Article checker (#182)

* Article checker

* seperate formatters file

.github/workflows/check-articles.yml

@@ -0,0 +1,65 @@
+name: Check articles are valid
+
+on:
+  workflow_call:
+    inputs:
+      datasource:
+        type: string
+        required: true
+  workflow_dispatch: # allow manual triggering
+    inputs:
+      datasource:
+        description: 'The datasource to process'
+        type: choice
+        options:
+          - all
+          - agentmodels
+          - agisf
+          - aisafety.info
+          - alignment_newsletter
+          - alignmentforum
+          - arbital
+          - arxiv
+          - blogs
+          - distill
+          - eaforum
+          - indices
+          - lesswrong
+          - special_docs
+          - youtube
+  schedule:
+    - cron: "0 */4 * * *"  # Every 4 hours
+
+jobs:
+  build-dataset:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+
+    - name: Setup Python environment
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.x'
+
+    - name: Install Pandoc
+      run: |
+        if [ "${{ inputs.datasource }}" = "gdocs" ]; then
+          sudo apt-get update
+          sudo apt-get -y install pandoc
+        fi
+
+    - name: Install dependencies
+      run: pip install -r requirements.txt
+
+    - name: Process dataset
+      env:
+        CODA_TOKEN: ${{ secrets.CODA_TOKEN }}
+        AIRTABLE_API_KEY: ${{ secrets.AIRTABLE_API_KEY }}
+        YOUTUBE_API_KEY: ${{ secrets.YOUTUBE_API_KEY }}
+        ARD_DB_USER: ${{ secrets.ARD_DB_USER }}
+        ARD_DB_PASSWORD: ${{ secrets.ARD_DB_PASSWORD }}
+        ARD_DB_HOST: ${{ secrets.ARD_DB_HOST }}
+        ARD_DB_NAME: alignment_research_dataset
+      run: python main.py fetch ${{ inputs.datasource }}

align_data/common/alignment_dataset.py

@@ -1,14 +1,16 @@
-import re
 from datetime import datetime
 from itertools import islice
 import logging
 import time
 from dataclasses import dataclass, field, KW_ONLY
 from pathlib import Path
-from typing import List, Optional, Set, Iterable, Tuple, Generator
+from typing import Iterable, List, Optional, Set, Tuple, Generator
+from sqlalchemy import select
+from sqlalchemy.exc import IntegrityError
+from sqlalchemy.orm import joinedload
 
 import pytz
-from sqlalchemy import select, Select, JSON
+from sqlalchemy import select, Select
 from sqlalchemy.exc import IntegrityError
 from sqlalchemy.orm import joinedload, Session
 import jsonlines
@@ -17,8 +19,7 @@
 
 from align_data.db.models import Article, Summary
 from align_data.db.session import make_session
-from align_data.settings import ARTICLE_MAIN_KEYS
-from align_data.sources.utils import merge_dicts
+from align_data.common.formatters import normalize_url, article_dict
 
 logger = logging.getLogger(__name__)
 
@@ -64,28 +65,10 @@ def __post_init__(self):
     def __str__(self) -> str:
         return self.name
 
-    def _add_authors(self, article: Article, authors: List[str]) -> Article:
-        # TODO: Don't keep adding the same authors - come up with some way to reuse them
-        article.authors = ",".join(authors)
-        if len(article.authors) > 1024:
-            article.authors = ",".join(article.authors[:1024].split(",")[:-1])
-        return article
-
     def make_data_entry(self, data, **kwargs) -> Article:
-        data = merge_dicts(data, kwargs)
-
-        summaries = data.pop("summaries", [])
-        summary = data.pop("summary", None)
-        summaries += [summary] if summary else []
-
-        authors = data.pop("authors", [])
-        data['title'] = (data.get('title') or '').replace('\n', ' ').replace('\r', '') or None
-
-        article = Article(
-            meta={k: v for k, v in data.items() if k not in ARTICLE_MAIN_KEYS and v is not None},
-            **{k: v for k, v in data.items() if k in ARTICLE_MAIN_KEYS},
-        )
-        self._add_authors(article, authors)
+        data = article_dict(data, **kwargs)
+        summaries = data.pop('summaries', [])
+        article = Article(**data)
         article.summaries += [Summary(text=summary, source=self.name) for summary in summaries]
         return article
 
@@ -109,7 +92,7 @@ def read_entries(self, sort_by=None) -> Iterable[Article]:
             query = self._query_items.options(joinedload(Article.summaries))
             if sort_by is not None:
                 query = query.order_by(sort_by)
-            
+
             result = session.scalars(query)
             for article in result.unique(): # removes duplicates
                 yield article
@@ -153,41 +136,14 @@ def get_item_key(self, item) -> str:
         """
         return item.name
 
-    @staticmethod
-    def _normalize_url(url: str | None) -> str | None:
-        if not url:
-            return url
-
-        # ending '/'
-        url = url.rstrip("/")
-
-        # Remove http and use https consistently
-        url = url.replace("http://", "https://")
-
-        # Remove www
-        url = url.replace("https://www.", "https://")
-
-        # Remove index.html or index.htm
-        url = re.sub(r'/index\.html?$', '', url)
-
-        # Convert youtu.be links to youtube.com
-        url = url.replace("https://youtu.be/", "https://youtube.com/watch?v=")
-
-        # Additional rules for mirror domains can be added here
-
-        # agisafetyfundamentals.com -> aisafetyfundamentals.com
-        url = url.replace("https://agisafetyfundamentals.com", "https://aisafetyfundamentals.com")
-
-        return url
-
     def _normalize_urls(self, urls: Iterable[str]) -> Set[str]:
-        return {self._normalize_url(url) for url in urls}
+        return {normalize_url(url) for url in urls}
 
 
     def _load_outputted_items(self) -> Set[str]:
         """
         Loads the outputted items from the database and returns them as a set.
-        
+
         if the done_key is not an attribute of Article, it will try to load it from the meta field.
         """
         with make_session() as session:
@@ -207,7 +163,7 @@ def not_processed(self, item) -> bool:
         # cause problems (e.g. massive RAM usage, big slow downs) then it will have to be switched around, so that
         # this function runs a query to check if the item is in the database rather than first getting all done_keys.
         # If it get's to that level, consider batching it somehow
-        return self._normalize_url(self.get_item_key(item)) not in self._outputted_items
+        return normalize_url(self.get_item_key(item)) not in self._outputted_items
 
     def unprocessed_items(self, items=None) -> list | filter:
         """Return a list of all items to be processed.

align_data/common/formatters.py

@@ -0,0 +1,60 @@
+import re
+from typing import Any, Dict, List
+
+from align_data.settings import ARTICLE_MAIN_KEYS
+from align_data.sources.utils import merge_dicts
+
+
+def normalize_url(url: str | None) -> str | None:
+    if not url:
+        return url
+
+    # ending '/'
+    url = url.rstrip("/")
+
+    # Remove http and use https consistently
+    url = url.replace("http://", "https://")
+
+    # Remove www
+    url = url.replace("https://www.", "https://")
+
+    # Remove index.html or index.htm
+    url = re.sub(r'/index\.html?$', '', url)
+
+    # Convert youtu.be links to youtube.com
+    url = url.replace("https://youtu.be/", "https://youtube.com/watch?v=")
+
+    # Additional rules for mirror domains can be added here
+
+    # agisafetyfundamentals.com -> aisafetyfundamentals.com
+    url = url.replace("https://agisafetyfundamentals.com", "https://aisafetyfundamentals.com")
+
+    return url
+
+
+def normalize_text(text: str | None) -> str | None:
+    return (text or '').replace('\n', ' ').replace('\r', '').strip() or None
+
+
+def format_authors(authors: List[str]) -> str:
+    # TODO: Don't keep adding the same authors - come up with some way to reuse them
+    authors_str = ",".join(authors)
+    if len(authors_str) > 1024:
+        authors_str = ",".join(authors_str[:1024].split(",")[:-1])
+    return authors_str
+
+
+def article_dict(data, **kwargs) -> Dict[str, Any]:
+    data = merge_dicts(data, kwargs)
+
+    summaries = data.pop("summaries", [])
+    summary = data.pop("summary", None)
+
+    data['summaries'] = summaries + [summary] if summary else []
+    data['authors'] = format_authors(data.pop("authors", []))
+    data['title'] = normalize_text(data.get('title'))
+
+    return dict(
+        meta={k: v for k, v in data.items() if k not in ARTICLE_MAIN_KEYS and v is not None},
+        **{k: v for k, v in data.items() if k in ARTICLE_MAIN_KEYS},
+    )

align_data/db/models.py

@@ -71,6 +71,7 @@ class Article(Base):
     date_updated: Mapped[Optional[datetime]] = mapped_column(
         DateTime, onupdate=func.current_timestamp()
     )
+    date_checked: Mapped[datetime] = mapped_column(DateTime, default=func.now())  # The timestamp when this article was last checked if still valid
     status: Mapped[Optional[str]] = mapped_column(String(256))
     comments: Mapped[Optional[str]] = mapped_column(LONGTEXT)  # Editor comments. Can be anything
 

align_data/sources/articles/datasets.py

@@ -12,6 +12,7 @@
 from sqlalchemy import select, Select
 
 from align_data.common.alignment_dataset import AlignmentDataset
+from align_data.common.formatters import normalize_url
 from align_data.db.models import Article
 from align_data.sources.articles.google_cloud import fetch_file, fetch_markdown
 from align_data.sources.articles.parsers import (
@@ -127,16 +128,16 @@ def not_processed(self, item: tuple) -> bool:
         url = self.maybe(item, "url")
         source_url = self.maybe(item, "source_url")
 
-        if item_key and self._normalize_url(item_key) in self._outputted_items:
+        if item_key and normalize_url(item_key) in self._outputted_items:
             return False
-        
+
         for given_url in [url, source_url]:
             if given_url:
-                norm_url = self._normalize_url(given_url)
+                norm_url = normalize_url(given_url)
                 if norm_url in self._outputted_items:
                     return False
 
-                norm_canonical_url = self._normalize_url(arxiv_canonical_url(given_url))
+                norm_canonical_url = normalize_url(arxiv_canonical_url(given_url))
                 if norm_canonical_url in self._outputted_items:
                     return False
 

align_data/sources/validate.py

@@ -0,0 +1,90 @@
+import logging
+from datetime import datetime, timedelta
+from typing import Any, List
+
+from tqdm import tqdm
+from sqlalchemy.exc import IntegrityError
+from align_data.common.formatters import normalize_url, normalize_text, article_dict
+from align_data.db.session import make_session
+from align_data.db.models import Article
+from align_data.sources.articles.parsers import item_metadata
+from align_data.sources.articles.html import fetch
+
+
+logger = logging.getLogger(__name__)
+
+
+def update_article_field(article: Article, field: str, value: Any):
+    if not value:
+        return
+
+    if field == 'url' and normalize_url(article.url) == normalize_url(value):
+        # This is pretty much the same url, so don't modify it
+        return
+    if field == 'title' and normalize_text(article.title) == normalize_text(value):
+        # If there are slight differences in the titles (e.g. punctuation), assume the
+        # database version is more correct
+        return
+    if field == 'meta':
+        article.meta = article.meta or {}
+        for k, v in value.items():
+            meta_val = article.meta.get(k)
+            try:
+                if not meta_val or v > meta_val:
+                    article.meta[k] = v
+            except Exception as e:
+                # Ignore exceptions here - the metadata isn't that important
+                logger.info('Error checking metadata value for article %s: %s', article.url, value)
+        return
+
+    article_val = getattr(article, field, None)
+    # Assume that if the provided value is larger (or later, in the case of dates), then it's
+    # better. This might very well not hold, but it seems like a decent heuristic?
+    if not article_val:
+        setattr(article, field, value)
+    elif isinstance(value, datetime) and value > article_val:
+        setattr(article, field, value)
+    elif isinstance(value, str) and len(normalize_text(value) or '') > len(normalize_text(article_val) or ''):
+        setattr(article, field, normalize_text(value))
+
+
+def update_article(article: Article) -> Article:
+    """Check whether there are better data for this article and whether its url is pointing somewhere decent."""
+    source_url = article.meta.get('source_url') or article.url
+    contents = {}
+    if source_url:
+        contents = item_metadata(source_url)
+
+    if 'error' not in contents:
+        for field, value in article_dict(contents).items():
+            update_article_field(article, field, value)
+    else:
+        logger.info('Error getting contents for %s: %s', article, contents.get('error'))
+
+    if 400 <= fetch(article.url).status_code < 500:
+        logger.info('Could not get url for %s', article)
+        article.status = 'Unreachable url'
+
+    article.date_checked = datetime.utcnow()
+
+    return article
+
+
+def check_articles(sources: List[str], batch_size=100):
+    """Check `batch_size` articles with the given `sources` to see if they have better data."""
+    logger.info('Checking %s articles for %s', batch_size, ', '.join(sources))
+    with make_session() as session:
+        for article in tqdm(
+            session.query(Article)
+            .filter(Article.date_checked < datetime.now() - timedelta(weeks=4))
+            .filter(Article.source.in_(sources))
+            .limit(batch_size)
+            .all()
+        ):
+            update_article(article)
+            session.add(article)
+        logger.debug('commiting')
+        try:
+            session.commit()
+        except IntegrityError as e:
+            logger.error(e)