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GinzburgLevGinzburgLev
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Merge pull request #580 from FAIRmat-NFDI/search_app_for_NXsensor_scan_and_inhereting_classes
Update NeXus search app in pynxtools
2 parents 09fb12d + c228e42 commit aa77148

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‎src/pynxtools/nomad/entrypoints.py‎

Lines changed: 187 additions & 34 deletions
Original file line numberDiff line numberDiff line change
@@ -73,13 +73,15 @@ def load(self):
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MenuItemHistogram,
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MenuItemPeriodicTable,
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MenuItemTerms,
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MenuSizeEnum,
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SearchQuantities,
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)
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schema = "pynxtools.nomad.schema.Root"
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82+
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nexus_app = AppEntryPoint(
82-
name="NexusApp",
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name="NeXus App",
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description="Simple Generic NeXus app.",
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app=App(
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# Label of the App
@@ -91,7 +93,7 @@ def load(self):
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# Brief description used in the app menu
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description="A simple search app customized for generic NeXus data.",
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# Longer description that can also use markdown
94-
readme="This is a simple App to support basic search for NeXus based Experiment Entries.",
96+
readme="This page allows to search for generic NeXus Experiment Entries. It is similar to the entries search, but with reduced filter set, modified menu on the left and different shown columns. The dashboard directly shows useful interactive statistics about the data",
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# If you want to use quantities from a custom schema, you need to load
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# the search quantities from it first here. Note that you can use a glob
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# syntax to load the entire package, or just a single schema from a
@@ -101,98 +103,249 @@ def load(self):
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),
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# Controls which columns are shown in the results table
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columns=[
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Column(quantity="entry_id", selected=True),
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Column(quantity=f"entry_type", selected=True),
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Column(title="Entry ID", search_quantity="entry_id", selected=True),
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Column(
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title="File Name",
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search_quantity=f"mainfile",
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selected=True,
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),
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Column(
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title="Start Time",
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search_quantity=f"data.ENTRY[*].start_time#{schema}",
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selected=True,
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),
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Column(
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title="Description",
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search_quantity=f"data.ENTRY[*].experiment_description__field#{schema}",
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selected=True,
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),
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Column(
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title="definition",
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quantity=f"data.ENTRY[*].definition__field#{schema}",
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title="Author",
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search_quantity=f"[data.ENTRY[*].USER[*].name__field, data.ENTRY[*].userID[*].name__field]#{schema}",
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selected=True,
110126
),
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Column(
112-
title="start_time",
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quantity=f"data.ENTRY[*].start_time__field#{schema}",
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title="Sample",
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search_quantity=f"data.ENTRY[*].SAMPLE[*].name__field#{schema}",
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selected=True,
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),
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Column(
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title="title",
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quantity=f"data.ENTRY[*].title__field#{schema}",
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title="Sample ID",
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search_quantity=f"data.ENTRY[*].SAMPLE[*].sample_id__field#{schema}",
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selected=False,
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),
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Column(
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title="Definition",
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search_quantity=f"data.ENTRY[*].definition__field#{schema}",
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selected=True,
120141
),
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],
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# Dictionary of search filters that are always enabled for queries made
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# within this app. This is especially important to narrow down the
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# results to the wanted subset. Any available search filter can be
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# targeted here. This example makes sure that only entries that use
126-
# MySchema are included.
145+
# results to the wanted subset.
127146
filters_locked={"section_defs.definition_qualified_name": [schema]},
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# Controls the menu shown on the left
129148
menu=Menu(
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title="Material",
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size=MenuSizeEnum.MD,
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title="Menu",
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items=[
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Menu(
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title="elements",
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title="Elements",
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size=MenuSizeEnum.XXL,
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items=[
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MenuItemPeriodicTable(
136-
quantity="results.material.elements",
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search_quantity="results.material.elements",
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),
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MenuItemTerms(
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search_quantity="results.material.chemical_formula_hill",
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width=6,
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options=0,
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),
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MenuItemTerms(
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quantity="results.material.chemical_formula_hill",
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search_quantity="results.material.chemical_formula_iupac",
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width=6,
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options=0,
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),
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MenuItemTerms(
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quantity="results.material.chemical_formula_iupac",
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search_quantity="results.material.chemical_formula_reduced",
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width=6,
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options=0,
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),
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MenuItemTerms(
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search_quantity="results.material.chemical_formula_anonymous",
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width=6,
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options=0,
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),
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MenuItemHistogram(
149180
x="results.material.n_elements",
150181
),
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],
152-
)
183+
),
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Menu(
185+
title="Experiment type",
186+
size=MenuSizeEnum.LG,
187+
items=[
188+
MenuItemTerms(
189+
title="Entry Type",
190+
search_quantity=f"entry_type",
191+
width=12,
192+
options=12,
193+
),
194+
MenuItemTerms(
195+
title="NeXus Class",
196+
search_quantity=f"data.ENTRY.definition__field#{schema}",
197+
width=12,
198+
options=12,
199+
),
200+
],
201+
),
202+
Menu(
203+
title="Instruments",
204+
size=MenuSizeEnum.LG,
205+
items=[
206+
MenuItemTerms(
207+
title="Model",
208+
search_quantity=f"data.ENTRY.INSTRUMENT.name__field#{schema}",
209+
width=12,
210+
options=12,
211+
),
212+
MenuItemTerms(
213+
name="Name",
214+
search_quantity=f"data.ENTRY.INSTRUMENT.name#{schema}",
215+
width=12,
216+
options=12,
217+
),
218+
],
219+
),
220+
Menu(
221+
title="Samples",
222+
size=MenuSizeEnum.LG,
223+
items=[
224+
MenuItemTerms(
225+
title="Name",
226+
search_quantity=f"data.ENTRY.SAMPLE.name__field#{schema}",
227+
width=12,
228+
options=12,
229+
),
230+
MenuItemTerms(
231+
title="Sample ID",
232+
search_quantity=f"data.ENTRY.SAMPLE.sample_id__field#{schema}",
233+
width=12,
234+
options=12,
235+
),
236+
],
237+
),
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Menu(
239+
title="Authors / Origin",
240+
size=MenuSizeEnum.LG,
241+
items=[
242+
MenuItemTerms(
243+
title="Entry Author",
244+
search_quantity=f"data.ENTRY.USER.name__field#{schema}",
245+
width=12,
246+
options=5,
247+
),
248+
MenuItemTerms(
249+
title="User ID / Entry Author",
250+
search_quantity=f"data.ENTRY.userID.name__field#{schema}#str",
251+
width=12,
252+
options=5,
253+
),
254+
MenuItemTerms(
255+
title="Upload Author",
256+
search_quantity=f"authors.name",
257+
width=12,
258+
options=5,
259+
),
260+
MenuItemTerms(
261+
title="Affiliation",
262+
search_quantity=f"data.ENTRY.USER.affiliation__field#{schema}",
263+
width=12,
264+
options=5,
265+
),
266+
],
267+
),
268+
MenuItemHistogram(
269+
title="Start Time",
270+
x=f"data.ENTRY.start_time#{schema}",
271+
autorange=True,
272+
),
273+
MenuItemHistogram(
274+
title="Upload Creation Time",
275+
x=f"upload_create_time",
276+
autorange=True,
277+
),
153278
],
154279
),
155280
# Controls the default dashboard shown in the search interface
156281
dashboard={
157282
"widgets": [
158283
{
159-
"type": "histogram",
160-
"show_input": False,
161-
"autorange": True,
162-
"nbins": 30,
284+
"type": "periodic_table",
163285
"scale": "linear",
164-
"quantity": f"data.ENTRY.start_time__field#{schema}",
165-
"title": "Start Time",
286+
"quantity": f"results.material.elements",
166287
"layout": {
167-
"lg": {"minH": 3, "minW": 3, "h": 4, "w": 12, "y": 0, "x": 0}
288+
"sm": {"minH": 3, "minW": 3, "h": 5, "w": 8, "y": 0, "x": 0},
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"md": {"minH": 3, "minW": 3, "h": 7, "w": 12, "y": 0, "x": 0},
290+
"lg": {"minH": 3, "minW": 3, "h": 10, "w": 14, "y": 0, "x": 0},
291+
"xl": {"minH": 3, "minW": 3, "h": 7, "w": 10, "y": 0, "x": 0},
292+
"xxl": {"minH": 3, "minW": 3, "h": 7, "w": 10, "y": 0, "x": 0},
168293
},
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},
170295
{
171296
"type": "terms",
172-
"show_input": False,
297+
"show_input": True,
173298
"scale": "linear",
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"quantity": f"entry_type",
175300
"title": "Entry Type",
176301
"layout": {
177-
"lg": {"minH": 3, "minW": 3, "h": 8, "w": 4, "y": 0, "x": 12}
302+
"sm": {"minH": 3, "minW": 3, "h": 5, "w": 4, "y": 0, "x": 8},
303+
"md": {"minH": 3, "minW": 3, "h": 7, "w": 6, "y": 0, "x": 12},
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"lg": {"minH": 3, "minW": 3, "h": 5, "w": 5, "y": 0, "x": 14},
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"xl": {"minH": 3, "minW": 3, "h": 7, "w": 4, "y": 0, "x": 10},
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"xxl": {"minH": 3, "minW": 3, "h": 7, "w": 4, "y": 0, "x": 10},
178307
},
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},
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{
181310
"type": "terms",
182-
"show_input": False,
311+
"show_input": True,
183312
"scale": "linear",
184313
"quantity": f"data.ENTRY.definition__field#{schema}",
185-
"title": "Definition",
314+
"title": "NeXus Class",
186315
"layout": {
187-
"lg": {"minH": 3, "minW": 3, "h": 8, "w": 4, "y": 0, "x": 16}
316+
"sm": {"minH": 3, "minW": 3, "h": 5, "w": 4, "y": 5, "x": 0},
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"md": {"minH": 3, "minW": 3, "h": 7, "w": 6, "y": 7, "x": 0},
318+
"lg": {"minH": 3, "minW": 3, "h": 5, "w": 5, "y": 0, "x": 19},
319+
"xl": {"minH": 3, "minW": 3, "h": 7, "w": 4, "y": 0, "x": 14},
320+
"xxl": {"minH": 3, "minW": 3, "h": 7, "w": 4, "y": 0, "x": 14},
188321
},
189322
},
190323
{
191-
"type": "periodic_table",
324+
"type": "terms",
325+
"show_input": True,
192326
"scale": "linear",
193-
"quantity": f"results.material.elements",
327+
"quantity": f"data.ENTRY.USER.name__field#{schema}",
328+
"title": "Author",
329+
"layout": {
330+
"sm": {"minH": 3, "minW": 3, "h": 5, "w": 4, "y": 5, "x": 4},
331+
"md": {"minH": 3, "minW": 3, "h": 7, "w": 6, "y": 7, "x": 6},
332+
"lg": {"minH": 3, "minW": 3, "h": 5, "w": 5, "y": 5, "x": 14},
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"xl": {"minH": 3, "minW": 3, "h": 7, "w": 4, "y": 0, "x": 18},
334+
"xxl": {"minH": 3, "minW": 3, "h": 7, "w": 4, "y": 0, "x": 18},
335+
},
336+
},
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{
338+
"type": "terms",
339+
"show_input": True,
340+
"scale": "linear",
341+
"quantity": f"data.ENTRY.SAMPLE.name__field#{schema}",
342+
"title": "Sample",
194343
"layout": {
195-
"lg": {"minH": 3, "minW": 3, "h": 4, "w": 12, "y": 4, "x": 0}
344+
"sm": {"minH": 3, "minW": 3, "h": 5, "w": 4, "y": 5, "x": 8},
345+
"md": {"minH": 3, "minW": 3, "h": 7, "w": 6, "y": 7, "x": 12},
346+
"lg": {"minH": 3, "minW": 3, "h": 5, "w": 5, "y": 5, "x": 19},
347+
"xl": {"minH": 3, "minW": 3, "h": 7, "w": 4, "y": 0, "x": 22},
348+
"xxl": {"minH": 3, "minW": 3, "h": 7, "w": 4, "y": 0, "x": 22},
196349
},
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},
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]

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