diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcImpl.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcImpl.java index 0f53d6688323..e5cc259c77eb 100644 --- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcImpl.java +++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcImpl.java @@ -62,18 +62,18 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc { public static final String SCT_FILE_CONCEPT = "Terminology/sct2_Concept_Full_"; public static final String SCT_FILE_DESCRIPTION = "Terminology/sct2_Description_Full-en"; public static final String SCT_FILE_RELATIONSHIP = "Terminology/sct2_Relationship_Full"; - public static final String LOINC_ANSWERLIST_FILE = "AnswerList_Beta_1.csv"; - public static final String LOINC_ANSWERLIST_LINK_FILE = "LoincAnswerListLink_Beta_1.csv"; + public static final String LOINC_ANSWERLIST_FILE = "AnswerList.csv"; + public static final String LOINC_ANSWERLIST_LINK_FILE = "LoincAnswerListLink.csv"; public static final String LOINC_DOCUMENT_ONTOLOGY_FILE = "DocumentOntology.csv"; public static final String LOINC_UPLOAD_PROPERTIES_FILE = "loincupload.properties"; - public static final String LOINC_FILE = "loinc.csv"; - public static final String LOINC_HIERARCHY_FILE = "MULTI-AXIAL_HIERARCHY.CSV"; - public static final String LOINC_PART_FILE = "Part_Beta_1.csv"; - public static final String LOINC_PART_LINK_FILE = "LoincPartLink_Beta_1.csv"; - public static final String LOINC_PART_RELATED_CODE_MAPPING_FILE = "PartRelatedCodeMapping_Beta_1.csv"; + public static final String LOINC_FILE = "Loinc.csv"; + public static final String LOINC_HIERARCHY_FILE = "MultiAxialHierarchy.csv"; + public static final String LOINC_PART_FILE = "Part.csv"; + public static final String LOINC_PART_LINK_FILE = "LoincPartLink.csv"; + public static final String LOINC_PART_RELATED_CODE_MAPPING_FILE = "PartRelatedCodeMapping.csv"; public static final String LOINC_RSNA_PLAYBOOK_FILE = "LoincRsnaRadiologyPlaybook.csv"; - public static final String LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE = "Top2000CommonLabResultsUS.csv"; - public static final String LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE = "Top2000CommonLabResultsSI.csv"; + public static final String LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE = "Top2000CommonLabResultsUs.csv"; + public static final String LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE = "Top2000CommonLabResultsSi.csv"; public static final String LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE = "LoincUniversalLabOrdersValueSet.csv"; public static final String LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_CSV = "LoincIeeeMedicalDeviceCodeMappingTable.csv"; public static final String LOINC_IMAGING_DOCUMENT_CODES_FILE = "ImagingDocumentCodes.csv"; diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/TerminologyUploaderProviderDstu3Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/TerminologyUploaderProviderDstu3Test.java index 60b94ec3d2c4..052af9d5d9bc 100644 --- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/TerminologyUploaderProviderDstu3Test.java +++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/TerminologyUploaderProviderDstu3Test.java @@ -37,10 +37,10 @@ private byte[] createLoincZip() throws IOException { ByteArrayOutputStream bos = new ByteArrayOutputStream(); ZipOutputStream zos = new ZipOutputStream(bos); - zos.putNextEntry(new ZipEntry("loinc.csv")); - zos.write(IOUtils.toByteArray(getClass().getResourceAsStream("/loinc/loinc.csv"))); - zos.putNextEntry(new ZipEntry("LOINC_2.54_MULTI-AXIAL_HIERARCHY.CSV")); - zos.write(IOUtils.toByteArray(getClass().getResourceAsStream("/loinc/LOINC_2.54_MULTI-AXIAL_HIERARCHY.CSV"))); + zos.putNextEntry(new ZipEntry("Loinc.csv")); + zos.write(IOUtils.toByteArray(getClass().getResourceAsStream("/loinc/Loinc.csv"))); + zos.putNextEntry(new ZipEntry("MultiAxialHierarchy.csv")); + zos.write(IOUtils.toByteArray(getClass().getResourceAsStream("/loinc/MultiAxialHierarchy.csv"))); zos.close(); byte[] packageBytes = bos.toByteArray(); diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/TerminologyUploaderProviderR4Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/TerminologyUploaderProviderR4Test.java index b732bf868005..560b3b082db6 100644 --- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/TerminologyUploaderProviderR4Test.java +++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/TerminologyUploaderProviderR4Test.java @@ -29,10 +29,10 @@ private byte[] createLoincZip() throws IOException { ByteArrayOutputStream bos = new ByteArrayOutputStream(); ZipOutputStream zos = new ZipOutputStream(bos); - zos.putNextEntry(new ZipEntry("loinc.csv")); - zos.write(IOUtils.toByteArray(getClass().getResourceAsStream("/loinc/loinc.csv"))); - zos.putNextEntry(new ZipEntry("LOINC_2.54_MULTI-AXIAL_HIERARCHY.CSV")); - zos.write(IOUtils.toByteArray(getClass().getResourceAsStream("/loinc/LOINC_2.54_MULTI-AXIAL_HIERARCHY.CSV"))); + zos.putNextEntry(new ZipEntry("Loinc.csv")); + zos.write(IOUtils.toByteArray(getClass().getResourceAsStream("/loinc/Loinc.csv"))); + zos.putNextEntry(new ZipEntry("MultiAxialHierarchy.csv")); + zos.write(IOUtils.toByteArray(getClass().getResourceAsStream("/loinc/MultiAxialHierarchy.csv"))); zos.close(); byte[] packageBytes = bos.toByteArray(); diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcLoincTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcLoincTest.java index d98f7a9f0ae0..20fd44822a3f 100644 --- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcLoincTest.java +++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcLoincTest.java @@ -341,19 +341,19 @@ public void testLoadLoincMissingMandatoryFiles() throws IOException { mySvc.loadLoinc(myFiles.getFiles(), details); fail(); } catch (UnprocessableEntityException e) { - assertEquals("Could not find the following mandatory files in input: [loinc.csv, MULTI-AXIAL_HIERARCHY.CSV]", e.getMessage()); + assertEquals("Could not find the following mandatory files in input: [Loinc.csv, MultiAxialHierarchy.csv]", e.getMessage()); } } static void addLoincMandatoryFilesToZip(ZipCollectionBuilder theFiles) throws IOException { - theFiles.addFileZip("/loinc/", "loinc.csv", TerminologyLoaderSvcImpl.LOINC_FILE); - theFiles.addFileZip("/loinc/", "hierarchy.csv", TerminologyLoaderSvcImpl.LOINC_HIERARCHY_FILE); + theFiles.addFileZip("/loinc/", "Loinc.csv", TerminologyLoaderSvcImpl.LOINC_FILE); + theFiles.addFileZip("/loinc/", "MultiAxialHierarchy.csv", TerminologyLoaderSvcImpl.LOINC_HIERARCHY_FILE); } static void addLoincOptionalFilesToZip(ZipCollectionBuilder theFiles) throws IOException { theFiles.addFileZip("/loinc/", "loincupload.properties"); - theFiles.addFileZip("/loinc/", "AnswerList_Beta_1.csv", TerminologyLoaderSvcImpl.LOINC_ANSWERLIST_FILE); + theFiles.addFileZip("/loinc/", "AnswerList.csv", TerminologyLoaderSvcImpl.LOINC_ANSWERLIST_FILE); theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_ANSWERLIST_LINK_FILE, TerminologyLoaderSvcImpl.LOINC_ANSWERLIST_LINK_FILE); theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_PART_FILE, TerminologyLoaderSvcImpl.LOINC_PART_FILE); theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_PART_LINK_FILE, TerminologyLoaderSvcImpl.LOINC_PART_LINK_FILE); @@ -368,8 +368,8 @@ static void addLoincOptionalFilesToZip(ZipCollectionBuilder theFiles) throws IOE * Top 2000 files have versions in the filename so don't use the * constant.. that way this is a better test */ - theFiles.addFilePlain("/loinc/", "LOINC_1.6_Top2000CommonLabResultsSI.csv"); - theFiles.addFilePlain("/loinc/", "LOINC_1.6_Top2000CommonLabResultsUS.csv"); + theFiles.addFilePlain("/loinc/", "Top2000CommonLabResultsSi.csv"); + theFiles.addFilePlain("/loinc/", "Top2000CommonLabResultsUs.csv"); } @AfterClass diff --git a/hapi-fhir-jpaserver-base/src/test/resources/loinc/AnswerList_Beta_1.csv b/hapi-fhir-jpaserver-base/src/test/resources/loinc/AnswerList.csv similarity index 100% rename from hapi-fhir-jpaserver-base/src/test/resources/loinc/AnswerList_Beta_1.csv rename to hapi-fhir-jpaserver-base/src/test/resources/loinc/AnswerList.csv diff --git a/hapi-fhir-jpaserver-base/src/test/resources/loinc/loinc.csv b/hapi-fhir-jpaserver-base/src/test/resources/loinc/Loinc.csv similarity index 100% rename from hapi-fhir-jpaserver-base/src/test/resources/loinc/loinc.csv rename to hapi-fhir-jpaserver-base/src/test/resources/loinc/Loinc.csv diff --git a/hapi-fhir-jpaserver-base/src/test/resources/loinc/LoincAnswerListLink_Beta_1.csv b/hapi-fhir-jpaserver-base/src/test/resources/loinc/LoincAnswerListLink.csv similarity index 100% rename from hapi-fhir-jpaserver-base/src/test/resources/loinc/LoincAnswerListLink_Beta_1.csv rename to hapi-fhir-jpaserver-base/src/test/resources/loinc/LoincAnswerListLink.csv diff --git a/hapi-fhir-jpaserver-base/src/test/resources/loinc/LoincPartLink_Beta_1.csv b/hapi-fhir-jpaserver-base/src/test/resources/loinc/LoincPartLink.csv similarity index 100% rename from hapi-fhir-jpaserver-base/src/test/resources/loinc/LoincPartLink_Beta_1.csv rename to hapi-fhir-jpaserver-base/src/test/resources/loinc/LoincPartLink.csv diff --git a/hapi-fhir-jpaserver-base/src/test/resources/loinc/LOINC_2.54_MULTI-AXIAL_HIERARCHY.CSV b/hapi-fhir-jpaserver-base/src/test/resources/loinc/MultiAxialHierarchy.csv similarity index 100% rename from hapi-fhir-jpaserver-base/src/test/resources/loinc/LOINC_2.54_MULTI-AXIAL_HIERARCHY.CSV rename to hapi-fhir-jpaserver-base/src/test/resources/loinc/MultiAxialHierarchy.csv diff --git a/hapi-fhir-jpaserver-base/src/test/resources/loinc/Part_Beta_1.csv b/hapi-fhir-jpaserver-base/src/test/resources/loinc/Part.csv similarity index 100% rename from hapi-fhir-jpaserver-base/src/test/resources/loinc/Part_Beta_1.csv rename to hapi-fhir-jpaserver-base/src/test/resources/loinc/Part.csv diff --git a/hapi-fhir-jpaserver-base/src/test/resources/loinc/PartRelatedCodeMapping_Beta_1.csv b/hapi-fhir-jpaserver-base/src/test/resources/loinc/PartRelatedCodeMapping.csv similarity index 100% rename from hapi-fhir-jpaserver-base/src/test/resources/loinc/PartRelatedCodeMapping_Beta_1.csv rename to hapi-fhir-jpaserver-base/src/test/resources/loinc/PartRelatedCodeMapping.csv diff --git a/hapi-fhir-jpaserver-base/src/test/resources/loinc/LOINC_1.6_Top2000CommonLabResultsSI.csv b/hapi-fhir-jpaserver-base/src/test/resources/loinc/Top2000CommonLabResultsSi.csv similarity index 100% rename from hapi-fhir-jpaserver-base/src/test/resources/loinc/LOINC_1.6_Top2000CommonLabResultsSI.csv rename to hapi-fhir-jpaserver-base/src/test/resources/loinc/Top2000CommonLabResultsSi.csv diff --git a/hapi-fhir-jpaserver-base/src/test/resources/loinc/LOINC_1.6_Top2000CommonLabResultsUS.csv b/hapi-fhir-jpaserver-base/src/test/resources/loinc/Top2000CommonLabResultsUs.csv similarity index 100% rename from hapi-fhir-jpaserver-base/src/test/resources/loinc/LOINC_1.6_Top2000CommonLabResultsUS.csv rename to hapi-fhir-jpaserver-base/src/test/resources/loinc/Top2000CommonLabResultsUs.csv diff --git a/hapi-fhir-jpaserver-base/src/test/resources/loinc/hierarchy.csv b/hapi-fhir-jpaserver-base/src/test/resources/loinc/hierarchy.csv deleted file mode 100644 index d7bd6d54884c..000000000000 --- a/hapi-fhir-jpaserver-base/src/test/resources/loinc/hierarchy.csv +++ /dev/null @@ -1,10 +0,0 @@ -PATH_TO_ROOT,SEQUENCE,IMMEDIATE_PARENT,CODE,CODE_TEXT -,1,,LP31755-9,Microbiology -LP31755-9,1,LP31755-9,LP14559-6,Microorganism -LP31755-9.LP14559-6,1,LP14559-6,LP98185-9,Bacteria -LP31755-9.LP14559-6.LP98185-9,1,LP98185-9,LP14082-9,Bacteria -LP31755-9.LP14559-6.LP98185-9.LP14082-9,1,LP14082-9,LP52258-8,Bacteria | Body Fluid -LP31755-9.LP14559-6.LP98185-9.LP14082-9.LP52258-8,1,LP52258-8,41599-2,Bacteria Fld Ql Micro -LP31755-9.LP14559-6.LP98185-9.LP14082-9,2,LP14082-9,LP52260-4,Bacteria | Cerebral spinal fluid -LP31755-9.LP14559-6.LP98185-9.LP14082-9.LP52260-4,1,LP52260-4,41602-4,Bacteria CSF Ql Micro -LP31755-9.LP14559-6.LP98185-9.LP14082-9,3,LP14082-9,LP52960-9,Bacteria | Cervix