From d7f9169c86b3d0ce58d2a4e9d9161cbf1f1e7651 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Oscar=20Arbel=C3=A1ez?= Date: Wed, 14 Oct 2020 13:05:38 -0500 Subject: [PATCH 01/10] Add scopus citation parser --- setup.py | 2 +- wostools/exceptions.py | 5 ++ wostools/scopus.py | 143 +++++++++++++++++++++++++++++++++++++++++ 3 files changed, 149 insertions(+), 1 deletion(-) create mode 100644 wostools/scopus.py diff --git a/setup.py b/setup.py index 3415e8f..d98d2ab 100644 --- a/setup.py +++ b/setup.py @@ -10,7 +10,7 @@ with open("HISTORY.md") as history_file: history = history_file.read() -requirements = ["Click>=7.0"] +requirements = ["Click>=7.0<8", "bibtexparser>=1.2.0<2"] setup_requirements = ["pytest-runner"] diff --git a/wostools/exceptions.py b/wostools/exceptions.py index cf059e3..1a7efc9 100644 --- a/wostools/exceptions.py +++ b/wostools/exceptions.py @@ -13,6 +13,11 @@ def __init__(self, reference: str): super().__init__(f"{reference} does not look like an ISI citation") +class InvalidScopusFile(WosToolsError, ValueError): + def __init__(self): + super().__init__(f"The file does not look like a valid bib file") + + class InvalidIsiLine(WosToolsError, ValueError): """ Raised when we encounter an invalid line when processing an ISI file. diff --git a/wostools/scopus.py b/wostools/scopus.py new file mode 100644 index 0000000..16960de --- /dev/null +++ b/wostools/scopus.py @@ -0,0 +1,143 @@ +import logging +import re +from typing import Dict, Iterable, List, Optional, Tuple, Type + +from bibtexparser.bparser import BibTexParser + +from wostools.article import Article +from wostools.exceptions import InvalidScopusFile + + +def _size(file) -> int: + file.seek(0, 2) + size = file.tell() + file.seek(0) + return size + + +def _int_or_nothing(value: Optional[str]) -> Optional[int]: + if not value: + return None + try: + return int(value) + except TypeError: + return None + + +def _parse_page(value: Optional[str]) -> Optional[str]: + if not value: + return None + first, *_ = value.split("-") + return first + + +def _find_volume_info(ref: str) -> Tuple[Dict[str, str], str]: + pattern = re.compile( + "(?P\d+)( \((?P.+)\))?(, pp?\. (?P\w+)(-\w+)?)?" + ) + result = re.search(pattern, ref) + if result is None: + return {}, ref + data = result.groupdict() + if "volume" in data and data["volume"]: + data["volume"] = f"V{data['volume']}" + if "page" in data and data["page"]: + data["page"] = f"P{data['page']}" + return data, ref[result.lastindex :] + + +def _find_doi(ref: str) -> Tuple[Optional[str], str]: + pattern = re.compile( + r"((DOI:?)|(doi.org\/)|(aps.org\/doi\/)) ?(?P[^\s,]+)", re.I + ) + result = re.search(pattern, ref) + if result is None or "doi" not in result.groupdict(): + if "doi" in ref.lower(): + print("doi not found in", ref, result) + return None, ref + return f"DOI {result.groupdict()['doi']}", ref[result.lastindex :] + + +def _scopus_ref_to_isi(scopusref: str) -> str: + authors, year, rest = re.split(r"(\(\d{4}\))", scopusref, maxsplit=1) + first_name, last_name, *_ = authors.split(", ") + # NOTE: The title might be between the authors and the year. + year = year[1:-1] + journal, rest = rest.split(", ", 1) + volume_info, rest = _find_volume_info(rest) + doi, _ = _find_doi(scopusref) + parts = { + "author": f"{first_name} {last_name.replace(' ', '').replace('.', '')}", + "yaer": year, + "journal": journal.strip().replace(".", "").upper() + if not journal.isspace() + else None, + "volume": volume_info.get("volume"), + "page": volume_info.get("page"), + "doi": doi, + } + return ", ".join(val for val in parts.values() if val is not None) + + +def parse_references(refstring: Optional[str]) -> List[str]: + if not refstring: + return [] + result = [] + for ref in refstring.split(";"): + try: + result.append(_scopus_ref_to_isi(ref)) + except (KeyError, IndexError, TypeError, ValueError) as e: + pass + # print(f"ignoring {ref}", e) + return result + + +def parse_file(file) -> Iterable[Article]: + if not _size(file): + return [] + + parser = BibTexParser() + bibliography = parser.parse_file(file) + + if not bibliography: + raise InvalidScopusFile() + + if any(entry.get("source") != "Scopus" for entry in bibliography): + logging.warn("This bib file doesn't come from scopus.") + + if any("abbrev_source_title" not in entry for entry in bibliography): + logging.warn( + "Source abreviation not found, maximum compatibility not guaranteed" + ) + + for entry in bibliography: + yield Article( + title=entry.get("title"), + authors=entry.get("author", "").split(" and "), + year=_int_or_nothing(entry.get("year")), + journal=entry.get("abbrev_source_title", entry.get("journal")), + volume=entry.get("volume"), + issue=entry.get("number"), + page=_parse_page(entry.get("pages")), + doi=entry.get("doi"), + keywords=entry.get("author_keywords"), + references=parse_references(entry.get("references")), + sources={entry.get("source")}, + extra=entry, + ) + + +if __name__ == "__main__": + with open("refs.txt") as refs: + data = [line.strip() for line in refs] + cit = [ref for line in data for ref in parse_references(line)] + print(sum("doi" in ref or "DOI" in ref for ref in data)) + print(sum("DOI" in ref for ref in cit)) + + with open("translated.txt", "w") as refs: + refs.write("\n".join(cit)) + + _scopus_ref_to_isi( + "Terris, B.D., Folks, L., Weller, D., Baglin, J.E.E., Kellock, A.J., Rothuizen, H., Vettiger, P., Ion beam patterning of magnetic films using stencil masks (1999) Appl. Phys. Lett., 75 (2), pp. 403-405. , July" + ) + From f94e02175d47a88a8308c296b4e9f648ac53d965 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Oscar=20Arbel=C3=A1ez?= Date: Thu, 15 Oct 2020 09:39:25 -0500 Subject: [PATCH 02/10] Use ris instead of bib for scopus --- wostools/article.py | 14 ++- wostools/base.py | 23 ++--- wostools/cached.py | 44 ++++++--- wostools/lazy.py | 20 ---- wostools/scopus.py | 143 --------------------------- wostools/sources/__file__.py | 0 wostools/sources/isi.py | 15 +++ wostools/sources/scopus.py | 181 +++++++++++++++++++++++++++++++++++ 8 files changed, 248 insertions(+), 192 deletions(-) delete mode 100644 wostools/scopus.py create mode 100644 wostools/sources/__file__.py create mode 100644 wostools/sources/isi.py create mode 100644 wostools/sources/scopus.py diff --git a/wostools/article.py b/wostools/article.py index 3cfe209..e219cfd 100644 --- a/wostools/article.py +++ b/wostools/article.py @@ -55,7 +55,7 @@ def __init__( self.extra: Mapping[str, Any] = extra or {} @property - def label(self): + def simple_label(self): if not (self.authors and self.year and self.journal): raise MissingLabelFields(self) pieces = { @@ -64,10 +64,15 @@ def label(self): "J9": str(self.journal), "VL": f"V{self.volume}" if self.volume else None, "BP": f"P{self.page}" if self.page else None, - "DI": f"DOI {self.doi}" if self.doi else None, } return ", ".join(value for value in pieces.values() if value) + @property + def label(self): + if self.doi: + return self.doi + return self.simple_label + def to_dict(self, simplified=True): """ Transform the article into some key value pairs for easy transportation. @@ -95,12 +100,13 @@ def to_dict(self, simplified=True): } def merge(self, other: "Article") -> "Article": - if self.label != other.label: - logger.warning( + if other.label not in {self.label, self.simple_label}: + logger.debug( "\n".join( [ "Mixing articles with different labels might result in tragedy", f" mine: {self.label}", + f" or: {self.simple_label}", f" others: {other.label}", ] ) diff --git a/wostools/base.py b/wostools/base.py index e41802e..a34f863 100644 --- a/wostools/base.py +++ b/wostools/base.py @@ -4,10 +4,11 @@ import glob import logging -from typing import Iterable, Iterator, Tuple +from typing import Iterable, Iterator, TextIO, Tuple from wostools.article import Article -from wostools.exceptions import InvalidReference +from wostools.exceptions import InvalidReference, WosToolsError +from wostools.sources import isi, scopus logger = logging.getLogger(__name__) @@ -49,7 +50,7 @@ def from_filenames(cls, *filenames): return cls(*files) @property - def _article_texts(self) -> Iterable[str]: + def _iter_files(self) -> Iterable[TextIO]: """Iterates over all the single article texts in the colection. Returns: @@ -57,19 +58,15 @@ def _article_texts(self) -> Iterable[str]: """ for filehandle in self._files: filehandle.seek(0) - data = filehandle.read() + yield filehandle filehandle.seek(0) - for article_text in data.split("\n\n"): - if article_text != "EF": - yield article_text def _articles(self) -> Iterable[Article]: - """ - Should iterate over all the articles in the ISI file, excluding references. - """ - raise NotImplementedError( - "Sub classes should know how to iterate over articles" - ) + for file in self._iter_files: + try: + yield from isi.parse_file(file) + except WosToolsError: + yield from scopus.parse_file(file) def __iter__(self) -> Iterator[Article]: """ diff --git a/wostools/cached.py b/wostools/cached.py index 85b2984..843bdcb 100644 --- a/wostools/cached.py +++ b/wostools/cached.py @@ -5,12 +5,14 @@ import itertools import logging from contextlib import suppress -from typing import Dict, Iterable, Iterator, Tuple +from typing import Dict, Iterable, Iterator, Set, Tuple from wostools.article import Article from wostools.base import BaseCollection from wostools.exceptions import InvalidReference, MissingLabelFields +from memory_profiler import profile + logger = logging.getLogger(__name__) @@ -23,18 +25,19 @@ def __init__(self, *files): super().__init__(*files) self._cache_key = None self._cache: Dict[str, Article] = {} + self._labels: Dict[str, Set[str]] = {} self._preheat() - def _articles(self) -> Iterable[Article]: - for article_text in self._article_texts: - yield Article.from_isi_text(article_text) - - def _add_article(self, article): - label = article.label - if label in self._cache: - article = article.merge(self._cache[label]) - self._cache[label] = article + def _add_article(self, article: Article): + labels = {article.label, article.simple_label} + for label in labels: + self._labels[label] = self._labels.get(label, set()).union(labels) + for label in labels: + if label in self._cache: + article = article.merge(self._cache[label]) + self._cache[article.label] = article + @profile def _preheat(self): # Preheat our cache key = ":".join(str(id(file) for file in self._files)) @@ -59,7 +62,12 @@ def __iter__(self) -> Iterator[Article]: generator: A generator of Articles according to the text articles. """ self._preheat() - yield from self._cache.values() + visited = set() + for label, article in self._cache.items(): + if label in visited: + continue + visited.update(self._labels[label]) + yield article @property def authors(self) -> Iterable[str]: @@ -94,7 +102,19 @@ def citation_pairs(self) -> Iterable[Tuple[Article, Article]]: labesl, where the firts element is the article which cites the second element. """ - for article in self._cache.values(): + for article in self: for reference in article.references: if reference in self._cache: yield (article, self._cache[reference]) + + +@profile +def main(): + collection = CachedCollection.from_filenames( + "./scratch/scopus.ris", "./scratch/bit-pattern-savedrecs.txt" + ) + print(collection) + + +if __name__ == "__main__": + main() diff --git a/wostools/lazy.py b/wostools/lazy.py index 3343f3f..d3c5afc 100644 --- a/wostools/lazy.py +++ b/wostools/lazy.py @@ -22,26 +22,6 @@ class LazyCollection(BaseCollection): articles. """ - @property - def _article_texts(self): - """Iterates over all the single article texts in the colection. - - Returns: - generator: A generator of strings with the text articles. - """ - for filehandle in self._files: - filehandle.seek(0) - data = filehandle.read() - filehandle.seek(0) - for article_text in data.split("\n\n"): - if article_text != "EF": - yield article_text - - def _articles(self) -> Iterable[Article]: - with suppress(MissingLabelFields): - for article_text in self._article_texts: - yield Article.from_isi_text(article_text) - @property def authors(self) -> Iterable[str]: """Iterates over all article authors, including duplicates diff --git a/wostools/scopus.py b/wostools/scopus.py deleted file mode 100644 index 16960de..0000000 --- a/wostools/scopus.py +++ /dev/null @@ -1,143 +0,0 @@ -import logging -import re -from typing import Dict, Iterable, List, Optional, Tuple, Type - -from bibtexparser.bparser import BibTexParser - -from wostools.article import Article -from wostools.exceptions import InvalidScopusFile - - -def _size(file) -> int: - file.seek(0, 2) - size = file.tell() - file.seek(0) - return size - - -def _int_or_nothing(value: Optional[str]) -> Optional[int]: - if not value: - return None - try: - return int(value) - except TypeError: - return None - - -def _parse_page(value: Optional[str]) -> Optional[str]: - if not value: - return None - first, *_ = value.split("-") - return first - - -def _find_volume_info(ref: str) -> Tuple[Dict[str, str], str]: - pattern = re.compile( - "(?P\d+)( \((?P.+)\))?(, pp?\. (?P\w+)(-\w+)?)?" - ) - result = re.search(pattern, ref) - if result is None: - return {}, ref - data = result.groupdict() - if "volume" in data and data["volume"]: - data["volume"] = f"V{data['volume']}" - if "page" in data and data["page"]: - data["page"] = f"P{data['page']}" - return data, ref[result.lastindex :] - - -def _find_doi(ref: str) -> Tuple[Optional[str], str]: - pattern = re.compile( - r"((DOI:?)|(doi.org\/)|(aps.org\/doi\/)) ?(?P[^\s,]+)", re.I - ) - result = re.search(pattern, ref) - if result is None or "doi" not in result.groupdict(): - if "doi" in ref.lower(): - print("doi not found in", ref, result) - return None, ref - return f"DOI {result.groupdict()['doi']}", ref[result.lastindex :] - - -def _scopus_ref_to_isi(scopusref: str) -> str: - authors, year, rest = re.split(r"(\(\d{4}\))", scopusref, maxsplit=1) - first_name, last_name, *_ = authors.split(", ") - # NOTE: The title might be between the authors and the year. - year = year[1:-1] - journal, rest = rest.split(", ", 1) - volume_info, rest = _find_volume_info(rest) - doi, _ = _find_doi(scopusref) - parts = { - "author": f"{first_name} {last_name.replace(' ', '').replace('.', '')}", - "yaer": year, - "journal": journal.strip().replace(".", "").upper() - if not journal.isspace() - else None, - "volume": volume_info.get("volume"), - "page": volume_info.get("page"), - "doi": doi, - } - return ", ".join(val for val in parts.values() if val is not None) - - -def parse_references(refstring: Optional[str]) -> List[str]: - if not refstring: - return [] - result = [] - for ref in refstring.split(";"): - try: - result.append(_scopus_ref_to_isi(ref)) - except (KeyError, IndexError, TypeError, ValueError) as e: - pass - # print(f"ignoring {ref}", e) - return result - - -def parse_file(file) -> Iterable[Article]: - if not _size(file): - return [] - - parser = BibTexParser() - bibliography = parser.parse_file(file) - - if not bibliography: - raise InvalidScopusFile() - - if any(entry.get("source") != "Scopus" for entry in bibliography): - logging.warn("This bib file doesn't come from scopus.") - - if any("abbrev_source_title" not in entry for entry in bibliography): - logging.warn( - "Source abreviation not found, maximum compatibility not guaranteed" - ) - - for entry in bibliography: - yield Article( - title=entry.get("title"), - authors=entry.get("author", "").split(" and "), - year=_int_or_nothing(entry.get("year")), - journal=entry.get("abbrev_source_title", entry.get("journal")), - volume=entry.get("volume"), - issue=entry.get("number"), - page=_parse_page(entry.get("pages")), - doi=entry.get("doi"), - keywords=entry.get("author_keywords"), - references=parse_references(entry.get("references")), - sources={entry.get("source")}, - extra=entry, - ) - - -if __name__ == "__main__": - with open("refs.txt") as refs: - data = [line.strip() for line in refs] - cit = [ref for line in data for ref in parse_references(line)] - print(sum("doi" in ref or "DOI" in ref for ref in data)) - print(sum("DOI" in ref for ref in cit)) - - with open("translated.txt", "w") as refs: - refs.write("\n".join(cit)) - - _scopus_ref_to_isi( - "Terris, B.D., Folks, L., Weller, D., Baglin, J.E.E., Kellock, A.J., Rothuizen, H., Vettiger, P., Ion beam patterning of magnetic films using stencil masks (1999) Appl. Phys. Lett., 75 (2), pp. 403-405. , July" - ) - diff --git a/wostools/sources/__file__.py b/wostools/sources/__file__.py new file mode 100644 index 0000000..e69de29 diff --git a/wostools/sources/isi.py b/wostools/sources/isi.py new file mode 100644 index 0000000..352f9d6 --- /dev/null +++ b/wostools/sources/isi.py @@ -0,0 +1,15 @@ +from typing import Iterable, TextIO +from wostools.article import Article + + +def _split(file) -> Iterable[str]: + parts = file.read().split("\n\n") + for part in parts: + if part != "ER": + yield part + + +def parse_file(file: TextIO) -> Iterable[Article]: + for raw in _split(file): + yield Article.from_isi_text(raw) + diff --git a/wostools/sources/scopus.py b/wostools/sources/scopus.py new file mode 100644 index 0000000..f909cee --- /dev/null +++ b/wostools/sources/scopus.py @@ -0,0 +1,181 @@ +from collections import defaultdict +import logging +import re +from typing import Dict, Iterable, List, Optional, TextIO, Tuple, Type + +from bibtexparser.bparser import BibTexParser + +from wostools.article import Article +from wostools.exceptions import InvalidScopusFile + + +def _size(file) -> int: + file.seek(0, 2) + size = file.tell() + file.seek(0) + return size + + +def _int_or_nothing(raw: Optional[List[str]]) -> Optional[int]: + if not raw: + return None + try: + return int(raw[0]) + except TypeError: + return None + + +def _joined(raw: Optional[List[str]]) -> Optional[str]: + if not raw: + return None + return " ".join(raw) + + +def _parse_page(value: Optional[str]) -> Optional[str]: + if not value: + return None + first, *_ = value.split("-") + return first + + +def _find_volume_info(ref: str) -> Tuple[Dict[str, str], str]: + volume_pattern = re.compile(r"(?P\d+)( \((?P.+?)\))?") + page_pattern = re.compile(r"(pp?\. (?P\w+)(-[^,\s]+)?)") + page = page_pattern.search(ref) + last_index = 0 + if page: + last_index = page.lastindex or 0 + first, *_ = ref.split(page.group()) + volume = volume_pattern.search(first) + else: + volume = volume_pattern.search(ref) + if volume: + last_index = volume.lastindex or 0 + + if not page and not volume: + return {}, ref + + data = {} + if page: + data.update(page.groupdict()) + if volume: + data.update(volume.groupdict()) + + if "volume" in data and data["volume"]: + data["volume"] = f"V{data['volume']}" + if "page" in data and data["page"]: + data["page"] = f"P{data['page']}" + + return data, ref[last_index:] + + +def _find_doi(ref: str) -> Tuple[Optional[str], str]: + pattern = re.compile( + r"((DOI:?)|(doi.org\/)|(aps.org\/doi\/)) ?(?P[^\s,]+)", re.I + ) + result = re.search(pattern, ref) + if result is None or "doi" not in result.groupdict(): + return None, ref + return f"DOI {result.groupdict()['doi']}", ref[result.lastindex :] + + +def _scopus_ref_to_isi(scopusref: str) -> str: + authors, year, rest = re.split(r"(\(\d{4}\))", scopusref, maxsplit=1) + first_name, last_name, *_ = authors.split(", ") + year = year[1:-1] + journal, rest = rest.split(", ", 1) + volume_info, rest = _find_volume_info(rest) + doi, _ = _find_doi(scopusref) + parts = { + "author": f"{first_name} {last_name.replace(' ', '').replace('.', '')}", + "yaer": year, + "journal": journal.strip().replace(".", "").upper() + if not journal.isspace() + else None, + "volume": volume_info.get("volume"), + "page": volume_info.get("page"), + "doi": doi, + } + return ", ".join(val for val in parts.values() if val is not None) + + +def parse_references(refs: List[str]) -> List[str]: + if not refs: + return [] + result = [] + for ref in refs: + try: + result.append(_scopus_ref_to_isi(ref)) + except (KeyError, IndexError, TypeError, ValueError) as e: + pass + # print(f"ignoring {ref}", e) + return result + + +def ris_to_dict(record: str) -> Dict[str, List[str]]: + RIS_PATTERN = re.compile(r"^(((?P[A-Z09]{2})) - )?(?P(.*))^") + parsed = defaultdict(list) + current = None + + for line in record.split("\n"): + match = RIS_PATTERN.match(line) + if not match: + raise InvalidScopusFile() + data = match.groupdict() + key = data.get("key") + value = data.get("value") + if "ER" in data: + break + if key: + if key == "N1" and value and ":" in value: + label, value = value.split(": ", 1) + current = f"{key}:{label}" + else: + current = data["key"] + if value and current: + parsed[current].append(data.get("value", "")) + + return dict(parsed) + + +def parse_record(record: str) -> Article: + data = ris_to_dict(record) + return Article( + title=_joined(data.get("TI")), + authors=data.get("AU", []), + year=_int_or_nothing(data.get("PY")), + journal=_joined(data.get("J2")), + volume=_joined(data.get("VL")), + issue=_joined(data.get("IS")), + page=_joined(data.get("SP")), + doi=_joined(data.get("DO")), + keywords=data.get("KW"), + references=parse_references(data.get("N1:References", [])), + sources={"scopus"}, + extra=data, + ) + + +def parse_file(file: TextIO) -> Iterable[Article]: + if not _size(file): + return [] + for item in file.read().split("\n\n"): + if item.isspace(): + continue + yield parse_record(item) + + +if __name__ == "__main__": + with open("./scratch/refs.txt") as refs: + data = [line.strip() for line in refs] + cit = [ref for line in data for ref in parse_references([line])] + print(sum("doi" in ref or "DOI" in ref for ref in data)) + print(sum("DOI" in ref for ref in cit)) + + with open("./scratch/translated.txt", "w") as refs: + refs.write("\n".join(cit)) + + _scopus_ref_to_isi( + "Terris, B.D., Folks, L., Weller, D., Baglin, J.E.E., Kellock, A.J., Rothuizen, H., Vettiger, P., Ion beam patterning of magnetic films using stencil masks (1999) Appl. Phys. Lett., 75 (2), pp. 403-405. , July" + ) + From 86cb81cfea89bfdfdd2278c8fd48cffba10715fb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Oscar=20Arbel=C3=A1ez?= Date: Thu, 15 Oct 2020 12:16:22 -0500 Subject: [PATCH 03/10] Start doing a better job of keeping just one article --- wostools/cached.py | 19 +++++++++++++++---- 1 file changed, 15 insertions(+), 4 deletions(-) diff --git a/wostools/cached.py b/wostools/cached.py index 843bdcb..3c46871 100644 --- a/wostools/cached.py +++ b/wostools/cached.py @@ -11,11 +11,17 @@ from wostools.base import BaseCollection from wostools.exceptions import InvalidReference, MissingLabelFields -from memory_profiler import profile - logger = logging.getLogger(__name__) +class Ref: + def __init__(self, current) -> None: + self.current = current + + def __hash__(self) -> int: + return id(self) + + class CachedCollection(BaseCollection): """ A collection of WOS text files. @@ -25,11 +31,18 @@ def __init__(self, *files): super().__init__(*files) self._cache_key = None self._cache: Dict[str, Article] = {} + self._refs: Dict[str, Ref] = {} self._labels: Dict[str, Set[str]] = {} self._preheat() def _add_article(self, article: Article): labels = {article.label, article.simple_label} + existing_labels = { + l for label in labels for l in self._labels.get(label, set()) + } + existing_refs = { + self._refs[label] for label in existing_labels if label in self._refs + } for label in labels: self._labels[label] = self._labels.get(label, set()).union(labels) for label in labels: @@ -37,7 +50,6 @@ def _add_article(self, article: Article): article = article.merge(self._cache[label]) self._cache[article.label] = article - @profile def _preheat(self): # Preheat our cache key = ":".join(str(id(file) for file in self._files)) @@ -108,7 +120,6 @@ def citation_pairs(self) -> Iterable[Tuple[Article, Article]]: yield (article, self._cache[reference]) -@profile def main(): collection = CachedCollection.from_filenames( "./scratch/scopus.ris", "./scratch/bit-pattern-savedrecs.txt" From 529988aae5a98de0e1c683741c3d65904b966735 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Oscar=20Arbel=C3=A1ez?= Date: Thu, 15 Oct 2020 22:38:44 -0500 Subject: [PATCH 04/10] Finish scopus support --- docs/examples/scopus.ris | 35808 +++++++++++++++++++++++++++++++++++ setup.py | 2 +- wostools/article.py | 40 +- wostools/cached.py | 52 +- wostools/cli.py | 4 +- wostools/sources/scopus.py | 43 +- 6 files changed, 35863 insertions(+), 86 deletions(-) create mode 100644 docs/examples/scopus.ris diff --git a/docs/examples/scopus.ris b/docs/examples/scopus.ris new file mode 100644 index 0000000..fe29598 --- /dev/null +++ b/docs/examples/scopus.ris @@ -0,0 +1,35808 @@ +TY - JOUR +TI - FORC signatures and switching-field distributions of dipolar coupled nanowire-based hysterons +T2 - Journal of Applied Physics +J2 - J Appl Phys +VL - 128 +IS - 9 +PY - 2020 +DO - 10.1063/5.0020407 +AU - Pierrot, A. +AU - Béron, F. +AU - Blon, T. +N1 - Export Date: 15 October 2020 +M3 - Article +DB - Scopus +C7 - 093903 +N1 - References: Mayergoyz, I.D., (1986) Phys. 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Lett. +VL - 56 +IS - 18 +SP - 931 +EP - 934 +PY - 2020 +DO - 10.1049/el.2020.1324 +AU - Nguyen, C.D. +N1 - Export Date: 15 October 2020 +M3 - Article +DB - Scopus +N1 - References: Park, K.-S., Park, Y.-P., Park, N.-C., 'Prospect of recording technologies for higher storage performance (2011) IEEE Trans. Magn, 47 (3), pp. 539-545; +Coughlin, T.M., (2018) 'Digital storage in consumer electronics: The essential guide', pp. 1-24. , (Springer International Publishing AG, Switzerland, 2nd edn); +Albrecht, T.R., Arona, H., Ayanoor-Vitikkate, V., 'Bit-patterned magnetic recording: Theory, media fabrication, and recording performance (2015) IEEE Trans. Magn, 51, pp. 1-42. , Art.no. 0800342; +Nguyen, C.D., Lee, J., 'Twin iterative detection for bit-patterned media recording systems' (2017) IEEE Trans. Magn, 53 (11), pp. 1-4. , Art 8109304; +Nguyen, C.D., Lee, J., '9/12 2-D modulation code for bit-patterned media recording (2017) IEEE Trans. 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Magn., , to be published +UR - https://www.scopus.com/inward/record.uri?eid=2-s2.0-85042049905&doi=10.1109%2fJPROC.2018.2795961&partnerID=40&md5=38a3dfa79923400c0ad28cbc30e8536f +ER - + +TY - CHAP +TI - Ferrimagnetic heterostructures for applications in magnetic recording +T2 - Novel Magnetic Nanostructures: Unique Properties and Applications +J2 - Novel Magnetic Nanostructures: Unique Properties and Applications +SP - 267 +EP - 331 +PY - 2018 +DO - 10.1016/B978-0-12-813594-5.00009-6 +AU - Radu, F. +AU - Sánchez-Barriga, J. +KW - All-optical switching +KW - Bit-patterned media +KW - Ferrimagnetic heterostructures +KW - Ferrimagnetic spin valves +KW - Ferrimagnetism +KW - Heat-assisted magnetic recording +KW - Helicity-dependent switching +KW - Magnetic memory bits +KW - Magnetic nanostructures +KW - Magnetic recording +KW - Magnetic thin films +KW - Noncollinear spin textures +KW - Percolated media +KW - Perpendicular magnetic recording +KW - Rear-earth transition-metal alloys +KW - Spintronics +KW - Temperature induced magnetic switching +KW - Ultrahigh density magnetic recording +N1 - Cited By :3 +N1 - Export Date: 15 October 2020 +M3 - Book Chapter +DB - Scopus +N1 - References: Wolf, S.A., Awschalom, D.D., Buhrman, R.A., Daughton, J.M., Von Molnár, S., Roukes, M.L., Chtchelkanova, A.Y., Treger, D.M., Spintronics: A spin-based electronics vision for the future (2001) Science, 294 (5546), pp. 1488-1495; +Žutić, I., Fabian, J., Das Sarma, S., Spintronics: Fundamentals and applications (2004) Rev. 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LaBrake; Solid State Tech Feb 2007; Wierer, J.J., Krames, M.R., Epier, J.E., Gardner, N.F., Wendt, J.R., Sigalas, M.M., Brueck, S.R.J., Shagam, M., (2005) Proc SPIE, 5739, p. 103; +Karlicek, R., (2007) Strategies in Light Symposium, , San Jose, February; +For more data on the Imprio-1100 see www.molecularimprints.comUR - https://www.scopus.com/inward/record.uri?eid=2-s2.0-35148889133&partnerID=40&md5=2582b93fae54a73f4f88759885c02951 +ER - + +TY - CONF +TI - Lithography beyond 32nm - A role for imprint? +C3 - Proceedings of SPIE - The International Society for Optical Engineering +J2 - Proc SPIE Int Soc Opt Eng +VL - 6518 +IS - PART 1 +SP - xxiii +EP - xxxvi +PY - 2007 +AU - Melliar-Smith, M. +KW - Bit patterned media +KW - Imprints lithography +KW - Photolithography +KW - Photonic crystals +N1 - Export Date: 15 October 2020 +M3 - Conference Paper +DB - Scopus +N1 - References: Colburn, M., Johnson, S., Stewart, M., Damle, S., Bailey, T., Choi, B.J., Wedlake, M., Willson, C.G., (1999) Proceedings of the SPIE's Int. Symp. on Microlithography, 3676, pp. 379-389. , March; +Chou, S.Y., Krauss, P.R., Renstrom, P.J., Nanoimprint lithography (1996) J. Vac. Sci., Tech. B, 14 (6); +Bender, M., (2002) Microelectronic Engineering, 61-62, pp. 407-413; +McMackin, I., Schumaker, P., Babbs, D., Choi, J., Wenli Collison, S.V.S., Schumaker, N., Watts, M., Voisin, R., (2003) Proc. of the SPIE's Int. Symp. on Microlithography, , Emerging Lithographic Technologies VII, Santa Clara, CA, February; +Resnick, D.J., Dauksher, W.J., Mancini, D., Nordquist, K.J., Johnson, S., Stacey, N., Ekhert, J.G., Schumaker, N., (2003) J.Vac. Sci. Tech B, 21, p. 2624. , November; +D.J.Resnick, D.P.Mancini, K.J.Norquist, W.J.Dauksher, I.McMackin, P.Schumaker, E.Thompson and S.V.Sreenivasan, J. Microlith, Microfab and Microsystems, 3, p316 April 2004; Hua, F., Sun, Y., Gaur, A., Meitl, M.A., Bilhaut, L., Rotkina, L., Wang, J., Rogers, J.A., (2004) Nano Letters, 4, p. 2467; +International Technology Roadmap for Semiconductors - 2006 Update - Table 78a Optical Mask Requirements; Scmid, G.M., Thompson, E., Stacey, N., Resnick, D., (2007) SPIE Emerging Lithographic Technologies Symposium, , Feb; +See www.vistec-semi.com for more details; Schmid, G.M., Thompson, E., Stacey, N., Resnick, D.J., Olynick, D.L., Anderson, E.H., Microlelectronic Engineering (2007), to be published; Sreenivasan, S.V., Schumaker, P., MaMackin, I., Choi, J., (2006), 5th International Conference on Nanoimprint and Nanoprint Technology, Nov; Myron, L.J., Thompson, E., McMackin, I., Resnick, D.J., Kitamura, T., Hasebe, T., Nakazawa, S., Dauksher, W., (2006) Proc SPIE, 6151, p. 173; +Dauksher, W., Nordquist, K., Le, N.V., Gehoski, K., Mancini, D., Resnick, D.J., Bozak, R., Lee, D., (2004) J. Vac. Sci Technology, p. 3306; +Schmid, G.M., Resnick, D.J., Fettig, R., Edinger, K., Young, S.R., Dauksher, W.J., (2007) European Mask and Lithography Conference, , January; +Moon, E.E., (1995) 2648 J. Vac. Sci. Technol. B, 13 (6). , Nov/Dec; +Choi, B.J., SPIE Intl (2001) Symp. Microlithography, , Emerging Lithographic Technologies, Santa Clara, CA; +Euclid E. Moon, et al; J. Vac. Sci. Technol. B, 21, No. 6, Nov'Dec 2003; Choi, J., (2004) Microelectronic Engineering, 78-79, p. 633; +Schumaker, P., Rafferty, T., Choi, J., McMackin, I., DiBiase, A., SPIE Intl Symp. Microlithography, , Emerging Lithographic Technologies, Poster Session 2006; +McMackin, I., private communication; Xu, F., Stacey, N., Watts, M., Truskett, V., McMackin, I., Choi, J., Schumaker, P., Schumaker, N., (2004) Proceedings of SPIE, 5374 (1), pp. 232-241. , Santa Clara, California, USA; +Kim, E.K., Stacey, N.A., Smith, B.J., Dickey, M.D., Johnson, S.C., Trinque, B.C., Willson, C.G., (2004) J. Vac. Sci. Technol. B, 22 (1), pp. 131-135. , Jan/Feb; +Reddy, S., Bonnecaze, R.T., (2005) Microeletronic Engineering, 82, pp. 60-70; +McMackin, I., LaBrake, D., private communication; Sreenivasan, S.V., McMackin, I., Xu, F., Wang, D., Stacey, N., Resnick, D.J., (2005) MICRO Magazine, , January; +Stewart, M.D., (2005) SPIE Intl Symp Microlithography Conference, March, , Paper 5751-21; +Willson, G., to be published; Willson, G., (2006) SEMATECH Litho Forum, May, , Vancouver, Canada; +Sooriyakumaran, R., (2006) SEMATECH Litho Forum, May, , Vancouver, Canada; +K. Gopalakrishnan et al, IEDM Tech. Digest 2005, p 471; R. S. Shenoy et al, Proc Symp VLSI Tech, June 2006, p 140. and Y. C Chen et al, IEEE Electron Device Meeting, December 2006; Hart, M., (2007) DARPA presentation January 22; +Z. Z. Bandic, E. A. Dobisz, T-W. Wu and T.R.Albrecht Soild State Technology Supplement Sept 2006; D. J. Resnick, G. M. Schmid and M. Miller MRS Proc Nov 2006; D. J. Resnick, G. M. Schmid, M. Miller, G. F. Doyle, C Jones and D. LaBrake; Solid State Tech Feb 2007; Wierer, J.J., Krames, M.R., Epier, J.E., Gardner, N.F., Wendt, J.R., Sigalas, M.M., Brueck, S.R.J., Shagam, M., (2005) Proc SPIE, 5739, p. 103; +Karlicek, R., (2007) Strategies in Light Symposium, , San Jose, February; +For more data on the Imprio-1100 see www.molecularimprints.comUR - https://www.scopus.com/inward/record.uri?eid=2-s2.0-35148875097&partnerID=40&md5=48209f99f6738ce72e7e4f1257971f53 +ER - + +TY - CONF +TI - Lithography beyond 32nm - A role for imprint? +C3 - Proceedings of SPIE - The International Society for Optical Engineering +J2 - Proc SPIE Int Soc Opt Eng +VL - 6521 +SP - xiii +EP - xxvi +PY - 2007 +AU - Melliar-Smith, M. +KW - Bit patterned media +KW - Imprints lithography +KW - Photolithography +KW - Photonic crystals +N1 - Export Date: 15 October 2020 +M3 - Conference Paper +DB - Scopus +N1 - References: Colburn, M., Johnson, S., Stewart, M., Damle, S., Bailey, T., Choi, B.J., Wedlake, M., Willson, C.G., (1999) Proceedings of the SPIE's Int. Symp. on Microlithography, 3676, pp. 379-389. , March; +Chou, S.Y., Krauss, P.R., Renstrom, P.J., Nanoimprint lithography (1996) J. Vac. Sci., Tech. B, 14 (6); +Bender, M., (2002) Microelectronic Engineering, 61-62, pp. 407-413; +McMackin, I., Schumaker, P., Babbs, D., Choi, J., Wenli Collison, S.V.S., Schumaker, N., Watts, M., Voisin, R., (2003) Proc. of the SPIE's Int. Symp. on Microlithography, , Emerging Lithographic Technologies VII, Santa Clara, CA, February; +Resnick, D.J., Dauksher, W.J., Mancini, D., Nordquist, K.J., Johnson, S., Stacey, N., Ekhert, J.G., Schumaker, N., (2003) J.Vac. Sci. Tech B, 21, p. 2624. , November; +D.J.Resnick, D.P.Mancini, K.J.Norquist, W.J.Dauksher, I.McMackin, P.Schumaker, E.Thompson and S.V.Sreenivasan, J. 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Nanotechnol. +VL - 7 +IS - 1 +SP - 13 +EP - 45 +PY - 2007 +AU - Li, K. +AU - Wu, Y. +AU - Guo, Z. +AU - Zheng, Y. +AU - Han, G. +AU - Qiu, J. +AU - Luo, P. +AU - An, L. +AU - Zhou, T. +KW - Current-Perpendicular-to-the-Plane (CPP) +KW - Exchange Bias +KW - Giant Magnetoresistive +KW - Interlayer Exchange Coupling +KW - Magnetic Media +KW - Magnetic Read Head +KW - Patterned Media +KW - Perpendicular Media +KW - Spin Valves +KW - Tunnel Magnetoresistance +N1 - Cited By :21 +N1 - Export Date: 15 October 2020 +M3 - Review +DB - Scopus +N1 - References: Thomposn, D.A., Best, J.S., (2000) IBM J. Res. Develop, 44, p. 311; +Tsang, C.H., Fontana Jr., R.E., Lin, T., Heim, D.E., Gurney, B.A., Williams, M.L., (1998) IBM J. Res. Develop, 42, p. 103; +Mao, S., Chen, Y., Liu, F., Chen, X., Xu, B., Lu, P., Patwari, M., Ryan, P., (2006) IEEE Trans. Magn, 42, p. 97; +A. Moser, C. Bonhote, Q. Dai, H. Do, B. Knigge, Y. Ikeda, Q. Le, B. Lengsfield, S. MacDonald, J. Li, V. Nayak, R. Payne, M. Schabes, N. 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Phys., 64, p. 5832 +UR - https://www.scopus.com/inward/record.uri?eid=2-s2.0-0001580052&doi=10.1063%2f1.364569&partnerID=40&md5=9a7287b9e74721d8dfd43196db034256 +ER - + +TY - JOUR +TI - External clocking PRML magnetic recording channel for discrete track media +T2 - IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences +J2 - IEICE Trans Fund Electron Commun Comput Sci +VL - E76-A +IS - 7 +SP - 1164 +EP - 1166 +PY - 1993 +AU - Yada, Hiroaki +AU - Yamakoshi, Takamichi +AU - Yamamoto, Noriyuki +AU - Erkocevic, Murat +AU - Hayashi, Nobuhiro +N1 - Cited By :3 +N1 - Export Date: 15 October 2020 +M3 - Article +DB - Scopus +UR - https://www.scopus.com/inward/record.uri?eid=2-s2.0-0027635379&partnerID=40&md5=61623bed8a53e2caad7dab09c9fa2f8a +ER - + +TY - JOUR +TI - HIGH-PERFORMANCE COLOUR GRAPHICS CONTROLLER. +T2 - Electronics & wireless world +J2 - Electron Wireless World +VL - 93 +IS - 1614 +SP - 368 +EP - 373 +PY - 1987 +AU - Adams, John +N1 - Export Date: 15 October 2020 +M3 - Article +DB - Scopus +UR - https://www.scopus.com/inward/record.uri?eid=2-s2.0-0023329368&partnerID=40&md5=26277b198a4733e1cb07f9ce2d6f3dcd +ER - + diff --git a/setup.py b/setup.py index d98d2ab..18a242d 100644 --- a/setup.py +++ b/setup.py @@ -10,7 +10,7 @@ with open("HISTORY.md") as history_file: history = history_file.read() -requirements = ["Click>=7.0<8", "bibtexparser>=1.2.0<2"] +requirements = ["Click>=7.0<8"] setup_requirements = ["pytest-runner"] diff --git a/wostools/article.py b/wostools/article.py index e219cfd..77eac63 100644 --- a/wostools/article.py +++ b/wostools/article.py @@ -14,11 +14,11 @@ ) ISI_CITATION_PATTERN = re.compile( - r"""^(?P[^,]+)?,[ ] # First author - (?P\d{4})?,[ ] # Publication year - (?P[^,]+)? # Journal + r"""^(?P[^,]+),[ ] # First author + (?P\d{4}),[ ] # Publication year + (?P[^,]+) # Journal (,[ ]V(?P[\w\d-]+))? # Volume - (,[ ][Pp](?P\d+))? # Start page + (,[ ][Pp](?P\w+))? # Start page (,[ ]DOI[ ](?P.+))? # The all important DOI """, re.X, @@ -55,23 +55,36 @@ def __init__( self.extra: Mapping[str, Any] = extra or {} @property - def simple_label(self): + def label(self) -> str: + if self.doi: + return self.doi + return self._label() + + def _label(self, exclude_doi=False, lower_p=False) -> str: if not (self.authors and self.year and self.journal): raise MissingLabelFields(self) + page_prefix = "p" if lower_p else "P" pieces = { "AU": self.authors[0].replace(",", ""), "PY": str(self.year), "J9": str(self.journal), "VL": f"V{self.volume}" if self.volume else None, - "BP": f"P{self.page}" if self.page else None, + "BP": f"{page_prefix}{self.page}" if self.page else None, + "DI": f"DOI {self.doi}" if self.doi else None, } return ", ".join(value for value in pieces.values() if value) @property - def label(self): - if self.doi: - return self.doi - return self.simple_label + def labels(self) -> Set[str]: + if not self.doi: + return {self.label, self._label(lower_p=True)} + return { + self.doi, + self.label, + self._label(exclude_doi=True), + self._label(lower_p=True), + self._label(exclude_doi=True, lower_p=True), + } def to_dict(self, simplified=True): """ @@ -100,13 +113,12 @@ def to_dict(self, simplified=True): } def merge(self, other: "Article") -> "Article": - if other.label not in {self.label, self.simple_label}: - logger.debug( + if other.label not in self.labels: + logger.warning( "\n".join( [ "Mixing articles with different labels might result in tragedy", - f" mine: {self.label}", - f" or: {self.simple_label}", + f" mine: {self.labels}", f" others: {other.label}", ] ) diff --git a/wostools/cached.py b/wostools/cached.py index 3c46871..268a39c 100644 --- a/wostools/cached.py +++ b/wostools/cached.py @@ -14,14 +14,6 @@ logger = logging.getLogger(__name__) -class Ref: - def __init__(self, current) -> None: - self.current = current - - def __hash__(self) -> int: - return id(self) - - class CachedCollection(BaseCollection): """ A collection of WOS text files. @@ -31,24 +23,27 @@ def __init__(self, *files): super().__init__(*files) self._cache_key = None self._cache: Dict[str, Article] = {} - self._refs: Dict[str, Ref] = {} self._labels: Dict[str, Set[str]] = {} + self._refs: Dict[str, str] = {} self._preheat() def _add_article(self, article: Article): - labels = {article.label, article.simple_label} existing_labels = { - l for label in labels for l in self._labels.get(label, set()) + l for label in article.labels for l in self._labels.get(label, set()) } + all_labels = existing_labels | article.labels existing_refs = { - self._refs[label] for label in existing_labels if label in self._refs + self._refs[label] for label in all_labels if label in self._refs } - for label in labels: - self._labels[label] = self._labels.get(label, set()).union(labels) - for label in labels: - if label in self._cache: - article = article.merge(self._cache[label]) + for ref in existing_refs: + other = self._cache.pop(ref, None) + if other is not None: + article = article.merge(other) + self._cache[article.label] = article + for label in all_labels: + self._labels[label] = all_labels + self._refs[label] = article.label def _preheat(self): # Preheat our cache @@ -74,12 +69,7 @@ def __iter__(self) -> Iterator[Article]: generator: A generator of Articles according to the text articles. """ self._preheat() - visited = set() - for label, article in self._cache.items(): - if label in visited: - continue - visited.update(self._labels[label]) - yield article + yield from self._cache.values() @property def authors(self) -> Iterable[str]: @@ -116,16 +106,6 @@ def citation_pairs(self) -> Iterable[Tuple[Article, Article]]: """ for article in self: for reference in article.references: - if reference in self._cache: - yield (article, self._cache[reference]) - - -def main(): - collection = CachedCollection.from_filenames( - "./scratch/scopus.ris", "./scratch/bit-pattern-savedrecs.txt" - ) - print(collection) - - -if __name__ == "__main__": - main() + if reference in self._refs: + label = self._refs[reference] + yield (article, self._cache[label]) diff --git a/wostools/cli.py b/wostools/cli.py index 2209f21..c03953f 100644 --- a/wostools/cli.py +++ b/wostools/cli.py @@ -41,7 +41,7 @@ def citation_pairs(sources, output): json.dump(pairs, output, indent=2) -@main.command("to-dict") +@main.command("to-json") @click.argument("sources", type=click.File("r"), nargs=-1) @click.option( "--output", @@ -58,7 +58,7 @@ def citation_pairs(sources, output): default=False, help="Add extra info to the output", ) -def to_dict(sources, output, more): +def to_json(sources, output, more): """ Build a collection by using the sources and print the citation pairs in json format or dumps them in the `output`. diff --git a/wostools/sources/scopus.py b/wostools/sources/scopus.py index f909cee..0c57937 100644 --- a/wostools/sources/scopus.py +++ b/wostools/sources/scopus.py @@ -1,5 +1,4 @@ from collections import defaultdict -import logging import re from typing import Dict, Iterable, List, Optional, TextIO, Tuple, Type @@ -31,13 +30,6 @@ def _joined(raw: Optional[List[str]]) -> Optional[str]: return " ".join(raw) -def _parse_page(value: Optional[str]) -> Optional[str]: - if not value: - return None - first, *_ = value.split("-") - return first - - def _find_volume_info(ref: str) -> Tuple[Dict[str, str], str]: volume_pattern = re.compile(r"(?P\d+)( \((?P.+?)\))?") page_pattern = re.compile(r"(pp?\. (?P\w+)(-[^,\s]+)?)") @@ -71,12 +63,13 @@ def _find_volume_info(ref: str) -> Tuple[Dict[str, str], str]: def _find_doi(ref: str) -> Tuple[Optional[str], str]: pattern = re.compile( - r"((DOI:?)|(doi.org\/)|(aps.org\/doi\/)) ?(?P[^\s,]+)", re.I + r"((doi.org\/)|(aps.org\/doi\/)|(DOI:?)) ?(?P[^\s,;:]{5,})", re.I ) result = re.search(pattern, ref) if result is None or "doi" not in result.groupdict(): return None, ref - return f"DOI {result.groupdict()['doi']}", ref[result.lastindex :] + doi = result.groupdict()["doi"] + return f"DOI {doi}", ref[result.lastindex :] def _scopus_ref_to_isi(scopusref: str) -> str: @@ -107,13 +100,12 @@ def parse_references(refs: List[str]) -> List[str]: try: result.append(_scopus_ref_to_isi(ref)) except (KeyError, IndexError, TypeError, ValueError) as e: - pass - # print(f"ignoring {ref}", e) + continue return result def ris_to_dict(record: str) -> Dict[str, List[str]]: - RIS_PATTERN = re.compile(r"^(((?P[A-Z09]{2})) - )?(?P(.*))^") + RIS_PATTERN = re.compile(r"^(((?P[A-Z0-9]{2}))[ ]{2}-[ ]{1})?(?P(.*))$") parsed = defaultdict(list) current = None @@ -128,13 +120,13 @@ def ris_to_dict(record: str) -> Dict[str, List[str]]: break if key: if key == "N1" and value and ":" in value: - label, value = value.split(": ", 1) - current = f"{key}:{label}" + label, value = value.split(":", 1) + value = value.strip() + current = f"{key}:{label.strip()}" else: current = data["key"] if value and current: parsed[current].append(data.get("value", "")) - return dict(parsed) @@ -162,20 +154,5 @@ def parse_file(file: TextIO) -> Iterable[Article]: for item in file.read().split("\n\n"): if item.isspace(): continue - yield parse_record(item) - - -if __name__ == "__main__": - with open("./scratch/refs.txt") as refs: - data = [line.strip() for line in refs] - cit = [ref for line in data for ref in parse_references([line])] - print(sum("doi" in ref or "DOI" in ref for ref in data)) - print(sum("DOI" in ref for ref in cit)) - - with open("./scratch/translated.txt", "w") as refs: - refs.write("\n".join(cit)) - - _scopus_ref_to_isi( - "Terris, B.D., Folks, L., Weller, D., Baglin, J.E.E., Kellock, A.J., Rothuizen, H., Vettiger, P., Ion beam patterning of magnetic films using stencil masks (1999) Appl. Phys. Lett., 75 (2), pp. 403-405. , July" - ) - + article = parse_record(item.strip()) + yield article From 45fef0d5b684310c3a2bd0016735654afabb12c9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Oscar=20Arbel=C3=A1ez?= Date: Thu, 15 Oct 2020 22:43:17 -0500 Subject: [PATCH 05/10] Drop lazi collection support --- README.md | 2 -- tests/conftest.py | 12 +------- wostools/__init__.py | 4 +-- wostools/base.py | 4 +-- wostools/lazy.py | 65 -------------------------------------------- 5 files changed, 5 insertions(+), 82 deletions(-) delete mode 100644 wostools/lazy.py diff --git a/README.md b/README.md index 4223c5b..de9b73e 100644 --- a/README.md +++ b/README.md @@ -43,8 +43,6 @@ $ wostools to-json docs/examples/bit-pattern-savedrecs.txt --output=document.jso - Free software: MIT license - Just parses an ISI Web of Knowledge file and produces a native python object. -- Through the `CollectionLazy` object it can do this using the minimum - amount of memory it can possibly do. - It has a cli to extract documents and citation pairs for you :smile: ## Credits diff --git a/tests/conftest.py b/tests/conftest.py index 64a4386..9b23926 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -2,7 +2,7 @@ Configuration file for python-wostools tests. """ -from wostools import Article, LazyCollection, CachedCollection +from wostools import Article, CachedCollection import pytest import io @@ -102,13 +102,3 @@ def filename_single_document(): @pytest.fixture def filename_many_documents(): return "docs/examples/bit-pattern-savedrecs.txt" - - -@pytest.fixture(params=[CachedCollection, LazyCollection]) -def collection_single_document(request, filename_single_document): - return request.param.from_filenames(filename_single_document) - - -@pytest.fixture(params=[CachedCollection, LazyCollection]) -def collection_many_documents(request, filename_many_documents): - return request.param.from_filenames(filename_many_documents) diff --git a/wostools/__init__.py b/wostools/__init__.py index 940d739..34cfb72 100644 --- a/wostools/__init__.py +++ b/wostools/__init__.py @@ -5,7 +5,7 @@ __version__ = "2.0.7" from wostools.article import Article -from wostools.lazy import LazyCollection from wostools.cached import CachedCollection +from wostools.cached import CachedCollection as Collection -__all__ = ["CachedCollection", "LazyCollection", "Article"] +__all__ = ["CachedCollection", "Collection", "Article"] diff --git a/wostools/base.py b/wostools/base.py index a34f863..6f63686 100644 --- a/wostools/base.py +++ b/wostools/base.py @@ -31,7 +31,7 @@ def from_glob(cls, pattern): pattern (str): String with the pattern to be passed to glob. Returns: - CollectionLazy: Collection with the articles by using the pattern. + BaseCollection: Collection with the articles by using the pattern. """ return cls.from_filenames(*glob.glob(pattern)) @@ -43,7 +43,7 @@ def from_filenames(cls, *filenames): filenames (str): String with the filename. Returns: - CollectionLazy: Collection with the articles by reading the + BaseCollection: Collection with the articles by reading the filenames. """ files = [open(filename, encoding="utf-8-sig") for filename in filenames] diff --git a/wostools/lazy.py b/wostools/lazy.py deleted file mode 100644 index d3c5afc..0000000 --- a/wostools/lazy.py +++ /dev/null @@ -1,65 +0,0 @@ -""" -The whole wostools thing. -""" - -import itertools -import logging -from contextlib import suppress -from typing import Iterable, Tuple - -from wostools.article import Article -from wostools.base import BaseCollection -from wostools.exceptions import InvalidReference, MissingLabelFields - -logger = logging.getLogger(__name__) - - -class LazyCollection(BaseCollection): - """A collection of WOS text files. - - Args: - filenames (str): Strings with the names of the files containing - articles. - """ - - @property - def authors(self) -> Iterable[str]: - """Iterates over all article authors, including duplicates - - Returns: - generator: A generator with the authors (one by one) of the - articles in the collection. - """ - for article in self: - yield from article.authors - - @property - def coauthors(self) -> Iterable[Tuple[str, str]]: - """Iterates over coauthor pairs. - - Returns: - generator: A generator with the pair of coauthors of the articles - in the collections. - """ - for article in self._articles(): - yield from ( - (source, target) - for source, target in itertools.combinations(sorted(article.authors), 2) - ) - - def citation_pairs(self) -> Iterable[Tuple[Article, Article]]: - """Computes the citation pairs for the articles in the collection. - - Returns: - genertator: A generator with the citation links: pairs of article - labesl, where the firts element is the article which cites the - second element. - """ - for article in self: - for reference in article.references: - try: - yield (article, Article.from_isi_citation(reference)) - except InvalidReference: - logger.info( - f"Ignoring malformed reference '{reference}' from '{article.label}'" - ) From 8f505b2c732a493db13d28e9f77fead862f03c4d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Oscar=20Arbel=C3=A1ez?= Date: Thu, 15 Oct 2020 23:05:43 -0500 Subject: [PATCH 06/10] Make the linter happy --- tests/conftest.py | 2 +- wostools/cached.py | 4 +++- wostools/exceptions.py | 2 +- wostools/sources/isi.py | 1 - wostools/sources/scopus.py | 12 +++++++----- 5 files changed, 12 insertions(+), 9 deletions(-) diff --git a/tests/conftest.py b/tests/conftest.py index 9b23926..c82391e 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -2,7 +2,7 @@ Configuration file for python-wostools tests. """ -from wostools import Article, CachedCollection +from wostools import Article import pytest import io diff --git a/wostools/cached.py b/wostools/cached.py index 268a39c..74bea07 100644 --- a/wostools/cached.py +++ b/wostools/cached.py @@ -29,7 +29,9 @@ def __init__(self, *files): def _add_article(self, article: Article): existing_labels = { - l for label in article.labels for l in self._labels.get(label, set()) + alias + for label in article.labels + for alias in self._labels.get(label, set()) } all_labels = existing_labels | article.labels existing_refs = { diff --git a/wostools/exceptions.py b/wostools/exceptions.py index 1a7efc9..0accfe4 100644 --- a/wostools/exceptions.py +++ b/wostools/exceptions.py @@ -15,7 +15,7 @@ def __init__(self, reference: str): class InvalidScopusFile(WosToolsError, ValueError): def __init__(self): - super().__init__(f"The file does not look like a valid bib file") + super().__init__("The file does not look like a valid bib file") class InvalidIsiLine(WosToolsError, ValueError): diff --git a/wostools/sources/isi.py b/wostools/sources/isi.py index 352f9d6..f178b95 100644 --- a/wostools/sources/isi.py +++ b/wostools/sources/isi.py @@ -12,4 +12,3 @@ def _split(file) -> Iterable[str]: def parse_file(file: TextIO) -> Iterable[Article]: for raw in _split(file): yield Article.from_isi_text(raw) - diff --git a/wostools/sources/scopus.py b/wostools/sources/scopus.py index 0c57937..547d411 100644 --- a/wostools/sources/scopus.py +++ b/wostools/sources/scopus.py @@ -1,13 +1,15 @@ from collections import defaultdict +import logging import re -from typing import Dict, Iterable, List, Optional, TextIO, Tuple, Type - -from bibtexparser.bparser import BibTexParser +from typing import Dict, Iterable, List, Optional, TextIO, Tuple from wostools.article import Article from wostools.exceptions import InvalidScopusFile +logger = logging.getLogger(__name__) + + def _size(file) -> int: file.seek(0, 2) size = file.tell() @@ -99,8 +101,8 @@ def parse_references(refs: List[str]) -> List[str]: for ref in refs: try: result.append(_scopus_ref_to_isi(ref)) - except (KeyError, IndexError, TypeError, ValueError) as e: - continue + except (KeyError, IndexError, TypeError, ValueError): + logging.error(f"Ignoring invalid reference {ref}") return result From d8c68caa85fa3cdec6abb34e9fba0aad894be38e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Oscar=20Arbel=C3=A1ez?= Date: Thu, 15 Oct 2020 23:19:01 -0500 Subject: [PATCH 07/10] Update our dev requirements --- requirements_dev.txt | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/requirements_dev.txt b/requirements_dev.txt index 64880c7..77bfd88 100644 --- a/requirements_dev.txt +++ b/requirements_dev.txt @@ -1,9 +1,9 @@ -flake8==3.8.3 -coverage==5.2.1 +flake8==3.8.4 +coverage==5.3 -pytest==6.0.1 +pytest==6.1.1 pytest-runner==5.2 pytest-watch==4.2.0 -pytest-bdd==3.4.0 +pytest-bdd==4.0.1 dataclasses==0.7; python_version < "3.7" From 8a2ca772ed461b82b1a81dff18a08dbfb1dd3318 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Oscar=20Arbel=C3=A1ez?= Date: Thu, 15 Oct 2020 23:23:32 -0500 Subject: [PATCH 08/10] Try for higher python version support --- .github/workflows/pythonpackage.yml | 2 +- setup.py | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml index 9c72c5e..3be565c 100644 --- a/.github/workflows/pythonpackage.yml +++ b/.github/workflows/pythonpackage.yml @@ -9,7 +9,7 @@ jobs: strategy: max-parallel: 4 matrix: - python-version: [3.6, 3.7, 3.8] + python-version: [3.6, 3.7, 3.8, 3.9] steps: - uses: actions/checkout@v1 diff --git a/setup.py b/setup.py index 18a242d..6d6c00b 100644 --- a/setup.py +++ b/setup.py @@ -28,6 +28,8 @@ "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.6", "Programming Language :: Python :: 3.7", + "Programming Language :: Python :: 3.8", + "Programming Language :: Python :: 3.9", ], entry_points={"console_scripts": ["wostools=wostools.cli:main"]}, description="Translates isi web of knowledge files into python objects.", From b3b72107b740652524ac38118e87b49f28e8d576 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Oscar=20Arbel=C3=A1ez?= Date: Thu, 15 Oct 2020 23:27:32 -0500 Subject: [PATCH 09/10] Python 3.6 is after it's final bugfix version now --- .github/workflows/pythonpackage.yml | 2 +- CONTRIBUTING.md | 3 --- setup.py | 1 - 3 files changed, 1 insertion(+), 5 deletions(-) diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml index 3be565c..06530c5 100644 --- a/.github/workflows/pythonpackage.yml +++ b/.github/workflows/pythonpackage.yml @@ -9,7 +9,7 @@ jobs: strategy: max-parallel: 4 matrix: - python-version: [3.6, 3.7, 3.8, 3.9] + python-version: [3.7, 3.8, 3.9] steps: - uses: actions/checkout@v1 diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index bbc149a..495ad66 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -110,9 +110,6 @@ Before you submit a pull request, check that it meets these guidelines: 2. If the pull request adds functionality, the docs should be updated. Put your new functionality into a function with a docstring, and add the feature to the list in README.md. -3. The pull request should work for Python 3.6, and for PyPy. Check - - and make sure that the tests pass for all supported Python versions. ## Tips diff --git a/setup.py b/setup.py index 6d6c00b..b61c43a 100644 --- a/setup.py +++ b/setup.py @@ -26,7 +26,6 @@ "License :: OSI Approved :: MIT License", "Natural Language :: English", "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.6", "Programming Language :: Python :: 3.7", "Programming Language :: Python :: 3.8", "Programming Language :: Python :: 3.9", From 1bb6e2d5d0c4fac6b3056c9086553603186fb380 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Oscar=20Arbel=C3=A1ez?= Date: Thu, 15 Oct 2020 23:42:39 -0500 Subject: [PATCH 10/10] Prepare for release --- .zenodo.json | 4 ++-- HISTORY.md | 8 ++++++++ README.md | 15 +++++++++------ setup.py | 2 +- wostools/__init__.py | 2 +- 5 files changed, 21 insertions(+), 10 deletions(-) diff --git a/.zenodo.json b/.zenodo.json index 8af3162..5be563b 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -2,7 +2,7 @@ "description": "Translates isi web of knowledge files into python objects.", "license": "MIT", "title": "coreofscience/python-wostools", - "version": "v2.0.7", + "version": "v3.0.0", "upload_type": "software", "publication_date": "2018-08-13", "creators": [ @@ -25,7 +25,7 @@ "related_identifiers": [ { "scheme": "url", - "identifier": "https://github.com/coreofscience/python-wostools/tree/v2.0.7", + "identifier": "https://github.com/coreofscience/python-wostools/tree/v3.0.0", "relation": "isSupplementTo" }, { diff --git a/HISTORY.md b/HISTORY.md index 08253b1..81aadc2 100644 --- a/HISTORY.md +++ b/HISTORY.md @@ -1,5 +1,13 @@ # History +## 3.0.0 (2020-10-15) + +- (!) Adds scopus RIS format support. +- Drops support for `LazyCollection`. +- Adds docummented support for Python 3.8 and 3.9 +- Drops docummented support for Python 3.6. +- Improves article matching in collections. + ## 2.0.7 (2020-08-23) - Remove from the collection those documents whose label is unknow or conflictive. diff --git a/README.md b/README.md index de9b73e..bd96613 100644 --- a/README.md +++ b/README.md @@ -18,8 +18,8 @@ Say you want to grab the title of all the articles in an ISI file, you can grab [this example file](docs/examples/bit-pattern-savedrecs.txt). ```python ->>> from wostools import CachedCollection ->>> collection = CachedCollection.from_filenames('docs/examples/bit-pattern-savedrecs.txt') +>>> from wostools import Cached +>>> collection = Cached.from_filenames('docs/examples/bit-pattern-savedrecs.txt') >>> for article in collection: ... print(article.title) In situ grazing incidence small-angle X-ray scattering study of solvent vapor annealing in lamellae-forming block copolymer thin films: Trade-off of defects in deswelling @@ -40,10 +40,11 @@ $ wostools to-json docs/examples/bit-pattern-savedrecs.txt --output=document.jso ## Features -- Free software: MIT license -- Just parses an ISI Web of Knowledge file and produces a native - python object. -- It has a cli to extract documents and citation pairs for you :smile: +- Free software: MIT license +- Parses an ISI Web of Knowledge file and produces a native python object. +- Parses RIS scopus files and produces a native python object. +- Merges ISI and RIS files into enriched collections. +- It has a cli to extract documents and citation pairs for you :smile: ## Credits @@ -51,3 +52,5 @@ This package was created with [Cookiecutter](https://github.com/audreyr/cookiecutter) and the [audreyr/cookiecutter-pypackage](https://github.com/audreyr/cookiecutter-pypackage) project template. + +Development of this package is supported by [Core of Science](https://coreofscience.com). \ No newline at end of file diff --git a/setup.py b/setup.py index b61c43a..f21c34c 100644 --- a/setup.py +++ b/setup.py @@ -43,7 +43,7 @@ test_suite="tests", tests_require=test_requirements, url="https://github.com/coreofscience/python-wostools", - version="2.0.7", + version="3.0.0", zip_safe=False, long_description_content_type="text/markdown", ) diff --git a/wostools/__init__.py b/wostools/__init__.py index 34cfb72..a2b08c6 100644 --- a/wostools/__init__.py +++ b/wostools/__init__.py @@ -2,7 +2,7 @@ __author__ = """Core of Science""" __email__ = "dev@coreofscience.com" -__version__ = "2.0.7" +__version__ = "3.0.0" from wostools.article import Article from wostools.cached import CachedCollection