Rename variant->variation services

.gitignore

@@ -168,6 +168,6 @@ data/
 # services
 therapy-normalization/
 gene-normalization/
-variant-normalization/
+variation-normalization/
 disease-normalization/
 metakb/

README.md

@@ -39,7 +39,7 @@ You will need to clone services repositories.
 git clone https://github.com/cancervariants/disease-normalization
 git clone https://github.com/cancervariants/gene-normalization
 git clone https://github.com/cancervariants/therapy-normalization
-git clone https://github.com/cancervariants/variant-normalization
+git clone https://github.com/cancervariants/variation-normalization
 ```
 
 
@@ -90,17 +90,17 @@ dc exec gene sh -c "pipenv run python3 -m gene.cli --update_all"
 ```
 
 
-* Variant
+* Variation
 
 ```
 #
-# Variant normalizer will read from variant/data/seqrepo/latest
+# Variation normalizer will read from variation/data/seqrepo/latest
 # so, in the host os, navigate to data/gene/seqrepo and `ln -s`
 #
 ln -s  2020-11-27 latest
 #
-# then, in docker compose, we map the seqrepo we setup for gene to the variant container
-# `- ./data/gene/seqrepo:/app/variant/data/seqrepo`
+# then, in docker compose, we map the seqrepo we setup for gene to the variation container
+# `- ./data/gene/seqrepo:/app/variation/data/seqrepo`
 #
 ```
 
@@ -122,7 +122,7 @@ dynamodb   /docker-entrypoint.py --sm ...   Up             10000/tcp, 22/tcp, 70
 gene       /bin/sh -c pipenv run uvic ...   Up (healthy)   0.0.0.0:8002->80/tcp
 test       /bin/sh -c tail -f /dev/null     Up
 therapy    /bin/sh -c pipenv run uvic ...   Up (healthy)   0.0.0.0:8001->80/tcp
-variant    /bin/sh -c pipenv run uvic ...   Up (healthy)   0.0.0.0:8003->80/tcp
+variation    /bin/sh -c pipenv run uvic ...   Up (healthy)   0.0.0.0:8003->80/tcp
 ```
 
 
@@ -155,7 +155,7 @@ du -sh ./data/*
  14G	./data/gene
 1.5G	./data/scylla
  20G	./data/therapy
- 38M	./data/variant
+ 38M	./data/variation
 ```
 
 
@@ -168,7 +168,7 @@ docker-compose  exec test sh -c "pipenv run pytest  tests/integration"
 tests/integration/test_disease.py ...
 tests/integration/test_gene.py ...
 tests/integration/test_therapy.py ...
-tests/integration/test_variant.py ...
+tests/integration/test_variation.py ...
 
 ```
 

docker-compose.yml

@@ -66,13 +66,13 @@ services:
       - "dynamodb"
     volumes:
      - ./data/gene:/app/gene/data
-  # The variant service
-  variant:
-    build: variant-normalization
-    hostname: variant
-    container_name: variant
+  # The variation service
+  variation:
+    build: variation-normalization
+    hostname: variation
+    container_name: variation
     environment:
-      # variant shares gene's db 
+      # variation shares gene's db 
       - GENE_NORM_DB_URL=http://dynamodb:8000
       # read from .env file
       - AWS_DEFAULT_REGION=${AWS_DEFAULT_REGION:-dev}
@@ -84,10 +84,10 @@ services:
     depends_on:
       - "dynamodb"
     volumes:
-     # The variant service has packaged data at variant/data,
-     # so we do not map a host directory to variant/data.
+     # The variation service has packaged data at variation/data,
+     # so we do not map a host directory to variation/data.
      # We do share seqrepo already harvested for gene
-     - ./data/gene/seqrepo:/app/variant/data/seqrepo
+     - ./data/gene/seqrepo:/app/variation/data/seqrepo
   # The disease service
   disease:
     build: disease-normalization
@@ -146,7 +146,7 @@ services:
     depends_on:
       - "neo4j"
       - "disease"
-      - "variant"
+      - "variation"
       - "gene"
       - "therapy"      
     volumes:
@@ -166,7 +166,7 @@ services:
      - ./test/tests:/app/tests
     depends_on:
       - "disease"
-      - "variant"
+      - "variation"
       - "gene"
       - "therapy"
 

test/tests/integration/test_variant.py → test/tests/integration/test_variation.py

@@ -4,21 +4,21 @@
 
 
 def test_server_alive():
-    """Variant server should return 200."""
-    response = requests.get("http://variant/variant")
+    """Variation server should return 200."""
+    response = requests.get("http://variation/variation")
     assert response.status_code == 200, test_server_alive.__doc__
 
 
 def test_swagger_ui():
-    """Variant server should return swagger UI 'FastAPI - Swagger UI'."""
-    response = requests.get("http://variant/variant")
+    """Variation server should return swagger UI 'FastAPI - Swagger UI'."""
+    response = requests.get("http://variation/variation")
     assert response.status_code == 200, test_swagger_ui.__doc__
     assert 'FastAPI - Swagger UI' in response.text, test_swagger_ui.__doc__
 
 
 def test_query():
-    """Variant server should find `BRAF V600E`."""
-    url = "http://variant/variant/normalize?q=BRAF%20V600E"
+    """Variation server should find `BRAF V600E`."""
+    url = "http://variation/variation/normalize?q=BRAF%20V600E"
     headers = {'accept': 'application/json'}
     response = requests.get(url, headers=headers)
     assert response.status_code == 200, test_query.__doc__