support notes

paperlibrary/api/api.py

@@ -1,8 +1,9 @@
-from typing import List
+from pathlib import Path
+from typing import List, Dict
 
 from requests import Session
 
-from paperlibrary.api.models import Author, PDF, Keyword
+from paperlibrary.api.models import Author, PDF, Keyword, PaperComplete
 
 
 class PaperLibraryAPI:
@@ -13,14 +14,35 @@ class PaperLibraryAPI:
         self.s = Session()
         self.s.headers.update({"Authorization": "Token " + auth_token})
 
+    def fetch_papers(self) -> List[PaperComplete]:
+        r = self.s.get(self.baseURL + "papers/")
+        return PaperComplete.schema().loads(r.text, many=True)
+
     def fetch_authors(self) -> List[Author]:
         r = self.s.get(self.baseURL + "authors/")
         return Author.schema().loads(r.text, many=True)
 
-    def fetch_keywords(self) -> List[Author]:
+    def fetch_keywords(self) -> List[Keyword]:
         r = self.s.get(self.baseURL + "keywords/")
         return Keyword.schema().loads(r.text, many=True)
 
+    def fetch_papers_by_year(self) -> Dict[int, List[PaperComplete]]:
+        papers = self.fetch_papers()
+        years: Dict[int, List[PaperComplete]] = {}
+        for paper in papers:
+            if paper.year in years:
+                years[paper.year].append(paper)
+            else:
+                years[paper.year] = [paper]
+        return years
+
     def fetch_pdfs(self) -> List[PDF]:
         r = self.s.get(self.baseURL + "pdfs/")
         return PDF.schema().loads(r.text, many=True)
+
+    def upload_pdf(self, pdf, file: Path) -> PDF:
+        with file.open("rb") as f:
+            r = self.s.put(pdf.url, files={
+                "file": f,
+            })
+        return PDF.schema().loads(r.text)

paperlibrary/api/models.py

@@ -6,13 +6,23 @@ from dataclasses_json import DataClassJsonMixin, config
 from marshmallow import fields
 
 
+@dataclass
+class Note(DataClassJsonMixin):
+    paper: int
+    recommended_by: List[str]
+    custom_title: str
+    notes_md: str
+    notes_html: str
+
+
 @dataclass
 class PDF(DataClassJsonMixin):
     id: int
+    url: str
     file: str
-    sha265: str
+    sha256: str
     type: str
-    preview: str
+    preview: Optional[str]
     updated_at: datetime = field(
         metadata=config(
             encoder=datetime.isoformat,
@@ -24,29 +34,52 @@ class PDF(DataClassJsonMixin):
 
 @dataclass
 class Paper(DataClassJsonMixin):
-    id: int
+    # id: int
     url: str
     title: str
     pdfs: List[PDF]
-    doi: str
+    doi: Optional[str]
+    note: Optional[Note]
 
     @property
-    def main_pdf(self) -> PDF:
+    def main_pdf(self) -> Optional[PDF]:
+        if not self.pdfs:
+            return None
         return self.pdfs[0]
 
 
+@dataclass
+class PaperComplete(Paper):
+    keywords: List[str]
+    authors: List[str]
+    first_author: str
+    publication: str
+    doctype: str
+    arxiv_id: str
+    bibcode: str
+    year: int
+    pubdate: str  # TODO: to datetime
+    entry_date: str  # TODO: to datetime
+    citation_count: int
+
+
 @dataclass
 class Author(DataClassJsonMixin):
     url: str
     papers: List[Paper]
     name: str
+    pretty_name: Optional[str]
     affiliation: Optional[str]
     orcid_id: Optional[str]
 
+    @property
+    def display_name(self):
+        return self.pretty_name if self.pretty_name else self.name
+
 
 @dataclass
 class Keyword(DataClassJsonMixin):
     url: str
     papers: List[Paper]
     name: str
-    schema: str
+    kw_schema: str

paperlibrary/library/library.py

@@ -1,10 +1,10 @@
 import hashlib
 import os
 import shutil
-import string
 from datetime import datetime
 from pathlib import Path
 
+from alive_progress import alive_bar
 from tzlocal import get_localzone
 
 from paperlibrary.api import PaperLibraryAPI
@@ -12,46 +12,94 @@ from paperlibrary.config import basedir
 
 
 def format_filename(s: str) -> str:
-    additional_letters = ["ä", "Ä", "ö", "Ö", "ü", "Ü"]
-    valid_chars = f"-_.() {string.ascii_letters}{string.digits}{''.join(additional_letters)}"
-    filename = ''.join(c for c in s if c in valid_chars)
+    invalid_chars = {"/"}
+    filename = ''.join(c for c in s if c not in invalid_chars)
     # filename = filename.replace(' ', '_')  # I don't like spaces in filenames.
+    if not filename:
+        raise ValueError("empty filename")
     return filename
 
 
 def write_symlinks(api: PaperLibraryAPI):
     ...
     pdf_dir = basedir / "pdfs"
+    pdf_dir.mkdir(exist_ok=True)
+
     author_dir = basedir / "by_author"
-    shutil.rmtree(author_dir, ignore_errors=True)
-    author_dir.mkdir()
+    keyword_dir = basedir / "by_keyword"
+    year_dir = basedir / "by_year"
+    title_dir = basedir / "by_title"
+    custom_title_dir = basedir / "by_custom_title"
+
+    for directory in [author_dir, keyword_dir, year_dir, title_dir, custom_title_dir]:
+        shutil.rmtree(directory, ignore_errors=True)
+        directory.mkdir()
 
     for author in api.fetch_authors():
-        author_subdir = author_dir / format_filename(author.name)
+        author_subdir = author_dir / format_filename(author.display_name)
         author_subdir.mkdir()
         for paper in author.papers:
+            if not paper.main_pdf:
+                continue
             sourcefile = pdf_dir / f"{paper.main_pdf.id}.pdf"
             targetfile = author_subdir / "{}.pdf".format(format_filename(paper.title))
             targetfile.symlink_to(sourcefile)
 
+    for keyword in api.fetch_keywords():
+        keyword_subdir = keyword_dir / format_filename(keyword.name)
+        keyword_subdir.mkdir()
+        for paper in keyword.papers:
+            if not paper.main_pdf:
+                continue
+            sourcefile = pdf_dir / f"{paper.main_pdf.id}.pdf"
+            targetfile = keyword_subdir / "{}.pdf".format(format_filename(paper.title))
+            targetfile.symlink_to(sourcefile)
+
+    for paper in api.fetch_papers():
+        if not paper.main_pdf:
+            continue
+
+        sourcefile = pdf_dir / f"{paper.main_pdf.id}.pdf"
+        targetfile = title_dir / "{}.pdf".format(format_filename(paper.title))
+        targetfile.symlink_to(sourcefile)
+
+        if not paper.note:
+            continue
+        sourcefile = pdf_dir / f"{paper.main_pdf.id}.pdf"
+        targetfile = custom_title_dir / "{}.pdf".format(format_filename(paper.note.custom_title))
+        targetfile.symlink_to(sourcefile)
+
+    for year, papers in api.fetch_papers_by_year().items():
+        year_subdir = year_dir / str(year)
+        year_subdir.mkdir()
+        for paper in papers:
+            if not paper.main_pdf:
+                continue
+            sourcefile = pdf_dir / f"{paper.main_pdf.id}.pdf"
+            targetfile = year_subdir / "{}.pdf".format(format_filename(paper.title))
+            targetfile.symlink_to(sourcefile)
+
 
 def download_file(api: PaperLibraryAPI, url: str, target_file: Path):
     r = api.s.get(url)
     r.raise_for_status()
+    with alive_bar(int(r.headers["Content-Length"])) as bar:
         with target_file.open("wb") as f:
             for chunk in r.iter_content(1024):
+                for _ in range(1024):
+                    bar()
                 f.write(chunk)
 
 
 def hash_file(file: Path, buffer_size=65536) -> str:
-    sha265 = hashlib.sha256()
+    sha256 = hashlib.sha256()
     with file.open("rb") as f:
         while True:
             data = f.read(buffer_size)
             if not data:
                 break
-            sha265.update(data)
-    return sha265.hexdigest()
+            sha256.update(data)
+    return sha256.hexdigest()
 
 
 def update_pdfs(api: PaperLibraryAPI):
@@ -63,16 +111,14 @@ def update_pdfs(api: PaperLibraryAPI):
         if not pdf_file.exists():
             download_file(api, pdf.file, pdf_file)
             continue
-        if hash_file(pdf_file) != pdf.sha265:
+        if hash_file(pdf_file) != pdf.sha256:
             modification_date = datetime.fromtimestamp(
                 os.path.getmtime(pdf_file),
                 get_localzone()
             )
-            print(modification_date)
-            print(pdf.updated_at)
-            # print(modification_date - pdf.updated_at)
             if modification_date > pdf.updated_at:
-                raise ValueError("local file is newer")
+                print("local file is newer")
+                api.upload_pdf(pdf, pdf_file)
             else:
-                raise ValueError("remote file is newer")
-            # TODO: check if file should be uploaded or downloaded
+                print("remote file is newer")
+                download_file(api, pdf.file, pdf_file)

paperlibrary/pap.py

@@ -9,6 +9,7 @@ from paperlibrary.library import write_symlinks, update_pdfs
 def cli():
     pass
 
+
 @cli.command()
 def update():
     api = PaperLibraryAPI(url, auth_token=auth_token)
@@ -16,5 +17,12 @@ def update():
     update_pdfs(api)
 
 
+@cli.command()
+def test():
+    api = PaperLibraryAPI(url, auth_token=auth_token)
+
+    print(api.fetch_papers())
+
+
 if __name__ == '__main__':
     cli()

poetry.lock

@@ -1,3 +1,11 @@
+[[package]]
+name = "alive-progress"
+version = "1.6.1"
+description = "A new kind of Progress Bar, with real-time throughput, eta and very cool animations!"
+category = "main"
+optional = false
+python-versions = ">=2.7, <4"
+
 [[package]]
 name = "certifi"
 version = "2020.6.20"
@@ -161,9 +169,13 @@ socks = ["PySocks (>=1.5.6,<1.5.7 || >1.5.7,<2.0)"]
 [metadata]
 lock-version = "1.1"
 python-versions = "^3.8"
-content-hash = "55c1b4123bca6c85380c21f1e6f5faa129bb1171aa2c9a45497e5916e8c4ac2e"
+content-hash = "8bb7dbfcc0d218d22ff3dcafae140daff4799bfeb988731a3759412a256d0e29"
 
 [metadata.files]
+alive-progress = [
+    {file = "alive-progress-1.6.1.tar.gz", hash = "sha256:2a0d7516ec0f596d5ce53755c0913a909eb1c91854e1d782e511ef5e1dd53218"},
+    {file = "alive_progress-1.6.1-py3-none-any.whl", hash = "sha256:9a0fae6b94fb4e4bcd9fb51760506d29a33358ebbfef2c6516dce3e359a661b5"},
+]
 certifi = [
     {file = "certifi-2020.6.20-py2.py3-none-any.whl", hash = "sha256:8fc0819f1f30ba15bdb34cceffb9ef04d99f420f68eb75d901e9560b8749fc41"},
     {file = "certifi-2020.6.20.tar.gz", hash = "sha256:5930595817496dd21bb8dc35dad090f1c2cd0adfaf21204bf6732ca5d8ee34d3"},

pyproject.toml

@@ -10,6 +10,7 @@ requests = "^2.24.0"
 click = "^7.1.2"
 dataclasses-json = "^0.5.2"
 tzlocal = "^2.1"
+alive-progress = "^1.6.1"
 
 [build-system]
 requires = ["poetry-core>=1.0.0"]