-3831 Add exp audit to flag standards violations (#2124)
15. ENCD-3766 Add submitter comments to certain js pages (#2123)
16. ENCD-3820 Biosample: PMI property (#2120)
17. ENCD-3798 Ontology Update Jan2018 (#2119)
18. ENCD-3816 Update selenium version to 3.8.1 (#2118)
19. ENCD-3803 Allow fastq_sig to accept 3 in SRR headers (#2113)
20. ENCD-3456 Stringify array and object items in a cell (#2111)
21. ENCD-3762 Add RegulomeDB internal_tag and badge (#2110)
22. ENCD-3421 Properly link home chart to matrix (#2108)
23. ENCD-2567 New report page column selector modal (#2105)
65.3 (released)
----------------
* ENCD-3851 Add max clause es5 updates
65.2 (unreleased)
-----------------
* Update to snovault 1.0.2 (#2128) -> ENCD-3845
65.1 (unreleased)
-----------------
* ENCD-3813 Update to snovault 1.0.1 (#2116)
65.0 (unreleased)
-----------------
1. ENCD-3815 Fix tests for facet aggregation set to 200 (#2109)
2. ENCD-3795 Fix spelling in histone and idr qm jsons (#2104)
3. ENCD-3810 Set facet aggregation to 200 in search (#2107)
4. ENCD 3749 Update README for ES5 and dependency requirements (#2087)
5. ENCD-3741 Search for objects based on associated grant number (#2103)
6. ENCD-3792 Add histone_chip_quality_metric PIP-198 (#2101)
7. Update to snovault v1.0.0 -> ENCD-3788
8. ENCD-3745 Add platform to file and exp facets (#2088)
9. ENCD-3765 Set max_result_window for annotations index (#2083)
10. ENCD-2488 ES5 Update aka RM3910
11. ENCD-3546 Create 'save and add' button to add forms (#2100)
12. ENCD-3700 Remove unreplicated exp audit for genetic mod DNase (#2096)
13. ENCD-3781 Resolve WGBS lambda audit error (#2095)
14. ENCD 3759 Fix WGBS coverage audit (#2093)
15. ENCD-3743 Fix read depth audits for DNase and ChIP (#2091)
16. ENCD-3760 Remove the NTR assay audit (#2089)
17. ENCD-3724 Adjust facet term display check (#2086)
18. ENCD-3755 Remove schemas for RNAi and construct characterizations (#2085)
19. ENCD-3737 Add M14 gencode annotations to file enums (#2084)
20. ENCD-3708 Update publication states (#2077)
21. ENCD-3699 Remove mixed run type audit from DNase (#2065)
22. ENCD-3661 Update drawing file graphs and JS Tests (#2080)
23. ENCD-3764 Fix message typo in Assay audit (#2081)
24. ENCD-3473 Fix for unknown error in batch_download
25. ENCD-3579 Fix for batch download error
26. ENCD-3566 Fix JS FileInput add document (#2076)
27. ENCD-3597 Use obj picker for user impersonation (#2068)
28. ENCD-3721 Allow 'in vitro sample' to have biosample_term_name (#2067)
29. ENCD-3734 file audit escalation (#2066)
0.1 (unreleased)
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