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Merge from master #60
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Commits on Oct 9, 2023
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Merge branch 'master' of github.com:SouthGreenPlatform/Gigwa2 into st…
…ore_runs_list_in_variants
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fix: summary of instance content in another jsp + empty database ok (…
…have to be verified)
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Commits on Oct 13, 2023
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Made group overlap problem more explicit for Fst calculation
... also disabling Show button when < 2 metadata values selected
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Commits on Oct 20, 2023
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Made number of groups only depend on declared "groupColors" array
sempere authored and sempere committedOct 20, 2023 Configuration menu - View commit details
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Commits on Oct 23, 2023
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Merge pull request #71 from SouthGreenPlatform/multipleGropus
Multiple gropus
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Commits on Oct 30, 2023
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Merge pull request #72 from SouthGreenPlatform/master
Merge from master
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Merge pull request #73 from SouthGreenPlatform/master
Fix: reset individual list before feeding it
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Merge pull request #74 from SouthGreenPlatform/master
Fix: slight bug in group memorizing when changing project
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Commits on Nov 2, 2023
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Reduction of the genotype column in the table and addition of known a…
…lleles for a variant
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Merge pull request #75 from SouthGreenPlatform/store_runs_list_in_var…
…iants Store runs list in variants
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Merge pull request #76 from SouthGreenPlatform/bookmarkMultiGroups
Bookmark multi groups + variant detail popup improvements
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Introduced VariantQueryWrapper...
as an attempt to manage variant-level query generation from a single piece of code, no matter if meant at being used with VariantData or VariantRunData documents
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Merge branch 'multipleGroups' of https://github.com/SouthGreenPlatfor…
…m/Gigwa2 into multipleGroups
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Merge pull request #78 from SouthGreenPlatform/multipleGroups
Made export and visualization queries support any group number
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Merge pull request #79 from SouthGreenPlatform/VariantQueryWrapper
Introduced VariantQueryWrapper...
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Merge pull request #80 from SouthGreenPlatform/multipleGroups
Multiple groups
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Merge pull request #82 from SouthGreenPlatform/query
load query fixed
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Commits on Dec 5, 2023
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- moved filter-by-variant-id checkbox - hid empty runs - added background color to sample names
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Merge pull request #85 from SouthGreenPlatform/master
Fix: Issue in attaching genotype pattern onchange to groups
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Merge pull request #86 from SouthGreenPlatform/master
Removed unwanted changes / unused stuff
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Merge pull request #87 from SouthGreenPlatform/geneLookup
Gene lookup
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Merge pull request #88 from SouthGreenPlatform/master
Merge from master
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Merge pull request #89 from SouthGreenPlatform/multipleGroups
Multiple groups
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Merge pull request #92 from SouthGreenPlatform/master
Merge from master
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Merge pull request #95 from SouthGreenPlatform/individualMetadata
Filter individual metadata from server queries
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Merge pull request #96 from SouthGreenPlatform/master
Merge from master
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Merge pull request #98 from SouthGreenPlatform/master
Merge from master
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Merge pull request #99 from SouthGreenPlatform/bundles
Added bundle creation scripts for each OS
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Fixed 2 bugs in chart interface...
- passing assembly to server - showing metadata field checkboxes even if no group selected
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Removed iframe-dialog resizing code that seems useless
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Now get list of list of level1Roles from moduleManager
(so it can customize it)
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added OAuth token compatibility for API requests, based on an OIDC di…
…scovery file (#112) Co-authored-by: GuilhemSempere <[email protected]>
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added OAuth token compatibility for API requests, based on an OIDC di…
…scovery file (#113) Co-authored-by: Peter Selby <[email protected]>
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Caching unzoomed results for fast zoom resets
... also reduced dot size and set default number of intervals to 1000
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* test push master * dartimport * Better manage file type identification (+ slight improvements) * Made DArTseq import support official (mentioned in UI) * Merge from master (#115) * Added support for SNPCLUST_EDITOR role * Added snpclust logo * SnpClust link functionality almost finalized * Update index.jsp Removed iframe-dialog resizing code that seems useless * Small bugfix * Now get list of list of level1Roles from moduleManager (so it can customize it) * Simplified areGroupsOverlapping() implementation * Gave more flexibility in designing Fst groups * Fixed bug in areGroupsOverlapping() * Simplified chart query payload * Minor fix * Added means to display MAF distribution chart * Moved standalone IGV download link to "Online output tools" dialog * added OAuth token compatibility for API requests, based on an OIDC discovery file (#112) Co-authored-by: GuilhemSempere <[email protected]> * Revert "added OAuth token compatibility for API requests, based on an OIDC discovery file (#112)" This reverts commit a899c7f. --------- Co-authored-by: Peter Selby <[email protected]> --------- Co-authored-by: Yoan BIGGIO <[email protected]> Co-authored-by: Peter Selby <[email protected]>
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fix importing metadata from BrAPI to manage the case of having severa…
…l individuals or samples linked to the same externalRefId (#122) Co-authored-by: Alice Boizet <[email protected]>
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Modified import UI to allow importing MD from single endpoint
... accounting for the fact that provided IDs match those in the BrAPI datasource. Started to handle new cases in the controller, still need to implement the actual import
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Re-added lost functionality (fast loading of IGV data without genotypes)
... probably lost while resolving conflicts
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Co-authored-by: GuilhemSempere <[email protected]>
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added build-test for staging --------- Co-authored-by: Dorian Grasset <[email protected]>
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Revert "added OAuth token compatibility for API requests, based on an
OIDC discovery file (#113)"
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Merge pull request #132 from SouthGreenPlatform/master
Merge from master
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Merge pull request #133 from SouthGreenPlatform/staging
Merge from staging
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Merge pull request #134 from SouthGreenPlatform/staging
Final adjustments before release, documentation update
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Merge pull request #135 from SouthGreenPlatform/GuilhemSempere-patch-3
Update build.yml
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* Update build.yml * Reverted back to original build.sh * Added missing file (possibly forgot to commmit/push it) (#136)
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added python build file to get dynamically current pom.xml dependenci…
…es, add build.sh deprecated and improve current github workflow (#138) Co-authored-by: Dorian Grasset <[email protected]>
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