1.6.3-beta

Minor
------
- Address security patch (update urllib3 to v1.24.3)
- Revert Metapub to v0.4.4 and Eutils to v0.5.0
- Utility bash script for deployment update

data/main/site_info.json

@@ -6,5 +6,5 @@
     "md_privacy": "",
     "md_terms": "",
     "md_usage_guide": "",
-    "version": "1.6.2-beta"
+    "version": "1.6.3-beta"
 }

metadata/models.py

@@ -284,7 +284,7 @@ def format_reference_html(self):
                 self.identifier
             )
         else:
-            reference = article.citation
+            reference = article.citation_html
         return reference
 
     def save(self, *args, **kwargs):

metadata/tests/test_models.py

@@ -298,7 +298,7 @@ def test_format_reference_url_hyperlinks_references(self):
         pubmed = PubmedIdentifierFactory(reference_html=None)
         fetch = metapub.PubMedFetcher()
         article = fetch.article_by_pmid(pubmed.identifier)
-        self.assertEqual(pubmed.reference_html, article.citation)
+        self.assertEqual(pubmed.reference_html, article.citation_html)
 
     def test_save_sets_dbname_as_PubMeD(self):
         pm = PubmedIdentifierFactory()

requirements/base.txt

@@ -15,17 +15,15 @@ social-auth-app-django==2.1.0
 tablib==0.13.0
 factory-boy==2.11.1
 celery==4.1.1
-flower==0.9.2
 pypandoc==1.4
-selenium>=3.4.3
 Faker==0.8.15
 coverage==4.5.1
 idutils==1.1.0
-urllib3==1.23
-hg+https://bitbucket.org/metapub/metapub@default
+urllib3==1.24.3
+hg+https://bitbucket.org/metapub/metapub@6fe5735
 git+https://github.com/VariantEffect/hgvs-patterns.git
 lxml==4.3.5
-eutils
+eutils==0.5.0
 psycopg2-binary
 pandas
 numpy

requirements/local.txt

@@ -1 +1,3 @@
--r base.txt
+-r base.txt
+
+selenium>=3.4.3

update.sh

@@ -1,11 +1,11 @@
 if [ "$1" != "" ]; then
-    settings="--settings=$1"
+    settings="--settings=settings.$1"
 else
     settings="--settings=settings.production"
 fi
 
 if [ "$2" != "" ]; then
-    requirements="$2"
+    requirements="$2.txt"
 else
     requirements="production.txt"
 fi