Initial code for a simple NOMAD app for atom probe

pyproject.toml

@@ -39,7 +39,6 @@ dev = [
     "pytest",
     "pytest-cov",
     "pytest-timeout",
-    "pytest-cov",
     "structlog",
     "types-pyyaml",
     "types-pytz",
@@ -65,6 +64,7 @@ apm = "pynxtools_apm.reader:APMReader"
 
 [project.entry-points.'nomad.plugin']
 apm_example = "pynxtools_apm.nomad.entrypoints:apm_example"
+apm_app = "pynxtools_apm.nomad.entrypoints:apm_app"
 
 [tool.setuptools.packages.find]
 where = [

src/pynxtools_apm/nomad/entrypoints.py

@@ -18,7 +18,19 @@
 """Entry points for XPS examples."""
 
 try:
-    from nomad.config.models.plugins import ExampleUploadEntryPoint
+    from nomad.config.models.plugins import (
+        AppEntryPoint,
+        ExampleUploadEntryPoint,
+    )
+    from nomad.config.models.ui import (
+        App,
+        Column,
+        Menu,
+        MenuItemHistogram,
+        MenuItemPeriodicTable,
+        MenuItemTerms,
+        SearchQuantities,
+    )
 except ImportError as exc:
     raise ImportError(
         "Could not import nomad package. Please install the package 'nomad-lab'."
@@ -39,3 +51,118 @@
     plugin_package="pynxtools_apm",
     resources=["nomad/examples/*"],
 )
+
+
+schema = "pynxtools.nomad.schema.NeXus"
+
+nexus_app = AppEntryPoint(
+    name="ApmApp",
+    description="Atom probe tomography app.",
+    app=App(
+        # Label of the App
+        label="Apm",
+        # Path used in the URL, must be unique
+        path="apmapp",
+        # Used to categorize apps in the explore menu
+        category="Experiment",
+        # Brief description used in the app menu
+        description="A simple search app customized for NeXus data from the research field of atom probe tomography.",
+        # 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.ENTRY.start_time__field#{schema}",
+                    "title": "Start 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}
+                    },
+                },
+            ]
+        },
+    ),
+)