FIx #1649 - Account for LOINC file format changes in 2.67
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@ -57,6 +57,10 @@
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title: "Several misleading comments in documentation code snippets were fixed. Thanks to
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Jafer Khan for the pull request!"
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- item:
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issue: "1603"
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type: "fix"
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title: "The client threw a NullPointerException in some circumstances when it received an HTTP 201 No Content response from the server. This has been corrected. Thanks to Petro Mykhailysyn for the pull request!"
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issue: "1603"
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type: "fix"
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title: "The client threw a NullPointerException in some circumstances when it received an HTTP 201 No Content response from the server. This has been corrected. Thanks to Petro Mykhailysyn for the pull request!"
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- item:
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issue: "1649"
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type: "add"
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title: "Support for LOINC 2.67 file format changes has been added to the JPA Server LOINC uploader. Thanks to Dan Vreeman for reporting!"
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@ -21,8 +21,8 @@ package ca.uhn.fhir.jpa.term.loinc;
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*/
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import ca.uhn.fhir.jpa.entity.TermConcept;
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import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
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import ca.uhn.fhir.jpa.term.IRecordHandler;
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import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
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import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
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import org.apache.commons.csv.CSVRecord;
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import org.hl7.fhir.r4.model.ConceptMap;
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@ -40,16 +40,13 @@ public class LoincPartRelatedCodeMappingHandler extends BaseLoincHandler impleme
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public static final String LOINC_SCT_PART_MAP_ID = "loinc-parts-to-snomed-ct";
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public static final String LOINC_SCT_PART_MAP_URI = "http://loinc.org/cm/loinc-parts-to-snomed-ct";
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private static final String LOINC_SCT_PART_MAP_NAME = "LOINC Part Map to SNOMED CT";
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public static final String LOINC_TERM_TO_RPID_PART_MAP_ID = "loinc-to-rpids";
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public static final String LOINC_TERM_TO_RPID_PART_MAP_URI = "http://loinc.org/cm/loinc-to-rpids";
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public static final String LOINC_TERM_TO_RPID_PART_MAP_NAME = "LOINC Terms to RadLex RPIDs";
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public static final String LOINC_PART_TO_RID_PART_MAP_ID = "loinc-part-to-rids";
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public static final String LOINC_PART_TO_RID_PART_MAP_URI = "http://loinc.org/cm/loinc-part-to-rids";
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public static final String LOINC_PART_TO_RID_PART_MAP_NAME = "LOINC Parts to RadLex RIDs";
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private static final String LOINC_SCT_PART_MAP_NAME = "LOINC Part Map to SNOMED CT";
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private static final String LOINC_RXNORM_PART_MAP_ID = "loinc-parts-to-rxnorm";
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private static final String LOINC_RXNORM_PART_MAP_URI = "http://loinc.org/cm/loinc-parts-to-rxnorm";
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private static final String LOINC_RXNORM_PART_MAP_NAME = "LOINC Part Map to RxNORM";
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@ -69,28 +66,26 @@ public class LoincPartRelatedCodeMappingHandler extends BaseLoincHandler impleme
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String partNumber = trim(theRecord.get("PartNumber"));
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String partName = trim(theRecord.get("PartName"));
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String partTypeName = trim(theRecord.get("PartTypeName"));
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String extCodeId = trim(theRecord.get("ExtCodeId"));
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// TODO: use hex code for ascii 160
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extCodeId = extCodeId.replace(" ", "");
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String extCodeDisplayName = trim(theRecord.get("ExtCodeDisplayName"));
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String extCodeSystem = trim(theRecord.get("ExtCodeSystem"));
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String mapType = trim(theRecord.get("MapType"));
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String contentOrigin = trim(theRecord.get("ContentOrigin"));
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String mapType = trim(theRecord.get("Equivalence"));
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String extCodeSystemVersion = trim(theRecord.get("ExtCodeSystemVersion"));
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String extCodeSystemCopyrightNotice = trim(theRecord.get("ExtCodeSystemCopyrightNotice"));
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Enumerations.ConceptMapEquivalence equivalence;
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switch (trim(defaultString(mapType))) {
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case "":
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case "Exact":
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case "equivalent":
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// 'equal' is more exact than 'equivalent' in the equivalence codes
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equivalence = Enumerations.ConceptMapEquivalence.EQUAL;
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break;
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case "LOINC broader":
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case "narrower":
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equivalence = Enumerations.ConceptMapEquivalence.NARROWER;
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break;
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case "LOINC narrower":
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case "wider":
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equivalence = Enumerations.ConceptMapEquivalence.WIDER;
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break;
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default:
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