Prez v4.0.0 (#229)

* Update permissions according to recommendations based on file type; fixes previous inadvertent permission changes.
Merge search endpoint with other listing functions.
Move to using sparql_grammar_pydantic as external dependency, black code, improve API documentation (examples, query params); remove unused code.
Update dependencies; minor changes to get tests passing.
Prez V4 architecture using SPARQL grammar library.

* Add CQL examples to /cql POST endpoint.
Example updates.
Fix shapely issue in Docker container

* Add mediatype examples

* fix path issue or loading CQL json

* Add example application/sparql-query MT

* Update documentation. Remove unused code. Split API extras/examples to separate file for clarity.

* Add annotations to cache on startup.

* Reverse TriplesSameSubjectPath lists in query generation for more performant queries - this was causing timeouts on link generation. Remove skos broader/narrower from extra predicates; there are concept scheme specific endpoints for these.

* Reverse TriplesSameSubjectPath lists in for performance.

* Limit Count queries to a configurable limit to prevent timeouts; defaulted to 1000.
Patch sparql-grammar-pydantic to support this.

* Group Triples with same subject to improve performance. Sort reverse order to put pattern matches with more variables last.

* Minor fixes to regressions from rebasing

* black repo

.gitignore

@@ -8,3 +8,7 @@ __pycache__/
 dist/
 !.env-template
 rdf/
+http/
+/.python-version
+http/
+.ropeproject/

.run/test_data pyoxigraph.run.xml

@@ -0,0 +1,34 @@
+<component name="ProjectRunConfigurationManager">
+  <configuration default="false" name="test_data pyoxigraph" type="PythonConfigurationType" factoryName="Python">
+    <module name="prez" />
+    <option name="ENV_FILES" value="" />
+    <option name="INTERPRETER_OPTIONS" value="" />
+    <option name="PARENT_ENVS" value="true" />
+    <envs>
+      <env name="PYTHONUNBUFFERED" value="1" />
+      <env name="LOCAL_RDF_DIR" value="test_data" />
+      <env name="LOG_LEVEL" value="DEBUG" />
+      <env name="PORT" value="8010" />
+      <env name="SPARQL_REPO_TYPE" value="pyoxigraph" />
+    </envs>
+    <option name="SDK_HOME" value="" />
+    <option name="WORKING_DIRECTORY" value="$PROJECT_DIR$/prez" />
+    <option name="IS_MODULE_SDK" value="true" />
+    <option name="ADD_CONTENT_ROOTS" value="true" />
+    <option name="ADD_SOURCE_ROOTS" value="true" />
+    <EXTENSION ID="PythonCoverageRunConfigurationExtension" runner="coverage.py" />
+    <EXTENSION ID="software.aws.toolkits.jetbrains.core.execution.PythonAwsConnectionExtension">
+      <option name="credential" />
+      <option name="region" />
+      <option name="useCurrentConnection" value="false" />
+    </EXTENSION>
+    <option name="SCRIPT_NAME" value="$PROJECT_DIR$/prez/app.py" />
+    <option name="PARAMETERS" value="" />
+    <option name="SHOW_COMMAND_LINE" value="false" />
+    <option name="EMULATE_TERMINAL" value="false" />
+    <option name="MODULE_MODE" value="false" />
+    <option name="REDIRECT_INPUT" value="false" />
+    <option name="INPUT_FILE" value="" />
+    <method v="2" />
+  </configuration>
+</component>

Dockerfile

@@ -1,6 +1,6 @@
 ARG PREZ_VERSION
 ARG PYTHON_VERSION=3.12.3
-ARG POETRY_VERSION=1.8.1
+ARG POETRY_VERSION=1.8.3
 ARG VIRTUAL_ENV=/opt/venv
 
 #
@@ -19,7 +19,9 @@ RUN apk add --no-cache \
       libffi-dev \
       musl-dev \
       pipx \
-      python3-dev
+      python3-dev \
+      geos \
+      geos-dev
 
 RUN pipx install poetry==${POETRY_VERSION}
 
@@ -47,7 +49,9 @@ COPY --from=base ${VIRTUAL_ENV} ${VIRTUAL_ENV}
 RUN apk update && \
     apk upgrade --no-cache && \
     apk add --no-cache \
-      bash
+      bash \
+      geos \
+      geos-dev
 
 WORKDIR /app
 # prez module is already built as a package and installed in $VIRTUAL_ENV as a library