Feat: add new SRS OC collections

aodn_cloud_optimised/bin/satellite_chlorophylla_gsm_1day_aqua.py

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+#!/usr/bin/env python3
+import subprocess
+
+
+def main():
+    command = [
+        "generic_cloud_optimised_creation",
+        "--paths",
+        "IMOS/SRS/OC/gridded/aqua/P1D/",
+        "--filters",
+        "aust.chl_gsm.nc",
+        "--dataset-config",
+        "satellite_chlorophylla_gsm_1day_aqua.json",
+        "--clear-existing-data",
+        "--cluster-mode",
+        "remote",
+    ]
+
+    # Run the command
+    subprocess.run(command, check=True)
+
+
+if __name__ == "__main__":
+    main()

aodn_cloud_optimised/bin/satellite_chlorophylla_oc3_1day_aqua.py

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+#!/usr/bin/env python3
+import subprocess
+
+
+def main():
+    command = [
+        "generic_cloud_optimised_creation",
+        "--paths",
+        "IMOS/SRS/OC/gridded/aqua/P1D/",
+        "--filters",
+        "aust.chl_oc3.nc",
+        "--dataset-config",
+        "satellite_chlorophylla_oc3_1day_aqua.json",
+        "--clear-existing-data",
+        "--cluster-mode",
+        "local",
+    ]
+
+    # Run the command
+    subprocess.run(command, check=True)
+
+
+if __name__ == "__main__":
+    main()

aodn_cloud_optimised/bin/satellite_chlorophylla_oci_1day_aqua.py

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+#!/usr/bin/env python3
+import subprocess
+
+
+## issue opening files in batch with h5netcdf. The ds does not have any variables, To investigate
+
+
+def main():
+    command = [
+        "generic_cloud_optimised_creation",
+        "--paths",
+        "IMOS/SRS/OC/gridded/aqua/P1D/2024",
+        "--filters",
+        "aust.chl_oc3.nc",
+        "--dataset-config",
+        "satellite_chlorophylla_oci_1day_aqua.json",
+        "--clear-existing-data",
+        "--cluster-mode",
+        "local",
+    ]
+
+    # Run the command
+    subprocess.run(command, check=True)
+
+
+if __name__ == "__main__":
+    main()

aodn_cloud_optimised/bin/satellite_diffuse_attenuation_coefficent_1day_aqua.py

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+#!/usr/bin/env python3
+import subprocess
+
+
+def main():
+    command = [
+        "generic_cloud_optimised_creation",
+        "--paths",
+        "IMOS/SRS/OC/gridded/aqua/P1D/",
+        "--filters",
+        "aust.K_490.nc",
+        "--dataset-config",
+        "satellite_diffuse_attenuation_coefficent_1day_aqua.json",
+        "--clear-existing-data",
+        "--cluster-mode",
+        "remote",
+    ]
+
+    # Run the command
+    subprocess.run(command, check=True)
+
+
+if __name__ == "__main__":
+    main()

aodn_cloud_optimised/bin/satellite_nanoplankton_fraction_oc3_1day_aqua.py

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+#!/usr/bin/env python3
+import subprocess
+
+
+def main():
+    command = [
+        "generic_cloud_optimised_creation",
+        "--paths",
+        "IMOS/SRS/OC/gridded/aqua/P1D/",
+        "--filters",
+        "aust.nanop_brewin2012in.nc",
+        "--dataset-config",
+        "satellite_nanoplankton_fraction_oc3_1day_aqua.json",
+        "--clear-existing-data",
+        "--cluster-mode",
+        "remote",
+    ]
+
+    # Run the command
+    subprocess.run(command, check=True)
+
+
+if __name__ == "__main__":
+    main()

aodn_cloud_optimised/bin/satellite_net_primary_productivity_gsm_1day_aqua.py

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+#!/usr/bin/env python3
+import subprocess
+
+
+def main():
+    command = [
+        "generic_cloud_optimised_creation",
+        "--paths",
+        "IMOS/SRS/OC/gridded/aqua/P1D/",
+        "--filters",
+        "aust.npp_vgpm_eppley_gsm.nc",
+        "--dataset-config",
+        "satellite_net_primary_productivity_gsm_1day_aqua.json",
+        "--clear-existing-data",
+        "--cluster-mode",
+        "remote",
+    ]
+
+    # Run the command
+    subprocess.run(command, check=True)
+
+
+if __name__ == "__main__":
+    main()

aodn_cloud_optimised/bin/satellite_net_primary_productivity_oc3_1day_aqua.py

@@ -0,0 +1,24 @@
+#!/usr/bin/env python3
+import subprocess
+
+
+def main():
+    command = [
+        "generic_cloud_optimised_creation",
+        "--paths",
+        "IMOS/SRS/OC/gridded/aqua/P1D/",
+        "--filters",
+        "aust.npp_vgpm_eppley_oc3.nc",
+        "--dataset-config",
+        "satellite_net_primary_productivity_oc3_1day_aqua.json",
+        "--clear-existing-data",
+        "--cluster-mode",
+        "remote",
+    ]
+
+    # Run the command
+    subprocess.run(command, check=True)
+
+
+if __name__ == "__main__":
+    main()

aodn_cloud_optimised/bin/satellite_optical_water_type_1day_aqua.py

@@ -0,0 +1,24 @@
+#!/usr/bin/env python3
+import subprocess
+
+
+def main():
+    command = [
+        "generic_cloud_optimised_creation",
+        "--paths",
+        "IMOS/SRS/OC/gridded/aqua/P1D/",
+        "--filters",
+        "aust.owtd_csiro.nc",
+        "--dataset-config",
+        "satellite_optical_water_type_1day_aqua.json",
+        "--clear-existing-data",
+        "--cluster-mode",
+        "remote",
+    ]
+
+    # Run the command
+    subprocess.run(command, check=True)
+
+
+if __name__ == "__main__":
+    main()

aodn_cloud_optimised/bin/satellite_picoplankton_fraction_oc3_1day_aqua.py

@@ -0,0 +1,24 @@
+#!/usr/bin/env python3
+import subprocess
+
+
+def main():
+    command = [
+        "generic_cloud_optimised_creation",
+        "--paths",
+        "IMOS/SRS/OC/gridded/aqua/P1D/",
+        "--filters",
+        "aust.picop_brewin2012in.nc",
+        "--dataset-config",
+        "satellite_picoplankton_fraction_oc3_1day_aqua.json",
+        "--clear-existing-data",
+        "--cluster-mode",
+        "remote",
+    ]
+
+    # Run the command
+    subprocess.run(command, check=True)
+
+
+if __name__ == "__main__":
+    main()

aodn_cloud_optimised/config/dataset/satellite_chlorophylla_gsm_1day_aqua.json

@@ -0,0 +1,77 @@
+{
+  "dataset_name": "satellite_chlorophylla_gsm_1day_aqua",
+  "logger_name": "satellite_chlorophylla_gsm_1day_aqua",
+  "parent_config": "satellite_ocean_colour_1day_aqua_main.json",
+  "metadata_uuid": "f73daf07-eb81-4995-a72a-ca903834509f",
+  "var_template_shape": "chl_gsm",
+  "schema": {
+    "time": {
+      "type": "timestamp[ns]",
+      "long_name": "time",
+      "standard_name": "time",
+      "axis": "T"
+    },
+    "latitude": {
+      "type": "double",
+      "long_name": "latitude",
+      "standard_name": "latitude",
+      "units": "degrees_north",
+      "axis": "Y"
+    },
+    "longitude": {
+      "type": "double",
+      "long_name": "longitude",
+      "standard_name": "longitude",
+      "units": "degrees_east",
+      "axis": "X"
+    },
+    "chl_gsm": {
+      "type": "float",
+      "units": "mg/m^3",
+      "long_name": "Chlorophyll Concentration, GSM model",
+      "flag_applied": "HISATZEN LAND CLDICE NAVFAIL"
+    }
+  },
+  "dataset_gattrs": {
+    "title": ""
+  },
+  "aws_opendata_registry": {
+    "Name": "IMOS - SRS - MODIS - 01 day - Chlorophyll-a concentration (GSM model)",
+    "Description": "The Aqua satellite platform carries a MODIS sensor that observes sunlight reflected from within the ocean surface layer at multiple wavelengths. These multi-spectral measurements are used to infer the concentration of chlorophyll-a (Chl-a), most typically due to phytoplankton, present in the water. \n\nThere are multiple retrieval algorithms for estimating Chl-a. These data use the Garver-Siegel-Maritorena (GSM) method   implemented in the SeaDAS processing software l2gen and described in \u201cChapter 11, and references therein, of IOCCG Report 5, 2006, (http://ioccg.org/wp-content/uploads/2015/10/ioccg-report-05.pdf).",
+    "Documentation": "https://catalogue-imos.aodn.org.au/geonetwork/srv/eng/catalog.search#/metadata/f73daf07-eb81-4995-a72a-ca903834509f",
+    "Contact": "[email protected]",
+    "ManagedBy": "AODN",
+    "UpdateFrequency": "As Needed",
+    "Tags": [
+      "FILL UP MANUALLY - CHECK DOCUMENTATION"
+    ],
+    "License": "http://creativecommons.org/licenses/by/4.0/",
+    "Resources": [
+      {
+        "Description": "Cloud Optimised AODN dataset of IMOS - SRS - MODIS - 01 day - Chlorophyll-a concentration (GSM model)",
+        "ARN": "arn:aws:s3:::aodn-cloud-optimised/satellite_chlorophylla_gsm_1day_aqua.zarr",
+        "Region": "ap-southeast-2",
+        "Type": "S3 Bucket"
+      }
+    ],
+    "DataAtWork": {
+      "Tutorials": [
+        {
+          "Title": "Accessing IMOS - SRS - MODIS - 01 day - Chlorophyll-a concentration (GSM model)",
+          "URL": "https://nbviewer.org/github/aodn/aodn_cloud_optimised/blob/main/notebooks/satellite_chlorophylla_gsm_1day_aqua.ipynb",
+          "NotebookURL": "https://githubtocolab.com/aodn/aodn_cloud_optimised/blob/main/notebooks/satellite_chlorophylla_gsm_1day_aqua.ipynb",
+          "AuthorName": "Laurent Besnard",
+          "AuthorURL": "https://github.com/aodn/aodn_cloud_optimised"
+        },
+        {
+          "Title": "Accessing and search for any AODN dataset",
+          "URL": "https://nbviewer.org/github/aodn/aodn_cloud_optimised/blob/main/notebooks/GetAodnData.ipynb",
+          "NotebookURL": "https://githubtocolab.com/aodn/aodn_cloud_optimised/blob/main/notebooks/GetAodnData.ipynb",
+          "AuthorName": "Laurent Besnard",
+          "AuthorURL": "https://github.com/aodn/aodn_cloud_optimised"
+        }
+      ]
+    },
+    "Citation": "IMOS [year-of-data-download], [Title], [data-access-URL], accessed [date-of-access]"
+  }
+}

aodn_cloud_optimised/config/dataset/satellite_chlorophylla_oc3_1day_aqua.json

@@ -0,0 +1,77 @@
+{
+  "dataset_name": "satellite_chlorophylla_oc3_1day_aqua",
+  "logger_name": "satellite_chlorophylla_oc3_1day_aqua",
+  "parent_config": "satellite_ocean_colour_1day_aqua_main.json",
+  "metadata_uuid": "d7a14921-8f3f-4522-9a54-e7d1df969c8a",
+  "var_template_shape": "chl_oc3",
+  "schema": {
+    "time": {
+      "type": "timestamp[ns]",
+      "long_name": "time",
+      "standard_name": "time",
+      "axis": "T"
+    },
+    "latitude": {
+      "type": "double",
+      "long_name": "latitude",
+      "standard_name": "latitude",
+      "units": "degrees_north",
+      "axis": "Y"
+    },
+    "longitude": {
+      "type": "double",
+      "long_name": "longitude",
+      "standard_name": "longitude",
+      "units": "degrees_east",
+      "axis": "X"
+    },
+    "chl_oc3": {
+      "type": "float",
+      "units": "mg/m^3",
+      "long_name": "Chlorophyll Concentration, OC3 Algorithm",
+      "flag_applied": "HISATZEN LAND CLDICE NAVFAIL"
+    }
+  },
+  "dataset_gattrs": {
+    "title": ""
+  },
+  "aws_opendata_registry": {
+    "Name": "IMOS - SRS - MODIS - 01 day - Chlorophyll-a concentration (OC3 model)",
+    "Description": "The Aqua satellite platform carries a MODIS sensor that observes sunlight reflected from within the ocean surface layer at multiple wavelengths. These multi-spectral measurements are used to infer the concentration of chlorophyll-a (Chl-a), most typically due to phytoplankton, present in the water. \n\nThere are multiple retrieval algorithms for estimating Chl-a. These data use the OC3 method recommended by the NASA Ocean Biology Processing Group and implemented in the SeaDAS processing software l2gen. The OC3 algorithm is described at http://oceancolor.gsfc.nasa.gov/cms/atbd/chlor_a (and links therein).",
+    "Documentation": "https://catalogue-imos.aodn.org.au/geonetwork/srv/eng/catalog.search#/metadata/d7a14921-8f3f-4522-9a54-e7d1df969c8a",
+    "Contact": "[email protected]",
+    "ManagedBy": "AODN",
+    "UpdateFrequency": "As Needed",
+    "Tags": [
+      "FILL UP MANUALLY - CHECK DOCUMENTATION"
+    ],
+    "License": "http://creativecommons.org/licenses/by/4.0/",
+    "Resources": [
+      {
+        "Description": "Cloud Optimised AODN dataset of IMOS - SRS - MODIS - 01 day - Chlorophyll-a concentration (OC3 model)",
+        "ARN": "arn:aws:s3:::aodn-cloud-optimised/satellite_chlorophylla_oc3_1day_aqua.zarr",
+        "Region": "ap-southeast-2",
+        "Type": "S3 Bucket"
+      }
+    ],
+    "DataAtWork": {
+      "Tutorials": [
+        {
+          "Title": "Accessing IMOS - SRS - MODIS - 01 day - Chlorophyll-a concentration (OC3 model)",
+          "URL": "https://nbviewer.org/github/aodn/aodn_cloud_optimised/blob/main/notebooks/satellite_chlorophylla_oc3_1day_aqua.ipynb",
+          "NotebookURL": "https://githubtocolab.com/aodn/aodn_cloud_optimised/blob/main/notebooks/satellite_chlorophylla_oc3_1day_aqua.ipynb",
+          "AuthorName": "Laurent Besnard",
+          "AuthorURL": "https://github.com/aodn/aodn_cloud_optimised"
+        },
+        {
+          "Title": "Accessing and search for any AODN dataset",
+          "URL": "https://nbviewer.org/github/aodn/aodn_cloud_optimised/blob/main/notebooks/GetAodnData.ipynb",
+          "NotebookURL": "https://githubtocolab.com/aodn/aodn_cloud_optimised/blob/main/notebooks/GetAodnData.ipynb",
+          "AuthorName": "Laurent Besnard",
+          "AuthorURL": "https://github.com/aodn/aodn_cloud_optimised"
+        }
+      ]
+    },
+    "Citation": "IMOS [year-of-data-download], [Title], [data-access-URL], accessed [date-of-access]"
+  }
+}