diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000000000000000000000000000000000000..e012fc16957d0eb9e662bb6cbe63ea056f7094e8 --- /dev/null +++ b/.gitignore @@ -0,0 +1,61 @@ +# 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 +photoemissionparser.egg-info/ + +.directory +*.annotate + +test.json diff --git a/LICENSE.txt b/LICENSE.txt new file mode 100644 index 0000000000000000000000000000000000000000..d645695673349e3947e8e5ae42332d0ac3164cd7 --- /dev/null +++ b/LICENSE.txt @@ -0,0 +1,202 @@ + + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. 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We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright [yyyy] [name of copyright owner] + + 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. diff --git a/README.md b/README.md index b903d5a592136c97df892e06fb607b29e24d6734..4b4cc5116311f0d9727c080879830c885578c6e5 100644 --- a/README.md +++ b/README.md @@ -1,2 +1,31 @@ # parser-photoemission +## Setup and run example + +We are currently targeting Python 3.6 + +Best use a virtual environment: +``` +virtualenv -p python3 .pyenv +source .pyenv/bin/activate +``` + +Clone and install the nomad infrastructure and the necessary dependencies (including this parser) +``` +git clone https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR nomad +git submodule update --init +pip install -r requirements.txt +./dependencies.sh -e +``` + +To run the parser: +``` +cd nomad/dependencies/parser/photoemission +python -m photoemissionparser <test_file> +``` + +## Docs + +[metainfo](https://metainfo.nomad-coe.eu/nomadmetainfo_public/archive.html) + +[nomad@fairdi, tmp.](http://enc-staging-nomad.esc.rzg.mpg.de/fairdi/nomad/migration/docs) diff --git a/photoemissionparser/__init__.py b/photoemissionparser/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..1adc9799517c03a60f74edca41b7ff1daf0279e7 --- /dev/null +++ b/photoemissionparser/__init__.py @@ -0,0 +1,51 @@ +# 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. + +import sys +import os.path + +from nomadcore.simple_parser import SimpleMatcher +from nomadcore.baseclasses import ParserInterface, AbstractBaseParser + +from nomad.parsing import LocalBackend + + +class PhotoemissionParserInterface(ParserInterface): + + def get_metainfo_filename(self): + """ The parser specific metainfo. This file must be part of the nomad-meta-info. """ + return os.path.join(os.path.dirname(__file__), 'photoemission.nomadmetainfo.json') + + def get_parser_info(self): + """ Basic info about parser used in archive data and logs. """ + return { + 'name': 'vaspoutcar_parser', + 'version': '1.0.0' + } + + def setup_version(self): + """ Can be used to call :func:`setup_main_parser` differently for different code versions. """ + self.setup_main_parser(None) + + def setup_main_parser(self, _): + """ Setup the actual parser (behind this interface) """ + self.main_parser = PhotoemissionParser(self.parser_context) + + +class PhotoemissionParser(AbstractBaseParser): + def parse(self, filepath): + backend = self.parser_context.super_backend + + root_gid = backend.openSection('section_root') + backend.addValue('experiment_location', 'here...') + backend.closeSection('section_root', root_gid) diff --git a/photoemissionparser/__main__.py b/photoemissionparser/__main__.py new file mode 100644 index 0000000000000000000000000000000000000000..a38401a0b27360bc8d1b811675313732985489d1 --- /dev/null +++ b/photoemissionparser/__main__.py @@ -0,0 +1,26 @@ +# 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. + +import sys + +from nomad.parsing import LocalBackend +from photoemissionparser import PhotoemissionParserInterface + +if __name__ == "__main__": + # instantiate the parser via its interface with a LocalBackend + parser = PhotoemissionParserInterface(backend=LocalBackend) + # call the actual parsing with the given mainfile + parser.parse(sys.argv[1]) + # print the results stored in the LocalBackend + parser.parser_context.super_backend.write_json( + sys.stdout, pretty=True, root_sections=['section_root']) diff --git a/photoemissionparser/photoemission.nomadmetainfo.json b/photoemissionparser/photoemission.nomadmetainfo.json new file mode 100644 index 0000000000000000000000000000000000000000..4c8e3da0daca8ab131000a47b6b4431e64a0f1ca --- /dev/null +++ b/photoemissionparser/photoemission.nomadmetainfo.json @@ -0,0 +1,16 @@ +{ + "type": "nomad_meta_info_1_0", + "description": "Public experimental material science meta info, not specific to any experimental method", + "metaInfos": [ { + "description": "Root section that contains all information about an experiment", + "kindStr": "type_section", + "name": "section_root", + "superNames": [] + }, { + "description": "Contains information relating to an archive.", + "name": "experiment_location", + "dtypeStr": "C", + "superNames": ["section_root"] + } + ] + } diff --git a/setup.py b/setup.py new file mode 100644 index 0000000000000000000000000000000000000000..27488f819508878d42ebb7389a87fb4c1b546482 --- /dev/null +++ b/setup.py @@ -0,0 +1,32 @@ +# 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='photoemissionparser', + version='0.1', + description='NOMAD parser implementation for photoemission experiment files.', + author='', + license='APACHE 2.0', + packages=find_packages(), + install_requires=[ + 'nomadcore' + ], + ) + + +if __name__ == '__main__': + main()