Merge pull request #191 from VariantEffect/release/2.2.2

Release/2.2.2

Author: afrubin

DEVELOPERS.md

@@ -127,11 +127,15 @@ python manage.py runserver 0.0.0.0:8000
 
 # Building a new image
 
-## MaveHGVS docs
-Place the `mavehgvs` sphinx documentation files into `/docs/mavehgvs/`. The build path in `Makefile` and `make.bat`
-must be `../build/docs/mavehgvs/`. Once the application starts, this documentation will be collected in the static file
-directory and served at `https://mavedb.org/docs/mavehgvs`.
-
-You can use the `./publish` script to build a new image and push it to the MaveDB [Docker Hub repository](https://hub.docker.com/). 
-The script takes the following arguments in the following order `IMAGE_NAME`, `TAG`, `REPOSITORY`', where `IMAGE_NAME` and `REPOSITORY`
-are both `mavedb` for now.
+The `mavehgvs` and MaveTools documentation will be automatically built and placed in the correct location as specified
+in the Dockerfile.
+
+To create the new image, follow these steps:
+```shell script
+MAVEDB_VERSION="2.2.2"  # update to the version being built
+
+docker build . -t mavedb/mavedb:$MAVEDB_VERSION --no-cache
+docker tag mavedb/mavedb:$MAVEDB_VERSION mavedb/mavedb:latest
+docker push mavedb/mavedb:$MAVEDB_VERSION
+docker push mavedb/mavedb:latest
+```

api/views.py

@@ -534,14 +534,19 @@ def _parse_reference_maps_data(data):
         request_data = json.loads(request.POST["request"])
         scoreset_request_data = request_data["scoreset"]
         target_request_data = request_data["target"]
-        uniprot_request_data = request_data["uniprot"]
-        ensembl_request_data = request_data["ensembl"]
-        refseq_request_data = request_data["refseq"]
+        # Accept none value for uniprot, ensemb and refseq.
+        uniprot_request_data = request_data.get("uniprot", None)
+        ensembl_request_data = request_data.get("ensembl", None)
+        refseq_request_data = request_data.get("refseq", None)
         reference_maps_request_data = request_data["reference_maps"]
         files = {
-            constants.variant_score_data: request.FILES["score_data"],
-            constants.variant_count_data: request.FILES["count_data"],
-            constants.meta_data: request.FILES["meta_data"],
+            constants.variant_score_data: request.FILES.get(
+                "score_data", None
+            ),
+            constants.variant_count_data: request.FILES.get(
+                "count_data", None
+            ),
+            constants.meta_data: request.FILES.get("meta_data", None),
         }
         if "fasta_file" in request.FILES:
             files["sequence_fasta"] = request.FILES["fasta_file"]

data/main/site_info.json

@@ -6,5 +6,5 @@
   "md_privacy": "",
   "md_terms": "",
   "md_usage_guide": "",
-  "version": "2.2.1"
+  "version": "2.2.2"
 }

main/urls.py

@@ -11,7 +11,7 @@
 urlpatterns = [
     url(r"^$", views.home_view, name="home"),
     # ------------ Documentation landing page ---------------------- #
-    url(r"^docs", views.documentation_view, name="docs-landing"),
+    url(r"^docs/$", views.documentation_view, name="docs-landing"),
     # ------------ MaveDB documentation ---------------------- #
     url(
         r"^docs/mavedb/$",