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Support additional filetypes #69

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Support additional filetypes #69

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2257963
Provided filename mappings for currently unsupported files
lukeswindale Jun 27, 2023
4c18912
Provided filename mappings for integer simple map refset
lukeswindale Jun 27, 2023
5bd6eee
Provided filename mappings for ccs and cci type refsets
lukeswindale Jun 27, 2023
a8a4f68
Added the create table scripts for the new tables
lukeswindale Jun 27, 2023
7bc49a7
Added crefset
lukeswindale Jun 28, 2023
6ec45df
Fix the failing test
senjo-aehrc Jul 4, 2023
0921b49
Resolving conflict
senjo-aehrc Jun 28, 2023
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8 changes: 5 additions & 3 deletions src/main/java/org/ihtsdo/rvf/core/service/AssertionExecutionService.java
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Original file line number Diff line number Diff line change
Expand Up @@ -196,10 +196,12 @@ private void executeCommand(final Assertion assertion, final MysqlExecutionConfi
}
}
else {
if (sqlStatement.startsWith("create table")
if (sqlStatement.startsWith("create table")) {
// only add engine if we do not create using a like statement
&& (!(sqlStatement.contains("like") || sqlStatement.contains("as")))){
sqlStatement = sqlStatement + " ENGINE = MyISAM";
if (!sqlStatement.toUpperCase().contains(" ENGINE") &&
!(sqlStatement.contains("like") || sqlStatement.contains("as"))) {
sqlStatement = sqlStatement + " ENGINE = MyISAM";
}
}
executeUpdateStatement(connection, sqlStatement);
}
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37 changes: 33 additions & 4 deletions src/main/java/org/ihtsdo/rvf/core/service/util/RF2FileTableMapper.java
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
package org.ihtsdo.rvf.core.service.util;

import java.util.Collection;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.Map;
import java.util.regex.Pattern;

Expand All @@ -11,6 +11,7 @@ public class RF2FileTableMapper {
private static final String STATED_RELATIONSHIP_FILE_HEADER = "sct2_StatedRelationship_";
private static final String SIMPLE_FILE_HEADER = "der2_Refset_.*Simple";
private static final String SIMPLE_MAP_FILE_HEADER = "der2_sRefset_.*SimpleMap";
private static final String INTEGER_SIMPLE_MAP_FILE_HEADER = "der2_iRefset_.*SimpleMap";
private static final String RELATIONSHIP_FILE_HEADER = "sct2_Relationship_";
private static final String RELATIONSHIP_CONCRETE_VALUES_FILE_HEADER = "sct2_RelationshipConcreteValues";
private static final String LANGUAGE_FILE_HEADER = "der2_cRefset_.*Language";
Expand All @@ -30,7 +31,14 @@ public class RF2FileTableMapper {
private static final String MRCM_ATRRIBUTE_RANGE_FILE_HEADER = "der2_ssccRefset_.*MRCMAttributeRange";
private static final String MRCM_DOMAIN_FILE_HEADER = "der2_sssssssRefset_.*MRCMDomain";
private static final String DESCRIPTION_TYPE_FILE_HEADER = "der2_ciRefset_.*DescriptionType";
private static final Map<String,String> tableNameMap = new HashMap<>();
private static final String ATTRIBUTE_VALUE_MAP_FILE_HEADER = "der2_csRefset_.*AttributeValueMap";
private static final String EXTENDED_ASSOCIATION_FILE_HEADER = "der2_ccRefset_.*ExtendedAssociation";
private static final String IDENTIFIER_FILE_HEADER = "sct2_Identifier_";
private static final String CCS_REFSET_FILE_HEADER = "der2_ccsRefset_";
private static final String CCI_REFSET_FILE_HEADER = "der2_cciRefset_";
private static final String C_REFSET_FILE_HEADER = "der2_cRefset_";

private static final Map<String,String> tableNameMap = new LinkedHashMap<>();
private static final String DELTA = ".*Delta.*_*_\\d{8}.txt";
private static final String SNAPSHOT = ".*Snapshot.*_*_\\d{8}.txt";
private static final String FULL = ".*Full.*_*_\\d{8}.txt";
Expand Down Expand Up @@ -60,7 +68,14 @@ public class RF2FileTableMapper {
tableNameMap.put(MRCM_ATRRIBUTE_RANGE_FILE_HEADER + DELTA, "mrcmattributerangerefset_d");
tableNameMap.put(MRCM_DOMAIN_FILE_HEADER + DELTA, "mrcmdomainrefset_d");
tableNameMap.put(DESCRIPTION_TYPE_FILE_HEADER + DELTA, "descriptiontyperefset_d");

tableNameMap.put(ATTRIBUTE_VALUE_MAP_FILE_HEADER + DELTA, "attributevaluemap_d");
tableNameMap.put(EXTENDED_ASSOCIATION_FILE_HEADER + DELTA, "extendedassociation_d");
tableNameMap.put(IDENTIFIER_FILE_HEADER + DELTA, "identifier_d");
tableNameMap.put(INTEGER_SIMPLE_MAP_FILE_HEADER + DELTA, "isimplemaprefset_d");
tableNameMap.put(CCS_REFSET_FILE_HEADER + DELTA, "ccsrefset_d");
tableNameMap.put(CCI_REFSET_FILE_HEADER + DELTA, "ccirefset_d");
tableNameMap.put(C_REFSET_FILE_HEADER + DELTA, "crefset_d");

//Full
tableNameMap.put(CONCEPT_FILE_HEADER + FULL, "concept_f");
tableNameMap.put(DESCRIPTION_FILE_HEADER + FULL, "description_f");
Expand All @@ -85,7 +100,14 @@ public class RF2FileTableMapper {
tableNameMap.put(MRCM_ATRRIBUTE_RANGE_FILE_HEADER + FULL, "mrcmattributerangerefset_f");
tableNameMap.put(MRCM_DOMAIN_FILE_HEADER + FULL, "mrcmdomainrefset_f");
tableNameMap.put(DESCRIPTION_TYPE_FILE_HEADER + FULL, "descriptiontyperefset_f");

tableNameMap.put(ATTRIBUTE_VALUE_MAP_FILE_HEADER + FULL, "attributevaluemap_f");
tableNameMap.put(EXTENDED_ASSOCIATION_FILE_HEADER + FULL, "extendedassociation_f");
tableNameMap.put(IDENTIFIER_FILE_HEADER + FULL, "identifier_f");
tableNameMap.put(INTEGER_SIMPLE_MAP_FILE_HEADER + FULL, "isimplemaprefset_f");
tableNameMap.put(CCS_REFSET_FILE_HEADER + FULL, "ccsrefset_f");
tableNameMap.put(CCI_REFSET_FILE_HEADER + FULL, "ccirefset_f");
tableNameMap.put(C_REFSET_FILE_HEADER + FULL, "crefset_f");

//Snapshot
tableNameMap.put(CONCEPT_FILE_HEADER + SNAPSHOT, "concept_s");
tableNameMap.put(DESCRIPTION_FILE_HEADER + SNAPSHOT, "description_s");
Expand All @@ -110,6 +132,13 @@ public class RF2FileTableMapper {
tableNameMap.put(MRCM_ATRRIBUTE_RANGE_FILE_HEADER + SNAPSHOT, "mrcmattributerangerefset_s");
tableNameMap.put(MRCM_DOMAIN_FILE_HEADER + SNAPSHOT, "mrcmdomainrefset_s");
tableNameMap.put(DESCRIPTION_TYPE_FILE_HEADER + SNAPSHOT, "descriptiontyperefset_s");
tableNameMap.put(ATTRIBUTE_VALUE_MAP_FILE_HEADER + SNAPSHOT, "attributevaluemap_s");
tableNameMap.put(EXTENDED_ASSOCIATION_FILE_HEADER + SNAPSHOT, "extendedassociation_s");
tableNameMap.put(IDENTIFIER_FILE_HEADER + SNAPSHOT, "identifier_s");
tableNameMap.put(INTEGER_SIMPLE_MAP_FILE_HEADER + SNAPSHOT, "isimplemaprefset_s");
tableNameMap.put(CCS_REFSET_FILE_HEADER + SNAPSHOT, "ccsrefset_s");
tableNameMap.put(CCI_REFSET_FILE_HEADER + SNAPSHOT, "ccirefset_s");
tableNameMap.put(C_REFSET_FILE_HEADER + SNAPSHOT, "crefset_s");
}

public static String getLegacyTableName(final String filename) {
Expand Down
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