From e7a9acec9b35e86e85740aef636f4729a6a23944 Mon Sep 17 00:00:00 2001 From: Ronak Shah Date: Mon, 17 Jun 2024 23:52:45 -0400 Subject: [PATCH 1/8] Updates for Biometrics and Genral Parse Stat --- cwl-commandlinetools | 2 +- cwl_subworkflows | 2 +- nucleo_aggregate_visualize.cwl | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/cwl-commandlinetools b/cwl-commandlinetools index cf66cd5..d61c917 160000 --- a/cwl-commandlinetools +++ b/cwl-commandlinetools @@ -1 +1 @@ -Subproject commit cf66cd5f0269b5a51adceda97c4f5cf046b31133 +Subproject commit d61c9170bf84b35368eadfb3a522c6d143b93b55 diff --git a/cwl_subworkflows b/cwl_subworkflows index d9bbc74..39dafc3 160000 --- a/cwl_subworkflows +++ b/cwl_subworkflows @@ -1 +1 @@ -Subproject commit d9bbc743d68baae2a0372358abaf82e465976b88 +Subproject commit 39dafc393cf6a7b7bea6f8cff12071e79ab0af06 diff --git a/nucleo_aggregate_visualize.cwl b/nucleo_aggregate_visualize.cwl index 0a1213a..3bb681e 100644 --- a/nucleo_aggregate_visualize.cwl +++ b/nucleo_aggregate_visualize.cwl @@ -178,7 +178,7 @@ steps: source: config out: - id: aggregate_parsed_stats - run: cwl-commandlinetools/cci_utils/0.3.1/general_stats_parse.cwl + run: cwl-commandlinetools/cci_utils/0.3.2/general_stats_parse.cwl label: general_stats_parse 'sbg:x': 870.1131591796875 'sbg:y': 520.0625 From a3ac58468b552a187b3e9e1f2c37a8093c4bcae6 Mon Sep 17 00:00:00 2001 From: Ronak Shah Date: Mon, 17 Jun 2024 23:55:26 -0400 Subject: [PATCH 2/8] Update test_nucleo_qc.yaml --- .github/workflows/test_nucleo_qc.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/test_nucleo_qc.yaml b/.github/workflows/test_nucleo_qc.yaml index 9d3f56d..78d9d77 100644 --- a/.github/workflows/test_nucleo_qc.yaml +++ b/.github/workflows/test_nucleo_qc.yaml @@ -22,12 +22,12 @@ jobs: python-version: [3.10.8] steps: - name: Checkout - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: ref: ${{ github.head_ref }} submodules: recursive - name: Set up Python - uses: actions/setup-python@v3 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - name : Set up NodeJS From 8c3259bc01829ddc66ed859058c54c74ced52711 Mon Sep 17 00:00:00 2001 From: Ronak Shah Date: Tue, 18 Jun 2024 00:19:50 -0400 Subject: [PATCH 3/8] Update Sub-modules --- cwl-commandlinetools | 2 +- cwl_subworkflows | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/cwl-commandlinetools b/cwl-commandlinetools index d61c917..24accf3 160000 --- a/cwl-commandlinetools +++ b/cwl-commandlinetools @@ -1 +1 @@ -Subproject commit d61c9170bf84b35368eadfb3a522c6d143b93b55 +Subproject commit 24accf3747b8698a66b3ec262dc44f9a18231e8d diff --git a/cwl_subworkflows b/cwl_subworkflows index 39dafc3..275a628 160000 --- a/cwl_subworkflows +++ b/cwl_subworkflows @@ -1 +1 @@ -Subproject commit 39dafc393cf6a7b7bea6f8cff12071e79ab0af06 +Subproject commit 275a62872353456a2e39ce0605bc90dc101cfd6e From 6be6e096be026c6b420921813b8e8db03ca65661 Mon Sep 17 00:00:00 2001 From: Ronak Shah Date: Tue, 18 Jun 2024 00:29:03 -0400 Subject: [PATCH 4/8] Update install_data.sh --- install_data.sh | 21 +++++++++++++++------ 1 file changed, 15 insertions(+), 6 deletions(-) diff --git a/install_data.sh b/install_data.sh index 70b3580..96a5413 100644 --- a/install_data.sh +++ b/install_data.sh @@ -4,15 +4,24 @@ # Test data is hosted on Google Drive at: # https://drive.google.com/u/0/uc?id=1i1GA4AZhuw6Si8RmPFPJxmejIUt3ZZ1D +fileid=1i1GA4AZhuw6Si8RmPFPJxmejIUt3ZZ1D + filename=test_nucleo_qc.tar.gz -# Note: Drive seems to change somewhat frequently how it handles endpoints for large files -# add confirm parameter to link for this to work -# previously used another wget scheme and gdown -wget -O $filename "https://drive.google.com/u/0/uc?id=1i1GA4AZhuw6Si8RmPFPJxmejIUt3ZZ1D&export=download&confirm=t" +foldername=test_nucleo_qc + +# Skip if already have test data +[[ -f $filename ]] && exit 0 +[[ -d $foldername ]] && exit 0 + +curl -c ./cookie -s -k -L "https://drive.google.com/uc?export=download&id=$fileid" > /dev/null + +curl -k -Lb ./cookie "https://drive.google.com/uc?export=download&confirm=`awk '/download/ {print $NF}' ./cookie`&id=${fileid}" -o ${filename} + # Suppress linux warnings for MacOS tar.gz files if [[ "$OSTYPE" == "linux-gnu" ]]; then - tar --warning=no-unknown-keyword -xzvf $filename -C tests/inputs/ + tar --warning=no-unknown-keyword -xzvf $filename elif [[ "$OSTYPE" == "darwin"* ]]; then - tar -xzvf $filename -C tests/inputs/ + tar -xzvf $filename fi + rm $filename \ No newline at end of file From fd86faa462a503d839a8f64837daca3d7b8045f0 Mon Sep 17 00:00:00 2001 From: Ronak Shah Date: Tue, 18 Jun 2024 01:52:18 -0400 Subject: [PATCH 5/8] Update install_data.sh --- install_data.sh | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/install_data.sh b/install_data.sh index 96a5413..ab1e884 100644 --- a/install_data.sh +++ b/install_data.sh @@ -13,9 +13,10 @@ foldername=test_nucleo_qc [[ -f $filename ]] && exit 0 [[ -d $foldername ]] && exit 0 -curl -c ./cookie -s -k -L "https://drive.google.com/uc?export=download&id=$fileid" > /dev/null +#curl -c ./cookie -s -k -L "https://drive.google.com/uc?export=download&id=$fileid" > /dev/null +#curl -k -Lb ./cookie "https://drive.google.com/uc?export=download&confirm=`awk '/download/ {print $NF}' ./cookie`&id=${fileid}" -o ${filename} -curl -k -Lb ./cookie "https://drive.google.com/uc?export=download&confirm=`awk '/download/ {print $NF}' ./cookie`&id=${fileid}" -o ${filename} +curl -L "https://drive.usercontent.google.com/download?id=${fileid}&confirm=xxx" -o ${filename} # Suppress linux warnings for MacOS tar.gz files if [[ "$OSTYPE" == "linux-gnu" ]]; then From 288e93a661b730741e2d6bae491360059f740935 Mon Sep 17 00:00:00 2001 From: Ronak Shah Date: Tue, 18 Jun 2024 02:10:42 -0400 Subject: [PATCH 6/8] Update install_data.sh --- install_data.sh | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/install_data.sh b/install_data.sh index ab1e884..f8f8975 100644 --- a/install_data.sh +++ b/install_data.sh @@ -1,13 +1,12 @@ #!/usr/bin/env bash - # Test data is hosted on Google Drive at: # https://drive.google.com/u/0/uc?id=1i1GA4AZhuw6Si8RmPFPJxmejIUt3ZZ1D fileid=1i1GA4AZhuw6Si8RmPFPJxmejIUt3ZZ1D filename=test_nucleo_qc.tar.gz -foldername=test_nucleo_qc +foldername=test_data # Skip if already have test data [[ -f $filename ]] && exit 0 @@ -15,7 +14,7 @@ foldername=test_nucleo_qc #curl -c ./cookie -s -k -L "https://drive.google.com/uc?export=download&id=$fileid" > /dev/null #curl -k -Lb ./cookie "https://drive.google.com/uc?export=download&confirm=`awk '/download/ {print $NF}' ./cookie`&id=${fileid}" -o ${filename} - +cd tests/inputs || exit curl -L "https://drive.usercontent.google.com/download?id=${fileid}&confirm=xxx" -o ${filename} # Suppress linux warnings for MacOS tar.gz files @@ -25,4 +24,4 @@ elif [[ "$OSTYPE" == "darwin"* ]]; then tar -xzvf $filename fi -rm $filename \ No newline at end of file +rm $filename From 24915e4116ae2236957a845bf8910b2c82f67cd6 Mon Sep 17 00:00:00 2001 From: Ronak Shah Date: Tue, 27 Aug 2024 10:51:23 -0400 Subject: [PATCH 7/8] Updating submodule to release branch --- cwl-commandlinetools | 2 +- cwl_subworkflows | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/cwl-commandlinetools b/cwl-commandlinetools index 24accf3..7275e19 160000 --- a/cwl-commandlinetools +++ b/cwl-commandlinetools @@ -1 +1 @@ -Subproject commit 24accf3747b8698a66b3ec262dc44f9a18231e8d +Subproject commit 7275e19ae7e64331fbd3c4489e25cf0b2dcf124b diff --git a/cwl_subworkflows b/cwl_subworkflows index 275a628..de06777 160000 --- a/cwl_subworkflows +++ b/cwl_subworkflows @@ -1 +1 @@ -Subproject commit 275a62872353456a2e39ce0605bc90dc101cfd6e +Subproject commit de0677791d883829f8e7d930b8b0ef0f4d687b79 From 9bb248dee694871ebedbd80ceb27983c31afc28f Mon Sep 17 00:00:00 2001 From: Ronak Shah Date: Tue, 27 Aug 2024 10:53:08 -0400 Subject: [PATCH 8/8] Updating submodule to release branch --- cwl-commandlinetools | 2 +- cwl_subworkflows | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/cwl-commandlinetools b/cwl-commandlinetools index 7275e19..082f3a3 160000 --- a/cwl-commandlinetools +++ b/cwl-commandlinetools @@ -1 +1 @@ -Subproject commit 7275e19ae7e64331fbd3c4489e25cf0b2dcf124b +Subproject commit 082f3a3177a845acfd717ad1783ae5b6a668095e diff --git a/cwl_subworkflows b/cwl_subworkflows index de06777..aeb7fec 160000 --- a/cwl_subworkflows +++ b/cwl_subworkflows @@ -1 +1 @@ -Subproject commit de0677791d883829f8e7d930b8b0ef0f4d687b79 +Subproject commit aeb7fec838db8abdfbdae7fbc617e2dd6bc5ae9c