notes-slide-upload-log

Test Pathology Cloud

(11/22/23)

export PROJECT_ID=gcp-pathology-poc1
gcloud init
gcloud auth login
gcloud auth application-default login # for terraform
gcloud config set project ${PROJECT_ID?}

Slides Uploaded

gsutil cp \
gs://dpas-external-assets-bucket/transformation/sample_metadata.csv \
gs://${PROJECT_ID?}-transformation-input-metadata/

gsutil cp \
/mnt/d/DataSets/JP2K-33003-2.svs \
gs://${PROJECT_ID?}-transformation-input-images/GO-1694041298474-1-A-0_JP2K-33003-2.svs

- using local storage: /mnt/d/DataSets/gcp-path-samples
gsutil cp \
/mnt/d/DataSets/gcp-path-samples/Nano-IHC1.csv \
gs://${PROJECT_ID?}-transformation-input-metadata/

gsutil cp \
/mnt/d/DataSets/gcp-path-samples/Nano-IHC1.ndpi \
gs://${PROJECT_ID?}-transformation-input-images/GS-123456-1-A-0_Nano-IHC1.ndpi

- DICOM Image
- IHC-PR-DICOM-01
gsutil cp \
/mnt/d/DataSets/gcp-path-samples/IHC-PR-DICOM-01/IHC-PR-DICOM-01.csv \
gs://${PROJECT_ID?}-transformation-input-metadata/

gsutil cp \
/mnt/d/DataSets/gcp-path-samples/IHC-PR-DICOM-01/IHC-PR-DICOM-01.zip \
gs://gcp-pathology-poc1-transformation-input-images/GS-123457-DCM-1_IHC-PR-DICOM-01.zip

- IHC-PR-DICOM-02
gsutil cp \
/mnt/d/DataSets/gcp-path-samples/IHC-PR-DICOM-02/IHC-PR-DICOM-02.csv \
gs://${PROJECT_ID?}-transformation-input-metadata/

gsutil cp \
/mnt/d/DataSets/gcp-path-samples/IHC-PR-DICOM-02/IHC-PR-DICOM-02_level-0.dcm \
gs://gcp-pathology-poc1-transformation-input-images/GS-123458-PR-DCM-2-A_IHC-PR-DICOM-02_level-0.dcm

gsutil cp \
/mnt/d/DataSets/gcp-path-samples/IHC-PR-DICOM-02/IHC-PR-DICOM-02_macro.dcm \
gs://gcp-pathology-poc1-transformation-input-images/GS-123458-PR-DCM-2-A_IHC-PR-DICOM-02_macro.dcm

- M01KBB05R-1322
gsutil cp \
/mnt/d/DataSets/gcp-path-samples/M01KBB05R-1322/M01KBB05R-1322.csv \
gs://${PROJECT_ID?}-transformation-input-metadata/

gsutil cp \
/mnt/d/DataSets/gcp-path-samples/M01KBB05R-1322/M01KBB05R-1322_level-0.dcm \
gs://gcp-pathology-poc1-transformation-input-images/GS-123456-1-A-1_M01KBB05R-1322_level-0.dcm

#### 11/28/2023
gsutil cp \
/mnt/d/DataSets/gcp-path-samples/IHCBio-H01CBC105P-207637/H01CBC105P-207637.csv \
gs://gcp-pathology-poc1-transformation-input-metadata/

gsutil cp \
/mnt/d/DataSets/gcp-path-samples/IHCBio-H01CBC105P-207637/H01CBC105P-207637_level-0.dcm \
gs://gcp-pathology-poc1-transformation-input-images/Bio-H01CBC105P-207637_level-0.dcm

#### 11/30/2023
gsutil cp \
/mnt/d/DataSets/gcp-path-samples/PR-M01KBB05R-1319/PR-M01KBB05R-1319.csv \
gs://gcp-pathology-poc1-transformation-input-metadata/

gsutil cp \
/mnt/d/DataSets/gcp-path-samples/PR-M01KBB05R-1319/PR-M01KBB05R-1319.zip \
gs://gcp-pathology-poc1-transformation-input-images/PR-M01KBB05R-1319_PR-M01KBB05R-1319.zip

gsutil cp \
/mnt/d/DataSets/gcp-path-samples/PR-M01KBB05R-1319/M01KBB05R-1319_level-0.dcm \
gs://gcp-pathology-poc1-transformation-input-images/PR-M01KBB05R-1319_M01KBB05R-1319_level-0.dcm

#### 12/05/2023
- NW Roche Samples
gsutil cp \
/mnt/d/DataSets/Northwell/Roche-Images/DP200-40x/NW_162CB793.csv \
gs://gcp-pathology-poc1-transformation-input-metadata/

gsutil cp \
/mnt/d/DataSets/Northwell/Roche-Images/DP200-40x//NW_162CB793.zip \
gs://gcp-pathology-poc1-transformation-input-images/NW_162CB793_NW_162CB793.zip

gsutil cp \
/mnt/d/DataSets/Northwell/Roche-Images/DP200-40x/NW_BIF_162CB794.csv \
gs://gcp-pathology-poc1-transformation-input-metadata/

gsutil cp \
/mnt/d/DataSets/Northwell/Roche-Images/DP200-40x/NW_BIF_162CB794.bif \
gs://gcp-pathology-poc1-transformation-input-images/NW_BIF_162CB794_NW_BIF_162CB794.bif

#### 01/02/2024
- GS TransformationSvc Samples
GS-TransSvc-00001A_gt450-01.dcm
gsutil cp \
/mnt/d/DataSets/gcp-path-samples/GS-TransSvc-00001A.csv \
gs://gcp-pathology-poc1-transformation-input-metadata/

gsutil cp \
/mnt/d/DataSets/gcp-path-samples/GS-TransSvc-00001A.dcm \
gs://gcp-pathology-poc1-transformation-input-images/GS-TransSvc-00001A.dcm

#### 01/03/2024
- GS TransformationSvc Samples
GS-TransSvc-00001A_gt450-01.dcm
gsutil cp \
/mnt/d/DataSets/gcp-path-samples/GS-TransSvc-00003A.csv \
gs://gcp-pathology-poc1-transformation-input-metadata/

gsutil cp \
/mnt/d/DataSets/gcp-path-samples/GS-TransSvc-00003A.dcm \
gs://gcp-pathology-poc1-transformation-input-images/GS-TransSvc-00003A.dcm

#### 05/21/2024
- JPG Transform Test
gsutil cp \
/mnt/d/DataSets/gcp-path-samples/OpenFlexure01.csv \
gs://gcp-pathology-poc1-transformation-input-metadata/

gsutil cp \
/mnt/d/Downloads/OpenFlexureScannerUploads/OpenFlexureScannerUploads/36.jpg \
gs://gcp-pathology-poc1-transformation-input-images/OpenFlexure01.jpg
- flat image failed to open

gsutil cp \
/mnt/d/Downloads/OpenFlexureScannerUploads/OpenFlexureScannerUploads/26.jpg \
gs://gcp-pathology-poc1-transformation-input-images/OpenFlexure01.jpg
- flat image failed to open

gsutil cp \
/mnt/d/Downloads/OpenFlexureScannerUploads/OpenFlexureScannerUploads/0.jpg \
gs://gcp-pathology-poc1-transformation-input-images/OpenFlexure01.jpg
- flat image failed to open

gsutil cp \
/mnt/d/Downloads/OpenFlexureScannerUploads/OpenFlexureScannerUploads/stitched.jpg \
gs://gcp-pathology-poc1-transformation-input-images/OpenFlexure01.jpg
- this image uploaded and was transformed to DICOM; but can't find BigQuery metadata

### 05/22/2024
#### Metadata
gsutil cp \
/mnt/d/DataSets/gcp-path-samples/OpenFlexure02.csv \
gs://gcp-pathology-poc1-transformation-input-metadata/

#### Image Upload to Bucket
gsutil cp \
/mnt/d/Downloads/OpenFlexureScannerUploads/OpenFlexureScannerUploads/stitched.jpg \
gs://gcp-pathology-poc1-transformation-input-images/OpenFlexure02.jpg
- this image uploaded and was transformed to DICOM; but can't find BigQuery metadata

#### Metadata
gsutil cp \
/mnt/d/DataSets/gcp-path-samples/JP2K-33003-2.csv \
gs://gcp-pathology-poc1-transformation-input-metadata/

#### Image Upload to Bucket
gsutil cp \
/mnt/d/DataSets/gcp-path-samples/JP2K-33003-2.svs \
gs://gcp-pathology-poc1-transformation-input-images/JP2K-33003-3.svs

#### OPenFlexure TIF Test1
gsutil cp \
/mnt/d/DataSets/gcp-path-samples/OpenFlexure03-TIF.csv \
gs://gcp-pathology-poc1-transformation-input-metadata/

gsutil cp \
/mnt/d/Downloads/OpenFlexureScannerUploads/OpenFlexureScannerUploads/lungTP.ome.tiff \
gs://gcp-pathology-poc1-transformation-input-images/OpenFlexure03-TIF.tiff
- flat image failed to open

#### OpenFlexure_pap_smear_57_stitched_JPG
gsutil cp \
/mnt/d/DataSets/gcp-path-samples/OpenFlexure_pap_smear_57_stitched_JPG.csv \
gs://gcp-pathology-poc1-transformation-input-metadata/

gsutil cp \
/mnt/d/DataSets/OpenFlexureScannerUploads/OpenFlexureScannerUploads/JK_OFM/pap_smear_57_stitched.jpg \
gs://gcp-pathology-poc1-transformation-input-images/OpenFlexure-pap-smear-57-stitched.jpg
- flat image failed to open

Test Pathology Cloud​

(11/22/23)​

Slides Uploaded​

Test Pathology Cloud

(11/22/23)

Slides Uploaded