Change the retractions API and resource name

indra/literature/pubmed_client.py

@@ -7,15 +7,14 @@
 import os
 import re
 import time
-from pathlib import Path
-
 import tqdm
 import logging
 import random
 import subprocess
 import requests
 from time import sleep
 from typing import List
+from pathlib import Path
 from functools import lru_cache
 import xml.etree.ElementTree as ET
 from indra.resources import RESOURCES_PATH
@@ -30,7 +29,7 @@
 pubmed_archive = "https://ftp.ncbi.nlm.nih.gov/pubmed"
 pubmed_archive_baseline = pubmed_archive + "/baseline/"
 pubmed_archive_update = pubmed_archive + "/updatefiles/"
-RETRACTIONS_FILE = RESOURCES_PATH + "/pmid_retractions.tsv"
+RETRACTIONS_FILE = os.path.join(RESOURCES_PATH, "pubmed_retractions.tsv")
 
 
 # Send request can't be cached by lru_cache because it takes a dict
@@ -966,20 +965,20 @@ def get_publication_types(article: ET.Element):
     return {pt.text for pt in article.find('.//PublicationTypeList')}
 
 
-def article_is_retracted(pmid: str) -> bool:
+def is_retracted(pubmed_id: str) -> bool:
     """Return True if the article with the given PMID has been retracted.
 
     Parameters
     ----------
-    pmid :
+    pubmed_id :
         The PMID of the paper to check.
 
     Returns
     -------
     :
         True if the paper has been retracted, False otherwise.
     """
-    return retractions.is_retracted(pmid)
+    return retractions.is_retracted(pubmed_id)
 
 
 def generate_retractions_file(xml_path: str, download_missing: bool = False):

indra/tests/test_pubmed_client.py

@@ -243,5 +243,5 @@ def test_get_substance_annotations():
 
 
 def test_is_retracted():
-    assert pubmed_client.article_is_retracted('35463694')
-    assert not pubmed_client.article_is_retracted('36938926')
+    assert pubmed_client.is_retracted('35463694')
+    assert not pubmed_client.is_retracted('36938926')

indra/tools/assemble_corpus.py

@@ -23,7 +23,7 @@
 from indra.preassembler import Preassembler, flatten_evidence
 from indra.resources import get_resource_path
 from indra.statements.validate import print_validation_report
-from indra.literature.pubmed_client import article_is_retracted
+from indra.literature.pubmed_client import is_retracted
 import indra.tools.fix_invalidities
 
 
@@ -1277,6 +1277,7 @@ def filter_retracted_sources(stmts_in, **kwargs):
         A list of statements to filter.
     save : Optional[str]
         The name of a pickle file to save the results (stmts_out) into.
+
     Returns
     -------
     stmts_out : list[indra.statements.Statement]
@@ -1287,7 +1288,7 @@ def filter_retracted_sources(stmts_in, **kwargs):
         ev_out = []
         for ev in stmt.evidence:
             pmid = ev.pmid or ev.text_refs.get('PMID')
-            if pmid and article_is_retracted(pmid):
+            if pmid and is_retracted(pmid):
                 continue
             ev_out.append(ev)