From b73d514a8d89756d1a9f959dd15a8c61c524e84f Mon Sep 17 00:00:00 2001
From: vkt1414 <vthiriveedhi@mgh.harvard.edu>
Date: Wed, 20 Sep 2023 08:13:46 -0400
Subject: [PATCH] Updated gh references from prsnl acc to IDC

---
 Terra/TotalSegmentator/splitWorkflow/oneVM.wdl   |  4 ++--
 Terra/TotalSegmentator/splitWorkflow/threeVM.wdl | 12 ++++++------
 Terra/TotalSegmentator/splitWorkflow/twoVM.wdl   |  8 ++++----
 3 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/Terra/TotalSegmentator/splitWorkflow/oneVM.wdl b/Terra/TotalSegmentator/splitWorkflow/oneVM.wdl
index 656e8c2..97bfa27 100644
--- a/Terra/TotalSegmentator/splitWorkflow/oneVM.wdl
+++ b/Terra/TotalSegmentator/splitWorkflow/oneVM.wdl
@@ -11,7 +11,7 @@ workflow TotalSegmentator {
    String dicomToNiftiConverterTool
 
    #Docker Images for each task
-   String totalSegmentatorDocker = "vamsithiriveedhi/totalsegmentator:end_to_end_v1" 
+   String totalSegmentatorDocker = "imagingdatacommons/totalsegmentator:end_to_end_v1" 
 
    #Preemptible retries
    Int totalSegmentatorPreemptibleTries = 3
@@ -83,7 +83,7 @@ task totalSegmentatorEndToEnd{
 
  }
  command {
-   wget https://raw.githubusercontent.com/vkt1414/Cloud-Resources-Workflows/main/Notebooks/Totalsegmentator/endToEndTotalSegmentatorNotebook.ipynb
+   wget https://raw.githubusercontent.com/ImagingDataCommons/Cloud-Resources-Workflows/main/Notebooks/Totalsegmentator/endToEndTotalSegmentatorNotebook.ipynb
    set -e
    papermill -p csvFilePath ~{seriesInstanceS5cmdUrls} -p converterType ~{dicomToNiftiConverterTool}  endToEndTotalSegmentatorNotebook.ipynb endToEndTotalSegmentatorOutputJupyterNotebook.ipynb || (>&2 echo "Killed" && exit 1)
  }
diff --git a/Terra/TotalSegmentator/splitWorkflow/threeVM.wdl b/Terra/TotalSegmentator/splitWorkflow/threeVM.wdl
index ebdf6e4..5a6f88d 100644
--- a/Terra/TotalSegmentator/splitWorkflow/threeVM.wdl
+++ b/Terra/TotalSegmentator/splitWorkflow/threeVM.wdl
@@ -11,9 +11,9 @@ workflow TotalSegmentator {
    String dicomToNiftiConverterTool
 
    #Docker Images for each task
-   String downloadDicomAndConvertDocker = "vamsithiriveedhi/totalsegmentator:task1_v1"
-   String inferenceTotalSegmentatorDocker = "vamsithiriveedhi/totalsegmentator:task2_v3"
-   String dicomsegAndRadiomicsSR_Docker = "vamsithiriveedhi/totalsegmentator:task3_v3"
+   String downloadDicomAndConvertDocker = "imagingdatacommons/totalsegmentator:task1_v1"
+   String inferenceTotalSegmentatorDocker = "imagingdatacommons/totalsegmentator:task2_v3"
+   String dicomsegAndRadiomicsSR_Docker = "imagingdatacommons/totalsegmentator:task3_v3"
 
    #Preemptible retries
    Int downloadAndConvertPreemptibleTries = 3
@@ -119,7 +119,7 @@ task downloadAndConvert {
     String downloadAndConvertCpuFamily
  }
  command {
-   wget https://raw.githubusercontent.com/vkt1414/Cloud-Resources-Workflows/main/Notebooks/Totalsegmentator/downloadDicomAndConvertNotebook.ipynb
+   wget https://raw.githubusercontent.com/ImagingDataCommons/Cloud-Resources-Workflows/main/Notebooks/Totalsegmentator/downloadDicomAndConvertNotebook.ipynb
    set -e
    papermill -p converterType ~{dicomToNiftiConverterTool} -p csvFilePath ~{seriesInstanceS5cmdUrls} downloadDicomAndConvertNotebook.ipynb downloadAndConvertOutputJupyterNotebook.ipynb 
  }
@@ -163,7 +163,7 @@ task inferenceTotalSegmentator {
  }
 
  command {
-   wget https://raw.githubusercontent.com/vkt1414/Cloud-Resources-Workflows/main/Notebooks/Totalsegmentator/inferenceTotalSegmentatorNotebook.ipynb
+   wget https://raw.githubusercontent.com/ImagingDataCommons/Cloud-Resources-Workflows/main/Notebooks/Totalsegmentator/inferenceTotalSegmentatorNotebook.ipynb
    set -e
    papermill -p converterType ~{dicomToNiftiConverterTool}  -p niftiFilePath ~{NiftiFiles} inferenceTotalSegmentatorNotebook.ipynb inferenceOutputJupyterNotebook.ipynb
  }
@@ -206,7 +206,7 @@ task dicomsegAndRadiomicsSR{
     File inferenceZipFile
  }
  command {
-   wget https://raw.githubusercontent.com/vkt1414/Cloud-Resources-Workflows/main/Notebooks/Totalsegmentator/dicomsegAndRadiomicsSR_Notebook.ipynb
+   wget https://raw.githubusercontent.com/ImagingDataCommons/Cloud-Resources-Workflows/main/Notebooks/Totalsegmentator/dicomsegAndRadiomicsSR_Notebook.ipynb
    set -e
    papermill -p csvFilePath ~{seriesInstanceS5cmdUrls} -p inferenceNiftiFilePath ~{inferenceZipFile}  dicomsegAndRadiomicsSR_Notebook.ipynb dicomsegAndRadiomicsSR_OutputJupyterNotebook.ipynb || (>&2 echo "Killed" && exit 1)
  }
diff --git a/Terra/TotalSegmentator/splitWorkflow/twoVM.wdl b/Terra/TotalSegmentator/splitWorkflow/twoVM.wdl
index ceee6b5..dc644d2 100644
--- a/Terra/TotalSegmentator/splitWorkflow/twoVM.wdl
+++ b/Terra/TotalSegmentator/splitWorkflow/twoVM.wdl
@@ -11,8 +11,8 @@ workflow TotalSegmentator {
    String dicomToNiftiConverterTool
 
    #Docker Images for each task
-   String downloadDicomAndConvertAndInferenceTotalSegmentatorDocker = "vamsithiriveedhi/totalsegmentator:task1and2_v4"
-   String dicomsegAndRadiomicsSR_Docker = "vamsithiriveedhi/totalsegmentator:task3_v4"
+   String downloadDicomAndConvertAndInferenceTotalSegmentatorDocker = "imagingdatacommons/totalsegmentator:task1and2_v4"
+   String dicomsegAndRadiomicsSR_Docker = "imagingdatacommons/totalsegmentator:task3_v4"
 
    #Preemptible retries
 
@@ -106,7 +106,7 @@ task downloadDicomAndConvertAndInferenceTotalSegmentator{
  }
 
  command {
-   wget https://raw.githubusercontent.com/vkt1414/Cloud-Resources-Workflows/main/Notebooks/Totalsegmentator/downloadDicomAndConvertAndInferenceTotalSegmentatorNotebook.ipynb
+   wget https://raw.githubusercontent.com/ImagingDataCommons/Cloud-Resources-Workflows/main/Notebooks/Totalsegmentator/downloadDicomAndConvertAndInferenceTotalSegmentatorNotebook.ipynb
    set -e
    papermill -p converterType ~{dicomToNiftiConverterTool}  -p csvFilePath ~{seriesInstanceS5cmdUrls} downloadDicomAndConvertAndInferenceTotalSegmentatorNotebook.ipynb downloadDicomAndConvertAndInferenceTotalSegmentatorOutputJupyterNotebook.ipynb
  }
@@ -150,7 +150,7 @@ task dicomsegAndRadiomicsSR{
     File inferenceZipFile
  }
  command {
-   wget https://raw.githubusercontent.com/vkt1414/Cloud-Resources-Workflows/main/Notebooks/Totalsegmentator/dicomsegAndRadiomicsSR_Notebook.ipynb
+   wget https://raw.githubusercontent.com/ImagingDataCommons/Cloud-Resources-Workflows/main/Notebooks/Totalsegmentator/dicomsegAndRadiomicsSR_Notebook.ipynb
    
    set -o xtrace
    # For any command failures in the rest of this script, return the error.