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Fix CI submodule checkout and set Dependabot to weekly #4

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Merged
jas88 merged 8 commits into from
Oct 25, 2025
Merged

Fix CI submodule checkout and set Dependabot to weekly #4

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7c008c1
Fix CI submodule checkout and set Dependabot to weekly
jas88 Oct 21, 2025
aa7f979
Downgrade SMI version from 5.2.0 to 5.1.3
jas88 Oct 21, 2025
e5090f8
Fix hardcoded version paths in Makefile
jas88 Oct 21, 2025
fdea637
Add -s flag to curl to suppress progress bar
jas88 Oct 21, 2025
c7f9053
Use && instead of ; in cd/tar command for proper error handling
jas88 Oct 21, 2025
84f8649
Replace deprecated AdoptOpenJDK with Eclipse Temurin
jas88 Oct 21, 2025
7ea8f06
Suppress wget progress bars and update libicu version
jas88 Oct 21, 2025
b19b8ab
Use libicu-dev instead of version-specific package
jas88 Oct 21, 2025
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4 changes: 2 additions & 2 deletions .github/dependabot.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,5 +4,5 @@ updates:
- package-ecosystem: "github-actions"
directory: "/"
schedule:
# Check for updates to GitHub Actions every weekday
interval: "daily"
# Check for updates to GitHub Actions every week
interval: "weekly"
3 changes: 2 additions & 1 deletion .github/workflows/dockerpush.yml
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Expand Up @@ -10,7 +10,8 @@ jobs:
steps:
- uses: actions/checkout@v4
with:
submodules: true
submodules: recursive
fetch-depth: 0
- name: ccache
uses: hendrikmuhs/ccache-action@v1
- name: Build containers
Expand Down
20 changes: 10 additions & 10 deletions Makefile
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@@ -1,4 +1,4 @@
SMIV := 5.2.0
SMIV := 5.1.3
RDMPV := 7.0.12

JARS := ctpanonymiser-1.0.0/CTPAnonymiser-portable-1.0.0.jar smi-nerd-v$(SMIV).jar
Expand All @@ -14,9 +14,9 @@ all: $(BINS)
minidocker: smi/smiinit smi/smiinit.sh smi/CTPAnonymiser-portable-1.0.0.jar smi/smi-nerd-v$(SMIV).jar smi/ctp-whitelist.script smi/eng.traineddata.gz
mkdir -p smi
touch smi/dummy.sh
(cd smi-services-v4.0.0-linux-x64;tar cf - .) | (cd smi ; tar xf -)
$(eval ctr1:=$(shell buildah from --name smidocker docker://docker.io/adoptopenjdk/openjdk11:debian-jre))
tar c -f - smi/ | buildah run "$(ctr1)" sh -c "tar xof - && apt-get update && apt-get install libicu63"
(cd smi-services-v$(SMIV)-linux-x64 && tar cf - .) | (cd smi && tar xf -)
$(eval ctr1:=$(shell buildah from --name smidocker docker://docker.io/eclipse-temurin:11-jre))
tar c -f - smi/ | buildah run "$(ctr1)" sh -c "tar xof - && apt-get update && apt-get install -y libicu-dev"
buildah config --cmd "/smi/smiinit.sh" "$(ctr1)"
buildah commit "$(ctr1)" "smidocker"

Expand Down Expand Up @@ -63,7 +63,7 @@ smi/eng.traineddata.gz:
curl -sL https://github.com/tesseract-ocr/tessdata/raw/main/eng.traineddata | gzip -9 > $@

smi-services-v$(SMIV)-linux-x64/default.yaml:
curl -L https://github.com/SMI/SmiServices/releases/download/v$(SMIV)/smi-services-v$(SMIV)-linux-x64.tgz | tar xzf -
curl -sL https://github.com/SMI/SmiServices/releases/download/v$(SMIV)/smi-services-v$(SMIV)-linux-x64.tgz | tar xzf -
sed -i -e 's:MappingTable'"'"':smi.MappingTable'"'"':' smi-services-v$(SMIV)-linux-x64/default.yaml
sed -i -e 's/CTPAnonymiserOptions:/CTPAnonymiserOptions:\n SRAnonTool: '\''\/smi\/dummy.sh'\''/' smi-services-v$(SMIV)-linux-x64/default.yaml

Expand All @@ -74,7 +74,7 @@ docker: smiinit $(JARS) $(HOME)/rdmp-cli/rdmp ctp-whitelist.script smi-services-
buildah copy "$(ctr1)" smiinit /bin/
buildah copy "$(ctr1)" $(HOME)/rdmp-cli /rdmp-cli
buildah copy "$(ctr1)" $(JARS) ctp-whitelist.script smi-services-v$(SMIV)-linux-x64/ /smi
./eqnames.pl < smi-services-v3.0.2-linux-x64/default.yaml | buildah run "$(ctr1)" -- bash 2>&1 | tee dockerbuild.log
./eqnames.pl < smi-services-v$(SMIV)-linux-x64/default.yaml | buildah run "$(ctr1)" -- bash 2>&1 | tee dockerbuild.log
buildah config --cmd "/bin/smiinit -c /smi -f /smi.yaml" "$(ctr1)"
buildah commit "$(ctr1)" "smifull"

Expand All @@ -83,19 +83,19 @@ $(HOME)/rdmp-cli/rdmp: rdmp-cli-linux-x64.zip
chmod +x $(HOME)/rdmp-cli/rdmp

rdmp-cli-linux-x64.zip:
wget https://github.com/HicServices/RDMP/releases/download/v$(RDMPV)/rdmp-cli-linux-x64.zip
wget -q https://github.com/HicServices/RDMP/releases/download/v$(RDMPV)/rdmp-cli-linux-x64.zip

ctpanonymiser-v$(SMIV).zip:
wget https://github.com/SMI/SmiServices/releases/download/v$(SMIV)/ctpanonymiser-v$(SMIV).zip
wget -q https://github.com/SMI/SmiServices/releases/download/v$(SMIV)/ctpanonymiser-v$(SMIV).zip

ctpanonymiser-1.0.0/CTPAnonymiser-portable-1.0.0.jar: ctpanonymiser-v$(SMIV).zip
[ -e $@ ] || unzip -DD $<

smi-nerd-v$(SMIV).jar:
wget https://github.com/SMI/SmiServices/releases/download/v$(SMIV)/smi-nerd-v$(SMIV).jar
wget -q https://github.com/SMI/SmiServices/releases/download/v$(SMIV)/smi-nerd-v$(SMIV).jar

ctp-whitelist.script:
wget https://raw.githubusercontent.com/SMI/SmiServices/v$(SMIV)/data/ctp/ctp-whitelist.script
wget -q https://raw.githubusercontent.com/SMI/SmiServices/v$(SMIV)/data/ctp/ctp-whitelist.script

smiinit: smiinit.cpp yaml-cpp/build/libyaml-cpp.a
ifeq ($(UNAME), Darwin)
Expand Down