From 87b4c90a765e0fee66badfe54a9d6431a2a44dd4 Mon Sep 17 00:00:00 2001
From: Lauri Himanen <lauri.himanen@gmail.com>
Date: Wed, 23 Oct 2024 10:24:58 +0000
Subject: [PATCH] Resolve "Issue with missing color markers in scatter plots"
---
examples/data/rdm_tutorial/tutorial.ipynb | 1240 ++---------------
.../editQuantity/QueryEditQuantity.js | 2 +-
.../entry/properties/SampleHistoryCard.js | 16 +-
gui/src/components/search/SearchContext.js | 10 +-
.../components/search/SearchContext.spec.js | 10 +-
gui/src/components/search/SearchResults.js | 2 +-
.../components/search/SearchResults.spec.js | 16 +-
gui/src/components/search/conftest.spec.js | 6 +-
.../search/widgets/WidgetScatterPlot.js | 2 +-
.../search/widgets/WidgetScatterPlot.spec.js | 15 +-
.../components/uploads/SectionSelectDialog.js | 2 +-
gui/tests/env.js | 248 ++--
nomad/config/models/ui.py | 12 +-
13 files changed, 282 insertions(+), 1299 deletions(-)
diff --git a/examples/data/rdm_tutorial/tutorial.ipynb b/examples/data/rdm_tutorial/tutorial.ipynb
index 7a3783f615..845cc22f24 100644
--- a/examples/data/rdm_tutorial/tutorial.ipynb
+++ b/examples/data/rdm_tutorial/tutorial.ipynb
@@ -6814,19 +6814,11 @@
},
{
"cell_type": "code",
- "execution_count": 1,
+ "execution_count": 2,
"metadata": {
"tags": []
},
- "outputs": [
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "Schema is deprecated, use plugins. ()\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"from nomad.metainfo import Quantity\n",
"from nomad.datamodel.data import Schema\n",
@@ -6881,40 +6873,11 @@
},
{
"cell_type": "code",
- "execution_count": 2,
+ "execution_count": null,
"metadata": {
"tags": []
},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "0.10000021008919545 electron_volt\n"
- ]
- },
- {
- "data": {
- "application/json": {
- "delayed_lifetime": 1,
- "peak_emission_wavelength": 470,
- "photoluminescence_quantum_yield": 0.9,
- "singlet_triplet_energy_splitting": 0.10000021008919545
- },
- "text/plain": [
- "<IPython.core.display.JSON object>"
- ]
- },
- "execution_count": 2,
- "metadata": {
- "application/json": {
- "expanded": false,
- "root": "root"
- }
- },
- "output_type": "execute_result"
- }
- ],
+ "outputs": [],
"source": [
"# Quantities can be instantiated in the constructor\n",
"molecule = TADFMolecule(\n",
@@ -6945,7 +6908,7 @@
},
{
"cell_type": "code",
- "execution_count": 3,
+ "execution_count": 4,
"metadata": {
"tags": []
},
@@ -6998,7 +6961,7 @@
},
{
"cell_type": "code",
- "execution_count": 4,
+ "execution_count": 5,
"metadata": {
"tags": []
},
@@ -7026,7 +6989,7 @@
},
{
"cell_type": "code",
- "execution_count": 5,
+ "execution_count": 6,
"metadata": {
"tags": []
},
@@ -7093,25 +7056,11 @@
},
{
"cell_type": "code",
- "execution_count": 6,
+ "execution_count": null,
"metadata": {
"tags": []
},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Collecting rdkit\n",
- " Downloading rdkit-2023.9.6-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (34.9 MB)\n",
- "\u001b[2K \u001b[90mâ”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”â”\u001b[0m \u001b[32m34.9/34.9 MB\u001b[0m \u001b[31m29.6 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m00:01\u001b[0m00:01\u001b[0m\n",
- "\u001b[?25hRequirement already satisfied: numpy in /opt/conda/lib/python3.10/site-packages (from rdkit) (1.22.4)\n",
- "Requirement already satisfied: Pillow in /opt/conda/lib/python3.10/site-packages (from rdkit) (9.4.0)\n",
- "Installing collected packages: rdkit\n",
- "Successfully installed rdkit-2023.9.6\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"! pip install rdkit"
]
@@ -7125,7 +7074,7 @@
},
{
"cell_type": "code",
- "execution_count": 7,
+ "execution_count": 8,
"metadata": {
"tags": []
},
@@ -7156,47 +7105,11 @@
},
{
"cell_type": "code",
- "execution_count": 8,
+ "execution_count": null,
"metadata": {
"tags": []
},
- "outputs": [
- {
- "data": {
- "application/json": {
- "DOI_number": "https://doi.org/10.1021/jp5126624",
- "journal": "The Journal of Physical Chemistry C",
- "m_def": "__main__.TADFMolecule",
- "molecular_formula": "C8H10N4O2",
- "molecular_mass": 194.08037556,
- "publication_authors": [
- "Dharani Sabba",
- "Hemant Kumar Mulmudi",
- "Rajiv Ramanujam Prabhakar",
- "Thirumal Krishnamoorthy",
- "Tom Baikie",
- "Pablo P. Boix",
- "Subodh Mhaisalkar",
- "Nripan Mathews"
- ],
- "publication_date": "2015-01-06T15:24:53+00:00",
- "publication_title": "Impact of Anionic Br<sup>–</sup> Substitution on Open Circuit Voltage in Lead Free Perovskite (CsSnI<sub>3-x</sub>Br<sub><i>x</i></sub>) Solar Cells",
- "smile": "CN1C=NC2=C1C(=O)N(C(=O)N2C)C"
- },
- "text/plain": [
- "<IPython.core.display.JSON object>"
- ]
- },
- "execution_count": 8,
- "metadata": {
- "application/json": {
- "expanded": false,
- "root": "root"
- }
- },
- "output_type": "execute_result"
- }
- ],
+ "outputs": [],
"source": [
"from nomad.datamodel.datamodel import EntryArchive\n",
"import logging\n",
@@ -7236,7 +7149,7 @@
},
{
"cell_type": "code",
- "execution_count": 9,
+ "execution_count": 10,
"metadata": {
"tags": []
},
@@ -7308,354 +7221,11 @@
},
{
"cell_type": "code",
- "execution_count": 10,
+ "execution_count": null,
"metadata": {
"tags": []
},
- "outputs": [
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "/opt/conda/lib/python3.10/site-packages/nomad/atomutils.py:548: RuntimeWarning: invalid value encountered in double_scalars\n",
- " angles[i] = np.dot(cell[j], cell[k]) / (lengths[j] * lengths[k])\n"
- ]
- },
- {
- "data": {
- "application/json": {
- "material": {
- "chemical_formula_anonymous": "A5B4C2D",
- "chemical_formula_descriptive": "C8H10N4O2",
- "chemical_formula_hill": "C8H10N4O2",
- "chemical_formula_iupac": "C4N2H5O",
- "chemical_formula_reduced": "C4H5N2O",
- "elemental_composition": [
- {
- "atomic_fraction": 0.3333333333333333,
- "element": "C",
- "mass": 1.994423656721262e-26,
- "mass_fraction": 0.4948004692297156
- },
- {
- "atomic_fraction": 0.4166666666666667,
- "element": "H",
- "mass": 1.673723746788804e-27,
- "mass_fraction": 0.05190467509755879
- },
- {
- "atomic_fraction": 0.16666666666666666,
- "element": "N",
- "mass": 2.325867254414622e-26,
- "mass_fraction": 0.28851448010356834
- },
- {
- "atomic_fraction": 0.08333333333333333,
- "element": "O",
- "mass": 2.656762874216004e-26,
- "mass_fraction": 0.1647803755691573
- }
- ],
- "elements": [
- "C",
- "H",
- "N",
- "O"
- ],
- "topology": [
- {
- "atoms": {
- "atomic_numbers": [
- 6,
- 7,
- 6,
- 7,
- 6,
- 6,
- 6,
- 8,
- 7,
- 6,
- 8,
- 7,
- 6,
- 6,
- 1,
- 1,
- 1,
- 1,
- 1,
- 1,
- 1,
- 1,
- 1,
- 1
- ],
- "labels": [
- "C",
- "N",
- "C",
- "N",
- "C",
- "C",
- "C",
- "O",
- "N",
- "C",
- "O",
- "N",
- "C",
- "C",
- "H",
- "H",
- "H",
- "H",
- "H",
- "H",
- "H",
- "H",
- "H",
- "H"
- ],
- "lattice_vectors": [
- [
- 0,
- 0,
- 0
- ],
- [
- 0,
- 0,
- 0
- ],
- [
- 0,
- 0,
- 0
- ]
- ],
- "m_def": "nomad.datamodel.metainfo.system.Atoms",
- "periodic": [
- false,
- false,
- false
- ],
- "positions": [
- [
- 3.267350695943137e-10,
- 6.127845346726945e-11,
- -2.3641309333764952e-11
- ],
- [
- 2.1264267420429976e-10,
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- ],
- [
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- ],
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- ],
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- ],
- [
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- 6.188581606168382e-11
- ],
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- ],
- [
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- 1.5590235176205895e-10
- ],
- [
- -2.657054148524369e-10,
- 2.610820200752254e-10,
- -1.8252875322965927e-11
- ],
- [
- -1.287739461582144e-10,
- 3.325435523001943e-10,
- 7.021912677971663e-11
- ]
- ],
- "species": [
- 6,
- 7,
- 6,
- 7,
- 6,
- 6,
- 6,
- 8,
- 7,
- 6,
- 8,
- 7,
- 6,
- 6,
- 1,
- 1,
- 1,
- 1,
- 1,
- 1,
- 1,
- 1,
- 1,
- 1
- ]
- },
- "cell": {
- "a": 0,
- "b": 0,
- "c": 0,
- "volume": 0
- },
- "chemical_formula_anonymous": "A5B4C2D",
- "chemical_formula_descriptive": "C8H10N4O2",
- "chemical_formula_hill": "C8H10N4O2",
- "chemical_formula_iupac": "C4N2H5O",
- "chemical_formula_reduced": "C4H5N2O",
- "description": "3D reconstruction of the molecule generated from the SMILES.",
- "dimensionality": "0D",
- "elemental_composition": [
- {
- "atomic_fraction": 0.3333333333333333,
- "element": "C",
- "mass": 1.994423656721262e-26,
- "mass_fraction": 0.4948004692297156
- },
- {
- "atomic_fraction": 0.16666666666666666,
- "element": "N",
- "mass": 2.325867254414622e-26,
- "mass_fraction": 0.28851448010356834
- },
- {
- "atomic_fraction": 0.08333333333333333,
- "element": "O",
- "mass": 2.656762874216004e-26,
- "mass_fraction": 0.1647803755691573
- },
- {
- "atomic_fraction": 0.4166666666666667,
- "element": "H",
- "mass": 1.673723746788804e-27,
- "mass_fraction": 0.05190467509755879
- }
- ],
- "elements": [
- "C",
- "H",
- "N",
- "O"
- ],
- "label": "Molecule reconstruction",
- "n_atoms": 24,
- "structural_type": "molecule",
- "system_id": "results/material/topology/0"
- }
- ]
- }
- },
- "text/plain": [
- "<IPython.core.display.JSON object>"
- ]
- },
- "execution_count": 10,
- "metadata": {
- "application/json": {
- "expanded": false,
- "root": "root"
- }
- },
- "output_type": "execute_result"
- }
- ],
+ "outputs": [],
"source": [
"archive = EntryArchive(\n",
" data=TADFMolecule(\n",
@@ -7680,7 +7250,7 @@
},
{
"cell_type": "code",
- "execution_count": 11,
+ "execution_count": 12,
"metadata": {
"tags": []
},
@@ -7758,7 +7328,7 @@
},
{
"cell_type": "code",
- "execution_count": 12,
+ "execution_count": 13,
"metadata": {
"tags": []
},
@@ -7829,7 +7399,7 @@
},
{
"cell_type": "code",
- "execution_count": 13,
+ "execution_count": 14,
"metadata": {
"tags": []
},
@@ -7871,7 +7441,7 @@
},
{
"cell_type": "code",
- "execution_count": 14,
+ "execution_count": 15,
"metadata": {
"tags": []
},
@@ -7933,35 +7503,11 @@
},
{
"cell_type": "code",
- "execution_count": 15,
+ "execution_count": null,
"metadata": {
"tags": []
},
- "outputs": [
- {
- "data": {
- "application/json": {
- "DOI_number": "https://doi.org/10.1039/D0TC02884C",
- "iupac_name": "5-(5-(dibenzo[b, d]furan-2-yl)-pyridin-2-yl)-5H-benzo[d]benzo-[4,5]imidazo[1,2-a]imidazole",
- "m_def": "TADFMolecules.TADFMolecule",
- "name": "5-(5-(dibenzo[b,d]furan-2-yl)-pyridin-2-yl)-5H-benzo[d]benzo-[4,5]imidazo[1,2-a]imidazole",
- "peak_emission_wavelength": 483,
- "smile": "c1ccc2c(c1)nc1n(-c3ccc(-c4ccc5oc6ccccc6c5c4)cn3)c3ccccc3n21"
- },
- "text/plain": [
- "<IPython.core.display.JSON object>"
- ]
- },
- "execution_count": 15,
- "metadata": {
- "application/json": {
- "expanded": false,
- "root": "root"
- }
- },
- "output_type": "execute_result"
- }
- ],
+ "outputs": [],
"source": [
"archive = EntryArchive()\n",
"parser = TADFMoleculesParser()\n",
@@ -7980,610 +7526,11 @@
},
{
"cell_type": "code",
- "execution_count": 16,
+ "execution_count": null,
"metadata": {
"tags": []
},
- "outputs": [
- {
- "data": {
- "application/json": {
- "data": {
- "DOI_number": "https://doi.org/10.1039/D0TC02884C",
- "iupac_name": "5-(5-(dibenzo[b, d]furan-2-yl)-pyridin-2-yl)-5H-benzo[d]benzo-[4,5]imidazo[1,2-a]imidazole",
- "journal": "Journal of Materials Chemistry C",
- "m_def": "TADFMolecules.TADFMolecule",
- "molecular_formula": "C30H18N4O",
- "molecular_mass": 450.1480611960005,
- "name": "5-(5-(dibenzo[b,d]furan-2-yl)-pyridin-2-yl)-5H-benzo[d]benzo-[4,5]imidazo[1,2-a]imidazole",
- "peak_emission_wavelength": 483,
- "publication_authors": [
- "Kyu Man Youn",
- "Hyuna Lee",
- "Han Jong Yoo",
- "Young Hun Jung",
- "Jae Do Park",
- "Hyein Jeong",
- "Jungsub Lee",
- "Ju Young Lee",
- "Jang Hyuk Kwon"
- ],
- "publication_date": "2020-09-11T02:25:56+00:00",
- "publication_title": "High triplet energy bipolar host materials with the combination of dibenzofuran and benziimidazobenzoimidazole moieties for blue thermally activated delayed fluorescence emitter",
- "smile": "c1ccc2c(c1)nc1n(-c3ccc(-c4ccc5oc6ccccc6c5c4)cn3)c3ccccc3n21"
- },
- "metadata": {
- "entry_type": "TADFMolecule",
- "references": [
- "https://doi.org/10.1039/D0TC02884C"
- ]
- },
- "results": {
- "material": {
- "chemical_formula_anonymous": "A30B18C4D",
- "chemical_formula_descriptive": "C30H18N4O",
- "chemical_formula_hill": "C30H18N4O",
- "chemical_formula_iupac": "C30N4H18O",
- "chemical_formula_reduced": "C30H18N4O",
- "elemental_composition": [
- {
- "atomic_fraction": 0.5660377358490566,
- "element": "C",
- "mass": 1.994423656721262e-26,
- "mass_fraction": 0.7998421807785707
- },
- {
- "atomic_fraction": 0.33962264150943394,
- "element": "H",
- "mass": 1.673723746788804e-27,
- "mass_fraction": 0.040273735637087894
- },
- {
- "atomic_fraction": 0.07547169811320754,
- "element": "N",
- "mass": 2.325867254414622e-26,
- "mass_fraction": 0.12436854331011744
- },
- {
- "atomic_fraction": 0.018867924528301886,
- "element": "O",
- "mass": 2.656762874216004e-26,
- "mass_fraction": 0.035515540274223996
- }
- ],
- "elements": [
- "C",
- "H",
- "N",
- "O"
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- "topology": [
- {
- "atoms": {
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- "labels": [
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- "H",
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- "H",
- "H",
- "H",
- "H",
- "H",
- "H",
- "H",
- "H",
- "H"
- ],
- "lattice_vectors": [
- [
- 0,
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- 0
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- [
- 0,
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- [
- 0,
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- ]
- ],
- "m_def": "nomad.datamodel.metainfo.system.Atoms",
- "periodic": [
- false,
- false,
- false
- ],
- "positions": [
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- ],
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- 5.744573231016062e-10,
- 2.834980926639528e-10,
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- ],
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- 3.420802181449816e-10,
- 1.0886772734583234e-10,
- -8.603153377599315e-12
- ],
- [
- 1.1532875058250963e-10,
- 9.217143137930445e-11,
- 1.4088389989047605e-10
- ],
- [
- -2.0100344860447588e-10,
- -1.2021609100621008e-10,
- -3.267025530339569e-10
- ],
- [
- -3.79195075451379e-10,
- -1.4856011757095024e-10,
- -4.958266255587795e-10
- ],
- [
- -6.159405453629103e-10,
- -1.0064321296382544e-10,
- -4.423215014756119e-10
- ],
- [
- -6.811731073907394e-10,
- -2.1000209556077262e-11,
- -2.152298862639582e-10
- ]
- ],
- "species": [
- 6,
- 6,
- 6,
- 6,
- 6,
- 6,
- 7,
- 6,
- 7,
- 6,
- 6,
- 6,
- 6,
- 6,
- 6,
- 6,
- 6,
- 8,
- 6,
- 6,
- 6,
- 6,
- 6,
- 6,
- 6,
- 6,
- 6,
- 7,
- 6,
- 6,
- 6,
- 6,
- 6,
- 6,
- 7,
- 1,
- 1,
- 1,
- 1,
- 1,
- 1,
- 1,
- 1,
- 1,
- 1,
- 1,
- 1,
- 1,
- 1,
- 1,
- 1,
- 1,
- 1
- ]
- },
- "cell": {
- "a": 0,
- "b": 0,
- "c": 0,
- "volume": 0
- },
- "chemical_formula_anonymous": "A30B18C4D",
- "chemical_formula_descriptive": "C30H18N4O",
- "chemical_formula_hill": "C30H18N4O",
- "chemical_formula_iupac": "C30N4H18O",
- "chemical_formula_reduced": "C30H18N4O",
- "description": "3D reconstruction of the molecule generated from the SMILES.",
- "dimensionality": "0D",
- "elemental_composition": [
- {
- "atomic_fraction": 0.5660377358490566,
- "element": "C",
- "mass": 1.994423656721262e-26,
- "mass_fraction": 0.7998421807785707
- },
- {
- "atomic_fraction": 0.07547169811320754,
- "element": "N",
- "mass": 2.325867254414622e-26,
- "mass_fraction": 0.12436854331011744
- },
- {
- "atomic_fraction": 0.018867924528301886,
- "element": "O",
- "mass": 2.656762874216004e-26,
- "mass_fraction": 0.035515540274223996
- },
- {
- "atomic_fraction": 0.33962264150943394,
- "element": "H",
- "mass": 1.673723746788804e-27,
- "mass_fraction": 0.040273735637087894
- }
- ],
- "elements": [
- "C",
- "H",
- "N",
- "O"
- ],
- "label": "Molecule reconstruction",
- "n_atoms": 53,
- "structural_type": "molecule",
- "system_id": "results/material/topology/0"
- }
- ]
- }
- }
- },
- "text/plain": [
- "<IPython.core.display.JSON object>"
- ]
- },
- "execution_count": 16,
- "metadata": {
- "application/json": {
- "expanded": false,
- "root": "root"
- }
- },
- "output_type": "execute_result"
- }
- ],
+ "outputs": [],
"source": [
"archive.data.normalize(archive, logger)\n",
"JSON(archive.m_to_dict())"
@@ -8605,19 +7552,11 @@
},
{
"cell_type": "code",
- "execution_count": 18,
+ "execution_count": null,
"metadata": {
"tags": []
},
- "outputs": [
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "could not generate representative structure\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"import os\n",
"import json\n",
@@ -8678,12 +7617,14 @@
" Column,\n",
" Columns,\n",
" Dashboard,\n",
- " FilterMenu,\n",
- " FilterMenus,\n",
- " Filters,\n",
" Format,\n",
" Layout,\n",
+ " Menu,\n",
+ " MenuItemHistogram,\n",
+ " MenuItemPeriodicTable,\n",
+ " MenuItemTerms,\n",
" Pagination,\n",
+ " SearchQuantities,\n",
" WidgetHistogram,\n",
" WidgetPeriodicTable,\n",
" WidgetScatterPlot,\n",
@@ -8696,7 +7637,7 @@
" path='tadf-molecules',\n",
" description='Search for thermally activated delayed fluorescent molecules.',\n",
" category='Experiment',\n",
- " filters=Filters(\n",
+ " search_quantities=SearchQuantities(\n",
" include=[f'*#{schema}'],\n",
" ),\n",
" filters_locked={'section_defs.definition_qualified_name': schema},\n",
@@ -8704,57 +7645,84 @@
" order_by=f'data.photoluminescence_quantum_yield#{schema}',\n",
" order='desc',\n",
" ),\n",
- " columns=Columns(\n",
- " selected=[\n",
- " 'results.material.chemical_formula_hill',\n",
- " f'data.photoluminescence_quantum_yield#{schema}',\n",
- " f'data.peak_emission_wavelength#{schema}',\n",
- " f'data.delayed_lifetime#{schema}',\n",
- " f'data.singlet_triplet_energy_splitting#{schema}',\n",
- " 'references',\n",
- " ],\n",
- " options={\n",
- " 'results.material.chemical_formula_hill': Column(),\n",
- " f'data.photoluminescence_quantum_yield#{schema}': Column(\n",
- " format=Format(decimals=2, mode='standard')\n",
- " ),\n",
- " f'data.peak_emission_wavelength#{schema}': Column(\n",
- " format=Format(decimals=2, mode='standard'), unit='nm'\n",
- " ),\n",
- " f'data.delayed_lifetime#{schema}': Column(\n",
- " format=Format(decimals=2, mode='standard'), unit='µs'\n",
+ " columns=[\n",
+ " Column(search_quantity='results.material.chemical_formula_hill', selected=True),\n",
+ " Column(\n",
+ " search_quantity=f'data.photoluminescence_quantum_yield#{schema}',\n",
+ " format=Format(decimals=2),\n",
+ " selected=True,\n",
+ " ),\n",
+ " Column(\n",
+ " search_quantity=f'data.peak_emission_wavelength#{schema}',\n",
+ " format=Format(decimals=2),\n",
+ " selected=True,\n",
+ " ),\n",
+ " Column(\n",
+ " search_quantity=f'data.delayed_lifetime#{schema}',\n",
+ " format=Format(decimals=2),\n",
+ " selected=True,\n",
+ " ),\n",
+ " Column(\n",
+ " search_quantity=f'data.singlet_triplet_energy_splitting#{schema}',\n",
+ " format=Format(decimals=2),\n",
+ " selected=True,\n",
+ " ),\n",
+ " Column(search_quantity='references', selected=True),\n",
+ " ],\n",
+ " menu=Menu(\n",
+ " items=[\n",
+ " Menu(\n",
+ " title='Elements / Formula',\n",
+ " size='xxl',\n",
+ " items=[\n",
+ " MenuItemPeriodicTable(\n",
+ " search_quantity='results.material.elements',\n",
+ " ),\n",
+ " MenuItemTerms(\n",
+ " search_quantity='results.material.chemical_formula_hill',\n",
+ " options=0,\n",
+ " ),\n",
+ " MenuItemHistogram(\n",
+ " x='results.material.n_elements',\n",
+ " ),\n",
+ " ],\n",
" ),\n",
- " f'data.singlet_triplet_energy_splitting#{schema}': Column(\n",
- " format=Format(decimals=2, mode='standard'),\n",
- " unit='eV',\n",
+ " Menu(\n",
+ " title='TADF Properties',\n",
+ " items=[\n",
+ " MenuItemHistogram(\n",
+ " x=f'data.photoluminescence_quantum_yield#{schema}',\n",
+ " ),\n",
+ " MenuItemHistogram(\n",
+ " x=f'data.peak_emission_wavelength#{schema}',\n",
+ " ),\n",
+ " MenuItemHistogram(\n",
+ " x=f'data.delayed_lifetime#{schema}',\n",
+ " ),\n",
+ " MenuItemHistogram(\n",
+ " x=f'data.singlet_triplet_energy_splitting#{schema}',\n",
+ " ),\n",
+ " ],\n",
" ),\n",
- " 'references': Column(),\n",
- " },\n",
- " ),\n",
- " filter_menus=FilterMenus(\n",
- " options={\n",
- " 'material': FilterMenu(label='Material'),\n",
- " 'elements': FilterMenu(label='Elements / Formula', level=1, size='xl'),\n",
- " 'custom_quantities': FilterMenu(label='Custom Quantities', size='l'),\n",
- " 'metadata': FilterMenu(label='Visibility / IDs / Schema'),\n",
- " }\n",
+ " ]\n",
" ),\n",
" dashboard=Dashboard(\n",
" widgets=[\n",
" WidgetPeriodicTable(\n",
" scale='linear',\n",
- " quantity='results.material.elements',\n",
+ " search_quantity='results.material.elements',\n",
" layout={'lg': Layout(w=11, h=7, x=0, y=0)},\n",
" ),\n",
" WidgetScatterPlot(\n",
" layout={'lg': Layout(w=7, h=7, x=11, y=0)},\n",
- " x=Axis(quantity=f'data.peak_emission_wavelength#{schema}', unit='nm'),\n",
- " y=Axis(quantity=f'data.photoluminescence_quantum_yield#{schema}'),\n",
+ " x=Axis(\n",
+ " search_quantity=f'data.peak_emission_wavelength#{schema}', unit='nm'\n",
+ " ),\n",
+ " y=Axis(search_quantity=f'data.delayed_lifetime#{schema}'),\n",
" ),\n",
" WidgetTerms(\n",
- " type='terms',\n",
" layout={'lg': Layout(w=6, h=7, x=18, y=0)},\n",
- " quantity='results.material.chemical_formula_hill',\n",
+ " search_quantity='results.material.chemical_formula_hill',\n",
" scale='linear',\n",
" ),\n",
" WidgetHistogram(\n",
@@ -8762,18 +7730,22 @@
" autorange=False,\n",
" nbins=30,\n",
" scale='1/4',\n",
- " quantity=f'data.delayed_lifetime#{schema}',\n",
+ " x=Axis(search_quantity=f'data.delayed_lifetime#{schema}'),\n",
" ),\n",
" WidgetHistogram(\n",
" layout={'lg': Layout(w=12, h=4, x=12, y=7)},\n",
" autorange=False,\n",
" nbins=30,\n",
" scale='linear',\n",
- " quantity=f'data.singlet_triplet_energy_splitting#{schema}',\n",
+ " x=Axis(\n",
+ " search_quantity=f'data.singlet_triplet_energy_splitting#{schema}',\n",
+ " unit='joule',\n",
+ " ),\n",
" ),\n",
" ]\n",
" ),\n",
- ")"
+ ")\n",
+ "\n"
]
},
{
@@ -8784,8 +7756,8 @@
"source": [
"We will not go very deep into app development, but here are the most important things to notice:\n",
"\n",
- " - `filters`: By default, apps will not load any additional schemas to avoid overcrowding the search bar. Only the \"standardized\" set of information found in `archive.metadata` and `archive.results` is available by default. To load our schema into the app, we define in `filters.include` a pattern that matches all information in our schema.\n",
- " - `filter_menus`: This controls which menus will be visible on the left. Currently, there is only a fixed set of available menus, but we are working on a more flexible customization for them as well.\n",
+ " - `search_quantities`: By default, apps will not load any additional schemas to avoid overcrowding the search bar. Only the \"standardized\" set of information found in `archive.metadata` and `archive.results` is available by default. To load our schema into the app, we define in `search_quantities.include` a pattern that matches all information in our schema.\n",
+ " - `menus`: This controls the menu layout on the left.\n",
" - `filters_locked`: Used to pre-filter the results that this app will show. In our case we say we only want entries that originate from the `TADFMolecule` schema.\n",
" - `columns`: This controls which columns will be shown in the results table.\n",
" - `dashboard`: Controls which widgets to show by default above the search results.\n",
@@ -8814,7 +7786,7 @@
],
"metadata": {
"kernelspec": {
- "display_name": "Python 3 (ipykernel)",
+ "display_name": "nomad",
"language": "python",
"name": "python3"
},
@@ -8828,7 +7800,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.10.10"
+ "version": "3.11.0"
}
},
"nbformat": 4,
diff --git a/gui/src/components/editQuantity/QueryEditQuantity.js b/gui/src/components/editQuantity/QueryEditQuantity.js
index 8417258974..31f6b82e3a 100644
--- a/gui/src/components/editQuantity/QueryEditQuantity.js
+++ b/gui/src/components/editQuantity/QueryEditQuantity.js
@@ -44,7 +44,7 @@ const shownColumns = [
]
const rows = context?.rows
const columns = (context?.columns || [])
- .map((column) => ({...column, selected: shownColumns.includes(column.quantity)}))
+ .map((column) => ({...column, selected: shownColumns.includes(column.search_quantity)}))
rows.details = {enabled: false}
rows.actions = {enabled: false}
diff --git a/gui/src/components/entry/properties/SampleHistoryCard.js b/gui/src/components/entry/properties/SampleHistoryCard.js
index 0dc26bbb66..0d454f7b0e 100644
--- a/gui/src/components/entry/properties/SampleHistoryCard.js
+++ b/gui/src/components/entry/properties/SampleHistoryCard.js
@@ -27,14 +27,14 @@ import { ui } from "../../../config"
const context = cloneDeep(ui?.apps?.options?.entries)
const columns = [
- {quantity: 'entry_name', title: 'Name', align: 'left', selected: true},
- {quantity: 'entry_type', title: 'Entry type', align: 'left', selected: true},
- {quantity: 'entry_create_time', title: 'Entry creation time', align: 'left', selected: true},
- {quantity: 'upload_name', title: 'Upload name', align: 'left'},
- {quantity: 'upload_id', title: 'Upload id', align: 'left'},
- {quantity: 'upload_create_time', title: 'Upload time', align: 'left'},
- {quantity: 'authors', title: 'Authors', align: 'left', sortable: false},
- {quantity: 'results.eln.lab_ids', title: 'IDs'}
+ {search_quantity: 'entry_name', title: 'Name', align: 'left', selected: true},
+ {search_quantity: 'entry_type', title: 'Entry type', align: 'left', selected: true},
+ {search_quantity: 'entry_create_time', title: 'Entry creation time', align: 'left', selected: true},
+ {search_quantity: 'upload_name', title: 'Upload name', align: 'left'},
+ {search_quantity: 'upload_id', title: 'Upload id', align: 'left'},
+ {search_quantity: 'upload_create_time', title: 'Upload time', align: 'left'},
+ {search_quantity: 'authors', title: 'Authors', align: 'left', sortable: false},
+ {search_quantity: 'results.eln.lab_ids', title: 'IDs'}
]
context.colums = columns
diff --git a/gui/src/components/search/SearchContext.js b/gui/src/components/search/SearchContext.js
index bbedb85215..c54c7457ac 100644
--- a/gui/src/components/search/SearchContext.js
+++ b/gui/src/components/search/SearchContext.js
@@ -249,11 +249,11 @@ export const SearchContextRaw = React.memo(({
let options = cloneDeep(initialColumns)
options.forEach(option => {
- const parseResults = parseJMESPath(option.quantity)
+ const parseResults = parseJMESPath(option.search_quantity)
if (parseResults.error) {
- throw Error(`Invalid JMESPath query in the app columns: ${option.quantity}`)
+ throw Error(`Invalid JMESPath query in the app columns: ${option.search_quantity}`)
}
- option.sortable = parseResults.quantity === option.quantity
+ option.sortable = parseResults.quantity === option.search_quantity
const filter = initialSearchQuantities[parseResults.quantity]
const storageUnit = filter?.unit
const displayUnit = option.unit
@@ -362,9 +362,9 @@ export const SearchContextRaw = React.memo(({
}
// Add key, defaults, and custom overrides
- options = options.map((column) => ({...column, key: column.quantity}))
+ options = options.map((column) => ({...column, key: column.search_quantity}))
addColumnDefaults(options, undefined, initialSearchQuantities)
- options = options.map((column) => ({...column, ...(overrides[column.quantity] || {})}))
+ options = options.map((column) => ({...column, ...(overrides[column.search_quantity] || {})}))
return options
}, [initialSearchQuantities, initialColumns, user, units])
diff --git a/gui/src/components/search/SearchContext.spec.js b/gui/src/components/search/SearchContext.spec.js
index 282c4fe9df..df4a3e1607 100644
--- a/gui/src/components/search/SearchContext.spec.js
+++ b/gui/src/components/search/SearchContext.spec.js
@@ -125,22 +125,22 @@ describe('reading query from URL', function() {
})
})
-describe.only('test that final column information is generated correctly', function() {
+describe('test that final column information is generated correctly', function() {
test.each([
['default unit, default label', {}, new Filter({name: 'test_filter'}, {group: 'test', unit: 'joule'}), 'Test filter (eV)'],
['custom label, default unit', {title: 'Testing'}, new Filter(undefined, {group: 'test', unit: 'joule'}), 'Testing (eV)'],
['default label, custom unit', {}, new Filter({name: 'test_filter'}, {group: 'test', unit: 'joule'}), 'Test filter (eV)'],
['custom label, custom unit', {title: 'Testing', unit: 'Ha'}, new Filter(undefined, {group: 'test', unit: 'joule'}), 'Testing (Ha)']
])('%s', async (name, column, filter, label) => {
- const quantity = 'test_filter'
+ const search_quantity = 'test_filter'
const { result: resultUseSearchContext } = renderHook(() => useSearchContext(), { wrapper: (props) => <Wrapper
- initialSearchQuantities={{[quantity]: filter}}
- initialColumns={[{quantity, ...column}]}
+ initialSearchQuantities={{[search_quantity]: filter}}
+ initialColumns={[{search_quantity, ...column}]}
{...props}
/>})
const columns = resultUseSearchContext.current.columns
for (const column of columns) {
- if (column.quantity === quantity) {
+ if (column.search_quantity === search_quantity) {
expect(column.label).toBe(label)
}
}
diff --git a/gui/src/components/search/SearchResults.js b/gui/src/components/search/SearchResults.js
index e0016f3b81..07969485b1 100644
--- a/gui/src/components/search/SearchResults.js
+++ b/gui/src/components/search/SearchResults.js
@@ -71,7 +71,7 @@ export const SearchResults = React.memo(({
const shownColumns = columns
? columns
.filter((column) => column.selected)
- .map((column) => column.quantity)
+ .map((column) => column.search_quantity)
: []
useEffect(() => {
diff --git a/gui/src/components/search/SearchResults.spec.js b/gui/src/components/search/SearchResults.spec.js
index cdfc0de37d..a51d3842e1 100644
--- a/gui/src/components/search/SearchResults.spec.js
+++ b/gui/src/components/search/SearchResults.spec.js
@@ -68,13 +68,13 @@ jest.mock('./SearchContext', () => ({
describe('test search columns', () => {
test.each([
- ['boolean scalar', {quantity: 'my_boolean', selected: true}, 'My boolean', 'True', true],
- ['float scalar', {quantity: 'my_float', selected: true, format: {decimals: 2}}, 'My float', '1.23', true],
- ['float from repeating section', {quantity: 'repeated_section[*].my_float', selected: true, format: {decimals: 2}}, 'My float', '1.23, 2.35', false],
- ['float from nested repeating section', {quantity: 'repeated_section_outer[*].repeated_section_inner[*].my_float', selected: true, format: {decimals: 2}}, 'My float', '1.23, 2.35, 3.46', false],
- ['float from array', {quantity: 'my_float_array', selected: true, format: {decimals: 2}}, 'My float array', '1.23, 2.35', false],
- ['custom title', {quantity: 'my_float', title: 'Custom', selected: true, format: {decimals: 2}}, 'Custom', '1.23', true],
- ['custom quantity', {quantity: 'data.my_float#my_plugin.schema_packages.my_schema.MySchema.my_float', selected: true, format: {decimals: 2}}, 'My float', '1.23', true]
+ ['boolean scalar', {search_quantity: 'my_boolean', selected: true}, 'My boolean', 'True', true],
+ ['float scalar', {search_quantity: 'my_float', selected: true, format: {decimals: 2}}, 'My float', '1.23', true],
+ ['float from repeating section', {search_quantity: 'repeated_section[*].my_float', selected: true, format: {decimals: 2}}, 'My float', '1.23, 2.35', false],
+ ['float from nested repeating section', {search_quantity: 'repeated_section_outer[*].repeated_section_inner[*].my_float', selected: true, format: {decimals: 2}}, 'My float', '1.23, 2.35, 3.46', false],
+ ['float from array', {search_quantity: 'my_float_array', selected: true, format: {decimals: 2}}, 'My float array', '1.23, 2.35', false],
+ ['custom title', {search_quantity: 'my_float', title: 'Custom', selected: true, format: {decimals: 2}}, 'Custom', '1.23', true],
+ ['custom quantity', {search_quantity: 'data.my_float#my_plugin.schema_packages.my_schema.MySchema.my_float', selected: true, format: {decimals: 2}}, 'My float', '1.23', true]
])('%s', async (name, column, expected_title, expected_value, sortable) => {
render(
<SearchContextRaw
@@ -95,7 +95,7 @@ describe('test search columns', () => {
)
screen.getByText(expected_title)
screen.getByText(expected_value)
- const sortButton = screen.queryByTestId(`sortable_${column.quantity}`)
+ const sortButton = screen.queryByTestId(`sortable_${column.search_quantity}`)
if (sortable) {
expect(sortButton).not.toBeNull()
} else {
diff --git a/gui/src/components/search/conftest.spec.js b/gui/src/components/search/conftest.spec.js
index 0e49362b7a..6a700ad967 100644
--- a/gui/src/components/search/conftest.spec.js
+++ b/gui/src/components/search/conftest.spec.js
@@ -343,9 +343,9 @@ export async function expectSearchResults(columns, root = screen) {
const columnLabels = columns
.filter((column) => column.selected)
.map((column) => {
- const quantity = column.quantity
- const unit = column.unit || defaultFilterData[quantity]?.unit
- const label = column.label || defaultFilterData[quantity]?.label || getDisplayLabel({name: quantity.split('.').slice(-1)[0]})
+ const searchQuantity = column.search_quantity
+ const unit = column.unit || defaultFilterData[searchQuantity]?.unit
+ const label = column.label || defaultFilterData[searchQuantity]?.label || getDisplayLabel({name: searchQuantity.split('.').slice(-1)[0]})
return unit
? `${label} (${new Unit(unit).label()})`
: label
diff --git a/gui/src/components/search/widgets/WidgetScatterPlot.js b/gui/src/components/search/widgets/WidgetScatterPlot.js
index 7f56fefdeb..04fd99367b 100644
--- a/gui/src/components/search/widgets/WidgetScatterPlot.js
+++ b/gui/src/components/search/widgets/WidgetScatterPlot.js
@@ -122,7 +122,7 @@ export const WidgetScatterPlot = React.memo((
yAxis: getAxisConfig(y, filterData, units),
colorAxis: markers?.color ? getAxisConfig(markers.color, filterData, units) : {}
}
- }, [error, filterData, markers.color, x, units, y])
+ }, [error, filterData, markers?.color, x, units, y])
const setXFilter = useSetFilter(xAxis.search_quantity)
const setYFilter = useSetFilter(yAxis.search_quantity)
diff --git a/gui/src/components/search/widgets/WidgetScatterPlot.spec.js b/gui/src/components/search/widgets/WidgetScatterPlot.spec.js
index 161994bbd9..b2fb9cd182 100644
--- a/gui/src/components/search/widgets/WidgetScatterPlot.spec.js
+++ b/gui/src/components/search/widgets/WidgetScatterPlot.spec.js
@@ -148,18 +148,19 @@ describe('test custom axis units', () => {
describe('test different colors', () => {
test.each([
- ['empty', undefined, undefined, []],
- ['scalar integer', 'results.material.n_elements', {search_quantity: 'results.material.n_elements'}, []],
- ['scalar float', 'results.properties.geometry_optimization.final_energy_difference', {search_quantity: 'results.properties.geometry_optimization.final_energy_difference'}, []],
- ['scalar string', 'results.material.chemical_formula_hill', undefined, ['Si2', 'CO2']],
- ['array string', 'results.material.elements', undefined, ['Si', 'C, O']]
- ])('%s', async (name, axis, colorTitle, legend) => {
+ ['empty markers', undefined, undefined, []],
+ ['empty color', {}, undefined, []],
+ ['scalar integer', {color: {search_quantity: 'results.material.n_elements'}}, {search_quantity: 'results.material.n_elements'}, []],
+ ['scalar float', {color: {search_quantity: 'results.properties.geometry_optimization.final_energy_difference'}}, {search_quantity: 'results.properties.geometry_optimization.final_energy_difference'}, []],
+ ['scalar string', {color: {search_quantity: 'results.material.chemical_formula_hill'}}, undefined, ['Si2', 'CO2']],
+ ['array string', {color: {search_quantity: 'results.material.elements'}}, undefined, ['Si', 'C, O']]
+ ])('%s', async (name, markers, colorTitle, legend) => {
const config = {
id: '0',
scale: 'linear',
x: {search_quantity: 'results.material.n_elements'},
y: {search_quantity: 'results.material.n_elements'},
- markers: {color: {search_quantity: axis}}
+ markers: markers
}
renderSearchEntry(<WidgetScatterPlot {...config} />)
await expectWidgetScatterPlot(config, false, colorTitle, legend)
diff --git a/gui/src/components/uploads/SectionSelectDialog.js b/gui/src/components/uploads/SectionSelectDialog.js
index 9187165cd6..acefa519c6 100644
--- a/gui/src/components/uploads/SectionSelectDialog.js
+++ b/gui/src/components/uploads/SectionSelectDialog.js
@@ -198,7 +198,7 @@ Details.propTypes = {
}
const columns = (context?.columns || [])
- .map((column) => ({...column, selected: shownColumns.includes(column.quantity)}))
+ .map((column) => ({...column, selected: shownColumns.includes(column.search_quantity)}))
const rows = context?.rows
rows.details = {enabled: true, render: Details}
rows.actions = {enabled: false}
diff --git a/gui/tests/env.js b/gui/tests/env.js
index 33faca4662..d0a3b27971 100644
--- a/gui/tests/env.js
+++ b/gui/tests/env.js
@@ -441,158 +441,158 @@ window.nomadEnv = {
},
"columns": [
{
- "quantity": "entry_name",
+ "search_quantity": "entry_name",
"selected": true,
"title": "Name",
"label": "Name",
"align": "left"
},
{
- "quantity": "results.material.chemical_formula_hill",
+ "search_quantity": "results.material.chemical_formula_hill",
"selected": true,
"title": "Formula",
"label": "Formula",
"align": "left"
},
{
- "quantity": "entry_type",
+ "search_quantity": "entry_type",
"selected": true,
"align": "left"
},
{
- "quantity": "entry_create_time",
+ "search_quantity": "entry_create_time",
"selected": false,
"align": "left"
},
{
- "quantity": "upload_name",
+ "search_quantity": "upload_name",
"selected": false,
"align": "left"
},
{
- "quantity": "upload_id",
+ "search_quantity": "upload_id",
"selected": false,
"align": "left"
},
{
- "quantity": "upload_create_time",
+ "search_quantity": "upload_create_time",
"selected": true,
"title": "Upload time",
"label": "Upload time",
"align": "left"
},
{
- "quantity": "authors",
+ "search_quantity": "authors",
"selected": true,
"align": "left"
},
{
- "quantity": "results.method.method_name",
+ "search_quantity": "results.method.method_name",
"selected": false,
"align": "left"
},
{
- "quantity": "results.method.simulation.program_name",
+ "search_quantity": "results.method.simulation.program_name",
"selected": false,
"align": "left"
},
{
- "quantity": "results.method.simulation.dft.xc_functional_type",
+ "search_quantity": "results.method.simulation.dft.xc_functional_type",
"selected": false,
"align": "left"
},
{
- "quantity": "results.method.simulation.precision.apw_cutoff",
+ "search_quantity": "results.method.simulation.precision.apw_cutoff",
"selected": false,
"align": "left"
},
{
- "quantity": "results.method.simulation.precision.basis_set",
+ "search_quantity": "results.method.simulation.precision.basis_set",
"selected": false,
"align": "left"
},
{
- "quantity": "results.method.simulation.precision.k_line_density",
+ "search_quantity": "results.method.simulation.precision.k_line_density",
"selected": false,
"align": "left"
},
{
- "quantity": "results.method.simulation.precision.native_tier",
+ "search_quantity": "results.method.simulation.precision.native_tier",
"selected": false,
"align": "left"
},
{
- "quantity": "results.method.simulation.precision.planewave_cutoff",
+ "search_quantity": "results.method.simulation.precision.planewave_cutoff",
"selected": false,
"align": "left"
},
{
- "quantity": "results.material.structural_type",
+ "search_quantity": "results.material.structural_type",
"selected": false,
"align": "left"
},
{
- "quantity": "results.material.symmetry.crystal_system",
+ "search_quantity": "results.material.symmetry.crystal_system",
"selected": false,
"align": "left"
},
{
- "quantity": "results.material.symmetry.space_group_symbol",
+ "search_quantity": "results.material.symmetry.space_group_symbol",
"selected": false,
"align": "left"
},
{
- "quantity": "results.material.symmetry.space_group_number",
+ "search_quantity": "results.material.symmetry.space_group_number",
"selected": false,
"align": "left"
},
{
- "quantity": "results.eln.lab_ids",
+ "search_quantity": "results.eln.lab_ids",
"selected": false,
"align": "left"
},
{
- "quantity": "results.eln.sections",
+ "search_quantity": "results.eln.sections",
"selected": false,
"align": "left"
},
{
- "quantity": "results.eln.methods",
+ "search_quantity": "results.eln.methods",
"selected": false,
"align": "left"
},
{
- "quantity": "results.eln.tags",
+ "search_quantity": "results.eln.tags",
"selected": false,
"align": "left"
},
{
- "quantity": "results.eln.instruments",
+ "search_quantity": "results.eln.instruments",
"selected": false,
"align": "left"
},
{
- "quantity": "mainfile",
+ "search_quantity": "mainfile",
"selected": false,
"align": "left"
},
{
- "quantity": "comment",
+ "search_quantity": "comment",
"selected": false,
"align": "left"
},
{
- "quantity": "references",
+ "search_quantity": "references",
"selected": false,
"align": "left"
},
{
- "quantity": "datasets",
+ "search_quantity": "datasets",
"selected": false,
"align": "left"
},
{
- "quantity": "published",
+ "search_quantity": "published",
"selected": false,
"title": "Access",
"label": "Access",
@@ -2409,113 +2409,113 @@ window.nomadEnv = {
},
"columns": [
{
- "quantity": "results.material.chemical_formula_hill",
+ "search_quantity": "results.material.chemical_formula_hill",
"selected": true,
"title": "Formula",
"label": "Formula",
"align": "left"
},
{
- "quantity": "results.method.simulation.program_name",
+ "search_quantity": "results.method.simulation.program_name",
"selected": true,
"align": "left"
},
{
- "quantity": "results.method.method_name",
+ "search_quantity": "results.method.method_name",
"selected": true,
"align": "left"
},
{
- "quantity": "results.method.simulation.dft.xc_functional_type",
+ "search_quantity": "results.method.simulation.dft.xc_functional_type",
"selected": true,
"align": "left"
},
{
- "quantity": "upload_create_time",
+ "search_quantity": "upload_create_time",
"selected": true,
"title": "Upload time",
"label": "Upload time",
"align": "left"
},
{
- "quantity": "authors",
+ "search_quantity": "authors",
"selected": true,
"align": "left"
},
{
- "quantity": "results.method.simulation.precision.apw_cutoff",
+ "search_quantity": "results.method.simulation.precision.apw_cutoff",
"selected": false,
"align": "left"
},
{
- "quantity": "results.method.simulation.precision.basis_set",
+ "search_quantity": "results.method.simulation.precision.basis_set",
"selected": false,
"align": "left"
},
{
- "quantity": "results.method.simulation.precision.k_line_density",
+ "search_quantity": "results.method.simulation.precision.k_line_density",
"selected": false,
"align": "left"
},
{
- "quantity": "results.method.simulation.precision.native_tier",
+ "search_quantity": "results.method.simulation.precision.native_tier",
"selected": false,
"align": "left"
},
{
- "quantity": "results.method.simulation.precision.planewave_cutoff",
+ "search_quantity": "results.method.simulation.precision.planewave_cutoff",
"selected": false,
"align": "left"
},
{
- "quantity": "results.material.structural_type",
+ "search_quantity": "results.material.structural_type",
"selected": false,
"align": "left"
},
{
- "quantity": "results.material.symmetry.crystal_system",
+ "search_quantity": "results.material.symmetry.crystal_system",
"selected": false,
"align": "left"
},
{
- "quantity": "results.material.symmetry.space_group_symbol",
+ "search_quantity": "results.material.symmetry.space_group_symbol",
"selected": false,
"align": "left"
},
{
- "quantity": "results.material.symmetry.space_group_number",
+ "search_quantity": "results.material.symmetry.space_group_number",
"selected": false,
"align": "left"
},
{
- "quantity": "entry_name",
+ "search_quantity": "entry_name",
"selected": false,
"title": "Name",
"label": "Name",
"align": "left"
},
{
- "quantity": "mainfile",
+ "search_quantity": "mainfile",
"selected": false,
"align": "left"
},
{
- "quantity": "comment",
+ "search_quantity": "comment",
"selected": false,
"align": "left"
},
{
- "quantity": "references",
+ "search_quantity": "references",
"selected": false,
"align": "left"
},
{
- "quantity": "datasets",
+ "search_quantity": "datasets",
"selected": false,
"align": "left"
},
{
- "quantity": "published",
+ "search_quantity": "published",
"selected": false,
"title": "Access",
"label": "Access",
@@ -4077,39 +4077,39 @@ window.nomadEnv = {
},
"columns": [
{
- "quantity": "chemical_formula_hill",
+ "search_quantity": "chemical_formula_hill",
"selected": true,
"title": "Formula",
"label": "Formula",
"align": "left"
},
{
- "quantity": "structural_type",
+ "search_quantity": "structural_type",
"selected": true,
"align": "left"
},
{
- "quantity": "symmetry.structure_name",
+ "search_quantity": "symmetry.structure_name",
"selected": true,
"align": "left"
},
{
- "quantity": "symmetry.space_group_number",
+ "search_quantity": "symmetry.space_group_number",
"selected": true,
"align": "left"
},
{
- "quantity": "symmetry.crystal_system",
+ "search_quantity": "symmetry.crystal_system",
"selected": true,
"align": "left"
},
{
- "quantity": "symmetry.space_group_symbol",
+ "search_quantity": "symmetry.space_group_symbol",
"selected": false,
"align": "left"
},
{
- "quantity": "material_id",
+ "search_quantity": "material_id",
"selected": false,
"align": "left"
}
@@ -5359,88 +5359,88 @@ window.nomadEnv = {
},
"columns": [
{
- "quantity": "entry_name",
+ "search_quantity": "entry_name",
"selected": true,
"title": "Name",
"label": "Name",
"align": "left"
},
{
- "quantity": "entry_type",
+ "search_quantity": "entry_type",
"selected": true,
"align": "left"
},
{
- "quantity": "upload_create_time",
+ "search_quantity": "upload_create_time",
"selected": true,
"title": "Upload time",
"label": "Upload time",
"align": "left"
},
{
- "quantity": "authors",
+ "search_quantity": "authors",
"selected": true,
"align": "left"
},
{
- "quantity": "results.material.chemical_formula_hill",
+ "search_quantity": "results.material.chemical_formula_hill",
"selected": false,
"title": "Formula",
"label": "Formula",
"align": "left"
},
{
- "quantity": "results.method.method_name",
+ "search_quantity": "results.method.method_name",
"selected": false,
"align": "left"
},
{
- "quantity": "results.eln.lab_ids",
+ "search_quantity": "results.eln.lab_ids",
"selected": false,
"align": "left"
},
{
- "quantity": "results.eln.sections",
+ "search_quantity": "results.eln.sections",
"selected": false,
"align": "left"
},
{
- "quantity": "results.eln.methods",
+ "search_quantity": "results.eln.methods",
"selected": false,
"align": "left"
},
{
- "quantity": "results.eln.tags",
+ "search_quantity": "results.eln.tags",
"selected": false,
"align": "left"
},
{
- "quantity": "results.eln.instruments",
+ "search_quantity": "results.eln.instruments",
"selected": false,
"align": "left"
},
{
- "quantity": "mainfile",
+ "search_quantity": "mainfile",
"selected": false,
"align": "left"
},
{
- "quantity": "comment",
+ "search_quantity": "comment",
"selected": false,
"align": "left"
},
{
- "quantity": "references",
+ "search_quantity": "references",
"selected": false,
"align": "left"
},
{
- "quantity": "datasets",
+ "search_quantity": "datasets",
"selected": false,
"align": "left"
},
{
- "quantity": "published",
+ "search_quantity": "published",
"selected": false,
"title": "Access",
"label": "Access",
@@ -5855,78 +5855,78 @@ window.nomadEnv = {
},
"columns": [
{
- "quantity": "results.material.chemical_formula_hill",
+ "search_quantity": "results.material.chemical_formula_hill",
"selected": true,
"title": "Formula",
"label": "Formula",
"align": "left"
},
{
- "quantity": "results.properties.spectroscopic.spectra.provenance.eels.detector_type",
+ "search_quantity": "results.properties.spectroscopic.spectra.provenance.eels.detector_type",
"selected": true,
"align": "left"
},
{
- "quantity": "results.properties.spectroscopic.spectra.provenance.eels.resolution",
+ "search_quantity": "results.properties.spectroscopic.spectra.provenance.eels.resolution",
"selected": true,
"align": "left"
},
{
- "quantity": "upload_create_time",
+ "search_quantity": "upload_create_time",
"selected": true,
"title": "Upload time",
"label": "Upload time",
"align": "left"
},
{
- "quantity": "authors",
+ "search_quantity": "authors",
"selected": true,
"align": "left"
},
{
- "quantity": "results.properties.spectroscopic.spectra.provenance.eels.min_energy",
+ "search_quantity": "results.properties.spectroscopic.spectra.provenance.eels.min_energy",
"selected": false,
"align": "left"
},
{
- "quantity": "results.properties.spectroscopic.spectra.provenance.eels.max_energy",
+ "search_quantity": "results.properties.spectroscopic.spectra.provenance.eels.max_energy",
"selected": false,
"align": "left"
},
{
- "quantity": "entry_name",
+ "search_quantity": "entry_name",
"selected": false,
"title": "Name",
"label": "Name",
"align": "left"
},
{
- "quantity": "entry_type",
+ "search_quantity": "entry_type",
"selected": false,
"align": "left"
},
{
- "quantity": "mainfile",
+ "search_quantity": "mainfile",
"selected": false,
"align": "left"
},
{
- "quantity": "comment",
+ "search_quantity": "comment",
"selected": false,
"align": "left"
},
{
- "quantity": "references",
+ "search_quantity": "references",
"selected": false,
"align": "left"
},
{
- "quantity": "datasets",
+ "search_quantity": "datasets",
"selected": false,
"align": "left"
},
{
- "quantity": "published",
+ "search_quantity": "published",
"selected": false,
"title": "Access",
"label": "Access",
@@ -7465,47 +7465,47 @@ window.nomadEnv = {
},
"columns": [
{
- "quantity": "entry_id",
+ "search_quantity": "entry_id",
"selected": false,
"align": "left"
},
{
- "quantity": "entry_type",
+ "search_quantity": "entry_type",
"selected": false,
"title": "Entry type",
"label": "Entry type",
"align": "left"
},
{
- "quantity": "authors",
+ "search_quantity": "authors",
"selected": true,
"title": "Authors",
"label": "Authors",
"align": "left"
},
{
- "quantity": "data.name#nomad_aitoolkit.schema.AIToolkitNotebook",
+ "search_quantity": "data.name#nomad_aitoolkit.schema.AIToolkitNotebook",
"selected": true,
"title": "Name",
"label": "Name",
"align": "left"
},
{
- "quantity": "data.category#nomad_aitoolkit.schema.AIToolkitNotebook",
+ "search_quantity": "data.category#nomad_aitoolkit.schema.AIToolkitNotebook",
"selected": true,
"title": "Category",
"label": "Category",
"align": "left"
},
{
- "quantity": "data.platform#nomad_aitoolkit.schema.AIToolkitNotebook",
+ "search_quantity": "data.platform#nomad_aitoolkit.schema.AIToolkitNotebook",
"selected": false,
"title": "Platform",
"label": "Platform",
"align": "left"
},
{
- "quantity": "data.date#nomad_aitoolkit.schema.AIToolkitNotebook",
+ "search_quantity": "data.date#nomad_aitoolkit.schema.AIToolkitNotebook",
"selected": true,
"title": "Last update",
"label": "Last update",
@@ -7905,41 +7905,41 @@ window.nomadEnv = {
},
"columns": [
{
- "quantity": "results.material.chemical_formula_iupac",
+ "search_quantity": "results.material.chemical_formula_iupac",
"selected": true,
"title": "Formula",
"label": "Formula",
"align": "left"
},
{
- "quantity": "mainfile",
+ "search_quantity": "mainfile",
"selected": true,
"align": "left"
},
{
- "quantity": "upload_create_time",
+ "search_quantity": "upload_create_time",
"selected": false,
"title": "Upload time",
"label": "Upload time",
"align": "left"
},
{
- "quantity": "authors",
+ "search_quantity": "authors",
"selected": true,
"align": "left"
},
{
- "quantity": "comment",
+ "search_quantity": "comment",
"selected": false,
"align": "left"
},
{
- "quantity": "datasets",
+ "search_quantity": "datasets",
"selected": false,
"align": "left"
},
{
- "quantity": "published",
+ "search_quantity": "published",
"selected": false,
"title": "Access",
"label": "Access",
@@ -8829,14 +8829,14 @@ window.nomadEnv = {
},
"columns": [
{
- "quantity": "results.material.chemical_formula_descriptive",
+ "search_quantity": "results.material.chemical_formula_descriptive",
"selected": true,
"title": "Descriptive formula",
"label": "Descriptive formula",
"align": "left"
},
{
- "quantity": "results.properties.optoelectronic.solar_cell.efficiency",
+ "search_quantity": "results.properties.optoelectronic.solar_cell.efficiency",
"selected": true,
"title": "Efficiency (%)",
"label": "Efficiency (%)",
@@ -8847,7 +8847,7 @@ window.nomadEnv = {
}
},
{
- "quantity": "results.properties.optoelectronic.solar_cell.open_circuit_voltage",
+ "search_quantity": "results.properties.optoelectronic.solar_cell.open_circuit_voltage",
"selected": true,
"align": "left",
"unit": "V",
@@ -8857,7 +8857,7 @@ window.nomadEnv = {
}
},
{
- "quantity": "results.properties.optoelectronic.solar_cell.short_circuit_current_density",
+ "search_quantity": "results.properties.optoelectronic.solar_cell.short_circuit_current_density",
"selected": true,
"align": "left",
"unit": "A/m**2",
@@ -8867,7 +8867,7 @@ window.nomadEnv = {
}
},
{
- "quantity": "results.properties.optoelectronic.solar_cell.fill_factor",
+ "search_quantity": "results.properties.optoelectronic.solar_cell.fill_factor",
"selected": true,
"align": "left",
"format": {
@@ -8876,24 +8876,24 @@ window.nomadEnv = {
}
},
{
- "quantity": "references",
+ "search_quantity": "references",
"selected": true,
"align": "left"
},
{
- "quantity": "results.material.chemical_formula_hill",
+ "search_quantity": "results.material.chemical_formula_hill",
"selected": false,
"title": "Formula",
"label": "Formula",
"align": "left"
},
{
- "quantity": "results.material.structural_type",
+ "search_quantity": "results.material.structural_type",
"selected": false,
"align": "left"
},
{
- "quantity": "results.properties.optoelectronic.solar_cell.illumination_intensity",
+ "search_quantity": "results.properties.optoelectronic.solar_cell.illumination_intensity",
"selected": false,
"title": "Illum. intensity",
"label": "Illum. intensity",
@@ -8905,71 +8905,71 @@ window.nomadEnv = {
}
},
{
- "quantity": "results.eln.lab_ids",
+ "search_quantity": "results.eln.lab_ids",
"selected": false,
"align": "left"
},
{
- "quantity": "results.eln.sections",
+ "search_quantity": "results.eln.sections",
"selected": false,
"align": "left"
},
{
- "quantity": "results.eln.methods",
+ "search_quantity": "results.eln.methods",
"selected": false,
"align": "left"
},
{
- "quantity": "results.eln.tags",
+ "search_quantity": "results.eln.tags",
"selected": false,
"align": "left"
},
{
- "quantity": "results.eln.instruments",
+ "search_quantity": "results.eln.instruments",
"selected": false,
"align": "left"
},
{
- "quantity": "entry_name",
+ "search_quantity": "entry_name",
"selected": false,
"title": "Name",
"label": "Name",
"align": "left"
},
{
- "quantity": "entry_type",
+ "search_quantity": "entry_type",
"selected": false,
"align": "left"
},
{
- "quantity": "mainfile",
+ "search_quantity": "mainfile",
"selected": false,
"align": "left"
},
{
- "quantity": "upload_create_time",
+ "search_quantity": "upload_create_time",
"selected": false,
"title": "Upload time",
"label": "Upload time",
"align": "left"
},
{
- "quantity": "authors",
+ "search_quantity": "authors",
"selected": false,
"align": "left"
},
{
- "quantity": "comment",
+ "search_quantity": "comment",
"selected": false,
"align": "left"
},
{
- "quantity": "datasets",
+ "search_quantity": "datasets",
"selected": false,
"align": "left"
},
{
- "quantity": "published",
+ "search_quantity": "published",
"selected": false,
"title": "Access",
"label": "Access",
diff --git a/nomad/config/models/ui.py b/nomad/config/models/ui.py
index d92e549ee9..3a1e20a7e2 100644
--- a/nomad/config/models/ui.py
+++ b/nomad/config/models/ui.py
@@ -259,7 +259,7 @@ class Column(ConfigBaseModel):
- Show instance that matches a criterion: `repeating_section[?label=='target'].quantity`
"""
- quantity: Optional[str] = Field(
+ search_quantity: Optional[str] = Field(
description="""
Path of the targeted quantity. Note that you can most of the features
JMESPath syntax here to further specify a selection of values. This
@@ -267,6 +267,9 @@ class Column(ConfigBaseModel):
statistical values.
"""
)
+ quantity: Optional[str] = Field(
+ deprecated='The "quantity" field is deprecated, use "search_quantity" instead.'
+ )
selected: bool = Field(
False, description="""Is this column initially selected to be shown."""
)
@@ -287,6 +290,13 @@ class Column(ConfigBaseModel):
@root_validator(pre=True)
def _validate(cls, values):
+ # Backwards compatibility for quantity.
+ quantity = values.get('quantity')
+ search_quantity = values.get('search_quantity')
+ if quantity is not None and search_quantity is None:
+ values['search_quantity'] = quantity
+ del values['quantity']
+
# Backwards compatibility for label
label = values.get('label')
title = values.get('title')
--
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