Fix 'experiment_instrument' component_set in Nomad Eln. (#41)

Author: RubelMozumder

src/pynxtools_spm/nomad/examples/afm/AFMExampleWithCustomization/AFMExample.archive.json

@@ -0,0 +1 @@
+{"data":{"m_def":"../upload/raw/afm.scheme.archive.yaml#/definitions/section_definitions/0","reader":"spm","nxdl":"NXafm","default":"current_forward","definition":"NXafm","input_files":["A151216.123306-02602.sxm","config.json"],"experiment_technique":"AFM","scan_mode":"tapping mode","experiment_description":"<div>\n<div>An demo NeXus example for AFM.</div>\n</div>","identifier_experiment":"D:\\\\\\\\Data\\\\\\\\123306\\\\A151216.123306-02602","identifier_collection":"D:\\\\\\\\Data\\\\\\\\123306","user":[{"name":"Rubel Mozumder","affiliation":["Dr. Cojal González, José David","Dr. Carlos-Andres Palma"],"email":["cojal@physik.hu-berlin.de","palma@physik.hu-berlin.de","mozumder@physik.hu-berlin.de"]}],"Instrument":{"hardware":{"vendor":"Nanonis","name":"Nanonis","model":"Generic 4","model/@version":"4"},"software":{"model":"Generic 4","model/@version":"4","vendor":"Nanonis","name":"Nanonis"}},"Sample":{"name":"diPAMY","Sample_component":[{"name":"Au(Mica)","description":"<div>\n<div>Gold on Mica.</div>\n</div>","chemical_formula":" KAl₂(AlSi₃O₁₀)(OH)₂)"}],"description":"<div>\n<div>We used the diPAMY sample used in this demo example.</div>\n</div>"}}}

src/pynxtools_spm/nomad/examples/afm/AFMExampleWithCustomization/AFMNeXusExample.archive.json

@@ -0,0 +1 @@
+{"data":{"m_def":"../upload/raw/stm.scheme.archive.yaml#/definitions/section_definitions/0","reader":"spm","nxdl":"NXstm","default":"current_forward","definition":"NXstm","experiment_description":"<div>\n<div>Experiment with</div>\n<div>Bias: -50mV</div>\n<div>Setpoint: 25pA</div>\n</div>","input_files":["Au_mica_2023_Y_A_diPAMY_195.sxm","config.json"],"experiment_technique":"STM","scan_mode":"constant current","identifier_experiment":"D:\\\\Data\\\\20230428\\\\Au_mica_2023_Y_A_diPAMY_154-211C_370C_1min_385C_30min_400C_1min_400C_30min_415_30min_430_30min_11min_30min_30min_20230419_1min_0420_30min_0425_30min_195.sxm","identifier_collection":"D:\\\\Data\\\\20230428\\\\Au_mica_2023_Y_A_diPAMY_154-211C_370C_1min_385C_30min_400C_1min_400C_30min_415_30min_430_30min_11min_30min_30min_20230419","user":{"name":"Yichen Jin","affiliation":["Rubel Mozumder","Dr. Cojal González, José David","Dr. Carlos-Andres Palma"],"email":["ycjin@physik.hu-berlin.de","rubel.mozumder@physik.hu-berlin.de","cojal@physik.hu-berlin.de","palma@physik.hu-berlin.de"]},"Instrument":{"hardware":{"name":"Nanonis","vendor":"Nanonis","model":"Generic 4.5","model/@version":"4.5"},"software":{"name":"Nanonis","vendor":"Nanonis","model":"Generic 4.5","model/@version":"4.5"}},"Sample":{"name":"diPAMY","Sample_component":{"name":"Au(Mica)","chemical_formula":"Au(KAl3Si3012H2)","description":"<div>\n<div>Substrate:</div>\n<div>Stack of two layers: Au(111) on Mica</div>\n</div>"}}}}

src/pynxtools_spm/nomad/examples/stm/STMExampleWithCustomization/STMExample.archive.json

@@ -109,7 +109,7 @@ definitions:
                     component: StringEditQuantity
                 description: |
                   List of emails from users who performed the experiment.
-        experiment_instrument:
+        Instrument:
           section:
             m_annotations:
               eln:
@@ -280,66 +280,60 @@ definitions:
                 description: |
                   Description of the sample or sample preparation.
             sub_sections:
-              sample_component_set:
+              Sample_component:
                 section:
                   m_annotations:
                     eln:
                       overview: true
-                  sub_sections:
-                    sample_component:
-                      section:
-                        m_annotations:
-                          eln:
-                            overview: true
-                        description: |
-                          A sample component is a part of the sample that is of interest.
-                          For example, a sample component could be a layer of a multilayer sample.
-                        quantities:
-                          name:
-                            type: str
-                            m_annotations:
-                              eln:
-                                component: StringEditQuantity
-                            description: |
-                              Name of the sample component.
-                          sample_id:
-                            type: str
-                            m_annotations:
-                              eln:
-                                component: StringEditQuantity
-                            description: |
-                              An unique identifier for the sample component.
-                          chemical_formula:
-                            type: str
-                            m_annotations:
-                              eln:
-                                component: StringEditQuantity
-                            description: |
-                              The chemical formula specified using CIF conventions.
-                              Abbreviated version of CIF standard:
-                              
-                              * Only recognized element symbols may be used.
-                              * Each element symbol is followed by a 'count' number. A count of '1' may be omitted.
-                              * A space or parenthesis must separate each cluster of (element symbol + count).
-                              * Where a group of elements is enclosed in parentheses, the multiplier for the
-                                group must follow the closing parentheses. That is, all element and group
-                                multipliers are assumed to be printed as subscripted numbers.
-                              * Unless the elements are ordered in a manner that corresponds to their chemical
-                                structure, the order of the elements within any group or moiety depends on
-                                whether or not carbon is present.
-                              * If carbon is present, the order should be:
-                              
-                                - C, then H, then the other elements in alphabetical order of their symbol.
-                                - If carbon is not present, the elements are listed purely in alphabetic order of their symbol.
-                                
-                              * This is the *Hill* system used by Chemical Abstracts.
-                          description:
-                            type: str
-                            m_annotations:
-                              eln:
-                                component: RichTextEditQuantity
-                            description: |
-                              Description of the sample component or sample preparation.
+                  description: |
+                    A sample component is a part of the sample that is of interest.
+                    For example, a sample component could be a layer of a multilayer sample.
+                  quantities:
+                    name:
+                      type: str
+                      m_annotations:
+                        eln:
+                          component: StringEditQuantity
+                      description: |
+                        Name of the sample component.
+                    sample_id:
+                      type: str
+                      m_annotations:
+                        eln:
+                          component: StringEditQuantity
+                      description: |
+                        An unique identifier for the sample component.
+                    chemical_formula:
+                      type: str
+                      m_annotations:
+                        eln:
+                          component: StringEditQuantity
+                      description: |
+                        The chemical formula specified using CIF conventions.
+                        Abbreviated version of CIF standard:
+                        
+                        * Only recognized element symbols may be used.
+                        * Each element symbol is followed by a 'count' number. A count of '1' may be omitted.
+                        * A space or parenthesis must separate each cluster of (element symbol + count).
+                        * Where a group of elements is enclosed in parentheses, the multiplier for the
+                          group must follow the closing parentheses. That is, all element and group
+                          multipliers are assumed to be printed as subscripted numbers.
+                        * Unless the elements are ordered in a manner that corresponds to their chemical
+                          structure, the order of the elements within any group or moiety depends on
+                          whether or not carbon is present.
+                        * If carbon is present, the order should be:
+                        
+                          - C, then H, then the other elements in alphabetical order of their symbol.
+                          - If carbon is not present, the elements are listed purely in alphabetic order of their symbol.
+                          
+                        * This is the *Hill* system used by Chemical Abstracts.
+                    description:
+                      type: str
+                      m_annotations:
+                        eln:
+                          component: RichTextEditQuantity
+                      description: |
+                        Description of the sample component or sample preparation.
               History:
                 section:
                   m_annotations:

src/pynxtools_spm/nomad/examples/stm/STMExampleWithCustomization/STMNeXusExample.archive.json

@@ -0,0 +1 @@
+{"data":{"m_def":"../upload/raw/sts.scheme.archive.yaml#/definitions/section_definitions/0","reader":"spm","nxdl":"NXsts","input_files":["config.json","Bias-Spectroscopy00015_20230420.dat"],"export":true,"nexus_view":"../upload/archive/vO8URld58Uv17CJzLgLCFkxng_rU#/data","default":"current_filter_grad","definition":"NXsts","experiment_technique":"STS","experiment_description":"<div>\n<div>The experiment with</div>\n<div>&nbsp;</div>\n<div>Bias: -50mA</div>\n<div>Setpoint: 25pA</div>\n</div>","identifier_experiment":"Au_mica_2023_Y_A_diPAMY_154-211C_370C_1min_385C_30min_400C_1min_400C_30min_415_30min_430_30min_11min_30min_30min_20230416_20230420","identifier_collection":"Au_mica_2023_Y_A_diPAMY_154-211C_370C_1min_385C_30min_400C_1min_400C_30min_415_30min_430_30min_11min_30min_30min_20230419","User":{"name":"Yichen Jin","affiliation":["Rubel Mozumder","Dr. Cojal Gonzalez","Dr. Carlos-Andres Palma"],"email":["ycjin@physik.hu-berlin.de","rubel.mozumder@physik.hu-berlin.de","cojal@physik.hu-berlin.de","palma@physik.hu-berlin.de"]},"Instrument":{"hardware":{"name":"Nanonis","vendor":"Nanonis","model":"Generic5","model/@version":"5"},"software":{"vendor":"Nanonis","name":"Nanonis","model":"Generic5","model/@version":"5"},"lockin_amplifier":{"modulation_signal":"Current","lockin_current_flip_sign":-1},"scan_environment":{"tip_temp":10}},"Sample":{"name":"diPAMY","Sample_component":{"name":"Au(Mica)","sample_id":"Au(KAl3Si3O12H2)","description":"<div>\n<div>Substrate:</div>\n<div>Two layers stack: Au-Mica</div>\n</div>"}}}}

src/pynxtools_spm/nomad/examples/stm/STMExampleWithCustomization/stm.scheme.archive.yaml

@@ -1,6 +1,6 @@
 {
   "ENTRY[entry]": {
-    "@default": { "raw_path": "@default:current_filter_grad" },
+    "@default": { "raw_path": "@default:current_grad" },
     "definition": { "@version": "" },
     "start_time": {
       "raw_path": "/Start time/value"