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many minor changes

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Lukas Winkler 2023-06-27 22:38:59 +02:00
parent c15883e801
commit 53c60a22b5
Signed by: lukas
GPG key ID: 54DE4D798D244853
7 changed files with 436 additions and 189 deletions
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1
.gitignore vendored
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@ -2,3 +2,4 @@
__pycache__/ __pycache__/
library/ library/
!paperlibrary/library !paperlibrary/library
*.bak

25
paperlibrary/api/api.py
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@ -1,9 +1,10 @@
from functools import lru_cache
from pathlib import Path from pathlib import Path
from typing import List, Dict from typing import List, Dict
from requests import Session from requests import Session
from paperlibrary.api.models import Author, PDF, Keyword, PaperComplete from paperlibrary.api.models import Author, PDF, Keyword, PaperComplete, Note
class PaperLibraryAPI: class PaperLibraryAPI:
@ -14,18 +15,25 @@ class PaperLibraryAPI:
self.s = Session() self.s = Session()
self.s.headers.update({"Authorization": "Token " + auth_token}) self.s.headers.update({"Authorization": "Token " + auth_token})
@lru_cache
def fetch_papers(self) -> List[PaperComplete]: def fetch_papers(self) -> List[PaperComplete]:
r = self.s.get(self.baseURL + "papers/") r = self.s.get(self.baseURL + "papers/")
r.raise_for_status()
return PaperComplete.schema().loads(r.text, many=True) return PaperComplete.schema().loads(r.text, many=True)
@lru_cache
def fetch_authors(self) -> List[Author]: def fetch_authors(self) -> List[Author]:
r = self.s.get(self.baseURL + "authors/") r = self.s.get(self.baseURL + "authors/")
r.raise_for_status()
return Author.schema().loads(r.text, many=True) return Author.schema().loads(r.text, many=True)
@lru_cache
def fetch_keywords(self) -> List[Keyword]: def fetch_keywords(self) -> List[Keyword]:
r = self.s.get(self.baseURL + "keywords/") r = self.s.get(self.baseURL + "keywords/")
r.raise_for_status()
return Keyword.schema().loads(r.text, many=True) return Keyword.schema().loads(r.text, many=True)
@lru_cache
def fetch_papers_by_year(self) -> Dict[int, List[PaperComplete]]: def fetch_papers_by_year(self) -> Dict[int, List[PaperComplete]]:
papers = self.fetch_papers() papers = self.fetch_papers()
years: Dict[int, List[PaperComplete]] = {} years: Dict[int, List[PaperComplete]] = {}
@ -36,12 +44,16 @@ class PaperLibraryAPI:
years[paper.year] = [paper] years[paper.year] = [paper]
return years return years
@lru_cache
def fetch_bibliography(self) -> str: def fetch_bibliography(self) -> str:
r = self.s.get(self.baseURL + "bibtex/") r = self.s.get(self.baseURL + "bibtex/")
r.raise_for_status()
return r.text return r.text
@lru_cache
def fetch_pdfs(self) -> List[PDF]: def fetch_pdfs(self) -> List[PDF]:
r = self.s.get(self.baseURL + "pdfs/") r = self.s.get(self.baseURL + "pdfs/")
r.raise_for_status()
return PDF.schema().loads(r.text, many=True) return PDF.schema().loads(r.text, many=True)
def upload_pdf(self, pdf, file: Path) -> PDF: def upload_pdf(self, pdf, file: Path) -> PDF:
@ -49,4 +61,15 @@ class PaperLibraryAPI:
r = self.s.put(pdf.url, files={ r = self.s.put(pdf.url, files={
"file": f, "file": f,
}) })
r.raise_for_status()
return PDF.schema().loads(r.text) return PDF.schema().loads(r.text)
def update_note(self, id: int, file_text: str) -> None:
r = self.s.put(self.baseURL + f"notes/{id}/", json={"paper": id, "text_md": file_text})
r.raise_for_status()
return Note.schema().loads(r.text)
def create_note(self, id: int, file_text: str) -> None:
r = self.s.post(self.baseURL + f"notes/", json={"paper": id, "text_md": file_text})
r.raise_for_status()
return Note.schema().loads(r.text)

19
paperlibrary/api/models.py
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@ -25,7 +25,7 @@ class PDF(DataClassJsonMixin):
@dataclass @dataclass
class Paper(DataClassJsonMixin): class Paper(DataClassJsonMixin):
# id: int id: int
url: str url: str
title: str title: str
custom_title: str custom_title: str
@ -47,6 +47,8 @@ class PaperComplete(Paper):
publication: str publication: str
doctype: str doctype: str
arxiv_id: Optional[str] arxiv_id: Optional[str]
arxiv_class: Optional[str]
ads_version: Optional[int]
bibcode: Optional[str] bibcode: Optional[str]
year: int year: int
pubdate: str # TODO: to datetime pubdate: str # TODO: to datetime
@ -56,12 +58,14 @@ class PaperComplete(Paper):
recommended_by: List[str] recommended_by: List[str]
tags: List[str] tags: List[str]
custom_title: str custom_title: str
notes_md: str notes_md: Optional[str]
notes_html: str notes_html: Optional[str]
notes_updated_at: Optional[str]
@dataclass @dataclass
class Author(DataClassJsonMixin): class Author(DataClassJsonMixin):
id: int
url: str url: str
papers: List[Paper] papers: List[Paper]
name: str name: str
@ -76,7 +80,16 @@ class Author(DataClassJsonMixin):
@dataclass @dataclass
class Keyword(DataClassJsonMixin): class Keyword(DataClassJsonMixin):
id: int
url: str url: str
papers: List[Paper] papers: List[Paper]
name: str name: str
kw_schema: str kw_schema: str
@dataclass
class Note(DataClassJsonMixin):
paper: int
text_md: str
text_html: str
updated_at: str

56
paperlibrary/library/library.py
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@ -1,7 +1,7 @@
import hashlib import hashlib
import os import os
import shutil import shutil
from datetime import datetime from datetime import datetime, timezone
from pathlib import Path from pathlib import Path
from alive_progress import alive_bar from alive_progress import alive_bar
@ -27,9 +27,15 @@ def link_file(pdf_dir: Path, directory: Path, paper: Paper, filename: str = None
if filename is None: if filename is None:
filename = paper.title filename = paper.title
notes_dir = pdf_dir.parent / "notes"
notes_file = notes_dir / f"{paper.id}.md"
meta_dir = pdf_dir.parent / "meta"
meta_file = meta_dir / f"{paper.id}.json"
sourcefile = pdf_dir / f"{paper.main_pdf.id}.pdf" sourcefile = pdf_dir / f"{paper.main_pdf.id}.pdf"
targetfile = directory / "{}.pdf".format(format_filename(filename)) targetfile = directory / "{}.pdf".format(format_filename(filename))
targetfile.symlink_to(sourcefile) targetfile.symlink_to(sourcefile)
targetfile.with_suffix(".md").symlink_to(notes_file)
targetfile.with_suffix(".json").symlink_to(meta_file)
def write_symlinks(api: PaperLibraryAPI, config: Config): def write_symlinks(api: PaperLibraryAPI, config: Config):
@ -40,11 +46,12 @@ def write_symlinks(api: PaperLibraryAPI, config: Config):
author_dir = basedir / "by_author" author_dir = basedir / "by_author"
keyword_dir = basedir / "by_keyword" keyword_dir = basedir / "by_keyword"
year_dir = basedir / "by_year" year_dir = basedir / "by_year"
tags_dir = basedir / "by_tags"
title_dir = basedir / "by_title" title_dir = basedir / "by_title"
custom_title_dir = basedir / "by_custom_title" custom_title_dir = basedir / "by_custom_title"
citation_key_dir = basedir / "by_citation_key" citation_key_dir = basedir / "by_citation_key"
for directory in [author_dir, keyword_dir, year_dir, title_dir, custom_title_dir, citation_key_dir]: for directory in [author_dir, keyword_dir, year_dir, title_dir, tags_dir, custom_title_dir, citation_key_dir]:
shutil.rmtree(directory, ignore_errors=True) shutil.rmtree(directory, ignore_errors=True)
directory.mkdir() directory.mkdir()
@ -60,12 +67,16 @@ def write_symlinks(api: PaperLibraryAPI, config: Config):
if not keyword.papers: if not keyword.papers:
continue continue
keyword_subdir = keyword_dir / format_filename(keyword.name) keyword_subdir = keyword_dir / format_filename(keyword.name)
keyword_subdir.mkdir() keyword_subdir.mkdir(exist_ok=True)
for paper in keyword.papers: for paper in keyword.papers:
link_file(pdf_dir, keyword_subdir, paper) link_file(pdf_dir, keyword_subdir, paper)
for paper in api.fetch_papers(): for paper in api.fetch_papers():
link_file(pdf_dir, title_dir, paper, paper.title) link_file(pdf_dir, title_dir, paper, paper.title)
for tag in paper.tags:
tag_dir = tags_dir / tag
tag_dir.mkdir(exist_ok=True, parents=True)
link_file(pdf_dir, tag_dir, paper, paper.title)
if not paper.custom_title: if not paper.custom_title:
continue continue
@ -126,6 +137,45 @@ def update_pdfs(api: PaperLibraryAPI, config: Config):
download_file(api, pdf.file, pdf_file) download_file(api, pdf.file, pdf_file)
def update_meta(api: PaperLibraryAPI, config: Config):
meta_dir = config.basedir_path / "meta"
meta_dir.mkdir(exist_ok=True)
for paper in api.fetch_papers():
with (meta_dir / f"{paper.id}.json").open("w") as f:
f.write(paper.to_json(indent=2, ensure_ascii=False))
def update_notes(api: PaperLibraryAPI, config: Config):
notes_dir = config.basedir_path / "notes"
notes_dir.mkdir(exist_ok=True)
for paper in api.fetch_papers():
if paper.notes_md is None:
paper.notes_md = ""
notes_file = notes_dir / f"{paper.id}.md"
if not notes_file.exists():
notes_file.write_text(paper.notes_md)
continue
file_text = notes_file.read_text()
if file_text == paper.notes_md:
continue
print(repr(file_text), repr(paper.notes_md))
if paper.notes_updated_at is None:
api.create_note(paper.id, file_text)
continue
online_change_date = datetime.fromisoformat(paper.notes_updated_at)
local_change_date = datetime.fromtimestamp(notes_file.stat().st_mtime, tz=timezone.utc)
print(online_change_date, local_change_date)
print(local_change_date - online_change_date)
if online_change_date > local_change_date:
print("fetching from online")
notes_file.write_text(paper.notes_md)
continue
print("updating online")
api.update_note(paper.id, file_text)
def write_bibliography(api: PaperLibraryAPI, config: Config): def write_bibliography(api: PaperLibraryAPI, config: Config):
bib = api.fetch_bibliography() bib = api.fetch_bibliography()
target_file = config.basedir_path / "bibliography.bib" target_file = config.basedir_path / "bibliography.bib"

9
paperlibrary/pap.py
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@ -1,11 +1,12 @@
import click import click
from click_default_group import DefaultGroup
from paperlibrary.api import PaperLibraryAPI from paperlibrary.api import PaperLibraryAPI
from paperlibrary.config import get_config, Config, save_config, config_check from paperlibrary.config import get_config, Config, save_config, config_check
from paperlibrary.library import write_symlinks, update_pdfs, write_bibliography from paperlibrary.library import write_symlinks, update_pdfs, write_bibliography, update_notes, update_meta
@click.group() @click.group(cls=DefaultGroup, default="update",default_if_no_args=True)
@click.pass_context @click.pass_context
def cli(ctx): def cli(ctx):
ctx.obj = get_config() ctx.obj = get_config()
@ -18,8 +19,10 @@ def update(config: Config):
config_check(config) config_check(config)
api = PaperLibraryAPI(config.url, auth_token=config.auth_token) api = PaperLibraryAPI(config.url, auth_token=config.auth_token)
write_bibliography(api, config) write_bibliography(api, config)
write_symlinks(api, config)
update_pdfs(api, config) update_pdfs(api, config)
update_meta(api, config)
update_notes(api, config)
write_symlinks(api, config)
@cli.command() @cli.command()

506
poetry.lock generated
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@ -1,278 +1,434 @@
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grapheme = "0.6.0"
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9
pyproject.toml
View file

@ -7,11 +7,12 @@ authors = ["Lukas Winkler <git@lw1.at>"]
[tool.poetry.dependencies] [tool.poetry.dependencies]
python = "^3.8" python = "^3.8"
requests = "^2.24.0" requests = "^2.24.0"
click = "^7.1.2" click = "^8.1.2"
dataclasses-json = "^0.5.2" dataclasses-json = "^0.5.2"
tzlocal = "^2.1" tzlocal = "^5.0"
alive-progress = "^1.6.1" alive-progress = "^3.1.2"
PyYAML = "^5.3.1" PyYAML = "^6.0.0"
click-default-group = "^1.2.2"
[build-system] [build-system]
requires = ["poetry-core>=1.0.0"] requires = ["poetry-core>=1.0.0"]