v85.2

Update to 85.2 (#2779)

v85.1

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)

v84.0 (released) snovault 1.0.28

v84.0 Release Notes

Addition of walkthrough tutorials
Reorganization of the 'Materials & Methods' and 'Help' drop-down menus
Updated help/about content and created some new pages
Created FAQ page (https://www.encodeproject.org/help/faq/)
Added a 'target' facet to the Antibody search page (https://www.encodeproject.org/search/?type=AntibodyLot&status=released)
Improved functionality of the recent 'typeahead' facets
Updated Characterizaiton schema based on feedback from reviewing labs
Site-wide reconciliation of facet headers names, property names, and report columns names across all object types
Bug fixes in the matrix and metadata.tsv

v84.0 (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)

v83.0 with 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)

v82.0

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)

v81.0 / sno 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)

v80.0 / Snovault 1.0.24

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)

v79.0

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)

v78.0

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)