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Tm 690 fix slowness#50

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rlreamy wants to merge 201 commits intotranSMART-Foundation:mastertranSMART-Foundation/transmartApp:masterfrom Kretzler-Lab:TM-690_FixSlownessKretzler-Lab/transmartApp:TM-690_FixSlownessCopy head branch name to clipboard

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Commits

Commits on Nov 29, 2016

• Fix for ui autocomplete

  

  dennyverbeeck

  authored and

  Ruslan Forostianov

  committed
  dc54db8

Commits on Dec 12, 2016

• version release 16.2

  ricepeterm

  committed
  04e906f

Commits on Dec 13, 2016

• application version 16.2

  ricepeterm

  committed
  b66ea48

Commits on Dec 14, 2016

• updated browse delete study/program with children messages

  ricepeterm

  committed
  ed40d77

• include GWAS-plink plugin

  ricepeterm

  committed
  39c15bb

• simple version number

  ricepeterm

  committed
  9b481cc

Commits on Dec 15, 2016

• Escape collision of jq versions on the qurypanel.

  Show description for fbf6ab3
  

  Ruslan Forostianov

  committed
  fbf6ab3

Commits on Dec 22, 2016

• Fix TRANSREL-153: ignore empty string variable values

  ricepeterm

  committed
  872abac

Commits on Jan 2, 2017

• updated SmartR version

  sherzinger

  committed
  d8533e6

• Merge pull request transmart#207 from transmart/transmart-SmartR

  Show description for 68c01cf
  sherzinger

  authored
  68c01cf

Commits on Jan 3, 2017

• use standard email contact for uploadData

  ricepeterm

  committed
  48fe62a

• unique name for activateTab in datasetExplorer

  ricepeterm

  committed
  03c0a77

• browserDetect script in case of future version issues

  ricepeterm

  committed
  b134ab8

Commits on Jan 4, 2017

• Update BuildConfig.groovy

  sherzinger

  authored
  b3012ee

Commits on Jan 23, 2017

• Merge branch 'master' of github.com:transmart/transmartApp

  ricepeterm

  committed
  ee542ce

• rename activateTab to be unique

  ricepeterm

  committed
  e1645c3

• Catch null and empty variable params

  ricepeterm

  committed
  37359c7

• browser version detect code in case of need

  ricepeterm

  committed
  f9b2cb1

• Merge master branch

  ricepeterm

  committed
  8b3968c

Commits on Feb 2, 2017

• Fixed restore comparison from workspace, for clinical and highdimensional concepts.

  dennyverbeeck

  committed
  bba635f

Commits on Feb 3, 2017

• Fixing an issue linked with SmartR importation of another version of jQuery: after a click on "Advanced Workflow", we could no more use the "Clear" button of "Active Filters", nor click on the resu…

  Show description for 2eed677
  anthony-o

  committed
  2eed677

• Merge pull request transmart#208 from dennyverbeeck/fix/restore-comparison

  Show description for ae1cdae
  ricepeterm

  authored
  ae1cdae

• Hidome Ffature: when search term left empty, you get a 'no-value' type filter. I.e. match all subjects who have the high dimensional concept (a.k.a. the original pre-Hidome behavior)

  Show description for acb4a7a
  dennyverbeeck

  committed
  acb4a7a

• Merge pull request transmart#210 from dennyverbeeck/feature/hidome-novalue

  Show description for 42a4fbe
  ricepeterm

  authored
  42a4fbe

• Merge pull request transmart#209 from anthony-o/fix-search-issues-involving-jquery

  Show description for 41fac62
  ricepeterm

  authored
  41fac62

• Catch empty search terms list

  ricepeterm

  committed
  a362123

• name of xnat import enable parameter

  ricepeterm

  committed
  24b25da

• xnat import enable parameter

  ricepeterm

  committed
  3b95368

• typo in error message

  ricepeterm

  committed
  0f9a306

Commits on Feb 5, 2017

• jQuery Noconflict updates; variable name typo

  ricepeterm

  committed
  020a20d

Commits on Feb 8, 2017

• Fix in repopulate filter window that caused not being able to create new high dimensional queries.

  Show description for 9d69e32
  dennyverbeeck

  committed
  9d69e32

• Add button for 'No filter' option in high dimensional data instead of clicking ok with no filter, as this is not clear to users.

  dennyverbeeck

  committed
  349727c

• Cosmetic change to query display

  dennyverbeeck

  committed
  d0d67b4

• Merge pull request transmart#212 from dennyverbeeck/fix/TRANSREL-168

  Show description for a80f09e
  ricepeterm

  authored
  a80f09e

• Merge pull request transmart#211 from dennyverbeeck/fix/TRANSREL-169

  Show description for b70e5a6
  ricepeterm

  authored
  b70e5a6

Commits on Feb 9, 2017

• Fix for using 'No filter' when dropping high dimensional concept into summary statistics or grid view

  dennyverbeeck

  committed
  1bf36e0

Commits on Mar 1, 2017

• Fixes for HiDome

  Show description for f6931c9
  dennyverbeeck

  committed
  f6931c9

• Merge branch 'fix/TRANSREL-168' into fix/hidome-fixes

  dennyverbeeck

  committed
  f7438f6

• Merge pull request transmart#214 from dennyverbeeck/fix/hidome-fixes

  Show description for 960c02c
  ricepeterm

  authored
  960c02c

• Fix an issue in Workspace (saved queries)

  Show description for c69d19e
  dennyverbeeck

  committed
  c69d19e

• Merge pull request transmart#215 from dennyverbeeck/fix/display-query-workspace

  Show description for 9302ccc
  ricepeterm

  authored
  9302ccc

Commits on Mar 9, 2017

• restore gene list functionality

  ricepeterm

  committed
  8659ebe

• fix for 1000 patient query in oracle from 17.1

  ricepeterm

  committed
  e0c3636

• Convert Oracle CLOB to parse XML

  ricepeterm

  committed
  0097380

• move AS to be accepted as SQL syntax on Oracle

  ricepeterm

  committed
  d0b2606

Commits on Mar 13, 2017

• Merge remote-tracking branch 'transmart/master' into release-16.2

  ricepeterm

  committed
  4852fbb

• GenePatternFiles class public

  ricepeterm

  committed
  38327be

• Merge remote-tracking branch 'transmart/master' into release-16.2

  ricepeterm

  committed
  f39c141

Commits on Mar 16, 2017

• Added alias for subquery, since postgres requires this. Omitted the 'AS' keyword, this way the syntax is supported by Postgres and Oracle.

  dennyverbeeck

  committed
  365fb47

• Add the gwas-plink plugin by default

  dennyverbeeck

  committed
  66e7023

Commits on Mar 17, 2017

• Merge pull request transmart#216 from dennyverbeeck/master

  Show description for ca2c689
  ricepeterm

  authored
  ca2c689

• Merge remote-tracking branch 'transmart/master' into release-16.2

  ricepeterm

  committed
  81bbab2

• correcting a few typos

  ricepeterm

  committed
  3ff36f4

Commits on Mar 22, 2017

• Add pretty names for probeId and transcriptId

  dennyverbeeck

  committed
  d059b55

Commits on Mar 31, 2017

• release-16.1-TraIT fixes

  

  Ruslan Forostianov

  committed
  383c7a7

Commits on Apr 7, 2017

• Browse fix for studies loaded below c_hlevel 1

  ricepeterm

  committed
  2fb86ec

• Merge pull request transmart#217 from dennyverbeeck/feature/hidome

  Show description for 6d1b8fc
  ricepeterm

  authored
  6d1b8fc

• Merge pull request transmart#218 from transmart/release-16.1-TraIT-fixes

  Show description for 17bfc70
  ricepeterm

  authored
  17bfc70

• Merge branch 'master' of github.com:transmart/transmartApp

  ricepeterm

  committed
  956244b

Commits on Apr 19, 2017

• Merge remote-tracking branch 'transmart/master' into release-16.2

  ricepeterm

  committed
  5ecc8e5

• Fix for probeid genesignatures

  ricepeterm

  committed
  4b17ab1

• redisplay programs after 'delete program'

  ricepeterm

  committed
  38c3188

• Option ui.jirareport.hide to hide 'report a bug' button

  ricepeterm

  committed
  8607434

• fix for 'delete program'; fix function name spellings

  ricepeterm

  committed
  889f243

• Merge remote-tracking branch 'transmart/master' into release-16.2

  ricepeterm

  committed
  14784c5

• remove console.log message

  ricepeterm

  committed
  5916266

• Merge remote-tracking branch 'transmart/master' into release-16.2

  ricepeterm

  committed
  75d78ca

Commits on May 24, 2017

• Fix typos in accessLog message

  ricepeterm

  committed
  843bcff

• Make gridview column label unambiguous

  ricepeterm

  committed
  8953388

• Merge remote-tracking branch 'transmart/master' into release-16.2

  ricepeterm

  committed
  3a25179

Commits on Oct 27, 2017

• TM-152: Data attestion page

  zwright

  committed
  0c990b2

• TM-152: Data attestion page null checks

  zwright

  committed
  e2992c8

Commits on Oct 30, 2017

• TM-152: Quick start link

  zwright

  committed
  0f01c51

• TM-152: Page title reset after Genome Browser

  zwright

  committed
  d3a7ec3

• TM-152: Fix jquery for closing utilities menu

  

  Becky Reamy

  committed
  f5da6f4

Commits on Oct 31, 2017

• TM-152: MOTD and config customizations

  zwright

  committed
  8f6a08a

• TM-152: Logos

  KingstonDuo

  committed
  72daae3

• TM-152: Added emails to configs

  

  kingstonduo@umich.edu

  committed
  be6d991

• TM-152: Contact emails

  KingstonDuo

  committed
  5b3fb72

• TM-152: App titles

  KingstonDuo

  committed
  baf7c9e

Commits on Nov 6, 2017

• TM 152: Platform dropdown

  KingstonDuo

  committed
  aaee4ec

Commits on Nov 7, 2017

• TM-152: Don't return unauthorized studies

  KingstonDuo

  committed
  1ecdc43

Commits on Nov 17, 2017

• TM 152: Across Trials security fixes

  KingstonDuo

  committed
  5b383d6

Commits on Nov 21, 2017

• TM 234: Move code from HTML to JS

  KingstonDuo

  committed
  2880ce9

Commits on Nov 22, 2017

• TM-234: Check before clearing data grid element

  KingstonDuo

  committed
  043ff56

Commits on Nov 30, 2017

• TM 234: Remove test file

  KingstonDuo

  committed
  68cd925

• Merge pull request #1 from Kretzler-Lab/TM_234_16_2_Bugs

  Show description for cd3f0ba
  KingstonDuo

  authored
  cd3f0ba

Commits on Dec 1, 2017

• TM 152: Across Trials tooltips, search limit

  KingstonDuo

  committed
  01a87ec

• Merge pull request #2 from Kretzler-Lab/TM-152_16_2_Upgrade

  Show description for 9e555b9
  rlreamy

  authored
  9e555b9

Commits on Dec 4, 2017

• TM-224: Thicken grid lines

  KingstonDuo

  committed
  f7fbaee

• TM-229: Added axis labels

  KingstonDuo

  committed
  01a99d2

• Merge pull request #3 from Kretzler-Lab/TM-224_Grid_Lines

  Show description for a295de2
  rlreamy

  authored
  a295de2

• Merge pull request #4 from Kretzler-Lab/TM-229_Axis_Labels

  Show description for 35f7693
  rlreamy

  authored
  35f7693

Commits on Dec 5, 2017

• TM-226: Update Jfree chart library

  KingstonDuo

  committed
  d72584f

• TM-226: Add new jFree jars

  KingstonDuo

  committed
  f35439d

• TM-226: Fixed missing user error

  KingstonDuo

  committed
  cfd7393

• Merge pull request #5 from Kretzler-Lab/TM-226_Chart_Tooltips

  Show description for 5b101e3
  rlreamy

  authored
  5b101e3

• TM-229: Add labels to numeric concept charts

  KingstonDuo

  committed
  7273c04

• Merge pull request #6 from Kretzler-Lab/TM-229_Axis_Labels

  Show description for 8b8b9f5
  rlreamy

  authored
  8b8b9f5

• Make tranSMART build on my machine

  

  kingstonduo@umich.edu

  committed
  f20fce6

Commits on Dec 7, 2017

• TM-245: Remove the em tag so that the user can click on the number and drag

  

  kingstonduo@umich.edu

  committed
  9e6ef8b

Commits on Dec 12, 2017

• TM-246: Adding changes so we can work on Zachs machine

  

  kingstonduo@umich.edu

  committed
  b8c86ba

• TM 246: Sort by category

  KingstonDuo

  committed
  ec011e5

• Merge pull request #8 from Kretzler-Lab/TM-246_RaceSummaryStatsSortOrder

  Show description for 32ba2fd
  rlreamy

  authored
  32ba2fd

• Merge pull request #7 from Kretzler-Lab/TM_245_GrabTermsIssue

  Show description for cf08b5c
  zwright

  authored
  cf08b5c

• TM 247: Put pvalues in scientific notation

  KingstonDuo

  committed
  e89f9df

Commits on Dec 13, 2017

• TM-247: Styling the stats

  KingstonDuo

  committed
  8ff202e

• TM-247: Vertical table

  KingstonDuo

  committed
  22f59ec

• TM-225: Use concept name for subset

  KingstonDuo

  committed
  bdee9c4

Commits on Dec 14, 2017

• TM-225: Use full concept path

  KingstonDuo

  committed
  a63722b

• Update _conceptsAnalysis.gsp

  Show description for 6bbbc97
  rlreamy

  authored
  6bbbc97

• Merge pull request #9 from Kretzler-Lab/TM-247_Summary_Stats_Pvalue

  Show description for 947d07e
  rlreamy

  authored
  947d07e

• TM-225: Remove extra Private Studies

  KingstonDuo

  committed
  98a9b70

Commits on Dec 15, 2017

• Merge pull request #10 from Kretzler-Lab/TM-225_Long_Subset_Name

  Show description for b99ccaa
  rlreamy

  authored
  b99ccaa

• TM-86: Add search icon

  KingstonDuo

  committed
  638b5ef

• TM-86: Placeholder text

  KingstonDuo

  committed
  421274e

• Merge pull request #11 from Kretzler-Lab/TM-86_Label_Search_Box

  Show description for 23d1fbb
  rlreamy

  authored
  23d1fbb

Commits on Dec 19, 2017

• TM-86: Use font-awesome instead

  KingstonDuo

  committed
  65db92e

• Merge pull request #12 from Kretzler-Lab/TM-86_Label_Search_Box

  Show description for 7b9c092
  rlreamy

  authored
  7b9c092

Commits on Dec 21, 2017

• TM-57: Make the labels on th pie chart readable

  

  kingstonduo@umich.edu

  committed
  5867a96

Commits on Dec 22, 2017

• TM-57: Make labels easier to read in bar charts

  

  kingstonduo@umich.edu

  committed
  286e3b5

• TM-222: Modify config to use relative path

  

  kingstonduo@umich.edu

  committed
  6c52e45

Commits on Jan 2, 2018

• TM-242: Hide upload data link

  

  kingstonduo@umich.edu

  committed
  a63ec75

• Merge pull request #14 from Kretzler-Lab/TM-222_FixHelpLink

  Show description for 3878744
  zwright

  authored
  3878744

• Merge pull request #13 from Kretzler-Lab/TM-57_FixVizLabels

  Show description for f9ee76e
  zwright

  authored
  f9ee76e

Commits on Feb 1, 2018

• TM-258: Formalize names

  KingstonDuo

  committed
  6e13169

Commits on Feb 2, 2018

• TM-272: Remove autocomplete code

  KingstonDuo

  committed
  cebfe93

• TM-272: Tweaks to get rid of errors

  KingstonDuo

  committed
  a534a3d

• TM-272: More tweaks to get rid of errors

  KingstonDuo

  committed
  e469143

• Merge pull request #15 from Kretzler-Lab/TM-258_Formalize_Stat_Words

  Show description for 2958d2e
  rlreamy

  authored
  2958d2e

• TM-271: Terms -> Concepts

  KingstonDuo

  committed
  7db405f

• TM-285: Disable GWAS

  KingstonDuo

  committed
  50a02fb

• Merge pull request #16 from Kretzler-Lab/TM-272_Remove_Autocomplete

  Show description for 68b54ba
  rlreamy

  authored
  68b54ba

• Merge pull request #17 from Kretzler-Lab/TM-271_Drag_Terms_Label

  Show description for 8c9d9b9
  rlreamy

  authored
  8c9d9b9

• Merge pull request #18 from Kretzler-Lab/TM-285_Disable_GWAS

  Show description for 7ceb27e
  rlreamy

  authored
  7ceb27e

Commits on Feb 5, 2018

• TM-284: Remove button

  KingstonDuo

  committed
  5382bcf

• TM-257: Set outline and whisker color to black

  KingstonDuo

  committed
  12f1389

• Merge pull request #19 from Kretzler-Lab/TM-284_Remove_Filter_Button

  Show description for f7e64f9
  rlreamy

  authored
  f7e64f9

• Merge pull request #20 from Kretzler-Lab/TM-257_Whisker_Color

  Show description for 6b7c581
  rlreamy

  authored
  6b7c581

Commits on Feb 6, 2018

• TM-217: Basic monitoring page

  KingstonDuo

  committed
  565b121

• TM-259: Added a couple of divs and moved all subset stats boxes into one cell

  

  kingstonduo@umich.edu

  committed
  e71f53e

• TM-259: Make subset boxes closer on big screen

  

  kingstonduo@umich.edu

  committed
  5b9cf05

• TM-214: Updated the version number to show that we have modified the app

  

  kingstonduo@umich.edu

  committed
  e0c1bb7

• TM-217: More monitoring info

  KingstonDuo

  committed
  ba06150

Commits on Feb 7, 2018

• Merge pull request #21 from Kretzler-Lab/TM-259_FixSubsetCharts

  Show description for c340524
  zwright

  authored
  c340524

• Merge pull request #22 from Kretzler-Lab/TM-214_ShowVersionNumber

  Show description for 03ff832
  zwright

  authored
  03ff832

• TM-217: Move things to service

  KingstonDuo

  committed
  dd84be5

• Merge pull request #23 from Kretzler-Lab/TM-217_Database_Monitor_Page

  Show description for 8633e43
  rlreamy

  authored
  8633e43

Commits on May 21, 2018

• TM-227: Removed the duplicated summary graph

  

  kingstonduo@umich.edu

  committed
  b77108f

Commits on May 22, 2018

• Merge pull request #24 from Kretzler-Lab/TM-227_DuplicatedSummary

  Show description for 6358ce4
  zwright

  authored
  6358ce4

Commits on May 24, 2018

• TM-299: Change the color of the box-plots to make the outliers more visible

  

  kingstonduo@umich.edu

  committed
  42b31da

Commits on May 25, 2018

• Merge pull request #25 from Kretzler-Lab/TM-299_BoxAndWhiskerPlotColors

  Show description for 65657e0
  zwright

  authored
  65657e0

• TM-298: CPROBE config

  KingstonDuo

  committed
  13e2315

• TM-298: CPROBE logo

  KingstonDuo

  committed
  5c5aaef

Commits on May 29, 2018

• TM 298: New email address

  KingstonDuo

  committed
  23da234

• Merge pull request #26 from Kretzler-Lab/TM-298_CPROBE_Config

  Show description for a6e6228
  rlreamy

  authored
  a6e6228

Commits on Jun 1, 2018

• A couple of tweaks to the config

  KingstonDuo

  committed
  0a58cab

Commits on Jun 6, 2018

• Merge pull request #27 from Kretzler-Lab/CPROBE_Config

  Show description for de074ac
  rlreamy

  authored
  de074ac

Commits on Jun 8, 2018

• TM 324: Updates to the Config

  KingstonDuo

  committed
  3e59272

• TM 327: Use the item!

  KingstonDuo

  committed
  351a12b

Commits on Jun 11, 2018

• Merge pull request #28 from Kretzler-Lab/TM-324_Update_Quick_Start

  Show description for 5e4ee7a
  rlreamy

  authored
  5e4ee7a

• Merge pull request #29 from Kretzler-Lab/TM-327_Cohort_Detail

  Show description for 51f5e41
  rlreamy

  authored
  51f5e41

Commits on Jul 24, 2018

• TM-333: update help link

  KingstonDuo

  committed
  3cab14a

Commits on Jul 25, 2018

• Merge pull request #30 from Kretzler-Lab/TM-333_New_Help_Doc

  Show description for 6b838ac
  rlreamy

  authored
  6b838ac

Commits on May 22, 2019

• TM-708: Added new menu items with links

  rlreamy

  committed
  2af08fd

Commits on May 24, 2019

• Merge pull request #31 from Kretzler-Lab/TM-408_UpdateUtilitiesMenu

  Show description for 001beda
  zwright

  authored
  001beda

• KPMP-409: Added logic to turn menu items on or off

  rlreamy

  committed
  e78a870

• KPMP-409: Added new items for KPMP-413 as well

  rlreamy

  committed
  8f117ac

• Merge pull request #32 from Kretzler-Lab/KPMP-409_UpdateUtilitiesCure

  Show description for a8dd1b9
  zwright

  authored
  a8dd1b9

• KPMP-384: Changed version number

  rlreamy

  committed
  4adfe25

• Merge pull request #33 from Kretzler-Lab/KPMP-384_RemovePathwayFromPopup

  Show description for 8a355b8
  zwright

  authored
  8a355b8

Commits on May 28, 2019

• TM-409: fix typo

  rlreamy

  committed
  1edef92

• TM-409: fix typo

  rlreamy

  committed
  2cc7b37

Commits on May 29, 2019

• TM-412: Initial stab at a fix

  rlreamy

  committed
  4ff9b7b

Commits on May 30, 2019

• TM-412: Changed the call to set the tooltip generator

  rlreamy

  committed
  5df19cd

• TM-412: Fix version number

  rlreamy

  committed
  bfef9f6

• Merge pull request #34 from Kretzler-Lab/TM-412_FixHistograms

  Show description for 554dd8e
  zwright

  authored
  554dd8e

• TM-421: Make points on box and points plot gray

  rlreamy

  committed
  2b020d6

Commits on May 31, 2019

• Merge pull request #35 from Kretzler-Lab/TM-421_ChangeColorOfPoints

  Show description for 3aa8c58
  zwright

  authored
  3aa8c58

• Update Config.rpc2.groovy

  zwright

  authored
  9eb8f37

Commits on Jul 10, 2019

• KPMP-435: Change front page message

  zwright

  committed
  1b8550d

• Merge pull request #36 from Kretzler-Lab/TM-435_Update_Front_Text

  Show description for cec78ec
  rlreamy

  authored
  cec78ec

Commits on Jan 23, 2020

• TM-482: Add files to dropdown and config

  zwright

  committed
  b75c163

Commits on Jan 24, 2020

• TM-483: Try just links

  zwright

  committed
  cdcf2e1

• TM-483: Try just links with no separate tab

  zwright

  committed
  5b3dd95

Commits on Feb 21, 2020

• Merge pull request #37 from Kretzler-Lab/TM-483_File_Links

  Show description for 53c54b4
  zwright

  authored
  53c54b4

• TM-467: H3Africa config file and logo

  zwright

  committed
  bdb16d8

Commits on Feb 24, 2020

• Merge pull request #38 from Kretzler-Lab/TM-467_H3Africa_Config

  Show description for 0130b81
  rlreamy

  authored
  0130b81

Commits on Feb 27, 2020

• TM-467: Fix email addres

  zwright

  committed
  e08f680

• Merge pull request #39 from Kretzler-Lab/TM-467_Config_Fix

  Show description for 0748951
  rlreamy

  authored
  0748951

Commits on Apr 6, 2020

• TM-496: Remove unused guides

  zwright

  committed
  5b8f0a3

Commits on Apr 7, 2020

• TM-496: Update data attestation

  zwright

  committed
  4854a10

Commits on Apr 8, 2020

• Merge pull request #40 from Kretzler-Lab/TM-496_Update_Config

  Show description for afdce0d
  rlreamy

  authored
  afdce0d

Commits on Apr 20, 2020

• TM-501: Turn off exporting

  zwright

  committed
  670ccde

• Merge pull request #41 from Kretzler-Lab/TM-501_No_Export

  Show description for bee18c9
  rlreamy

  authored
  bee18c9

Commits on Apr 9, 2024

• Update Config.curegn.groovy

  rlreamy

  authored
  e5af828

• Update Config.rpc2.groovy

  rlreamy

  authored
  70041e6

• Update Config.neptune.groovy

  rlreamy

  authored
  9e40db8

• Update Config.cprobe.groovy

  rlreamy

  authored
  6235b3f

• Update Config.h3africa.groovy

  rlreamy

  authored
  b1ba69b

• Update Config.groovy

  rlreamy

  authored
  78fed82