Merge pull request #7 from ImagingDataCommons/iteration2

Updated gh references from prsnl acc to IDC
ImagingDataCommons · Sep 20, 2023 · 34c31df · 34c31df
2 parents a48f38a + b73d514
commit 34c31df
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Showing 3 changed files with 12 additions and 12 deletions.
diff --git 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
@@ -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
@@ -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.