initial skeleton for NeXus App (#474)

* initial skeleton for NeXus App

* a minimalistic App

* fix merge

* comments added as suggested in code review

pyproject.toml

@@ -96,6 +96,7 @@ xrd = [
 nexus_parser = "pynxtools.nomad.entrypoints:nexus_parser"
 nexus_schema = "pynxtools.nomad.entrypoints:nexus_schema"
 nexus_data_converter = "pynxtools.nomad.entrypoints:nexus_data_converter"
+nexus_app = "pynxtools.nomad.entrypoints:nexus_app"
 iv_temp_example = "pynxtools.nomad.entrypoints:iv_temp_example"
 
 [project.scripts]

src/pynxtools/nomad/entrypoints.py

@@ -17,9 +17,10 @@
 #
 try:
     from nomad.config.models.plugins import (
+        AppEntryPoint,
+        ExampleUploadEntryPoint,
         ParserEntryPoint,
         SchemaPackageEntryPoint,
-        ExampleUploadEntryPoint,
     )
 except ImportError as exc:
     raise ImportError(
@@ -65,6 +66,130 @@ def load(self):
     mainfile_mime_re="application/x-hdf5",
 )
 
+from nomad.config.models.ui import (
+    App,
+    Column,
+    Menu,
+    MenuItemHistogram,
+    MenuItemPeriodicTable,
+    MenuItemTerms,
+    SearchQuantities,
+)
+
+schema = "pynxtools.nomad.schema.NeXus"
+
+nexus_app = AppEntryPoint(
+    name="NexusApp",
+    description="Simple Generic NeXus app.",
+    app=App(
+        # Label of the App
+        label="NeXus",
+        # Path used in the URL, must be unique
+        path="nexusapp",
+        # Used to categorize apps in the explore menu
+        category="Experiment",
+        # Brief description used in the app menu
+        description="A simple search app customized for generic NeXus data.",
+        # Longer description that can also use markdown
+        readme="This is a simple App to support basic search for NeXus based Experiment Entries.",
+        # If you want to use quantities from a custom schema, you need to load
+        # the search quantities from it first here. Note that you can use a glob
+        # syntax to load the entire package, or just a single schema from a
+        # package.
+        search_quantities=SearchQuantities(
+            include=[f"*#{schema}"],
+        ),
+        # Controls which columns are shown in the results table
+        columns=[
+            Column(quantity="entry_id", selected=True),
+            Column(quantity=f"entry_type", selected=True),
+            Column(
+                title="definition",
+                quantity=f"data.*.ENTRY[*].definition__field#{schema}",
+                selected=True,
+            ),
+            Column(
+                title="start_time",
+                quantity=f"data.*.ENTRY[*].start_time__field#{schema}",
+                selected=True,
+            ),
+            Column(
+                title="title",
+                quantity=f"data.*.ENTRY[*].title__field#{schema}",
+                selected=True,
+            ),
+        ],
+        # Dictionary of search filters that are always enabled for queries made
+        # within this app. This is especially important to narrow down the
+        # results to the wanted subset. Any available search filter can be
+        # targeted here. This example makes sure that only entries that use
+        # MySchema are included.
+        filters_locked={"section_defs.definition_qualified_name": [schema]},
+        # Controls the menu shown on the left
+        menu=Menu(
+            title="Material",
+            items=[
+                Menu(
+                    title="elements",
+                    items=[
+                        MenuItemPeriodicTable(
+                            quantity="results.material.elements",
+                        ),
+                        MenuItemTerms(
+                            quantity="results.material.chemical_formula_hill",
+                            width=6,
+                            options=0,
+                        ),
+                        MenuItemTerms(
+                            quantity="results.material.chemical_formula_iupac",
+                            width=6,
+                            options=0,
+                        ),
+                        MenuItemHistogram(
+                            x="results.material.n_elements",
+                        ),
+                    ],
+                )
+            ],
+        ),
+        # Controls the default dashboard shown in the search interface
+        dashboard={
+            "widgets": [
+                {
+                    "type": "histogram",
+                    "show_input": False,
+                    "autorange": True,
+                    "nbins": 30,
+                    "scale": "linear",
+                    "quantity": f"data.Root.datetime#{schema}",
+                    "title": "Procesing Time",
+                    "layout": {
+                        "lg": {"minH": 3, "minW": 3, "h": 4, "w": 12, "y": 0, "x": 0}
+                    },
+                },
+                {
+                    "type": "terms",
+                    "show_input": False,
+                    "scale": "linear",
+                    "quantity": f"entry_type",
+                    "title": "Entry Type",
+                    "layout": {
+                        "lg": {"minH": 3, "minW": 3, "h": 8, "w": 4, "y": 0, "x": 12}
+                    },
+                },
+                {
+                    "type": "periodic_table",
+                    "scale": "linear",
+                    "quantity": f"results.material.elements",
+                    "layout": {
+                        "lg": {"minH": 3, "minW": 3, "h": 4, "w": 12, "y": 4, "x": 0}
+                    },
+                },
+            ]
+        },
+    ),
+)
+
 iv_temp_example = ExampleUploadEntryPoint(
     title="Sensor Scan - IV Temperature Curve",
     category="FAIRmat examples",

src/pynxtools/nomad/schema.py

@@ -33,7 +33,7 @@
 try:
     from nomad import utils
     from nomad.datamodel import EntryArchive, EntryMetadata
-    from nomad.datamodel.data import EntryData
+    from nomad.datamodel.data import EntryData, Schema
     from nomad.datamodel.metainfo.basesections import (
         BaseSection,
         Component,
@@ -775,6 +775,7 @@ def __create_package_from_nxdl_directories(nexus_section: Section) -> Package:
     """
     Creates a metainfo package from the given nexus directory. Will generate the
     respective metainfo definitions from all the nxdl files in that directory.
+    The parent Schema is also populated with all AppDefs and then is is also added to the package.
     """
     package = Package(name=__PACKAGE_NAME)
 
@@ -799,6 +800,7 @@ def __create_package_from_nxdl_directories(nexus_section: Section) -> Package:
                 SubSection(section_def=section, name=section.name)
             )
 
+    package.section_definitions.append(nexus_section)
     return package
 
 
@@ -832,9 +834,11 @@ def init_nexus_metainfo():
 
     # We take the application definitions and create a common parent section that allows
     # to include nexus in an EntryArchive.
+    # To be able to register it into data section, it is expected that this section inherits from Schema.
     nexus_section = Section(
         validate=VALIDATE, name=__GROUPING_NAME, label=__GROUPING_NAME
     )
+    nexus_section.base_sections = [Schema.m_def]
 
     # try:
     #     load_nexus_schema('')
@@ -846,8 +850,6 @@ def init_nexus_metainfo():
     #         pass
     nexus_metainfo_package = __create_package_from_nxdl_directories(nexus_section)
 
-    nexus_metainfo_package.section_definitions.append(nexus_section)
-
     # We need to initialize the metainfo definitions. This is usually done automatically,
     # when the metainfo schema is defined though MSection Python classes.
     nexus_metainfo_package.init_metainfo()