xas dataset and schema update

Dataset/p65_example_data.yaml

-experimentID: EXP-001
-sample:
-      sampleID: SAMPLE-001
-      material: Platinum on Alumina
-      preparationMethod: Impregnation
-      catalyst: Platinum (1 wt%)
-      reactionConditions: 
-        temperature:
-            unit: degC
-            value: 300
-        pressure:
-            unit: atm
-            value: 1
-        gas: H2
-      description: A sample of platinum nanoparticles dispersed on gamma-alumina support.
-      dSpacing: 3.54  # in angstroms
-      crystalType: Cubic
-instrument:
-      instrumentID: INSTR-001
-      name: Synchrotron Beamline Instrument
-      facility: DESY
-      beamline: P65
-      energyRange:
-        minEnergy: 
-            value: 5000
-            unit: eV
-        maxEnergy:
-            value: 25000
-            unit: eV  # in eV
-technique:
-      techniqueType: EXAFS
-      edge: K-edge
-      detector: Fluorescence
-      monochromator: Si111
-dataProcessing:
-      software: Athena
-      version: 0.9.26
-      method: Background subtraction and Fourier transform
-metadata:
-      project: "Catalysis Study for Platinum-Based Catalysts"
-      experimenter: "Dr. John Doe"
-startTime: "2024-08-01T09:00:00"
-endTime: "2024-08-01T12:00:00"
+datasetName: "P65 XAS"
+description: "XAS dataset."
+principalInvestigator: "Dr. Anjali"
+owner: "Anjali"
+contactEmail: "anjali@example.com"
+sourceFolder: "/tmp"
+size: 123456
+creationLocation: "Hamburg"
+creationTime: "2024-06-26T12:00:00Z"
+type: "raw"
+instrumentId: "Instrument001"
+proposalId: "20010161"
+dataFormat: "HDF5"
+isPublished: False
+ownerGroup: "hasylab"
+accessGroups: ["FS-EC"]
+keywords: ["XAS", "data", "keywords"]
+license: "CC BY 4.0"
+scientificMetadata:
+      experimentID: EXP-001
+      sample:
+            sampleID: SAMPLE-001
+            material: Platinum on Alumina
+            preparationMethod: Impregnation
+            catalyst: Platinum (1 wt%)
+            reactionConditions: 
+              temperature:
+                  unit: degC
+                  value: 300
+              pressure:
+                  unit: atm
+                  value: 1
+              gas: H2
+            description: A sample of platinum nanoparticles dispersed on gamma-alumina support.
+            dSpacing: 3.54  # in angstroms
+            crystalType: Cubic
+      instrument:
+            instrumentID: INSTR-001
+            name: Synchrotron Beamline Instrument
+            facility: DESY
+            beamline: P65
+            energyRange:
+              minEnergy: 
+                  value: 5000
+                  unit: eV
+              maxEnergy:
+                  value: 25000
+                  unit: eV  # in eV
+      technique:
+            techniqueType: EXAFS
+            edge: K-edge
+            detector: Fluorescence
+            monochromator: Si111
+      dataProcessing:
+            software: Athena
+            version: 0.9.26
+            method: Background subtraction and Fourier transform
+      metadata:
+            project: "Catalysis Study for Platinum-Based Catalysts"
+            experimenter: "Dr. John Doe"
+      startTime: "2024-08-01T09:00:00"
+      endTime: "2024-08-01T12:00:00"
 
 

schema/base_scicat_dataset.yaml

@@ -116,6 +116,7 @@ classes:
         description: The ID of the proposal to which the dataset belongs.
       isPublished:
         description: The ID of the proposal to which the dataset belongs.
+        range: bool
       #~ sampleId:
         #~ description: ID of the sample used when collecting the data.
       instrumentId:
@@ -125,6 +126,7 @@ classes:
       accessGroups: 
         description: Defines the group which owns the data, and therefore has unrestricted access to this data. Usually a pgroup like p12151
     #   #~ instrumentGroup: {}
+        range: list
 
 
   SciCatProposal:

schema/beamline_p65.yaml → schema/beamline_p65_xas.yaml

@@ -18,19 +18,23 @@ imports:
   - base_scicat_dataset
   - base_sample
   - rockit
+  - technique_xas_catalysis
+  
 default_range: string
 classes:
   P65ScientificMetadata:
     description: The metadata associated with P65
     is_a: PetraScientificMetadata
-    mixins: [rockit_Container]
-    attributes:
-      # special_p65_parameter:
-      #   description: something that only exists at P65
-      catalyst: 
-        description: Name of the catalyst used for experiment
-      sample:
-        range: SolidStateSample 
+    # mixins: [rockit_Container]
+    mixins: [CatalysisExperiment]
+    # attributes:
+    #   # special_p65_parameter:
+    #   #   description: something that only exists at P65
+    #   catalyst: 
+    #     description: Name of the catalyst used for experiment
+    #   sample:
+    #     range: SolidStateSample 
+
   P65Dataset:
     tree_root: true
     is_a: ScicatDataset

schema/technique_xas_catalysis.yaml

@@ -10,6 +10,10 @@ imports:
   - linkml:types
   - base_types
   - base_sample
+  # - base_scicat_dataset
+  # - base_catalogue_metadata
+
+
 
 default_prefix: xas_catalysis
 
@@ -20,6 +24,21 @@ types:
     base: datetime
 
 classes:
+
+  # P65ScientificMetadata:
+  #   description: The metadata associated with P65
+  #   is_a: PetraScientificMetadata
+  #   mixins: [CatalysisExperiment]
+
+  # P65Dataset:
+  #   tree_root: true
+  #   is_a: ScicatDataset
+  #   description: The metadata associated with P65
+  #   attributes:
+  #     scientificMetadata:
+  #       range: P65ScientificMetadata
+  #       required: true
+
   CatalysisExperiment:
     description: Information about the catalysis experiment using XAS at the DESY P65 beamline
     attributes:

scripts/validate_p65_data.sh

 # linkml-validate -s ./schema/beamline_p08.yaml -C P08Dataset  ./Dataset/p08_example_data.yaml   
-linkml-validate -s ../schema/technique_xas_catalysis.yaml -C CatalysisExperiment ../Dataset/p65_example_data.yaml 
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+linkml-validate -s ../schema/beamline_p65.yaml -C P65Dataset ../Dataset/p65_example_data.yaml 
\ No newline at end of file