Update Parse Grant ID function name

README.md

@@ -166,7 +166,7 @@ To extract month and day information from PubDate, set `year_info_only=True`. We
 
 ### Parse MEDLINE Grant ID
 
-Use `parse_medline_grant_id` in order to parse MEDLINE grant IDs from XML file. This will return a list of dictionaries, each containing
+Use `parse_grant_id` in order to parse MEDLINE grant IDs from XML file. This will return a list of dictionaries, each containing
 
 * `pmid` : PubMed ID
 * `grant_id` : Grant ID

docs/api.rst

@@ -11,7 +11,7 @@ Parse MEDLINE XML
 -----------------
 
 .. autofunction:: parse_medline_xml
-.. autofunction:: parse_medline_grant_id
+.. autofunction:: parse_grant_id
 
 Parse PubMed OA XML
 -------------------

docs/conf.py

@@ -16,7 +16,6 @@
 import sys
 import os
 import sphinx
-import pubmed_parser
 import sphinx_gallery
 
 

pubmed_parser/__init__.py

@@ -12,7 +12,11 @@
     parse_pubmed_caption,
     parse_pubmed_table,
 )
-from .medline_parser import parse_medline_xml, split_mesh
+from .medline_parser import (
+    parse_medline_xml,
+    parse_grant_id,
+    split_mesh,
+)
 from .pubmed_web_parser import (
     parse_xml_web,
     parse_citation_web,

pubmed_parser/medline_parser.py

@@ -9,7 +9,7 @@
 from collections import defaultdict
 from pubmed_parser.utils import read_xml, stringify_children, month_or_day_formater
 
-__all__ = ["parse_medline_xml",  "split_mesh"]
+__all__ = ["parse_medline_xml",  "parse_grant_id", "split_mesh"]
 
 
 def parse_pmid(pubmed_article):

scripts/medline_spark.py

@@ -70,7 +70,7 @@ def process_file(date_update):
                       mode='overwrite')
 
     # parse grant database
-    parse_grant_rdd = path_rdd.flatMap(lambda x: pp.parse_medline_grant_id(x))\
+    parse_grant_rdd = path_rdd.flatMap(lambda x: pp.parse_grant_id(x))\
         .filter(lambda x: x is not None)\
         .map(lambda x: Row(**x))
     grant_df = parse_grant_rdd.toDF()

tests/test_medline_parser.py

@@ -206,18 +206,6 @@ def test_parse_medline_xml():
     assert parsed_medline[0]["vernacular_title"] == ""
 
 
-def test_parse_medline_grant_id():
-    """
-    Test parsing grants from MEDLINE XML
-    """
-    grants = pp.parse_medline_grant_id(os.path.join("data", "pubmed20n0014.xml.gz"))
-    assert isinstance(grants, list)
-    assert isinstance(grants[0], dict)
-    assert grants[0]["pmid"] == "399300"
-    assert grants[0]["grant_id"] == "HL17731"
-    assert len(grants) == 484, "Expect number of grants in a given file to be 484"
-
-
 def test_parse_medline_mesh_terms():
     """
     Test parsing MeSH headings from MEDLINE XML