add pocH-100i analyzer

I-TECH-UW · Jun 14, 2024 · 0f79b28 · 0f79b28
1 parent c227043
commit 0f79b28
Show file tree

Hide file tree

Showing 7 changed files with 817 additions and 0 deletions.
diff --git a/analyzers/pocH-100i/.vscode/settings.json b/analyzers/pocH-100i/.vscode/settings.json
@@ -0,0 +1,5 @@
+{
+    "java.project.sourcePaths": [
+        "src/main/java"
+    ]
+}
diff --git a/analyzers/pocH-100i/pom.xml b/analyzers/pocH-100i/pom.xml
@@ -0,0 +1,89 @@
+<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.openelisglobal.plugins</groupId>
+	<artifactId>pocH-100iAnalyzer</artifactId>
+	<parent>
+		<groupId>org.openelisglobal</groupId>
+		<artifactId>openelisglobal-plugins</artifactId>
+		<version>1.0</version>
+		<relativePath>../../pom.xml</relativePath>
+	</parent>
+
+	<version>0.1</version>
+	<properties>
+		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+		<hapi.version>2.3</hapi.version>
+	</properties>
+
+	<dependencies>
+		<dependency>
+			<groupId>javax.servlet</groupId>
+			<artifactId>javax.servlet-api</artifactId>
+			<version>4.0.1</version>
+			<scope>provided</scope>
+		</dependency>
+		<dependency>
+			<groupId>commons-fileupload</groupId>
+			<artifactId>commons-fileupload</artifactId>
+			<version>1.4</version>
+		</dependency>
+		<dependency>
+			<groupId>org.springframework</groupId>
+			<artifactId>spring-webmvc</artifactId>
+			<version>${springframework.version}</version>
+		</dependency>
+	</dependencies>
+
+	<build>
+		<sourceDirectory>src/main/java</sourceDirectory>
+		<resources>
+			<resource>
+				<directory>src/main/filtered-resources</directory>
+				<filtering>true</filtering>
+			</resource>
+			<resource>
+				<directory>src/main/resources</directory>
+			</resource>
+		</resources>
+		<plugins>
+			<plugin>
+				<artifactId>maven-compiler-plugin</artifactId>
+				<version>3.8.0</version>
+				<configuration>
+					<source>1.8</source>
+					<target>1.8</target>
+				</configuration>
+			</plugin>
+			<plugin>
+				<artifactId>maven-resources-plugin</artifactId>
+				<version>2.4.3</version>
+				<executions>
+					<execution>
+						<id>copy-resources</id>
+						<!-- here the phase you need -->
+						<phase>install</phase>
+						<goals>
+							<goal>copy-resources</goal>
+						</goals>
+						<configuration>
+							<outputDirectory>${project.basedir}/../../plugins</outputDirectory>
+							<resources>
+								<resource>
+									<!-- Get main artifact -->
+									<directory>target/</directory>
+									<includes>
+										<include>${project.build.finalName}.jar</include>
+									</includes>
+									<!-- Don't filter binary files -->
+									<filtering>false</filtering>
+								</resource>
+							</resources>
+						</configuration>
+					</execution>
+				</executions>
+			</plugin>
+		</plugins>
+	</build>
+</project>
diff --git a/analyzers/pocH-100i/src/main/java/oe/plugin/analyzer/PocH100iAnalyzer.java b/analyzers/pocH-100i/src/main/java/oe/plugin/analyzer/PocH100iAnalyzer.java
@@ -0,0 +1,167 @@
+/*
+ * The contents of this file are subject to the Mozilla Public License
+ * Version 1.1 (the "License"); you may not use this file except in
+ * compliance with the License. You may obtain a copy of the License at
+ * http://www.mozilla.org/MPL/
+ *
+ * Software distributed under the License is distributed on an "AS IS"
+ * basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the
+ * License for the specific language governing rights and limitations under
+ * the License.
+ *
+ * The Original Code is OpenELIS code.
+ *
+ * Copyright (C) ITECH, University of Washington, Seattle WA.  All Rights Reserved.
+ */
+
+package oe.plugin.analyzer;
+
+import static org.openelisglobal.common.services.PluginAnalyzerService.getInstance;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.regex.Pattern;
+
+import org.openelisglobal.analyzerimport.analyzerreaders.AnalyzerLineInserter;
+import org.openelisglobal.common.services.PluginAnalyzerService;
+import org.openelisglobal.plugin.AnalyzerImporterPlugin;
+import org.openelisglobal.analyzerimport.analyzerreaders.AnalyzerResponder;
+import org.openelisglobal.common.log.LogEvent;
+
+public class PocH100iAnalyzer implements AnalyzerImporterPlugin {
+
+	public static final String ANALYZER_NAME = "PocH100iAnalyzer";
+
+	@Override
+	public boolean connect() {
+		List<PluginAnalyzerService.TestMapping> nameMapping = new ArrayList<>();
+		nameMapping.add(
+				new PluginAnalyzerService.TestMapping(PocH100iAnalyzerImplementation.ANALYZER_TEST_WBC, "White Blood Cells Count (WBC)",
+						PocH100iAnalyzerImplementation.LOINC_WBC));
+		nameMapping.add(
+				new PluginAnalyzerService.TestMapping(PocH100iAnalyzerImplementation.ANALYZER_TEST_RBC, "Red Blood Cells Count (RBC)",
+						PocH100iAnalyzerImplementation.LOINC_RBC));
+		nameMapping.add(
+				new PluginAnalyzerService.TestMapping(PocH100iAnalyzerImplementation.ANALYZER_TEST_HGB, "Hemoglobin",
+				PocH100iAnalyzerImplementation.LOINC_HGB));
+		nameMapping.add(
+				new PluginAnalyzerService.TestMapping(PocH100iAnalyzerImplementation.ANALYZER_TEST_HCT, "Hematocrit",
+						PocH100iAnalyzerImplementation.LOINC_HCT));
+		nameMapping.add(
+				new PluginAnalyzerService.TestMapping(PocH100iAnalyzerImplementation.ANALYZER_TEST_MCV, "Medium corpuscular volum",
+						PocH100iAnalyzerImplementation.LOINC_MCV));
+		nameMapping.add(
+				new PluginAnalyzerService.TestMapping(PocH100iAnalyzerImplementation.ANALYZER_TEST_MCH, "",
+						PocH100iAnalyzerImplementation.LOINC_MCH));
+		nameMapping
+				.add(new PluginAnalyzerService.TestMapping(PocH100iAnalyzerImplementation.ANALYZER_TEST_MCHC, "",
+						PocH100iAnalyzerImplementation.LOINC_MCHC));
+		nameMapping
+				.add(new PluginAnalyzerService.TestMapping(PocH100iAnalyzerImplementation.ANALYZER_TEST_RDWSD, "",
+						PocH100iAnalyzerImplementation.LOINC_RDWSD));
+		nameMapping.add(
+				new PluginAnalyzerService.TestMapping(PocH100iAnalyzerImplementation.ANALYZER_TEST_RDWCV, "",
+						PocH100iAnalyzerImplementation.LOINC_RDWCV));
+		nameMapping
+				.add(new PluginAnalyzerService.TestMapping(PocH100iAnalyzerImplementation.ANALYZER_TEST_PLT, "Platelets",
+						PocH100iAnalyzerImplementation.LOINC_PLT));
+		nameMapping.add(
+				new PluginAnalyzerService.TestMapping(PocH100iAnalyzerImplementation.ANALYZER_TEST_MPV, "",
+						PocH100iAnalyzerImplementation.LOINC_MPV));
+		nameMapping.add(
+				new PluginAnalyzerService.TestMapping(PocH100iAnalyzerImplementation.ANALYZER_TEST_NEUT_COUNT, "Neutrophiles",
+				PocH100iAnalyzerImplementation.LOINC_NEUT_COUNT));
+		nameMapping.add(
+				new PluginAnalyzerService.TestMapping(PocH100iAnalyzerImplementation.ANALYZER_TEST_NEUT_PERCENT, "Neutrophiles (%)",
+						PocH100iAnalyzerImplementation.LOINC_NEUT_PERCENT));
+		nameMapping.add(
+				new PluginAnalyzerService.TestMapping(PocH100iAnalyzerImplementation.ANALYZER_TEST_LYMPH_COUNT, "Lymphocytes (Abs)",
+						PocH100iAnalyzerImplementation.LOINC_LYMPH_COUNT));
+		nameMapping.add(
+				new PluginAnalyzerService.TestMapping(PocH100iAnalyzerImplementation.ANALYZER_TEST_LYMPH_PERCENT, "Lymphocytes (%)",
+						PocH100iAnalyzerImplementation.LOINC_LYMPH_PERCENT));
+		nameMapping.add(
+				new PluginAnalyzerService.TestMapping(PocH100iAnalyzerImplementation.ANALYZER_TEST_MONO_COUNT, "Monocytes (Abs)",
+						PocH100iAnalyzerImplementation.LOINC_MONO_COUNT));
+		nameMapping.add(
+				new PluginAnalyzerService.TestMapping(PocH100iAnalyzerImplementation.ANALYZER_TEST_MONO_PERCENT, "Monocytes (%)",
+						PocH100iAnalyzerImplementation.LOINC_MONO_PERCENT));
+		nameMapping.add(
+				new PluginAnalyzerService.TestMapping(PocH100iAnalyzerImplementation.ANALYZER_TEST_EO_COUNT, "Eosinophiles",
+						PocH100iAnalyzerImplementation.LOINC_EO_COUNT));
+		nameMapping.add(
+				new PluginAnalyzerService.TestMapping(PocH100iAnalyzerImplementation.ANALYZER_TEST_EO_PERCENT, "Eosinophiles (%)",
+						PocH100iAnalyzerImplementation.LOINC_EO_PERCENT));
+		nameMapping.add(
+				new PluginAnalyzerService.TestMapping(PocH100iAnalyzerImplementation.ANALYZER_TEST_BASO_COUNT, "Basophiles",
+						PocH100iAnalyzerImplementation.LOINC_BASO_COUNT));
+		nameMapping.add(
+				new PluginAnalyzerService.TestMapping(PocH100iAnalyzerImplementation.ANALYZER_TEST_BASO_PERCENT, "Basophiles (%)",
+						PocH100iAnalyzerImplementation.LOINC_BASO_PERCENT));
+		nameMapping.add(
+				new PluginAnalyzerService.TestMapping(PocH100iAnalyzerImplementation.ANALYZER_TEST_IG_COUNT, "",
+						PocH100iAnalyzerImplementation.LOINC_IG_COUNT));
+		nameMapping.add(
+				new PluginAnalyzerService.TestMapping(PocH100iAnalyzerImplementation.ANALYZER_TEST_IG_PERCENT, "",
+						PocH100iAnalyzerImplementation.LOINC_IG_PERCENT));
+		nameMapping.add(
+				new PluginAnalyzerService.TestMapping(PocH100iAnalyzerImplementation.ANALYZER_TEST_MXD_COUNT, "",
+						PocH100iAnalyzerImplementation.LOINC_MXD_COUNT));
+		nameMapping.add(
+				new PluginAnalyzerService.TestMapping(PocH100iAnalyzerImplementation.ANALYZER_TEST_MXD_PERCENT, "",
+						PocH100iAnalyzerImplementation.LOINC_MXD_PERCENT));
+		getInstance().addAnalyzerDatabaseParts(ANALYZER_NAME, ANALYZER_NAME, nameMapping, true);
+		getInstance().registerAnalyzer(this);
+		return true;
+	}
+
+	@Override
+	public boolean isTargetAnalyzer(List<String> lines) {
+		for (String line : lines) {
+			if (line.startsWith(PocH100iAnalyzerImplementation.HEADER_RECORD_IDENTIFIER)) {
+				String[] headerRecord = line.split(Pattern.quote(PocH100iAnalyzerImplementation.FD));
+				if (headerRecord.length < 5) {
+					LogEvent.logTrace(this.getClass().getSimpleName(), "isTargetAnalyzer", "incoming message is not PocH100i: header record not long enough");
+					return false;
+				}
+				String[] senderNameFields = headerRecord[4].split(Pattern.quote(PocH100iAnalyzerImplementation.CD));
+				if (senderNameFields.length < 1) {
+					LogEvent.logTrace(this.getClass().getSimpleName(), "isTargetAnalyzer", "incoming message is not PocH100i: sender name field not long enough");
+					return false;
+				}
+				String senderName = senderNameFields[0].trim();
+				LogEvent.logTrace(this.getClass().getSimpleName(), "isTargetAnalyzer", "incoming message analyzer name is " + senderName);
+				if (senderName.equalsIgnoreCase("pocH-100i")) {
+					LogEvent.logTrace(this.getClass().getSimpleName(), "isTargetAnalyzer", "incoming message is PocH100i");
+					return true;
+				}
+				LogEvent.logTrace(this.getClass().getSimpleName(), "isTargetAnalyzer", "incoming message is not PocH100i: sender name doesn't match");
+				return false;
+			}
+		}
+		LogEvent.logTrace(this.getClass().getSimpleName(), "isTargetAnalyzer", "incoming message is not PocH100i: no header line");
+		return false;
+	}
+
+	@Override
+	public boolean isAnalyzerResult(List<String> lines) {
+		for (String line : lines) {
+			if (line.startsWith(PocH100iAnalyzerImplementation.RESULT_RECORD_IDENTIFIER)) {
+				return true;
+			}
+		}
+		LogEvent.logDebug(this.getClass().getSimpleName(), "isAnalyzerResult", "no result recoord identifier located");
+		return false;
+	}
+
+	@Override
+	public AnalyzerLineInserter getAnalyzerLineInserter() {
+		return new PocH100iAnalyzerImplementation();
+	}
+
+	@Override
+	public AnalyzerResponder getAnalyzerResponder() {
+		return new PocH100iAnalyzerImplementation();
+	}
+
+}