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improve ASTM analyzers #28

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merged 6 commits into from
Jun 14, 2024
Merged

improve ASTM analyzers #28

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4cd630a
add ability for returning results
CalebSLane Apr 15, 2024
a18c5ea
specify java version
CalebSLane Apr 24, 2024
b93a71c
move geneXpert to an ASTM approach but keep old files in case
CalebSLane Jun 14, 2024
c227043
modify sysmex analyzers under development
CalebSLane Jun 14, 2024
0f79b28
add pocH-100i analyzer
CalebSLane Jun 14, 2024
4947d09
fix lib path for github action build
CalebSLane Jun 14, 2024
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5 changes: 5 additions & 0 deletions analyzers/GeneXpert/.vscode/settings.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
{
"java.project.sourcePaths": [
"src/main/java"
]
}
15 changes: 5 additions & 10 deletions analyzers/GeneXpert/pom.xml
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Original file line number Diff line number Diff line change
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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