From 774327c4a9dc77c58167f035e26b9d18df821566 Mon Sep 17 00:00:00 2001 From: Brian Shand Date: Tue, 19 May 2026 14:09:08 +0100 Subject: [PATCH 1/3] Germline refresh should ignore new RJ1 (Guy's) data files [NDRS2-3673] --- lib/import/brca/scripts/bash/Import_all_brca_interactive.sh | 1 + 1 file changed, 1 insertion(+) diff --git a/lib/import/brca/scripts/bash/Import_all_brca_interactive.sh b/lib/import/brca/scripts/bash/Import_all_brca_interactive.sh index 74a91f25..1db5ebd4 100755 --- a/lib/import/brca/scripts/bash/Import_all_brca_interactive.sh +++ b/lib/import/brca/scripts/bash/Import_all_brca_interactive.sh @@ -152,6 +152,7 @@ MBIS=$1 PROV='RJ1' IFS=$'\n' for x in $(find $DIRPATH/$FILEPATH -type f -name "*.pseudo" -path "*/$PROV/*" \ +-not -path "*/2026/*" \ ! -name ""Dummy_Pseudo_RJ1.pseudo) do IFS="$OIFS" From 84c02708b22478155c6541f025c65e9735b88378 Mon Sep 17 00:00:00 2001 From: Brian Shand Date: Wed, 20 May 2026 15:20:25 +0100 Subject: [PATCH 2/3] Germline refresh should ignore new RQ3 (Birmingham) data files with mixed BRCA and colorectal data [NDRS2-3673] --- lib/import/brca/scripts/bash/Import_all_brca_interactive.sh | 3 +++ 1 file changed, 3 insertions(+) diff --git a/lib/import/brca/scripts/bash/Import_all_brca_interactive.sh b/lib/import/brca/scripts/bash/Import_all_brca_interactive.sh index 1db5ebd4..27087bfc 100755 --- a/lib/import/brca/scripts/bash/Import_all_brca_interactive.sh +++ b/lib/import/brca/scripts/bash/Import_all_brca_interactive.sh @@ -134,7 +134,10 @@ done RQ3 () { PROV='RQ3' IFS=$'\n' +# Ignore 2 RQ3 files submitted in 2026 which contain both BRCA and Germline data. +# Our plan is not to load these as pseudonymised data, but rather into live encore. for x in $(find $DIRPATH/$FILEPATH -type f -name "*.pseudo" -path "*/$PROV/*" \ +-not -path "*/2026/*" \ -not -path "*/2018-02-06/*" \ ! -iname "*Rare*" \ ! -iname "*Colon*" \ From 986aaec68c298dde426c4810604b320e8eb60edb Mon Sep 17 00:00:00 2001 From: Brian Shand Date: Wed, 20 May 2026 15:22:29 +0100 Subject: [PATCH 3/3] Germline refresh should ignore new RJ1 (Guy's) data files [NDRS2-3673] --- lib/import/brca/scripts/bash/Import_all_brca_interactive.sh | 1 + 1 file changed, 1 insertion(+) diff --git a/lib/import/brca/scripts/bash/Import_all_brca_interactive.sh b/lib/import/brca/scripts/bash/Import_all_brca_interactive.sh index 27087bfc..8e09383e 100755 --- a/lib/import/brca/scripts/bash/Import_all_brca_interactive.sh +++ b/lib/import/brca/scripts/bash/Import_all_brca_interactive.sh @@ -154,6 +154,7 @@ RJ1 () { MBIS=$1 PROV='RJ1' IFS=$'\n' +# Germline refresh should ignore new RJ1 data files submitted in 2026 in a new format. for x in $(find $DIRPATH/$FILEPATH -type f -name "*.pseudo" -path "*/$PROV/*" \ -not -path "*/2026/*" \ ! -name ""Dummy_Pseudo_RJ1.pseudo)