Initial commit

.gitignore

+eels-data.zip
+
+# use glob syntax.
+syntax: glob
+*~
+*.bak
+*.off
+*.old
+*.pyc
+*.bk
+*.swp
+.DS_Store
+__pycache__/
+
+# logging files
+detailed.log
+
+# eclipse conf file
+.settings
+.classpath
+.project
+.manager
+.scala_dependencies
+
+# idea
+.idea
+*.iml
+
+# building
+target
+build
+null
+tmp*
+temp*
+dist
+test-output
+build.log
+
+# other scm
+.svn
+.CVS
+.hg*
+
+# switch to regexp syntax.
+#  syntax: regexp
+#  ^\.pc/
+
+#SHITTY output not in target directory
+build.log
+
+#emacs TAGS
+TAGS
+
+lib/
+env/
+
+# Setuptools install folder
+*.egg-info/
+
+.directory
+*.annotate
+
+test.json

LICENSE.txt

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README.md

+# NOMAD EELSDB crawler/converter
+
+This project contains code to retrieve EELS data and add it to NOMAD.
\ No newline at end of file

eelsdbconverter/__init__.py

+# Copyright 2016-2018 Markus Scheidgen
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
+
+import sys
+import os.path
+import json
+import ase
+import numpy as np
+from datetime import datetime
+import time
+import ast
+import logging
+import re
+
+from .metainfo import eels as meels
+from nomad.datamodel.metainfo.general_experimental import (
+    section_experiment as Experiment,
+    section_sample as Sample,
+    section_method as Method,
+    section_data as Data)
+from nomad.parsing.parser import FairdiParser
+
+
+logger = logging.getLogger(__name__)
+
+
+class EELSApiJsonConverter(FairdiParser):
+    def __init__(self):
+        super().__init__(
+            name='parsers/eelsdb', code_name='eels', code_homepage='https://eelsdb.eu/',
+            domain='ems',
+            mainfile_mime_re=r'application/json',
+            mainfile_contents_re=(r'https://eelsdb.eu/spectra')
+        )
+
+    def parse(self, filepath, archive, logger=logger):
+        with open(filepath) as f:
+            data = json.load(f)
+
+        experiment = archive.m_create(Experiment)
+        experiment.raw_metadata = data
+
+        experiment.experiment_publish_time = datetime.strptime(
+            data.get('published'), '%Y-%m-%d %H:%M:%S')
+
+        sample = experiment.m_create(Sample)
+        sample.sample_chemical_formula = data.get('formula')
+        sample.sample_atom_labels = data.get('elements')
+        sample.sample_chemical_name = data.get('title')
+
+        experiment.m_create(
+            Method,
+            experiment_method_name='electron energy loss spectroscopy',
+            experiment_method_abbreviation='EELS')
+
+        section_data = experiment.m_create(Data)
+
+        archive.section_metadata.external_id = str(data.get('id'))
+        archive.section_metadata.external_db = 'EELSDB'
+
+        author = data.get('author')['name']
+        author = re.sub(r'\(.*\)', '', author).strip()
+        archive.section_metadata.coauthors = [dict(
+            first_name=' '.join(author.split(' ')[0:-1]),
+            last_name=author.split(' ')[-1])]
+        archive.section_metadata.comment = data.get('description')
+        archive.section_metadata.references = [
+            data.get('permalink'),
+            data.get('api_permalink'),
+            data.get('download_link')
+        ]
+
+        reference = data.get('reference')
+        if reference:
+            if isinstance(reference, str):
+                archive.section_metadata.references.append(reference)
+            elif isinstance(reference, dict):
+                if 'freetext' in reference:
+                    archive.section_metadata.references.append(
+                        re.sub(r'\r+\n+', '; ', reference['freetext']))
+                else:
+                    archive.section_metadata.references.append('; '.join([
+                        str(value).strip() for value in reference.values()
+                    ]))
+
+        section_data.data_repository_name = 'Electron Energy Loss Spectroscopy (EELS) database'
+        section_data.data_repository_url = 'https://eelsdb.eu'
+        section_data.entry_repository_url = data.get('permalink')

eelsdbconverter/__main__.py

+# Copyright 2016-2018 Markus Scheidgen
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
+
+import sys
+import json
+
+from eelsdbconverter import EELSApiJsonParser
+
+if __name__ == "__main__":
+    archive = EELSApiJsonParser.main(sys.argv[1])
+    print(json.dumps(archive.m_to_dict(), indent=2))

eelsdbconverter/crawl.py

+# Copyright 2016-2018 Markus Scheidgen
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
+
+import requests
+import json
+import zipfile
+import os.path
+
+
+def download_eels(max: int = 1000):
+    ''' Downloads all EELS data. '''
+    zf = zipfile.ZipFile('eels-data.zip', mode='x')
+
+    eelsdb = requests.get('https://api.eelsdb.eu/spectra?per_page=%d' % max).json()
+    for entry in eelsdb:
+        path = entry['permalink'].strip('https://').strip('/')
+        with zf.open(os.path.join(path, 'metadata.json'), mode='w') as f:
+            f.write(json.dumps(entry, indent=2).encode('utf-8'))
+
+        try:
+            data = requests.get(entry['download_link']).content
+            with zf.open(os.path.join(path, 'data.msa'), mode='w') as f:
+                f.write(data)
+
+        except Exception:
+            print('Could not download spectra for %s' % entry['permalink'])
+
+    zf.close()
+
+
+if __name__ == '__main__':
+    download_eels(max=10)

eelsdbconverter/metainfo/__init__.py

+import sys
+from nomad.metainfo import Environment
+from nomad.metainfo.legacy import LegacyMetainfoEnvironment
+import eelsparser.metainfo.eels
+import nomad.datamodel.metainfo.general
+import nomad.datamodel.metainfo.general_experimental
+
+m_env = LegacyMetainfoEnvironment()
+m_env.m_add_sub_section(Environment.packages, sys.modules['eelsparser.metainfo.eels'].m_package)  # type: ignore
+m_env.m_add_sub_section(Environment.packages, sys.modules['nomad.datamodel.metainfo.general'].m_package)  # type: ignore
+m_env.m_add_sub_section(Environment.packages, sys.modules['nomad.datamodel.metainfo.general_experimental'].m_package)  # type: ignore

eelsdbconverter/metainfo/eels.py

+import numpy as np            # pylint: disable=unused-import
+import typing                 # pylint: disable=unused-import
+from nomad.metainfo import (  # pylint: disable=unused-import
+    MSection, MCategory, Category, Package, Quantity, Section, SubSection, SectionProxy,
+    Reference
+)
+
+m_package = Package(
+    name='eelsdb',
+    description='Metadata for the EELS database (https://eelsdb.eu)')
+
+m_package.__init_metainfo__()

setup.py

+# Copyright 2016-2018 R. Patrick Xian
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
+
+from setuptools import setup, find_packages
+
+
+def main():
+    setup(
+        name='eelsdbconverter',  # replace with new name for parser's python package
+        version='0.1',
+        description='NOMAD converter/parser for metadata from EELS database',  # change accordingly
+        author='Markus Scheidgen',  # add your names
+        license='APACHE 2.0',
+        packages=find_packages(),
+        install_requires=[
+            'nomad-lab'
+        ],
+    )
+
+
+if __name__ == '__main__':
+    main()

tests/all.json

+{
+  "id": 21601,
+  "title": "Yttria stabilized Zirconia",
+  "permalink": "https://eelsdb.eu/spectra/yttria-stabilized-zirconia/",
+  "author": {
+    "name": "(Dr) Marie Cheynet",
+    "profile_url": "https://eelsdb.eu/author/mcheynet/",
+    "profile_api_url": "https://api.eelsdb.eu/author/mcheynet/"
+  },
+  "published": "2005-05-26 00:00:00",
+  "description": "the cubic structure is stabilized by addition of 8.5mol% of Y2O3 Analyst: M. Cheynet. Temperature: Room. ",
+  "comment_count": 0,
+  "api_permalink": "https://api.eelsdb.eu/spectra/yttria-stabilized-zirconia/",
+  "keywords": [
+    "imported from old site"
+  ],
+  "download_link": "https://eelsdb.eu/wp-content/uploads/2015/09/DspectVJrUq.msa",
+  "type": "Low Loss",
+  "formula": "ZrO2-8.5mol%Y2O3",
+  "elements": [
+    "Zr",
+    "O",
+    "Y"
+  ],
+  "microscope": "Tecnai F20",
+  "max_energy": "91.6 eV",
+  "min_energy": "-6.1 eV",
+  "source_purity": "Spray-pyrolysis nanocrystallized powders",
+  "edges": [
+    "Zr_L1",
+    "Zr_L2,3"
+  ],
+  "guntype": "feg Schottky",
+  "beamenergy": "200 kV",
+  "stepSize": "0.1 eV/pixel",
+  "acquisition_mode": "STEM",
+  "convergence": "13.5 mrad",
+  "collection": "1.2 mrad",
+  "probesize": "1 nm^2",
+  "integratetime": "1 secs",
+  "readouts": "2",
+  "detector": "Parallel: GIF",
+  "darkcurrent": "Yes",
+  "gainvariation": "Yes",
+  "reference": {
+    "freetext": "Electronic structure and electron energy-loss spectroscopy of ZrO2 zirconia\r\nL.K. Dash, N. Vast, P. Baranek, M.C. Cheynet, L. Reining\r\nPhys. Rev. B 70, 245116 (2004)"
+  },
+  "other_links": [
+    {
+      "url": "http://pc-web.cemes.fr/eelsdb/index.php?page=displayspec.php&id=84",
+      "title": "Old EELS DB"
+    }
+  ],
+  "monochromated": "No",
+  "resolution": "0.8 eV",
+  "calibration": "Low loss + drift tube",
+  "deconvolutions": [
+    "Fourier-ratio"
+  ],
+  "thickness": "0.76 t/λ",
+  "beamcurrent": "200",
+  "associated_spectra": [
+    {
+      "name": "Zr",
+      "link": "https://eelsdb.eu/spectra/zr/",
+      "type": "Core Loss"
+    }
+  ]
+}