Merge pull request #403 from broadinstitute/development

Release 1.43.1

Author: bistline

Dockerfile

@@ -10,7 +10,8 @@
 # Use a managed base image from Google.  It is continually updated for
 # security fixes (thus the "latest" tag).
 # https://github.com/GoogleContainerTools/base-images-docker/tree/master/ubuntu
-FROM marketplace.gcr.io/google/ubuntu2004:latest
+FROM marketplace.gcr.io/google/ubuntu2204:latest
+ENV DEBIAN_FRONTEND=noninteractive
 
 # RUN echo "Uncomment to clear cached layers below this statement (2022-03-14-1441)"
 
@@ -21,7 +22,8 @@ RUN apt-get -y update && \
   apt-get -y install python3-pip && \
   apt-get -y install python3.10 && \
   apt-get -y install python3.10-dev && \
-  apt-get -y install python3.10-distutils
+  apt-get -y install python3.10-distutils && \
+  apt-get -y remove python3-blinker # due to pip install errors of distutils package
 
 RUN apt-get -y update && apt-get -y install curl
 

README.md

@@ -29,6 +29,14 @@ source env/bin/activate
 pip install -r requirements.txt
 source scripts/setup-mongo-dev.sh
 ```
+Note: if you encounter the following error:
+```
+AttributeError: module 'coverage' has no attribute 'types'
+```
+You can run the following to address this:
+```
+pip install --upgrade coverage
+```
 
 ### Docker
 

ingest/validation/ontologies/cl.min.tsv.gz

@@ -1 +1 @@
-1752088054 # validation cache key
+1764620615 # validation cache key

ingest/validation/ontologies/efo.min.tsv.gz

@@ -476,8 +476,17 @@ def retrieve_label_and_synonyms(
     :param property_type: attribute type for term (string, array, boolean)
     """
     ontology_name = re.split("[_:]", ontology_id)[0].lower()
-    if ontology_is_local(ontology_name):
+    # use OLS fallback for taxon IDs since minified version is not authoritative
+    use_fallback = ontology_name == "ncbitaxon"
+    if ontology_is_local(ontology_name) and not use_fallback:
         return minified_reader.find_ontology_entry(ontology_name, ontology_id, property_name)
+    elif ontology_is_local(ontology_name) and use_fallback:
+        try:
+            return minified_reader.find_ontology_entry(ontology_name, ontology_id, property_name)
+        except ValueError:
+            return retriever.retrieve_ontology_term_label_and_synonyms(
+                ontology_id, property_name, convention, property_type
+            )
     else:
         return retriever.retrieve_ontology_term_label_and_synonyms(
             ontology_id, property_name, convention, property_type