From c311c48e5ea6cc3a815b19ded625dcd7c56dbffd Mon Sep 17 00:00:00 2001
From: daniaki <danielce90@gmail.com>
Date: Wed, 7 Aug 2019 12:25:49 +1000
Subject: [PATCH 1/4] Resume using `citation_html`

---
 metadata/models.py            | 2 +-
 metadata/tests/test_models.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/metadata/models.py b/metadata/models.py
index fa876d50..cb612dfe 100644
--- a/metadata/models.py
+++ b/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):
diff --git a/metadata/tests/test_models.py b/metadata/tests/test_models.py
index 6ed5edb5..706075fe 100644
--- a/metadata/tests/test_models.py
+++ b/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()

From ac66027dbfe3ea233364cbcfceaac100c8e0c3c6 Mon Sep 17 00:00:00 2001
From: daniaki <danielce90@gmail.com>
Date: Wed, 7 Aug 2019 12:25:58 +1000
Subject: [PATCH 2/4] Security patches

---
 data/main/site_info.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/data/main/site_info.json b/data/main/site_info.json
index 29d76207..f470def3 100644
--- a/data/main/site_info.json
+++ b/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"
 }

From 743bec2aa0476f15e5c4077a589723a17ba872d0 Mon Sep 17 00:00:00 2001
From: daniaki <danielce90@gmail.com>
Date: Wed, 7 Aug 2019 12:26:16 +1000
Subject: [PATCH 3/4] Security patches; metapub and eutils revert

---
 requirements/base.txt  | 8 +++-----
 requirements/local.txt | 4 +++-
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/requirements/base.txt b/requirements/base.txt
index 71ec2cc3..ff57b2c5 100644
--- a/requirements/base.txt
+++ b/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
\ No newline at end of file
diff --git a/requirements/local.txt b/requirements/local.txt
index 9c9dec9e..430ef449 100644
--- a/requirements/local.txt
+++ b/requirements/local.txt
@@ -1 +1,3 @@
--r base.txt
\ No newline at end of file
+-r base.txt
+
+selenium>=3.4.3
\ No newline at end of file

From 8ddf46da5b306e0b2f30e0bdc745fe567a64886f Mon Sep 17 00:00:00 2001
From: daniaki <danielce90@gmail.com>
Date: Wed, 7 Aug 2019 12:48:20 +1000
Subject: [PATCH 4/4] Updated args

---
 update.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/update.sh b/update.sh
index 10aec3eb..8cda817f 100644
--- a/update.sh
+++ b/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