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Merge pull request #28 from CalebSLane/develop
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improve ASTM analyzers
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@CalebSLane
CalebSLane authored Jun 14, 2024
2 parents f7c18f6 + 4947d09 commit 63c4ff1
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Showing 44 changed files with 2,280 additions and 266 deletions.
5 changes: 5 additions & 0 deletions analyzers/GeneXpert/.vscode/settings.json
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@@ -0,0 +1,5 @@
{
"java.project.sourcePaths": [
"src/main/java"
]
}
15 changes: 5 additions & 10 deletions analyzers/GeneXpert/pom.xml
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Expand Up @@ -3,15 +3,15 @@
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>GeneXpert</artifactId>
<artifactId>GeneXpertAnalyzer</artifactId>
<parent>
<groupId>org.openelisglobal</groupId>
<artifactId>openelisglobal-plugins</artifactId>
<version>1.0</version>
<relativePath>../../pom.xml</relativePath>
</parent>

<version>0.3</version>
<version>0.4</version>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<hapi.version>2.3</hapi.version>
Expand All @@ -25,14 +25,9 @@
<scope>provided</scope>
</dependency>
<dependency>
<groupId>ca.uhn.hapi</groupId>
<artifactId>hapi-hl7overhttp</artifactId>
<version>${hapi.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi</groupId>
<artifactId>hapi-structures-v25</artifactId>
<version>${hapi.version}</version>
<groupId>commons-fileupload</groupId>
<artifactId>commons-fileupload</artifactId>
<version>1.4</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
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159 changes: 145 additions & 14 deletions analyzers/GeneXpert/src/main/java/oe/plugin/analyzer/GeneXpertAnalyzer.java
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Expand Up @@ -5,7 +5,7 @@
* 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
* basis, WITHOUT WARRANTY OF ANY KIND, either eXNLress or implied. See the
* License for the specific language governing rights and limitations under
* the License.
*
Expand All @@ -20,39 +20,165 @@

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 GeneXpertAnalyzer implements AnalyzerImporterPlugin {

public static final String ANALYZER_NAME = "GeneXpertAnalyzer";

@Override
public boolean connect() {
@Override
public boolean connect() {
List<PluginAnalyzerService.TestMapping> nameMapping = new ArrayList<>();
nameMapping.add(
new PluginAnalyzerService.TestMapping(GeneXpertAnalyzerImplementation.HBV, "HEPATITIS B VIRAL LOAD",
GeneXpertAnalyzerImplementation.HBV_LOINC));
new PluginAnalyzerService.TestMapping(GeneXpertAnalyzerImplementation.ANALYZER_TEST_WBC, "White Blood Cells Count (WBC)",
GeneXpertAnalyzerImplementation.LOINC_WBC));
nameMapping.add(
new PluginAnalyzerService.TestMapping(GeneXpertAnalyzerImplementation.ANALYZER_TEST_RBC, "Red Blood Cells Count (RBC)",
GeneXpertAnalyzerImplementation.LOINC_RBC));
nameMapping.add(
new PluginAnalyzerService.TestMapping(GeneXpertAnalyzerImplementation.ANALYZER_TEST_HGB, "Hemoglobin",
GeneXpertAnalyzerImplementation.LOINC_HGB));
nameMapping.add(
new PluginAnalyzerService.TestMapping(GeneXpertAnalyzerImplementation.ANALYZER_TEST_HCT, "Hematocrit",
GeneXpertAnalyzerImplementation.LOINC_HCT));
nameMapping.add(
new PluginAnalyzerService.TestMapping(GeneXpertAnalyzerImplementation.ANALYZER_TEST_MCV, "Medium corpuscular volum",
GeneXpertAnalyzerImplementation.LOINC_MCV));
nameMapping.add(
new PluginAnalyzerService.TestMapping(GeneXpertAnalyzerImplementation.HCV, "HEPATITIS C VIRAL LOAD",
GeneXpertAnalyzerImplementation.HCV_LOINC));
new PluginAnalyzerService.TestMapping(GeneXpertAnalyzerImplementation.ANALYZER_TEST_MCH, "",
GeneXpertAnalyzerImplementation.LOINC_MCH));
nameMapping
.add(new PluginAnalyzerService.TestMapping(GeneXpertAnalyzerImplementation.ANALYZER_TEST_MCHC, "",
GeneXpertAnalyzerImplementation.LOINC_MCHC));
nameMapping
.add(new PluginAnalyzerService.TestMapping(GeneXpertAnalyzerImplementation.ANALYZER_TEST_RDWSD, "",
GeneXpertAnalyzerImplementation.LOINC_RDWSD));
nameMapping.add(
new PluginAnalyzerService.TestMapping(GeneXpertAnalyzerImplementation.HIV_QUAL, "​Xpert HIV-1 Qual",
GeneXpertAnalyzerImplementation.HIV_QUAL_LOINC));
new PluginAnalyzerService.TestMapping(GeneXpertAnalyzerImplementation.ANALYZER_TEST_RDWCV, "",
GeneXpertAnalyzerImplementation.LOINC_RDWCV));
nameMapping
.add(new PluginAnalyzerService.TestMapping(GeneXpertAnalyzerImplementation.HIV_VIRAL, "HIV VIRAL LOAD",
GeneXpertAnalyzerImplementation.HIV_VIRAL_LOINC));
.add(new PluginAnalyzerService.TestMapping(GeneXpertAnalyzerImplementation.ANALYZER_TEST_PLT, "Platelets",
GeneXpertAnalyzerImplementation.LOINC_PLT));
nameMapping.add(
new PluginAnalyzerService.TestMapping(GeneXpertAnalyzerImplementation.ANALYZER_TEST_MPV, "",
GeneXpertAnalyzerImplementation.LOINC_MPV));
nameMapping.add(
new PluginAnalyzerService.TestMapping(GeneXpertAnalyzerImplementation.ANALYZER_TEST_NEUT_COUNT, "Neutrophiles",
GeneXpertAnalyzerImplementation.LOINC_NEUT_COUNT));
nameMapping.add(
new PluginAnalyzerService.TestMapping(GeneXpertAnalyzerImplementation.ANALYZER_TEST_NEUT_PERCENT, "Neutrophiles (%)",
GeneXpertAnalyzerImplementation.LOINC_NEUT_PERCENT));
nameMapping.add(
new PluginAnalyzerService.TestMapping(GeneXpertAnalyzerImplementation.ANALYZER_TEST_LYMPH_COUNT, "Lymphocytes (Abs)",
GeneXpertAnalyzerImplementation.LOINC_LYMPH_COUNT));
nameMapping.add(
new PluginAnalyzerService.TestMapping(GeneXpertAnalyzerImplementation.ANALYZER_TEST_LYMPH_PERCENT, "Lymphocytes (%)",
GeneXpertAnalyzerImplementation.LOINC_LYMPH_PERCENT));
nameMapping.add(
new PluginAnalyzerService.TestMapping(GeneXpertAnalyzerImplementation.ANALYZER_TEST_MONO_COUNT, "Monocytes (Abs)",
GeneXpertAnalyzerImplementation.LOINC_MONO_COUNT));
nameMapping.add(
new PluginAnalyzerService.TestMapping(GeneXpertAnalyzerImplementation.ANALYZER_TEST_MONO_PERCENT, "Monocytes (%)",
GeneXpertAnalyzerImplementation.LOINC_MONO_PERCENT));
nameMapping.add(
new PluginAnalyzerService.TestMapping(GeneXpertAnalyzerImplementation.ANALYZER_TEST_EO_COUNT, "Eosinophiles",
GeneXpertAnalyzerImplementation.LOINC_EO_COUNT));
nameMapping.add(
new PluginAnalyzerService.TestMapping(GeneXpertAnalyzerImplementation.ANALYZER_TEST_EO_PERCENT, "Eosinophiles (%)",
GeneXpertAnalyzerImplementation.LOINC_EO_PERCENT));
nameMapping.add(
new PluginAnalyzerService.TestMapping(GeneXpertAnalyzerImplementation.ANALYZER_TEST_BASO_COUNT, "Basophiles",
GeneXpertAnalyzerImplementation.LOINC_BASO_COUNT));
nameMapping.add(
new PluginAnalyzerService.TestMapping(GeneXpertAnalyzerImplementation.ANALYZER_TEST_BASO_PERCENT, "Basophiles (%)",
GeneXpertAnalyzerImplementation.LOINC_BASO_PERCENT));
nameMapping.add(
new PluginAnalyzerService.TestMapping(GeneXpertAnalyzerImplementation.ANALYZER_TEST_IG_COUNT, "",
GeneXpertAnalyzerImplementation.LOINC_IG_COUNT));
nameMapping.add(
new PluginAnalyzerService.TestMapping(GeneXpertAnalyzerImplementation.ANALYZER_TEST_IG_PERCENT, "",
GeneXpertAnalyzerImplementation.LOINC_IG_PERCENT));
nameMapping.add(
new PluginAnalyzerService.TestMapping(GeneXpertAnalyzerImplementation.COV_2, "COVID-19 PCR",
GeneXpertAnalyzerImplementation.COV_2_LOINC));
new PluginAnalyzerService.TestMapping(GeneXpertAnalyzerImplementation.ANALYZER_TEST_RET_COUNT, "",
GeneXpertAnalyzerImplementation.LOINC_RET_COUNT));
nameMapping.add(
new PluginAnalyzerService.TestMapping(GeneXpertAnalyzerImplementation.ANALYZER_TEST_RET_PERCENT, "",
GeneXpertAnalyzerImplementation.LOINC_RET_PERCENT));
nameMapping.add(
new PluginAnalyzerService.TestMapping(GeneXpertAnalyzerImplementation.ANALYZER_TEST_IRF, "",
GeneXpertAnalyzerImplementation.LOINC_IRF));
nameMapping.add(
new PluginAnalyzerService.TestMapping(GeneXpertAnalyzerImplementation.ANALYZER_TEST_RETHE, "",
GeneXpertAnalyzerImplementation.LOINC_RETHE));
nameMapping.add(
new PluginAnalyzerService.TestMapping(GeneXpertAnalyzerImplementation.ANALYZER_TEST_WBCBF, "",
GeneXpertAnalyzerImplementation.LOINC_WBCBF));
nameMapping.add(
new PluginAnalyzerService.TestMapping(GeneXpertAnalyzerImplementation.ANALYZER_TEST_RBCBF, "",
GeneXpertAnalyzerImplementation.LOINC_RBCBF));
nameMapping.add(
new PluginAnalyzerService.TestMapping(GeneXpertAnalyzerImplementation.ANALYZER_TEST_MN_COUNT, "",
GeneXpertAnalyzerImplementation.LOINC_MN_COUNT));
nameMapping.add(
new PluginAnalyzerService.TestMapping(GeneXpertAnalyzerImplementation.ANALYZER_TEST_MN_PERCENT, "",
GeneXpertAnalyzerImplementation.LOINC_MN_PERCENT));
nameMapping.add(
new PluginAnalyzerService.TestMapping(GeneXpertAnalyzerImplementation.ANALYZER_TEST_PMN_COUNT, "",
GeneXpertAnalyzerImplementation.LOINC_PMN_COUNT));
nameMapping.add(
new PluginAnalyzerService.TestMapping(GeneXpertAnalyzerImplementation.ANALYZER_TEST_PMN_PERCENT, "",
GeneXpertAnalyzerImplementation.LOINC_PMN_PERCENT));
nameMapping.add(
new PluginAnalyzerService.TestMapping(GeneXpertAnalyzerImplementation.ANALYZER_TEST_TCBF_COUNT, "",
GeneXpertAnalyzerImplementation.LOINC_TCBF_COUNT));
getInstance().addAnalyzerDatabaseParts("GeneXpertAnalyzer", "GeneXpertAnalyzer", nameMapping, true);
getInstance().registerAnalyzer(this);
return true;
}

@Override
// this plugin does not work for flat files, so we disable it in that workflow
public boolean isTargetAnalyzer(List<String> lines) {
for (String line : lines) {
if (line.startsWith(GeneXpertAnalyzerImplementation.HEADER_RECORD_IDENTIFIER)) {
String[] headerRecord = line.split(Pattern.quote(GeneXpertAnalyzerImplementation.FD));
if (headerRecord.length < 5) {
LogEvent.logTrace(this.getClass().getSimpleName(), "isTargetAnalyzer", "incoming message is not GeneXpert: header record not long enough");
return false;
}
String[] senderNameFields = headerRecord[4].split(Pattern.quote(GeneXpertAnalyzerImplementation.CD));
if (senderNameFields.length < 2) {
LogEvent.logTrace(this.getClass().getSimpleName(), "isTargetAnalyzer", "incoming message is not GeneXpert: sender name field not long enough");
return false;
}
String systemName = senderNameFields[1].trim();

LogEvent.logTrace(this.getClass().getSimpleName(), "isTargetAnalyzer", "incoming message analyzer name is " + systemName);
if (systemName.equalsIgnoreCase("GeneXpert")) {
LogEvent.logTrace(this.getClass().getSimpleName(), "isTargetAnalyzer", "incoming message is GeneXpert ");
return true;
}
LogEvent.logTrace(this.getClass().getSimpleName(), "isTargetAnalyzer", "incoming message is not GeneXpert: sender name doesn't match");
return false;
}
}
LogEvent.logTrace(this.getClass().getSimpleName(), "isTargetAnalyzer", "incoming message is not GeneXpert: no header line");
return false;
}

@Override
public boolean isAnalyzerResult(List<String> lines) {
for (String line : lines) {
if (line.startsWith(GeneXpertAnalyzerImplementation.RESULT_RECORD_IDENTIFIER)) {
return true;
}
}
LogEvent.logDebug(this.getClass().getSimpleName(), "isAnalyzerResult", "no result recoord identifier located");
return false;
}

Expand All @@ -61,4 +187,9 @@ public AnalyzerLineInserter getAnalyzerLineInserter() {
return new GeneXpertAnalyzerImplementation();
}

@Override
public AnalyzerResponder getAnalyzerResponder() {
return new GeneXpertAnalyzerImplementation();
}

}
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