Initial

README.md

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+# pynxtools-rii_database
+Converts refractiveindex.info yaml files to nexus

pynxtools_rii_database/README.md

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+# A reader for the refractive index database
+
+## Contact person in FAIRmat for this reader
+The FAIRmat Area B team

pynxtools_rii_database/citation_parser.py

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+#
+# Copyright The NOMAD Authors.
+#
+# This file is part of NOMAD. See https://nomad-lab.eu for further info.
+#
+# 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.
+#
+"""Parse references from rii yaml files"""
+from dataclasses import dataclass, field
+import re
+from typing import Any, Dict, Optional
+import requests_cache
+
+
+@dataclass
+class Citation:
+    """A representation for a citation"""
+
+    _raw_str: str = field(repr=False)
+    ref_str: str
+    url: Optional[str]
+    doi: Optional[str]
+    session: Optional[requests_cache.CachedSession] = None
+    bibtex: Optional[str] = None
+
+    @staticmethod
+    def parse_citations(reference: str, download_bibtex: bool = False):
+        """Parses a reference string into its components"""
+        cites = re.split(r"<br\s*\/?\s*>", reference)
+
+        clean_cites = []
+        for cite in cites:
+            clean_cites.append(Citation(cite, download_bibtex))
+        return clean_cites
+
+    def __init__(
+        self, ref_str: str, download_bibtex: bool = False, desc: Optional[str] = None
+    ):
+        self._raw_str = ref_str
+        self.ref_str = re.sub(
+            r"\<\/?[^\<\>]*\>",
+            "",
+            re.search(r"(?:\d\))?\s*(.*)", ref_str).group(1),
+        )
+        self.get_non_doi_url()
+        self.get_doi()
+
+        if desc:
+            self.description = desc
+        else:
+            self.description = (
+                "Literature reference from which this "
+                "dispersion function was extracted."
+            )
+
+        if download_bibtex:
+            self.download_bibtex()
+
+    def download_bibtex(self):
+        """Requests the bibtext entry for a given doi"""
+        if not self.doi:
+            return
+
+        if self.session is None:
+            self.session = requests_cache.CachedSession("rii_bibtex")
+
+        req = self.session.get(
+            f"https://doi.org/{self.doi}",
+            timeout=30,
+            headers={"Accept": "application/x-bibtex"},
+        )
+        if req.status_code == 200:
+            self.bibtex = req.text
+
+    def get_non_doi_url(self):
+        """Extract urls which are not dois"""
+        url = re.search(r"href\=\"([^\"]+)\"", self._raw_str)
+        self.url = url.group(1) if url and "doi.org" not in url.group(1) else None
+
+    def get_doi(self):
+        """Extracts doi from a reference string"""
+        doi_match = re.search(r"\".*doi\.org\/([^\"]+)\"", self._raw_str)
+        self.doi = doi_match.group(1) if doi_match else None
+
+    def write_entries(self, template: Dict[str, Any], path: str):
+        """Write entries to pynxtools template"""
+        reference_identifier = "REFERENCES"
+        name = basename = "reference"
+
+        while f"{path}/{reference_identifier}[{name}]/text" in template:
+            count = locals().get("count", 0) + 1
+            name = f"{basename}{count}"
+
+        base_path = f"{path}/{reference_identifier}[{name}]"
+        if self.url:
+            template[f"{base_path}/url"] = self.url
+        if self.doi:
+            template[f"{base_path}/doi"] = self.doi
+        if self.bibtex:
+            template[f"{base_path}/bibtex"] = self.bibtex
+
+        template[f"{base_path}/text"] = self.ref_str
+        template[f"{base_path}/description"] = self.description