Merge pull request #1000 from rhausam/update-filenames
Updated LOINC filenames to match 2.64 and future releases.
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commit
e63604afc9
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@ -62,18 +62,18 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
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public static final String SCT_FILE_CONCEPT = "Terminology/sct2_Concept_Full_";
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public static final String SCT_FILE_DESCRIPTION = "Terminology/sct2_Description_Full-en";
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public static final String SCT_FILE_RELATIONSHIP = "Terminology/sct2_Relationship_Full";
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public static final String LOINC_ANSWERLIST_FILE = "AnswerList_Beta_1.csv";
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public static final String LOINC_ANSWERLIST_LINK_FILE = "LoincAnswerListLink_Beta_1.csv";
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public static final String LOINC_ANSWERLIST_FILE = "AnswerList.csv";
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public static final String LOINC_ANSWERLIST_LINK_FILE = "LoincAnswerListLink.csv";
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public static final String LOINC_DOCUMENT_ONTOLOGY_FILE = "DocumentOntology.csv";
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public static final String LOINC_UPLOAD_PROPERTIES_FILE = "loincupload.properties";
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public static final String LOINC_FILE = "loinc.csv";
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public static final String LOINC_HIERARCHY_FILE = "MULTI-AXIAL_HIERARCHY.CSV";
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public static final String LOINC_PART_FILE = "Part_Beta_1.csv";
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public static final String LOINC_PART_LINK_FILE = "LoincPartLink_Beta_1.csv";
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public static final String LOINC_PART_RELATED_CODE_MAPPING_FILE = "PartRelatedCodeMapping_Beta_1.csv";
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public static final String LOINC_FILE = "Loinc.csv";
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public static final String LOINC_HIERARCHY_FILE = "MultiAxialHierarchy.csv";
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public static final String LOINC_PART_FILE = "Part.csv";
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public static final String LOINC_PART_LINK_FILE = "LoincPartLink.csv";
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public static final String LOINC_PART_RELATED_CODE_MAPPING_FILE = "PartRelatedCodeMapping.csv";
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public static final String LOINC_RSNA_PLAYBOOK_FILE = "LoincRsnaRadiologyPlaybook.csv";
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public static final String LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE = "Top2000CommonLabResultsUS.csv";
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public static final String LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE = "Top2000CommonLabResultsSI.csv";
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public static final String LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE = "Top2000CommonLabResultsUs.csv";
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public static final String LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE = "Top2000CommonLabResultsSi.csv";
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public static final String LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE = "LoincUniversalLabOrdersValueSet.csv";
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public static final String LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_CSV = "LoincIeeeMedicalDeviceCodeMappingTable.csv";
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public static final String LOINC_IMAGING_DOCUMENT_CODES_FILE = "ImagingDocumentCodes.csv";
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@ -37,10 +37,10 @@ public class TerminologyUploaderProviderDstu3Test extends BaseResourceProviderDs
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ByteArrayOutputStream bos = new ByteArrayOutputStream();
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ZipOutputStream zos = new ZipOutputStream(bos);
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zos.putNextEntry(new ZipEntry("loinc.csv"));
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zos.write(IOUtils.toByteArray(getClass().getResourceAsStream("/loinc/loinc.csv")));
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zos.putNextEntry(new ZipEntry("LOINC_2.54_MULTI-AXIAL_HIERARCHY.CSV"));
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zos.write(IOUtils.toByteArray(getClass().getResourceAsStream("/loinc/LOINC_2.54_MULTI-AXIAL_HIERARCHY.CSV")));
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zos.putNextEntry(new ZipEntry("Loinc.csv"));
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zos.write(IOUtils.toByteArray(getClass().getResourceAsStream("/loinc/Loinc.csv")));
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zos.putNextEntry(new ZipEntry("MultiAxialHierarchy.csv"));
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zos.write(IOUtils.toByteArray(getClass().getResourceAsStream("/loinc/MultiAxialHierarchy.csv")));
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zos.close();
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byte[] packageBytes = bos.toByteArray();
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@ -29,10 +29,10 @@ public class TerminologyUploaderProviderR4Test extends BaseResourceProviderR4Tes
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ByteArrayOutputStream bos = new ByteArrayOutputStream();
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ZipOutputStream zos = new ZipOutputStream(bos);
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zos.putNextEntry(new ZipEntry("loinc.csv"));
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zos.write(IOUtils.toByteArray(getClass().getResourceAsStream("/loinc/loinc.csv")));
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zos.putNextEntry(new ZipEntry("LOINC_2.54_MULTI-AXIAL_HIERARCHY.CSV"));
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zos.write(IOUtils.toByteArray(getClass().getResourceAsStream("/loinc/LOINC_2.54_MULTI-AXIAL_HIERARCHY.CSV")));
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zos.putNextEntry(new ZipEntry("Loinc.csv"));
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zos.write(IOUtils.toByteArray(getClass().getResourceAsStream("/loinc/Loinc.csv")));
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zos.putNextEntry(new ZipEntry("MultiAxialHierarchy.csv"));
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zos.write(IOUtils.toByteArray(getClass().getResourceAsStream("/loinc/MultiAxialHierarchy.csv")));
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zos.close();
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byte[] packageBytes = bos.toByteArray();
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@ -341,19 +341,19 @@ public class TerminologyLoaderSvcLoincTest {
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mySvc.loadLoinc(myFiles.getFiles(), details);
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fail();
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} catch (UnprocessableEntityException e) {
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assertEquals("Could not find the following mandatory files in input: [loinc.csv, MULTI-AXIAL_HIERARCHY.CSV]", e.getMessage());
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assertEquals("Could not find the following mandatory files in input: [Loinc.csv, MultiAxialHierarchy.csv]", e.getMessage());
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}
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}
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static void addLoincMandatoryFilesToZip(ZipCollectionBuilder theFiles) throws IOException {
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theFiles.addFileZip("/loinc/", "loinc.csv", TerminologyLoaderSvcImpl.LOINC_FILE);
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theFiles.addFileZip("/loinc/", "hierarchy.csv", TerminologyLoaderSvcImpl.LOINC_HIERARCHY_FILE);
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theFiles.addFileZip("/loinc/", "Loinc.csv", TerminologyLoaderSvcImpl.LOINC_FILE);
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theFiles.addFileZip("/loinc/", "MultiAxialHierarchy.csv", TerminologyLoaderSvcImpl.LOINC_HIERARCHY_FILE);
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}
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static void addLoincOptionalFilesToZip(ZipCollectionBuilder theFiles) throws IOException {
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theFiles.addFileZip("/loinc/", "loincupload.properties");
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theFiles.addFileZip("/loinc/", "AnswerList_Beta_1.csv", TerminologyLoaderSvcImpl.LOINC_ANSWERLIST_FILE);
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theFiles.addFileZip("/loinc/", "AnswerList.csv", TerminologyLoaderSvcImpl.LOINC_ANSWERLIST_FILE);
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theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_ANSWERLIST_LINK_FILE, TerminologyLoaderSvcImpl.LOINC_ANSWERLIST_LINK_FILE);
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theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_PART_FILE, TerminologyLoaderSvcImpl.LOINC_PART_FILE);
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theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_PART_LINK_FILE, TerminologyLoaderSvcImpl.LOINC_PART_LINK_FILE);
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@ -368,8 +368,8 @@ public class TerminologyLoaderSvcLoincTest {
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* Top 2000 files have versions in the filename so don't use the
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* constant.. that way this is a better test
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*/
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theFiles.addFilePlain("/loinc/", "LOINC_1.6_Top2000CommonLabResultsSI.csv");
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theFiles.addFilePlain("/loinc/", "LOINC_1.6_Top2000CommonLabResultsUS.csv");
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theFiles.addFilePlain("/loinc/", "Top2000CommonLabResultsSi.csv");
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theFiles.addFilePlain("/loinc/", "Top2000CommonLabResultsUs.csv");
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}
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@AfterClass
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Can't render this file because it contains an unexpected character in line 1 and column 31.
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Can't render this file because it contains an unexpected character in line 1 and column 23.
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Can't render this file because it contains an unexpected character in line 1 and column 30.
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@ -1,10 +0,0 @@
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PATH_TO_ROOT,SEQUENCE,IMMEDIATE_PARENT,CODE,CODE_TEXT
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,1,,LP31755-9,Microbiology
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LP31755-9,1,LP31755-9,LP14559-6,Microorganism
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LP31755-9.LP14559-6,1,LP14559-6,LP98185-9,Bacteria
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LP31755-9.LP14559-6.LP98185-9,1,LP98185-9,LP14082-9,Bacteria
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LP31755-9.LP14559-6.LP98185-9.LP14082-9,1,LP14082-9,LP52258-8,Bacteria | Body Fluid
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LP31755-9.LP14559-6.LP98185-9.LP14082-9.LP52258-8,1,LP52258-8,41599-2,Bacteria Fld Ql Micro
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LP31755-9.LP14559-6.LP98185-9.LP14082-9,2,LP14082-9,LP52260-4,Bacteria | Cerebral spinal fluid
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LP31755-9.LP14559-6.LP98185-9.LP14082-9.LP52260-4,1,LP52260-4,41602-4,Bacteria CSF Ql Micro
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LP31755-9.LP14559-6.LP98185-9.LP14082-9,3,LP14082-9,LP52960-9,Bacteria | Cervix
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