Merge pull request #62 from jdkent/fix/new_source_tests

[FIX] new source tests

Author: jdkent

ace/ingest.py

@@ -54,6 +54,8 @@ def _parse_article(args):
                 return f, None
 
         article = source.parse_article(html, pmid, metadata_dir=metadata_dir, **kwargs)
+        if not article:
+            return f, None
         return f, article
     except Exception as e:
         logger.info("Error parsing article %s: %s", f, str(e))
@@ -63,13 +65,41 @@ def _parse_article(args):
 def add_articles(db, files, commit=True, table_dir=None, limit=None,
     pmid_filenames=False, metadata_dir=None, force_ingest=True, num_workers=None, 
     use_readability=None, **kwargs):
-    ''' Process articles and add their data to the DB. '''
+    ''' Process articles and add their data to the DB.
+    
+     Args:
+        files: The path to the article(s) to process. Can be a single
+            filename (string), a list of filenames, or a path to pass
+            to glob (e.g., "article_ls  dir/NIMG*html")
+        commit: Whether or not to save records to DB file after adding them.
+        table_dir: Directory to store downloaded tables in (if None, tables
+            will not be saved.)
+        limit: Optional integer indicating max number of articles to add
+            (selected randomly from all available). When None, will add all
+            available articles.
+        pmid_filenames: When True, assume that the file basename is a PMID.
+            This saves us from having to retrieve metadata from PubMed When
+            checking if a file is already in the DB, and greatly speeds up
+            batch processing when overwrite is off.
+        metadata_dir: Location to read/write PubMed metadata for articles.
+            When None (default), retrieves new metadata each time. If a
+            path is provided, will check there first before querying PubMed,
+            and will save the result of the query if it doesn't already
+            exist.
+        force_ingest: Ingest even if no source is identified.
+        num_workers: Number of worker processes to use when processing in parallel.
+            If None (default), uses the number of CPUs available on the system.
+        use_readability: When True, use readability.py for HTML cleaning if available.
+            When False, use fallback HTML processing by default. If None (default),
+            uses the value from config.USE_READABILITY.
+        kwargs: Additional keyword arguments to pass to parse_article.
+    '''
     manager = sources.SourceManager(
-        table_dir, 
+        table_dir,
         use_readability=use_readability if use_readability is not None 
             else get_config('USE_READABILITY')
     )
-    
+
     # Prepare source configurations for parallel processing
     source_configs = {name: source.identifiers for name, source in manager.sources.items()}
 

ace/sources.py

@@ -203,14 +203,14 @@ def parse_article(self, html, pmid=None, metadata_dir=None):
 
         # did our best to find PMID, but failed
         if not pmid:
-            return False
+            return None
 
         metadata = scrape.get_pubmed_metadata(pmid, store=metadata_dir, save=True)
 
         # Remove all scripts and styles
         for script in soup(["script", "style"]):
             script.extract()
-        
+
         # Get text using readability
         text = self._clean_html_with_readability(str(soup))
 
@@ -2230,4 +2230,4 @@ def extract_pmid(self, soup):
             return scrape.get_pmid_from_doi(doi)
 
         logger.warning("AmPsychSource could not extract PMID.")
-        return None
+        return None

ace/tests/cassettes/test_ace/test_ampsych_source.yaml

@@ -0,0 +1,225 @@
+interactions:
+- request:
+    body: null
+    headers:
+      Accept:
+      - '*/*'
+      Accept-Encoding:
+      - gzip, deflate
+      Connection:
+      - keep-alive
+      User-Agent:
+      - Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36 (KHTML,
+        like Gecko) Chrome/124.0.6367.78 Safari/537.36
+    method: GET
+    uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=21078707&retmode=xml&rettype=medline
+  response:
+    body:
+      string: !!binary |
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