Fixes for issue 160 (#161)

* various version updates to fix issue 160

* add servers.zip

* add xml libraries to Alpine linux docker

* Update python-flask templates

* Increment version

* Revert "Increment version"

This reverts commit 2fe39d7.

* Revert "Update python-flask templates"

This reverts commit 647bae7.

* Update with fixes to moustache templates because of openapi version increment

* Update Open API generator version
Add curl to docker instance to help with health check

* Add comment about servers folder

* Put back the docs file

pom.xml

@@ -6,7 +6,7 @@
     <packaging>jar</packaging>
     <groupId>edu.isi.oba</groupId>
     <artifactId>oba</artifactId>
-    <version>3.6.0</version>
+    <version>3.6.0.04</version>
     <name>core</name>
     <url>https://github.com/KnowledgeCaptureAndDiscovery/OBA</url>
 

src/main/resources/README.md

@@ -0,0 +1,10 @@
+# Servers directory
+
+Note servers.zip file is used to generate the python flask server, so any changes to files in the folder need to be replicated into a new servers.zip file. eg.
+
+```
+rm servers.zip
+zip -r servers.zip servers
+```
+
+Also note the moustache template files in the hidden folder: OBA/src/main/resources/servers/python/.openapi-generator were copied from https://github.com/OpenAPITools/openapi-generator/tree/master/modules/openapi-generator/src/main/resources/python-flask on 17 Jul 2020, and have not followed changes to that project so that a full refactor would be required to get back in sync.

src/main/resources/servers/python/.openapi-generator/template/Dockerfile.mustache

@@ -5,7 +5,7 @@ FROM python:2-alpine
 FROM python:3-alpine
 {{/supportPython2}}
 
-RUN apk add build-base libffi-dev openssl-dev git
+RUN apk add build-base libffi-dev openssl-dev git libxml2-dev libxslt-dev curl
 RUN mkdir -p /usr/src/app
 WORKDIR /usr/src/app
 
@@ -29,4 +29,4 @@ ENTRYPOINT ["python"]
 ENTRYPOINT ["python3"]
 {{/supportPython2}}
 
-CMD ["-m", "{{packageName}}"]
+CMD ["-m", "{{packageName}}"]

src/main/resources/servers/python/.openapi-generator/template/__init__.mustache

@@ -11,13 +11,10 @@ except:
 logger = logging.getLogger(__name__)
 
 query_manager = QueryManager(queries_dir=QUERY_DIRECTORY,
-                             context_dir=CONTEXT_DIRECTORY,
-                             queries_types=QUERIES_TYPES,
-                             endpoint=ENDPOINT,
-                             endpoint_username=ENDPOINT_USERNAME,
-                             endpoint_password=ENDPOINT_PASSWORD,
-                             graph_base=ENDPOINT_GRAPH_BASE,
-                             prefix=ENDPOINT_RESOURCE_PREFIX)
-
-
+               context_dir=CONTEXT_DIRECTORY,
+               endpoint=ENDPOINT,
+               endpoint_username=ENDPOINT_USERNAME,
+               endpoint_password=ENDPOINT_PASSWORD,
+               named_graph_base=ENDPOINT_GRAPH_BASE,
+               uri_prefix=ENDPOINT_RESOURCE_PREFIX)
 

src/main/resources/servers/python/.openapi-generator/template/controller.mustache

@@ -9,7 +9,7 @@ from {{packageName}} import util
 {{#operations}}
 {{#operation}}
 
-def {{operationId}}({{#allParams}}{{paramName}}{{^required}}=None{{/required}}{{#hasMore}}, {{/hasMore}}{{/allParams}}):  # noqa: E501
+def {{operationId}}({{#allParams}}{{paramName}}{{^required}}=None{{/required}}{{^-last}}, {{/-last}}{{/allParams}}):  # noqa: E501
     """{{#summary}}{{.}}{{/summary}}{{^summary}}{{operationId}}{{/summary}}
 
     {{#notes}}{{.}}{{/notes}} # noqa: E501
@@ -110,9 +110,9 @@ def {{operationId}}({{#allParams}}{{paramName}}{{^required}}=None{{/required}}{{
         {{/isMapContainer}}
     {{/allParams}}
 
-    return query_manager.{{#lambda.lowercase}}{{httpMethod}}_resource{{/lambda.lowercase}}({{#pathParams}}{{paramName}}={{paramName}}{{#hasMore}},{{/hasMore}}{{#-last}},{{/-last}}{{/pathParams}}{{#queryParams}}
-        {{paramName}}={{paramName}}{{#hasMore}},{{/hasMore}}{{#-last}},{{/-last}}{{/queryParams}}{{#bodyParams}}
-        body={{paramName}}{{#hasMore}},{{/hasMore}}{{#-last}},{{/-last}}{{/bodyParams}}
+    return query_manager.{{#lambda.lowercase}}{{httpMethod}}_resource{{/lambda.lowercase}}({{#pathParams}}{{paramName}}={{paramName}},{{/pathParams}}{{#queryParams}}
+        {{paramName}}={{paramName}},{{/queryParams}}{{#bodyParams}}
+        body={{paramName}},{{/bodyParams}}
         rdf_type_uri={{#lambda.uppercase}}{{baseName}}_type_uri{{/lambda.uppercase}},
         rdf_type_name={{#lambda.uppercase}}{{baseName}}_type_name{{/lambda.uppercase}}, 
         kls={{baseName}})

src/main/resources/servers/python/.openapi-generator/template/model.mustache

@@ -47,13 +47,13 @@ class {{classname}}(Model):
 
         self.openapi_types = {
 {{#vars}}
-            '{{name}}': {{{dataType}}}{{#hasMore}},{{/hasMore}}
+            '{{name}}': {{{dataType}}}{{^-last}},{{/-last}}
 {{/vars}}
         }
 
         self.attribute_map = {
 {{#vars}}
-            '{{name}}': '{{baseName}}'{{#hasMore}},{{/hasMore}}
+            '{{name}}': '{{baseName}}'{{^-last}},{{/-last}}
 {{/vars}}
         }
 {{#vars}}{{#-first}}

src/main/resources/servers/python/.openapi-generator/template/requirements.mustache

@@ -1,9 +1,10 @@
 pythonql3==0.9.61
 connexion >= 2.6.0
 obasparql >= 3.4.2
-werkzeug==0.16.1
+werkzeug>=2.0
 swagger-ui-bundle >= 0.0.2
 python_dateutil >= 2.6.0
 setuptools >= 21.0.0
 validators >= 0.14.2
 python-jose >= 3.0.1
+markupsafe==2.0.1

src/main/resources/servers/python/generate-server.sh

@@ -20,9 +20,9 @@ cp ../openapi.yaml ${PWD}
 SERVER_DIR=server
 
 
-docker run -ti --rm -v ${PWD}:/local \
+docker run --rm -v ${PWD}:/local \
      -u "$(id -u):$(id -u)" \
-     openapitools/openapi-generator-cli:v4.1.2 \
+     openapitools/openapi-generator-cli:v6.0.0 \
      generate  \
      -i /local/openapi.yaml\
      -g python-flask  \