Revision c46ff3376e06d900588e0d0ab2211b3bf65819ba authored by keenangraham on 12 November 2021, 17:36:37 UTC, committed by GitHub on 12 November 2021, 17:36:37 UTC
1 parent 209be2f
CHANGES.rst
Changes
=======
124.0 (released) snovault 1.0.62
--------------------------------
1. ENCD-6224-fix-hicqualitymetric-dependencies (#4174)
2. ENCD-6218 Add facets and facet groups to donor (#4170)
3. REVERT ENCD-6179 (#4172)
4. ENCD-6223 pin responses to 0.14.0 (#4173)
5. ENCD-6217-report-list-crash (#4169)
6. ENCD-6220-deeply-profile-missing-facets (#4171)
7. update-snovault-1.0.62 (#4165)
8. ENCD-6209-updating-FCS-assay-title (#4164)
9. SNO-217-register-search-config-pieces-from-item (#4160)
10. ENCD-6208 remove control (#4161)
11. ENCD-6179-fcc-menu (#4157)
12. ENCD-6183-hic-scatac-qc (#4149)
13. ENCD-6197-devcontainer (#4137)
14 ENCD-6207-remove-columns-from-dataset-schema (#4156)
15. ENCD-6202-add-enums-for-restriction-enzymes (#4153)
16. ENCD-6205-fix-browser-track-in-region-search (#4152)
17. ENCD-6192-cart-schema-updates (#4135)
18. ENCD-6196-examined-loci-dependency-include-readout (#4154)
19. ENCD-6206-appended-exists-facet (#4155)
20. ENCD-6178-library-property-updates-Yu-lab (#4146)
21. ENCD-6117-cell-line-matrix (#4133)
22. ENCD-6182-scrna-output-types (#4145)
23. ENCD-6187 fix legend for ccres (#4151)
24. ENCD-4287 update d3 (#4144)
25. ENCD-6201-add-purpose-treatment-UI (#4147)
26. ENCD-6145-more-facet-headers (#4129)
27. ENCD-6194-relax-unreplicated-audit-on-long-read-scRNA-seq (#4150)
28. SNO-214-upgrade-node-to-version-12-for-circleci-tests (#4136)
29. ENCD-6175-support-collection-series-and-transgenic-enhancer-experiments-in-cart (#4138)
30. SNO-210-read-columns-from-configs (#4114)
31. ENCD-6199-fixed-deep-biosample-crash (#4141)
32. ENCD-6131-update-donor-ethnicity-enum (#4143)
33. SNO-212-support-gzip-attachment (#4126)
34. ENCD-6195 Add datapoint to Transgenic Enhancer Experiment (#4139)
35. ENCD-6168-update-fc-series-search-title (#4142)
36. ENCD-6189-add-experimental-input-UI (#4140)
37. ENCD-5893-cart-reclassify-non-raw-files-without-assembly-as-processed (#4074)
38. ENCD-6157-allow-multiple-types-for-report-view-button (#4122)
39. ENCD-6138-fix-mixed-title-not-appearing (#4088)
40. ENCD-5869-add-missing-control_type-in-url (#4124)
41. ENCD-6190-html-editor-crash (#4128)
123.0 (released) snovault 1.0.60
--------------------------------
1. ENCD-6180-matrix-search (#4123)
2. ENCD-6181-move-warning-facet-to-quality-group (#4125)
3. ENCD-6142-biosample-summary-updates (#4105)
4. ENCD-6035 add body map (#4093)
5. ENCD-6160-snatac (#4120)
6. ENCD-6169 gkm-SVM-model (#4118)
7. ENCD-6148 exclude fcc datapoints (#4117)
8. ENCD-6154-collection-series (#4111)
9. ENCD-6159-updates-to-reference-data-table (#4096)
10. ENCD-6097-allow-series-and-related-datasets-in-cart (#4119)
11. ENCD-6173-circle-node-install-fix (#4121)
12. ENCD-6143-upgrade-encyclopedia-version-enums (#4102)
13. ENCD-6166-Filtering out unnecessary Region Search fields (#4113)
14. ENCD-6141-update-fc-title-search (#4115)
15. ENCD-6134-add-elements-selection-method-enums (#4109)
16. ENCD-6093-facets-appear-in-groups-on-certain-search-result-pages (#4104)
17. ENCD-6144 tracks batch (#4106)
18. ENCD-6150 Removing both lifestage and run_type from facets (#4110)
19. ENCD-6162-fix-single-cell-unit-schema-link (#4103)
20. ENCD-6158-treatment-details-add-purpose-enum (#4108)
21. ENCD-5758-cart-rep-facet (#4079)
22. ENCD-6149-add-hic-file-output-types (#4097)
122.0 (released) snovault 1.0.60
--------------------------------
1. ENCD-6161-fix genome browser pinned files in sessionStorage (#4098)
2. ENCD-6005-region-search-display-bug-fixes (#4095)
3. ENCD-6113 FCC search updates (#4091)
4. ENCD-6129 Removing facets (#4092)
5. ENCD-6135-cart-view-update (#4089)
6. ENCD-6005-region-search-dserv-genome-browser (#4052)
7. ENCD-6136-gkm-svm-annotation-type-file-output-type (#4090)
8. ENCD-5219-add-deleted-and-inserted-gene-details (#4087)
9. ENCD-6121-add-screen-tiling-reference (#4081)
10. ENCD-6109-origin-biosample-property (#4076)
11. ENCD-6077-perturbations (#4072)
12. ENCD-6130 file detail title not showing (#4086)
13. ENCD-6067-update-ontology-slimming-terms (#4080)
14. ENCD-5687-add-replication-count-to-experiments-and-fcc-experiments (#4078)
15. ENCD-6096-remove-region-indexer (#4083)
16. ENCD-6108-controlled-cell-growth-tag (#4070)
17. ENCD-6099-audit-index-reads-no-read-structure (#4071)
18. ENCD-6102-change-regex-lot-id-product-id (#4069)
19. ENCD-6125-specify-location-constraint-in-moto-tests (#4077)
20. ENCD-5908-add-formatted-biorep-property-to-experiments-and-fcc-experiments (#4065)
21. ENCD-6105-disable-viz-btn-mouse-dev-matrix (#4066)
22. ENCD-6103-fix-rush-matrix-urls (#4067)
23. ENCD-6095-add-mEGFP-tag (#4073)
121.0 (released) snovault 1.0.60
--------------------------------
1. update-snovault-1.0.59 (#4026)
2. SNO-209-move-search-code-to-independent-package (#4059)
3. ENCD-6100 removing trailing slash for rnaget link (#4063)
4. ENCD-6071 fragments file addition (#4061)
5. ENCD-6090-singlecellunit-cart (#4056)
6. ENCD-6094-update-azure-link (#4062)
7. ENCD-6091-add-Hongkai-Ji-submission-properties (#4060)
8. ENCD-6092 Add embedding of originated_from.biosample_ontology to Experiment (#4058)
9. ENCD-6076-gender-symbols (#4057)
10. ENCD-6049 pooled clone sequencing dependency (#4055)
11. ENCD-6073-add-sparse-matrix-output-type-genome-compartment-id-analysis-step-type (#4054)
12. ENCD-6055-FCC-series-search-update (#4039)
13. ENCD-5981-change-filegallery-defaults (#4047)
14. ENCD-5921-sc-paging (#4051)
15. ENCD-6050-loci-fcc-search-list-view (#4049)
16. SNO-206-use-redis-cache-for-rnget-view (#4045)
17. ENCD-6084-mouse-matrix-crash (#4053)
18. ENCD-6069-add-redacted-transcriptome-alignments (#4042)
19. ENCD-4448-audit-annotations-without-original-files (#4048)
20. ENCD-5984-fix-mixed-analysis-title (#4040)
21. ENCD-5927-audit-raw-data-lacking-step-run (#4044)
22. ENCD-6041-remove-ie11-from-babel (#4028)
23. ENCD-6080-update-robots-txt (#4043)
24. ENCD-6066-show-series-experiment-tables-controls (#4031)
25. ENCD-6048-audit-CRISPR-not-in-series (#4046)
26. ENCD-6057-reconcile-biosample-summary (#4041)
27. ENCD-5889-brain-disease-matrix (#3996)
28. SNO-205-allow-customization-of-default-sort (#4038)
29. ENCD-6058-single-cell-nav (#4033)
30. ENCD-6059-update-reagent-regex-thermo (#4034)
31. ENCD-6064-make-elements-mapping-an-array (#4032)
32. ENCD-6063-add-fce-table-to-reference-page (#4037)
33. ENCD-5837-project-bio-term-name-bug (#4036)
34. ENCD-6053-file-view-update (#4029)
35. ENCD-5723-term-name-erasure (#4035)
120.0 (released) snovault 1.0.59
--------------------------------
1. ENCD-6065 fix post diff table crash (#4027)
2. update-snovault-1.0.59 (#4026)
3. ENCD-6036 reset chr range in cart (#4025)
4. ENCD-6039-software-cleanup (#4018)
5. ENCD-6052-add-rnaget-search-and-report-views (#4022)
6. ENCD-6038-biosample-summary-series-header (#4017)
7. ENCD-6056-cart-upgrade-error (#4024)
8. ENCD-6024-make-search-results-targets-into-links (#4015)
9. ENCD-5876-series-updates (#4023)
10. ENCD-5851 single cell landing page (#4021)
11. ENCD-6008-convert-nuc-acid-start-quant-to-number (#4014)
12. ENCD-6047-ENTEx-annotation (#4019)
13. ENCD-5968-add-MOI-guide-type-to-GM (#3987)
14. ENCD-6045-add-david-hafler-to-alias-prefix (#4013)
15. ENCD-6046-add-RUSH-AD-internal_tags-donor (#4016)
16. ENCD-6042-search-dl-options (#4012)
17. ENCD-5724 differentiation series (#4009)
18. ENCD-5982-file-cart-views (#4011)
19. ENCD-6043-slim-perturb-snATAC-seq (#4010)
20. ENCD-6040-document-embedding-in-annotations (#4007)
119.0 (released)
--------------------------------
1. ENCD-5974 biosample summary summary (#4004)
2. ENCD-5990-embed-docs (#3986)
3. ENCD-6037-annotation-target (#4006)
4. ENCD-5618 encyclopedia page (#3998)
5. ENCD-5955-analysis-titles (#4002)
6. ENCD-6031-add-DHS-to-annotation-subtype (#3999)
7. ENCD-6028-visualizable-filter (#3997)
8. ENCD-5926-adjust-biosample-characterizations-audit-to-check-parents (#3958)
9. ENCD-5995-update-rnaget-ui (#3980)
10. ENCD-6032-adding-link-to-official-rnaget-api-docs (#3978)
11. ENCD-6022-add-filter-type-and-filter-value-properties (#3990)
12. ENCD-5971-split-experiments-in-disease-series (#3989)
13. ENCD-6013-bump-queue-worker get size (#3968)
14. ENCD-5994-long-read-scrna-assay-slim (#3976)
15. ENCD-5993 Exclude long read single-cell RNA-seq from audit (#3973)
16. ENCD-5969-reference-elements-sel-method (#3985)
17. ENCD-6021-allow-txt-for-sequence-barcodes-add-polyA-sites-output (#3991)
18. ENCD-6023-expression-readout-fcc-series-table (#3993)
19. ENCD-6025-cart-valis-targets (#3992)
20. ENCD-6019-increase-sts-token-expiration (#3977)
21. ENCD-6006-add-facs-expression-measurement-method (#3982)
22. ENCD-5720-target-cart-facet (#3971)
23. ENCD-5970-fcc-series-elements-references (#3974)
24. ENCD-5996-add-enum-analysis-step-type (#3979)
25. ENCD-5986-set-status-transgenic-enhancer-expt (#3981)
26. ENCD-5967-use-biosample-summary-series-tables (#3970)
27. ENCD-5965-enable-association-graph-in-series (#3949)
28. ENCD-5918-cart-analyses (#3966)
29. ENCD-6020 disable email sending (#3975)
118.0 (released) snovault 1.0.58
--------------------------------
1. ENCD-6012-regulome-validation-error (#3969)
2. ENCD-6011-ontology-efo-bug-fix (#3967)
3. ENCD-6002-publicationdata-dl (#3965)
4. ENCD-5992-cart-analysis-dl (#3964)
5. update-snovault-1.0.58 (#3963)
6. ENCD-5886-add-ccre-default-tracks (#3960)
7. ENCD-5989-fix-analysis-embed (#3961)
8. ENCD-5949-add-file-output-types-unidirectional-bidirectional-peaks-and-entex (#3957)
9. SNO-170-avoid-rendering-from-database-3 (#3954)
10. ENCD-5776-new-batch-download-ui (#3941)
11. ENCD-5888-accept-regions-in-examined-loci-on-reference (#3959)
12. ENCD-5929-analysis-audits (#3951)
13. ENCD-5975-adjust-file-schema-ultima-fastqs (#3953)
14. ENCD-5972 entex references (#3952)
15. ENCD-5964-add-assays-update-ontology (#3942)
16. ENCD-5978-hic-qc (#3945)
17. ENCD-5980-fix-download-button (#3950)
18. ENCD-5976-nagios-configuration (#3947)
19. ENCD-5952-add-new-internal-tags (#3935)
20. ENCD-5962-avoid-results-from-stale-request (#3943)
21. ENCD-5977 pairs file addition (#3944)
22. ENCD-5939-bdd-tests (#3946)
23. ENCD-5943 Update relevant_life_stage enums for Annotation (#3936)
24. ENCD-5948-fcc-ucsc-visualization (#3938)
25. ENCD-5617-new-software-page (#3922)
26. SNO-202-python3.8.5-upgrade (#3937)
27. ENCD-5933-add-promoter-details-to-gm-reagents (#3931)
28. ENCD-5953-update-fcc-table (#3934)
29. ENCD-5690-add-azure-uri-to-file-metadata (#3939)
30. ENCD-4549-wildtype-biosample-title-update (#3927)
31. ENCD-5966-fix-series-table-target-bug (#3933)
32. ENCD-5940-cart-dataset-target (#3930)
33. ENCD-5932 fix regulome tags (#3928)
34. ENCD-5808 facet for biochemical inputs (#3869)
35. ENCD-5942-display-disease-name-on-series (#3926)
36. ENCD-5959-fix-series-page-crash (#3932)
117.0 (released) snovault 1.0.57
--------------------------------
1. ENCD-5945-index-annotations-logging (#3920)
2. ENCD-5954-fix-matrix-chip-seq-urls (#3923)
3. ENCD-5951-annotation-labels (#3924)
4. ENCD-5957-wale-broken (#3925)
5. ENCD-5947-series-search-ban-robots (#3921)
6. ENCD-5903-audit-mixed-expression-measurement-methods (#3914)
7. ENCD-5757-multisearch-within-collections (#3917)
8. ENCD-5941-update-robots-txt (#3919)
9. ENCD-5938-control-crispr-screens-incorrectly-calculated-as-proliferation (#3918)
10. ENCD-5930-add-enum-to-software-type (#3909)
11. ENCD-5920-change-machine-size (#3915)
12. ENCD-5935-fix-file-audit-error (#3916)
13. ENCD-5912-FCC-series-search-update (#3908)
14. ENCD-5614-cart-dataset-filters (#3911)
15. ENCD-5923-fix-chromatin-genome-browser-bug (#3910)
16. ENCD-5917-add-guide-locations-output-type (#3913)
17. ENCD-5689-updates-to-chip-matrix (#3906)
18. ENCD-5914-rna-get-beta (#3901)
19. ENCD-5909-single-cell-series-UI (#3897)
20. ENCD-5924-deafult analysis (#3900)
21. ENCD-5861-add-annotation-types-subtypes-to-glossary (#3912)
22. ENCD-5911-update-crispr-screen-methods-in-fcc-faceting (#3907)
23. ENCD-4945-status-color-key (#3903)
24. ENCD-5919-elements-ref-embedding-to-fce (#3905)
25. ENCD-5898-separate-ami-demo-prod (#3879)
26. ENCD-5814-add-donor-to-metadata-tsv (#3899)
27. ENCD-5854-series-dl (#3883)
28. ENCD-5915-update-software-schema (#3904)
29. ENCD-5871-exclude-deleted-inconsistent-analysis (#3887)
30. ENCD-5897-add-disease-term-in-biosample-page (#3891)
31. ENCD-5916-encyclopedia-v6 (#3898)
32. ENCD-5873-remove-single-cell-classification (#3890)
33. ENCD-5805-collections-tag-link (#3885)
116.0 (released) snovault 1.0.57
--------------------------------
1. update snovault 1.0.57 (#3882)
2. SNO-201-add-search-config-registry (#3855)
3. ENCD-5858-add-single-cell-units-to-series (#3858)
4. ENCD-5561-organize-pyramid-config (#3781)
5. ENCD-5896-add-MultiomicsSeries-object (#3873)
6. ENCD-5147-add-expression-measurement-method-to-examined-loci-FCE (#3876)
7. VALIS-36 remove expander (#3805)
8. ENCD-5863-speed-up-chip-matrix (#3868)
9. revert SNO-202-python3.8.5-upgrade (#3881)
11. VALIS-40-dbSNP-track (#3866)
12. ENCD-5770 add legend to browser (#3829)
13. ENCD-5892-add-ManateeDonor-object (#3872)
14. ENCD-5874-disease-series (#3875)
15. ENCD-5895-adjust-strand-specificity-display (#3871)
16. ENCD-5891-exclude-rrbs-from-audits (#3860)
17. ENCD-5902 bam mapped run type and read length (#3877)
18. ENCD-5880 analysis title (#3874)
19. ENCD-5900-fix-smallrna-cage-audit-detail (#3870)
20. ENCD-5728-add-gene-target-page (#3863)
21. ENCD-5867-add-R2C2-subreads-output-type (#3864)
22. ENCD-5830-autocomplete-rnaget-ui (#3839)
23. NCD-5840-analysis-objects-to-analyses-move-to-dataset (#3834)
24. ENCD-5820-select-better-analysis-by-default (#3809)
25. ENCD-5894-restrict-strand-specificity-requirement-to-RNA-libraries (#3867)
26. ENCD-5857 Add audits for analyses with multiple rfas or datasets (#3856)
27. ENCD-5860 Add repeat elements annotation file output type (#3852)
28. ENCD-5887-crispr-file-format-types (#3862)
29. ENCD-5804-add-ctl_type-to-FCC-n-Exp-search-pg (#3831)
30. ENCD-5865-add-ana-conesa-to-alias-regex (#3861)
31. ENCD-5834-add-default-analysis-calculation (#3842)
32. SNO-202-python3.8.5-upgrade (#3865)
33. ENCD-5885-update-snovault-link-readme (#3851)
34. ENCD-5685-stacked-buttons (#3847)
35. ENCD-5853-ihec-json-updates (#3849)
36. ENCD-5872-usable-fragments (#3846)
37. ENCD-5866-python-36-circleci (#3845)
38. ENCD-5884 Add spaces in audit details (#3850)
115.0 (released) snovault 1.0.56
--------------------------------
1. ENCD-5870-fix-bdd-submitter-test
2. ENCD-5864-add-analysis-objects-to-fce (#3840)
3. ENCD-5827-migrate-audits-to-analysis (#3813)
4. SNO-200-remove-nonsubstring-filter-from-mapping (#3837)
5. ENCD-5856-TSTAN-not-showing (#3835)
6. ENCD-5828-single-cell-experiments (#3828)
7. SNO-199-allow-customization-of-search-fields (#3841)
8. ENCD-5825-series-files (#3836)
9. ENCD-5806-cCRE-annotation-subtypes-and-other-file-output-types (#3838)
10. ENCD-5154-print-base-branch-deploy (#3832)
11. ENCD-5831-add-metadata-columns-and-small-improvements-to-rnaget-ui (#3825)
12. ENCD-5850-fix-analysis-title-and-permission (#3824)
13. ENCD-5750-update-glossary-with-file-output-types (#3833)
14. ENCD-5841-remove-redundant-originated-from (#3823)
15. ENCD-5829-allow-batch-download-from-more-dataset-pages (#3827)
16. SNO-197-add-range-queries-and-min-max-aggs (#3812)
17. ENCD-5847-add-azure-link (#3818)
18. SNO-198-allow-configuration-of-reserved-search-params (#3816)
19. SNO-138-fix-pytest-warnings (#3826)
20. ENCD-5807 compare to literal with == instead of is in experiment_series audit (#3778)
21. ENCD-5842 do not clone the private config repo in runcmd_all (#3821)
22. ENCD-5844-add-unstranded-enum-to-library-objects (#3822)
23. ENCD-5778-add-pulse-chase-series-and-pulse-chase-properties (#3817)
24. ENCD-5843-add-disease-facet (#3815)
25. ENCD-5833-analysis-audits (#3810)
26. ENCD-5836 Remove duplicate definition (#3806)
27. ENCD-5818 Remove ssh key copying from app-final.sh (#3800)
114.0 (released) snovault 1.0.55
--------------------------------
1. ENCD-5832 Consider assembly when choosing pseudo-default files (#3804)
2. ENCD-5824-bug-fix-dnase-analysis-audits (#3801)
3. ENCD-5819-related-files (#3802)
4. update snovault 1.0.55 (#3798)
5. ENCD-5789 Cart pseudo-default files (#3786)
6. ENCD-5786-move-dnase-audits-to-analysis (#3783)
7. ENCD-5787-add-assays-GROcap-GROseq-long-read-scRNAseq-remove-snRNAseq-genotyping-HTS (#3791)
8. ENCD-5745-embed-assay-title-and-annotation-type-in-file (#3794)
9. ENCD-5718-add-rna-get-ui (#3776)
10. ENCD-5817-remove-dup-boost-dataset-award (#3797)
11. ENCD-5803-update-wgbs-vis-def (#3785)
12. ENCD-4612-add-Valis-tracks-GRCm39-M26-V33-dm3-genes-ce10-genes (#3790)
13. ENCD-5773-exp-series-tables-dnase-rna (#3789)
14. ENCD-5790-add-split-seq-library-file-terms (#3782)
15. ENCD-5167-fix-gene-search (#3795)
16. ENCD-5746-deploy-valis-03-08-21 (#3788)
17. ENCD-5729-walkme-in-menu (#3787)
18. SNO-192-update-pip-install (#3750)
19. ENCD-5775-update-biosample-summary (#3773)
20. ENCD-4931-revert-ENCD-4251 (#3784)
21. ENCD-5749-make-bigbed9-collapsible (#3741)
22. ENCD-5784-modify-pearson-audit-encode3-wgbs (#3769)
23. ENCD-5771-add-v33-m39 (#3772)
24. ENCD-5794 Add calculated property read_depth for STAR quality metric (#3770)
25. ENCD-5799-bdd-cart (#3779)
26. ENCD-5774-update-crispr-assay-calc (#3762)
27. ENCD-5792-remove-java-from-cloud-config (#3774)
28. ENCD-5753-adjust-library-linkers-add-extraction-enum (#3771)
29. ENCD-5751-improve-transgenic-enhancer-expt-facets (#3754)
30. ENCD-5732-mapped-run-type (#3748)
31. ENCD-5788-block-new-WGBS-bigBeds (#3764)
32. ENCD-5766 Add audit for differentiation series time units (#3761)
33. ENCD-5744 Display DOI of all datasets (#3760)
34. ENCD-5742-fix-valis-track-sticking (#3755)
35. ENCD-5765-add-enum-gm-introduced-tags (#3758)
36. ENCD-5764-add-pip-version-to-readme (#3747)
37. ENCD-5783-deprecrated-files-crashing-file-details (#3763)
38. ENCD-5791-add-analysis-in-annotations (#3768)
39. ENCD-5740 fix mouse colors (#3766)
40. ENCD-5793 Fix cart downloads for selected analysis and default files (#3767)
113.0 (released) snovault 1.0.54
--------------------------------
1. ENCD-5772-modify-wgbs-audit (#3751)
2. ENCD-5782-browser-label (#3757)
3. ENCD-5780-cart-analysis-crash (#3756)
4. ENCD-5767-fix-file-details-facets-viz-files (#3749)
5. Update snovault 1.0.54 (#3746)
6. ENCD-5726-file-gallery-analysis-display-update (#3723)
7. SNO-27-pip-installable (#3707)
8. SNO-191-pyramid-env-vars (#3738)
9. ENCD-4302-fix-dbxref-jest-errors (#3711)
10. ENCD-5711-add-regulome-output-type-to-analysis-step (#3718)
11. SNO-117-top-hits-search (#3710)
12. ENCD-5699-filter-report-by-analyses (#3744)
13. ENCD-5743 add glossary link (#3745)
14. ENCD-5717-convert-cCRE-annotation-biochemical-inputs-property (#3740)
15. ENCD-5736-pin-wale (#3731)
16. ENCD-5701-cart-analysis-selection (#3743)
17. ENCD-5739-fix-elasticsearch-install-circleci (#3732)
18. ENCD-4573-documentation-links-for-facets (#3735)
19. ENCD-5738-making-analysis-step-run-submittable (#3737)
20. ENCD-5693 clickable mouse diagram (#3733)
21. ENCD-5706-exempt-mixed-biosample-from-undetermined-replication-audit (#3742)
22. ENCD-5712-chia-pet-audits (#3734)
23. ENCD-5716-differentiation-series (#3720)
24. ENCD-5735-add-guide-quantifications-output-type (#3730)
25. ENCD-5705-add-audit-flag-experiments-with-inconsistent-analysis-status (#3736)
26. ENCD-5714-add-defect-mode-property-dnase (#3722)
27. ENCD-5675 Display all children of a biosample including grandchildren (#3709)
28. ENCD-5676-add-doi-to-dataset (#3725)
29. ENCD-2753-slim-embed-analysis-in-file (#3728)
30. ENCD-5731-add-accession-to-analysis-boost (#3726)
31. ENCD-5707-relax-unreplicated-audit-on-PCS (#3729)
32. ENCD-5725-analysis-title (#3727)
33. ENCD-5708-release-documents-with-released-analysis-objects (#3724)
34. ENCD-5612-paste-deploy-scripts-static (#3714)
35. ENCD-5475-fix-modal-font (#3713)
36. ENCD-5715-do-not-mess-with-cluster-name (#3712)
37. ENCD-5348 WGBS audit (#3715)
38. ENCD-5652-AMI-based-deployment (#3664)
112.0 (released) snovault 1.0.53
--------------------------------
1. ENCD-5719 fix breadcrumbs and treatments (#3716)
2. ENCD-5713-snovault update to 1.0.53 (#3708)
3. ENCD-5247-experiment- series-table-update (#3704)
4. ENCD-4179-batchdownload-link-on-dataset-pages (#3666)
5. ENCD-5673-add-scss-linter (#3684)
6. ENCD-4018-update-regulome-related-schema (#3706)
7. ENCD-5686-move-stimulation-to-purpose (#3695)
8. ENCD-5337 Fix downloaded graphs (#3699)
9. ENCD-5709-form-selects (#3705)
10. SNO-158-create-minimally-indexed-deploy (#3399)
11. ENCD-5606 update series searches (#3685)
12. ENCD-5674-allow-submission-of-library-with-mixed-biosamples (#3698)
13. ENCD-5700-add-index-reads-to-input-file-types-analysis-step (#3703)
14. ENCD-5691-add -element-enrichments-file-format-type (#3700)
15. ENCD-5678-update-frontend-documentation (#3689)
16. ENCD-5592-chia-pet-quality-metrics (#3696)
17. ENCD-5660-remove-antibody-NTR-audit-expt (#3687)
18. ENCD-5683-exp-series-hotfix (#3691)
19. ENCD-5694-fix-experiment-report-columns-for-cart-test (#3702)
20. ENCD-5684-fix-download-from-cart-report (#3692)
21. ENCD-5649 add series to nav (#3688)
22. ENCD-5661-upgrade-js-pkg (#3677)
23. ENCD-5593-move-install-to-setup (#3657)
24. ENCD-5655-page-editor-fix (#3690)
25. ENCD-5672-update-schema-columns-amount (#3682)
26. ENCD-5680 Pin setuptools version in circle-ci (#3686)
111.0 (released) snovault 1.0.52
--------------------------------
1. ENCD-5665-tie-eslint-to-circleci (#3671)
2. ENCD-5670-manual-slim-transcription-assays (#3681)
3. ENCD-5671-fix-stacked-buttons (#3679)
4. SNO-185-log-connection-error (#3659)
5. ENCD-5615-dataset-search (#3676)
6. ENCD-5647-add-capped-mRNA-to-nucleic-acid-term-name (#3655)
7. ENCD-5666-add-nanopore-signal-to-file-output-types (#3675)
8. ENCD-5667-update-ebs-volume-type (#3674)
9. ENCD-5663-login-dropdown-misaligned (#3673)
10. ENCD-5644-footprints-audit (#3672)
11. ENCD-5657-exclusion-list (#3660)
13. ENCD-5664-juicebox-availability-fix (#3670)
14. ENCD-5653-signin-location-and-text-update (#3651)
15. ENCD-5623 add section breaks to glossary (#3668)
16. ENCD-5650-jan-2021-ontology-update (#3665)
17. ENCD-5518-change-navbar-color (#3661)
18. ENCD-5640-new-internal-tag-LRGASP (#3662)
19. ENCD-5543-add-series-page (#3647)
20. ENCD-5662-pseudoreplicated-peaks (#3663)
21. ENCD-5659-display-library-construction-method (#3667)
22. ENCD-5629-add-file-output-type-entries-to-glossary (#3627)
23. ENCD-5639-library-property-construction-method (#3654)
24. SNO-183-allow-specification-of-cart-in-search (#3650)
25. ENCD-5654-adjust-nic-audit-for-mapping-award (#3656)
26. ENCD-5607-warning-about-cart-title-private-info (#3638)
27. ENCD-5634-logged-out-carts (#3652)
28. ENCD-5586-make-donor-ethnicity-list-add-enums (#3645)
29. ENCD-5648-email-user-name-as-last-name-in-auth (#3648)
30. ENCD-4551-disable-visit-sharable-cart-during-cart-ops (#3646)
31. ENCD-5583-reorder-pipeline-on-experiment (#3642)
32. ENCD-5642-circleci-test-results (#3643)
110.0 (released) snovault 1.0.51
--------------------------------
1. ENCD-5645-pin-pip-version (#3644)
2. ENCD-5636-missing-processed-data-audit (#3639)
3. ENCD-5638-add-LRGASP-labs-to-alias-regex (#3640)
4. VALIS-26-enable-plotting-of-ENCD-bigbed-types (#3583)
5. ENCD-5631 Add audit for treatment series for mixed units (#3631)
6. ENCD-5595-avoid-inheriting-references-audits (#3637)
7. ENCD-5596-Valis-deploy-sprint-11-09-2020 (#3635)
8. ENCD-5356-add-examined-loci-on-FCC-experiments (#3624)
9. ENCD-5632 preserve coordinate on tab out (#3630)
10. ENCD-5573-unify-file-output-types (#3629)
11. ENCD-4525-cart-improvements (#3632)
12. ENCD-5600-add-Capture-Hi-C-and-snRNA-seq (#3626)
13. ENCD-5444 Rewrite the report page (#3616)
14. ENCD-5570-audit-outdated-analysis-update (#3633)
15. ENCD-5625-series-schema-pages-updates (#3625)
16. ENCD-5599-adjust-madqc-auditing-for-technical-replicates (#3617)
17. ENCD-5539 analysis set status (#3621)
18. ENCD-4660-hide-leave-modal-on-download (#3613)
19. ENCD-5619-fix-terser-circleci (#3622)
20. ENCD-5616-update-ckeditor (#3618)
21. ENCD-5566 fix cropped tooltips (#3588)
22. ENCD-5608-embed-Gene-in-examined-loci (#3614)
109.0 (released) snovault 1.0.51
--------------------------------
1. update-snovault-1.0.51 (#3609)
2. ENCD-5562 add screen links (#3577)
3. SNO-174-add-local-storage-redis (#3599)
4. ENCD-5274-QC-report (#3605)
5. ENCD-5559 FCC processed data facet (#3584)
6. SNO-176-invalidate-object-when-unlinked (#3607)
7. ENCD-5590-add-starch-file-format (#3602)
8. ENCD-5579-dataset-search (#3597)
9. ENCD-5494-update-gene-annotations (#3514)
10. ENCD-5457-lower-audit-severity-RNA-frag-size-for-Bru (#3604)
11. ENCD-5584-file-output-types-gene-stabilities-preprocessed-alignments (#3600)
12. SNO-177-add-view-with-specified-fields (#3592)
13. ENCD-5589-allow-Genbank-reagents-in-GeneticModification-objects (#3606)
14. SNO-178-dont-print-to-logs-during-ES-test (#3608)
15. ENCD-5345-pipeline-prop-in-reference-fileset (#3593)
16. ENCD-5546-use-terms-remove-slims-ontology (#3595)
17. ENCD-5585-fix-views-with-no-at-type (#3594)
18. ENCD-5576-matrix-arrows (#3585)
19. ENCD-5567-analysis-supersedes (#3587)
20. ENCD-5554-add-audit-mixed-strand-specific-libraries (#3590)
21. ENCD-5571-display-location-Gene (#3596)
22. ENCD-5569-biosample-char-doc-details (#3589)
23. ENCD-4700-hide-checkbx-in-proceeded-data (#3586)
108.0 (released) snovault 1.0.50
--------------------------------
1. ENCD-5534 Allow annotations and FCCs in carts (#3574)
2. ENCD-5574-update-snovault-version-1.0.50 (#3581)
3. ENCD-5572-Add-jesse-engreitz-to-aliases-name-space (#3579)
4. ENCD-5513-gm-doc-in-exp-page (#3568)
5. ENCD-5374 tooltip improvements (#3546)
6. ENCD-5531 adding h5ad file format (#3566)
7. SNO-168-stream-heterogeneous-uuids (#3548)
8. ENCD-5568-valis-deployment-09-28-2020 (#3576)
9. ENCD-5545 adding Gene Silencing Series (#3567)
10. ENCD-5347-show-strand-specificity (#3550)
11. ENCD-5515-ucsc-visualization-fcc-files (#3563)
12. ENCD-5555-Split-out-apache-indexer-config (#3561)
13. ENCD-5541-linkers-library-property (#3551)
14. ENCD-5551 Replace all instances of smoothed (#3565)
15. ENCD-5529-add-SOP-for-adding-new-assay (#3560)
16. ENCD-5550-fetch-origin-on-deploy (#3564)
17. ENCD-5492-remove-cloud-config-dir
18. ENCD-5491-remove-internal-deploy-docs
19. ENCD-5497 Add missing reqs for python osx
20. ENCD-5537 save browser position on sort (#3555)
21. ENCD-5547-add-FDR-cut-rate-and-footprints-UCSC-tracks (#3559)
22. ENCD-5487-tissue-organoid-expt-biosample-summary (#3538)
23. ENCD-5532-polyA-plus-RNA-seq-bug (#3557)
24. ENCD-5558-remove-redundant-analysis-file-audit (#3558)
25. ENCD-5526-gm-geneid (#3556)
26. ENCD-5542 Display average fragment size (#3547)
27. ENCD-5501 update gemBS alignment QC (#3549)
28. ENCD-5548 Remove duplicate line in DNase alignment quality metric changelog (#3544)
29. ENCD-4780-raw-seq-data-not-showing (#3541)
30. ENCD-5575-fce-bdd-test (#3582)
107.0 (released) snovault 1.0.49
--------------------------------------------------------------------
1. ENCD-5538 fix mouse dev queries (#3539)
2. ENCD-4275-encore-matrix (#3543) (note: not ENCD-3078)
3. ENCD-5544-chip-matrix-remove-x-result-and-add-mint (#3542)
4. ENCD-5549-exclude-mixed-assembly-or-annotation-for-file-graph (#3545)
5. ENCD-5354-update-schema-replace-analyses-with-analysis-objects (#3536)
6. ENCD-5527-add-cut-and-tag-assay (#3524)
7. ENCD-5504 fourier transform min value (#3512)
8. ENCD-5488-add-valis-1-3-x-update (#3537)
9. ENCD-5442-improve-factorbook-integration (#3522)
10. ENCD-5536-empty-average-fragment-size-variable-compared-to-int (#3535)
11. ENCD-5530 Badges for all matrix pages (#3530)
12. ENCD-5524 use new life stage age property for mouse dev matrix (#3533)
13. ENCD-5514-fix-miRNA-experiment-audits-on-miRNA-quant-files (#3534)
14. ENCD-5499-new-output-types-for-Bru-WGBS-sc (#3532)
15. ENCD-5535-pipeline-arrows (#3531)
16. ENCD-5502-modENCODE-to-chip-matrix (#3511)
17. ENCD-5522-add-cutadapt-to-trimmingqm (#3525)
18. ENCD-5519-change-calculation-contributing-files (#3517)
19. ENCD-5498-allow-average-fragment-size-remove-small-RNA-title-calc (#3518)
20. ENCD-5468-IDR-thresholded-peaks-ATAC-audit (#3499)
21. ENCD-5377-generate-glossary-page-from-glossary-json (#3526)
22. ENCD-5523-life-stage-age-calc-property (#3521)
23. ENCD-5509 wgbs analysis step types update (#3515)
24. ENCD-5493-adjust-GM-schema-CRISPR (#3520)
25. ENCD-5507 RSC NSC values and audit (#3519)
26. ENCD-5344-fix-phone-issue-on-lab-update (#3508)
27. ENCD-5528-use-analysis-objects-to-draw-file-graph (#3523)
28. ENCD-5500-bdd-fixes (#3510)
106.0 (released) snovault 1.0.49
--------------------------------------------------------------------
1. ENCD-5510-set-file-permissions-nagios (#3513)
2. ENCD-5512 Set type for cluster size in deploy (#3513)
3. update-snovault 1.0.49 (#3509)
4. ENCD-5462-qc-grouping (#3503)
5. SNO-166-update-query-string (#3475)
6. ENCD-5414 Update FCC menus (#3504)
7. ENCD-5469-switch-batch-download-mechanism (#3500)
8. ENCD-5495-cart-test (#3505)
9. ENCD-5464-sprite-ip (#3490)
10. ENCD-5437 Highlight file graph arrows (#3492)
11. ENCD-5451-add-nagios-monitor-deploy (#3498)
12. ENCD-5480-replace-stable-peaks-with-pseudo-replicated-peaks (#3485)
13. ENCD-5407-trans-enhancerpage (#3477)
14. ENCD-5473-update-biosample-characterization-audit (#3486)
15. ENCD-5334-add-analysis-step-audit (#3494)
16. ENCD-5467 Update Genetic Modification UI for new property (#3481)
17. ENCD-5463-make-target-import_items (#3480)
18. ENCD-5466-make-disease-term-id-name-list (#3482)
19. ENCD-5489-use-ramdisk-on-circleci (#3495)
20. ENCD-5459-transgenic-enhancer-expt-schema-changes (#3488)
21. ENCD-5481 Fix wrong audit detail (#3484)
22. ENCD-5471-lower-default-chunksize (#3476)
23. ENCD-5476-fix-indexing-tests (#3489)
24. ENCD-5472-as-file-form-submission (#3483)
105.0 (released) snovault 1.0.48
--------------------------------------------------------------------
1. update-snovault-1.0.48 (#3474)
2. SNO-163-install-graphviz (#3460)
3. ENCD-5439-optimize-metadata-endpoint (#3462)
4. ENCD-5372-gm-delivery (#3465)
5. ENCD-5453-fix-missing-read-depth-audit (#3470)
6. ENCD-5447 dnase reference updates (#3473)
7. ENCD-5458-use-analysis-objects-for-file-graph (#3468)
8. ENCD-5431-add-bigInteract-to-file (#3466)
9. ENCD-5350-encode4-atac-qc-audits (#3469)
10. ENCD-5440-update-analysis-step-run-set-status (#3467)
11. ENCD-4957-view-control (#3463)
12. ENCD-5456-table-shift (#3464)
13. ENCD-5443-add-ng-to-biosample-starting-amount-units (#3459)
14. ENCD-5424-remove-assembly-for-gtf-files (#3461)
15. ENCD-5311-dnase-specific-alignment-quality-metric (#3396)
16. ENCD-5410 pseudo replicated peaks (#3457)
17. ENCD-5287-archived-file (#3455)
18. ENCD-5316-add-workflow-ID (#3458)
19. ENCD-5436-audit-idr-enc3-enc4 (#3454)
20. ENCD-5447 dnase reference file updates (#3451)
21. ENCD-5425-fix-tooltip-in-edge-and-ie (#3456)
22. ENCD-5445-fix-typos-experiment-audits (#3453)
23. ENCD-5423-modify-GM-reagents-regex (#3452)
24. ENCD-5416-misc-font-updates (#3450)
25. ENCD-5432-walkme-test (#3446)
26. ENCD-5062-add-image-icon-on-report-page (#3449)
27. ENCD-5433-refactor-not-bdd-not-indexing-tests (#3445)
28. ENCD-5418-adjust-fonts (#3444)
104.0 (released) snovault 1.0.47
--------------------------------------------------------------------
1. Update snovault 1.0.47 (#3447)
2. ENCD-5427-fix-title-underlines (#3442)
3. ENCD-5415-audits-in-annotation-metadata (#3439)
4. ENCD-5426-classic-img-update (#3441)
5. ENCD-5386-reverse-link-publications-in-dataset.references (#3423)
6. ENCD-5409-lower-chunksize-option-demo (#3437)
7. ENCD-5420-fix-bottom-shading (#3440)
8. ENCD-5421-annotation-test (#3436)
9. ENCD-5403-annotation-meta-columns (#3433)
10. SNO-159 Allow remote indexing (#3412)
11. ENCD-5288-create-facet-for-cCREs (#3427)
12. ENCD-5393-publication-dataset-download (#3435)
13. ENCD-5404-add-mint-to-chip-audits (#3430)
14. ENCD-5395-check-biosample-characterizations-from-pooled-from-biosample (#3421)
15. ENCD-5398-add-cut-and-run-assay (#3425)
16. ENCD-5400-analysis-update (#3426)
17. ENCD-5371-biosample-disease-ontology (#3420)
18. ENCD-5401-Restrict-batch-download-to-certain-types (#3432)
19. ENCD-5394-cart-experiments-only (#3429)
20. ENCD-5390 update fonts sitewide (#3418)
21. ENCD-5413-hide-download-btn-for-large-search (#3431)
22. ENCD-5382-update-robots-txt (#3424)
23. ENCD-5405-cart-dl-metadata-url (#3422)
24. ENCD-5385 facets updates (#3416)
25. ENCD-5389-correct-audit-details-for-missing-input-control-audit (#3409)
26. ENCD-5381-fix-publication-object-publication-year (#3414)
27. ENCD-5367 clean up body map styles (#3407)
28. ENCD-5290-homepage-update (#3413)
29. ENCD-5378-fix-metadata-tsv-assay-col (#3411)
30. ENCD-5252-add-index-reads-audit (#3391)
31. ENCD-5359 add-hover-definitions-to-menu (#3401)
32. ENCD-5391-fix-internal-status-facet-not-opening (#3410)
33. ENCD-5304-major-ontology-update-scRNA-seq-assay-change (#3394)
103.0 (unreleased) snovault 1.0.46
--------------------------------------------------------------------
1. Update snovault 1.0.46 (#3406)
2. SNO-160-use-boolean-values-in-facets (#3402)
3. SNO-116-fix-summary-naming-conflict (#3404)
4. ENCD-5241-search-scroll (#3367)
5. ENCD-5370-add-pagination-to-publication-dataset (#3403)
6. ENCD-5369-change-annotation-v5 (#3398)
7. ENCD-5365-add-document-to-publication-obj (#3405)
8. ENCD-5373 fix mouse development matrix (#3397)
9. ENCD-5245-adjust-ChIP-control-audit (#3400)
10. ENCD-5363-Fix-tags-on-cluster-deployments (#3381)
11. ENCD-4519-in-series-change-relative-age-to-age (#3373)
12. SNO-157-make-page-facets-collapsable (#3385)
13. ENCD-5368-lib-dependency-depleted-nucleic-acid-term (#3395)
14. ENCD-5193 additions to set_status_up for datasets (#3392)
15. ENCD-4350-make-antibody-label-clearer (#3374)
16. ENCD-5360-atac-output-types (#3389)
17. ENCD-5358 fix body map thumbnail (#3390)
18. ENCD-5286-subreads-bam-should-require-replicate (#3393)
19. ENCD-5280-lower-audit-severity-missing-characterization (#3386)
102.0 (released) snovault 1.0.45
--------------------------------------------------------------------
1. ENCD-5361-bug-fix-biosample-summary (#3378)
2. Update to snovault 1.0.45 (#3376)
3. ENCD-5268-analysis-object (#3323)
SNO-154 fix magic to add json types
5. SNO-156 Use pyramid_retry 2.1.1 (#3359)
6. ENCD-5353-cart-limit (#3375)
7. ENCD-5237 add body map to reference epigenome (#3366)
8. ENCD-5255-add-encode4-atac-seq-qc-audits (#3368)
9. ENCD-5331-target-factorbook-dbxref (#3360)
10. ENCD-5343-adjusting-internal-status-property (#3372)
11. ENCD-5185-fix-replication-type-for-pooled-clone-sequencing-experiments (#3361)
12. ENCD-5329-read-depth-audit-update (#3369)
13. ENCD-5315 gemBS alignment QC (#3365)
14. ENCD-5272-Model-donor-age-when-biosample-is-collected (#3362)
15. ENCD-5341-update-deployment-tags (#3371)
16. ENCD-5314-add-new-output-types (#3354)
17. ENCD-5298-add-fileset-to-pipeline-object (#3358)
18. ENCD-5336-matrix-desc (#3370)
19. ENCD-5309-cart-locks (#3355)
20. ENCD-5308-fix-react-error-on-summary-page (#3348)
21. ENCD-5307-add-dnase-footprints-quality-metric (#3356)
22. ENCD-5303-remove-other-plasmid-lib-type (#3347)
23. ENCD-5239-fix-css-problem-on-examine-loci-reference-form(#3318)
24. ENCD-3470-blocked-out-facet-setting (#3357)
25. ENCD-5342-remove-page-titles (#3363)
26. ENCD-5349-add-element-location-transgenic-expt (#3364)
27. ENCD-5297-add-ATAC-adapters-to-library (#3353)
28. ENCD-4438-remove-stage-timepoint (#3349)
29. ENCD-5338-add-idr-ranked-peak-file-format-type (#3350)
30. ENCD-5333-fix-google-dataset-author (#3344)
31. ENCD-5327-fastq-demultiplex-analysis-step-type (#3342)
32. ENCD-5113 fix curl command to get metadata.tsv(#3343)
33. ENCD-5320-fix-sescc-element-url (#3337)
34. ENCD-5321-remove-lib-frag-method-enum (#3339)
35. ENCD-5306-update-hotspot-qc-metric (#3352)
36. ENCD-5310-choose-analysis (#3340)
37. ENCD-5285-table-lines (#3330)
38. ENCD-5332-sequence-barcodes-reference-type (#3351)
39. ENCD-4857-add-biosample_ontology.classification-to-matrix (#3331)
40. ENCD-5328 fix released start date (#3346)
v101.0 (released) snovault 1.0.44
--------------------------------------------------------------------
1. ENCD-5324-experiment-perturbed (#3338)
2. ENCD-5296-fix-matrix-header-link (#3329)
3. ENCD-5317-fix-bug-biosample-summary (#3332)
4. ENCD-5319 fix date released link (#3335)
5. ENCD-5322-fix-table-capitalization (#3334)
6. ENCD-5191 add ENCSR id to cart (#3336)
7. ENCD-5294-move-4-read-fraction-QMs (#3320)
8. ENCD-5302-cart-link (#3328)
9. ENCD-5181-perturbed-facet-normal (#3325)
10. ENCD-5267 body map updates (#3326)
11. ENCD-5270-library-adapter (#3312)
12. ENCD-5278-add-binding-to-category-property (#3310)
13. ENCD-5214-in-vivo-enhancer-screen (#3314)
14. ENCD-5271-add-atac-dnase-output-types (#3309)
15. ENCD-5243 fix crash on date submitted (#3300)
16. ENCD-5281 Remove extra files.assembly column (#3324)
17. ENCD-5276-add-kallisto-properties-to-library (#3321)
18. ENCD-5292 Change txt extension to txt.gz (#3319)
19. ENCD-5277 Update amis v100 and typos (#3307)
20. ENCD-5300-add-audit-field-to-metadata-tsv (#3322)
21. ENCD-5265-correct-stem-cell-matrix-links (#3298)
22. ENCD-5289-fcc-remove-assay-type-facet (#3316)
23. ENCD-5254-add-pseudoalignment-analysis-step-type (#3317)
24. ENCD-5238-organ-system-slims-assay-update (#3297)
25. ENCD-4913-fix-filtered-url-in-matrix (#3294)
26. ENCD-5262 add skinny tracks (#3306)
27. ENCD-5236-display-fcc-prop (#3315)
28. ENCD-5261-copy-schema (#3311)
29. ENCD-5269-audit-annotation-file-derived-from-revoked (#3302)
30. ENCD-5225-display-cropped-read-length-and-tolerance (#3287)
31. ENCD-4614-no-assembly-graph (#3299)
32. ENCD-4927 Internal Audit details not showing up for GM
33. ENCD-5260 Cart auto-save
34. ENCD-5159-show-donor-on-ref-page (#3289)
35. ENCD-5136-hide-nih-in-facets-on-0-results (#3290)
v100.0 (released) snovault 1.0.44
--------------------------------------------------------------------
1. ENCD-5216 deploy demo pointing at pg (#3273)
⁃ ENCD-5242 refactor cloud config
⁃ ENCD-5235 fix wale backup error
⁃ ENCD-5240 fix lib magic dependency
⁃ ENCD-5212 deploy demo at ES cluster
⁃ ENCD-5234 fix key validation upload bucket
2. ENCD-5275-fix-json-ld-exploding-without-at-type (#3301)
3. ENCD-4215-enable-google-set (#3282)
4. ENCD-5258-add-file-upgrade (#3292)
5. ENCD-5264 fix error on pages missing @type (#3293)
6. ENCD-5259-fix-validation-fail-reference-objects (#3291)
7. ENCD-5266 change description to title for index_of property
8. ENCD-5116-pipeline-graph (#3278)
9. ENCD-5178 add body map to summary page (#3285)
10. ENCD-5228-add-enc4-chip-pipeline-to-audits (#3288)
11. ENCD-5229-fix-run-type-dependency (#3270)
12. ENCD-5244-add-new-enums-for-DAC-pipeline (#3286)
13. ENCD-5226-add-bulk-RNA-seq-pipeline-to-audits (#3276)
14. ENCD-5217-expt-fcc-audit-inconsistent-gms (#3284)
15. ENCD-5157-add-to-biosample-summary-and-display (#3280)
16. ENCD-4378-remove-restrict-target-dbxref (#3271)
17. ENCD-5100-index-reads-grouping (#3281)
18. ENCD-5215-improve-Publication-link-to-PublicationData (#3283)
19. ENCD-5204-fix-ExperimentSeries-QC-table-crash-for-no-target-experiments (#3269)
20. ENCD-4644-add-details-about-fastq-signatures (#3272)
21. ENCD-5220-add-crop-length-tolerance-to-file (#3277)
22. ENCD-5230-change-tech-replicate-field-of-metadata-tsv (#3268)
23. ENCD-5211-add-Mint-ChIP-control-title (#3262)
24. ENCD-5201-biosample-organ-system-slims (#3275)
25. ENCD-5209-add-elements-ref-to-analysis-step-schema (#3264)
26. ENCD-5232-add-rDHSs-to-rep-DNase-hypersensitivity-sites (#3267)
27. ENCD-5203-biosample-audit-inconsistent-GMs (#3274)
28. ENCD-5151-fix-software-breadcrumb (#3245)
29. ENCD-5099-add-index-read-on-file-page (#3256)
30. ENCD-5105-SECC-Stem-cell-matrix (#3203)
31. ENCD-5200-add-FCC-ExperimentTable (#3266)
32. ENCD-5210-make-documents-searchable (#3263)
33. ENCD-5206-add-element-quantification-to-file-output-type (#3265)
34. ENCD-4991-display-assembly-N-gene_annot-on-UI (#3248)
35. ENCD-5218-batch-dl-issue (#3259)
36. ENCD-5070-missing-img (#3260)
v99.0 (released) snovault 1.0.44
--------------------------------------------------------------------
1. ENCD-5223-metadata-shift (#3258)
2. ENCD-5221-smaller-es-cluster-master (#3257)
3. ENCD-5171-download-fastq-files (#3252)
4. ENCD-5184-comp-model-software-version-unique (#3250)
5. ENCD-5152-add-app-json-to-attachments (#3247)
6. ENCD-5148-adjust-GM-for-homologous-recombination-and-CRISPR-intro (#3242)
7. ENCD-5111-cleanup-deploy-output (#3251)
8. ENCD-5194-add-grnas-file-output-type (#3234)
9. ENCD-5169-humandonor-external-ids (#3226)
10. ENCD-5195-add-gene-to-reference-page (#3244)
11. ENCD-5208-circle-ci-install-fix (#3249)
12. ENCD-5207-update-snovault-1.0.44 (#3246)
13. ENCD-4374-fix-restrict-file-edit-checkbx (#3237)
14. ENCD-5006-Fix-target-breadcrumb (#3241)
15. ENCD-5140-add-clear-classification-of-related-datasets (#3239)
16. ENCD-5127-add-biosample-ontology-fce-requirement (#3240)
17. ENCD-5160-cropped-read-length-bam (#3232)
18. ENCD-5198-update-libmagic-ubuntu-with-amis (#3238)
19. ENCD-5202-lower-indexing-RAM-footprint (#3243)
20. ENCD-5164 add production amis (#3229)
21. ENCD-5199-add-ref-epig-bdd-and-polish (#3233)
22. SNO-143-switch-update-readmes (#3221)
23. ENCD-5018 Change tagged target audits severity to Warning (#3230)
24. ENCD-5149-gene-and-target-dbxrefs-for-GeneCards (#3220)
25. ENCD-5128-calculate-crispr-assay-titles (#3224)
26. ENCD-5172-add-output-type-regulatory-elements (#3227)
27. ENCD-5161-add-fragmentation-duration-props-to-library (#3235)
28. ENCD-5173-add-to-reference-summary-page (#3228)
29. ENCD-5197 return paths from library calculated property
30. SNO-144-redirect-downloads-through-nginx-or-apache (#3182)
31. ENCD-5166 change organoid color (#3213)
32. ENCD-5189-additional-pytest-cleanup (#3223)
33. ENCD-5131-add-sprite-assay-ontology-update (#3215)
34. ENCD-5163 deemphasize hg19 screen link (#3211)
v98.0 (released) snovault 1.0.43
--------------------------------------------------------------------
1. ENCD-5186-Fix-FCC-audit-script-error-with-biosample-ontology (#3219)
2. ENCD-5175-fix-validation-error-crispr-insertion (#3214)
3. ENCD-5180-re-matrix-left-align-term-names (#3216)
4. ENCD-5182 respect filters for viz (#3217)
5. ENCD-5039-reorganize-pytest-fixtures-set (#3206)
6. Update snovault 1.0.43 (#3212)
7. ENCD-4540 Cart visualizations (#3205)
8. SNO-146-clean-up-threadmanager-on-pyramid-retry-exception (#3207)
9. ENCD-5133-calculate-for-analyses (#3200)
10. ENCD-5145-remove-gRNA-tiled-loci-update-examined-loci (#3183)
11. ENCD-5150-rendering-error (#3209)
12. ENCD-5168-allow-apache-status-monitoring (#3210)
13. ENCD-5123-expt-audit-processed-files-analyses (#3192)
14. ENCD-2666 mouse dev matrix (#3198)
15. ENCD-5090-apply-experiment-audits-to-fcc-experiments (#3169)
16. ENCD-5117-update-mixed-read-length-audit (#3193)
17. ENCD-5110-add-gm-categories (#3181)
18. ENCD-5125-add-factorbook (#3191)
19. ENCD-5087-add-subreads-dependencies (#3180)
20. ENCD-5082-file-pagination (#3201)
21. ENCD-5051-generating-QC-table-for-experimental-series (#3138)
22. ENCD-5129-check-if-view-has-type (#3199)
23. ENCD-5143-remove-properties-gene_type_quant_qc (#3185)
24. ENCD-5144-add-dna-cloning-biosampletype (#3184)
25. ENCD-5139-add-post-nucleic-acid-time-biosample (#3188)
26. ENCD-5122-add-Donor-to-Reference (#3197)
27. ENCD-5109-fix-file-validation-audit-for-annotations (#3194)
28. ENCD-5080-add-library-property-strandedness (#3186)
29. ENCD-5069 fix error in gene search (#3166)
30. ENCD-5118-adjust-unreplicated-experiment-audit (#3187)
31. ENCD-5130-Add-download-btn-to-FCC (#3179)
v97.0 (unreleased) snovault 1.0.42 ubuntu18/py376 merge
--------------------------------------------------------------------
1. SNO-145 handle missing _stats on request
2. ENCD-5137-Fix-ENTEx-text-issue (#3178)
3. ENCD-5132-update-deployment-amis (#3174)
4. update-to-v97rc1 (#3172)
5. update-to-v96.1 (#3171)
6. ENCD-5071-audit-script-error-when-control-is-series (#3164)
7. ENCD-4626-fix-test-save-change-antibody (#3145)
8. ENCD-4365-roadmap-collection-view (#3142)
9. ENCD-5121-doc-section-publication-data (#3162)
10. ENCD-5073-multiple-targets-FCC (#3154)
11. ENCD-5097-add-Ingrid-to-AntibodyCharacterization-reviewed-by (#3148)
12. ENCD-5033-index-user-made-accounts (#3158)
13. ENCD-4953-calculated-tags-property-experiment (#3155)
14. ENCD-5072 Library construction platform display (#3168)
15. SNO-142 Minor fixes for ubutnu 18 on v96x1rc1
16. ENCD-5106-add-control-link-FCE (#3151)
17. ENCD-5101-add-target-to-annotation-summary-page (#3165)
18. ENCD-5124-fix-vis-indexing-failure-on-RNA-seq-annotation (#3161)
19. ENCD-5074-exclude-single-cell-from-read-count-audit (#3153)
20. ENCD-5083-restrict-IHEC-dbxref-to-RefEpi-and-Annotation (#3147)
21. ENCD-5034-encyclopedia-v6-addition (#3152)
22. SNO-141-update-osx-catalina-readme
23. ENCD-4917-new-target-matrix (#3071)
24. ENCD-5120-1st-post-master-merge-fix-u18-py369 (#3160)
25. ENCD-3983-update-to-ubuntu-18
26. ENCD-5112 Update deploy ami map for all builds
27. SNO-140 Allow shorting uuids with flag
28. ENCD-5075 Adding the change for depmap (#3141)
29. SNO-139 Log detailed initial indexing times
30. ENCD-3983-update-to-ubuntu-18
31. ENCD-4961-make-base-amis-encd-deployment
32. ENCD-4960-add-aws-pems-for-deployment
33. SNO-132 Update to py37 lrowe pr with fixes
34. ENCD-5061-echo-filenames-in-deploy-scirpt
35. ENCD-5060-add-py-requirements-file
36. ENCD-5059-fix-pylint-in-deploy-script
37. ENCD-5081 add-pooled-clone-sequencing-types (#3144)
38. ENCD-5084-draft-1 (#3149)
39. ENCD-5096-draft-1 (#3150)
40. ENCD-5091 Rebuilt package-lock.json (#3140)
41. ENCD-5077 Remove unnecessary prints (#3146)
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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