From 187a81aed068191825f2079e59e1ff3560169c9c Mon Sep 17 00:00:00 2001 From: LizBaldo Date: Wed, 28 Aug 2024 10:26:25 -0400 Subject: [PATCH 1/4] chamge permission so GHA runner can execute script --- build_all.sh | 0 1 file changed, 0 insertions(+), 0 deletions(-) mode change 100644 => 100755 build_all.sh diff --git a/build_all.sh b/build_all.sh old mode 100644 new mode 100755 From 44cb066d9410b7986a1f5252a583791f2fa87231 Mon Sep 17 00:00:00 2001 From: LizBaldo Date: Wed, 28 Aug 2024 10:58:49 -0400 Subject: [PATCH 2/4] make sure arguments are passed to bash script --- build_all.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/build_all.sh b/build_all.sh index db22942d..16a96043 100755 --- a/build_all.sh +++ b/build_all.sh @@ -17,8 +17,8 @@ images=(terra-jupyter-base terra-jupyter-python terra-jupyter-r terra-jupyter-ga # Loop over each image to build in the correct order for image in images; do # Call build.sh with the image to build - echo 'Building and publishing the following image to GCR: $image' - ./build.sh "$image" "true" + echo "Building and publishing the following image to GCR: $image" + ./build.sh $image true done # Once all images have been built, generate and push the 'terra-docker-versions-new' doc From 759f2b34bdef68d03c9ea5034b8f6baaf4e16a01 Mon Sep 17 00:00:00 2001 From: LizBaldo Date: Wed, 28 Aug 2024 11:09:22 -0400 Subject: [PATCH 3/4] fixed the bash syntax --- build_all.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/build_all.sh b/build_all.sh index 16a96043..1faa8d6b 100755 --- a/build_all.sh +++ b/build_all.sh @@ -12,10 +12,10 @@ # 7- terra-jupyter-bioconductor # 8- terra-rstudio-aou # 9- wondershaper -images=(terra-jupyter-base terra-jupyter-python terra-jupyter-r terra-jupyter-gatk terra-jupyter-hail terra-jupyter-aou terra-jupyter-bioconductor terra-rstudio-aou wondershaper) +images=("terra-jupyter-base" "terra-jupyter-python" "terra-jupyter-r" "terra-jupyter-gatk" "terra-jupyter-hail" "terra-jupyter-aou" "terra-jupyter-bioconductor" "terra-rstudio-aou" "wondershaper") # Loop over each image to build in the correct order -for image in images; do +for image in "${images[@]}"; do # Call build.sh with the image to build echo "Building and publishing the following image to GCR: $image" ./build.sh $image true From e86a2e3b34ffbeec00e0354f8963faf82ec6a826 Mon Sep 17 00:00:00 2001 From: LizBaldo Date: Wed, 28 Aug 2024 11:17:35 -0400 Subject: [PATCH 4/4] filter behavior returns an iterative not a list in python 3 --- scripts/generate_version_docs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/generate_version_docs.py b/scripts/generate_version_docs.py index da95f900..a8957501 100755 --- a/scripts/generate_version_docs.py +++ b/scripts/generate_version_docs.py @@ -29,7 +29,7 @@ def generate_docs(): print("current versions detected: " + str(remote_versions)) - legacy_gatk_doc = filter(lambda remote_doc: remote_doc["id"] == "terra-jupyter-gatk_legacy", remote_docs)[0] + legacy_gatk_doc = list(filter(lambda remote_doc: remote_doc["id"] == "terra-jupyter-gatk_legacy", remote_docs))[0] legacy_bioconductor_doc = utils.read_json_file(static_config_location)[0] # hard coding this until next bioconductor release (~06/2022) for image_config in image_configs: