fairdataihub · aaronm-2112 · Jul 14, 2025 · Jul 15, 2025 · Jul 15, 2025 · Jul 15, 2025
@@ -7,7 +7,7 @@ on:
       - main
       - staging
       - pre-staging
-      - folder-build
+      - sds3-demo
 
 jobs:
   deploy-on-linux:

@@ -7,7 +7,7 @@ on:
       - main
       - staging
       - pre-staging
-      - folder-build
+      - sds3-demo
 
 jobs:
   deploy-on-mac:

@@ -7,7 +7,7 @@ on:
       - main
       - staging
       - pre-staging
-      - folder-build
+      - sds3-demo
 
 jobs:
   deploy-on-windows:

diff --git a/SDS3-Dataset/README.md b/SDS3-Dataset/README.md
@@ -0,0 +1,9 @@
+# Sample Experimental Dataset
+
+This directory contains research data organized as follows:
+
+- 10 subjects (Subject01 through Subject10)
+- Each subject has 2 tissue samples
+- Each sample has 2 regions of interest (RegionA, RegionB)
+
+This dataset is designed for testing folder/file annotation workflows in SODA for SPARC.
diff --git a/SDS3-Dataset/dataset_description.xlsx b/SDS3-Dataset/dataset_description.xlsx
@@ -0,0 +1,41 @@
+Subject ID,Sample ID,Region,Collection Date
+Subject01,Tissue01,RegionA,2023-06-01
+Subject01,Tissue01,RegionB,2023-06-01
+Subject01,Tissue02,RegionA,2023-06-01
+Subject01,Tissue02,RegionB,2023-06-01
+Subject02,Tissue03,RegionA,2023-06-16
+Subject02,Tissue03,RegionB,2023-06-16
+Subject02,Tissue04,RegionA,2023-06-16
+Subject02,Tissue04,RegionB,2023-06-16
+Subject03,Tissue05,RegionA,2023-07-01
+Subject03,Tissue05,RegionB,2023-07-01
+Subject03,Tissue06,RegionA,2023-07-01
+Subject03,Tissue06,RegionB,2023-07-01
+Subject04,Tissue07,RegionA,2023-07-16
+Subject04,Tissue07,RegionB,2023-07-16
+Subject04,Tissue08,RegionA,2023-07-16
+Subject04,Tissue08,RegionB,2023-07-16
+Subject05,Tissue09,RegionA,2023-07-31
+Subject05,Tissue09,RegionB,2023-07-31
+Subject05,Tissue10,RegionA,2023-07-31
+Subject05,Tissue10,RegionB,2023-07-31
+Subject06,Tissue11,RegionA,2023-08-15
+Subject06,Tissue11,RegionB,2023-08-15
+Subject06,Tissue12,RegionA,2023-08-15
+Subject06,Tissue12,RegionB,2023-08-15
+Subject07,Tissue13,RegionA,2023-08-30
+Subject07,Tissue13,RegionB,2023-08-30
+Subject07,Tissue14,RegionA,2023-08-30
+Subject07,Tissue14,RegionB,2023-08-30
+Subject08,Tissue15,RegionA,2023-09-14
+Subject08,Tissue15,RegionB,2023-09-14
+Subject08,Tissue16,RegionA,2023-09-14
+Subject08,Tissue16,RegionB,2023-09-14
+Subject09,Tissue17,RegionA,2023-09-29
+Subject09,Tissue17,RegionB,2023-09-29
+Subject09,Tissue18,RegionA,2023-09-29
+Subject09,Tissue18,RegionB,2023-09-29
+Subject10,Tissue19,RegionA,2023-10-14
+Subject10,Tissue19,RegionB,2023-10-14
+Subject10,Tissue20,RegionA,2023-10-14
+Subject10,Tissue20,RegionB,2023-10-14
diff --git a/SDS3-Dataset/experiment/Subject01/Tissue01/RegionA/image_data.jpg b/SDS3-Dataset/experiment/Subject01/Tissue01/RegionA/image_data.jpg
diff --git a/SDS3-Dataset/experiment/Subject01/Tissue01/RegionA/measurements.csv b/SDS3-Dataset/experiment/Subject01/Tissue01/RegionA/measurements.csv
@@ -0,0 +1,5 @@
+Time,Position,Measurement,Value
+1,RegionA,Temperature,37.52 °C
+2,RegionA,pH,7.49
+3,RegionA,Pressure,98.00 mmHg
+4,RegionA,Flow Rate,124.80 ml/min
diff --git a/SDS3-Dataset/experiment/Subject01/Tissue01/RegionA/metadata.txt b/SDS3-Dataset/experiment/Subject01/Tissue01/RegionA/metadata.txt
@@ -0,0 +1,6 @@
+Site ID: RegionA
+Related Subject: Subject01
+Related Sample: Tissue01
+Collection Date: 5/28/2025
+Anatomical Location: RegionA
+Coordinates: X:38, Y:25, Z:23
diff --git a/SDS3-Dataset/experiment/Subject01/Tissue01/RegionA/results/analysis_output.csv b/SDS3-Dataset/experiment/Subject01/Tissue01/RegionA/results/analysis_output.csv
@@ -0,0 +1,4 @@
+Parameter,Value,Unit
+Temperature,38.83,°C
+pH,7.28,pH
+Volume,4.04,mL
diff --git a/SDS3-Dataset/experiment/Subject01/Tissue01/RegionA/results/notes.txt b/SDS3-Dataset/experiment/Subject01/Tissue01/RegionA/results/notes.txt
@@ -0,0 +1,4 @@
+Analysis performed: 5/28/2025
+Analyst: J. Researcher
+Results: Normal parameters detected
+Quality check: Passed
diff --git a/SDS3-Dataset/experiment/Subject01/Tissue01/RegionA/run_1.txt b/SDS3-Dataset/experiment/Subject01/Tissue01/RegionA/run_1.txt
@@ -0,0 +1,5 @@
+# Raw RegionA data - Run 1
+Sample ID: Subject01
+Date: 5/28/2025
+Values: 50.87, 33.00, 44.64, 52.99, 10.64
+Notes: Standard collection protocol followed
diff --git a/SDS3-Dataset/experiment/Subject01/Tissue01/RegionA/site_notes.txt b/SDS3-Dataset/experiment/Subject01/Tissue01/RegionA/site_notes.txt
@@ -0,0 +1,10 @@
+Site: RegionA
+Subject: Subject01
+Sample: Tissue01
+Date: 2023-06-01
+Researcher: Dr. M. Researcher
+
+Site-specific Notes:
+- Measurements taken according to SOP-onA
+- Site appears healthy and normal
+- Processing completed successfully
diff --git a/SDS3-Dataset/experiment/Subject01/Tissue01/RegionB/image_data.jpg b/SDS3-Dataset/experiment/Subject01/Tissue01/RegionB/image_data.jpg
diff --git a/SDS3-Dataset/experiment/Subject01/Tissue01/RegionB/measurements.csv b/SDS3-Dataset/experiment/Subject01/Tissue01/RegionB/measurements.csv
@@ -0,0 +1,5 @@
+Time,Position,Measurement,Value
+1,RegionB,Temperature,36.16 °C
+2,RegionB,pH,7.82
+3,RegionB,Pressure,94.42 mmHg
+4,RegionB,Flow Rate,145.80 ml/min
diff --git a/SDS3-Dataset/experiment/Subject01/Tissue01/RegionB/metadata.txt b/SDS3-Dataset/experiment/Subject01/Tissue01/RegionB/metadata.txt
@@ -0,0 +1,6 @@
+Site ID: RegionB
+Related Subject: Subject01
+Related Sample: Tissue01
+Collection Date: 5/28/2025
+Anatomical Location: RegionB
+Coordinates: X:11, Y:12, Z:10
diff --git a/SDS3-Dataset/experiment/Subject01/Tissue01/RegionB/results/analysis_output.csv b/SDS3-Dataset/experiment/Subject01/Tissue01/RegionB/results/analysis_output.csv
@@ -0,0 +1,4 @@
+Parameter,Value,Unit
+Temperature,36.26,°C
+pH,7.47,pH
+Volume,5.22,mL
diff --git a/SDS3-Dataset/experiment/Subject01/Tissue01/RegionB/results/notes.txt b/SDS3-Dataset/experiment/Subject01/Tissue01/RegionB/results/notes.txt
@@ -0,0 +1,4 @@
+Analysis performed: 5/28/2025
+Analyst: J. Researcher
+Results: Normal parameters detected
+Quality check: Passed
diff --git a/SDS3-Dataset/experiment/Subject01/Tissue01/RegionB/run_1.txt b/SDS3-Dataset/experiment/Subject01/Tissue01/RegionB/run_1.txt
@@ -0,0 +1,5 @@
+# Raw RegionB data - Run 1
+Sample ID: Subject01
+Date: 5/28/2025
+Values: 23.68, 37.54, 43.30, 40.49, 39.22
+Notes: Standard collection protocol followed
diff --git a/SDS3-Dataset/experiment/Subject01/Tissue01/RegionB/site_notes.txt b/SDS3-Dataset/experiment/Subject01/Tissue01/RegionB/site_notes.txt
@@ -0,0 +1,10 @@
+Site: RegionB
+Subject: Subject01
+Sample: Tissue01
+Date: 2023-06-01
+Researcher: Dr. M. Researcher
+
+Site-specific Notes:
+- Measurements taken according to SOP-onB
+- Site appears healthy and normal
+- Processing completed successfully
diff --git a/SDS3-Dataset/experiment/Subject01/Tissue01/Tissue01_data.csv b/SDS3-Dataset/experiment/Subject01/Tissue01/Tissue01_data.csv
@@ -0,0 +1,2 @@
+Subject,Measurement Type,Value 1,Value 2,Value 3
+Subject01,Tissue01,19.58,20.51,14.29
diff --git a/SDS3-Dataset/experiment/Subject01/Tissue01/lab_notes.txt b/SDS3-Dataset/experiment/Subject01/Tissue01/lab_notes.txt
@@ -0,0 +1,12 @@
+Lab Notes - Tissue01 Sample
+Subject: Subject01
+Sample: Tissue01
+Date: 2023-06-01
+Collected by: J. Smith
+
+Processing Notes:
+- Sample processed according to protocol
+- Stored at -80°C (Freezer #2)
+- Quality check: Passed
+
+Observations: Sample appears normal with no visible contamination
diff --git a/SDS3-Dataset/experiment/Subject01/Tissue01/run_1.txt b/SDS3-Dataset/experiment/Subject01/Tissue01/run_1.txt
@@ -0,0 +1,5 @@
+# Raw Tissue01 data - Run 1
+Sample ID: Subject01
+Date: 5/28/2025
+Values: 10.30, 54.56, 29.53, 55.98, 49.34
+Notes: Standard collection protocol followed
diff --git a/SDS3-Dataset/experiment/Subject01/Tissue01/run_2.txt b/SDS3-Dataset/experiment/Subject01/Tissue01/run_2.txt
@@ -0,0 +1,5 @@
+# Raw Tissue01 data - Run 2
+Sample ID: Subject01
+Date: 5/28/2025
+Values: 23.46, 25.27, 20.26, 27.23, 16.06
+Notes: Standard collection protocol followed
diff --git a/SDS3-Dataset/experiment/Subject01/Tissue02/RegionA/image_data.jpg b/SDS3-Dataset/experiment/Subject01/Tissue02/RegionA/image_data.jpg
diff --git a/SDS3-Dataset/experiment/Subject01/Tissue02/RegionA/measurements.csv b/SDS3-Dataset/experiment/Subject01/Tissue02/RegionA/measurements.csv
@@ -0,0 +1,5 @@
+Time,Position,Measurement,Value
+1,RegionA,Temperature,35.55 °C
+2,RegionA,pH,7.23
+3,RegionA,Pressure,106.49 mmHg
+4,RegionA,Flow Rate,102.70 ml/min
diff --git a/SDS3-Dataset/experiment/Subject01/Tissue02/RegionA/metadata.txt b/SDS3-Dataset/experiment/Subject01/Tissue02/RegionA/metadata.txt
@@ -0,0 +1,6 @@
+Site ID: RegionA
+Related Subject: Subject01
+Related Sample: Tissue02
+Collection Date: 5/28/2025
+Anatomical Location: RegionA
+Coordinates: X:42, Y:38, Z:36
diff --git a/SDS3-Dataset/experiment/Subject01/Tissue02/RegionA/results/analysis_output.csv b/SDS3-Dataset/experiment/Subject01/Tissue02/RegionA/results/analysis_output.csv
@@ -0,0 +1,4 @@
+Parameter,Value,Unit
+Temperature,35.61,°C
+pH,7.88,pH
+Volume,5.46,mL
diff --git a/SDS3-Dataset/experiment/Subject01/Tissue02/RegionA/results/notes.txt b/SDS3-Dataset/experiment/Subject01/Tissue02/RegionA/results/notes.txt
@@ -0,0 +1,4 @@
+Analysis performed: 5/28/2025
+Analyst: J. Researcher
+Results: Normal parameters detected
+Quality check: Passed
diff --git a/SDS3-Dataset/experiment/Subject01/Tissue02/RegionA/run_1.txt b/SDS3-Dataset/experiment/Subject01/Tissue02/RegionA/run_1.txt
@@ -0,0 +1,5 @@
+# Raw RegionA data - Run 1
+Sample ID: Subject01
+Date: 5/28/2025
+Values: 38.73, 33.40, 54.07, 10.75, 10.84
+Notes: Standard collection protocol followed
diff --git a/SDS3-Dataset/experiment/Subject01/Tissue02/RegionA/site_notes.txt b/SDS3-Dataset/experiment/Subject01/Tissue02/RegionA/site_notes.txt
@@ -0,0 +1,10 @@
+Site: RegionA
+Subject: Subject01
+Sample: Tissue02
+Date: 2023-06-01
+Researcher: Dr. M. Researcher
+
+Site-specific Notes:
+- Measurements taken according to SOP-onA
+- Site appears healthy and normal
+- Processing completed successfully
diff --git a/SDS3-Dataset/experiment/Subject01/Tissue02/RegionB/image_data.jpg b/SDS3-Dataset/experiment/Subject01/Tissue02/RegionB/image_data.jpg
diff --git a/SDS3-Dataset/experiment/Subject01/Tissue02/RegionB/measurements.csv b/SDS3-Dataset/experiment/Subject01/Tissue02/RegionB/measurements.csv
@@ -0,0 +1,5 @@
+Time,Position,Measurement,Value
+1,RegionB,Temperature,35.87 °C
+2,RegionB,pH,7.35
+3,RegionB,Pressure,115.78 mmHg
+4,RegionB,Flow Rate,108.94 ml/min
diff --git a/SDS3-Dataset/experiment/Subject01/Tissue02/RegionB/metadata.txt b/SDS3-Dataset/experiment/Subject01/Tissue02/RegionB/metadata.txt
@@ -0,0 +1,6 @@
+Site ID: RegionB
+Related Subject: Subject01
+Related Sample: Tissue02
+Collection Date: 5/28/2025
+Anatomical Location: RegionB
+Coordinates: X:5, Y:1, Z:1
diff --git a/SDS3-Dataset/experiment/Subject01/Tissue02/RegionB/results/analysis_output.csv b/SDS3-Dataset/experiment/Subject01/Tissue02/RegionB/results/analysis_output.csv
@@ -0,0 +1,4 @@
+Parameter,Value,Unit
+Temperature,36.72,°C
+pH,7.59,pH
+Volume,1.40,mL
diff --git a/SDS3-Dataset/experiment/Subject01/Tissue02/RegionB/results/notes.txt b/SDS3-Dataset/experiment/Subject01/Tissue02/RegionB/results/notes.txt
@@ -0,0 +1,4 @@
+Analysis performed: 5/28/2025
+Analyst: J. Researcher
+Results: Normal parameters detected
+Quality check: Passed
diff --git a/SDS3-Dataset/experiment/Subject01/Tissue02/RegionB/run_1.txt b/SDS3-Dataset/experiment/Subject01/Tissue02/RegionB/run_1.txt
@@ -0,0 +1,5 @@
+# Raw RegionB data - Run 1
+Sample ID: Subject01
+Date: 5/28/2025
+Values: 26.95, 53.27, 16.85, 32.31, 51.13
+Notes: Standard collection protocol followed
diff --git a/SDS3-Dataset/experiment/Subject01/Tissue02/RegionB/site_notes.txt b/SDS3-Dataset/experiment/Subject01/Tissue02/RegionB/site_notes.txt
@@ -0,0 +1,10 @@
+Site: RegionB
+Subject: Subject01
+Sample: Tissue02
+Date: 2023-06-01
+Researcher: Dr. M. Researcher
+
+Site-specific Notes:
+- Measurements taken according to SOP-onB
+- Site appears healthy and normal
+- Processing completed successfully
diff --git a/SDS3-Dataset/experiment/Subject01/Tissue02/Tissue02_data.csv b/SDS3-Dataset/experiment/Subject01/Tissue02/Tissue02_data.csv
@@ -0,0 +1,2 @@
+Subject,Measurement Type,Value 1,Value 2,Value 3
+Subject01,Tissue02,13.25,22.89,48.86
diff --git a/SDS3-Dataset/experiment/Subject01/Tissue02/lab_notes.txt b/SDS3-Dataset/experiment/Subject01/Tissue02/lab_notes.txt
@@ -0,0 +1,12 @@
+Lab Notes - Tissue02 Sample
+Subject: Subject01
+Sample: Tissue02
+Date: 2023-06-01
+Collected by: J. Smith
+
+Processing Notes:
+- Sample processed according to protocol
+- Stored at -80°C (Freezer #2)
+- Quality check: Passed
+
+Observations: Sample appears normal with no visible contamination
diff --git a/SDS3-Dataset/experiment/Subject01/Tissue02/run_1.txt b/SDS3-Dataset/experiment/Subject01/Tissue02/run_1.txt
@@ -0,0 +1,5 @@
+# Raw Tissue02 data - Run 1
+Sample ID: Subject01
+Date: 5/28/2025
+Values: 52.69, 46.16, 33.23, 16.07, 29.56
+Notes: Standard collection protocol followed
diff --git a/SDS3-Dataset/experiment/Subject01/Tissue02/run_2.txt b/SDS3-Dataset/experiment/Subject01/Tissue02/run_2.txt
@@ -0,0 +1,5 @@
+# Raw Tissue02 data - Run 2
+Sample ID: Subject01
+Date: 5/28/2025
+Values: 32.69, 32.48, 34.57, 15.59, 37.95
+Notes: Standard collection protocol followed
diff --git a/SDS3-Dataset/experiment/Subject01/subject_info.txt b/SDS3-Dataset/experiment/Subject01/subject_info.txt
@@ -0,0 +1,4 @@
+Subject ID: Subject01
+Collection Date: 2023-06-01
+Experimenter: J. Smith
+Project: Experiment-2023
diff --git a/SDS3-Dataset/experiment/Subject02/Tissue03/RegionA/image_data.jpg b/SDS3-Dataset/experiment/Subject02/Tissue03/RegionA/image_data.jpg
diff --git a/SDS3-Dataset/experiment/Subject02/Tissue03/RegionA/measurements.csv b/SDS3-Dataset/experiment/Subject02/Tissue03/RegionA/measurements.csv
@@ -0,0 +1,5 @@
+Time,Position,Measurement,Value
+1,RegionA,Temperature,39.38 °C
+2,RegionA,pH,7.41
+3,RegionA,Pressure,82.81 mmHg
+4,RegionA,Flow Rate,144.44 ml/min
diff --git a/SDS3-Dataset/experiment/Subject02/Tissue03/RegionA/metadata.txt b/SDS3-Dataset/experiment/Subject02/Tissue03/RegionA/metadata.txt
@@ -0,0 +1,6 @@
+Site ID: RegionA
+Related Subject: Subject02
+Related Sample: Tissue03
+Collection Date: 5/28/2025
+Anatomical Location: RegionA
+Coordinates: X:25, Y:20, Z:5
diff --git a/SDS3-Dataset/experiment/Subject02/Tissue03/RegionA/results/analysis_output.csv b/SDS3-Dataset/experiment/Subject02/Tissue03/RegionA/results/analysis_output.csv
@@ -0,0 +1,4 @@
+Parameter,Value,Unit
+Temperature,38.16,°C
+pH,7.76,pH
+Volume,2.93,mL
diff --git a/SDS3-Dataset/experiment/Subject02/Tissue03/RegionA/results/notes.txt b/SDS3-Dataset/experiment/Subject02/Tissue03/RegionA/results/notes.txt
@@ -0,0 +1,4 @@
+Analysis performed: 5/28/2025
+Analyst: J. Researcher
+Results: Normal parameters detected
+Quality check: Passed
diff --git a/SDS3-Dataset/experiment/Subject02/Tissue03/RegionA/run_1.txt b/SDS3-Dataset/experiment/Subject02/Tissue03/RegionA/run_1.txt
@@ -0,0 +1,5 @@
+# Raw RegionA data - Run 1
+Sample ID: Subject02
+Date: 5/28/2025
+Values: 38.94, 31.13, 38.63, 10.96, 57.49
+Notes: Standard collection protocol followed
diff --git a/SDS3-Dataset/experiment/Subject02/Tissue03/RegionA/site_notes.txt b/SDS3-Dataset/experiment/Subject02/Tissue03/RegionA/site_notes.txt
@@ -0,0 +1,10 @@
+Site: RegionA
+Subject: Subject02
+Sample: Tissue03
+Date: 2023-06-16
+Researcher: Dr. M. Researcher
+
+Site-specific Notes:
+- Measurements taken according to SOP-onA
+- Site appears healthy and normal
+- Processing completed successfully
diff --git a/SDS3-Dataset/experiment/Subject02/Tissue03/RegionB/image_data.jpg b/SDS3-Dataset/experiment/Subject02/Tissue03/RegionB/image_data.jpg
diff --git a/SDS3-Dataset/experiment/Subject02/Tissue03/RegionB/measurements.csv b/SDS3-Dataset/experiment/Subject02/Tissue03/RegionB/measurements.csv
@@ -0,0 +1,5 @@
+Time,Position,Measurement,Value
+1,RegionB,Temperature,38.68 °C
+2,RegionB,pH,7.12
+3,RegionB,Pressure,100.14 mmHg
+4,RegionB,Flow Rate,139.79 ml/min
diff --git a/SDS3-Dataset/experiment/Subject02/Tissue03/RegionB/metadata.txt b/SDS3-Dataset/experiment/Subject02/Tissue03/RegionB/metadata.txt
@@ -0,0 +1,6 @@
+Site ID: RegionB
+Related Subject: Subject02
+Related Sample: Tissue03
+Collection Date: 5/28/2025
+Anatomical Location: RegionB
+Coordinates: X:6, Y:43, Z:33
diff --git a/SDS3-Dataset/experiment/Subject02/Tissue03/RegionB/results/analysis_output.csv b/SDS3-Dataset/experiment/Subject02/Tissue03/RegionB/results/analysis_output.csv
@@ -0,0 +1,4 @@
+Parameter,Value,Unit
+Temperature,36.10,°C
+pH,7.80,pH
+Volume,2.56,mL
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		Subject,Measurement Type,Value 1,Value 2,Value 3
		Subject01,Tissue01,19.58,20.51,14.29
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		Subject,Measurement Type,Value 1,Value 2,Value 3
		Subject01,Tissue02,13.25,22.89,48.86