Merge pull request #192 from nr23730/regexId

Regex
buschlab · Dec 17, 2021 · 94e60bf · 94e60bf
2 parents 78c1058 + d522b9a
commit 94e60bf
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Showing 4 changed files with 76 additions and 11 deletions.
diff --git a/src/main/java/fhirspark/JsonFhirMapper.java b/src/main/java/fhirspark/JsonFhirMapper.java
@@ -89,6 +89,7 @@ public class JsonFhirMapper {
     private static String patientUri;
     private static String therapyRecommendationUri;
     private static String mtbUri;
+    private static List<Regex> regex;
 
     private FhirContext ctx = FhirContext.forR4();
     private IGenericClient client;
@@ -113,6 +114,7 @@ public JsonFhirMapper(Settings settings) {
         patientUri = settings.getPatientSystem();
         mtbUri = settings.getDiagnosticReportSystem();
         therapyRecommendationUri = settings.getObservationSystem();
+        regex = settings.getRegex();
     }
 
     /**
@@ -171,7 +173,8 @@ public String toJson(String patientId) throws JsonProcessingException {
             // REBIOPSY HERE
             mtb.getSamples().clear();
             for (Reference specimen : diagnosticReport.getSpecimen()) {
-                mtb.getSamples().add(((Specimen) specimen.getResource()).getIdentifierFirstRep().getValue());
+                mtb.getSamples().add(
+                        applyRegexToCbioportal(((Specimen) specimen.getResource()).getIdentifierFirstRep().getValue()));
             }
 
             for (Reference reference : diagnosticReport.getResult()) {
@@ -204,7 +207,7 @@ public String toJson(String patientId) throws JsonProcessingException {
                             ClinicalDatum cd = new ClinicalDatum().withAttributeName(attr[0]).withValue(attr[1]);
                             if (obs.getSpecimen().getResource() != null) {
                                 Specimen specimen = (Specimen) obs.getSpecimen().getResource();
-                                cd.setSampleId(specimen.getIdentifierFirstRep().getValue());
+                                cd.setSampleId(applyRegexToCbioportal(specimen.getIdentifierFirstRep().getValue()));
                             }
                             therapyRecommendation.getReasoning().getClinicalData()
                                     .add(cd);
@@ -417,10 +420,11 @@ public void addOrEditMtb(String patientId, List<Mtb> mtbs) throws DataFormatExce
             }
 
             mtb.getSamples().forEach(sample -> {
-                Specimen s = specimenAdapter.process(fhirPatient, sample);
+                String sampleId = applyRegexFromCbioportal(sample);
+                Specimen s = specimenAdapter.process(fhirPatient, sampleId);
                 bundle.addEntry().setFullUrl(s.getIdElement().getValue()).setResource(s)
-                        .getRequest().setUrl("Specimen?identifier=https://cbioportal.org/specimen/|" + sample)
-                        .setIfNoneExist("identifier=identifier=https://cbioportal.org/specimen/|" + sample)
+                        .getRequest().setUrl("Specimen?identifier=https://cbioportal.org/specimen/|" + sampleId)
+                        .setIfNoneExist("identifier=identifier=https://cbioportal.org/specimen/|" + sampleId)
                         .setMethod(Bundle.HTTPVerb.PUT);
                 diagnosticReport.addSpecimen(new Reference(s));
             });
@@ -461,12 +465,13 @@ public void addOrEditMtb(String patientId, List<Mtb> mtbs) throws DataFormatExce
                     therapyRecommendation.getReasoning().getClinicalData().forEach(clinical -> {
                         Specimen s = null;
                         if (clinical.getSampleId() != null && clinical.getSampleId().length() > 0) {
-                            s = specimenAdapter.process(fhirPatient, clinical.getSampleId());
+                            String sampleId = applyRegexFromCbioportal(clinical.getSampleId());
+                            s = specimenAdapter.process(fhirPatient, sampleId);
                             bundle.addEntry().setFullUrl(s.getIdElement().getValue()).setResource(s)
                                 .getRequest().setUrl("Specimen?identifier=https://cbioportal.org/specimen/|"
-                                        + clinical.getSampleId())
+                                        + sampleId)
                                 .setIfNoneExist("identifier=identifier=https://cbioportal.org/specimen/|"
-                                        + clinical.getSampleId()).setMethod(Bundle.HTTPVerb.PUT);
+                                        + sampleId).setMethod(Bundle.HTTPVerb.PUT);
                         }
                         try {
                             Method m = Class.forName("fhirspark.adapter.clinicaldata." + clinical.getAttributeId())
@@ -643,6 +648,22 @@ private String harmonizeId(IAnyResource resource) {
         }
     }
 
+    private String applyRegexToCbioportal(String input) {
+        String output = input;
+        for (Regex r : regex) {
+            output = output.replaceAll(r.getHis(), r.getCbio());
+        }
+        return output;
+    }
+
+    private String applyRegexFromCbioportal(String input) {
+        String output = input;
+        for (Regex r : regex) {
+            output = output.replaceAll(r.getCbio(), r.getHis());
+        }
+        return output;
+    }
+
     /**
      * Fetched Pubmed IDs that have been previously associated with the same alteration.
      *

diff --git a/src/main/java/fhirspark/Regex.java b/src/main/java/fhirspark/Regex.java
@@ -0,0 +1,27 @@
+package fhirspark;
+
+/**
+ * Regular expressions to convert cBioPortal IDs to HIS IDs.
+ */
+public class Regex {
+
+    private String cbio;
+    private String his;
+
+    public String getCbio() {
+        return cbio;
+    }
+
+    public void setCbio(String cbio) {
+        this.cbio = cbio;
+    }
+
+    public String getHis() {
+        return his;
+    }
+
+    public void setHis(String his) {
+        this.his = his;
+    }
+
+}
diff --git a/src/main/java/fhirspark/Settings.java b/src/main/java/fhirspark/Settings.java
@@ -21,7 +21,8 @@
     "portalUrl",
     "loginRequired",
     "oncokbPath",
-    "hl7v2config"
+    "hl7v2config",
+    "regex"
 })
 public final class Settings {
 
@@ -47,6 +48,8 @@ public final class Settings {
     private String oncokbPath;
     @JsonProperty("hl7v2config")
     private List<Hl7v2config> hl7v2config;
+    @JsonProperty("regex")
+    private List<Regex> regex;
 
     @JsonProperty("port")
     public Integer getPort() {
@@ -158,4 +161,14 @@ public void setHl7v2config(List<Hl7v2config> hl7v2config) {
         this.hl7v2config = hl7v2config;
     }
 
+    @JsonProperty("regex")
+    public List<Regex> getRegex() {
+        return regex;
+    }
+
+    @JsonProperty("regex")
+    public void setRegex(List<Regex> newRegex) {
+        regex = newRegex;
+    }
+
 }
diff --git a/src/main/resources/settings.yaml b/src/main/resources/settings.yaml
@@ -4,11 +4,15 @@ specimenSystem: ${FHIRSPARK_SPECIMENSYSTEM:-https://cbioportal.org/specimen/}
 diagnosticReportSystem: ${FHIRSPARK_DIAGNOSTICREPORTSYSTEM:-https://cbioportal.org/mtb/}
 observationSystem: ${FHIRSPARK_OBSERVATIONSYSTEM:-https://cbioportal.org/therapyrecommendation/}
 patientSystem: ${FHIRSPARK_PATIENTSYSTEM:-https://cbioportal.org/patient/}
-portalUrl: ${FHIRSPARK_PORTALURL:-http://cbioportal/}
-loginRequired: ${FHIRSPARK_LOGINREQUIRED:-true}
+portalUrl: ${FHIRSPARK_PORTALURL:-http://localhost:8080/}
+loginRequired: ${FHIRSPARK_LOGINREQUIRED:-false}
 hgncPath: ${FHIRSPARK_HGNCPATH:-hgnc.csv}
 oncokbPath: ${FHIRSPARK_ONCOKBPATH:-drugs.json}
 hl7v2config:
  - sendv2: ${FHIRSPARK_SENDHL7V2:-false}
    server: ${FHIRSPARK_HL7V2SERVER:-localhost}
    port: ${FHIRSPARK_HL7V2PORT:-1011}
+regex:
+  -
+    cbio: ${FHIRSPARK_REGEX_CBIO:-/}
+    his: ${FHIRSPARK_REGEX_HIS:-/}