Taxon resolver wip

duui-taxon-resolver/.gitignore

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+### IDE Files ###
+.idea/
+.vscode/
+
+### Java Environment ###
+target/
+
+### Python Environment ###
+__pycache__/
+*.pyc
+.venv/

duui-taxon-resolver/DOCKERFILE

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+FROM python:3.12.3
+
+WORKDIR /app
+
+RUN pip install --upgrade pip
+
+COPY requirements.txt .
+RUN pip install -r requirements.txt
+
+COPY src/main/python/*.py ./
+COPY src/main/lua/communication_layer.lua ./
+COPY src/main/resources/typesystem.xml ./
+
+# Preload the backbone data to avoid doing it at runtime when the first request arrives
+RUN python -c "import taxref_loader; taxref_loader.preload_backbone()"
+
+ENV TAXON_RESOLVER_EXECUTION_MODE=production
+
+EXPOSE 9714
+ENTRYPOINT ["uvicorn", "taxon-resolver:app", "--host", "0.0.0.0", "--port", "9714"]
+CMD ["--workers", "1"]

duui-taxon-resolver/docker_build.sh

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+#!/usr/bin/env bash
+set -euo pipefail
+
+# set default values for build args if not provided
+ANNOTATOR_NAME="${ANNOTATOR_NAME:-duui-taxon-resolver}"
+ANNOTATOR_VERSION="${ANNOTATOR_VERSION:-1.0.0}"
+LOG_LEVEL="${LOG_LEVEL:-INFO}"
+
+# Check if BUILD_TOOL is set, otherwise check for podman or docker
+if [ -n "${BUILD_TOOL:-}" ]; then
+    echo "⚙️  Using build tool: ${BUILD_TOOL}"
+# Test if docker is available and can be used
+elif (command -v docker > /dev/null 2>&1;) && (docker info > /dev/null 2>&1;) then
+    BUILD_TOOL="docker"
+    echo "⚙️  Using Docker as build tool"
+elif (command -v podman > /dev/null 2>&1;) && (podman info > /dev/null 2>&1;) then
+    BUILD_TOOL="podman"
+    echo "⚙️  Using Podman as build tool"
+else
+    echo "❌ Error: No build tool found or permissions missing. Please install Docker or Podman and ensure you have permission to run it."
+    exit 1
+fi
+
+${BUILD_TOOL} build \
+    --env TAXON_RESOLVER_ANNOTATOR_NAME="${ANNOTATOR_NAME}" \
+    --env TAXON_RESOLVER_ANNOTATOR_VERSION="${ANNOTATOR_VERSION}" \
+    --env TAXON_RESOLVER_LOG_LEVEL="${LOG_LEVEL}" \
+    -t "${ANNOTATOR_NAME}:${ANNOTATOR_VERSION}" \
+    -f DOCKERFILE \

duui-taxon-resolver/pom.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+
+    <groupId>org.texttechnologylab</groupId>
+    <artifactId>taxon-resolver</artifactId>
+    <version>1.0-SNAPSHOT</version>
+
+    <properties>
+        <maven.compiler.source>21</maven.compiler.source>
+        <maven.compiler.target>21</maven.compiler.target>
+        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+        <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
+        <ttlab.duui.version>1.5.5</ttlab.duui.version>
+        <ttlab.typesystem.version>3.0.14</ttlab.typesystem.version>
+    </properties>
+
+    <build>
+        <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-compiler-plugin</artifactId>
+                <configuration>
+                    <forceJavacCompilerUse>true</forceJavacCompilerUse>
+                </configuration>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-surefire-plugin</artifactId>
+                <version>2.22.0</version>
+                <configuration>
+                    <argLine>
+                        --illegal-access=permit
+                        --add-opens java.base/java.util=ALL-UNNAMED
+                    </argLine>
+                </configuration>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-failsafe-plugin</artifactId>
+                <version>2.22.0</version>
+                <configuration>
+                    <argLine>
+                        --illegal-access=permit
+                        --add-opens java.base/java.util=ALL-UNNAMED
+                    </argLine>
+                </configuration>
+            </plugin>
+        </plugins>
+    </build>
+
+    <repositories>
+        <repository>
+            <id>jitpack.io</id>
+            <url>https://jitpack.io</url>
+        </repository>
+    </repositories>
+
+    <dependencies><dependency>
+            <groupId>com.github.texttechnologylab</groupId>
+            <artifactId>DockerUnifiedUIMAInterface</artifactId>
+            <version>${ttlab.duui.version}</version>
+            <exclusions>
+                <exclusion>
+                    <groupId>com.github.texttechnologylab</groupId>
+                    <artifactId>UIMATypeSystem</artifactId>
+                </exclusion>
+            </exclusions>
+        </dependency>
+
+        <dependency>
+            <groupId>com.github.texttechnologylab</groupId>
+            <artifactId>UIMATypeSystem</artifactId>
+            <version>${ttlab.typesystem.version}</version>
+        </dependency>
+
+        <dependency>
+            <groupId>org.junit.jupiter</groupId>
+            <artifactId>junit-jupiter</artifactId>
+            <version>6.1.0-M1</version>
+            <scope>test</scope>
+        </dependency>
+
+        <dependency>
+            <groupId>org.dkpro.core</groupId>
+            <artifactId>dkpro-core-io-xmi-asl</artifactId>
+            <version>2.4.0</version>
+            <scope>test</scope>
+        </dependency>
+    </dependencies>
+
+</project>

duui-taxon-resolver/requirements.txt

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+annotated-types==0.7.0
+anyio==3.7.1
+attrs==25.4.0
+fastapi==0.104.1
+ipykernel==7.2.0
+pandas==3.0.3
+pydantic==2.13.4
+pydantic-settings==2.0.3
+python-dotenv==1.2.2
+requests==2.34.2
+# Taxoniq resolves NCBI taxonomic identifiers
+taxoniq==1.0.3
+urllib3==2.6.3
+uvicorn==0.46.0