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Merge pull request #1000 from rhausam/update-filenames 

Updated LOINC filenames to match 2.64 and future releases.
This commit is contained in:
James Agnew 2018-06-21 10:18:36 -04:00 committed by GitHub
parent 32e1feb484 215e224e3d
commit e63604afc9
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GPG Key ID: 4AEE18F83AFDEB23
14 changed files with 23 additions and 33 deletions
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18
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcImpl.java
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@ -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";

8
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/TerminologyUploaderProviderDstu3Test.java
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@ -37,10 +37,10 @@ public class TerminologyUploaderProviderDstu3Test extends BaseResourceProviderDs
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();

8
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/TerminologyUploaderProviderR4Test.java
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@ -29,10 +29,10 @@ public class TerminologyUploaderProviderR4Test extends BaseResourceProviderR4Tes
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();

12
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcLoincTest.java
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@ -341,19 +341,19 @@ public class TerminologyLoaderSvcLoincTest {
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 @@ public class TerminologyLoaderSvcLoincTest {
* 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

0
hapi-fhir-jpaserver-base/src/test/resources/loinc/AnswerList_Beta_1.csv → hapi-fhir-jpaserver-base/src/test/resources/loinc/AnswerList.csv
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Can't render this file because it contains an unexpected character in line 1 and column 31.

0
hapi-fhir-jpaserver-base/src/test/resources/loinc/loinc.csv → hapi-fhir-jpaserver-base/src/test/resources/loinc/Loinc.csv
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Can't render this file because it contains an unexpected character in line 1 and column 23.

0
hapi-fhir-jpaserver-base/src/test/resources/loinc/LoincAnswerListLink_Beta_1.csv → hapi-fhir-jpaserver-base/src/test/resources/loinc/LoincAnswerListLink.csv
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Can't render this file because it contains an unexpected character in line 1 and column 30.

0
hapi-fhir-jpaserver-base/src/test/resources/loinc/LoincPartLink_Beta_1.csv → hapi-fhir-jpaserver-base/src/test/resources/loinc/LoincPartLink.csv
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0
hapi-fhir-jpaserver-base/src/test/resources/loinc/LOINC_2.54_MULTI-AXIAL_HIERARCHY.CSV → hapi-fhir-jpaserver-base/src/test/resources/loinc/MultiAxialHierarchy.csv
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0
hapi-fhir-jpaserver-base/src/test/resources/loinc/Part_Beta_1.csv → hapi-fhir-jpaserver-base/src/test/resources/loinc/Part.csv
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0
hapi-fhir-jpaserver-base/src/test/resources/loinc/PartRelatedCodeMapping_Beta_1.csv → hapi-fhir-jpaserver-base/src/test/resources/loinc/PartRelatedCodeMapping.csv
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0
hapi-fhir-jpaserver-base/src/test/resources/loinc/LOINC_1.6_Top2000CommonLabResultsSI.csv → hapi-fhir-jpaserver-base/src/test/resources/loinc/Top2000CommonLabResultsSi.csv
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0
hapi-fhir-jpaserver-base/src/test/resources/loinc/LOINC_1.6_Top2000CommonLabResultsUS.csv → hapi-fhir-jpaserver-base/src/test/resources/loinc/Top2000CommonLabResultsUs.csv
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10
hapi-fhir-jpaserver-base/src/test/resources/loinc/hierarchy.csv
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@ -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
1 PATH_TO_ROOT SEQUENCE IMMEDIATE_PARENT CODE CODE_TEXT
2 1 LP31755-9 Microbiology
3 LP31755-9 1 LP31755-9 LP14559-6 Microorganism
4 LP31755-9.LP14559-6 1 LP14559-6 LP98185-9 Bacteria
5 LP31755-9.LP14559-6.LP98185-9 1 LP98185-9 LP14082-9 Bacteria
6 LP31755-9.LP14559-6.LP98185-9.LP14082-9 1 LP14082-9 LP52258-8 Bacteria | Body Fluid
7 LP31755-9.LP14559-6.LP98185-9.LP14082-9.LP52258-8 1 LP52258-8 41599-2 Bacteria Fld Ql Micro
8 LP31755-9.LP14559-6.LP98185-9.LP14082-9 2 LP14082-9 LP52260-4 Bacteria | Cerebral spinal fluid
9 LP31755-9.LP14559-6.LP98185-9.LP14082-9.LP52260-4 1 LP52260-4 41602-4 Bacteria CSF Ql Micro
10 LP31755-9.LP14559-6.LP98185-9.LP14082-9 3 LP14082-9 LP52960-9 Bacteria | Cervix