Merge pull request #439 from elifesciences/develop

PR for version 0.40.0 release

elifetools/__init__.py

@@ -1 +1 @@
-__version__ = "0.39.0"
+__version__ = "0.40.0"

elifetools/parseJATS.py

@@ -5361,6 +5361,11 @@ def funding_awards_json(soup):
                     utils.set_if_value(
                         award_content, "awardId", award_group.get("award-id")
                     )
+                    # set awardDoi if applicable
+                    if award_group.get("award-id-type") == "doi":
+                        utils.set_if_value(
+                            award_content, "awardDoi", award_group.get("award-id")
+                        )
 
                 if len(award_content) > 0:
                     awards.append(award_content)

tests/fixtures/test_funding_awards_json/content_08.xml

@@ -0,0 +1,22 @@
+<root xmlns:xlink="http://www.w3.org/1999/xlink">
+    <front>
+        <journal-meta>
+            <journal-id journal-id-type="publisher-id">eLife</journal-id>
+        </journal-meta>
+        <article-meta>
+            <article-id pub-id-type="publisher-id">90959</article-id>
+            <article-id pub-id-type="doi">10.7554/eLife.90959</article-id>
+            <funding-group>
+                <award-group id="fund3">
+                    <funding-source>
+                        <institution-wrap>
+                            <institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/100010269</institution-id>
+                            <institution>Wellcome Trust</institution>
+                        </institution-wrap>
+                    </funding-source>
+                    <award-id award-id-type="doi">10.35802/212242</award-id>
+                </award-group>
+            </funding-group>
+        </article-meta>
+    </front>
+</root>

tests/fixtures/test_funding_awards_json/content_08_expected.py

@@ -0,0 +1,18 @@
+# coding=utf-8
+from collections import OrderedDict
+
+expected = [
+    OrderedDict(
+        [
+            ("id", "fund3"),
+            (
+                "source",
+                OrderedDict(
+                    [("funderId", "10.13039/100010269"), ("name", ["Wellcome Trust"])]
+                ),
+            ),
+            ("awardId", "10.35802/212242"),
+            ("awardDoi", "10.35802/212242"),
+        ]
+    )
+]

tests/test_parse_jats.py

@@ -438,6 +438,11 @@ def test_funding_awards_json_by_file(self, filename, expected_len):
             read_fixture("test_funding_awards_json", "content_07.xml"),
             read_fixture("test_funding_awards_json", "content_07_expected.py"),
         ),
+        # 90959 v1 example funding award with an award DOI, sans recipients
+        (
+            read_fixture("test_funding_awards_json", "content_08.xml"),
+            read_fixture("test_funding_awards_json", "content_08_expected.py"),
+        ),
     )
     def test_funding_awards_json(self, xml_content, expected):
         soup = parser.parse_xml(xml_content)